ALBERT

Description: We present CO observations towards a sample of six H i-rich Ultradiffuse galaxies (UDGs) as well as one UDG (VLSB-A) in the Virgo Cluster with the Institut de RadioAstronomie Millimétrique (IRAM) 30-m telescope. CO J = 1–0 is marginally detected at 4σ level in AGC 122966, as the first detection of CO emission in UDGs. We estimate upper limits of molecular mass in other galaxies from the non-detection of CO lines. These upper limits and the marginal CO detection in AGC 122966 indicate low mass ratios between molecular and atomic gas masses. With the star formation efficiency derived from the molecular gas, we suggest that the inefficiency of star formation in such H i-rich UDGs is likely caused by the low efficiency in converting molecules from atomic gas, instead of low efficiency in forming stars from molecular gas.

Description: We find that the minor axes of the ultra-diffuse galaxies (UDGs) in Abell 2634 tend to be aligned with the major axis of the central dominant galaxy, at a $gtrsim 95{{ m per cent}}$ confidence level. This alignment is produced by the bright UDGs with the absolute magnitudes Mr 〈 −15.3 mag, and outer-region UDGs with R 〉 0.5R200. The alignment signal implies that these bright, outer-region UDGs are very likely to acquire their angular momenta from the vortices around the large-scale filament before they were accreted into A2634, and form their extended stellar bodies outside of the cluster; in this scenario, the orientations of their primordial angular momenta, which are roughly shown by their minor axes on the images, should tend to be parallel to the elongation of the large-scale filament. When these UDGs fell into the unrelaxed cluster A2634 along the filament, they could still preserve their primordial alignment signal before violent relaxation and encounters. These bright, outer-region UDGs in A2634 are very unlikely to be the descendants of the high-surface-brightness dwarf progenitors under tidal interactions with the central dominant galaxy in the cluster environment. Our results indicate that the primordial alignment could be a useful probe of the origin of UDGs in large-scale structures.

Description: We present a detailed analysis of the gaseous component of the Si K edge using high-resolution Chandra spectra of low-mass X-ray binaries. We fit the spectra with a modified version of the ISMabs model, including new photoabsorption cross-sections computed for all Si ionic species. We estimate column densities for Si i, Si ii, Si iii, Si xii, and Si xiii, which trace the warm, intermediate temperature, and hot phases of the Galactic interstellar medium. We find that the ionic fractions of the first two phases are similar. This may be due to the physical state of the plasma determined by the temperature or due to the presence of absorber material in the close vicinity of the sources. Our findings highlight the need for accurate modelling of the gaseous component before attempting to address the solid component.

Description: Using state-of-the-art high-resolution fully GPU N-body simulations, we demonstrate for the first time that the infall of a dark matter-rich satellite naturally explains a present black hole offset by subparsecs in M31. Observational data of the tidal features provide stringent constraints on the initial conditions of our simulations. The heating of the central region of M31 by the satellite via dynamical friction entails a significant black hole offset after the first pericentric passage. After having reached its maximum offset, the massive black hole sinks towards the M31 centre due to dynamical friction and it is determined to be offset by subparsecs as derived by observations.

Description: In two recent papers published in MNRAS, Namouni and Morais claimed evidence for the interstellar origin of some small Solar system bodies, including: (i) objects in retrograde co-orbital motion with the giant planets and (ii) the highly inclined Centaurs. Here, we discuss the flaws of those papers that invalidate the authors’ conclusions. Numerical simulations backwards in time are not representative of the past evolution of real bodies. Instead, these simulations are only useful as a means to quantify the short dynamical lifetime of the considered bodies and the fast decay of their population. In light of this fast decay, if the observed bodies were the survivors of populations of objects captured from interstellar space in the early Solar system, these populations should have been implausibly large (e.g. about 10 times the current main asteroid belt population for the retrograde co-orbital of Jupiter). More likely, the observed objects are just transient members of a population that is maintained in quasi-steady state by a continuous flux of objects from some parent reservoir in the distant Solar system. We identify in the Halley-type comets and the Oort cloud the most likely sources of retrograde co-orbitals and highly inclined Centaurs.

Description: Strong gravitational lensing has been a powerful probe of cosmological models and gravity. To date, constraints in either domain have been obtained separately. We propose a new methodology through which the cosmological model, specifically the Hubble constant, and post-Newtonian parameter can be simultaneously constrained. Using the time-delay cosmography from strong lensing combined with the stellar kinematics of the deflector lens, we demonstrate that the Hubble constant and post-Newtonian parameter are incorporated in two distance ratios that reflect the lensing mass and dynamical mass, respectively. Through the re-analysis of the four publicly released lenses distance posteriors from the H0LiCOW (H0 Lenses in COSMOGRAIL’s Wellspring) collaboration, the simultaneous constraints of Hubble constant and post-Newtonian parameter are obtained. Our results suggest no deviation from the general relativity; $gamma _{t {PPN}}=0.87^{+0.19}_{-0.17}$ with a Hubble constant that favours the local Universe value, $H_0=73.65^{+1.95}_{-2.26}$ km s−1 Mpc−1. Finally, we forecast the robustness of gravity tests by using the time-delay strong lensing for constraints we expect in the next few years. We find that the joint constraint from 40 lenses is able to reach the order of $7.7{{ m per cent}}$ for the post-Newtonian parameter and $1.4{{ m per cent}}$ for the Hubble constant.

Description: One of the proposed channels of binary black hole mergers involves dynamical interactions of three black holes. In such scenarios, it is possible that all three black holes merge in a so-called hierarchical merger chain, where two of the black holes merge first and then their remnant subsequently merges with the remaining single black hole. Depending on the dynamical environment, it is possible that both mergers will appear within the observable time window. Here, we perform a search for such merger pairs in the public available LIGO and Virgo data from the O1/O2 runs. Using a frequentist p-value assignment statistics, we do not find any significant merger pair candidates, the most significant being GW170809-GW151012 pair. Assuming no observed candidates in O3/O4, we derive upper limits on merger pairs to be ∼11–110 yr−1 Gpc−3, corresponding to a rate that relative to the total merger rate is ∼0.1−1.0. From this, we argue that both a detection and a non-detection within the next few years can be used to put useful constraints on some dynamical progenitor models.

Description: We present extremely deep upper limits on the radio emission from 4U 1957+11, an X-ray binary that is generally believed to be a persistently accreting black hole that is almost always in the soft state. We discuss a more comprehensive search for Type I bursts than in past work, revealing a stringent upper limit on the burst rate, bolstering the case for a black hole accretor. The lack of detection of this source at the 1.07 μJy/beam noise level indicates jet suppression that is stronger than expected even in the most extreme thin disc models for radio jet production – the radio power here is 1500–3700 times lower than the extrapolation of the hard state radio/X-ray correlation, with the uncertainties depending primarily on the poorly constrained source distance. We also discuss the location and velocity of the source and show that it must have either formed in the halo or with a strong asymmetric natal kick.

Description: Swift J004427.3−734801 is an X-ray source in the Small Magellanic Cloud (SMC) that was first discovered as part of the Swift S-CUBED programme in 2020 January. It was not detected in any of the previous 3 yr worth of observations. The accurate positional determination from the X-ray data has permitted an optical counterpart to be identified that has the characteristics of an O9V−B2III star. Evidence for the presence of an infrared excess and significant I-band variability strongly suggests that this is an OBe-type star. Over 17 yr worth of optical monitoring by the OGLE (Optical Gravitational Lensing Experiment) project reveals periods of time in which quasi-periodic optical flares occur at intervals of ∼21.5 d. The X-ray data obtained from the S-CUBED project reveal a very soft spectrum, too soft to be that from accretion on to a neutron star or black hole. It is suggested here that this is a rarely identified Be star–white dwarf binary in the SMC.

Description: Gravitational microlensing can detect isolated stellar-mass black holes (BHs), which are believed to be the dominant form of Galactic BHs according to population synthesis models. Previous searches for BH events in microlensing data focused on long time-scale events with significant microlensing parallax detections. Here we show that, although BH events preferentially have long time-scales, the microlensing parallax amplitudes are so small that in most cases the parallax signals cannot be detected statistically significantly. We then identify OGLE-2006-BLG-044 to be a candidate BH event because of its long time-scale and small microlensing parallax. Our findings have implications to future BH searches in microlensing data.

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: We present a sub-100 pc-scale analysis of the CO molecular gas emission and kinematics of the gravitational lens system SDP.81 at redshift 3.042 using Atacama Large Millimetre/submillimetre Array (ALMA) science verification data and a visibility-plane lens reconstruction technique. We find clear evidence for an excitation-dependent structure in the unlensed molecular gas distribution, with emission in CO (5–4) being significantly more diffuse and structured than in CO (8–7). The intrinsic line luminosity ratio is r 8–7/5–4  = 0.30 ± 0.04, which is consistent with other low-excitation starbursts at z  ~ 3. An analysis of the velocity fields shows evidence for a star-forming disc with multiple velocity components that is consistent with a merger/post-coalescence merger scenario, and a dynamical mass of M (〈1.56 kpc) = 1.6 ± 0.6  x  10 10 M . Source reconstructions from ALMA and the Hubble Space Telescope show that the stellar component is offset from the molecular gas and dust components. Together with Karl G. Jansky Very Large Array CO (1–0) data, they provide corroborative evidence for a complex ~2 kpc-scale starburst that is embedded within a larger ~15 kpc structure.

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: Regardless of the physical origin of stellar magnetic fields – fossil or dynamo induced - an inclination angle between the magnetic and rotation axes is very often observed. Absence of observational evidence in this direction in the solar case has led to generally assume that its global magnetic field and rotation axes are well aligned. We present the detection of a monthly periodic signal of the photospheric solar magnetic field at all latitudes, and especially near the poles, revealing that the main axis of the Sun's magnetic field is not aligned with the surface rotation axis. This result reinforces the view of our Sun as a common intermediate-mass star. Furthermore, this detection challenges and imposes a strong observational constraint to modern solar dynamo theories.

Description: We use the ‘Evolution and Assembly of GaLaxies and their Environments’ ( eagle ) suite of hydrodynamical cosmological simulations to measure offsets between the centres of stellar and dark matter components of galaxies. We find that the vast majority (〉95 per cent) of the simulated galaxies display an offset smaller than the gravitational softening length of the simulations (Plummer-equivalent  = 700 pc), both for field galaxies and satellites in clusters and groups. We also find no systematic trailing or leading of the dark matter along a galaxy's direction of motion. The offsets are consistent with being randomly drawn from a Maxwellian distribution with  ≤ 196 pc. Since astrophysical effects produce no feasible analogues for the $1.62^{+0.47}_{-0.49}$  kpc offset recently observed in Abell 3827, the observational result is in tension with the collisionless cold dark matter model assumed in our simulations.

Description: The solar wind magnetic field contains rotations at a broad range of scales, which have been extensively studied in the magnetohydrodynamics range. Here, we present an extension of this analysis to the range between ion and electron kinetic scales. The distribution of rotation angles was found to be approximately lognormal, shifting to smaller angles at smaller scales almost self-similarly, but with small, statistically significant changes of shape. The fraction of energy in fluctuations with angles larger than α was found to drop approximately exponentially with α, with e-folding angle 9.8° at ion scales and 0 $_{.}^{\circ}$ 66 at electron scales, showing that large angles (α 〉 30°) do not contain a significant amount of energy at kinetic scales. Implications for kinetic turbulence theory and the dissipation of solar wind turbulence are discussed.

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 broad-band spectral properties of the X-ray pulsar Cep X-4 by using a Suzaku observation in 2014 July. The 0.8–70 keV spectrum was found to be well described by three continuum models – Negative and Positive power-law with Exponential cut-off (NPEX), high-energy cut-off power-law and CompTT models. Additional components such as a cyclotron line at ~28 keV and two Gaussian components for iron lines at 6.4 and 6.9 keV were required in the spectral fitting. Apart from these, an additional absorption feature at ~45 keV was clearly detected in residuals obtained from the spectral fitting. This additional feature at ~45 keV was clearly seen in phase-resolved spectra of the pulsar. We identified this feature as the first harmonic of the fundamental cyclotron line at ~28 keV. The ratio between the first harmonic and fundamental line energies (1.7) was found to be in disagreement with the conventional factor of 2, indicating that the heights of line-forming regions are different or viewed at larger angles. The phase-resolved spectroscopy of the fundamental and first harmonic cyclotron lines shows significant pulse-phase variation of the line parameters. This can be interpreted as the effect of viewing angle or the role of complicated magnetic field of the pulsar.

Description: The spin-down of a neutron star, e.g. due to magneto-dipole losses, results in compression of the stellar matter and induces nuclear reactions at phase transitions between different nuclear species in the crust. We show that this mechanism is effective in heating recycled pulsars, in which the previous accretion process has already been compressing the crust, so it is not in nuclear equilibrium. We calculate the corresponding emissivity and confront it with available observations, showing that it might account for the likely thermal ultraviolet emission of PSR J0437–4715.

Description: New insights into the formation of interstellar formamide, a species of great relevance in prebiotic chemistry, are provided by electronic structure and kinetic calculations for the reaction NH 2 + H 2 CO -〉 NH 2 CHO + H. Contrarily to what previously suggested, this reaction is essentially barrierless and can, therefore, occur under the low temperature conditions of intestellar objects thus providing a facile formation route of formamide. The rate coefficient parameters for the reaction channel leading to NH 2 CHO + H have been calculated to be A = 2.6 x 10 –12  cm 3  s –1 , β = –2.1 and = 26.9 K in the range of temperatures 10–300 K. Including these new kinetic data in a refined astrochemical model, we show that the proposed mechanism can well reproduce the abundances of formamide observed in two very different interstellar objects: the cold envelope of the Sun-like protostar IRAS16293–2422 and the molecular shock L1157-B2. Therefore, the major conclusion of this Letter is that there is no need to invoke grain-surface chemistry to explain the presence of formamide provided that its precursors, NH 2 and H 2 CO, are available in the gas phase.

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: 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: Recent Low-Frequency Array (LOFAR) observations at 115–175 MHz of a field at medium Galactic latitudes (centred at the bright quasar 3C196) have shown striking filamentary structures in polarization that extend over more than 4° across the sky. In addition, the Planck satellite has released full sky maps of the dust emission in polarization at 353 GHz. The LOFAR data resolve Faraday structures along the line of sight, whereas the Planck dust polarization maps probe the orientation of the sky projected magnetic field component. Hence, no apparent correlation between the two is expected. Here we report a surprising, yet clear, correlation between the filamentary structures, detected with LOFAR, and the magnetic field orientation, probed by the Planck satellite. This finding points to a common, yet unclear, physical origin of the two measurements in this specific area in the sky. A number of follow-up multifrequency studies are proposed to shed light on this unexpected finding.

Description: Protoplanetary discs are now routinely observed and exoplanets, after the numerous indirect discoveries, are starting to be directly imaged. To better understand the planet formation process, the next step is the detection of forming planets or of signposts of young planets still in their disc, such as gaps. A spectacular example is the Atacama Large Millimeter/submillimeter Array (ALMA) science verification image of HL Tau showing numerous gaps and rings in its disc. To study the observability of planet gaps, we ran 3D hydrodynamical simulations of a gas and dust disc containing a 5 M J gap-opening planet and characterized the spatial distribution of migrating, growing and fragmenting dust grains. We then computed the corresponding synthetic images for ALMA. For a value of the dust fragmentation threshold of 15 m s –1 for the collisional velocity, we identify for the first time a self-induced dust pile-up in simulations taking fragmentation into account. This feature, in addition to the easily detected planet gap, causes a second apparent gap that could be mistaken for the signature of a second planet. It is therefore essential to be cautious in the interpretation of gap detections.

Description: Recent observations have discovered a number of extremely gas-rich very faint dwarf galaxies possibly embedded in low-mass dark matter haloes. We investigate star formation histories of these gas-rich dwarf (‘almost dark’) galaxies both for isolated and interacting/merging cases. We find that although star formation rates (SFRs) are very low (〈10 –5 M  yr –1 ) in the simulated dwarfs in isolation for the total halo masses ( M h ) of 10 8 -10 9 M , they can be dramatically increased to be ~10 –4 M  yr –1 when they interact or merge with other dwarfs. These interacting faint dwarfs with central compact H ii regions can be identified as isolated emission line dots (‘ELdots’) owing to their very low surface brightness envelopes of old stars. The remnant of these interacting and merging dwarfs can finally develop central compact stellar systems with very low metallicities ( Z /Z  〈 0.1), which can be identified as extremely metal-deficient (‘XMD’) dwarfs. These results imply that although there would exist many faint dwarfs that can be hardly detected in the current optical observations, they can be detected as isolated ELdots or XMD dwarfs, when they interact with other galaxies and their host environments. We predict that nucleated ultrafaint dwarfs formed from the darkest dwarf merging can be identified as low-mass globular clusters owing to the very low surface brightness stellar envelopes.

Description: The BRITE ( BRIght Target Explorer ) constellation of nanosatellites performs seismology of bright stars via high-precision photometry. In this context, we initiated a high-resolution, high signal-to-noise, high-sensitivity, spectropolarimetric survey of all stars brighter than V = 4. The goal of this survey is to detect new bright magnetic stars and provide prime targets for both detailed magnetic studies and asteroseismology with BRITE . Circularly polarized spectra were acquired with Narval at TBL (Bernard Lyot Telescope, France) and HARPSpol at ESO (European Southern Observatory) in La Silla (Chile). We discovered two new magnetic B stars: the B3V star i Car and the B8V component of the binary star Atlas. Each star was observed twice to confirm the magnetic detections and check for variability. These bright magnetic B stars are prime targets for asteroseismology and for flux-demanding techniques, such as interferometry.

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: Accreting neutron stars exhibit Type I X-ray bursts from both frequent hydrogen/helium flashes as well as rare carbon flashes. The latter (superbursts) ignite in the ashes of the former. Hydrogen/helium bursts, however, are thought to produce insufficient carbon to power superbursts. Stable burning could create the required carbon, but this was predicted to only occur at much larger accretion rates than where superbursts are observed. We present models of a new steady-state regime of stable hydrogen and helium burning that produces pure carbon ashes. Hot CNO burning of hydrogen heats the neutron star envelope and causes helium to burn before the conditions of a helium flash are reached. This takes place when the mass accretion rate is around 10 per cent of the Eddington limit: close to the rate where most superbursts occur. We find that increased heating at the base of the envelope sustains steady-state burning by steepening the temperature profile, which increases the amount of helium that burns before a runaway can ensue.

Description: We present new late-time near-infrared imaging of the site of the nearby core-collapse supernova SN 2012aw, confirming the disappearance of the point source identified by Fraser et al. and Van Dyk et al. as a candidate progenitor in both J and Ks filters. We remeasure the progenitor photometry, and find that both the J and Ks magnitudes of the source are consistent with those quoted in the literature. We also recover a marginal detection of the progenitor in H -band, for which we measure H = 19.67 ± 0.40 mag. Comparing the luminosity of the progenitor to stellar evolutionary models, SN 2012aw appears to have resulted from the explosion of a 12.5 ± 1.5 M red supergiant.

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: We derive the carbon monoxide (CO) luminosity function (LF) for different rotational transitions [i.e. (1–0), (3–2), (5–4)] starting from the Herschel LF by Gruppioni et al. and using appropriate L CO – L IR conversions for different galaxy classes. Our predicted LFs fit the data so far available at z 0 and 2. We compare our results with those obtained by semi-analytical models (SAMs): while we find a good agreement over the whole range of luminosities at z 0, at z 1 and z 2, the tension between our LFs and SAMs in the faint and bright ends increases. We finally discuss the contribution of luminous active galactic nucleus ( L X 〉 10 44 erg s – 1 ) to the bright end of the CO LF concluding that they are too rare to reproduce the actual CO LF at z 2.

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: The formation of the Milky Way stellar halo is thought to be the result of merging and accretion of building blocks such as dwarf galaxies and massive globular clusters. Recently, Deason et al. suggested that the Milky Way outer halo formed mostly from big building blocks, such as dwarf spheroidal galaxies, based on the similar number ratio of blue straggler (BS) stars to blue horizontal branch (BHB) stars. Here we demonstrate, however, that this result is seriously biased by not taking into detailed consideration on the formation mechanism of BHB stars from helium-enhanced second-generation population. In particular, the high BS-to-BHB ratio observed in the outer halo fields is most likely due to a small number of BHB stars provided by globular clusters (GCs) rather than to a large number of BS stars. This is supported by our dynamical evolution model of GCs which shows preferential removal of first-generation stars in GCs. Moreover, there are a sufficient number of outer halo GCs which show very high BS-to-BHB ratio. Therefore, the BS-to-BHB number ratio is not a good indicator to use in arguing that more massive dwarf galaxies are the main building blocks of the Milky Way outer halo. Several lines of evidence still suggest that GCs can contribute a significant fraction of the outer halo stars.

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: Nuclear star clusters (NCs) are found to exist in the centres of many galaxies and appear to follow scaling relations similar to those of supermassive black holes. Previous analytical work has suggested that such relations are a consequence of feedback-regulated growth. We explore this idea using high-resolution hydrodynamical simulations, focusing on the validity of the simplifying assumptions made in analytical models. In particular, we investigate feedback emanating from multiple stellar sources rather than from a single source, as is usually assumed, and show that collisions between shells of gas swept up by feedback leads to momentum cancellation and the formation of high-density clumps and filaments. This high-density material is resistant both to expulsion from the galaxy potential and to disruption by feedback; if it falls back on to the NC, we expect the gas to be available for further star formation or for feeding a central black hole. We also note that our results may have implications for the evolution of globular clusters and stellar clusters in high-redshift dark matter haloes.

Description: We explain the axisymmetric gaps seen in recent long-baseline observations of the HL Tau protoplanetary disc with the Atacama Large Millimetre/Submillimetre Array (ALMA) as being due to the different response of gas and dust to embedded planets in protoplanetary discs. We perform global, three-dimensional dusty smoothed particle hydrodynamics calculations of multiple planets embedded in dust/gas discs which successfully reproduce most of the structures seen in the ALMA image. We find a best match to the observations using three embedded planets with masses of 0.2, 0.27 and 0.55 M J in the three main gaps observed by ALMA, though there remain uncertainties in the exact planet masses from the disc model.

Description: Using deep Herschel and ALMA observations, we investigate the star formation rate (SFR) distributions of X-ray-selected active galactic nucleus (AGN) host galaxies at 0.5 〈  z  〈 1.5 and 1.5 〈  z  〈 4, comparing them to that of normal, star-forming (i.e. ‘main-sequence’, or MS) galaxies. We find that 34–55 per cent of AGNs in our sample have SFRs at least a factor of 2 below that of the average MS galaxy, compared to 15 per cent of all MS galaxies, suggesting significantly different SFR distributions. Indeed, when both are modelled as lognormal distributions, the mass and redshift-normalized SFR distributions of X-ray AGNs are roughly twice as broad, and peak 0.4 dex lower, than that of MS galaxies. However, like MS galaxies, the normalized SFR distribution of AGNs in our sample appears not to evolve with redshift. Despite X-ray AGNs and MS galaxies having different SFR distributions, the linear-mean SFR of AGNs derived from our distributions is remarkably consistent with that of MS galaxies, and thus with previous results derived from stacked Herschel data. This apparent contradiction is due to the linear-mean SFR being biased by bright outliers, and thus does not necessarily represent a true characterization of the typical SFR of X-ray AGNs.

Description: We investigate the density–shear instability in Hall-magnetohydrodynamics (Hall-MHD) via numerical simulation of the full non-linear problem in the context of magnetar activity. We confirm the development of the instability of a plane-parallel magnetic field with an appropriate intensity and electron density profile, in accordance with analytic theory. We find that the instability also appears for a monotonically decreasing electron number density and magnetic field, a plane-parallel analogue of an azimuthal or meridional magnetic field in the crust of a magnetar. The growth rate of the instability depends on the Hall properties of the field (magnetic field intensity, electron number density and the corresponding scaleheights), while being insensitive to weak resistivity. Since the Hall effect is the driving process for the evolution of the crustal magnetic field of magnetars, we argue that this instability is critical for systems containing strong meridional or azimuthal fields. We find that this process mediates the formation of localized structures with much stronger magnetic field than the average, which can lead to magnetar activity and accelerate the dissipation of the field and consequently the production of Ohmic heating. Assuming a 5  x  10 14  G magnetic field at the base of crust, we anticipate that magnetic field as strong as 10 15  G will easily develop in regions of typical size of a few hundred metres, containing magnetic energy of 10 43  erg, sufficient to power magnetar bursts. These active regions are more likely to appear in the magnetic equator where the tangential magnetic field is stronger.

Description: Long expected transition states between the rotation powered and accretion powered non-thermal emission in the millisecond pulsar binary systems have been recently observed in the case of three objects PSR J1023+0038, PSR J1824–2452, and PSR J1227–4859. Surprisingly, the transition is related to the significant change in the -ray flux being a factor of a few higher with the presence of an accretion disc. The origin of this enhanced emission seems to be related to the penetration of the inner pulsar magnetosphere by the accretion disc. We propose that the radiation processes, characteristic for the rotation powered pulsar, can co-exist with the presence of an accretion disc in the inner pulsar magnetosphere. In our scenario additional -ray emission is produced by secondary leptons, originated close to the acceleration gap, which Compton up-scatter thermal radiation from the accretion disc to GeV energies. The accretion disc penetrates deep into the pulsar magnetosphere allowing the matter to fall on to the neutron star surface producing pulsed X-ray emission. We show that the sum of the rotation powered pulsar -ray emission, produced by the primary electrons in the curvature process, and the -ray emission, produced by secondary leptons, can explain the observed high-energy radiation from the redback binary pulsar PSR J1227–4853 in the state with evidences of the accretion disc.

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: In the context of the ASAI (Astrochemical Surveys At IRAM) project, we carried out an unbiased spectral survey in the millimetre window towards the well known low-mass Class I source SVS13-A. The high sensitivity reached (3–12 mK) allowed us to detect at least six HDO broad (full width at half-maximum ~4–5 km s –1 ) emission lines with upper level energies up to E u = 837 K. A non-local thermodynamic equilibrium Large Velocity Gradient (LVG) analysis implies the presence of very hot (150–260 K) and dense (≥3  x  10 7  cm –3 ) gas inside a small radius (~25 au) around the star, supporting, for the first time, the occurrence of a hot corino around a Class I protostar. The temperature is higher than expected for water molecules are sublimated from the icy dust mantles (~100 K). Although we cannot exclude we are observing the effects of shocks and/or winds at such small scales, this could imply that the observed HDO emission is tracing the water abundance jump expected at temperatures ~220–250 K, when the activation barrier of the gas phase reactions leading to the formation of water can be overcome. We derive X ( HDO ) ~ 3  x  10 –6 , and a H 2 O deuteration ≥1.5  x  10 –2 , suggesting that water deuteration does not decrease as the protostar evolves from the Class 0 to the Class I stage.

Description: Evidence for the presence of quasi-periodic oscillations (QPOs) in the optical polarization of the blazar PKS 2155–304, during a period of enhanced gamma-ray brightness, is presented. The periodogram of the polarized flux revealed the existence of a prominent peak at T ~ 13 min, detected at 〉99.7 per cent significance, and T ~ 30 min, which was nominally significant at 〉99 per cent. This is the first evidence of QPOs in the polarization of an active galactic nucleus, potentially opening up a new avenue of studying this phenomenon.

Description: The spectrum and morphology of the diffuse Galactic -ray emission carries valuable information on cosmic ray (CR) propagation. Recent results obtained by analyzing Fermi -LAT data accumulated over 7 yr of observation show a substantial variation of the CR spectrum as a function of the distance from the Galactic Centre. The spatial distribution of the CR density in the outer Galaxy appears to be weakly dependent upon the galactocentric distance, as found in previous studies as well, while the density in the central region of the Galaxy was found to exceed the value measured in the outer Galaxy. At the same time, Fermi -LAT data suggest a gradual spectral softening while moving outwards from the centre of the Galaxy to its outskirts. These findings represent a challenge for standard calculations of CR propagation based on assuming a uniform diffusion coefficient within the Galactic volume. Here, we present a model of non-linear CR propagation in which transport is due to particle scattering and advection off self-generated turbulence. We find that for a realistic distribution of CR sources following the spatial distribution of supernova remnants and the space dependence of the magnetic field on galactocentric distance, both the spatial profile of CR density and the spectral softening can easily be accounted for.

Description: The correlation between the frequency and the absolute value of the frequency derivative of the kilohertz quasi-periodic oscillations (QPOs) observed for the first time from 4U 1636-53 is a simple consequence and indicator of the existence of a non-Keplerian rotation rate in the accretion disc boundary layer. This Letter interprets the observed correlation, showing that the observations provide strong evidence in support of the fundamental assumption of disc accretion models around slow rotators, that the boundary layer matches the Keplerian disc to the neutron star magnetosphere.

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: During their formation phase, stars gain most of their mass in violent episodic accretion events, such as observed in FU Orionis (FUor) and EXor stars. V346 Normae is a well-studied FUor that underwent a strong outburst beginning around 1980. Here, we report on photometric and spectroscopic observations, which show that the visual/near-infrared brightness has decreased dramatically between the 1990s and 2010 ( R 10.9 mag, J 7.8 mag and K 5.8 mag). The spectral properties of this fading event cannot be explained by variable extinction alone, but indicate a drop in accretion rate by two to three orders of magnitude. This is the first time that a member of the FUor class has been observed to switch to a very low accretion phase. Remarkably, in the last few years (2011–2015) V346 Nor has brightened again at all near-infrared wavelengths, indicating the onset of a new outburst event. The observed behaviour might be consistent with the clustered luminosity bursts that have been predicted by recent gravitational instability and fragmentation models for the early stages of protostellar evolution. Given V346 Nor's unique characteristics (concerning outburst duration, repetition frequency and spectroscopic diagnostics), our results also highlight the need to revisit the FUor/EXor classification scheme.

Description: Approximately 0.2 ± 0.2 of white dwarfs (WDs) show signs of pollution by metals, which is likely due to the accretion of tidally disrupted planetary material. Models invoking planet–planet interactions after WD formation generally cannot explain pollution at cooling times of several Gyr. We consider a scenario in which a planet is perturbed by Lidov–Kozai oscillations induced by a binary companion and exacerbated by stellar mass-loss, explaining pollution at long cooling times. Our computed accretion rates are consistent with observations assuming planetary masses between ~0.01 and 1 M Mars , although non-gravitational effects may already be important for masses 0.3 M Mars . The fraction of polluted WDs in our simulations, ~0.05, is consistent with observations of WDs with intermediate cooling times between ~0.1 and 1 Gyr. For cooling times 0.1 Gyr and 1 Gyr, our scenario cannot explain the high observed pollution fractions of up to 0.7. Nevertheless, our results motivate searches for companions around polluted WDs.

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: We present high resolution observations of fine structures at pore boundaries. The inner part of granules towards umbra show dark striations which evolve into a filamentary structure with dark core and ‘Y’ shape at the head of the filaments. These filaments migrate into the umbra similar to penumbral filaments. These filaments show higher temperature, lower magnetic field strength and more inclined field compared to the background umbra. The optical depth stratification of physical quantities suggests their similarity with penumbral filaments. However, line-of-sight velocity pattern is different from penumbral filaments where they show downflows in the deeper layers of the atmosphere while the higher layers show upflows. These observations show filamentation in a simple magnetic configuration.

Description: A large number of supernova remnants (SNRs) in our Galaxy and galaxies nearby have been resolved in various radio bands. This radio emission is thought to be produced via synchrotron emission from electrons accelerated by the shock that the supernova ejecta drives into the external medium. Here we consider the sample of radio SNRs in the Magellanic Clouds. Given the size and radio flux of an SNR, we seek to constrain the fraction of shocked fluid energy in non-thermal electrons ( e ) and magnetic field ( B ), and find e B ~ 10 –3 . These estimates do not depend on the largely uncertain values of the external density and the age of the SNR. We develop a Monte Carlo scheme that reproduces the observed distribution of radio fluxes and sizes of the population of radio SNRs in the Magellanic Clouds. This simple model provides a framework that could potentially be applied to other galaxies with complete radio SNRs samples.

Description: We present a line survey of the ultraluminous infrared galaxy Arp 220, taken with the newly installed SEPIA (Swedish-European Southern Observatory PI receiver for APEX) Band 5 instrument on APEX (Atacama Pathfinder Experiment). We illustrate the capacity of SEPIA to detect the 183.3 GHz H 2 O 3 1,3 –2 2,0 line against the atmospheric H 2 O absorption feature. We confirm the previous detection of the HCN(2–1) line, and detect new transitions of standard dense gas tracers such as HNC(2–1), HCO + (2–1), CS(4–3), C 34 S(4–3) and HC 3 N(20–19). We also detect HCN(2–1) v 2 = 1 and the 193.5 GHz methanol (4–3) group for the first time. The absence of time variations in the megamaser water line compared to previous observations seems to rule out an AGN nuclear origin for the line. It could, on the contrary, favour a thermal origin instead, but also possibly be a sign that the megamaser emission is associated with star-forming cores washed out in the beam. We finally discuss how the new transitions of HCN, HNC and HCO + refine our knowledge of the interstellar medium physical conditions in Arp 220.

Description: We present and test a method that dramatically reduces variance arising from the sparse sampling of wavemodes in cosmological simulations. The method uses two simulations which are fixed (the initial Fourier mode amplitudes are fixed to the ensemble average power spectrum) and paired (with initial modes exactly out of phase). We measure the power spectrum, monopole and quadrupole redshift-space correlation functions, halo mass function and reduced bispectrum at z  = 1. By these measures, predictions from a fixed pair can be as precise on non-linear scales as an average over 50 traditional simulations. The fixing procedure introduces a non-Gaussian correction to the initial conditions; we give an analytic argument showing why the simulations are still able to predict the mean properties of the Gaussian ensemble. We anticipate that the method will drive down the computational time requirements for accurate large-scale explorations of galaxy bias and clustering statistics, and facilitating the use of numerical simulations in cosmological data interpretation.

Description: Using a specialized technique sensitive to the presence of expanding ionized gas, we have detected a set of three concentric expanding shells in an H ii region in the nearby spiral galaxy M33. After mapping the kinematics in Hα with Fabry–Perot spectroscopy, we used slit spectra to measure the intensities of the [S ii ] doublet at 671.9, 673.1 nm and the [N ii ] doublet at 645.8, 658.3 nm to corroborate the kinematics and apply diagnostic tests using line ratios. These showed that the expanding shells are shock dominated as would be the case if they had originated with supernova explosions. Estimating their kinetic energies, we find fairly low values, indicating a fairly advanced stage of evolution. We obtain density, mass and parent star mass estimates, which, along with the kinetic energies, are inconsistent with the simplest models of shock–interstellar medium interaction. We propose that the presence and properties of an inhomogeneous medium offer a scenario which can account for these observations, and discuss the implications. Comparing our results with data from the literature supports the combined presence of an H ii region and supernova remnant material at the observed position.

Description: We study the origin of the stellar α-element-to-iron abundance ratio, [α/Fe] * , of present-day central galaxies, using cosmological, hydrodynamical simulations from the Evolution and Assembly of GaLaxies and their Environments (EAGLE) project. For galaxies with stellar masses of M * 〉 10 10.5 M , [α/Fe] * increases with increasing galaxy stellar mass and age. These trends are in good agreement with observations of early-type galaxies, and are consistent with a ‘downsizing’ galaxy formation scenario: more massive galaxies have formed the bulk of their stars earlier and more rapidly, hence from an interstellar medium that was mostly α-enriched by massive stars. In the absence of feedback from active galactic nuclei (AGNs), however, [α/Fe] * in M * 〉 10 10.5 M galaxies is roughly constant with stellar mass and decreases with mean stellar age, extending the trends found for lower mass galaxies in both simulations with and without AGN. We conclude that AGN feedback can account for the α-enhancement of massive galaxies, as it suppresses their star formation, quenching more massive galaxies at earlier times, thereby preventing the iron from longer lived intermediate-mass stars (supernova Type Ia) from being incorporated into younger stars.

Description: We report broad-band spectral properties of the high-mass X-ray binary pulsar SMC X-2 by using three simultaneous Nuclear Spectroscopy Telescope Array and Swift /XRT observations during its 2015 outburst. The pulsar was significantly bright, reaching a luminosity up to as high as ~5.5 x 10 38 erg s –1 in 1–70 keV range. Spin period of the pulsar was estimated to be 2.37 s. Pulse profiles were found to be strongly luminosity dependent. The 1–70 keV energy spectrum of the pulsar was well described with three different continuum models such as (i) negative and positive power law with exponential cutoff, (ii) Fermi -Dirac cutoff power law and (iii) cutoff power-law models. Apart from the presence of an iron line at ~6.4 keV, a model independent absorption like feature at ~27 keV was detected in the pulsar spectrum. This feature was identified as a cyclotron absorption line and detected for the first time in this pulsar. Corresponding magnetic field of the neutron star was estimated to be ~2.3 x 10 12  G. The cyclotron line energy showed a marginal negative dependence on the luminosity. The cyclotron line parameters were found to be variable with pulse phase and interpreted as due to the effect of emission geometry or complicated structure of the pulsar magnetic field.

Description: We analyse structural decompositions of 500 late-type galaxies (Hubble T -type ≥6) from the Spitzer Survey of Stellar Structure in Galaxies ( S 4 G ; Salo et al.), spanning stellar mass range of about 10 7 to a few times 10 10 M . Their decomposition parameters are compared with those of the early-type dwarfs in the Virgo cluster from Janz et al. They have morphological similarities, including the fact that the fraction of simple one-component galaxies in both samples increases towards lower galaxy masses. We find that in the late-type two-component galaxies both the inner and outer structures are by a factor of 2 larger than in the early-type dwarfs, for the same stellar mass of the component. While dividing the late-type galaxies to low- and high-density environmental bins, it is noticeable that both the inner and outer components of late types in the high local density galaxies are smaller, and lie closer in size to those of the early-type dwarfs. This suggests that, although structural differences between the late- and early-type dwarfs are observed, environmental processes can plausibly transform their sizes sufficiently, thus linking them evolutionarily.

Description: We calculate the microlensing event rate and typical time-scales for the free-floating planet (FFP) population that is predicted by the core accretion theory of planet formation. The event rate is found to be ~1.8  x  10 –3 of that for the stellar population. While the stellar microlensing event time-scale peaks at around 20 d, the median time-scale for FFP events (~0.1 d) is much shorter. Our values for the event rate and the median time-scale are significantly smaller than those required to explain the Sumi et al. result, by factors of ~13 and ~16, respectively. The inclusion of planets at wide separations does not change the results significantly. This discrepancy may be too significant for standard versions of both the core accretion theory and the gravitational instability model to explain satisfactorily. Therefore, either a modification to the planet formation theory is required or other explanations to the excess of short-time-scale microlensing events are needed. Our predictions can be tested by ongoing microlensing experiment such as Korean Microlensing Telescope Network, and by future satellite missions such as WFIRST and Euclid .

Description: The recent discovery of three Earth-sized, potentially habitable planets around a nearby cool star, TRAPPIST-1, has provided three key targets for the upcoming James Webb Space Telescope (JWST) . Depending on their atmospheric characteristics and precise orbit configurations, it is possible that any of the three planets may be in the liquid water habitable zone, meaning that they may be capable of supporting life. We find that present-day Earth levels of ozone, if present, would be detectable if JWST observes 60 transits for innermost planet 1b and 30 transits for 1c and 1d.

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.