ALBERT

Description: Transformation of refractory cratonic mantle into more fertile lithologies is the key to the fate of cratonic lithosphere. This process has been extensively studied in the eastern North China Craton (NCC) while that of its western part is still poorly constrained. A comprehensive study of newly-found pyroxenite xenoliths from the Langshan area, in the northwestern part of this craton is integrated with a regional synthesis of pyroxenite and peridotite xenoliths to constrain the petrogenesis of the pyroxenites and provide an overview of the processes involved in the modification of the deep lithosphere. The Langshan pyroxenites are of two types, high-Mg# [Mg2+/(Mg2++Fe2+)*100 = ∼ 90, atomic ratios] olivine-bearing websterites with high equilibration temperatures (880 ∼ 970 oC), and low-Mg# (70 ∼ 80) plagioclase-bearing websterites with low equilibration temperatures (550 ∼ 835 oC). The high-Mg# pyroxenites show trade-off abundances of olivine and orthopyroxene, highly depleted bulk Sr-Nd (ƐNd = +11.41, 87Sr/86Sr = ∼0.7034) and low clinopyroxene Sr isotopic ratios (mean 87Sr/86Sr = ∼0.703). They are considered to reflect the reaction of mantle peridotites with silica-rich silicate melts derived from the convective mantle. Their depletion in fusible components (e.g., FeO, TiO2 and Na2O) and progressive exhaustion of incompatible elements suggest melt extraction after their formation. The low-Mg# pyroxenites display layered structures, convex-upward rare earth element patterns, moderately enriched bulk Sr-Nd isotopic ratios (ƐNd = -14.20 ∼ -16.74, 87Sr/86Sr = 0.7070 ∼ 0.7078) and variable clinopyroxene Sr-isotope ratios (87Sr/86Sr = 0.706-0.711). They are interpreted to be crustal cumulates from hypersthene-normative melts generated by interaction between the asthenosphere and heterogeneous lithospheric mantle. Combined with studies on regional peridotite xenoliths, it is shown that the thinning and refertilization of the lithospheric mantle was accompanied by crustal rejuvenation and that such processes occurred ubiquitously in the northwestern part of the NCC. A geodynamic model is proposed for the evolution of the deep lithosphere, which includes long-term mass transfer through a mantle wedge into the deep crust from the Paleozoic to the Cenozoic, triggered by subduction of the Paleo-Asian ocean and the Late Mesozoic lithospheric extension of eastern Asia.

Description: The orogenic development after the continental collision between Laurussia and Gondwana, led to two contrasting associations of mantle-derived magmatic rocks on the territory of the Bohemian Massif: (i) a 340–310 Ma lamprophyre-lamproite orogenic association and (ii) a 300–275 Ma lamprophyre association of anorogenic affinity. Major types of potassic mantle-derived magmatic rocks recognised in the orogenic and anorogenic associations include: (i) calc-alkaline to alkaline lamprophyres, (ii) alkaline “orthopyroxene minettes” (and geochemically related rocks), and (iii) peralkaline lamproites. These three types significantly differ with respect to mineral, whole-rock and Sr–Nd–Pb–Li isotope composition, and spatial distribution. The calc-alkaline lamprophyres occur throughout the entire Saxo-Thuringian and Moldanubian zones, whereas the different types of malte-derived potassic rocks are spatially restricted to particular zones. Rocks of the Carboniferous lamprophyre-lamproite orogenic association are characterised by variable negative εNd(i) and variably radiogenic Sr(i), whereas the rocks of the Permian lamprophyre association of anorogenic affinity are characterised by positive εNd(i) and relatively young depleted-mantle Nd-model ages reflecting increasing input from upwelling asthenospheric mantle. The small variation in the Pb isotopic composition of post-collisional potassic mantle-derived magmatic rocks (of both the orogenic and anorogenic series) implies that the Pb budget of the mantle beneath the Bohemian Massif is dominated by the same crust-derived material, which itself may include material derived from several sources. The source rocks of “orthopyroxene minettes” are characterised by isotopically light (“eclogitic”) Li and strongly radiogenic (crustal) Sr and may have been metasomatised by high-pressure fluids along the edge of a subduction zone. In contrast, the strongly Al2O3 and CaO depleted mantle source of the lamproites is characterised by isotopically heavy Li and high SiO2 and extreme K2O contents. This mantle source may have been metasomatised predominantly by melts. The mantle source of the lamprophyres may have undergone metasomatism by both fluids and melts.

Description: The Lu–Hf isotope system and Sr–Nd–Hf–Os isotope systematics of mantle rocks are capable of unravelling the early processes in collision belts, especially in a hot subduction context where the Sm–Nd and U–Pb systems in crustal rocks are prone to resetting owing to high temperatures and interaction with melts during exhumation. To improve models of the Devonian–Carboniferous evolution of the Bohemian Massif, we investigated in detail mafic and ultramafic rocks (eclogite, pyroxenite, and peridotite) from the ultrahigh-pressure and ultrahigh-temperature Kutná Hora Crystalline Complex (KHCC: Úhrov, Bečváry, Doubrava, and Spačice localities). Petrography, multiphase solid inclusions, major and trace element compositions of rocks and minerals, and radiogenic isotopic data document contrasting sources and protoliths as well as effects of subduction-related processes for these rocks. The Úhrov peridotite has a depleted composition corresponding to the suboceanic asthenospheric mantle, whereas Bečváry and Doubrava peridotites represent lithospheric mantle that underwent melt refertilization by basaltic and SiO2-undersaturated melts, respectively. Multiphase solid inclusions enclosed in garnet from Úhrov and Bečváry peridotites represent trapped H2O ± CO2-bearing metasomatizing agents and Fe–Ti-rich melts. The KHCC eclogites either formed by high-pressure crystal accumulation from mantle-derived basaltic melts (Úhrov) or represent a fragment of mid-ocean ridge basalt-like gabbroic cumulate (Spačice) and crustal-derived material (Doubrava) both metamorphosed at high P–T conditions. The Lu–Hf age of 395 ± 23 Ma obtained for the Úhrov peridotite reflects garnet growth related to burial of the asthenospheric mantle during subduction of the oceanic slab. By contrast, Spačice and Doubrava eclogites yield younger Lu–Hf ages of ∼350 and 330 Ma, respectively, representing mixed ages as demonstrated by the strong granulite-facies overprint and trace element zoning in garnet grains. We propose a refined model for the Early Variscan evolution of the Bohemian Massif starting with the subduction of the oceanic crust (Saxothuringian ocean) and associated oceanic asthenospheric mantle (Úhrov) beneath the Teplá–Barrandian at ≥380 Ma, which was responsible for melt refertilization of the associated mantle wedge (Bečváry, Doubrava). This was followed by continental subduction (∼370–360 Ma?) accompanied by the oceanic slab break-off and incorporation of the upwelling asthenospheric mantle into the Moldanubian lithospheric mantle and subsequent coeval exhumation of mantle and crustal rocks at ∼350–330 Ma.

Description: The Changning–Menglian orogenic belt (CMOB) in the southeastern Tibetan Plateau is an important link between the Longmu Co–Shuanghu suture (LCSS) in the northern Tibetan Plateau and the Chiang Mai–Inthanon and Bentong–Raub sutures in Thailand and Peninsular Malaysia. These belts and sutures are generally regarded as containing the remnants of the oceanic crust of the Palaeo-Tethys that formed by seafloor spreading as a result of the separation of Gondwana- and Eurasia-derived blocks during the Middle Cambrian. In this paper we report the first discovery of abundant unaltered and retrograde eclogites that occur as irregular lenses and blocks in metasedimentary rocks of the CMOB, and these eclogites form an elongate and almost north–south-trending high-pressure (HP)–ultrahigh-pressure (UHP) metamorphic belt that is ∼200 km long and ∼50 km wide. The newly discovered phengite/talc/epidote–glaucophane eclogites, lawsonite–talc–phengite eclogites, dolomite/magnesite–kyanite eclogites and phengite–kyanite-bearing retrograde eclogites have enriched (E-) and normal mid-ocean ridge basalt (N-MORB)-like affinities and mainly positive as well as some negative whole-rock εNd values (–4·34 to +7·89), which suggest an enriched and depleted oceanic lithosphere source for their protoliths. Magmatic zircons separated from the epidote–glaucophane, magnesite–kyanite and (phengite–kyanite-bearing) retrograde eclogites gave protolith ages of 317–250 Ma, which fit well within the time frame of the opening of the Palaeo-Tethys during the Middle Cambrian and its closure during the Triassic. Abundant metamorphic zircons in the eclogites indicate a Triassic metamorphic event related to the subduction of the Palaeo-Tethys oceanic crust from 235 to 227 Ma. Taking into account previous isotopic age data, we now establish the periods of Early–Middle Triassic (246–227 Ma) and Late Triassic (222–209 Ma) as the ages of subduction and exhumation of the Palaeo-Tethyan oceanic crust, respectively. Thermodynamic modelling revealed that the eclogites record distinct HP–UHP peak metamorphic conditions of 23·0–25·5 kbar and 582–610 °C for the phengite–glaucophane eclogites, 24·0–25·5 kbar and 570–586 °C for the talc–glaucophane eclogites, 29·0–31·0 kbar and 675–712 °C for the dolomite–kyanite eclogites, and 30·0–32·0 kbar and 717–754 °C for the magnesite–kyanite eclogites. These P–T estimates and geochronological data indicate that the Palaeo-Tethys oceanic slab was subducted to different mantle depths from 75 km down to 95 km, forming distinct types of eclogite with a variety of peak eclogite-facies mineral assemblages. The eclogites consistently record clockwise metamorphic P–T–t paths characterized by a heating–compression prograde loop under a low geothermal gradient of 5–10 °C km–1, indicating the rapid subduction of cold oceanic crust at a rate of 4·5–6·0 km Ma–1, followed by isothermal or cooling–decompressive retrogression and exhumation at an average rate of 3·2–4·2 km Ma–1. The newly discovered eclogites of the CMOB with their signatures of ocean-crust subduction are petrologically, geochemically and geochronologically comparable with those of the LCSS, providing powerful support for the idea that a nearly 2000 km long HP–UHP eclogite belt extends from the northern Tibetan Plateau to the southeastern Tibetan Plateau, and that it represents the main boundary suture of the Palaeo-Tethyan domain. These results have far-reaching implications for the tectonic framework and complex metamorphic evolution of the Palaeo-Tethyan domain.

Description: Replacive symplectites (vermicular intergrowths of two or more minerals) are an important feature of layered igneous intrusions, recording evidence of late-stage reactions between interstitial liquid and crystals. They are common throughout the Layered Series of the 564 Ma Sept Iles layered intrusion in Quebec, Canada, and fall into three types: oxy-symplectites, ‘Type I’ symplectites, and ‘Type II’ symplectites. Oxy-symplectites are comprised of magnetite and orthopyroxene, nucleate on olivine primocrysts, and form via the reaction Olivine + O2 → Orthopyroxene + Magnetite; Type I symplectites (of which there are 3 distinct categories) are comprised of anorthitic plagioclase with pyroxene, amphibole, or olivine vermicules, grow from primocryst oxide grains, and replace primary plagioclase; and Type II symplectites (of which there are 2 distinct categories) are comprised of anorthitic plagioclase with orthopyroxene ± amphibole vermicules, grow from primocryst olivine grains, and replace primocryst plagioclase. Rare symplectites composed of biotite and plagioclase are also present. Symplectite growth occurred at 700-1030 °C with pressure constraints of 1-2 kbar. We propose that Type I symplectites, and some Type II symplectites, formed from interaction of primocrysts with residual Fe-rich liquid as a consequence of differential loss of an immiscible Si-rich liquid conjugate from the crystal mush. However, redistribution and concentration of hydrous fluids in incompletely solidified rock, or an increase in water activity of the interstitial melt, may be more plausible processes responsible for the formation of replacive symplectites comprising abundant hydrous mineral assemblages.

Description: Some of the most dangerous pathogens such as Mycobacterium tuberculosis and Yersinia pestis evolve clonally . This means that little or no recombination occurs between strains belonging to these species. Paradoxically, although different members of these species show extreme sequence similarity of orthologous genes, some show considerable intraspecies phenotypic variation, the source of which remains elusive. To examine the possible sources of phenotypic variation within clonal pathogenic bacterial species, we carried out an extensive genomic and pan-genomic analysis of the sources of genetic variation available to a large collection of clonal and nonclonal pathogenic bacterial species. We show that while nonclonal species diversify through a combination of changes to gene sequences, gene loss and gene gain, gene loss completely dominates as a source of genetic variation within clonal species. Indeed, gene loss is so prevalent within clonal species as to lead to levels of gene content variation comparable to those found in some nonclonal species that are much more diverged in their gene sequences and that acquire a substantial number of genes horizontally. Gene loss therefore needs to be taken into account as a potential dominant source of phenotypic variation within clonal bacterial species.

Description: Obligate bacterial symbionts are widespread in many invertebrates, where they are often confined to specialized host cells and are transmitted directly from mother to progeny. Increasing numbers of these bacteria are being characterized but questions remain about their population structure and evolution. Here we take a comparative genomics approach to investigate two prominent bacterial symbionts (BFo1 and BFo2) isolated from geographically separated populations of western flower thrips, Frankliniella occidentalis. Our multifaceted approach to classifying these symbionts includes concatenated multilocus sequence analysis (MLSA) phylogenies, ribosomal multilocus sequence typing (rMLST), construction of whole-genome phylogenies, and in-depth genomic comparisons. We showed that the BFo1 genome clusters more closely to species in the genus Erwinia, and is a putative close relative to Erwinia aphidicola . BFo1 is also likely to have shared a common ancestor with Erwinia pyrifoliae/Erwinia amylovora and the nonpathogenic Erwinia tasmaniensis and genetic traits similar to Erwinia billingiae . The BFo1 genome contained virulence factors found in the genus Erwinia but represented a divergent lineage. In contrast, we showed that BFo2 belongs within the Enterobacteriales but does not group closely with any currently known bacterial species. Concatenated MLSA phylogenies indicate that it may have shared a common ancestor to the Erwinia and Pantoea genera, and based on the clustering of rMLST genes, it was most closely related to Pantoea ananatis but represented a divergent lineage. We reconstructed a core genome of a putative common ancestor of Erwinia and Pantoea and compared this with the genomes of BFo bacteria. BFo2 possessed none of the virulence determinants that were omnipresent in the Erwinia and Pantoea genera. Taken together, these data are consistent with BFo2 representing a highly novel species that maybe related to known Pantoea .

Description: Gene expression evolution occurs through changes in cis - or trans -regulatory elements or both. Interactions between transcription factors (TFs) and their binding sites (TFBSs) constitute one of the most important points where these two regulatory components intersect. In this study, we investigated the evolution of TFBSs in the promoter regions of different Saccharomyces strains and species. We divided the promoter of a gene into the proximal region and the distal region, which are defined, respectively, as the 200-bp region upstream of the transcription starting site and as the 200-bp region upstream of the proximal region. We found that the predicted TFBSs in the proximal promoter regions tend to be evolutionarily more conserved than those in the distal promoter regions. Additionally, Saccharomyces cerevisiae strains used in the fermentation of alcoholic drinks have experienced more TFBS losses than gains compared with strains from other environments (wild strains, laboratory strains, and clinical strains). We also showed that differences in TFBSs correlate with the cis component of gene expression evolution between species (comparing S. cerevisiae and its sister species Saccharomyces paradoxus ) and within species (comparing two closely related S. cerevisiae strains).

Description: Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (~7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (~10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes.

Description: Viruses rely completely on the hosts’ machinery for translation of viral transcripts. However, for most viruses infecting humans, codon usage preferences (CUPrefs) do not match those of the host. Human papillomaviruses (HPVs) are a showcase to tackle this paradox: they present a large genotypic diversity and a broad range of phenotypic presentations, from asymptomatic infections to productive lesions and cancer. By applying phylogenetic inference and dimensionality reduction methods, we demonstrate first that genes in HPVs are poorly adapted to the average human CUPrefs, the only exception being capsid genes in viruses causing productive lesions. Phylogenetic relationships between HPVs explained only a small proportion of CUPrefs variation. Instead, the most important explanatory factor for viral CUPrefs was infection phenotype, as orthologous genes in viruses with similar clinical presentation displayed similar CUPrefs. Moreover, viral genes with similar spatiotemporal expression patterns also showed similar CUPrefs. Our results suggest that CUPrefs in HPVs reflect either variations in the mutation bias or differential selection pressures depending on the clinical presentation and expression timing. We propose that poor viral CUPrefs may be central to a trade-off between strong viral gene expression and the potential for eliciting protective immune response.

Description: Historically, genome-wide and molecular characterization of the genus Listeria has concentrated on the important human pathogen Listeria monocytogenes and a small number of closely related species, together termed Listeria sensu strictu. More recently, a number of genome sequences for more basal, and nonpathogenic, members of the Listeria genus have become available, facilitating a wider perspective on the evolution of pathogenicity and genome level evolutionary dynamics within the entire genus (termed Listeria sensu lato). Here, we have sequenced the genomes of additional Listeria fleischmannii and Listeria newyorkensis isolates and explored the dynamics of genome evolution in Listeria sensu lato. Our analyses suggest that acquisition of genetic material through gene duplication and divergence as well as through lateral gene transfer (mostly from outside Listeria ) is widespread throughout the genus. Novel genetic material is apparently subject to rapid turnover. Multiple lines of evidence point to significant differences in evolutionary dynamics between the most basal Listeria subclade and all other congeners, including both sensu strictu and other sensu lato isolates. Strikingly, these differences are likely attributable to stochastic, population-level processes and contribute to observed variation in genome size across the genus. Notably, our analyses indicate that the common ancestor of Listeria sensu lato lacked flagella, which were acquired by lateral gene transfer by a common ancestor of Listeria grayi and Listeria sensu strictu, whereas a recently functionally characterized pathogenicity island, responsible for the capacity to produce cobalamin and utilize ethanolamine/propane-2-diol, was acquired in an ancestor of Listeria sensu strictu.

Description: Taeniid cestodes (including the human parasites Echinococcus spp. and Taenia solium ) have very few mobile genetic elements (MGEs) in their genome, despite lacking a canonical PIWI pathway. The MGEs of these parasites are virtually unexplored, and nothing is known about their expression and silencing. In this work, we report the discovery of a novel family of small nonautonomous long terminal repeat retrotransposons (also known as terminal-repeat retrotransposons in miniature, TRIMs) which we have named ta-TRIM (taeniid TRIM). ta-TRIM s are only the second family of TRIM elements discovered in animals, and are likely the result of convergent reductive evolution in different taxonomic groups. These elements originated at the base of the taeniid tree and have expanded during taeniid diversification, including after the divergence of closely related species such as Echinococcus multilocularis and Echinococcus granulosus . They are massively expressed in larval stages, from a small proportion of full-length copies and from isolated terminal repeats that show transcriptional read-through into downstream regions, generating novel noncoding RNAs and transcriptional fusions to coding genes. In E. multilocularis , ta-TRIM s are specifically expressed in the germinative cells (the somatic stem cells) during asexual reproduction of metacestode larvae. This would provide a developmental mechanism for insertion of ta-TRIM s into cells that will eventually generate the adult germ line. Future studies of active and inactive ta-TRIM elements could give the first clues on MGE silencing mechanisms in cestodes.

Description: Even though mitochondrial genomes, which characterize eukaryotic cells, were first discovered more than 50 years ago, mitochondrial genomics remains an important topic in molecular biology and genome sciences. The Phylum Alveolata comprises three major groups (ciliates, apicomplexans, and dinoflagellates), the mitochondrial genomes of which have diverged widely. Even though the gene content of dinoflagellate mitochondrial genomes is reportedly comparable to that of apicomplexans, the highly fragmented and rearranged genome structures of dinoflagellates have frustrated whole genomic analysis. Consequently, noncoding sequences and gene arrangements of dinoflagellate mitochondrial genomes have not been well characterized. Here we report that the continuous assembled genome (~326 kb) of the dinoflagellate, Symbiodinium minutum , is AT-rich (~64.3%) and that it contains three protein-coding genes. Based upon in silico analysis, the remaining 99% of the genome comprises transcriptomic noncoding sequences. RNA edited sites and unique, possible start and stop codons clarify conserved regions among dinoflagellates. Our massive transcriptome analysis shows that almost all regions of the genome are transcribed, including 27 possible fragmented ribosomal RNA genes and 12 uncharacterized small RNAs that are similar to mitochondrial RNA genes of the malarial parasite, Plasmodium falciparum . Gene map comparisons show that gene order is only slightly conserved between S. minutu m and P. falciparum . However, small RNAs and intergenic sequences share sequence similarities with P. falciparum , suggesting that the function of noncoding sequences has been preserved despite development of very different genome structures.

Description: Evolutionary studies usually use a two-step process to investigate sequence data. Step one estimates a multiple sequence alignment (MSA) and step two applies phylogenetic methods to ask evolutionary questions of that MSA. Modern phylogenetic methods infer evolutionary parameters using maximum likelihood or Bayesian inference, mediated by a probabilistic substitution model that describes sequence change over a tree. The statistical properties of these methods mean that more data directly translates to an increased confidence in downstream results, providing the substitution model is adequate and the MSA is correct. Many studies have investigated the robustness of phylogenetic methods in the presence of substitution model misspecification, but few have examined the statistical properties of those methods when the MSA is unknown. This simulation study examines the statistical properties of the complete two-step process when inferring sequence divergence and the phylogenetic tree topology. Both nucleotide and amino acid analyses are negatively affected by the alignment step, both through inaccurate guide tree estimates and through overfitting to that guide tree. For many alignment tools these effects become more pronounced when additional sequences are added to the analysis. Nucleotide sequences are particularly susceptible, with MSA errors leading to statistical support for long-branch attraction artifacts, which are usually associated with gross substitution model misspecification. Amino acid MSAs are more robust, but do tend to arbitrarily resolve multifurcations in favor of the guide tree. No inference strategies produce consistently accurate estimates of divergence between sequences, although amino acid MSAs are again more accurate than their nucleotide counterparts. We conclude with some practical suggestions about how to limit the effect of MSA uncertainty on evolutionary inference.

Description: The evolution of mitochondrial information processing pathways, including replication, transcription and translation, is characterized by the gradual replacement of mitochondrial-encoded proteins with nuclear-encoded counterparts of diverse evolutionary origins. Although the ancestral enzymes involved in mitochondrial transcription and replication have been replaced early in eukaryotic evolution, mitochondrial translation is still carried out by an apparatus largely inherited from the α-proteobacterial ancestor. However, variation in the complement of mitochondrial-encoded molecules involved in translation, including transfer RNAs (tRNAs), provides evidence for the ongoing evolution of mitochondrial protein synthesis. Here, we investigate the evolution of the mitochondrial translational machinery using recent genomic and transcriptomic data from animals that have experienced the loss of mt-tRNAs, including phyla Cnidaria and Ctenophora, as well as some representatives of all four classes of Porifera. We focus on four sets of mitochondrial enzymes that directly interact with tRNAs: Aminoacyl-tRNA synthetases, glutamyl-tRNA amidotransferase, tRNA Ile lysidine synthetase, and RNase P. Our results support the observation that the fate of nuclear-encoded mitochondrial proteins is influenced by the evolution of molecules encoded in mitochondrial DNA, but in a more complex manner than appreciated previously. The data also suggest that relaxed selection on mitochondrial translation rather than coevolution between mitochondrial and nuclear subunits is responsible for elevated rates of evolution in mitochondrial translational proteins.

Description: The expansion of DUF1220 domain copy number during human evolution is a dramatic example of rapid and repeated domain duplication. Although patterns of expression, homology, and disease associations suggest a role in cortical development, this hypothesis has not been robustly tested using phylogenetic methods. Here, we estimate DUF1220 domain counts across 12 primate genomes using a nucleotide Hidden Markov Model. We then test a series of hypotheses designed to examine the potential evolutionary significance of DUF1220 copy number expansion. Our results suggest a robust association with brain size, and more specifically neocortex volume. In contradiction to previous hypotheses, we find a strong association with postnatal brain development but not with prenatal brain development. Our results provide further evidence of a conserved association between specific loci and brain size across primates, suggesting that human brain evolution may have occurred through a continuation of existing processes.

Description: Alternative splicing and gene duplication are the two main processes responsible for expanding protein functional diversity. Although gene duplication can generate new genes and alternative splicing can introduce variation through alternative gene products, the interplay between the two processes is complex and poorly understood. Here, we have carried out a study of the evolution of alternatively spliced exons after gene duplication to better understand the interaction between the two processes. We created a manually curated set of 97 human genes with mutually exclusively spliced homologous exons and analyzed the evolution of these exons across five distantly related vertebrates (lamprey, spotted gar, zebrafish, fugu, and coelacanth). Most of these exons had an ancient origin (more than 400 Ma). We found examples supporting two extreme evolutionary models for the behaviour of homologous axons after gene duplication. We observed 11 events in which gene duplication was accompanied by splice isoform separation, that is, each paralog specifically conserved just one distinct ancestral homologous exon. At other extreme, we identified genes in which the homologous exons were always conserved within paralogs, suggesting that the alternative splicing event cannot easily be separated from the function in these genes. That many homologous exons fall in between these two extremes highlights the diversity of biological systems and suggests that the subtle balance between alternative splicing and gene duplication is adjusted to the specific cellular context of each gene.

Description: There is widespread interest today in understanding enhancers, which are regulatory elements typically harboring several transcription factor binding sites and mediating the combinatorial effect of transcription factors on gene expression. The evolution of enhancers poses interesting unanswered questions, for example, the evolutionary time taken for a typical enhancer to emerge or the factors shaping its evolution. Existing approaches to cis -regulatory evolution have often ignored the combinatorial nature and varied biochemical mechanisms of gene regulation encoded in enhancers. We report on our investigation of enhancer evolution through the use of PEBCRES, a framework for evolutionary simulation of enhancers that employs a mechanistic and well-supported sequence-to-expression model to assign fitness to the evolving enhancer genotype. We estimated the time necessary to evolve, from genomic background, enhancers capable of driving complex gene expression patterns similar to those involved in early development in Drosophila. We found the time-to-evolve to range between 0.5 and 10 Myr, and to vary greatly with the target expression pattern, complexity of the real enhancer known to encode that pattern, and the strength of input from specific transcription factors. To our knowledge, this is the first estimate of waiting times for realistic enhancers to evolve. The in silico evolved enhancers had, with a few interesting exceptions, site compositions similar to those seen in real enhancers for the same patterns. Our simulations also revealed that certain features of an enhancer might evolve not due to their biological function but as aids to the evolutionary process itself.

Description: Despite significant progress in the structural and functional characterization of the human genome, understanding of the mechanisms underlying the genetic basis of human phenotypic uniqueness remains limited. Here, I report that transposable element-derived sequences, most notably LTR7/HERV-H, LTR5_Hs, and L1HS, harbor 99.8% of the candidate human-specific regulatory loci (HSRL) with putative transcription factor-binding sites in the genome of human embryonic stem cells (hESC). A total of 4,094 candidate HSRL display selective and site-specific binding of critical regulators (NANOG [Nanog homeobox], POU5F1 [POU class 5 homeobox 1], CCCTC-binding factor [CTCF], Lamin B1), and are preferentially located within the matrix of transcriptionally active DNA segments that are hypermethylated in hESC. hESC-specific NANOG-binding sites are enriched near the protein-coding genes regulating brain size, pluripotency long noncoding RNAs, hESC enhancers, and 5-hydroxymethylcytosine-harboring regions immediately adjacent to binding sites. Sequences of only 4.3% of hESC-specific NANOG-binding sites are present in Neanderthals’ genome, suggesting that a majority of these regulatory elements emerged in Modern Humans. Comparisons of estimated creation rates of novel TF-binding sites revealed that there was 49.7-fold acceleration of creation rates of NANOG-binding sites in genomes of Chimpanzees compared with the mouse genomes and further 5.7-fold acceleration in genomes of Modern Humans compared with the Chimpanzees genomes. Preliminary estimates suggest that emergence of one novel NANOG-binding site detectable in hESC required 466 years of evolution. Pathway analysis of coding genes that have hESC-specific NANOG-binding sites within gene bodies or near gene boundaries revealed their association with physiological development and functions of nervous and cardiovascular systems, embryonic development, behavior, as well as development of a diverse spectrum of pathological conditions such as cancer, diseases of cardiovascular and reproductive systems, metabolic diseases, multiple neurological and psychological disorders. A proximity placement model is proposed explaining how a 33–47% excess of NANOG, CTCF, and POU5F1 proteins immobilized on a DNA scaffold may play a functional role at distal regulatory elements.

Description: Organisms can adapt to local environmental conditions as a plastic response or become adapted through natural selection on genetic variation. The ability to adapt to increased water temperatures will be of paramount importance for many fish species as the climate continues to warm and water resources become limited. Because increased water temperatures will reduce the dissolved oxygen available for fish, we hypothesized that adaptation to low oxygen environments would involve improved respiration through oxidative phosphorylation (OXPHOS). To test this hypothesis, we subjected individuals from two ecologically divergent populations of inland (redband) rainbow trout ( Oncorhynchus mykiss gairdneri ) with historically different temperature regimes (desert and montane) and their F1 progeny to diel cycles of temperature stress and then examined gene expression data for 80 nuclear- and mitochondrial-encoded OXPHOS subunits that participate in respiration. Of the 80 transcripts, 7 showed ≥ 2-fold difference in expression levels in gill tissue from desert fish under heat stress whereas the montane fish had none and the F1 only had one differentially expressed gene. A structural analysis of the proteins encoded by those genes suggests that the response could coordinate the formation of supercomplexes and oligomers. Supercomplexes may increase the efficiency of respiration because complexes I, III, and IV are brought into close proximity and oligomerization of complex V alters the macrostructure of mitochondria to improve respiration. Significant differences in gene expression patterns in response to heat stress in a common environment indicate that the response was not due to plasticity but had a genetic basis.

Description: The enigmatic monocot family Triuridaceae provides a potentially useful model system for studying the effects of an ancient loss of photosynthesis on the plant plastid genome, as all of its members are mycoheterotrophic and achlorophyllous. However, few studies have placed the family in a comparative context, and its phylogenetic placement is only partly resolved. It was also unclear whether any taxa in this family have retained a plastid genome. Here, we used genome survey sequencing to retrieve plastid genome data for Sciaphila densiflora (Triuridaceae) and ten autotrophic relatives in the orders Dioscoreales and Pandanales. We recovered a highly reduced plastome for Sciaphila that is nearly colinear with Carludovica palmata , a photosynthetic relative that belongs to its sister group in Pandanales, Cyclanthaceae–Pandanaceae. This phylogenetic placement is well supported and robust to a broad range of analytical assumptions in maximum-likelihood inference, and is congruent with recent findings based on nuclear and mitochondrial evidence. The 28 genes retained in the S. densiflora plastid genome are involved in translation and other nonphotosynthetic functions, and we demonstrate that nearly all of the 18 protein-coding genes are under strong purifying selection. Our study confirms the utility of whole plastid genome data in phylogenetic studies of highly modified heterotrophic plants, even when they have substantially elevated rates of substitution.

Description: We report the identification of a novel gene family (named MgCRP-I) encoding short secreted cysteine-rich peptides in the Mediterranean mussel Mytilus galloprovincialis . These peptides display a highly conserved pre-pro region and a hypervariable mature peptide comprising six invariant cysteine residues arranged in three intramolecular disulfide bridges. Although their cysteine pattern is similar to cysteines-rich neurotoxic peptides of distantly related protostomes such as cone snails and arachnids, the different organization of the disulfide bridges observed in synthetic peptides and phylogenetic analyses revealed MgCRP-I as a novel protein family. Genome- and transcriptome-wide searches for orthologous sequences in other bivalve species indicated the unique presence of this gene family in Mytilus spp. Like many antimicrobial peptides and neurotoxins, MgCRP-I peptides are produced as pre-propeptides, usually have a net positive charge and likely derive from similar evolutionary mechanisms, that is, gene duplication and positive selection within the mature peptide region; however, synthetic MgCRP-I peptides did not display significant toxicity in cultured mammalian cells, insecticidal, antimicrobial, or antifungal activities. The functional role of MgCRP-I peptides in mussel physiology still remains puzzling.

Description: Most sequenced eukaryotic genomes show a large excess of recent duplicates. As duplicates age, both the population genetic process of failed fixation and the mutation-driven process of nonfunctionalization act to reduce the observed number of duplicates. Understanding the processes generating the age distributions of recent duplicates is important to also understand the role of duplicate genes in the functional divergence of genomes. To date, mechanistic models for duplicate gene retention only account for the mutation-driven nonfunctionalization process. Here, a neutral model for the distribution of synonymous substitutions in duplicated genes which are segregating and expected to never fix in a population is introduced. This model enables differentiation of neutral loss due to failed fixation from loss due to mutation-driven nonfunctionalization. The model has been validated on simulated data and subsequent analysis with the model on genomic data from human and mouse shows that conclusions about the underlying mechanisms for duplicate gene retention can be sensitive to consideration of population genetic processes.

Description: Stenotrophomonas maltophilia , a ubiquitous Gram-negative -proteobacterium, has emerged as an important opportunistic pathogen responsible for nosocomial infections. A major characteristic of clinical isolates is their high intrinsic or acquired antibiotic resistance level. The aim of this study was to decipher the genetic determinism of antibiotic resistance among strains from different origins (i.e., natural environment and clinical origin) showing various antibiotic resistance profiles. To this purpose, we selected three strains isolated from soil collected in France or Burkina Faso that showed contrasting antibiotic resistance profiles. After whole-genome sequencing, the phylogenetic relationships of these 3 strains and 11 strains with available genome sequences were determined. Results showed that a strain’s phylogeny did not match their origin or antibiotic resistance profiles. Numerous antibiotic resistance coding genes and efflux pump operons were revealed by the genome analysis, with 57% of the identified genes not previously described. No major variation in the antibiotic resistance gene content was observed between strains irrespective of their origin and antibiotic resistance profiles. Although environmental strains generally carry as many multidrug resistant (MDR) efflux pumps as clinical strains, the absence of resistance–nodulation–division (RND) pumps (i.e., SmeABC) previously described to be specific to S. maltophilia was revealed in two environmental strains (BurA1 and PierC1). Furthermore the genome analysis of the environmental MDR strain BurA1 showed the absence of SmeABC but the presence of another putative MDR RND efflux pump, named EbyCAB on a genomic island probably acquired through horizontal gene transfer.

Description: The expansion of Bantu-speaking agropastoralist populations had a great impact on the genetic, linguistic, and cultural variation of sub-Saharan Africa. It is generally accepted that Bantu languages originated in an area around the present border between Cameroon and Nigeria approximately 5,000 years ago, from where they spread South and East becoming the largest African linguistic branch. The demic consequences of this event are reflected in the relatively high genetic homogeneity observed across most of sub-Saharan Africa populations. In this work, we explored genome-wide single nucleotide polymorphism data from 28 populations to characterize the genetic components present in sub-Saharan African populations. Combining novel data from four Southern African populations with previously published results, we reject the hypothesis that the "non-Bantu" genetic component reported in South-Eastern Africa (Mozambique) reflects extensive gene flow between incoming agriculturalist and resident hunter-gatherer communities. We alternatively suggest that this novel component is the result of demographic dynamics associated with the Bantu dispersal.

Description: Dietary shifts can drive molecular evolution in mammals and a major transition in human history, the agricultural revolution, favored carbohydrate consumption. We investigated the evolutionary history of nine genes encoding brush-border proteins involved in carbohydrate digestion/absorption. Results indicated widespread adaptive evolution in mammals, with several branches experiencing episodic selection, particularly strong in bats. Many positively selected sites map to functional protein regions (e.g., within glucosidase catalytic crevices), with parallel evolution at SI (sucrase-isomaltase) and MGAM (maltase-glucoamylase). In human populations, five genes were targeted by positive selection acting on noncoding variants within regulatory elements. Analysis of ancient DNA samples indicated that most derived alleles were already present in the Paleolithic. Positively selected variants at SLC2A5 (fructose transporter) were an exception and possibly spread following the domestication of specific fruit crops. We conclude that agriculture determined no major selective event at carbohydrate metabolism genes in humans, with implications for susceptibility to metabolic disorders.

Description: Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (~0.4X to 2X) for six fern species from the Polypodiales ( Ceratopteris , Pteridium , Polypodium , Cystopteris ), Cyatheales ( Plagiogyria ), and Gleicheniales ( Dipteris ). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.

Description: The evolution of heterogametic sex chromosomes is often—but not always—accompanied by the evolution of dosage compensating mechanisms that mitigate the impact of sex-specific gene dosage on levels of gene expression. One emerging view of this process is that such mechanisms may only evolve in male-heterogametic (XY) species but not in female-heterogametic (ZW) species, which will consequently exhibit "incomplete" sex chromosome dosage compensation. However, recent results suggest that at least some Lepidoptera (moths and butterflies) may prove to be an exception to this prediction. Studies in bombycoid moths indicate the presence of a chromosome-wide epigenetic mechanism that effectively balances Z chromosome gene expression between the sexes by reducing Z-linked expression in males. In contrast, strong sex chromosome dosage effects without any reduction in male Z-linked expression were previously reported in a pyralid moth, suggesting a lack of any such dosage compensating mechanism. Here we report an analysis of sex chromosome dosage compensation in Heliconius butterflies, sampling multiple individuals for several different adult tissues (head, abdomen, leg, mouth, and antennae). Methodologically, we introduce a novel application of linear mixed-effects models to assess dosage compensation, offering a unified statistical framework that can estimate effects specific to chromosome, to sex, and their interactions (i.e., a dosage effect). Our results show substantially reduced Z-linked expression relative to autosomes in both sexes, as previously observed in bombycoid moths. This observation is consistent with an increasing body of evidence that some lepidopteran species possess an epigenetic dosage compensating mechanism that reduces Z chromosome expression in males to levels comparable with females. However, this mechanism appears to be imperfect in Heliconius , resulting in a modest dosage effect that produces an average 5–20% increase in male expression relative to females on the Z chromosome, depending on the tissue. Thus our results in Heliconius reflect a mixture of previous patterns reported for Lepidoptera. In Heliconius, a moderate pattern of incomplete dosage compensation persists apparently despite the presence of an epigenetic dosage compensating mechanism. The chromosomal distributions of sex-biased genes show an excess of male-biased and a dearth of female-biased genes on the Z chromosome relative to autosomes, consistent with predictions of sexually antagonistic evolution.

Description: Mycobacterium avium ( M. a. ) subsp. paratuberculosis (MAP)—the etiologic agent of Johne’s disease—affects cattle, sheep, and other ruminants worldwide. To decipher phenotypic differences among sheep and cattle strains (belonging to MAP-S [Type-I/III], respectively, MAP-C [Type-II]), comparative genome analysis needs data from diverse isolates originating from different geographic regions of the world. This study presents the so far best assembled genome of a MAP-S-strain: Sheep isolate JIII-386 from Germany. One newly sequenced cattle isolate (JII-1961, Germany), four published MAP strains of MAP-C and MAP-S from the United States and Australia, and M. a. subsp. hominissuis (MAH) strain 104 were used for assembly improvement and comparisons. All genomes were annotated by BacProt and results compared with NCBI (National Center for Biotechnology Information) annotation. Corresponding protein-coding sequences (CDSs) were detected, but also CDSs that were exclusively determined by either NCBI or BacProt. A new Shine–Dalgarno sequence motif (5'-AGCTGG-3') was extracted. Novel CDSs including PE-PGRS family protein genes and about 80 noncoding RNAs exhibiting high sequence conservation are presented. Previously found genetic differences between MAP-types are partially revised. Four of ten assumed MAP-S-specific large sequence polymorphism regions (LSP S s) are still present in MAP-C strains; new LSP S s were identified. Independently of the regional origin of the strains, the number of individual CDSs and single nucleotide variants confirms the strong similarity of MAP-C strains and shows higher diversity among MAP-S strains. This study gives ambiguous results regarding the hypothesis that MAP-S is the evolutionary intermediate between MAH and MAP-C, but it clearly shows a higher similarity of MAP to MAH than to Mycobacterium intracellulare .

Description: Eukaryotic organelles depend on nuclear genes to perpetuate their biochemical integrity. This is true for mitochondria in all eukaryotes and plastids in plants and algae. Then how do kleptoplasts, plastids that are sequestered by some sacoglossan sea slugs, survive in the animals’ digestive gland cells in the absence of the algal nucleus encoding the vast majority of organellar proteins? For almost two decades, lateral gene transfer (LGT) from algae to slugs appeared to offer a solution, but RNA-seq analysis, later supported by genome sequencing of slug DNA, failed to find any evidence for such LGT events. Yet, isolated reports continue to be published and are readily discussed by the popular press and social media, making the data on LGT and its support for kleptoplast longevity appear controversial. However, when we take a sober look at the methods used, we realize that caution is warranted in how the results are interpreted. There is no evidence that the evolution of kleptoplasty in sea slugs involves LGT events. Based on what we know about photosystem maintenance in embryophyte plastids, we assume kleptoplasts depend on nuclear genes. However, studies have shown that some isolated algal plastids are, by nature, more robust than those of land plants. The evolution of kleptoplasty in green sea slugs involves many promising and unexplored phenomena, but there is no evidence that any of these require the expression of slug genes of algal origin.

Description: The Matachewan Large Igneous Province (LIP) is interpreted to have formed during the early stages of mantle plume-induced continental break-up in the early Proterozoic. When the Matachewan LIP is reconstructed to its original configuration with units from the Superior Craton and other formerly adjacent blocks (Karelia, Kola, Wyoming and Hearne), the dyke swarms, layered intrusions and flood basalts, emplaced over the lifetime of the province, form one of the most extensive magmatic provinces recognized in the geological record. New geochemical data allow, for the first time, the Matachewan LIP to be considered as a single, coherent entity and show that Matachewan LIP rocks share a common tholeiitic composition and trace element geochemistry, characterized by enrichment in the most incompatible elements and depletion in the less incompatible elements. This signature, ubiquitous in early Proterozoic continental magmatic rocks, may indicate that the Matachewan LIP formed through contamination of the primary magmas with lithospheric material or that the early Proterozoic mantle had a fundamentally different composition from the modern mantle. In addition to the radiating geometry of the dyke swarms, a plume origin for the Matachewan LIP is consistent with the geochemistry of some of the suites; these suites are used to constrain a source mantle potential temperature of c. 1500–1550°C. Comparison of these mantle potential temperatures with estimated temperatures for the early Proterozoic upper mantle indicates that they are consistent with a hot mantle plume source for the magmatism. Geochemical data from coeval intrusions suggest that the plume head was compositionally heterogeneous and sampled material from both depleted and enriched mantle. As has been documented with less ancient but similarly vast LIPs, the emplacement of the Matachewan LIP probably had a significant impact on the early Proterozoic global environment. Compilation of the best age estimates for various suites shows that the emplacement of the Matachewan LIP occurred synchronously with the Great Oxidation Event. We explore the potential for the eruption of this LIP and the emission of its associated volcanic gases to have been a driver of the irreversible oxygenation of the Earth.

Description: Olivine major and trace element compositions from 12 basalts from the southern Payenia volcanic province in Argentina have been analyzed by electron microprobe and laser ablation inductively coupled plasma mass spectrometry. The olivines have high Fe/Mn and low Ca/Fe and many fall at the end of the global olivine array, indicating that they were formed from a pyroxene-rich source distinct from typical mantle peridotite. The olivines with the highest Fe/Mn have higher Zn/Fe, Zn and Co and lower Co/Fe than the olivines with lower Fe/Mn, also suggesting contributions from a pyroxene-rich source. Together with whole-rock radiogenic isotopes and elemental concentrations, the samples indicate mixing between two mantle sources: (1) a pyroxene-rich source with EM-1 ocean island basalt type trace element and isotope characteristics; (2) a peridotitic source with more radiogenic Pb that was metasomatized by subduction-zone fluids and/or melts. The increasing contributions from the pyroxene-rich source in the southern Payenia basalts are correlated with an increasing Fe-enrichment, which caused the olivines to have lower forsterite contents at a given Ni content. Al-in-olivine crystallization temperatures measured on olivine–spinel pairs are between 1155 and 1243°C and indicate that the magmas formed at normal upper mantle (asthenospheric) temperatures of ~1350°C. The pyroxene-rich material is interpreted to have been brought up from the deeper parts of the upper mantle by vigorous asthenospheric upwelling caused by break-off of the Nazca slab south of Payenia during the Pliocene and roll-back of the subducting slab beneath Payenia. The pyroxene-rich mantle mixed with peridotitic metasomatized South Atlantic mantle in the mantle wedge beneath Payenia.

Description: To reconstruct the magmatic–hydrothermal processes leading to porphyry Mo ore formation at the Climax Mo mine, Colorado, four magma units that were emplaced before, during and shortly after the mineralization events were investigated: (1) a pre-mineralization white dike of the Alma district; (2) the syn-mineralization Chalk Mountain Rhyolite; (3) a late- to post-mineralization rhyolite porphyry dyke; (4) a mafic enclave within the productive Bartlett stock. Melt inclusions, mineral inclusions and fluid inclusions in quartz phenocrysts were investigated by means of laser ablation inductively coupled plasma mass spectrometry, electron microprobe and microthermometry. Based on melt inclusion data both the Chalk Mountain Rhyolite and the rhyolite porphyry were ~10 times more fractionated than average granite and show geochemical characteristics of topaz rhyolites. They were saturated in magnetite, Mn-rich ilmenite, fluorite, aeschynite, monazite, pyrrhotite and thorite, and crystallized predominantly at 710–730°C, 1·2–2·6 kbar and log f O 2 FMQ + 2·2 (where FMQ is fayalite–magnetite–quartz). The silicate melt of the Chalk Mountain Rhyolite contained 3·5 ± 0·4 wt % F, 0·09 ± 0·03 wt % Cl, ≥ 3·0 wt % H 2 O, 15–90 µg g –1 Cs, 500–1500 µg g –1 Rb and 5–7 µg g –1 Mo, whereas that of the rhyolite porphyry contained 1·1 ± 0·3 wt % F and 4·9 ± 1·2 wt % H 2 O, but otherwise had a virtually identical major and trace element composition. The fluid exsolving from the latter melt had a bulk salinity of 10 ± 2 wt % NaCl equiv and contained of the order of 100 µg g –1 Mo. After emplacement of the Chalk Mountain Rhyolite magma at subvolcanic levels, extremely fractionated silicate melts coexisting with hypersaline brines (salt melts) and low-density vapor percolated at near-solidus conditions through the rock. These silicate melts contained 6·6 ± 0·4 wt % F, ≥ 7·5 ± 0·6 wt % H 2 O, 0·51 ± 0·05 wt % Cl, and up to 0·5 wt % Cs and 100 µg g –1 Mo, whereas the hypersaline brines contained 1–2 wt % Cs and 0·3–0·6 wt % Mo. However, owing to their negligible masses these liquids are unlikely to have played a major role in the mineralization process. The majority of Mo in the Climax deposit appears to have been derived from melts containing 5–7 µg g –1 Mo and bulk fluids containing ~100 µg g –1 Mo. These concentrations are similar to those found in similarly fractionated melts and fluids in barren and sub-economically mineralized intrusions. However, whereas in the latter intrusions fractionated melts occurred in a rather dispersed state, they seem to have been present as large, coherent masses in the apical parts of Climax-type porphyry Mo-forming magma systems. Efficient segregation of fractionated melts and fluids into the top of mineralizing magma chambers appears to have been promoted by high fluorine concentrations in the silicate melt, which was partly a primary feature, and partly an indirect consequence of other characteristics of within-plate magmatism.

Description: The Skaergaard intrusion, Greenland, is the type locality for Skaergaard-type mineralizations. Mineralization levels are perfectly concordant with igneous layering, up to 5 m thick, internally fractionated, and contain crystallized sulphide droplets and precious metal alloys, sulphides, arsenides and telluride. Immiscible Cu-rich sulphide droplets, formed in a mush zone below the roof, scavenged precious metals. They were subsequently dissolved and transported to the floor in late-formed, immiscible, Fe-rich mush melts. Mineralized stratigraphic intervals of floor gabbro formed in ‘proto-macrolayers‘, owing to local sulphide saturation in melt concentrated between floating plagioclase and sinking clinopyroxene. The floor mineralization is divided into four stratigraphic sections. Formation of the Lower Platinum Group Element Mineralization (LPGEM) involved: (1) crystallization of the bulk liquid liquidus paragenesis and in situ fractionation; (2) sulphide saturation and formation of sulphide droplets in melt in the upper part of ‘proto-macrolayers‘. After further in situ fractionation, the following steps occurred: (3) the onset of silicate–silicate immiscibility and the consequent loss of buoyant and immiscible Si-rich melt; (4) dissolution of unprotected droplets of sulphide melt present in the Fe-rich mush melt; (5) compaction-driven upwards loss of residual mush melt enriched in, for example, Au. The LPGEM preserves upward increasing bulk Pd/Pt (~6–13) owing to a continued supply of PGE and Au, with high Pd/Pt. The further development of the LPGEM ceased as the supply of precious metals to the floor waned. The Upper PGE Mineralization (UPGEM) subsequently formed from precious metals recycled in the floor. The UPGEM is characterized by increasing Au substitution in PGE phases, and a decrease in total PGE and Pd/Pt owing to upward fractionation in migrating mush melts and exhaustion of Pd and Pt. An upper Au-rich mineralization level (UAuM) was caused by late remobilization of Au and deposition on grain boundaries in fully crystallized gabbro. Cu concentrations (~150 ppm) are not correlated with PGE and Au. Repeated Cu mineralization levels (CuM), attaining 〉1000 ppm, occur above the Au levels, caused by local mush layer sulphide saturation. PGE, Au and Cu distributions in the floor mineralization reflect sub-liquidus, but supra-solidus, processes and reactions in mushes at the roof, wall and floor. Constraints provided by a new model for the mineralization provide the basis for re-evaluation of the solidification processes in the Skaergaard intrusion. We have identified the importance of extensive in situ fractionation and intrusion-wide elemental redistributions in immiscible Fe- and Si-rich silicate melts. Our model characterizes the floor cumulates as bulk liquid orthocumulates containing an upwards-increasing proportion crystallized from Fe-rich, immiscible mush melt. The roof-rocks are complementary to the floor, with downwards increasing proportions crystallized from the conjugate Si-rich melt. Petrographic observations and the relative timing of crystallization support the hypothesis that crystallization was restricted to marginal mush zones. Bulk melt remaining in the magma chamber evolved not, as generally assumed, as a result of loss of crystals grown from the bulk melt, but as the consequence of mixing with recycled and evolved melt expelled from the mush by compaction. Redistribution of Fe in immiscible melts may be common to mafic intrusions and puts into question the validity of petrogenetic modelling of bulk liquids in mafic intrusions based only on consideration of floor cumulates.

Description: We have determined experimentally the hydrous phase relations and trace element partitioning behaviour of ocean floor basalt protoliths at pressures and temperatures (3 GPa, 750–1000°C) relevant to melting in subduction zones. To avoid potential complexities associated with trace element doping of starting materials we have used natural, pristine mid-ocean ridge basalt (MORB from Kolbeinsey Ridge) and altered oceanic crust (AOC from Deep Sea Drilling Project leg 46, ~20°N Atlantic). Approximately 15 wt % water was added to starting materials to simulate fluid fluxing from dehydrating serpentinite underlying the oceanic crust. The vapour-saturated solidus is sensitive to basalt K 2 O content, decreasing from 825 ± 25°C in MORB (~0·04 wt % K 2 O) to 750°C in AOC (~0·25 wt % K 2 O). Textural evidence indicates that near-solidus fluids are sub-critical in nature. The residual solid assemblage in both MORB and AOC experiments is dominated by garnet and clinopyroxene, with accessory kyanite, epidote, Fe–Ti oxide and rutile (plus quartz–coesite, phengite and apatite below the solidus). Trace element analyses of quenched silica-rich melts show a strong temperature dependence of key trace elements. In contrast to the trace element-doped starting materials of previous studies, we do not observe residual allanite. Instead, abundant residual epidote provides the host for thorium and light rare earth elements (LREE), preventing LREE from being released (LREE 〈3 ppm at 750–900°C). Elevated Ba/Th ratios, characteristic of many arc basalts, are found to be generated within a narrow temperature field above the breakdown temperature of phengite, but below exhaustion of epidote. Melts with Ba/Th 〉1500 and La/Sm PUM (where PUM indicates primitive upper mantle) ~1, most closely matching the geochemical signal of arc lavas worldwide, were generated from AOC at 800–850°C.

Description: We constrain the physical nature of the magma reservoir and the mechanisms of rhyolite generation at Yellowstone caldera via detailed characterization of zircon and sanidine crystals hosted in three rhyolites erupted during the ( c . 170–70 ka) Central Plateau Member eruptive episode—the most recent post-caldera magmatism at Yellowstone. We present 238 U– 230 Th crystallization ages and trace-element compositions of the interiors and surfaces (i.e. unpolished rims) of single zircon crystals from each rhyolite. We compare these zircon data with 238 U– 230 Th crystallization ages of bulk sanidine separates coupled with chemical and isotopic data from single sanidine crystals. Zircon age and trace-element data demonstrate that the magma reservoir that sourced the Central Plateau Member rhyolites was long-lived (150–250 kyr) and genetically related to the preceding episode of magmatism, which occurred c . 256 ka. The interiors of most zircons in each rhyolite were inherited from unerupted material related to older stages of Central Plateau Member magmatism or the preceding late Upper Basin Member magmatism (i.e. are antecrysts). Conversely, most zircon surfaces crystallized near the time of eruption from their host liquids (i.e. are autocrystic). The repeated recycling of zircon interiors from older stages of magmatism demonstrates that sequentially erupted Central Plateau Member rhyolites are genetically related. Sanidine separates from each rhyolite yield 238 U– 230 Th crystallization ages at or near the eruption age of their host magmas, coeval with the coexisting zircon surfaces, but are younger than the coexisting zircon interiors. Chemical and isotopic data from single sanidine crystals demonstrate that the sanidines in each rhyolite are in equilibrium with their host melts, which considered along with their near-eruption crystallization ages suggests that nearly all Central Plateau Member sanidines are autocrystic. The paucity of antecrystic sanidine crystals relative to antecrystic zircons requires a model in which eruptible rhyolites are generated by extracting melt and zircons from a long-lived mush of immobile crystal-rich magma. In this process the larger sanidine crystals remain trapped in the locked crystal network. The extracted melts (plus antecrystic zircon) amalgamate into a liquid-dominated (i.e. eruptible) magma body that is maintained as a physically distinct entity relative to the bulk of the long-lived crystal mush. Zircon surfaces and sanidines in each rhyolite crystallize after melt extraction and amalgamation, and their ages constrain the residence time of eruptible magmas at Yellowstone. Residence times of the large-volume rhyolites (~40–70 km 3 ) are ≤1 kyr (conservatively 〈6 kyr), which suggests that large volumes of rhyolite can be generated rapidly by extracting melt from a crystal mush. Because the lifespan of the crystal mush that sourced the Central Plateau Member rhyolites is two orders of magnitude longer than the residence time of eruptible magma bodies within the reservoir, it is apparent that the Yellowstone magma reservoir spends most of its time in a largely crystalline (i.e. uneruptible) state, similar to the present-day magma reservoir, and that eruptible magma bodies are ephemeral features.

Description: We report and interpret new geochemical and Pb–Sr–Nd isotopic data from 325 samples of shield, late-shield, postshield, and rejuvenated stage lavas from Kauai and Niihau, the two most northwesterly islands in the Hawaiian island chain. Kauai is unique in the Hawaiian chain in that it exhibits a near-continuous geochemical transition from shield to postshield to rejuvenated stage volcanism between 4·4 and 3·6 Ma and has been continuously active over ~6 Myr. From c . 5·7 to 4·3 Ma, the shield stage of both islands produced tholeiitic basalts typical of other Hawaiian shield volcanoes. The Niihau basalts are more evolved and have high Gd/Yb compared with Kauai, indicating a higher residual garnet content in the source. Both Kauai and Niihau shield basalts have Kea-like trace element ratios, but isotopic ratios are transitional between Kea- and Loa-like compositions. The geochemical similarity of the two shields indicates that mantle sources in different regions of the plume source were similar, and that the 〈2 Ma Loa and Kea trends of the southeastern Hawaiian volcanoes are not observed. More Loa-like compositions are evident in shield lavas from eastern Kauai, where the enhanced Loa composition may reflect melting of low-melting temperature plume components as the island migrates off the hotter, more Kea-like, center of the Hawaiian plume. Postshield lavas and intrusive rocks on both islands are rare: Kauai includes alkalic basalts, hawaiites and mugearites that are isotopically homogeneous and include a significant depleted mantle component compared with the shield basalts, whereas the Niihau late-shield and postshield rocks consist of highly contrasting transitional tholeiites or basanites with variable but shield-like isotopic compositions. The Niihau postshield rocks represent variable, but lower degrees of melting of the shield mantle source. Large volumes of rejuvenated stage lavas cover both islands and also form submarine cone fields, but lava compositions are different. On Kauai, rejuvenated lavas range from melilitite to alkalic basalt with trace element, Nd isotope, and Pb isotope ratios that vary as a function of Th and SiO 2 content. Low-degree (high-Th) melts are dominated by a mixed Kea–Loihi component and high-degree (low-Th) melts include more of a depleted rejuvenated component (DRC) typified by rejuvenated stage lavas and xenoliths from nearby Kaula Island. With the exception of a single basanite, the Niihau rejuvenated stage lavas are uniformly alkalic basalt, with Sr and Ba excesses combined with depleted Th and Nb abundances relative to the light rare earth elements. Rejuvenated stage alkalic basalts from both islands are dominated by contributions from the DRC, which have high Sr/Ce and 87 Sr/ 86 Sr but low 206 Pb/ 204 Pb. The Sr-rich, possibly carbonate-bearing, DRC component may be distributed patchily in the rejuvenated stage mantle source such that, where present, the degree of partial melting was enhanced compared with the degree of partial melting of the Sr-poor, mixed Kea–Loihi component. Given the lack of a hiatus between postshield and rejuvenated stages on Kauai, the rejuvenated mantle source is already able to melt at the tail end of shield stage activity and no secondary melting mechanism is required to explain the rejuvenated stage.

Description: A number of sap-sucking insects harbor endosymbionts, which are thought to play an important role in the development of their hosts. One of the most important rice pests, the brown planthopper (BPH), Nilaparvata lugens (Stål), harbors an obligatory yeast-like symbiont (YLS) that cannot be cultured in vitro. Genomic information on this YLS would be useful to better understand its evolution. In this study, we performed genome sequencing of the YLS using both 454 and Illumina approaches, generating a draft genome that shows a slightly smaller genome size and relatively higher GC content than most ascomycete fungi. A phylogenomic analysis of the YLS supported its close relationship with insect pathogens. We analyzed YLS-specific genes and the categories of genes that are likely to have changed in the YLS during its evolution. The loss of mating type locus demonstrated in the YLS sheds light on the evolution of eukaryotic symbionts. This information about the YLS genome provides a helpful guide for further understanding endosymbiotic associations in hemiptera and the symbiotic replacement of ancient bacteria with a multifunctional YLS seems to have been a successful change.

Description: The RNA-directed DNA methylation (RdDM) pathway can be divided into three phases: 1) small interfering RNA biogenesis, 2) de novo methylation, and 3) chromatin modification. To determine the degree of conservation of this pathway we searched for key genes among land plants. We used OrthoMCL and the OrthoMCL Viridiplantae database to analyze proteomes of species in bryophytes, lycophytes, monilophytes, gymnosperms, and angiosperms. We also analyzed small RNA size categories and, in two gymnosperms, cytosine methylation in ribosomal DNA. Six proteins were restricted to angiosperms, these being NRPD4/NRPE4, RDM1, DMS3 (defective in meristem silencing 3), SHH1 (SAWADEE homeodomain homolog 1), KTF1, and SUVR2, although we failed to find the latter three proteins in Fritillaria persica , a species with a giant genome. Small RNAs of 24 nt in length were abundant only in angiosperms. Phylogenetic analyses of Dicer-like (DCL) proteins showed that DCL2 was restricted to seed plants, although it was absent in Gnetum gnemon and Welwitschia mirabilis . The data suggest that phases (1) and (2) of the RdDM pathway, described for model angiosperms, evolved with angiosperms. The absence of some features of RdDM in F. persica may be associated with its large genome. Phase (3) is probably the most conserved part of the pathway across land plants. DCL2, involved in virus defense and interaction with the canonical RdDM pathway to facilitate methylation of CHH, is absent outside seed plants. Its absence in G. gnemon , and W. mirabilis coupled with distinctive patterns of CHH methylation, suggest a secondary loss of DCL2 following the divergence of Gnetales.

Description: Comparisons of draft genome sequences of three geographically distinct isolates of Fusarium fujikuroi with two recently published genome sequences from the same species suggest diverse profiles of secondary metabolite production within F. fujikuroi . Species- and lineage-specific genes, many of which appear to exhibit expression profiles that are consistent with roles in host–pathogen interactions and adaptation to environmental changes, are concentrated in subtelomeric regions. These genomic compartments also exhibit distinct gene densities and compositional characteristics with respect to other genomic partitions, and likely play a role in the generation of molecular diversity. Our data provide additional evidence that gene duplication, divergence, and differential loss play important roles in F. fujikuroi genome evolution and suggest that hundreds of lineage-specific genes might have been acquired through horizontal gene transfer.

Description: Passerines are the largest avian order, and the 6,000 species comprise more than half of all extant bird species. This successful radiation probably had its origin in the Australasian region, but dating this origin has been difficult due to a scarce fossil record and poor biogeographic assumptions. Many of New Zealand’s endemic passerines fall within the deeper branches of the passerine radiation, and a well resolved phylogeny for the modern New Zealand element in the deeper branches of the oscine lineage will help us understand both oscine and passerine biogeography. To this end we present complete mitochondrial genomes representing all families of New Zealand passerines in a phylogenetic framework of over 100 passerine species. Dating analyses of this robust phylogeny suggest Passeriformes originated in the early Paleocene, with the major lineages of oscines "escaping" from Australasia about 30 Ma, and radiating throughout the world during the Oligocene. This independently derived conclusion is consistent with the passerine fossil record.

Description: Triplophysa fishes are the primary component of the fish fauna on the Tibetan Plateau and are well adapted to the high-altitude environment. Despite the importance of Triplophysa fishes on the plateau, the genetic mechanisms of the adaptations of these fishes to this high-altitude environment remain poorly understood. In this study, we generated the transcriptome sequences for three Triplophysa fishes, that is, Triplophysa siluroides , Triplophysa scleroptera , and Triplophysa dalaica , and used these and the previously available transcriptome and genome sequences from fishes living at low altitudes to identify potential genetic mechanisms for the high-altitude adaptations in Triplophysa fishes. An analysis of 2,269 orthologous genes among cave fish ( Astyanax mexicanus ), zebrafish ( Danio rerio ), large-scale loach ( Paramisgurnus dabryanus ), and Triplophysa fishes revealed that each of the terminal branches of the Triplophysa fishes had a significantly higher ratio of nonsynonymous to synonymous substitutions than that of the branches of the fishes from low altitudes, which provided consistent evidence for genome-wide rapid evolution in the Triplophysa genus. Many of the GO (Gene Ontology) categories associated with energy metabolism and hypoxia response exhibited accelerated evolution in the Triplophysa fishes compared with the large-scale loach. The genes that exhibited signs of positive selection and rapid evolution in the Triplophysa fishes were also significantly enriched in energy metabolism and hypoxia response categories. Our analysis identified widespread Triplophysa -specific nonsynonymous mutations in the fast evolving genes and positively selected genes. Moreover, we detected significant evidence of positive selection in the HIF (hypoxia-inducible factor)-1A and HIF-2B genes in Triplophysa fishes and found that the Triplophysa -specific nonsynonymous mutations in the HIF-1A and HIF-2B genes were associated with functional changes. Overall, our study provides new insights into the adaptations and evolution of fishes in the high-altitude environment of the Tibetan Plateau and complements previous findings on the adaptations of mammals and birds to high altitudes.

Description: Sponges harbor a complex consortium of microbial communities living in symbiotic relationship benefiting each other through the integration of metabolites. The mechanisms influencing a successful microbial association with a sponge partner are yet to be fully understood. Here, we sequenced the genome of Pseudovibrio sp. POLY-S9 strain isolated from the intertidal marine sponge Polymastia penicillus sampled from the Atlantic coast of Portugal to identify the genomic features favoring the symbiotic relationship. The draft genome revealed an exceptionally large genome size of 6.6 Mbp compared with the previously reported genomes of the genus Pseudovibrio isolated from a coral and a sponge larva. Our genomic study detected the presence of several biosynthetic gene clusters—polyketide synthase, nonribosomal peptide synthetase and siderophore—affirming the potential ability of the genus Pseudovibrio to produce a wide variety of metabolic compounds. Moreover, we identified a repertoire of genes encoding adaptive symbioses factors (eukaryotic-like proteins), such as the ankyrin repeats, tetratrico peptide repeats, and Sel1 repeats that improve the attachment to the eukaryotic hosts and the avoidance of the host’s immune response . The genome also harbored a large number of mobile elements (~5%) and gene transfer agents, which explains the massive genome expansion and suggests a possible mechanism of horizontal gene transfer. In conclusion, the genome of POLY-S9 exhibited an increase in size, number of mobile DNA, multiple metabolite gene clusters, and secretion systems, likely to influence the genome diversification and the evolvability.

Description: Gene regulatory networks (GRN) are central to developmental processes. They are composed of transcription factors and signaling molecules orchestrating gene expression modules that tightly regulate the development of organisms. The neural crest (NC) is a multipotent cell population that is considered a key innovation of vertebrates. Its derivatives contribute to shaping the astounding morphological diversity of jaws, teeth, head skeleton, or pigmentation. Here, we study the molecular evolution of the NC GRN by analyzing patterns of molecular divergence for a total of 36 genes in 16 species of bony fishes. Analyses of nonsynonymous to synonymous substitution rate ratios (d N /d S ) support patterns of variable selective pressures among genes deployed at different stages of NC development, consistent with the developmental hourglass model. Model-based clustering techniques of sequence features support the notion of extreme conservation of NC-genes across the entire network. Our data show that most genes are under strong purifying selection that is maintained throughout ray-finned fish evolution. Late NC development genes reveal a pattern of increased constraints in more recent lineages. Additionally, seven of the NC-genes showed signs of relaxation of purifying selection in the famously species-rich lineage of cichlid fishes. This suggests that NC genes might have played a role in the adaptive radiation of cichlids by granting flexibility in the development of NC-derived traits—suggesting an important role for NC network architecture during the diversification in vertebrates.

Description: Cymbomonas tetramitiformis —a marine prasinophyte—is one of only a few green algae that still retain an ancestral particulate-feeding mechanism while harvesting energy through photosynthesis. The genome of the alga is estimated to be 850 Mb–1.2 Gb in size—the bulk of which is filled with repetitive sequences—and is annotated with 37,366 protein-coding gene models. A number of unusual metabolic pathways (for the Chloroplastida) are predicted for C. tetramitiformis , including pathways for Lipid-A and peptidoglycan metabolism. Comparative analyses of the predicted peptides of C. tetramitiformis to sets of other eukaryotes revealed that nonphagocytes are depleted in a number of genes, a proportion of which have known function in feeding. In addition, our analysis suggests that obligatory phagotrophy is associated with the loss of genes that function in biosynthesis of small molecules (e.g., amino acids). Further, C. tetramitiformis and at least one other phago-mixotrophic alga are thus unique, compared with obligatory heterotrophs and nonphagocytes, in that both feeding and small molecule synthesis-related genes are retained in their genomes. These results suggest that early, ancestral host eukaryotes that gave rise to phototrophs had the capacity to assimilate building block molecules from inorganic substances (i.e., prototrophy). The loss of biosynthesis genes, thus, may at least partially explain the apparent lack of instances of permanent incorporation of photosynthetic endosymbionts in later-divergent, auxotrophic eukaryotic lineages, such as metazoans and ciliates.

Description: Chlamydiaceae are obligate intracellular bacteria that cause a diversity of severe infections among humans and livestock on a global scale. Identification of new species since 1989 and emergence of zoonotic infections, including abortion in women, underscore the need for genome sequencing of multiple strains of each species to advance our knowledge of evolutionary dynamics across Chlamydiaceae . Here, we genome sequenced isolates from avian, lower mammalian and human hosts. Based on core gene phylogeny, five isolates previously classified as Chlamydia abortus were identified as members of Chlamydia psittaci and Chlamydia pecorum. Chlamydia abortus is the most recently emerged species and is a highly monomorphic group that lacks the conserved virulence-associated plasmid. Low-level recombination and evidence for adaptation to the placenta echo evolutionary processes seen in recently emerged, highly virulent niche-restricted pathogens, such as Bacillus anthracis . In contrast, gene flow occurred within C. psittaci and other Chlamydiaceae species. The C. psittaci strain RTH, isolated from a red-tailed hawk ( Buteo jamaicensis ), is an outlying strain with admixture of C. abortus , C. psittaci , and its own population markers. An average nucleotide identity of less than 94% compared with other Chlamydiaceae species suggests that RTH belongs to a new species intermediary between C. psittaci and C. abortus . Hawks, as scavengers and predators, have extensive opportunities to acquire multiple species in their intestinal tract. This could facilitate transformation and homologous recombination with the potential for new species emergence. Our findings indicate that incubator hosts such as birds-of-prey likely promote Chlamydiaceae evolution resulting in novel pathogenic lineages.

Description: The causes of the great variation in nucleotide composition of prokaryotic genomes have long been disputed. Here, we use extensive metagenomic and whole-genome data to demonstrate that both phylogeny and the environment shape prokaryotic nucleotide content. We show that across environments, various phyla are characterized by different mean guanine and cytosine (GC) values as well as by the extent of variation on that mean value. At the same time, we show that GC-content varies greatly as a function of environment, in a manner that cannot be entirely explained by disparities in phylogenetic composition. We find environmentally driven differences in nucleotide content not only between highly diverged environments (e.g., soil, vs. aquatic vs. human gut) but also within a single type of environment. More specifically, we demonstrate that some human guts are associated with a microbiome that is consistently more GC-rich across phyla, whereas others are associated with a more AT-rich microbiome. These differences appear to be driven both by variations in phylogenetic composition and by environmental differences—which are independent of these phylogenetic composition differences. Combined, our results demonstrate that both phylogeny and the environment significantly affect nucleotide composition and that the environmental differences affecting nucleotide composition are far subtler than previously appreciated.

Description: Brachiopods are a lineage of invertebrates well known for the breadth and depth of their fossil record. Although the quality of this fossil record attracts the attention of paleontologists, geochemists, and paleoclimatologists, modern day brachiopods are also of interest to evolutionary biologists due to their potential to address a variety of questions ranging from developmental biology to biomineralization. The brachiopod shell is a composite material primarily composed of either calcite or calcium phosphate in close association with proteins and polysaccharides which give these composite structures their material properties. The information content of these biomolecules, sequestered within the shell during its construction, has the potential to inform hypotheses focused on describing how brachiopod shell formation evolved. Here, using high throughput proteomic approaches and next generation sequencing, we have surveyed and characterized the first shell-proteome and shell-forming transcriptome of any brachiopod, the South American Magellania venosa (Rhynchonelliformea: Terebratulida) . We find that the seven most abundant proteins present in the shell are unique to M. venosa , but that these proteins display biochemical features found in other metazoan biomineralization proteins. We can also detect some M. venosa proteins that display significant sequence similarity to other metazoan biomineralization proteins, suggesting that some elements of the brachiopod shell-forming proteome are deeply evolutionarily conserved. We also employed a variety of preparation methods to isolate shell proteins and find that in comparison to the shells of other spiralian invertebrates (such as mollusks) the shell ultrastructure of M. venosa may explain the effects these preparation strategies have on our results.

Description: Free fatty acid receptors (FFAR) belong to a family of five G-protein coupled receptors that are involved in the regulation of lipid metabolism, so that their loss of function increases the risk of obesity. The aim of this study was to determine the expansion of genes encoding paralogs of FFAR2 in the chicken, considered as a model organism for developmental biology and biomedical research. By estimating the gene copy number using quantitative polymerase chain reaction, genomic DNA resequencing, and RNA sequencing data, we showed the existence of 23 ± 1.5 genes encoding FFAR2 paralogs in the chicken genome. The FFAR2 paralogs shared an identity from 87.2% up to 99%. Extensive gene conversion was responsible for this high degree of sequence similarities between these genes, and this concerned especially the four amino acids known to be critical for ligand binding. Moreover, elevated nonsynonymous/synonymous substitution ratios on some amino acids within or in close-vicinity of the ligand-binding groove suggest that positive selection may have reduced the effective rate of gene conversion in this region, thus contributing to diversify the function of some FFAR2 paralogs. All the FFAR2 paralogs were located on a microchromosome in a same linkage group. FFAR2 genes were expressed in different tissues and cells such as spleen, peripheral blood mononuclear cells, abdominal adipose tissue, intestine, and lung, with the highest rate of expression in testis. Further investigations are needed to determine whether these chicken-specific events along evolution are the consequence of domestication and may play a role in regulating lipid metabolism in this species.

Description: A new thermodynamic model is presented for calculating phase relations in peridotite, from 0·001 to 60 kbar and from 800°C to liquidus temperatures, in the system NCFMASOCr. This model system is large enough to simulate phase relations and melting of natural peridotite and basaltic liquids. Calculations in the program thermocalc illustrate mantle phase relationships and melting conditions, specifically for the peridotite composition KLB-1. The garnet–spinel transition zone intersects the solidus at 21·4–21·7 kbar, where both Fe 3+ and Cr increase spinel stability, expanding the width of the transition. Orthopyroxene is lost at the solidus at 42 kbar in KLB-1, although this pressure is very sensitive to bulk composition. Calculated oxidation states are in excellent agreement with measured log f O 2 for xenolith suites with mantle Fe 2 O 3 contents in the range 0·1–0·3 wt %. It appears that mantle oxidation state is not just a simple function of P and T , but depends on phase assemblage, and may vary in a complex way within a single assemblage. The liquid model performs well, such that calculated solidus, melt productivity and liquid compositions compare favourably with those of experimental studies, permitting its use in interpolating between, and extrapolating from, experimental P–T conditions. Experimentally challenging but geologically useful regimes can be explored, such as subsolidus samples and very low melt fractions, with application to both mantle xenoliths and the origin of basalt.

Description: The anorthositic members of the Mealy Mountains Intrusive Suite (MMIS; Labrador, Canada) are host to 0·5–5 m diameter pegmatitic, pod-like segregations, originally described as graphic granite pods. U–Pb zircon geochronology confirms that the pods are coeval with the 1650–1630 Ma emplacement age range for the MMIS, yielding ages of 1654 ± 8 to 1628 ± 3·5 Ma. Petrographic and geochemical analysis of five pods from anorthositic rocks of the MMIS reveals that the pods have a diverse compositional range from monzodiorite to granite, varying from Fe-rich and Si-poor, to Fe-poor and Si-rich compositions. Fe-rich, Si-poor pods in the MMIS and other massifs (e.g. Laramie Anorthosite Complex) tend to be hosted by olivine-bearing anorthosites, whereas Si-rich, Fe-poor pods are hosted by pyroxene-bearing anorthosites. Each pod shows a range of graphic, myrmekitic and symplectitic textures, along with distinctive mineral assemblages (e.g. apatite and zircon) and highly enriched trace-element compositions. Evolved mineral assemblages, high concentrations of Fe, Ti and P (and in some cases SiO 2 ), and 10–1000 x chondrite enrichment in light rare earth elements, U, Th and Rb indicate that many of the pods are highly fractionated. The array of textural intergrowths provides clues about the final stages of crystallization in the pods and, by extension, the anorthosites. Macroscopic quartz–K-feldspar graphic intergrowths indicate high-viscosity, fluid-bearing and significantly undercooled magmatic conditions, whereas microscopic myrmekitic (plagioclase–quartz) and symplectitic (plagioclase–orthopyroxene) intergrowths on primary grain boundaries indicate replacement of phases in the presence of reactive fluids. In assessing the nature of these pegmatitic pods based on field, petrographic and geochemical evidence, we conclude that they represent the fluid-bearing, late-stage crystallization products of a residual liquid in the massif anorthosite system. The Fe and Si compositional variations observed in these late-stage pods can be linked to a fundamental olivine–pyroxene dichotomy observed in most Proterozoic anorthosite massifs, suggesting that pulses of magma experience variable contamination (in amount and/or composition) leading to varying differentiation paths. A range of lithologies (monzonites, monzonorites, ferrodiorites and jotunites) observed in similar pod-like structures, as well as dykes and plutons, has been observed in other Proterozoic anorthosite massifs and all have, at one time or another, been interpreted as the residual liquids of anorthosite crystallization. Our observation of in situ pods with similar compositions to all of the aforementioned lithologies, and displaying textures indicative of late-stage crystallization, supports the notion that all of these associated lithologies can be interpreted as comagmatic with, but variably contaminated and isolated residual liquids of, anorthosite crystallization. However, using isotopic evidence we cannot support the notion that the far larger granitic plutons associated with Proterozoic anorthosites are also residual liquids of anorthositic magma fractionation.

Description: We report the results of experiments on two natural marine sediments with different carbonate contents (calcareous clay: CO 2 = 6·1 wt %; marl: CO 2 = 16·2 wt %) at subduction-zone conditions (3 GPa, 750–1200°C). Water (7–15 wt %) was added to the starting materials to simulate the effects of external water addition from within the subducting slab. The onset of melting is at 760°C in water-rich experiments; melt becomes abundant by 800°C. In contrast, the onset of melting in published, water-poor experiments occurs at variable temperatures with the production of significant melt fractions being restricted to more than 900°C (phengite-out). The different solidus temperatures ( T solidus ) can be ascribed to variable fluid X H2O [H 2 O/(CO 2 + H 2 O)], which, in turn, depends on bulk K 2 O, H 2 O and CO 2 . Partial melts in equilibrium with residual garnet, carbonate, quartz/coesite, epidote, rutile, kyanite, phengite, and clinopyroxene are granitic in composition, with substantial dissolved volatiles. Supersolidus runs always contain both silicate melt and solute-rich fluid, indicating that experimental conditions lie below the second critical endpoint in the granite–H 2 O–CO 2 system. Carbonatite melt coexists with silicate melt and solute-rich fluid above 1100°C in the marl. The persistence of carbonate to high temperature, in equilibrium with CO 2 -rich hydrous melts, provides a mechanism to both supply CO 2 to arc magmas and recycle carbon into the deep Earth. The trace element compositions of the experimental glasses constrain the potential contribution of calcareous sediment to arc magmas. The presence of residual epidote and carbonate confers different trace element characteristics when compared with the trace element signal of Ca-poor marine sediments (e.g. pelagic clays). Notably, epidote retains Th and light rare earth elements, such that some melts derived from calcareous sediments have elevated Ba/Th and U/Th, and low La/Sm PUM , thereby resembling fluids conventionally ascribed to altered oceanic crust. Our results emphasize the importance of residual mineralogy, rather than source lithology, in controlling the trace element characteristics of slab-derived fluids.

Description: Three crystal-poor obsidian samples (one dacite, 67 wt % SiO 2 ; two rhyolites, 73 and 75 wt % SiO 2 ), which erupted effusively from monogenetic vents, contain sparse (〈2%) plagioclase phenocrysts that span a remarkably wide and continuous range in composition (≤30 mol % An). Many, but not all, of the plagioclase crystals display diffusion-limited growth textures (e.g. swallow-tails, skeletal, vermiform). Hypotheses to explain the paradox of a wide compositional range despite a low abundance of plagioclase include (1) incorporation of xenocrysts and/or magma mingling, (2) slow crystallization of plagioclase driven by slow cooling in a magma chamber, (3) slow crystallization of plagioclase followed by a resorption (e.g. heating) event, and (4) crystallization driven by rapid degassing (i.e. loss of melt H 2 O) ± rapid cooling during ascent. To test these hypotheses, a series of phase equilibrium experiments were conducted under pure-H 2 O fluid-saturated conditions in a cold-seal pressure vessel between 30 and 300 MPa and 750 and 950°C. The results show that the plagioclase population in each obsidian sample could have grown from their respective melts, with the exception of a single calcic core (An 60–63 ) in one sample. The results additionally rule out slow cooling in a magma chamber, because this would lead to equilibrium abundances of plagioclase (≤20%), which are far higher than what is observed in the samples (〈2%). Nor can resorption (i.e. heating) explain the low abundance of plagioclase, because this would eliminate the more sodic plagioclase crystals and hence the wide compositional range of plagioclase that is observed. The most viable hypothesis is that the sparse plagioclase phenocrysts grew relatively rapidly during magma ascent to the surface; this is consistent with the results of isothermal (850°C) continuous decompression experiments (2·9, 1·0, 0·8, and 0·1 MPa h –1 ), under pure-H 2 O fluid-saturated conditions, which were performed on one of the rhyolites (MLV-36; 73 wt % SiO 2 ) and quenched at P H2O = 89, 58 and 40 MPa. The four decompression rates correspond to degassing rates of 1·6, 0·56, 0·45 and 0·06 wt % H 2 O per day. Decompressions ≥1·0 MPa( P H2O ) h –1 , initiated above the liquidus, quenched to 100% glass at all final P H2O . Decompressions at 0·8 MPa( P H2O ) h –1 , also initiated above the liquidus, led to plagioclase crystals nearly five times larger than those grown in runs decompressed at the same rate, but initiated just below the plagioclase-in curve. It is the kinetic hindrance to nucleation that permits crystal growth to be concentrated on relatively few crystals, leading to larger crystals. Plagioclase growth rates from these experiments show that the largest phenocrysts (~1 mm) in the MLV-36 obsidian could have grown in 〈42 h. A cooling rate of ~1·2°C h –1 closely matches both the increase in melt viscosity with time and the effective undercooling with time that occurs during the 0·8 MPa( P H2O ) h –1 decompression over the first 50 h. The combined results point to crystallization of sparse plagioclase driven by relatively rapid rates of degassing ± cooling during ascent to the surface of melts that were initially above their liquidus. The obsidian samples must have been efficiently segregated as nearly 100% liquids from their respective source regions at H 2 O-fluid undersaturated conditions to attain a degree of superheating upon ascent before reaching fluid saturation.

Description: The Jurassic Vestfjella dyke swarm at the volcanic rifted margin of western Dronning Maud Land represents magmatism related to the incipient Africa–Antarctica rift zone; that is, rift-assemblage magmatism of the Karoo continental flood basalt (CFB) province. Geochemical and Nd–Sr isotopic data for basaltic and picritic dyke samples indicate diverse low-Ti and high-Ti tholeiitic compositions with Nd (180 Ma) ranging from +8 to –17. Combined with previously reported data on a subcategory of ferropicritic dykes, our new data facilitate grouping of the Vestfjella dyke swarm into seven geochemically distinct types. The majority of the dykes exhibit geochemical affinity to continental lithosphere and can be correlated with two previously identified chemical types (CT) of the wall-rock CFB lavas and are accordingly referred to as the CT1 and CT3 dykes. The less abundant Low-Nb and High-Nb dykes, a relatively enriched subtype of CT3 (CT3-E) dykes, and dykes belonging to the depleted and enriched ferropicrite suites represent magma types found only as intrusions. The chemically mid-ocean ridge basalt (MORB)-like Low-Nb and the depleted ferropicrite suite dykes represent, respectively, relatively high- and low-degree partial melting of the same overall depleted mantle (DM)-affinity source in the sublithospheric mantle. In contrast, we ascribe the chemically ocean island basalt (OIB)-like High-Nb dykes and the enriched ferropicrite suite dykes to melting of enriched components in the sublithospheric mantle. Geochemical modelling suggests that the low-Ti affinity CT1 and CT3, and high-Ti affinity CT3-E magma types of Vestfjella dyke may predominantly result from mixing of DM-sourced Low-Nb type magmas with 〈10 wt % of crust- and lithospheric mantle-derived melts. U/Pb zircon dating confirms synchronous emplacement of CT1 dykes and Karoo main-stage CFBs at 182·2 ± 0·9 and 182·2 ± 0·8 Ma, whereas two 40 Ar/ 39 Ar plagioclase plateau ages of 189·2 ± 2·3 Ma (CT1) and 185·5 ± 1·8 Ma (depleted ferropicrite suite), and a mini-plateau age of 186·9 ± 2·8 Ma (CT3-E) for the Vestfjella dykes raise the question of whether the onset of rift-zone magmatism could predate the province-wide c. 179–183 Ma main stage of Karoo magmatism. Notably variable Ca/K spectra suggest that younger 40 Ar/ 39 Ar plagioclase plateau ages of 173, 170, 164, and 154 Ma are related to crystallization of secondary minerals during the late-stage tectono-magmatic development of the Antarctic rifted margin. The occurrence of rare MORB- and OIB-like magma types in Vestfjella and along the African and Antarctic rifted margins suggests melting of geochemically variable depleted and enriched sublithospheric mantle beneath the Africa–Antarctica rift zone. Our models for the Vestfjella dyke swarm indicate that the voluminous lithosphere-affinity low-Ti and high-Ti rift-assemblage tholeiites could have been derived from MORB-like parental magmas by contamination, which implies sublithospheric depleted mantle as the principal source of the CFB magmas of the Africa–Antarctica rift zone.

Description: Monazite laser ablation–split-stream inductively coupled plasma–mass spectrometry (LASS) was used to date monazite in situ in Barrovian-type micaschists of the Moravian zone in the Thaya window, Bohemian Massif. Petrography and garnet zoning combined with pseudosection modelling show that rocks from staurolite–chlorite, staurolite, kyanite and kyanite–sillimanite zones record burial in the S 1 fabric under a moderate geothermal gradient from 4–4·5 kbar and ~530–540°C to 5 kbar and 570°C, 6–7 kbar and 600–640°C, 7·5–8 kbar and 630–650°C, and 8 kbar and 650°C, respectively. In the kyanite and kyanite–sillimanite zones, garnet rim chemistry and local syntectonic replacement of garnet by sillimanite–biotite aggregates point to re-equilibration at 5·5–6 kbar and 630–650°C in the S 2 fabric. Heterogeneously developed retrograde shear zones (S 3 ) are marked by widespread chloritization, but minor chlorite is present in the studied samples. Monazite abundance and size increase with metamorphic grade from 5 µm in the staurolite–chlorite zone to 〉100 µm in the kyanite and kyanite–sillimanite zones. Irrespective of the monazite-forming reaction, this is interpreted as the onset of limited prograde monazite growth at staurolite grade, and continued prograde monazite growth after the kyanite-in reaction, compatible with conditions of about 5·5 kbar and 570°C and 7·5 kbar and 630°C from pseudosection modelling. Monazite is zoned, showing embayments and sharp boundaries between zones, with low Y in the staurolite zone, high-Y cores and low-Y rims in the kyanite zone, and high-Y cores, a low-Y mantle and a high-Y rim in the sillimanite zone. The 207 Pb-corrected 238 U/ 206 Pb ages from three samples range from 344 ± 7 to 330 ± 7 Ma, irrespective of metamorphic grade. The dates from monazite inclusions are interpreted as the ages of the staurolite- and kyanite-in reactions along the prograde path at 340 and 337 ± 7 Ma, respectively. The monazite in the matrix (and some inclusions) is interpreted as dating the prograde crystallization at (340–337) ± 7 Ma within the S 1 fabric, and then being affected by recrystallization at or down to 332 ± 7 Ma in the S 2 and S 3 fabrics. The two groups of data, for 340–337 and 332 Ma, are significantly different when only their in-run uncertainties (±1–3 Myr) are compared and indicate a 9 ± 3 Myr period of monazite (re)crystallization. A systematic increase in heavy rare earth element (HREE) content with decreasing monazite age from 344 to 335 Ma is correlated with growth on the prograde P–T path; the drop in HREE of monazite at 335–328 Ma is assigned to recrystallization. The presence of chlorite even in the least retrogressed samples witnesses limited external fluid availability on the retrograde P–T path. Migration of this fluid was probably responsible for heterogeneous fluid-assisted recrystallization and resetting of original prograde monazite, even where included in garnet, staurolite or kyanite. It is suggested that the rocks passed the chlorite-in reaction on the retrograde path at 332 ± 7 Ma. The timing of burial in the Thaya window, a deformed part of the underthrust Brunia microcontinent, was coeval with exhumation of granulites and migmatites of the Moldanubian orogenic root at c. 340 Ma.

Description: The Fanshan intrusion in the North China Craton (NCC) is concentrically zoned with syenite in the core (Unit 1), surrounded by ultramafic rocks (clinopyroxenite and biotite clinopyroxenite; Unit 2), and an outer rim of garnet-rich clinopyroxenite and orthoclase clinopyroxenite and syenite (Unit 3). The intrusive rocks are composed of variable amounts of Ca-rich augite, biotite, orthoclase, melanite, garnet, magnetite and apatite, with minor primary calcite. Monomineralic apatite rocks, nelsonite and glimmerite exclusively occur in Unit 2. Geochemically, the Fanshan rocks are highly enriched in light rare earth elements (LREE) and large ion lithophile elements (LILE), moderately depleted in high field strength elements (HFSE), and have a limited range of Sr–Nd–O isotopic compositions. The similar mineralogy, mineral compositions, and trace element characteristics of the three units suggest that all the rocks are co-magmatic. The parental magma is ultrapotassic and is akin to kamafugite. Very low-degree partial melting of metasomatized lithospheric mantle best explains the geochemistry and petrogenesis of the parental magmas of the Fanshan intrusion. We propose that the mantle source may have been metasomatized by a hydrous carbonate-bearing melt, which has imprinted the enriched Sr–Nd isotopic signature and incompatible element enrichment with conspicuous negative Nb–Ta–Zr–Hf–Ti anomalies and LREE enrichments. The mantle source enrichment may be correlated with oceanic sediment recycling during southward subduction of the Paleo-Asian oceanic plate during the Carboniferous and Permian. We propose that crystal settling and mechanical sorting combined with repeated primitive magma replenishment and mixing with previously fractionated magma is the predominant process responsible for the formation of the apatite ores.

Description: Experimental studies of mantle petrology find that small concentrations of water and carbon dioxide have a large effect on the solidus temperature and distribution of melting in the upper mantle. However, it has remained unclear what effect small fractions of deep, volatile-rich melts have on melt transport and reactive melting in the shallow asthenosphere. Here we present theory and computations indicating that low-degree, reactive, volatile-rich melts cause channelization of magmatic flow at depths approximately corresponding to the anhydrous solidus temperature. These results are obtained with a novel method to simulate the thermochemical evolution of the upper mantle in the presence of volatiles. The method uses a thermodynamically consistent framework for reactive, disequilibrium, multi-component melting. It is coupled with a system of equations representing conservation of mass, momentum, and energy for a partially molten grain aggregate. Application of this method in two-phase, three-component upwelling-column models demonstrates that it reproduces leading-order features of hydrated and carbonated peridotite melting; in particular, it captures the production of low-degree, volatile-rich melt at depths far below the volatile-free solidus. The models predict that segregation of volatile-rich, deep melts promotes a reactive channelling instability that creates fast and chemically isolated pathways of melt extraction. Reactive channelling occurs where volatile-rich melts flux the base of the silicate melting region, enhancing dissolution of fusible components from the ambient mantle. We find this effect to be similarly expressed for models of both hydrated and carbonated mantle melting. These findings indicate that despite their small concentrations, water and carbon dioxide have an important control on the extent and style of magma genesis, as well as on the dynamics of melt transport.

Description: Loss of introns in plant mitochondrial genes is commonly explained by retroprocessing. Under this model, an mRNA is reverse transcribed and integrated back into the genome, simultaneously affecting the contents of introns and edited sites. To evaluate the extent to which retroprocessing explains intron loss, we analyzed patterns of intron content and predicted RNA editing for whole mitochondrial genomes of 30 species in the monocot order Alismatales. In this group, we found an unusually high degree of variation in the intron content, even expanding the hitherto known variation among angiosperms. Some species have lost some two-third of the cis -spliced introns. We found a strong correlation between intron content and editing frequency, and detected 27 events in which intron loss is consistent with the presence of nucleotides in an edited state, supporting retroprocessing. However, we also detected seven cases of intron loss not readily being explained by retroprocession. Our analyses are also not consistent with the entire length of a fully processed cDNA copy being integrated into the genome, but instead indicate that retroprocessing usually occurs for only part of the gene. In some cases, several rounds of retroprocessing may explain intron loss in genes completely devoid of introns. A number of taxa retroprocessing seem to be very common and a possibly ongoing process. It affects the entire mitochondrial genome.

Description: The luminous bacterial symbionts of anomalopid flashlight fish are thought to be obligately dependent on their hosts for growth and share several aspects of genome evolution with unrelated obligate symbionts, including genome reduction. However, in contrast to most obligate bacteria, anomalopid symbionts have an active environmental phase that may be important for symbiont transmission. Here we investigated patterns of evolution between anomalopid symbionts compared with patterns in free-living relatives and unrelated obligate symbionts to determine if trends common to obligate symbionts are also found in anomalopid symbionts. Two symbionts, " Candidatus Photodesmus katoptron" and " Candidatus Photodesmus blepharus," have genomes that are highly similar in gene content and order, suggesting genome stasis similar to ancient obligate symbionts present in insect lineages. This genome stasis exists in spite of the symbiont’s inferred ability to recombine, which is frequently lacking in obligate symbionts with stable genomes. Additionally, we used genome comparisons and tests of selection to infer which genes may be particularly important for the symbiont’s ecology compared with relatives. In keeping with obligate dependence, substitution patterns suggest that most symbiont genes are experiencing relaxed purifying selection compared with relatives. However, genes involved in motility and carbon storage, which are likely to be used outside the host, appear to be under increased purifying selection. Two chemoreceptor chemotaxis genes are retained by both species and show high conservation with amino acid sensing genes, suggesting that the bacteria may actively seek out hosts using chemotaxis toward amino acids, which the symbionts are not able to synthesize.

Description: Cynomoriaceae, one of the last unplaced families of flowering plants, comprise one or two species or subspecies of root parasites that occur from the Mediterranean to the Gobi Desert. Using Illumina sequencing, we assembled the mitochondrial and plastid genomes as well as some nuclear genes of a Cynomorium specimen from Italy. Selected genes were also obtained by Sanger sequencing from individuals collected in China and Iran, resulting in matrices of 33 mitochondrial, 6 nuclear, and 14 plastid genes and rDNAs enlarged to include a representative angiosperm taxon sampling based on data available in GenBank. We also compiled a new geographic map to discern possible discontinuities in the parasites’ occurrence. Cynomorium has large genomes of 13.70–13.61 (Italy) to 13.95–13.76 pg (China). Its mitochondrial genome consists of up to 49 circular subgenomes and has an overall gene content similar to that of photosynthetic angiosperms, while its plastome retains only 27 of the normally 116 genes. Nuclear, plastid and mitochondrial phylogenies place Cynomoriaceae in Saxifragales, and we found evidence for several horizontal gene transfers from different hosts, as well as intracellular gene transfers.

Description: The male-specific regions of primate Y-chromosomes (MSY) are enriched for multi-copy genes highly expressed in the testis. These genes are located in large repetitive sequences arranged as palindromes, inverted-, and tandem repeats termed amplicons. In humans, these genes have critical roles in male fertility and are essential for the production of sperm. The structure of human and chimpanzee amplicon sequences show remarkable difference relative to the remainder of the genome, a difference that may be the result of intense selective pressure on male fertility. Four subspecies of common chimpanzees have undergone extended periods of isolation and appear to be in the early process of subspeciation. A recent study found amplicons enriched for testis-expressed genes on the primate X-chromosome the target of hard selective sweeps, and male-fertility genes on the Y-chromosome may also be the targets of selection. However, little is understood about Y-chromosome amplicon diversity within and across chimpanzee populations. Here, we analyze nine common chimpanzee (representing three subspecies: Pan troglodytes schweinfurthii , Pan troglodytes ellioti , and Pan troglodytes verus ) and two bonobo ( Pan paniscus) male whole-genome sequences to assess Y ampliconic copy-number diversity across the Pan genus. We observe that the copy number of Y chromosome amplicons is variable among chimpanzees and bonobos, and identify several lineage-specific patterns, including variable copy number of azoospermia candidates RBMY and DAZ . We detect recurrent switchpoints of copy-number change along the ampliconic tracts across chimpanzee populations, which may be the result of localized genome instability or selective forces.

Description: De novo genes, which originate from ancestral nongenic sequences, are one of the most important sources of protein-coding genes. This origination process is crucial for the adaptation of organisms. However, how de novo genes arise and become fixed in a population or species remains largely unknown. Here, we identified 782 de novo genes from the model plant Arabidopsis thaliana and divided them into three types based on the availability of translational evidence, transcriptional evidence, and neither transcriptional nor translational evidence for their origin. Importantly, by integrating multiple types of omics data, including data from genomes, epigenomes, transcriptomes, and translatomes, we found that epigenetic modifications (DNA methylation and histone modification) play an important role in the origination process of de novo genes. Intriguingly, using the transcriptomes and methylomes from the same population of 84 accessions, we found that de novo genes that are transcribed in approximately half of the total accessions within the population are highly methylated, with lower levels of transcription than those transcribed at other frequencies within the population. We hypothesized that, during the origin of de novo gene alleles, those neutralized to low expression states via DNA methylation have relatively high probabilities of spreading and becoming fixed in a population. Our results highlight the process underlying the origin of de novo genes at the population level, as well as the importance of DNA methylation in this process.

Description: Halophilic microbes living in hypersaline environments must counteract the detrimental effects of low water activity and salt interference. Some halophilic prokaryotes equilibrate their intracellular osmotic strength with the extracellular milieu by importing inorganic solutes, mainly potassium. These "salt-in" organisms characteristically have proteins that are highly enriched with acidic and hydrophilic residues. In contrast, "salt-out" halophiles accumulate large amounts of organic solutes like amino acids, sugars and polyols, and lack a strong signature of halophilicity in the amino acid composition of cytoplasmic proteins. Studies to date have examined halophilic prokaryotes, yeasts, or algae, thus virtually nothing is known about the molecular adaptations of the other eukaryotic microbes, that is, heterotrophic protists (protozoa), that also thrive in hypersaline habitats. We conducted transcriptomic investigations to unravel the molecular adaptations of two obligately halophilic protists, Halocafeteria seosinensis and Pharyngomonas kirbyi . Their predicted cytoplasmic proteomes showed increased hydrophilicity compared with marine protists. Furthermore, analysis of reconstructed ancestral sequences suggested that, relative to mesophiles, proteins in halophilic protists have undergone fewer substitutions from hydrophilic to hydrophobic residues since divergence from their closest relatives. These results suggest that these halophilic protists have a higher intracellular salt content than marine protists. However, absence of the acidic signature of salt-in microbes suggests that Haloc. seosinensis and P. kirbyi utilize organic osmolytes to maintain osmotic equilibrium. We detected increased expression of enzymes involved in synthesis and transport of organic osmolytes, namely hydroxyectoine and myo-inositol, at maximal salt concentration for growth in Haloc. seosinensis , suggesting possible candidates for these inferred organic osmolytes.

Description: MicroRNAs are small (~22 nt) noncoding RNAs that repress translation and therefore regulate the production of proteins from specific target mRNAs. microRNAs have been found to function in diverse aspects of gene regulation within animal development and many other processes. Among invertebrates, both conserved and novel, lineage specific, microRNAs have been extensively studied predominantly in holometabolous insects such as Drosophila melanogaster . However little is known about microRNA repertoires in other arthropod lineages such as the chelicerates. To understand the evolution of microRNAs in this poorly sampled subphylum, we characterized the microRNA repertoire expressed during embryogenesis of the common house spider Parasteatoda tepidariorum . We identified a total of 148 microRNAs in P. tepidariorum representing 66 families. Approximately half of these microRNA families are conserved in other metazoans, while the remainder are specific to this spider. Of the 35 conserved microRNAs families 15 had at least two copies in the P. tepidariorum genome. A BLAST-based approach revealed a similar pattern of duplication in other spiders and a scorpion, but not among other chelicerates and arthropods, with the exception of a horseshoe crab. Among the duplicated microRNAs we found examples of lineage-specific tandem duplications, and the duplication of entire microRNA clusters in three spiders, a scorpion, and in a horseshoe crab. Furthermore, we found that paralogs of many P. tepidariorum microRNA families exhibit arm switching, which suggests that duplication was often followed by sub- or neofunctionalization. Our work shows that understanding the evolution of microRNAs in the chelicerates has great potential to provide insights into the process of microRNA duplication and divergence and the evolution of animal development.

Description: Family Hominidae, which includes humans and great apes, is recognized for unique complex social behavior and intellectual abilities. Despite the increasing genome data, however, the genomic origin of its phenotypic uniqueness has remained elusive. Clade-specific genes and highly conserved noncoding sequences (HCNSs) are among the high-potential evolutionary candidates involved in driving clade-specific characters and phenotypes. On this premise, we analyzed whole genome sequences along with gene orthology data retrieved from major DNA databases to find Hominidae-specific (HS) genes and HCNSs. We discovered that Down syndrome critical region 4 ( DSCR4 ) is the only experimentally verified gene uniquely present in Hominidae. DSCR4 has no structural homology to any known protein and was inferred to have emerged in several steps through LTR/ERV1, LTR/ERVL retrotransposition, and transversion. Using the genomic distance as neutral evolution threshold, we identified 1,658 HS HCNSs. Polymorphism coverage and derived allele frequency analysis of HS HCNSs showed that these HCNSs are under purifying selection, indicating that they may harbor important functions. They are overrepresented in promoters/untranslated regions, in close proximity of genes involved in sensory perception of sound and developmental process, and also showed a significantly lower nucleosome occupancy probability. Interestingly, many ancestral sequences of the HS HCNSs showed very high evolutionary rates. This suggests that new functions emerged through some kind of positive selection, and then purifying selection started to operate to keep these functions.

Description: To progress our understanding of molecular evolution from a collection of well-studied genes toward the level of the cell, we must consider whole systems. Here, we reveal the evolution of an important intracellular signaling system. The calcium-signaling toolkit is made up of different multidomain proteins that have undergone duplication, recombination, sequence divergence, and selection. The picture of evolution, considering the repertoire of proteins in the toolkit of both extant organisms and ancestors, is radically different from that of other systems. In eukaryotes, the repertoire increased in both abundance and diversity at a far greater rate than general genomic expansion. We describe how calcium-based intracellular signaling evolution differs not only in rate but in nature, and how this correlates with the disparity of plants and animals.

Description: A study of whole-rock major and trace element and Sr–Nd–Pb–Hf isotope compositions, combined with zircon U–Pb ages and Hf–O isotopes, for postcollisional intermediate volcanic rocks from the Dabie orogen, China provides constraints on the origin of andesitic magmas and insights into slab–mantle interaction in continental subduction channels. The volcanic rocks exhibit variable contents of SiO 2 (50·28–63·86 wt %), MgO (1·18–4·65 wt %), (Fe 2 O 3 ) T (3·60–8·53 wt %), Al 2 O 3 (12·92–18·95 wt %), Na 2 O (2·08–6·30 wt %) and K 2 O (0·73–5·25 wt %). They are mainly trachyandesites, with lesser amounts of basaltic trachyandesite, andesite, dacite and trachyte, characterized by subduction-like trace element distribution patterns showing enrichment of large ion lithophile elements and light rare earth elements but depletion of high field strength elements. The volcanic rocks have relatively enriched Sr–Nd–Pb–Hf isotope compositions, with high initial 87 Sr/ 86 Sr ratios of 0·7075–0·7110, highly negative Nd ( t ) values of –23·1 to –15·0, Hf ( t ) values of –29·8 to –18·3 and elevated 207 Pb/ 204 Pb and 208 Pb/ 204 Pb ratios at given 206 Pb/ 204 Pb ratios. Zircon Hf–O isotope analyses yield negative Hf ( t ) values of –31·0 to –17·8 and 18 O values of 4·4–6·8 for syn-magmatic domains. Zircon U–Pb dating yields consistent Early Cretaceous ages of 124 ± 3 to 130 ± 2 Ma for magma emplacement. Residual zircon cores yield Triassic, Neoproterozoic and Paleoproterozoic U–Pb ages, consistent with the ages of tectonothermal events involving ultrahigh-pressure metamorphism and protolith formation in the Dabie orogen. The zircon cores also yield a few low to negative 18 O values. An integrated interpretation of these geochemical characteristics is that the andesitic magmas were derived by partial melting of metasomatized zones in the orogenic lithospheric mantle. The metasomatites were generated by reaction of subcontinental lithospheric mantle wedge peridotite with felsic melts that originated from deeply subducted continental crust during continental collision in the Triassic. Melt–peridotite reaction in a subduction channel is therefore a key to the origin of the mantle sources of andesitic magmas in collisional orogens.

Description: The late Proterozoic Ntaka Ultramafic Complex is a body of dominantly pyroxenitic cumulate rocks containing cyclic alternations of olivine–orthopyroxene cumulates. Chemical zoning in the pyroxenes has been imaged at 25–40 µm resolution using desktop microbeam X-ray fluorescence mapping followed up with laser ablation–inductively coupled plasma mass spectrometry analysis for minor and trace elements on selected samples. Poikilitic and granular harzburgites are finely intermingled, in some cases on a centimetre scale in the same thin section. Poikilitic varieties display spectacular textures, ranging from isolated equant orthopyroxene oikocrysts within olivine-rich heteradcumulate harzburgites to rocks composed entirely of interlocking centimetre-sized anhedral orthopyroxene oikocrysts containing sharply bounded idiomorphic Cr-enriched cores. The poikilitic harzburgites are interlayered with cumulate pyroxenites in which orthopyroxene grains show a variety of zoning patterns: Cr-rich cores similar to those in the oikocrysts; sharply bounded oscillatory zoned cores; and reverse zoning with Cr-poor cores and Cr-enriched rims. A further variation is the presence of a mingled harzburgite lithology in which dunite or poikilitic harzburgite is invaded on a centimetre scale by diffuse vein networks or patches of coarse orthopyroxenite. This range of textures and lithologies attests to a more complex set of processes than implied by the standard cumulus theory model in which oikocrysts are considered to have crystallized from intercumulus liquid within a permeable crystal mush. A range of hypotheses is proposed, including infiltration metasomatism of original olivine cumulates by migrating orthopyroxene-saturated pore fluid; however, the textural relationships, whole-rock chemistry and Cr zoning within the grains can best be explained by a model in which the orthopyroxene oikocrysts form in part or whole as mechanically accumulated cumulus grains. The complexity of zoning patterns is attributed to stirring of entrained olivine and orthopyroxene crystals within a heterogeneous flowing crystal mush, where the transporting magma has a wide range of silica contents owing to poorly stirred incorporation of siliceous country-rock material. The Cr-rich orthopyroxenite component grew from Si-enriched chromite-saturated magma. Mingled lithologies developed after accumulation as a result of percolation and infiltration metasomatism by Si-enriched liquid derived by melting of xenoliths within the crystal pile. The model may be more generally applicable: dunite–harzburgite cycles, common in many layered intrusions, may reflect variable degrees of contamination rather than cycles of fractional crystallization and replenishment.

Description: New thermodynamic data for skiagite garnet (Fe 3 Fe 2 3+ Si 3 O 12 ) are derived from experimental phase-equilibrium data that extend to 10 GPa and are applied to oxybarometry of mantle peridotites using a revised six-component garnet mixing model. Skiagite is more stable by 12 kJ mol –1 than in a previous calibration of the equilibrium 2 skiagite = 4 fayalite + ferrosilite + O 2 , and this leads to calculated oxygen fugacities that are higher (more oxidized) by around 1–1·5 logfO2 units. A new calculation method and computer program incorporates four independent oxybarometers (including 2 pyrope + 2 andradite + 2 ferrosilite = 2 grossular + 4 fayalite + 3 enstatite + O 2 ) for use on natural peridotite samples to yield optimum logfO2 estimates by the method of least squares. These estimates should be more robust than those based on any single barometer and allow assessment of possible disequilibrium in assemblages. A new set of independent oxybarometers for spinel-bearing peridotites is also presented here, including a new reaction 2 magnetite + 3 enstatite = 3 fayalite + 3 forsterite + O 2 . These recalibrations combined with internally consistent PT determinations for published analyses of mantle peridotites with analysed Fe 2 O 3 data for garnets, from both cratonic (Kaapvaal, Siberia and Slave) and circumcratonic (Baikal Rift) regions, provide revised estimates of oxidation state in the lithospheric mantle. Estimates of logfO2 for spinel assemblages are more reduced than those based on earlier calibrations, whereas garnet-bearing assemblages are more oxidized. Importantly, this lessens considerably the difference between garnet and spinel oxybarometry that was observed with previous published calibrations.

Description: The Kidnappers [~1200 km 3 dense rock equivalent (DRE)] and Rocky Hill (~200 km 3 DRE) caldera-forming events in the Taupo Volcanic Zone, New Zealand, were erupted in close succession from the Mangakino volcanic centre. They have identical radiometric ages at ~1 Ma, yet erosion along the contact between the two deposits suggests that some years to decades separated the two eruptions. Field constraints and the similarities of crystal textures and compositions and glass chemistries of both eruption deposits demonstrate that they came from one overall magmatic system with a common crystal mush source. However, second-order variations in these parameters confirm that the Kidnappers and Rocky Hill deposits represent distinct events and are not the products of a single zoned magma chamber. The systematically zoned Kidnappers fall deposits provide evidence for the tapping of three discrete magma bodies, whereas the succeeding Kidnappers ignimbrite is compositionally more diverse. The transition from fall to flow deposition marks a change in the style of caldera collapse and the simultaneous evacuation of discrete but compositionally diverse melts, each of which underwent a distinct evolution and was held at slightly different P–T conditions prior to eruption. Contrasting plagioclase and orthopyroxene zonation patterns are present in pumices originating from three discrete magma bodies. Less evolved mafic melts interacted with the system, which mobilized portions of the final erupted melt through heating and volatile or chemical exchange in the mush. The two largest Kidnappers melt-dominant bodies were re-tapped in modified form, or re-established from their common mush source, prior to the Rocky Hill event. Rocky Hill pumices contain common, fluid-affected antecrystic crystal clots derived from chamber wall material. Amphibole compositions from each eruption reflect melt evolution processes and, in particular, the contemporaneous crystallization of biotite and breakdown of orthopyroxene. Plagioclase and orthopyroxene from Rocky Hill pumices share common zonation patterns with those from the two largest magma bodies in the Kidnappers. The rapid production of new melt-dominant bodies and the triggering of the Rocky Hill eruption reflect the ability of the magmatic system to rejuvenate on a geologically short timescale. The Mangakino centre did not follow a typical cycle of decreased activity after the supervolcanic Kidnappers event, instead producing a second caldera-forming eruption, within years to decades from the same system.

Description: Ambrym, a basaltic volcano in the Vanuatu Arc, has displayed variable eruptive behaviour throughout the past century, with major eruptions occurring both on the volcano flanks and at multiple vents within its caldera. These have been interspersed with periods of relative quiescence marked by extensive passive degassing at active, intra-caldera lava lakes, which experience occasional Strombolian explosions. Volcanic rocks from all vents and eruptive styles display similar isotope and incompatible trace element compositions, suggesting that all are derived from the same primary melt by fractional crystallization. Major eruptions are commonly responsible for effusion of the least evolved lavas examined (SiO 2 ~ 50 wt %; MgO ~ 5 wt %). Although all are geochemically similar, petrological differences discriminate between lavas erupted during flank and intra-caldera eruptions. Phyric basalts with homogeneous mineral compositions are common to flank eruptions, whereas crystal-rich basalts with variable mineral compositions, many not in equilibrium with their host liquid, are a feature of intra-caldera lavas. Lava lake samples are slightly more evolved than those from effusive eruptions (SiO 2 ~ 51–52 wt %; MgO ~ 4 wt %), as a result of additional crystallization during periods of relative quiescence. The diverse petrology of the intra-caldera lavas can be explained by mixing of replenishment magmas similar to those erupted from the volcano flanks with residual magma from lava lake activity. Flank eruptions exploit dykes that bypass the shallow reservoir involved with lava lake activity, limiting their interaction with this component.

Description: The generation and evolution of basaltic magmas at Usu volcano, located at the junction between the NE Japan arc and the Kuril arc, have been investigated. The mafic products, which form the somma edifice of the volcano, consist of basalt (49·6–51·3 wt % SiO 2 ) and basaltic andesite (52·0–54·9 wt % SiO 2 ) lavas. The basaltic lavas show relatively tight compositional trends, and 87 Sr/ 86 Sr ratios tend to decrease with increasing whole-rock SiO 2 content. The water content of the basaltic magmas was determined to be ~4·8 wt % based on plagioclase–melt thermodynamic equilibrium. Using this information and an olivine maximum fractionation model, the water content of the primary Usu magma was estimated to be 3·9 wt %. Multi-component thermodynamic calculations suggest that the primary magma was generated by ~23% melting of the source mantle with ~0·94 wt % H 2 O at ~1300°C and ~1·4 GPa. The 0·94 wt % water content of the source mantle is significantly higher than that beneath volcanoes in the main NE Japan arc (generally 〈0·7 wt % H 2 O); this implies that the wedge mantle at the arc–arc junction is intensively hydrated. The temperature of the wedge mantle of ~1300°C at ~1·4 GPa is also significantly higher than that of the mantle in the main NE Japan arc. Unlike the basaltic lavas, the whole-rock compositions of the basaltic andesite lavas are scattered in Harker variation diagrams. This observation suggests that the compositional diversity was produced by at least two independent processes. To elucidate the processes responsible for this compositional diversity, principal component analysis was applied to the major element compositions of the samples. This suggests that 47% of the diversity of the whole-rock compositions can be explained by mixing with partial melts of lower crustal materials, 25% is explained by redistribution of plagioclase phenocrysts, and 16% is explained by fractionation of accessory minerals.

Description: Endosymbiosis is an important evolutionary event for organisms, and there is widespread interest in understanding the evolution of endosymbiosis establishment. Hydra is one of the most suitable organisms for studying the evolution of endosymbiosis. Within the genus Hydra , H. viridissima and H. vulgaris show endosymbiosis with green algae. Previous studies suggested that the endosymbiosis in H. vulgaris took place much more recently than that in H. viridissima , noting that the establishment of the interaction between H. vulgaris and its algae is not as stable as in H. viridissima. To investigate the on-going process of endosymbiosis, we first compared growth and tolerance to starvation in symbiotic and aposymbiotic polyps of both species. The results revealed that symbiotic H. viridissima had a higher growth rate and greater tolerance to starvation than aposymbiotic polyps. By contrast, growth of symbiotic H. vulgaris was identical to that of aposymbiotic polyps, and symbiotic H. vulgaris was less tolerant to starvation. Moreover, our gene expression analysis showed a pattern of differential gene expression in H. viridissima similar to that in other endosymbiotically established organisms, and contrary to that observed in H. vulgaris . We also showed that H. viridissima could cope with oxidative stress that caused damage, such as cell death, in H. vulgaris . These observations support the idea that oxidative stress related genes play an important role in the on-going process of endosymbiosis evolution. The different evolutionary stages of endosymbiosis studied here provide a deeper insight into the evolutionary processes occurring toward a stable endosymbiosis.

Description: The plastid genome (plastome) of heterotrophic plants like mycoheterotrophs and parasites shows massive gene losses in consequence to the relaxation of functional constraints on photosynthesis. To understand the patterns of this convergent plastome reduction syndrome in heterotrophic plants, we studied 12 closely related orchids of three different lifeforms from the tribe Neottieae (Orchidaceae). We employ a comparative genomics approach to examine structural and selectional changes in plastomes within Neottieae. Both leafy and leafless heterotrophic species have functionally reduced plastid genome. Our analyses show that genes for the NAD(P)H dehydrogenase complex, the photosystems, and the RNA polymerase have been lost functionally multiple times independently. The physical reduction proceeds in a highly lineage-specific manner, accompanied by structural reconfigurations such as inversions or modifications of the large inverted repeats. Despite significant but minor selectional changes, all retained genes continue to evolve under purifying selection. All leafless Neottia species, including both visibly green and nongreen members, are fully mycoheterotrophic, likely evolved from leafy and partially mycoheterotrophic species. The plastomes of Neottieae span many stages of plastome degradation, including the longest plastome of a mycoheterotroph, providing invaluable insights into the mechanisms of plastome evolution along the transition from autotrophy to full mycoheterotrophy.

Description: Numerous models have been developed to simulate the reaction of magmas to changes of thermodynamic variables, such as pressure, temperature, oxygen fugacity, and water activity. However, the extensive experimental database still lacks information on the distinct effect of small amounts of H 2 O on olivine + plagioclase + clinopyroxene cotectic crystallization in tholeiitic basalt. We present an experimental study addressing the effects of pressure (at 100, 200, 400, and 700 MPa) and small amounts of H 2 O on phase relations and liquid lines of descent in three tholeiitic basalts representing different evolutionary stages of the Shatsky Rise oceanic plateau magmatic system (compositions AH6, AH3, and AH5 with 8·6, 8·0, and 6·4 wt % MgO, respectively). Two experimental approaches (dry and low H 2 O) are designed to maintain contrasting H 2 O activities during crystallization using (1) graphite–platinum double capsules to perform nearly anhydrous experiments (〈0·15 wt % H 2 O in the melt) and (2) Fe pre-saturated Au 20 Pd 80 capsules to obtain low melt H 2 O contents ranging from 0·4 to 1·1 wt % H 2 O. Under dry conditions, at lower pressures (≤400 MPa), the crystallization in the MgO-rich AH6 and intermediate AH3 basalts follows the typical sequence of tholeiitic differentiation with olivine crystallization at the liquidus followed by olivine + plagioclase and olivine + plagioclase + clinopyroxene. Both basalts are close to multiple saturation at pressures between 400 and 700 MPa. At high pressure (700 MPa) the crystallization sequence is reversed, starting with clinopyroxene at the liquidus. Under low-H 2 O conditions, AH6 and AH3 are very close to multiple saturation, even at the low pressures of 100 and 200 MPa, and the reversed crystallization sequence (clinopyroxene, plagioclase + clinopyroxene, olivine + plagioclase + clinopyroxene) is observed already at 400 MPa. In contrast to the two more MgO-rich basalts, in the most evolved AH5 basalt, clinopyroxene is the liquidus phase at all investigated pressures and under both dry and low-H 2 O conditions, followed by crystallization of plagioclase + clinopyroxene and olivine + plagioclase + clinopyroxene. The most striking observation in our experiments is that the stability of clinopyroxene increases not only with pressure increase but also in the presence of small amounts of H 2 O (when compared with dry counterparts at similar pressures). Small amounts of H 2 O increase the proportion of clinopyroxene in the olivine + plagioclase + clinopyroxene phase assemblage. Our experiments clearly show that the effect of adding 0·4 wt % H 2 O to cotectic melt compositions (e.g. CaO/Al 2 O 3 ratio at a given MgO) is similar to that caused by an increase of pressure from 100 to ~ 300 MPa. This implies that small amounts of H 2 O can lead to significant overestimation of cotectic crystallization pressures (by up to 300 MPa) and that H 2 O contents need to be taken into account in geobarometric models. Our new experiments emphasize the role of low melt H 2 O contents in stabilizing clinopyroxene and provide some new insights into the problem of the ‘pyroxene paradox’. The apparent mantle pressures obtained for some mid-ocean ridge basalts using ‘dry’ geobarometric approaches can actually represent depths within the lower crust, if small amounts of H 2 O are present. The application of our experimental data to natural Shatsky Rise basalts implies that the magmas record partial crystallization processes occurring mainly at low pressure (100 MPa), corresponding to depths of ~3 km beneath the former spreading center, although the more primitive lavas show evidence of differentiation in a deeper reservoir at ~14 km depth (400 MPa).

Description: Mantle-derived xenoliths hosted by melilitite lavas from In Teria (Ahaggar, SE Algeria) include garnet and spinel peridotites, pyroxenite and phlogopite megacrysts. The spinel and garnet peridotites record an early deformation event, which formed porphyroclastic microstructures and olivine crystal preferred orientations, followed by static infiltration of hydrous alkaline melts. This metasomatic stage (stage 1) is characterized by the crystallization of phlogopite in the garnet and spinel peridotites, amphibole in the spinel peridotites and clinopyroxene in the garnet peridotite, which record chemical equilibration with an alkaline silicate melt. These early events were largely overprinted by carbonatitic metasomatism (stage 2), which is observed only in the spinel peridotites. Spinel peridotite major and trace element compositions, as well as the compositions of newly formed minerals, are characteristic of interaction with carbonate melt, associated with strong enrichment in incompatible trace elements in clinopyroxene. This second stage was followed by crystallization of pyroxenites (stage 3) in vein conduits, probably segregated from alkaline melts. We propose a scenario in which the different metasomatic imprints record successive stages of interaction between lithospheric mantle and sublithospheric melts throughout the Cenozoic. In Sr–Nd isotope space, the host melilitites and several xenoliths are clustered and plot close to the HIMU mantle end-member. However, some peridotite xenoliths are shifted towards more radiogenic 87 Sr/ 86 Sr values. In 207 Pb/ 204 Pb– 206 Pb/ 204 Pb and 208 Pb/ 204 Pb– 06 Pb/ 204 Pb space the In Teria samples define a relatively large domain characterized by high 206 Pb/ 204 Pb and 208 Pb/ 204 Pb, consistent with a contribution of an HIMU component, considered to represent a sublithospheric signature. The highest 87 Sr/ 86 Sr values are comparable with those ascribed to the EM1 mantle end-member, representing the signature of the lower continental lithosphere, and are probably inherited from the pre-metasomatic lithospheric mantle beneath In Teria. Numerical modelling of porous percolation of melt of sublithospheric origin through an EM1-like lithospheric mantle protolith reproduces the In Teria peridotite compositions, using moderately sub-chondritic Sr/Nd values for the peridotite (e.g. In Teria garnet peridotite) and moderately super-chondritic Sr/Nd values in the melt (approximately ocean island basalt values). A few spinel peridotites require a component characterized by a 143 Nd/ 144 Nd signature higher than both the EM1 end-member and the local Ahaggar basalts; the 208 Pb/ 204 Pb compositions of several samples point to a component with a depleted mid-ocean ridge basalt (MORB) mantle (DMM) signature. Thus the lithospheric mantle beneath In Teria probably did not have a uniform EM1 signature before the onset of metasomatism; it included a DMM peridotite component as well as some peridotites with elevated 143 Nd/ 144 Nd values recording long-term LREE depletion.

Description: Modelled primary magma compositions of Palaeogene basalts from the North Atlantic Igneous Province (NAIP) require melting at mantle potential temperatures ( T P ) in the range 1480–1550°C. Modern lavas from Icelandic rift zones require T P ~ 1500°C and those from the rift flanks T P ~ 1450°C. Secular cooling of the NAIP thermal anomaly was therefore of the order of ~50°C over the past 61 Myr. There were systematic variations in T P of 50–100°C from the centre of the thermal anomaly to its margins at any one time, although limits on the stratigraphical distribution of T P determinations do not rule out thermal pulsing on a timescale of millions of years. Variation in extent of melting at similar T P was controlled by local variability in lithospheric thickness. In the west of the NAIP, lithosphere thickness varied from ~90 km at Disko Island to ~65 km at Baffin Island, with similar thickness variations being evident for magmatism in the Faroe Islands, Faroe–Shetland Basin and the British Palaeogene Igneous Province (BPIP). Mean pressure of melting was greater than or equal to the final pressure of melting; the two values converge for melting columns with a melting interval of 〈1·5 GPa, regardless of T P . The majority of the BPIP magmas were generated in the garnet–spinel transition in the upper mantle. Calculated and observed rare earth element distributions in NAIP lavas are entirely consistent with the melting regimes derived from major element melting models. This allows a calibration of rare earth element fractionation and melting conditions that can be applied to other flood basalt provinces.

Description: In the experimental evolution of microbes such as Escherichia coli , many replicate populations are evolved from a common ancestor. Freezing a population sample supplemented with the cryoprotectant glycerol permits later analysis or restarting of an evolution experiment. Typically, each evolving population, and thus each sample archived in this way, consists of many unique genotypes and phenotypes. The effect of archiving on such a heterogeneous population is unknown. Here, we identified optimal archiving conditions for E. coli. We also used genome sequencing of archived samples to study the effects that archiving has on genomic population diversity. We observed no allele substitutions and mostly small changes in allele frequency. Nevertheless, principal component analysis of genome-scale allelic diversity shows that archiving affects diversity across many loci. We showed that this change in diversity is due to selection rather than drift. In addition, ~1% of rare alleles that occurred at low frequencies were lost after treatment. Our observations imply that archived populations may be used to conduct fitness or other phenotypic assays of populations, in which the loss of a rare allele may have negligible effects. However, caution is appropriate when sequencing populations restarted from glycerol stocks, as well as when using glycerol stocks to restart or replay evolution. This is because the loss of rare alleles can alter the future evolutionary trajectory of a population if the lost alleles were strongly beneficial.

Description: PIWI proteins and PIWI-interacting RNAs (piRNAs) are part of a cellular pathway that has evolved to protect genomes against the proliferation of transposable elements (TEs). PIWIs and piRNAs assemble into complexes that are involved in epigenetic and post-transcriptional repression of TEs. Most of our understanding of the mechanisms of piRNA-mediated TE silencing comes from fruit fly and mouse models. However, even in these well-studied animals it is unclear how piRNA responses relate to variable TE expression and whether the strength of the piRNA response affects TE content over time. Here, we assessed the evolutionary interactions between TE and piRNAs in a statistical framework using three nonmodel laurasiatherian mammals as a study system: dog, horse, and a vesper bat. These three species diverged ~80 million years ago and have distinct genomic TE contents. By comparing species with distinct TE landscapes, we aimed to identify clear relationships among TE content, expression, and piRNAs. We found that the TE subfamilies that are the most transcribed appear to elicit the strongest "ping-pong" response. This was most evident among long interspersed elements, but the relationships between expression and ping-pong pilRNA (piRNA-like) expression were more complex among SINEs. SINE transcripts were equally abundant in the dog and horse yet new SINE insertions were relatively rare in the horse genome, where we identified a stronger piRNA response. Our analyses suggest that the piRNA response can have a strong impact on the TE composition of a genome. However, our results also suggest that the presence of a robust piRNA response is apparently not sufficient to stop TE mobilization and accumulation.

Description: We introduce a gene tree simulator that is designed for use in conjunction with approximate Bayesian computation approaches. We show that it can be used to determine the relative importance of hybrid speciation and introgression compared with incomplete lineage sorting (ILS) in producing patterns of incongruence across gene trees. Important features of the new simulator are (1) a choice of models to capture the decreasing probability of successful hybrid species formation or introgression as a function of genetic distance between potential parent species; (2) the ability for hybrid speciation to result in asymmetrical contributions of genetic material from each parent species; (3) the ability to vary the rates of hybrid speciation, introgression, and divergence speciation in different epochs; and (4) incorporation of the coalescent, so that patterns of incongruence due to ILS can be compared with those due to hybrid evolution. Given a set of gene trees generated by the simulator, we calculate a set of statistics, each measuring in a different way the discordance between the gene trees. We show that these statistics can be used to differentiate whether the gene tree discordance was largely due to hybridization, or only due to lineage sorting.

Description: Beetles represent the largest insect order and they display extreme morphological, ecological and behavioral diversity, which makes them ideal models for evolutionary studies. Here, we present the draft genome of the scarab beetle Oryctes borbonicus , which has a more basal phylogenetic position than the two previously sequenced pest species Tribolium castaneum and Dendroctonus ponderosae providing the potential for sequence polarization. Oryctes borbonicus is endemic to La Réunion, an island located in the Indian Ocean, and is the host of the nematode Pristionchus pacificus , a well-established model organism for integrative evolutionary biology. At 518 Mb, the O. borbonicus genome is substantially larger and encodes more genes than T. castaneum and D. ponderosae . We found that only 25% of the predicted genes of O. borbonicus are conserved as single copy genes across the nine investigated insect genomes, suggesting substantial gene turnover within insects. Even within beetles, up to 21% of genes are restricted to only one species, whereas most other genes have undergone lineage-specific duplications and losses. We illustrate lineage-specific duplications using detailed phylogenetic analysis of two gene families. This study serves as a reference point for insect/coleopteran genomics, although its original motivation was to find evidence for potential horizontal gene transfer (HGT) between O. borbonicus and P. pacificus . The latter was previously shown to be the recipient of multiple horizontally transferred genes including some genes from insect donors. However, our study failed to provide any clear evidence for additional HGTs between the two species.

Description: Collembola (springtails) are detritivorous hexapods that inhabit the soil and its litter layer. The ecology of the springtail Orchesella cincta is extensively studied in the context of adaptation to anthropogenically disturbed areas. Here, we present a draft genome of an O. cincta reference strain with an estimated size of 286.8 Mbp, containing 20,249 genes. In total, 446 gene families are expanded and 1,169 gene families evolved specific to this lineage. Besides these gene families involved in general biological processes, we observe gene clusters participating in xenobiotic biotransformation. Furthermore, we identified 253 cases of horizontal gene transfer (HGT). Although the largest percentage of them originated from bacteria (37.5%), we observe an unusually high percentage (30.4%) of such genes of fungal origin. The majority of foreign genes are involved in carbohydrate metabolism and cellulose degradation. Moreover, some foreign genes (e.g., bacillopeptidases) expanded after HGT. We hypothesize that horizontally transferred genes could be advantageous for food processing in a soil environment that is full of decaying organic material. Finally, we identified several lineage-specific genes, expanded gene families, and horizontally transferred genes, associated with altered gene expression as a consequence of genetic adaptation to metal stress. This suggests that these genome features may be preadaptations allowing natural selection to act on. In conclusion, this genome study provides a solid foundation for further analysis of evolutionary mechanisms of adaptation to environmental stressors.

Description: The predicted effect of effective population size on the distribution of fitness effects and substitution rate is critically dependent on the relationship between sequence and fitness. This highlights the importance of using models that are informed by the molecular biology, biochemistry, and biophysics of the evolving systems. We describe a computational model based on fundamental aspects of biophysics, the requirement for (most) proteins to be thermodynamically stable. Using this model, we find that differences in population size have minimal impact on the distribution of population-scaled fitness effects, as well as on the rate of molecular evolution. This is because larger populations result in selection for more stable proteins that are less affected by mutations. This reduction in the magnitude of the fitness effects almost exactly cancels the greater selective pressure resulting from the larger population size. Conversely, changes in the population size in either direction cause transient increases in the substitution rate. As differences in population size often correspond to changes in population size, this makes comparisons of substitution rates in different lineages difficult to interpret.

Description: Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation.

Description: The dihedral angle formed at junctions between two plagioclase grains and a grain of augite is only very rarely in textural equilibrium in gabbros from kilometre-scale crustal layered intrusions. The median of a population of these disequilibrium angles, cpp , varies systematically within a single layered intrusion, remaining constant over large stretches of stratigraphy with significant increases and decreases associated with the addition or reduction respectively of the number of phases on the liquidus of the bulk magma. The stepwise changes in cpp are present in the Upper Zone of the Bushveld Complex, the Megacyclic Unit I of the Sept Iles Intrusion, and the Layered Series of the Skaergaard intrusion. The plagioclase-bearing cumulates of Rum have a bimodal distribution of cpp , dependent on whether the cumulus assemblage includes clinopyroxene. The presence of the stepwise changes is independent of the order of arrival of cumulus phases and of the composition of either the cumulus phases or the inferred composition of the interstitial liquid. The only parameter that behaves in an exactly analogous manner to cpp is the rate of change in enthalpy with temperature ( H / T ) during crystallization. Both H / T and cpp increase with the addition of a liquidus phase, and decrease with the removal of a liquidus phase. The replacement of one phase by another has little effect on H / T and no discernible effect on cpp . An increase of H / T results in an increase in the fraction of the total enthalpy budget that is the latent heat of crystallization (the fractional latent heat). It also increases the mass crystallized in each incremental temperature drop (the crystal productivity). These increases of both fractional latent heat and crystal productivity are likely to cause an increase in the time taken to form three-grain junctions in the mush via thermal buffering of a thickened mushy layer. We suggest these are the underlying causes of stepwise increases in cpp . Stepwise changes in the geometry of three-grain junctions in fully solidified gabbros thus provide a clear microstructural marker for the progress of fractionation down the liquid line of descent in layered intrusions.

Description: High-resolution sampling in monogenetic fields has the potential to reveal fine-scale heterogeneity of the mantle, a feature that may be overwhelmed by larger fluxes of magma, or missed by under-sampling. The Quaternary Auckland Volcanic Field (AVF) in northern New Zealand is a basaltic field of 51 small-volume volcanic centres, and is one of the best-sampled examples of a monogenetic volcanic field. We present data for 12 centres in the volcanic field. These show the large compositional variations between volcanoes as well as through single eruptive sequences. Whole-rock compositions range from subalkaline basalt in the larger centres, through alkali basalt to nephelinite in the smallest centres. Fractional crystallization has had a limited effect in many of the centres, but high-pressure clinopyroxene crystallization may have occurred in others. Three end-members are observed in Pb isotope space, indicating that distinct mantle source components are involved in the petrogenesis of the magmas. Whole-rock multi-element patterns show that the larger centres have prominent positive Sr anomalies and lack K anomalies, whereas the smaller centres have prominent negative K anomalies and lack Sr anomalies. The melting parameters and compositions of the sources involved are modelled using trace element ratios and multi-element patterns, and three components are characterized: (1) fertile peridotite with a Pb-isotope composition similar to Pacific mid-ocean ridge basalt; (2) eclogite domains with a HIMU-like isotope composition dispersed within the fertile peridotite; (3) slightly depleted subduction-metasomatized peridotitic lithospheric mantle (containing c . 3% subduction fluids). Modelling shows that melting in the AVF begins in garnet-bearing fertile asthenosphere (with preferential melting of eclogite domains) and that melts are variably diluted by melts of the lithospheric source. The U–Th isotope compositions of the end-members in the AVF show 230 Th excess [( 230 Th/ 232 Th) ratios of 1·11–1·38], with the samples of lower ( 230 Th/ 232 Th) exhibiting higher ( 238 U/ 232 Th), which we attribute to the dilution effect of the melts from the lithospheric mantle source. Modelling reveals a correlation between melting in the asthenosphere, the degree of melting and incorporation of the metasomatized lithospheric mantle source, and the resultant size of the volcanic centre. This suggests that the scale of the eruption may essentially be controlled by asthenospheric mantle dynamics.

Description: The origin of mafic and ultramafic sills exhibiting different whole-rock compositional profiles (e.g. I-, C-, D-, M- and S-shaped profiles) remains controversial. We have addressed this issue by revisiting three ~100 m thick Siberian dolerite sills (Vavukansky, Kuz’movsky and Vilyuysky) that display remarkable internal differentiation. The Vavukansky sill has an M-shaped profile with prominent basal and top reversals showing inward increases in whole-rock MgO, Mg-number [100Mg/(Mg + Fe)] and normative An content [100An/(An + Ab)], followed by the Layered and Upper Border Series with inward decreases in these indices. The Kuz’movsky and Vilyuysky sills both show S-shaped profiles similar to the Vavukansky sill, but lack a top reversal. These whole-rock M- and S-shaped profiles are accompanied by similar profiles in mineral compositions. Plagioclase and, to a lesser extent, olivine show systematic inward increases in An content and Mg-number, respectively, across basal and top reversals. These compositional trends are followed by inward decreases in these ratios in the interiors of the Vavukansky and Kuz’movsky sills. Currently accepted models attribute whole-rock M- and S-shaped compositional profiles to crystal settling, compositional convection or compaction operating in closed systems. Our observations challenge these traditional interpretations because variations in mineral compositions observed in marginal reversals cannot result from closed-system fractionation. We suggest instead that initially the sills evolved as open systems that were slowly inflated by magmas that became gradually more primitive with time. The inflation was accompanied by in situ crystallization that preserved the preceding fractionation history of the injected magmas by forming basal and top reversals with minerals becoming more primitive inwards. This process culminated with rapid inflation of the sills to their current size owing to a major influx of primitive magma. Subsequently, magma flow through the sills ceased and they evolved as closed systems by fractional crystallization. This resulted in the Layered and Upper Border Series with minerals becoming more evolved inwards. This model can be extended to explain other compositional profiles and petrological features in mafic and ultramafic sills.

Description: Wolbachia , endosymbiotic bacteria of the order Rickettsiales, are widespread in arthropods but also present in nematodes. In arthropods, A and B supergroup Wolbachia are generally associated with distortion of host reproduction. In filarial nematodes, including some human parasites, multiple lines of experimental evidence indicate that C and D supergroup Wolbachia are essential for the survival of the host, and here the symbiotic relationship is considered mutualistic. The origin of this mutualistic endosymbiosis is of interest for both basic and applied reasons: How does a parasite become a mutualist? Could intervention in the mutualism aid in treatment of human disease? Correct rooting and high-quality resolution of Wolbachia relationships are required to resolve this question. However, because of the large genetic distance between Wolbachia and the nearest outgroups, and the limited number of genomes so far available for large-scale analyses, current phylogenies do not provide robust answers. We therefore sequenced the genome of the D supergroup Wolbachia endosymbiont of Litomosoides sigmodontis , revisited the selection of loci for phylogenomic analyses, and performed a phylogenomic analysis including available complete genomes (from isolates in supergroups A, B, C, and D). Using 90 orthologous genes with reliable phylogenetic signals, we obtained a robust phylogenetic reconstruction, including a highly supported root to the Wolbachia phylogeny between a (A + B) clade and a (C + D) clade. Although we currently lack data from several Wolbachia supergroups, notably F, our analysis supports a model wherein the putatively mutualist endosymbiotic relationship between Wolbachia and nematodes originated from a single transition event.

Description: Many insects rely on bacterial symbionts with tiny genomes specialized for provisioning nutrients lacking in host diets. Xylem sap and phloem sap are both deficient as insect diets, but differ dramatically in nutrient content, potentially affecting symbiont genome evolution. For sap-feeding insects, sequenced symbiont genomes are available only for phloem-feeding examples from the suborder Sternorrhyncha and xylem-feeding examples from the suborder Auchenorrhyncha, confounding comparisons. We sequenced genomes of the obligate symbionts, Sulcia muelleri and Nasuia deltocephalinicola , of the phloem-feeding pest insect, Macrosteles quadrilineatus (Auchenorrhyncha: Cicadellidae). Our results reveal that Nasuia- ALF has the smallest bacterial genome yet sequenced (112 kb), and that the Sulcia- ALF genome (190 kb) is smaller than that of Sulcia in other insect lineages. Together, these symbionts retain the capability to synthesize the 10 essential amino acids, as observed for several symbiont pairs from xylem-feeding Auchenorrhyncha. Nasuia retains genes enabling synthesis of two amino acids, DNA replication, transcription, and translation. Both symbionts have lost genes underlying ATP synthesis through oxidative phosphorylation, possibly as a consequence of the enriched sugar content of phloem. Shared genomic features, including reassignment of the UGA codon from Stop to tryptophan, and phylogenetic results suggest that Nasuia -ALF is most closely related to Zinderia , the betaproteobacterial symbiont of spittlebugs. Thus, Nasuia / Zinderia and Sulcia likely represent ancient associates that have co-resided in hosts since the divergence of leafhoppers and spittlebugs 〉200 Ma, and possibly since the origin of the Auchenorrhyncha, 〉260 Ma.

Description: Thanks to the microarray technology, our understanding of transcriptome evolution at the genome level has been considerably advanced in the past decade. Yet, further investigation was challenged by several technical limitations of this technology. Recent innovation of next-generation sequencing, particularly the invention of RNA-seq technology, has shed insightful lights on resolving this problem. Though a number of statistical and computational methods have been developed to analyze RNA-seq data, the analytical framework specifically designed for evolutionary genomics remains an open question. In this article we develop a new method for estimating the genome expression distance from the RNA-seq data, which has explicit interpretations under the model of gene expression evolution. Moreover, this distance measure takes the data overdispersion, gene length variation, and sequencing depth variation into account so that it can be applied to multiple genomes from different species. Using mammalian RNA-seq data as example, we demonstrated that this expression distance is useful in phylogenomic analysis.

Description: The control of RNA splicing is often modulated by exonic motifs near splice sites. Chief among these are exonic splice enhancers (ESEs). Well-described ESEs in mammals are purine rich and cause predictable skews in codon and amino acid usage toward exonic ends. Looking across species, those with relatively abundant intronic sequence are those with the more profound end of exon skews, indicative of exonization of splice site recognition. To date, the only intron-rich species that have been analyzed are mammals, precluding any conclusions about the likely ancestral condition. Here, we examine the patterns of codon and amino acid usage in the vicinity of exon–intron junctions in the brown alga Ectocarpus siliculosus , a species with abundant large introns, known SR proteins, and classical splice sites. We find that amino acids and codons preferred/avoided at both 3' and 5' ends in Ectocarpus , of which there are many, tend, on average, to also be preferred/avoided at the same exon ends in humans. Moreover, the preferences observed at the 5' ends of exons are largely the same as those at the 3' ends, a symmetry trend only previously observed in animals. We predict putative hexameric ESEs in Ectocarpus and show that these are purine rich and that there are many more of these identified as functional ESEs in humans than expected by chance. These results are consistent with deep phylogenetic conservation of SR protein binding motifs. Assuming codons preferred near boundaries are "splice optimal" codons, in Ectocarpus , unlike Drosophila, splice optimal and translationally optimal codons are not mutually exclusive. The exclusivity of translationally optimal and splice optimal codon sets is thus not universal.

Description: Autonomous retrotransposons lacking long terminal repeats (LTR) account for much of the variation in genome size and structure among vertebrates. Mammalian genomes contain hundreds of thousands of non-LTR retrotransposon copies, mostly resulting from the amplification of a single clade known as L1. The genomes of teleost fish and squamate reptiles contain a much more diverse array of non-LTR retrotransposon families, whereas copy number is relatively low. The majority of non-LTR retrotransposon insertions in nonmammalian vertebrates also appear to be very recent, suggesting strong purifying selection limits the accumulation of non-LTR retrotransposon copies. It is however unclear whether this turnover model, originally proposed in Drosophila , applies to nonmammalian vertebrates. Here, we studied the population dynamics of L1 in the green anole lizard ( Anolis carolinensis ). We found that although most L1 elements are recent in this genome, truncated insertions accumulate readily, and many are fixed at both the population and species level. In contrast, full-length L1 insertions are found at lower population frequencies, suggesting that the turnover model only applies to longer L1 elements in Anolis . We also found that full-length L1 inserts are more likely to be fixed in populations of small effective size, suggesting that the strength of purifying selection against deleterious alleles is highly dependent on host demographic history. Similar mechanisms seem to be controlling the fate of non-LTR retrotransposons in both Anolis and teleostean fish, which suggests that mammals have considerably diverged from the ancestral vertebrate in terms of how they interact with their intragenomic parasites.

Description: Increasing evidence from sequence data from various environments, including the human gut, suggests the existence of a previously unknown putative seventh order of methanogens. The first genomic data from members of this lineage, Methanomassiliicoccus luminyensis and " Candidatus Methanomethylophilus alvus," provide insights into its evolutionary history and metabolic features. Phylogenetic analysis of ribosomal proteins robustly indicates a monophyletic group independent of any previously known methanogenic order, which shares ancestry with the Marine Benthic Group D, the Marine Group II, the DHVE2 group, and the Thermoplasmatales. This phylogenetic position, along with the analysis of enzymes involved in core methanogenesis, strengthens a single ancient origin of methanogenesis in the Euryarchaeota and indicates further multiple independent losses of this metabolism in nonmethanogenic lineages than previously suggested. Genomic analysis revealed an unprecedented loss of the genes coding for the first six steps of methanogenesis from H 2 /CO 2 and the oxidative part of methylotrophic methanogenesis, consistent with the fact that M. luminyensis and " Ca. M. alvus" are obligate H 2 -dependent methylotrophic methanogens. Genomic data also suggest that these methanogens may use a large panel of methylated compounds. Phylogenetic analysis including homologs retrieved from environmental samples indicates that methylotrophic methanogenesis (regardless of dependency on H 2 ) is not restricted to gut representatives but may be an ancestral characteristic of the whole order, and possibly also of ancient origin in the Euryarchaeota. 16S rRNA and McrA trees show that this new order of methanogens is very diverse and occupies environments highly relevant for methane production, therefore representing a key lineage to fully understand the diversity and evolution of methanogenesis.

Description: Magma dynamics and time scales during the VEI 5, 2000 bp eruption of El Misti volcano, southern Peru (EM2000BP) are investigated to address cyclic explosive activity at this hazardous volcano. The 1·4 km 3 of pumice falls and flows have abundant mingled pumice of high-K, calc-alkaline rhyolite and andesite composition. Phenocryst zoning and compositions reveal mutual exchange of plagioclase between the two magmas; amphibole in the rhyolite was derived from the andesite. Amphiboles in the andesite are predominantly unrimmed crystals whereas those in the rhyolite mostly exhibit reaction rims. Phase equilibria indicate that the andesite formed at ~900–950°C and 2–3 kbar pressure and was water-saturated with 5·1–6·0 wt % H 2 O, broadly similar to El Misti magmas overall. Amphibole, plagioclase, Ti-magnetite, and two pyroxenes were the crystallizing phases. A separate rhyolite magma existed higher in the crust at a temperature of 816 ± 30°C and ~5% H 2 O in which only plagioclase and Fe–Ti oxides were stable. The lack of cognate amphibole in the rhyolite despite H 2 O saturation requires that it staged above the stability limit of amphibole (〈100 MPa). Exchange reactions in amphibole (dominantly pargasitic) and trace element partitioning in plagioclase indicate that both andesite and rhyolite magmas were broadly constant in temperature and H 2 O content. These constraints suggest that the initially separate rhyolite and deeper andesite magmas interacted by an initial andesite recharge event that resulted in mingling and crystal exchange. A period of 50–60 days is required for amphibole introduced into the rhyolite to develop reaction rims owing to decompression. These rims are dominated by plagioclase, a consequence of the Al-rich nature of the amphibole. The lack of reaction rims on amphibole in the andesite implicates a second, more-forceful and voluminous eruption-triggering recharge event during which andesite rose rapidly from source to surface in ≤5 days at ascent rates of at least 0·023 m s –1 . Further decompression-driven crystallization is recorded in plagioclase rims and microlite growth that may have contributed to a rapid increase in viscosity leading to explosive eruption. This VEI 5 plinian eruption shares characteristics with other explosive events at El Misti on a time scale of 2000–4000 years, suggesting periodic recharge-driven explosive activity.

Description: We report structural evidence of ductile strain localization in mantle pyroxenite from the spinel to plagioclase websterite transition in the Ronda Peridotite (southern Spain). Mapping shows that, in this domain, small-scale shear zones occurring at the base of the lithospheric section are systematically located within thin pyroxenite layers, suggesting that the pyroxenite was locally weaker than the host peridotite. Strain localization is associated with a sudden decrease of grain size and increasing volume fractions of plagioclase and amphibole as a result of a spinel to plagioclase phase transformation reaction during decompression. This reaction also fostered hydrogen extraction (‘dehydroxylation’) from clinopyroxene producing effective fluid saturation that catalyzed the synkinematic net-transfer reaction. This reaction produced fine-grained olivine and plagioclase, allowing the onset of grain-size sensitive creep and further strain localization in these pyroxenite bands. The strain localization in the pyroxenites is thus explained by their more fertile composition, which allowed earlier onset of the phase transition reactions. Geothermobarometry undertaken on compositionally zoned constituent minerals suggests that this positive feedback between reactions and deformation is associated with cooling from at least 1000°C to 700°C and decompression from 1·0 to 0·5 GPa.

Description: Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging human pathogen that causes life-threatening invasive infections such as streptococcal toxic shock syndrome. Recent epidemiological studies reveal that invasive SDSE infections have been increasing in Asia, Europe, and the United States. Almost all SDSE carry Lancefield group G or C antigen. We have determined the complete genome sequence of a human group C SDSE 167 strain. A comparison of its sequence with that of four SDSE strains, three in Lancefield group G and one in Lancefield group A, showed approximately 90% coverage. Most regions showing little or no homology were located in the prophages. There was no evidence of massive rearrangement in the genome of SDSE 167. Bayesian phylogeny using entire genome sequences showed that the most recent common ancestor of the five SDSE strains appeared 446 years ago. Interestingly, we found that SDSE 167 harbors sugar metabolizing enzymes in a unique region and streptodornase in the phage region, which presumably contribute to the degradation of host tissues and the prompted covRS mutation, respectively. A comparison of these five SDSE strains, which differ in Lancefield group antigens, revealed a gene cluster presumably responsible for the synthesis of the antigenic determinant. These results may provide the basis for molecular epidemiological research of SDSE.