ALBERT

Description: Fishermen are known to try to avoid fishing in stormy weather, as storms pose a physical threat to fishers, their vessels, and their gear. In this article, a dataset and methods are developed to investigate the degree to which fishers avoid storms, estimate storm aversion parameters, and explore how this response varies across vessel characteristics and across regions of the United States. The data consist of vessel-level trip-taking decisions from six federal fisheries across the United States combined with marine storm warning data from the National Weather Service. The estimates of storm aversion can be used to parameterize predictive models. Fishers’ aversion to storms decreases with increasing vessel size and increases with the severity of the storm warning. This information contributes to our understanding of the risk-to-revenue trade-off that fishers evaluate every time they consider going to sea, and of the propensity of fishers to take adaptive actions to avoid facing additional physical risk.

Description: Sardine Sardinops sagax is an ecologically and economically important Clupeid found off the entire South African coast that includes both coastal upwelling and western boundary current systems. Although the management of the sardine fisheries historically assumed a single, panmictic population, the existence of three, semi-discrete subpopulations has recently been hypothesized. We conducted otolith δ18O and microstructure analyses to investigate nursery habitat temperatures and early life growth rates, respectively, of sardine collected from three biogeographic regions around South Africa’s coast to test that hypothesis. Analyses indicated that for both summer- and winter-captured adults and summer-captured juveniles, fishes from the west coast grew significantly slower in water that was several degrees cooler than those from the south and east coasts. This suggests that mixing of sardines between regions, particularly the west and other coasts, is relatively limited and supports the hypothesis of semi-discrete subpopulations. However, the west-south differences disappeared in the results for winter-captured juveniles, suggesting that differences in early life conditions between regions may change seasonally, and/or that all or most winter-captured juveniles originated from the west coast. Further elucidating the interactions between South African sardine subpopulations and the mechanisms thereof is important for sustainable harvesting of this species.

Description: Progress towards ecosystem-based fisheries management calls for useful tools to prioritize actions. To select suitable methods for local circumstances, evaluating approaches used in other jurisdictions can be a cost-effective first step. We tested Productivity Susceptibility Analysis (PSA) to assess the potential vulnerability of the marine fish community in the Skagerrak–Kattegat (Eastern North Sea) to possible interactions with all Swedish fisheries operating in the area. This analysis combines attributes for a species productivity with attributes related to the susceptibility to capture to quantify a single score for vulnerability: high, medium, or low risk. Results indicate that demersal trawl and gillnet fisheries were associated with the highest risk levels if interaction occurs, i.e. having the highest prevalence of species with potentially high vulnerability to the fisheries. Mixed results were seen when comparing the assessment results with available data. The main benefit of utilizing PSA in the area is the comprehensiveness of the assessment, including data-deficient fisheries and species. Drawbacks include potential overestimation of actual risks. Overall, together with available data, PSA in the studied area provides a comprehensive map of potential risks for further actions and may progress a science-based, precautionary management of the area.

Description: While fisheries provide food and employment for hundreds of millions of people, they also can have significant impact on biodiversity. We explore the potential of area-based fisheries management to simultaneously maintain biodiversity and high levels of sustainable food production. We used two illustrative examples of fisheries that have different gear types, areas, and species to evaluate the trade-off between biodiversity and harvest. We calculate the optimal effort by gear and area that maximizes a weighted objective function of biodiversity and harvest, ranging from 100% of the weight on harvest to 100% on biodiversity. We found for both case studies that the trade-off was highly convex, with win–win solutions allowing for high levels of both fishery harvest and conservation. This is achieved by reducing or eliminating fishing effort that negatively impacts high conservation value species while maintaining fishing effort with gears and in areas where there is low conservation impact. We suggest that, in most fisheries, such situations can be found and that effective area-based management can provide for high levels of biodiversity protection and food production.

Description: Recent application of Fourier transform near infra-red spectroscopy (FT-NIRS) to predict age in fish otoliths has gained attention among fisheries managers as a potential alternative to costly production ageing of managed species. We assessed the age prediction capability of FT-NIRS scans in whole otoliths from red snapper, Lutjanus campechanus, collected from the US Gulf of Mexico and US Atlantic Ocean (South Atlantic). Otoliths were scanned with an FT-NIR spectrometer and resulting spectral signatures were regressed with traditionally estimated ages via partial least squares regression to produce calibration models, which were validated for predictive capability against test sets of otoliths. Calibration models successfully predicted age with R2 ranging 0.94–0.95, mean squared error ≤1.8 years, and bias 31 years were not well predicted, possibly due to light attenuation in the thickest otoliths. Our results suggest that FT-NIRS can improve efficiency in production ageing for fisheries management while maintaining data quality standards.

Description: This article investigates the diet of the snow crab (Chionoecetes opilio) and its feeding intensity in the Barents Sea. Data show that snow crab has a diverse diet that includes almost all types of benthic invertebrates living in the Barents Sea. There are differences between the diets of females and males and of juveniles and adults. Juveniles and females typically occupy shallow areas with communities of bivalve molluscs, while males typically live deeper on slopes and depressions where polychaetes and crustaceans are the most abundant groups. Stomach contents were analysed to determine the species composition and frequency of occurrence of various benthic taxa. Consumption of food was estimated and compared with data from the Russian seas of the Pacific region. The total annual consumption of macrozoobenthos by snow crab was calculated in accordance with its current distribution in the Barents Sea. Snow crab consumes at least 30 000 tonnes of benthos annually, which amounts to 0.1–0.2% of the total macrozoobenthic biomass in the investigated area. The population of snow crab causes the largest impact on the benthic communities in the northeastern part of the Barents Sea and near the south side of the Novaya Zemlya archipelago.

Description: Until the late 19th century, extensive beds of flat oyster Ostrea edulis populated the Central North Sea, which have vanished after intensive fisheries. At present, various initiatives are being carried out to investigate the potential to restore this former key species in the area. This historical ecological study contributes by delineating the former oyster bed area and through an assessment of its limits against known gradients in the North Sea. Extensive data from historical maps, texts, and ship-based surveys were used to synthesize our knowledge on the former beds. It was revealed that the area with oyster beds covered ∼6.2% of the total North Sea bottom, with a delineation that could partly be explained by hydrodynamic and temperature gradients. The position and extent of the area are notably different from the area that is used in recent feasibility studies on the restoration of North Sea oyster beds. The offshore oysters lived on muddy sand in relatively cold conditions, and there are several indications that their reproductive rate was low. The apparent disappearance of cold water adapted flat oysters will challenge restoration projects. This study provides indispensable information for the future restoration of flat oyster beds in the North Sea.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Description: Successful implementation of Ecosystem-Based Fisheries Management (EBFM) requires appropriate action as informed by reference points in an ecosystem context. Thresholds in the response of ecological indicators to system drivers have been suggested as reference points for EBFM, though the management performance of these indicators and possible values for their reference points have not been widely evaluated. We used Management Strategy Evaluation to test the performance of control rules that used ecological indicators to adjust the advice from single-species stock assessments, using the Georges Bank finfish fishery as a case study. We compare the performance of control rules that used ecological indicators to that of single-species F MSY control rules when the system dynamics were governed by the same multispecies population model. Control rules that used indicator-based reference points were able to perform better against catch and biodiversity objectives than when harvests were based on single-species advice alone. Indicators and values for reference points associated with good performance varied depending on the management objective. We quantified tradeoffs between total catch, biodiversity, and interannual variability in catch, noting that it was possible in some instances to achieve higher than average biodiversity while maintaining high catches using indicator-based control rules. While improved performance was noted using ecological indicators, outcomes were variable, and the gains in performance obtained may be similar to alternative methods of implementing precaution in single-species fishery control rules.

Description: Climate change and fishing can have major impacts on the distribution of natural marine resources. Climate change alters the distribution of suitable habitat, forcing organisms to shift their range or attempt to survive under suboptimal conditions. Fishing reduces the abundance of marine populations and truncates their age structure leading to range contractions or shifts. Along the east coast of the United States, there have been major changes in fish populations due to the impacts of fishing and subsequent regulations, as well as changes in the climate. Black sea bass, scup, summer flounder, and winter flounder are important commercial and recreational species, which utilize inshore and offshore waters on the northeast shelf. We examined the distributions of the four species with the Northeast Fisheries Science Center trawl surveys to determine if the along-shelf centres of biomass had changed over time and if the changes were attributed to changes in temperature or fishing pressure through changes in abundance and length structure. Black sea bass, scup, and summer flounder exhibited significant poleward shifts in distributions in at least one season while the Southern New England/Mid-Atlantic Bight stock of winter flounder did not shift. Generalized additive modelling indicated that the changes in the centres of biomass for black sea bass and scup in spring were related to climate, while the change in the distribution of summer flounder was largely attributed to a decrease in fishing pressure and an expansion of the length–age structure. While the changes in ocean temperatures will have major impacts on the distribution of marine taxa, the effects of fishing can be of equivalent magnitude and on a more immediate time scale. It is important for management to take all factors into consideration when developing regulations for natural marine resources.

Description: Many snow crab fisheries have fluctuated widely over time in a quasi-cyclic way due to highly variable recruitment. The causes of this variability are still debated. Bottom-up processes related to climate variability may strongly affect growth and survival during early life, whereas top-down predator effects may be a major source of juvenile mortality. Moreover, intrinsic density-dependent processes, which have received much less attention, are hypothetically responsible for the cycles in recruitment. This study explored how climate, larval production, intercohort cannibalism and groundfish predation may have affected recruitment of early juvenile snow crab in the northwest Gulf of St Lawrence (eastern Canada) over a period of 23 years. Abundance of early juvenile snow crabs (2.5–22.9 mm in carapace width), representing the first 3 years of benthic life, came from an annual trawl survey and was used to determine cohort strength. Analyses revealed a cyclic pattern in abundance of 0 + crabs that may arise from cohort resonant effects. This pattern consisted of three recruitment pulses but was reduced to two pulses by age 2 + , while the interannual variability of cohort strength was dampened. This reconfiguration of the earliest recruitment pattern was dictated primarily by bottom water temperature and cannibalism, which progressively overruled the pre-settlement factors of larval production and surface water temperature that best explained abundance of 0 + crabs. The results strongly suggest that bottom-up and density-dependent processes prevail over top-down control in setting the long-term trends and higher-frequency oscillations of snow crab early recruitment patterns.

Description: Fisheries biology encompasses a tremendous diversity of research questions, methods, and models. Many sub-fields use observational or experimental data to make inference about biological characteristics that are not directly observed (called "latent states"), such as heritability of phenotypic traits, habitat suitability, and population densities to name a few. Latent states will generally cause model residuals to be correlated, violating the assumption of statistical independence made in many statistical modelling approaches. In this exposition, we argue that mixed-effect modelling (i) is an important and generic solution to non-independence caused by latent states; (ii) provides a unifying framework for disparate statistical methods such as time-series, spatial, and individual-based models; and (iii) is increasingly practical to implement and customize for problem-specific models. We proceed by summarizing the distinctions between fixed and random effects, reviewing a generic approach for parameter estimation, and distinguishing general categories of non-linear mixed-effect models. We then provide four worked examples, including state-space, spatial, individual-level variability, and quantitative genetics applications (with working code for each), while providing comparison with conventional fixed-effect implementations. We conclude by summarizing directions for future research in this important framework for modelling and statistical analysis in fisheries biology.

Description: While the impact of environmental forcing on recruitment variability in marine populations remains largely elusive, studies spanning large spatial areas and many stocks are able to identify patterns common to different regions and species. In this study, we investigate the effects of the environment on the residuals of a Ricker stock–recruitment (SR) model, used as a proxy of prerecruits' survival, of 18 assessed stocks in the Baltic and North Seas. A probabilistic principal components (PCs) analysis permits the identification of groups of stocks with shared variability in the prerecruits' survival, most notably a group of pelagics in the Baltic Sea and a group composed of gadoids and herring in the North Sea. The first two PCs generally grouped the stocks according to their localizations: the North Sea, the Kattegat–Western Baltic, and the Baltic Sea. This suggests the importance of the local environmental variability on the recruitment strength. Hence, the prerecruits' survival variability is studied according to geographically disaggregated and potentially impacting abiotic or biotic variables. Time series (1990–2009) of nine environmental variables consistent with the spawning locations and season for each stock were extracted from a physical–biogeochemical model to evaluate their ability to explain the survival of prerecruits. Environmental variables explained 〉70% of the survival variability for eight stocks. The variables water current, salinity, temperature, and biomass of other fish stocks are regularly significant in the models. This study shows the importance of the local environment on the dynamics of SR. The results provide evidence of the necessity of including environmental variables in stock assessment for a realistic and efficient management of fisheries.

Description: Ecosystem-based fisheries management seeks to consider trade-offs among management objectives for interacting species, such as those that arise through predator–prey linkages. In particular, fisheries-targeting forage fish (small and abundant pelagic fish) might have a detrimental effect on fisheries-targeting predators that consume them. However, complexities in ecological interactions might dampen, negate, or even reverse this trade-off, because small pelagic fish can be important predators on egg stages of piscivorous fish. Further, the strength of this trade-off might depend on the extent to which piscivorous fish targeted by fisheries regulate forage species productivity. Here, we developed a novel delay-differential bioeconomic model of predator–prey and fishing dynamics to quantify how much egg predation or weak top-town control affects the strength of trade-off between forage and piscivore fisheries, and to measure how ecological interactions dictate policies that maximize steady-state profits. We parameterized the model based on ecological and economic data from the North Sea Atlantic cod ( Gadus morhua ) and Atlantic herring ( Clupea harengus ). The optimal policy was very sensitive to the ecological interactions (either egg predation or weak top-down control of forage by predators) at relatively low forage prices but was less sensitive at high forage fish prices. However, the optimal equilibrium harvest rates on forage and piscivores were not substantially different from what might be derived through analyses that did not consider species interactions. Applying the optimal multispecies policy would produce substantial losses (〉25%) in profits in the piscivore fishery, and the extent of loss was sensitive to ecological scenarios. While our equilibrium analysis is informative, a dynamic analysis under similar ecological scenarios is necessary to reveal the full economic and ecological benefits of applying ecosystem-based fishery management policies to predator–prey fishery systems.

Description: Leptocephali, the larvae of eels, grow to large sizes and are widely distributed in tropical and subtropical oceans. Their role in oceanic food webs is poorly known because they are rarely reported as food items in fish stomach content studies. Data from 13 years of research on the trophic dynamics of Pacific Ocean predatory fish indicate that among 8746 fish of 76 species/taxa (33 families) that had been feeding, only 16 fish of 6 species had remains of 34 leptocephali in their stomachs. Only 0.013% of the 256 308 total prey items were leptocephalus larvae, and 0.03% of the total prey items were juvenile or adult eels (mostly snipe eels: Nemichthyidae). There were 10 fish of 2 species of lancetfish ( Alepisaurus spp., n = 152), 2 rainbow runners ( Elagatis bipinnulata , n = 222), and 2 yellowfin tuna ( Thunnus albacares , n = 3103) that had leptocephali in their stomach contents, but all except one T. albacares (contained 15 leptocephali) had each eaten ≤3 leptocephali. A swallower, Pseudoscopelus sp., and a frigate tuna, Auxis thazard , had eaten single leptocephali. Twenty-eight bigeye tuna, Thunnus obesus , had eaten 76 juvenile/adult nemichthyid or serrivomerid eels. A literature survey found that only 15 out of 75 examined publications listed leptocephali in the stomach contents of a total of 6 species out of ~ 42 300 predatory fish of 40 species. The transparency of leptocephali and their apparent mimicry of gelatinous zooplankton could contribute to lower rates of predation. Their soft bodies likely digest rapidly, so although this study and existing literature indicate that leptocephali sometimes contribute to predatory fish diets, particularly for fish that do not exclude gelatinous prey types, and fish with low digestion rates in their stomachs such as lancetfish, their levels of contribution to fish diets and the impacts of predators on eel recruitment remain uncertain.

Description: Effective individual transferable quotas (ITQ) systems rebuild stocks and allow transfer of quotas to more efficient operators. This process requires functional markets for both quota sales and temporary quota leases. These markets are expected to respond to changes in economic rent from the fishery, which is influenced by stock abundance and the international rock lobster price. This research used multistate Markov modelling and Granger causality test to examine changes in the permanent and temporary quota trade in the Tasmanian rock lobster fishery quota market, during periods of both increasing and decreasing stock abundance. The permanent quota trade market was more active during the period of stock growth, while the quota lease market was active in both periods of stock growth and decline. In contrast to theoretical trends in ITQ fisheries, trades in both markets were not linked to the technical efficiency (i.e. catching capability) of operators, but were more driven by the quota owners' financial capacity (i.e. number of owned quotas). Prolonged and unexpected stock decline affected the quota market so that it deviated from the theoretical pattern of ITQ fisheries. Operators previously active in the market reduced their activity, while smaller operators and firms that previously had not traded became more active, so the fleet expanded with smaller operators entering.

Description: Jellyfish disruption of fisheries has been described in some coastal systems, but few thorough investigations have been conducted. To ascertain the economic impact and trend of jellyfish blooms in the Northern California Current (NCC), we mailed surveys to resident commercial shrimpers, salmon trollers, rockfish (blue, black), and groundfish fishers ( n = 872). We asked fishers to estimate the damages caused by jellyfish—including costs of relocating to avoid blooms, lost fishing time, time lost to bycatch sorting, fish depreciation, and gear damage. Of the total respondents ( n = 111), 67% reported that jellyfish reduce their seasonal revenue, but the degree of impact ranged considerably by fishery and location. Highest jellyfish nuisance corresponded to regions with the most salmon trolling effort. Using the mean revenue losses provided by respondents, we estimate that the combined economic impact of jellyfish on Oregon's salmon and pink shrimp fishers was over $650 000 in peak jellyfish season (June–September) in 2012. Fishers reported that jellyfish biomass varies annually, but most respondents (51%) reported observing no appreciable change in jellyfish populations in the last 5 years. Since economic impact analyses have been conducted primarily in areas with anomalous, high-density blooms, data from the NCC, which is not known to be experiencing increases in jellyfish abundance, provides baseline information on the socio-economic impact of jellyfish blooms in this region. In addition, the finding that jellyfish impact hook and line fisheries—not solely net fisheries—has implications for many other regions where fishers employ this gear type.

Description: Odontocete depredation on longlines involves socioeconomic and conservation issues with significant losses for fisheries and potential impacts on wild populations of depredating species. As technical solutions to this conflict are limited and difficult to implement, this study aimed to identify fishing practices that could reduce odontocete depredation, with a focus on killer whales (Orcinus orca) interacting with Patagonian toothfish (Dissostichus eleginoides) longliners off the Crozet islands. Data collected by fishery observers from 6013 longline sets between 2003 and 2013 allowed us to statistically detect the significant influence of five operational variables using GLMMs. The probability of interactions between vessels and killer whales was decreased by (i) the number of vessels operating simultaneously in the area: the limited number of depredating killer whales may induce a dilution effect with increased fleet size, and (ii) depth of longline sets: vessels operating in shallow waters may be more accessible to whales that are initially distributed on peri-insular shelves. The cpue was negatively influenced by (iii) length of longlines: longer sets may provide killer whales access to a greater proportion of hooked fish per set, and positively influenced by (iv) hauling speed: increased speed may shorten the time during which toothfish are accessible to whales during hauling. The time it takes for killer whales to reach vessels was positively correlated to (v) the distance travelled between longline sets with an estimated threshold of 100 km beyond which whales seem to temporarily lose track of vessels. These findings provide insightful guidelines about what fishing strategy to adopt given these variables to reduce killer whale depredation here and in similar situations elsewhere. To a greater extent, this study is illustrative of how collaborative work with fishermen in a fully controlled fishery framework may lead to the definition of cost-limited and easy-to-implement mitigation solutions when facing such human-wildlife conflict.

Description: In Alaskan waters, depredation on sablefish longline gear by sperm whales increases harvesting cost, negatively biases stock assessments, and presents a risk of entanglement for whales. The Southeast Alaska Sperm Whale Avoidance Project (SEASWAP), a collaborative effort involving industry, scientists, and managers, since 2003 has undertaken research to evaluate depredation with a goal of recommending measures to reduce interactions. Prior to 2003, little was known about sperm whale distribution and behaviour in the Gulf of Alaska (GOA). Although fishers were reporting increasing interactions, the level of depredation varied with no apparent predictor of occurrence across vessels. Between 2003 and 2007, fishers were provided with fishery logbooks and recorded information on whale behaviour, whale presence and absence, during the set, soak, and haul for 319 sets in the GOA. Data were evaluated for a vessel, area, and seasonal (month) effect in the presence and absence of sperm whales. Using catch per unit effort ( cpue ) as a metric, in kg/100 hooks, results indicated that depredation depended on both the vessel and the area. More whales associated with vessels from April to August. Sperm whales were also likely to be present when cpue was high, revealing that whales and fishers both knew the most productive fishing areas, but confounding the use of cpue as a metric for depredation. Using a Bayesian mark-recapture analysis and the sightings histories of photo-identified whales, an estimated $$\hat{N}=135$$ (95% CI 124, 153) sperm whales were associating with vessels in 2014. A spatial model was fitted to 319 longline sets and quantified a 3% loss in cpue , comparable to other global studies on sperm whale depredation. Through all phases of SEASWAP, our understanding of depredation has gained significantly. This successful collaboration should be considered as a model to create partnerships and build collaborations between researchers and fisherpeople encountering marine mammal interactions with fishing gear.

Description: This paper provides a synthesis of results obtained as part of a long-term collaborative study involving biologists, fishers, and resource managers—centring on the occurrence of killer whales in the Crozet Archipelago before and after the implementation of a demersal longline fishery for Patagonian toothfish. Depredation behaviour was reported as soon as the fishery was initiated, with dramatic effects on both the demographic trajectories of the killer whales and on the amount of fish lost by the fishers. Killer whales interacting with the fishery exhibited very high mortality rates when illegal fishing took place, while killer whales not interacting were unaffected. However, after illegal fishing ended, killer whales interacting with the fishery exhibited both higher fecundity and survival rates compared with killer whales not interacting. Since whales typically removed fish entirely from the hooks, an adapted methodology that did not rely on determining the number of damaged fish was developed to estimate depredation rates. In the Crozet EEZ over a 10-year period, 33.9% of the total amount of Patagonian toothfish caught, representing a total of 28 million , was estimated to be lost due to the combined effects of killer whale and sperm whale depredation. In an effort to reduce depredation losses, modifications to fishing methods, such as changing the fishing season, changing fishing areas when exposed to depredation and changing longline length and hauling speed were successfully tested. Acoustic deterrent devices were ineffective in deterring killer whales from depredating longlines. Alternative fishing gears, such as fish pots, were also tested. However, while providing encouraging results regarding the suppression of depredation and seabird bycatch, fish pots were not efficient enough to sustain an economically viable fishery. In conclusion, we discuss how the findings of this comprehensive study can be used elsewhere in fisheries confronted with depredation.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Description: A model combining qualitative and historical quantitative data in an innovative rule-based fuzzy cognitive map framework is used to assess and compare the long-term bioeconomic impact of adopting gear modifications aimed at reducing bycatch in the Portuguese crustacean trawl fishery. The impact of codend-related changes (mesh size and shape) and the introduction of a sorting device (sorting grid system) on the main target crustacean species (deepwater rose shrimp Parapenaeus longirostris and Norway lobster Nephrops norvegicus ) and the main fish bycatch species (blue whiting Micromesistius poutassou , horse mackerel Trachurus trachurus , and European hake Merluccius merluccius ) were evaluated. Horse mackerel was the only fish species for which changing codends negatively affected landings per unit of effort by large percentages. The use of a sorting grid system, only evaluated for blue whiting and Norway lobster, led to a strong decrease in landings per unit of effort, especially for the former species. The impact of gear alterations was negligible on fish spawning-stock biomass, but was significant for crustaceans, particularly rose shrimp. A straightforward evaluation of the economic impact (fishers' revenues) of the three bycatch reduction options showed these to be negligible or small.

Description: The difficulty of ensuring adequate statistical coverage of whole fleets is a challenge for the implementation of observer programmes and may reduce the usefulness of the data they obtain for management purposes. This makes it necessary to find cost-effective alternatives. Electronic monitoring (EM) systems are being used in some fisheries as an alternative or a complement to human observers. The objective of this study was to test the use and reliability of EM on the tropical tuna purse-seine fishery. To achieve this objective, seven trips of tuna purse seiners operating in the three Oceans were closely monitored to compare the information provided by EM and on-board observers to determine if EM can reliably document fishing effort, set type, tuna catch, and bycatch. Total tuna catch per set was not significantly different between EM and observer datasets; however, regarding species composition, only main species matched between EM and observers. Success on set-type identification using EM varied between 98.3 and 56.3%, depending on the camera placement. Overall, bycatch species were underestimated by EM, but large bodied species, such as billfishes, were well documented. The analyses in this study showed that EM can be used to determine the fishing effort (number of sets) and total tuna catch as reliably as observers can. Set-type identification also had very promising results, but indicated that refinement of the methods is still needed. To be fully comparable with observer data, improvements for accurately estimating the bycatch will need to be developed in the application and use of the EM system. Operational aspects that need to be improved for an EM programme to be implemented include standardizing installation and on-board catch handling methodology as well as improvements in video technology deployment.

Description: In this paper, we synthesize information presented at the 2nd Fishery Dependent Information (FDI) Conference, held in Rome, Italy, from 2 to 6 March 2014. We review current issues and advances in the collection, interpretation and application of fishery-dependent data, and highlight emergent findings in the field. Key issues include (i) the design and collection of data associated with commercial and recreational fisheries and the use of these data to support conventional and novel approaches to fisheries science and management and (ii) the role of fishers in co-management and policy setting. We noted that since the 2010 FDI conference a paradigm shift towards full engagement of key stakeholders started to take place. It also became evident that trust between stakeholders, managers, and scientists is necessary to develop efficient fishery monitoring programmes. While building such trust among key players often begins in informal settings, eventually one must evolve structured, formalized, and agreed processes for such interactions. We also conclude that because of the diversity of fisheries any determination of "best practices" may be difficult. Instead, we provide a list of "best principles" emerged from the conference.

Description: The walleye pollock ( Gadus chalcogrammus ) fishery in the Bering Sea is one of the largest fisheries in the world. The North Pacific Fishery Management Council (NPFMC) provides management advice for this fishery, including the development of measures to minimize salmon bycatch to the extent practicable, one of the stated objectives of the US Magnuson–Stevens Fishery Conservation and Management Act National Standard Guidelines. Salmon have a unique cultural and nutritional importance in the State of Alaska and are the subject of fully allocated mixed commercial, recreational, and subsistence fisheries. Chinook salmon ( Oncorhynchus tshawytscha ) stocks in Alaska have been declining for the last decade, and all sources of mortality are being considered to help in rebuilding stocks. Given the extensive scientific National Marine Fisheries Service observer data collection programme, the NPFMC has developed bycatch management measures that place limits by fishery sector on the allowable catch of Chinook salmon. Part of this programme includes industry-proposed incentive programmes designed to encourage lower bycatch. Evaluating the efficacy of the new measures poses a number of challenges, particularly in light of changing ocean conditions (perhaps affecting the degree of overlap between pollock and salmon). In this study, data on pre- and post-programme implementation were evaluated to determine if the programme is meeting stated goals and objectives or if modifications are needed. These evaluations included consideration of fleet-level bycatch numbers and rates, seasonality of bycatch by sector, and individual vessel bycatch rates. Results suggest that revised management regulations appear to have resulted in reduced bycatch of salmon overall. Also, lower bycatch rates seem to reflect changing behaviour in response to new management measures. However, the extent to which the programme is effective at the vessel level remains difficult to ascertain without explicit vessel-specific benchmarks developed for evaluating programme efficacy.

Description: Part of the European Union (EU) Common Fisheries Policy revision of 2013 is a commitment to implement a land-all policy, under which the practice of discarding caught fish back into the sea will be forbidden. This measure will be applied first to the pelagic fleet in 2015, with a phased implementation for the demersal fleet between 2016 and 2019. As part of trials to determine the efficacy of a land-all policy for North Sea cod ( Gadus morhua L.), Remote Electronic Monitoring (REM) systems were installed on seven Scottish demersal vessels in 2008. Vessels were permitted additional days-at-sea and cod quota, and were obliged to land all cod caught in the North Sea. This arrangement has been renewed each year as part of the Scottish Cod Conservation Credits scheme, and while the list of vessels involved has not remained constant, the scheme remains attractive to skippers (27 vessels in 2014), has always been oversubscribed, and is likely to remain a key part of the Scottish Government's approach to land-all enforcement. Marine Scotland Science is granted access to all REM data collected from Scottish vessels. This paper summarizes the scientific analyses carried out using these data from 2008 onwards, including the installation and operation of REM systems for scientific purposes; the programme developed to train REM analysts; systems for combining length measurements with fish counts; the potential use of REM data in management advice; and studies on such aspects as discard-rate estimation, activity mapping, estimating the relative costs of on-board and REM observation, morphometric length inference, and automated image analysis. We conclude that, while further development work is certainly needed, REM provides a rich source of fisheries information for science as well as for compliance and management. However, care will need to be taken to ensure that science monitoring and analysis resources do not become overwhelmed.

Description: Chinook salmon ( Oncorhynchus tshawytscha ) are taken as bycatch in the Bering Sea pollock ( Gadus chalcogrammus ) fishery, with recently revised management measures in place to limit the overall Chinook salmon catch. Historical impact of the bycatch on regional salmon stocks is made difficult because, until recently, sampling for the stock composition of the bycatch was patchy and diverse in approaches. In this study, extensive observer data on the biological attributes (size and age composition) of the bycatch were used to estimate the impact on specific regional stock groups (RSGs), as defined given available genetic stock identification estimates. Our model provides estimates of the impact on Chinook salmon RSGs, given seasonal and spatial variability in the bycatch, and accounts for observed in-river age compositions, uncertainty in age-specific oceanic natural mortality of Chinook salmon, and between-year variability in genetic information. The upper Yukon River stock is transboundary and subject to heightened management interest and international management agreements on escapement goals. Our study updates results from an earlier analysis used to develop the management regulations that went into place in 2011. It shows that the new data result in slight changes in previous estimates, and that the lower overall Chinook salmon bycatch since 2008 has resulted in lower impacts to the main western Alaskan RSGs.

Description: Change is an important feature of commercial fisheries; yet the fishing industry, including fishers, fishery management authorities, and other stakeholders, is, in many respects, highly resistant to change. Examples of this include the application of conservation engineering solutions to bycatch problems and transitions towards ecosystem-based fishery management. A key reason for this resistance may be conditioning, cultural conservatism, and uncertainty. Change is often considered uncontrollable and unpredictable and a threat to established processes and systems that forces individuals to face an unknown future. In the business world, many models of change management have been applied to assist individuals and corporations in responding to an ever-changing environment. While fragments of these models have been applied in a fisheries context, the deliberate application of entire models has not. The application of these models could help to improve many aspects of fishery-dependent data collection such as using fishery-dependent information in stock assessment, implementing technologies such as vessel monitoring systems and electronic logbooks, and sharing information that is traditionally not shared. We present a well-known model for change management and describe how its application in a fisheries context can guide change initiatives and produce enhanced outcomes. We also explore how competing commitments and big assumptions influence a fisher's resistance to change, including conservation engineering initiatives, and posit how this can influence their involvement in the collection of fishery-dependent data.

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: During the last centuries, populations of marine megafauna—such as seabirds, turtles, and mammals—were intensively exploited. At present, other threats such as bycatch and pollution affect these species, which play key ecological roles in marine ecosystems as apex consumers and/or nutrient transporters. This study analyses the distribution of six megafaunal species ( Chelonia mydas , Caretta caretta , Dermochelys coriacea , Thalassarche melanophris , Otaria flavescens , and Arctocephalus australis ) coexisting in the Southwestern Atlantic to discuss their protection in terms of current management strategies in the region. Through the prediction of the species potential distributions and their relation to bathymetry, sea temperature and oceanographic fronts, key ecological areas are defined from a multi-taxa perspective. Information on the distribution of 70 individuals (18 sea turtles, 19 albatrosses, and 33 otariids) was obtained through satellite tracking conducted during 2007–2013 and analysed using a Geographic Information System and maximum entropy models. During the autumn–winter period, megafaunal species were distributed over the continental shelves of Argentina, Uruguay, and Brazil, mainly over the Argentine Exclusive Economic Zone and the Argentina-Uruguay Common Fishing Zone. Despite some differences, all megafaunal species seems to have similar environmental requirements during the autumn–winter period. Mostly waters shallower than 50 m were identified as key ecological areas, with the Río de la Plata as the habitat with the highest suitability for all the species. This area is highly productive and sustains the main coastal fisheries of Uruguay and Argentina, yet its role as a key ecological area for megafaunal species has been underestimated until now. This approach provides a basis to analyse the effect of anthropic activities on megafaunal species through risk maps and, ultimately, to generate knowledge to improve national and bi-national management plans between Argentina and Uruguay.

Description: In the North Sea flatfish fishery, electric pulse trawls have been introduced to replace the conventional mechanical method. Pulse trawls reduce the fuel consumption, reduce adverse impact on the ecosystem but cause injuries in gadoids. We describe the design and electrical properties of pulse trawls currently in use and study the behavioural response and injuries in cod exposed to electrical pulses under controlled conditions. Pulse trawls operate at an average power of 0.7 kW m –1 beam length and a duty cycle of ~2%. The electric field is heterogeneous with highest field strength occurring close to the conductors. Cod were exposed to three different pulse types for a range of field strengths, frequencies, and duty cycles. Two size classes were tested representing cod that escape through the meshes (11–17 cm) and market-sized cod that are retained in the net (34–56 cm). Cod exposed to a field strength of ≥37 V m –1 responded by moderate-to-strong muscular contractions. Some of the large cod ( n = 260) developed haemorrhages and fractures in the spine, and haemal and neural arches in the tail part of the body. The probability of injuries increased with field strength and decreased when frequency was increased from 100 to 180 Hz. None of the small cod ( n = 132) were injured and all survived. The field strength at the lateral boundaries of the trawl was too low to inflict injuries in cod.

Description: A coupled biophysical model is used to explore the physical controls involved in the timing of the spring phytoplankton bloom in fjords. Observations from Rivers Inlet, British Columbia, are used to force and evaluate the model. It is found that the interannual variation in timing is due primarily to variations in retention, in particular, to variations in horizontal advection out of the fjord. The two dominant processes are (i) strong outflow winds rapidly advecting the surface layer and thus the phytoplankton population out of the fjord and (ii) losses due to high river flux increasing the estuarine circulation. Both processes delay the timing of spring bloom. Smaller effects on the interannual variation are due to increased wind mixing which deepens the mixing layer and reduces light to phytoplankton, and increased river flow which increases the stratification and decreases the mixing layer depth. Observed interannual variations in cloudiness were small. Strong outflow winds are common in winter along the British Columbia coast, but generally cease after the spring wind transition. Thus, observed interdecadal variations in the spring transition date probably imply strong variations in the timing of spring phytoplankton blooms in British Columbia fjords.

Description: Since "balanced harvest" was proposed in 2010 as a possible tool in the operationalization of the ecosystem approach to fisheries (EAF), the concept gained extensive international attention. Because maintaining ecosystem structure and achieving maximum sustainable yields have become two of the key international legal obligations in fisheries management, balanced harvest is as topical as ever. An international workshop on balanced harvest, organized by the IUCN Fisheries Expert Group at FAO headquarters in 2014, reviewed the progress in the field and discussed its prospects and challenges. Several articles in this theme set, mostly based on presentations from the workshop, discuss ecological, economical, legal, social, and operational issues surrounding the key management goals. Progress is being made on understanding of the theoretical underpinnings of balanced harvest and its practical feasibility. Yet, a basic debate on the concept of balanced harvest continues. To move the EAF forward, we anticipate and encourage further research and discussion on balanced harvest and similar ideas.

Description: Sampling of euphausiids is difficult because of their intermediate size between macrozooplankton and micronekton. The Barents Sea is one of the few marine areas where there have been long-term studies of euphausiids. We have examined three monitoring datasets on euphausiids and consider likely sources of errors associated with the sampling. Results indicated a high degree of patchiness in the distribution of euphausiids, even at the largest scale of sampling with a pelagic trawl. This indicates that euphausiids may occur in large, but infrequent, swarms that have a low probability of being sampled by small nets. The mean biomass of euphausiids sampled with MOCNESS was 2 g wet weight m –2 integrated over the water column, which is an underestimate due to avoidance of large individuals. The mean biomass obtained with pelagic trawl in the upper 60 m of water at night during an autumn survey was 10 g wet weight m –2 . The plankton net on bottom trawl collected mean and median density of euphausiids (0.1–0.2 g wet weight m –3 ) near bottom during a winter survey similar to the values found with pelagic trawl in the upper layer during autumn. The mean density for the autumn survey showed an increase from 2000 to 2011, while the winter survey showed generally a decrease from 2000–2007 to 2011. The increase in the autumn series coincided with a general warming trend presumably with a larger influx of euphausiids with Atlantic water, notably of Meganyctiphanes norvegica . In contrast, the decline during winter may reflect a decrease, particularly of Thysanoessa raschii in the southeastern Barents Sea in the most recent years. Improvements in sampling gears combined with more and better use of acoustical and optical technologies offer great promise for improved monitoring and quantification of the roles of euphausiids in the Barents Sea ecosystem.

Description: Balanced fishing proposes a considerable change to current fisheries management to increase overall biomass harvested while reducing the ecosystem impacts of large-scale fisheries. However, to date, the work to a large degree has focused on simplified models, which exclude much of the variability in real ecosystems, as well as basing harvesting rates on a perfect, but unrealistic, knowledge on stock productivity. Furthermore, the published studies have avoided examining the practicalities of implementing balanced fishing in a real world. This has resulted in a gap that remains to be overcome before balanced fishing can be considered a viable management strategy for large marine ecosystems. We discuss variability in recruitment, in biology and life history characteristics, in data quality, and in fishing practice and management, and their implications for implementation of balanced fishing, using examples from the Barents Sea. We try to outline the complexities that need to be investigated as a precursor to moving balanced fishing from an academic exercise to a practical management scheme. Given the difficulties in moving to "full" balanced fishing, we highlight the importance of investigating to what extent benefits can be gained by implementing only the most achievable parts of a balanced fishing regime.

Description: European eel ( Anguilla anguilla ) is considered as critical endangered and even under the best circumstances it may take decades before the stock recovers. Estimation of eel escapement biomass, B escapement , is of critical importance to evaluate management schemes and to predict the recovery potential for the eel stock. Westerberg and Wickström (2015. Stock assessment of eels in the Baltic: reconciling survey estimates to achieve quantitative analysis. ICES Journal of Marine Science, 73: 75–83) attempt to estimate potential B escapement based on the assumptions that all elvers at the entrance of the Baltic also migrate into the Baltic Sea and that natural mortality is low under the whole growth stage (close to 0.02 at the age of 10 years and older). As a consequence, Westerberg and Wickström estimated the present potential B escapement at ~10–20 000 tonnes and fishing mortality close to 0.05–0.10, while it was also suggested that other sources of anthropogenic mortality may reduce the actual escapement to unknown levels. Here we argue that these conclusions are entirely speculative and contradicted by tagging experiment and fishery data, which instead indicate a much higher fishing mortality (mortality induced by legal professional fishery) rates and a considerably smaller eel biomass.

Description: Discard bans have been proposed as part of management policies aimed at balanced harvest (BH). Nationwide discard bans exist in several countries, including Chile, the European Union, Norway, and New Zealand. We analysed experiences from these countries to determine whether or not discard bans are in contradiction with BH, based on six aspects: policy objectives, species/sizes applicability, accompanying technical measures, at-sea monitoring and control, and possible impacts. When discard bans are fully implemented, fishing operations change to more selective fishing, typically targeting bigger individuals of main commercial species. This is consistent with the primary objective of many discard policies, i.e. to reduce unwanted catch. In contrast, proponents of BH argue that broader catch diversity, a product of a widespread harvest strategy, should be sought to avoid major impacts on the ecosystem. Our analysis demonstrates that the scope of discard bans is often limited to main commercial species, although usually they can be extended to include more ecosystem components. Some of the policies examined also prohibit the use of unwanted catches for human consumption, thus limiting their effective use. However, the implementation of discard bans requires high levels of at-sea monitoring and effective control, and/or strong incentives to fish more selectively, neither of which applied in most cases examined. We conclude that if discard bans were set differently, they could contribute to fishery management policies aiming at BH. Their goals should be in line with BH, i.e. to reach a wider global harvest pattern, or at least be established within management regimes that promote high compliance. Finally, the extent to which a discard ban contributes to achieve BH depends also on the relative importance of the ecosystem benthic and megafauna components.

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: Energy allocation models have proved useful for clarifying the ecological mechanisms which influence growth and reproduction schemes in species with indeterminate growth and for understanding how traits correlate with generate the life history of specific species. In view of the need to understand how exploitation affects species for which few data on key population parameters such as reproductive potential and population growth rate are available, it would be helpful if simple energy allocation schemes parametrized by easily obtainable data could be used to estimate parameters such as reproductive effort and output. Testing the predictions of three such models on fecundity data from a range of species, we show how the simplifications required in a generalized energy allocation scheme are reflected in the deviations between model predictions and empirical data, and discuss the validity of the assumptions underlying these models. We caution against over-reliance on generalized and simplified models to predict reproductive effort.

Description: Since 2007, the biomass of sardine and anchovy in the NW Mediterranean has remained persistently low, whereas the biomass of the commercially low-valued sprat has exploded. Also, simultaneous decreases in condition, size, and/or age of these populations were observed. Altogether, this resulted in a drop in landings of small pelagics. To understand the amplitude of these events and to provide a baseline scenario against which current changes can be compared, we compiled exceptionally long landing series (1865–2013) of sardine, anchovy, and mackerel for different subregions of the southern French coast. We characterized the fluctuations of these landings and compared these with environmental drivers (sea surface temperature, Rhône river discharge, North Atlantic Oscillation, Western Mediterranean Oscillation—WeMO, and Atlantic Multidecadal Oscillation—AMO), using different time-series analyses. We also collated historical data to infer qualitative changes in fishing effort over time. A fishing effort related increase in landings was observed around 1962 for all three species, although current sardine landings have dropped below levels observed before this period. Sardine and anchovy landings were, respectively, positively and negatively related to the AMO index and anchovy landings were also positively related to the WeMO. We finished by discussing the potential role of the environmental variables and fishing on long-term fishery landings trends.

Description: We examine whether the landing rates of Belgian beam trawlers in the Southern Bight of the North Sea were affected through competitive interactions with the Dutch beam trawler fleet and whether the development of a pulse trawler fleet has altered competitive interactions between both fleets. Effects of competition were investigated through a natural experiment based on the different weekly exploitation patterns of both fleets. Logbook data were used to fit a generalized additive mixed model for the daily landing rates of the target species sole ( Solea solea ) and plaice ( Pleuronectes platessa ). Results showed that landing rates of sole by the Belgian beam trawlers (〉221 kW) from 2006 to 2013 were lower during weekdays than during weekends when the Dutch trawler fleet is in harbour, while no such an effect was found for plaice. After the development of a pulse trawler fleet in 2011, the negative weekday effect in the sole landing rates was much more pronounced in 2012 and 2013. This increased loss of efficiency during weekdays, as a result of increased competition with the Dutch trawler fleet, coincided with a reallocation of fishing effort by the Belgian beam trawler fleet.

Description: Fishers' knowledge research (FKR) aims to enhance the use of experiential knowledge of fish harvesters in fisheries research, assessment, and management. Fishery participants are able to provide unique knowledge, and that knowledge forms an important part of "best available information" for fisheries science and management. Fishers' knowledge includes, but is much greater than, basic biological fishery information. It includes ecological, economic, social, and institutional knowledge, as well as experience and critical analysis of experiential knowledge. We suggest that FKR, which may in the past have been defined quite narrowly, be defined more broadly to include both fishery observations and fishers "experiential knowledge" provided across a spectrum of arrangements of fisher participation. FKR is part of the new and different information required in evolving "ecosystem-based" and "integrated" management approaches. FKR is a necessary element in the integration of ecological, economic, social, and institutional considerations of future management. Fishers' knowledge may be added to traditional assessment with appropriate analysis and explicit recognition of the intended use of the information, but fishers' knowledge is best implemented in a participatory process designed to receive and use it. Co-generation of knowledge in appropriately designed processes facilitates development and use of fishers' knowledge and facilitates the participation of fishers in assessment and management, and is suggested as best practice in improved fisheries governance.

Description: The origin and life history of 186 Atlantic salmon caught at sea within Icelandic waters were investigated using microsatellites to assess the origin and scales and otoliths to assess freshwater and sea age. A total of 184 samples were aged using scales or otolithes or both. Most of the samples were from individuals in their first year at sea (72.8%). The freshwater age varied from 1 to 5 years with an average of 2.6 years. The most common freshwater age was 2 years (42%), with a further substantial proportion of 3-year-old fish (28%). Genetic assignment of individual fish to their most likely population of origin was performed using Bayesian genetic individual assignments with a baseline consisting of 284 Eastern Atlantic rivers and 466 sample sites genotyped at the 14 microsatellite. A total of 186 samples of salmon caught at sea were assigned to their origin. Eight samples, from post-smolts and caught close to land, were assigned as having come from Iceland. Of the remaining 178 samples, 121 individuals (68%) were from the Southern Group, i.e. from mainland Europe, the UK, and Ireland, 53 individuals (30%) were from the Northern Group, i.e. Scandinavia and Northern Russia, and 4 individuals were from Iceland (2%). Stock mixture proportions were estimated for four periods using ONCOR and cBAYES. Stock mixture analysis generally supported the individual assignments, but did not suggest a seasonal component to the distribution of salmon stocks. These results indicate that the sea south and east of Iceland are important as feeding areas for migrating Atlantic salmon, particularly for salmon originating in the UK, Ireland, and southern Europe. Furthermore, the lack of adult Icelandic fish so close to Iceland is remarkable and suggests that Atlantic salmon from Icelandic stocks are using different feeding grounds.

Description: Demands for management advice on mixed and multispecies fisheries pose many challenges, further complicated by corresponding requests for advice on the environmental impacts of alternate management options. Here, we develop, and apply to North Sea fisheries, a method for collectively assessing the effects of, and interplay between, technical interactions, multispecies interactions, and the environmental effects of fishing. Ecological interactions involving 21 species are characterized with an ensemble of 188 plausible parameterizations of size-based multispecies models, and four fleets (beam trawl, otter trawl, industrial, and pelagic) characterized with catch composition data. We use the method to evaluate biomass and economic yields, alongside the risk of stock depletion and changes in the value of community indicators, for 10 000 alternate fishing scenarios (combinations of rates of fishing mortality F and fleet configuration) and present the risk vs. reward trade-offs. Technical and multispecies interactions linked to the beam and otter trawl fleets were predicted to have the strongest effects on fisheries yield and value, risk of stock collapse and fish community indicators. Increasing beam trawl effort led to greater increases in beam trawl yield when otter trawl effort was low. If otter trawl effort was high, increases in beam trawl effort led to reduced overall yield. Given the high value of demersal species, permutations of fleet effort leading to high total yield (generated primarily by pelagic species) were not the same as permutations leading to high catch values. A transition from F for 1990 to 2010 to F MSY , but without changes in fleet configuration, reduced risk of stock collapse without affecting long-term weight or value of yield. Our approach directly addresses the need for assessment methods that treat mixed and multispecies issues collectively, address uncertainty, and take account of trade-offs between weight and value of yield, state of stocks and state of the environment.

Description: Underwater video recordings in the mouth of a squid trawl were used to evaluate the effectiveness of a trawl configured with drop-chain groundgear to catch longfin inshore squid ( Doryteuthis pealeii ) and reduce bycatch of finfish in the Nantucket Sound squid fishery off Cape Cod, Massachusetts, USA. Entrance through the trawl mouth or escape underneath the fishing line and between drop chains was quantified for targeted squid, and two major bycatch species, summer flounder ( Paralichthys dentatus ) and skates (family Rajidae). Additionally, contact and impingement between animals and groundgear were also quantified. Fish and squid swimming behaviours, positions, orientations, and time in the trawl mouth were quantified and related to capture or escape at the trawl mouth. Squid entered the trawl singly and in schools, and no squid were observed escaping under the fishing line. Most squid entered the trawl in the upper portion of the trawl mouth; mantle orientated away from the trawl and swimming in the same direction, and were gradually overtaken, not actively attempting to escape. Summer flounder and skates were observed to remain on or near the seabed, orientated, and swimming in the same direction as the approaching trawl. The majority (60.5%) of summer flounder entered the trawl above the fishing line. Summer flounder that changed their orientation and turned 180° were significantly more likely to enter the trawl ( p 〈 0.05). Most skates (89.7%) avoided trawl entrance and escaped under the fishing line. Neither squid nor summer flounder were observed to make contact or become impinged to the groundgear; however, 35.4% of skates had substantial contact with groundgear, with 12.3% becoming impinged. Video analysis results showed that the drop-chain trawl is effective at retaining targeted squid while allowing skates to escape. However, it is ineffective at avoiding the capture of summer flounder.

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: Species-transformation provisions allow fishers to convert quota of one species to that of another species at prescribed conversion rates. These provisions, along with other catch-quota balancing mechanisms, are meant to aid fishers in matching available quota to actual catch so that incentives to discard are reduced. In this paper, we use a bioeconomic model to examine how species-transformation provisions affect sustainability and profitability of a multispecies fishery. We base parameterization of the model loosely on management of the Icelandic demersal fishery, which currently employs one of the broadest implementations of species transformations. To represent fisher behaviour in each year, effort is allocated among two or three métiers, such that total profit for that year is maximized. Each métier represents a combination of three species’ catchability rates that define which species are targeted by each métier and how independent a species’ catch rate is from that of other species. Assumptions regarding the degree to which fishers can target specific species by shifting effort between métiers, as well as how relative profitability among métiers varies, are paramount to understanding more generally how fishing regulations such as species transformations can be expected to change fishing patterns. This constraint depends not only on how strongly associated species catches are within a métier but also on relative species abundance and what alternate métiers are available.

Description: Based on previous work, dome-shaped fishery selectivity patterns are expected in place of asymptotic patterns when one-way fish movements among areas are considered. It is less clear if this occurs when the "round-trip" seasonal movements are considered. A simulation of a long-distance migrating fish stock (Atlantic menhaden) was used to study the influence of life history and fishery processes on selectivity, under an "areas as fleet" stock assessment context. When age-constant two-way migration was assumed to occur at a low rate, a domed selectivity pattern in the area experiencing the highest fishing mortality was produced, consistent with previous work. However, as the two-way migration rate increased, the domed selectivity pattern diminished and eventually disappeared. When age-varying migration was introduced, with a higher movement probability for older fish, domed selectivity prevailed in the source (i.e. spawning) area. If movement away from the spawning area occurs at younger ages than are selected by the fishing gear, the extent of the dome in this area is reduced. When movement away from the spawning area occurs at ages that are already available to the fishing gear, the dome in the spawning area is exaggerated. The area in which domed selectivity occurred was primarily determined by whether the probability of movement increased or decreased with age. In contrast to previous work that considered one-way or diffusive movement, the temporal or spatial distribution of recruitment and overall fishing mortality did not have a significant influence on selectivity. Building simulations that reflect the life history of the stock can guide assessment efforts by placing priors and constraints on model fits to selectivity patterns and be used to explore trade-offs between model complexity and the ability to produce reasonable management advice. Their development is encouraged as a standard feature in the assessment of migratory fish stocks.

Description: Fish stock assessment models often rely on size- or age-specific observations that are assumed to be statistically independent of each other. In reality, these observations are not raw observations, but rather they are estimates from a catch-standardization model or similar summary statistics based on observations from many fishing hauls and subsamples of the size and age composition of the data. Although aggregation mitigates the strong intra-haul correlation between sizes/ages that is usually found in haul-by-haul data, violations of the independence assumption can have a large impact on the results and specifically on reported confidence bounds. A state-space assessment model that allows for correlations between age groups within years in the observation model for catches and surveys is presented and applied to data on several North Sea fish stocks using various correlation structures. In all cases the independence assumption is rejected. Less fluctuating estimates of the fishing mortality is obtained due to a reduced process error. The improved model does not suffer from correlated residuals unlike the independent model, and the variance of forecasts is decreased.

Description: The northern shrimp ( Pandalus borealis L.) stock in the Skagerrak is shared by Sweden, Norway, and Denmark. Although the fishery is regulated by an annual agreement between the EU and Norway, there are also national regulations as well as differences in fleet composition and shrimp markets. In early 2014, the World Wildlife Fund gave all Skagerrak shrimp a red light in their seafood consumer guide, which led to an extensive debate, especially in Sweden, about the sustainability of this fishery. The aim of this study was to quantify a set of indicators that together give a broad picture of the sustainability of the three fisheries to provide an objective basis for a discussion on needed measures. The different indicators concerned environmental, economic or social aspects of sustainability and were quantified per tonne of shrimp landed by each country in 2012. The Danish fishery was most efficient in terms of environmental and economic indicators, while the Swedish fishery provided most employment per tonne of shrimp landed. Fuel use in all fisheries was high, also when compared with other shrimp fisheries. Interesting patterns emerged, with smaller vessels being more fuel efficient than larger ones in Sweden and Norway, with the opposite trend in Denmark. The study also demonstrated major data gaps and differences between the countries in how data are collected and made available. Various improvement options in the areas data collection and publication, allocation of quotas and enforcement of regulations resulted. Product-oriented studies could be useful to follow-up performance of fisheries over time and to identify how to best utilize the Skagerrak shrimp stock. This could involve evaluating novel solutions in terms of technology and management, based on current and future scenarios aiming to maximize societal benefits generated from this limited resource, at minimized environmental impacts.

Description: The capacity to observe, retrieve, and model the physiographical and hydrographical features of the sea (i.e. seascapes) has surpassed our ability to integrate this information into the assessment and stewardship of marine ecosystems. However, current marine policy that mandates integrated ecosystem assessments demands temporally intensive and spatially extensive predictions of key populations and ecosystem processes and services, particularly those related to habitat use and distribution. In this sense, seascape ecology represents an operational linkage between basic oceanography and applied ecology and management that embraces spatially explicit models of the dynamic distributions of populations, communities and foodwebs through a joint consideration of observational data and ecological processes. For these reasons, the ICES Journal of Marine Science solicited contributions to the article theme set, " Frontiers in seascape ecology ". In this introduction, we present current concepts and developments in seascape ecology, briefly summarize the 10 articles that appear herein, and discuss the most relevant challenges to this nascent discipline. The contributions included in this theme set illustrate the growing relevance of seascape ecology in the multidisciplinary management of marine ecosystems.

Description: A shift towards ecosystem-based management in recent decades has led to new analytical tools such as end-to-end marine ecosystem models. End-to-end models are complex and typically simulate full ecosystems from oceanography to foodwebs and fisheries, operate on a spatial framework, and link to physical oceanographic models. Most end-to-end approaches allow multiple ways to implement human behaviours involving fishery catch, fleet movement, or other impacts such as nutrient loading or climate change effects. Though end-to-end ecosystem models were designed specifically for marine management, their novelty makes them unfamiliar to most decision makers. Before such models can be applied within the context of marine management decisions, additional levels of vetting will be required, and a dialogue with decision makers must be initiated. Here we summarize a review of an Atlantis end-to-end model, which involved a multi-day, expert review panel with local and international experts, convened to challenge models and data used in the management context. We propose nine credibility and quality control standards for end-to-end models intended to inform management, and suggest two best practice guidelines for any end-to-end modelling application. We offer our perspectives (as recent test subjects or "guinea pigs") on how a review could be motivated and structured and on the evaluation criteria that should be used, in the most specific terms possible.

Description: Accounting for connectivity is essential in marine spatial planning and the proper design and management of marine protected areas, given that their effectiveness depends on the patterns of dispersal and colonization between protected and non-protected areas. The genetic structure of populations is commonly used to infer connectivity among distant populations. Here, we explore how population genetic structure is affected by pre- and settlement limitations with a spatially explicit coupled metapopulation-gene flow model that simulates the effect of demographic fluctuations on the allele frequencies of a set of populations. We show that in closed populations, regardless of population growth rate, the maintenance of genetic diversity at saturating initial population density increases with species life expectancy as a result of density-dependent recruitment control. Correlatively, at low initial population density, the time at which a population begins to lose its genetic diversity is driven larval and post-settlement mortality (comprised in the recruitment success parameter)—the larger the recruitment success, the stronger the genetic drift. Different spatial structures of connectivity established for soft bottom benthic invertebrates in the Gulf of Lions (NW Mediterranean, France) lead to very different results in the spatial patterns of genetic structuration of the metapopulation, with high genetic drift in sites where the local retention rate was larger than 2%. The effect of recruitment failure and the loss of key source populations on heterozygosity confirm that transient demographic fluctuations help maintain genetic diversity in a metapopulation. This study highlights the role of intraspecific settlement limitations due to lack of space when the effective number of breeders approaches saturating capacity, causing a strong reduction in effective reproduction. The present model allows to: (i) disentangle the relative contribution of local demography and environmental connectivity in shaping seascape genetics, and (ii) perform in silico evaluations of different scenarios for marine spatial planning.

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: The potential influence of climate change on the future distribution and abundance of fish (and therefore commercial fisheries and food security) is increasingly recognized in the fishery management community. A changing climate will likely have differing effects on different species; some will flourish, some will flounder. Management targets for fishing mortality and spawning biomass are often calculated by assuming stationary population processes, but under climate change, this assumption may be violated. Non-stationary population processes can introduce bias into estimates of biomass from stock assessments and calculations of target fishing mortalities and biomasses. However, few accepted frameworks exist for incorporating the changing influence of the environment on exploited populations into management strategies. Identifying changes in population processes due to environmental influences is important in order to enable climate-enhanced management strategy evaluations to elucidate the potential benefits and costs of changing management targets. Cost/benefit analyses will also be useful when coincidentally caught species respond differently to environmental change.

Description: For decades, many Australian coastal communities have been changing, in varying degrees, from traditional "fishing towns" to "mining", "tourism", or "retirement" towns. However, environmental changes, such as climate change, have increased the vulnerability of these communities and their capacity to continue to successfully adapt is unknown. A framework for the assessment of socio-ecological vulnerability is used to provide information on the response to change in Geraldton, Western Australia. Geraldton has traditionally been a port and fishing town and has recently become a hub for the expanding mining industry. An innovative historical assessment of adaptive capacity using sustainable livelihoods analysis with indicators of social, economic, human, financial, physical, and natural capital is used to calculate socio-ecological vulnerability over time. The framework integrates adaptive capacity with environmental change, resource dependence, and the socio-economic importance of the fished species during four census years: 1921, 1954, 1981, and 2011. The earlier years are characterized by high adaptive capacity and low socio-ecological vulnerability in keeping with strong economic growth and low unemployment rates following the First and Second World Wars. The years 1981 and 2011 showed markedly higher socio-ecological vulnerability and lower adaptive capacities. This result was due to progressively greater exposure to climate change and the high socio-economic importance of fished species, as well as relatively poor physical, social, and natural capital. With continuing environmental and economic change, the fishing industry and the broader Geraldton population is likely to become increasingly vulnerable. Proactive rather than passive adaptation may speed the recovery and reduce a decline in the fishing industry and local economies. The paper briefly discusses potential adaptation in Geraldton which may be useful as a guideline for other coastal communities.