ALBERT

Beschreibung: In this study, we extended the original work of Kotwicki et al. (2013. Combining bottom trawl and acoustic data to model acoustic dead zone correction and bottom trawl efficiency parameters for semipelagic species. Canadian Journal of Fisheries and Aquatic Sciences 70: 208–219) to jointly estimate the acoustic dead-zone correction, the bias ratio, and the gear efficiency for multiple species by using simultaneously collected acoustic and bottom-trawl data. The model was applied to cod ( Gadus morhua ) and haddock ( Melanogrammus aeglefinus ) in the Barents Sea and demonstrated a better or similar performance compared with a single species approach. The vertical distribution of cod and haddock was highly variable and was influenced by light level, water temperature, salinity, and depth. Temperature and sunlight were the most influential factors in this study. Increase in temperature resulted in decreasing catch and fish density in the acoustic dead zone (ADZ), while increasing sun altitude (surrogate for light level) increased the catch and fish density in the ADZ. The catch and density of haddock in the ADZ also increased at the lowest sun altitude level (shortly after midnight). Generally, the density of cod and haddock changed more rapidly in the ADZ than in the catch (from bottom to the effective fishing height) indicating the importance of modelling fish density in the ADZ. Finally, the uncorrelated variability in the annual residual variance of cod and haddock further strengthen the conclusion that species vertical distribution changes frequently and that there are probably many other unobserved environmental variables that affect them independently.

Beschreibung: Coastal commercial fisheries targeting Pacific salmon inevitably capture a mix of co-migrating species and genetically distinct populations within each species, only some of which are sufficiently abundant to sustain exploitation. Species-specific release measures are implemented as a conservation measure, but there remains little understanding of the resulting mortality. A purse seine fishery for Pacific salmon in British Columbia, Canada, was simulated with the goal of estimating post-release mortality for coho salmon, a species commonly released from commercial fisheries. Landed coho salmon ( n = 220) were tagged with acoustic transmitters and tracked along their coastal approach and into freshwater. Survival analyses accounting for variable migration pathways among populations revealed population-specific survival, with the population of greatest conservation concern having the best survival. Condition assessments revealed scale loss to be the strongest predictor of success. Physically exhausted fish, identified via reflex impairment tests, also experienced higher mortality. Results highlight the complexity of estimating release mortality in mixed-population commercial fisheries and are discussed in the context of management implications.

Beschreibung: As the summer minimum in Arctic sea ice cover reduces in area year by year due to anthropogenic global climate change, so interest grows in the un-tapped oil, gas and fisheries resources that were previously concealed beneath. We show that existing marine protected areas in the Arctic Ocean offer little or no protection to many habitats and deep seafloor features that coincide spatially with areas likely to be of interest to industry. These habitats are globally unique, hosting Arctic species within pristine environments that are currently undergoing rapid adjustment to climate-induced changes in ocean dynamics, species migration and primary production. They are invaluable as reference points for conservation monitoring and assessment. The existing Arctic marine protected area network needs to be expanded in order to protect these habitats and be fully coordinated with other spatial and non-spatial measures intended to protect Arctic habitats and ensure any uses of Arctic marine or subsea resources are sustainable.

Beschreibung: The Natura 2000 network forms the cornerstone of the biodiversity conservation strategy of the European Union and is the largest coordinated network of protected areas (PAs) in the world. Here, we demonstrated that the network fails to adequately cover the marine environment and meet the conservation target of 10% set by the Convention on Biological Diversity. The relative percentage of marine surface cover varies significantly among member states. Interestingly, the relative cover of protected seascape was significantly lower for member states with larger exclusive economic zones. Our analyses demonstrated that the vast majority (93%) of the Natura 2000 sites that cover marine waters include both a terrestrial and a marine component. As a result, the majority of the protected surfaces is adjacent to the coastline, and decreases offshore; only 20% of Natura marine PAs is at depths 〉200 m. The lack of systematic planning processes is further reflected by the great variability in the distances among protected sites and the limited number of shared Natura sites among member states. Moreover, 〈40% of the marine sites have management plans, indicating the absence of active, or limited management in most sites. This work highlights the gaps in coverage and spatial design of the European conservation network in the marine environment, and raises questions on the unevenly treatment of marine vs. terrestrial areas.

Beschreibung: Knowing movement and structure of fish populations is a prerequisite for effective spatial fisheries management. The study evaluates migration patterns and connectivity of two groups of cod ( Gadus morhua ) associated with offshore feeding and nursery grounds. This was achieved by investigating (i) migration pathways of cod tagged at the feeding areas, (ii) immigration of cod to the areas based on mark-recapture data covering a period of two decades, and (iii) depth and temperature data from data storage tags (DSTs). Despite undertaking long-distance migrations after attaining sexual maturity, the cod aggregations in the two study areas appear to be largely separated from each other. This conclusion is supported by DSTs, indicating that mature fish associated with the two areas occupy different thermal-bathymetric niches. Low levels of connectivity suggest that effective spatial management in the two study areas would preserve fish of different origin. For the highly migratory adults, however, spatial management would need to focus on migration pathways and the areas where the fish are particularly vulnerable to fishing.

Beschreibung: Size-based indicators are well established as a management tool in shelf seas as they respond to changes in fishing pressure and describe important aspects of community function. In the deep sea, however, vital rates are much slower and body size relationships vary with depth, making it less clear how size-based indicators can be applied and whether they are appropriate for detecting changes through time. The deep-sea fish stocks of the North Atlantic underwent a period of exploitation followed by management and conservation action that relieved this pressure. We used data from a deep-water bottom trawl survey in the Rockall Trough, at depths of 300–2000 m, to test whether size-based indicators changed over a 16-year period, during which fishing pressure decreased. We applied four indicators to these data: mean body length, mean maximum length, large fish indicator (LFI), and the slope of the biomass spectrum. Patterns were analysed within four different depth bands. The LFI and slope of the biomass spectrum showed positive change over time, suggesting recovery from fishing pressure. This response was generally most apparent in the shallowest depth band, where most fishing activity has been distributed. Values of the LFI were much higher overall than in shelf seas, so the same reference points cannot be applied to all marine ecosystems. These findings imply that size-based indicators can be usefully applied to the deep sea and that they potentially track changes in fishing pressure in the medium term.

Beschreibung: Forage fish undergo dramatic changes in abundance through time. Long-term fluctuations, which have historically been attributed to changes in recruitment, may also be due to changes in adult mortality. Pacific herring, a lightly exploited forage fish in Puget Sound, WA, have exhibited shifts in age structure and decreases in spawning biomass during the past 30 years. Here, we investigate changes in adult mortality as a potential explanation for these shifts. Using a hierarchical, age-structured population model, we indicate that adult natural mortality for Puget Sound Pacific herring has increased since 1973. We find that natural mortality has increased for every age class of adult (age 3+), especially age 4 fish, whose estimated mortality has doubled over the survey time period (from M = 0.84–1.76). We demonstrate that long-term shifts in mortality explain changes in age structure, and may explain biomass declines and failure to reach management thresholds for two spawning sites in Puget Sound (Cherry Point and Squaxin Pass). Temporal shifts in natural adult mortality could have negative implications for herring and herring predators. We demonstrate that adult mortality, in addition to recruitment variation, is an important driver for forage fish, which face exceptionally high natural mortality compared with other fishes.

Beschreibung: Commercial fisheries and oil and gas extraction are both spatially extensive industries in the North Sea (NS), and inevitably there is physical interaction where the two activities coincide. Regular contact between fishing gear and pipelines may risk pipeline integrity and could lead to gear snagging. It is also known, anecdotally, that some vessels target pipelines, potentially benefiting from local artificial reef effects. The impacts of pipeline decommissioning options (removal vs. in situ ) on commercial fisheries must be evaluated as part of the consenting process, but the degree of interaction between the two is presently unknown in the NS. Vessel Monitoring System (VMS) data for the Scottish demersal fleet were analysed with spatial data on pipelines. Approximately one-third (36.1%) of trips fished within 200 m of a pipeline over a 5-year period, suggesting that pipelines are subjected to regular interaction with fishing gear. The fishing effort (in hours) associated with pipelines was 2.52% of the total effort, compared to 1.33% in an equivalent area of seabed 1 km away, implying modest aggregation of fishing around pipelines. Only a small percentage (0.93%) of fishing trips actively targeted pipelines as fishing grounds. The highest level of fishing around pipelines occurred in the northeast NS. Pipeline sections with 〉100 h of fishing were typically larger diameter pipelines. The results suggest that pipeline decommissioning may have both negative (displacement of aggregated effort) and positive (reduced snagging potential) outcomes for commercial fisheries. It is recommended that where there is little or no fishing activity associated with pipelines, receptors other than fishing should be prioritized when selecting decommissioning strategies. Additionally, the intensity of fishing around pipelines should be used to inform the frequency of post-decommissioning integrity monitoring for any pipelines left in situ.

Beschreibung: Successful management of small pelagic fisheries is critical in integrated ecosystem based approaches and requires understanding of how the ecological dynamics of pelagic stocks mesh with the economic and social dynamics of commercial fisheries and the larger systems within which they operate. Combining insights from stock assessments with those from local fishers, scientists, and managers, can help identify knowledge gaps that could jeopardize stock resilience. This article presents results from a social-ecological, mixed-methods study that combines insights from science and from interviews with fishermen, scientists, and managers of small pelagic fisheries in western Newfoundland, Canada (NAFO division 4R) and in NAFO division 4X. Different approaches to herring management are used in the two areas. In area 4R fishing for herring ( Clupea harengus ) is part of a complex multi-species, multi-gear fishery; most harvesters who target herring also target Atlantic mackerel ( Scomber scombrus ). Harvester interviews indicate herring in 4R, like herring in 4X and elsewhere, have substantial within-species stock structure, but that it is not well-documented in science and not well protected under the current management system. Further, fishing strategies in the competitive mackerel fishery in which the herring vessels are involved may contribute to the risk of over-fishing on some herring populations.

Beschreibung: Spatial management of vulnerable benthic ecosystem components such as deep-sea corals and sponges requires adequate maps of their distribution. These maps are often based on statistical models of survey data. The objective of this project was to validate the predictions of existing presence or absence and abundance models of deep-sea corals and sponges in the Aleutian Islands that were based on bottom trawl survey data. Model validation was conducted by comparing bottom trawl survey model predictions to the observations of an in situ camera survey conducted at randomly selected locations. The measures of goodness of fit (area-under-the-receiver-operator-curve, AUC) for the bottom trawl survey model predictions of camera survey observations ranged from 0.59 to 0.77 (for sponges and coral, respectively) and indicated that the bottom trawl survey models predicted the probability of presence for corals accurately across the Aleutian Islands. The bottom trawl survey models explained as little as 3% of the variability in Stylasteridae density and up to 17% of the variability in coral density. These results indicate that models of deep-sea coral distributions based on presence and absence data from bottom trawl surveys can be accurate and can provide useful information for spatial management of these vulnerable taxa. However, for some other taxa, such as sponges, care should be taken interpreting the results of bottom trawl survey models. An interesting finding of this study was that the residuals from the bottom trawl survey model-camera density relationships were negative in areas that remained open to fishing after 2005, possibly indicating an effect of continued bottom trawling on the abundance of corals in these areas. This study highlights the importance of validating models of species distribution using independent surveys, so that the results can be used with confidence to support decision-making processes.

Beschreibung: States have acknowledged that the new internationally legally binding instrument (ILBI) for the conservation and sustainable use of marine biodiversity beyond national jurisdiction must take account of the interests of coastal states with continental shelves that extend beyond 200 nautical miles. This article argues that the ILBI should go beyond repeating the existing legal position as set out in international treaties and customary international law. In particular, the concept of sedentary species is unhelpful in the context of a legal regime governing the use of marine genetic resources. The article makes a number of suggestions for possible inclusions in the ILBI to clarify the relationship between the continental shelf regime and the regime for biodiversity beyond national jurisdiction.

Beschreibung: The giant Australian cuttlefish, Sepia apama , forms a dense spawning aggregation at a single known location across its wide southern Australian distribution. After a rapid increase in fishing pressure on the aggregation in the late 1990s, a series of fishing closures were introduced before any biological information could be collected. We surveyed the habitats, timing, and spatial distribution of the spawning aggregation over 4 years, using underwater visual transects and passive tagging, to assess the suitability of the closures. We found that the annual aggregation was both temporally (April–August) and spatially (over 8   km of coastline) localized and predictable, with a consistent peak in abundances in late May–early June. Cuttlefish densities were generally highest over the shallow, broken bedrock habitat, which was more extensive in several sites left open to fishing. Although the original closure covered about 43% of the hard substrate, it accounted for only 23–37% of the total cuttlefish abundance. The extremely high densities recorded during this study verified that this is a massive spawning aggregation for cuttlefish species worldwide, and that it could be highly vulnerable to overexploitation in the absence of adequate protection, because it is so spatiotemporally predictable and localized.

Beschreibung: The effects of sea lice on the marine survival of wild salmonids are widely debated. In Norway this debate has reached a crescendo as the Norwegian government has recently ratified a management system where the growth in the salmonid aquaculture industry will be conditional on regional estimated impact of salmon lice on wild fish. Sea lice have thus become the most prominent obstacle to the stated political aim of quintupling aquaculture production in Norway by 2050. Scientific documentation that salmon lice impact the marine survival of salmon is robust. However, it is also evident that marine survival of salmon is strongly impacted by other factors, and that the effect of salmon lice is most likely an integral part of these other mortality factors. In this paper, our goal is to discuss and give advice on how managers and policy makers should handle this complexity, and to identify the greatest challenges in using scientific results to construct robust management rules. Inadequate extrapolation from the scale of known effects to the scale of management implementation may initially give a false impression of scientific certainty, but will eventually fuel upsetting disagreements among stakeholders as they gradually uncover the shaky foundation of the implemented policy. Thus, using a single model and parameter to determine management advice is not warranted, as no single data point reflects the natural complexity of nature. Furthermore, robust management rules should be based on unambiguous definitions of key concepts. Finally, despite the scientific consensus that salmon lice are a risk to salmon, studies on wild populations in situ that accurately quantify the impact of salmon lice are still urgently needed. We give advice on how this can be accomplished.

Beschreibung: A faster rate of adaptive evolution of X-linked genes compared with autosomal genes (the faster-X effect) can be caused by the fixation of recessive or partially recessive advantageous mutations. This effect should be largest for advantageous mutations that affect only male fitness, and least for mutations that affect only female fitness. We tested these predictions in Drosophila melanogaster by using coding and functionally significant noncoding sequences of genes with different levels of sex-biased expression. Consistent with theory, nonsynonymous substitutions in most male-biased and unbiased genes show faster adaptive evolution on the X. However, genes with very low recombination rates do not show such an effect, possibly as a consequence of Hill–Robertson interference. Contrary to expectation, there was a substantial faster-X effect for female-biased genes. After correcting for recombination rate differences, however, female-biased genes did not show a faster X-effect. Similar analyses of noncoding UTRs and long introns showed a faster-X effect for all groups of genes, other than introns of female-biased genes. Given the strong evidence that deleterious mutations are mostly recessive or partially recessive, we would expect a slower rate of evolution of X-linked genes for slightly deleterious mutations that become fixed by genetic drift. Surprisingly, we found little evidence for this after correcting for recombination rate, implying that weakly deleterious mutations are mostly close to being semidominant. This is consistent with evidence from polymorphism data, which we use to test how models of selection that assume semidominance with no sex-specific fitness effects may bias estimates of purifying selection.

Beschreibung: miRNAs play essential roles in the mechanics of gene regulation, however, on an organismal-scale, the processes in which they are deployed are not well understood. Here, we adopt an evolutionary developmental approach to study miRNA function by examining their expression throughout embryogenesis in both Caenorhabditis elegans and Drosophila melanogaster . We find that, in both species, miRNA transcriptomic shifts in a punctuated fashion during the mid-developmental transition, specifying two dominant modes of early and late expression profiles. Strikingly, late-expressed miRNAs are enriched for phylogenetic conservation and function by fine-tuning the expression of their targets, implicating a role in the canalization of cell types during differentiation. In contrast, early expressed miRNAs are inversely expressed with their targets suggesting strong target-inhibition. Taken together, our work exposes a bimodal role for miRNA function during animal development, involving late-expressed physiological roles and early expressed repressive roles.

Beschreibung: Recent studies have reported evidence suggesting that portions of contemporary human genomes introgressed from archaic hominin populations went to high frequencies due to positive selection. However, no study to date has specifically addressed the postintrogression population dynamics of these putative cases of adaptive introgression. Here, for the first time, we specifically define cases of immediate adaptive introgression (iAI) in which archaic haplotypes rose to high frequencies in humans as a result of a selective sweep that occurred shortly after the introgression event. We define these cases as distinct from instances of selection on standing introgressed variation (SI), in which an introgressed haplotype initially segregated neutrally and subsequently underwent positive selection. Using a geographically diverse data set, we report novel cases of selection on introgressed variation in living humans and shortlist among these cases those whose selective sweeps are more consistent with having been the product of iAI rather than SI. Many of these novel inferred iAI haplotypes have potential biological relevance, including three that contain immune-related genes in West Siberians, South Asians, and West Eurasians. Overall, our results suggest that iAI may not represent the full picture of positive selection on archaically introgressed haplotypes in humans and that more work needs to be done to analyze the role of SI in the archaic introgression landscape of living humans.

Beschreibung: The measurement of synonymous and nonsynonymous substitution rates (d S and d N ) is useful for assessing selection operating on protein sequences or for investigating mutational processes affecting genomes. In particular, the ratio dNdS is expected to be a good proxy for ω , the ratio of fixation probabilities of nonsynonymous mutations relative to that of neutral mutations. Standard methods for estimating d N , d S , or ω rely on the assumption that the base composition of sequences is at the equilibrium of the evolutionary process. In many clades, this assumption of stationarity is in fact incorrect, and we show here through simulations and analyses of empirical data that nonstationarity biases the estimate of d N , d S , and ω . We show that the bias in the estimate of ω can be fixed by explicitly taking into consideration nonstationarity in the modeling of codon evolution, in a maximum likelihood framework. Moreover, we propose an exact method for estimating d N and d S on branches, based on stochastic mapping, that can take into account nonstationarity. This method can be directly applied to any kind of codon evolution model, as long as neutrality is clearly parameterized.

Beschreibung: Defense against infection incurs costs as well as benefits that are expected to shape the evolution of optimal defense strategies. In particular, many theoretical studies have investigated contexts favoring constitutive versus inducible defenses. However, even when one immune strategy is theoretically optimal, it may be evolutionarily unachievable. This is because evolution proceeds via mutational changes to the protein interaction networks underlying immune responses, not by changes to an immune strategy directly. Here, we use a theoretical simulation model to examine how underlying network architectures constrain the evolution of immune strategies, and how these network architectures account for desirable immune properties such as inducibility and robustness. We focus on immune signaling because signaling molecules are common targets of parasitic interference but are rarely studied in this context. We find that in the presence of a coevolving parasite that disrupts immune signaling, hosts evolve constitutive defenses even when inducible defenses are theoretically optimal. This occurs for two reasons. First, there are relatively few network architectures that produce immunity that is both inducible and also robust against targeted disruption. Second, evolution toward these few robust inducible network architectures often requires intermediate steps that are vulnerable to targeted disruption. The few networks that are both robust and inducible consist of many parallel pathways of immune signaling with few connections among them. In the context of relevant empirical literature, we discuss whether this is indeed the most evolutionarily accessible robust inducible network architecture in nature, and when it can evolve.

Beschreibung: The distribution of fitness effects of mutations is a factor of fundamental importance in evolutionary biology. We determined the distribution of fitness effects of 510 mutants that each carried between 1 and 10 mutations (synonymous and nonsynonymous) in the hisA gene, encoding an essential enzyme in the l -histidine biosynthesis pathway of Salmonella enterica . For the full set of mutants, the distribution was bimodal with many apparently neutral mutations and many lethal mutations. For a subset of 81 single, nonsynonymous mutants most mutations appeared neutral at high expression levels, whereas at low expression levels only a few mutations were neutral. Furthermore, we examined how the magnitude of the observed fitness effects was correlated to several measures of biophysical properties and phylogenetic conservation.We conclude that for HisA: (i) The effect of mutations can be masked by high expression levels, such that mutations that are deleterious to the function of the protein can still be neutral with regard to organism fitness if the protein is expressed at a sufficiently high level; (ii) the shape of the fitness distribution is dependent on the extent to which the protein is rate-limiting for growth; (iii) negative epistatic interactions, on an average, amplified the combined effect of nonsynonymous mutations; and (iv) no single sequence-based predictor could confidently predict the fitness effects of mutations in HisA, but a combination of multiple predictors could predict the effect with a SD of 0.04 resulting in 80% of the mutations predicted within 12% of their observed selection coefficients.

Beschreibung: A central feature of pathogen genomics is that different infectious particles (virions and bacterial cells) within an infected individual may be genetically distinct, with patterns of relatedness among infectious particles being the result of both within-host evolution and transmission from one host to the next. Here, we present a new software tool, phyloscanner, which analyses pathogen diversity from multiple infected hosts. phyloscanner provides unprecedented resolution into the transmission process, allowing inference of the direction of transmission from sequence data alone. Multiply infected individuals are also identified, as they harbor subpopulations of infectious particles that are not connected by within-host evolution, except where recombinant types emerge. Low-level contamination is flagged and removed. We illustrate phyloscanner on both viral and bacterial pathogens, namely HIV-1 sequenced on Illumina and Roche 454 platforms, HCV sequenced with the Oxford Nanopore MinION platform, and Streptococcus pneumoniae with sequences from multiple colonies per individual. phyloscanner is available from https://github.com/BDI-pathogens/phyloscanner .

Beschreibung: Bacterial transformation can insert or delete genomic islands (GIs), depending on the donor and recipient genotypes, if an homologous recombination spans the GI’s integration site and includes sufficiently long flanking homologous arms. Combining mathematical models of recombination with experiments using pneumococci found GI insertion rates declined geometrically with the GI’s size. The decrease in acquisition frequency with length (1.08×10 −3  bp −1 ) was higher than a previous estimate of the analogous rate at which core genome recombinations terminated. Although most efficient for shorter GIs, transformation-mediated deletion frequencies did not vary consistently with GI length, with removal of 10-kb GIs ∼50% as efficient as acquisition of base substitutions. Fragments of 2 kb, typical of transformation event sizes, could drive all these deletions independent of island length. The strong asymmetry of transformation, and its capacity to efficiently remove GIs, suggests nonmobile accessory loci will decline in frequency without preservation by selection.

Beschreibung: Inference of how evolutionary forces have shaped extant genetic diversity is a cornerstone of modern comparative sequence analysis. Advances in sequence generation and increased statistical sophistication of relevant methods now allow researchers to extract ever more evolutionary signal from the data, albeit at an increased computational cost. Here, we announce the release of Datamonkey 2.0, a completely re-engineered version of the Datamonkey web-server for analyzing evolutionary signatures in sequence data. For this endeavor, we leveraged recent developments in open-source libraries that facilitate interactive, robust, and scalable web application development. Datamonkey 2.0 provides a carefully curated collection of methods for interrogating coding-sequence alignments for imprints of natural selection, packaged as a responsive (i.e. can be viewed on tablet and mobile devices), fully interactive, and API-enabled web application. To complement Datamonkey 2.0, we additionally release HyPhy Vision, an accompanying JavaScript application for visualizing analysis results. HyPhy Vision can also be used separately from Datamonkey 2.0 to visualize locally executed HyPhy analyses. Together, Datamonkey 2.0 and HyPhy Vision showcase how scientific software development can benefit from general-purpose open-source frameworks. Datamonkey 2.0 is freely and publicly available at http://www.datamonkey.org , and the underlying codebase is available from https://github.com/veg/datamonkey-js .

Beschreibung: Pathogen traits, such as the virulence of an infection, can vary significantly between patients. A major challenge is to measure the extent to which genetic differences between infecting strains explain the observed variation of the trait. This is quantified by the trait’s broad-sense heritability, H 2 . A recent discrepancy between estimates of the heritability of HIV-virulence has opened a debate on the estimators’ accuracy. Here, we show that the discrepancy originates from model limitations and important lifecycle differences between sexually reproducing organisms and transmittable pathogens. In particular, current quantitative genetics methods, such as donor–recipient regression of surveyed serodiscordant couples and the phylogenetic mixed model (PMM), are prone to underestimate H 2 , because they neglect or do not fit to the loss of resemblance between transmission partners caused by within-host evolution. In a phylogenetic analysis of 8,483 HIV patients from the United Kingdom, we show that the phenotypic correlation between transmission partners decays with the amount of within-host evolution of the virus. We reproduce this pattern in toy-model simulations and show that a phylogenetic Ornstein–Uhlenbeck model (POUMM) outperforms the PMM in capturing this correlation pattern and in quantifying H 2 . In particular, we show that POUMM outperforms PMM even in simulations without selection—as it captures the mentioned correlation pattern—which has not been appreciated until now. By cross-validating the POUMM estimates with ANOVA on closest phylogenetic pairs, we obtain H 2  ≈ 0.2, meaning ∼20% of the variation in HIV-virulence is explained by the virus genome both for European and African data.

Beschreibung: S.G. Seabra, I. Fragata, M.A. Antunes, G.S. Faria, M.A. Santos, V.C. Sousa, and P. Simões, M. Matos

Beschreibung: Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic data sets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org ). The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments. The original six lineage assessment data sets have been updated with improved species sampling, 34 new subsets have been built for vertebrates, arthropods, fungi, and prokaryotes that greatly enhance resolution, and data sets are now also available for nematodes, protists, and plants. Here, we present BUSCO v3 with example analyses that highlight the wide-ranging utility of BUSCO assessments, which extend beyond quality control of genomics data sets to applications in comparative genomics analyses, gene predictor training, metagenomics, and phylogenomics.

Beschreibung: New genes, with novel protein functions, can evolve “from scratch” out of intergenic sequences. These de novo genes can integrate the cell's genetic network and drive important phenotypic innovations. Therefore, identifying de novo genes and understanding how the transition from noncoding to coding occurs are key problems in evolutionary biology. However, identifying de novo genes is a difficult task, hampered by the presence of remote homologs, fast evolving sequences and erroneously annotated protein coding genes. To overcome these limitations, we developed a procedure that handles the usual pitfalls in de novo gene identification and predicted the emergence of 703 de novo gene candidates in 15 yeast species from 2 genera whose phylogeny spans at least 100 million years of evolution. We validated 85 candidates by proteomic data, providing new translation evidence for 25 of them through mass spectrometry experiments. We also unambiguously identified the mutations that enabled the transition from noncoding to coding for 30 Saccharomyces de novo genes. We established that de novo gene origination is a widespread phenomenon in yeasts, only a few being ultimately maintained by selection. We also found that de novo genes preferentially emerge next to divergent promoters in GC-rich intergenic regions where the probability of finding a fortuitous and transcribed ORF is the highest. Finally, we found a more than 3-fold enrichment of de novo genes at recombination hot spots, which are GC-rich and nucleosome-free regions, suggesting that meiotic recombination contributes to de novo gene emergence in yeasts.

Beschreibung: Methylation of the adenosine base at the nitrogen-6 position (m 6 A) is the most prevalent internal posttranscriptional modification of mRNAs in many eukaryotes. Despite the rapid progress in the transcriptome-wide mapping of m 6 As, identification of proteins responsible for writing, reading, and erasing m 6 As, and elucidation of m 6 A functions in splicing, RNA stability, translation, and other processes, it is unknown whether most observed m 6 A modifications are functional. To address this question, we respectively analyze the evolutionary conservation of yeast and human m 6 As in protein-coding regions. Relative to comparable unmethylated As, m 6 As are overall no more conserved in yeasts and only slightly more conserved in mammals. Furthermore, yeast m 6 As and comparable unmethylated As have no significant difference in single nucleotide polymorphism (SNP) density or SNP site frequency spectrum. The same is true in human. The methylation status of a gene, not necessarily the specific sites methylated in the gene, is subject to purifying selection for no more than ∼20% of m 6 A-modified genes. These observations suggest that most m 6 A modifications in protein-coding regions are nonfunctional and nonadaptive, probably resulting from off-target activities of m 6 A methyltransferases. In addition, our reanalysis invalidates the recent claim of positive selection for newly acquired m 6 A modifications in human evolution. Regarding the small number of evolutionarily conserved m 6 As, evidence suggests that a large proportion of them are likely functional; they should be prioritized in future functional characterizations of m 6 As. Together, these findings have important implications for understanding the biological significance of m 6 A and other posttranscriptional modifications.

Beschreibung: The study of model organisms on islands may shed light on rare long-range dispersal events, uncover signatures of local evolutionary processes, and inform demographic inference on the mainland. Here, we sequenced the genomes of Arabidopsis thaliana samples from the oceanic island of Madeira. These samples include the most diverged worldwide, likely a result of long isolation on the island. We infer that colonization of Madeira happened between 70 and 85 ka, consistent with a propagule dispersal model (of size ≥10), or with an ecological window of opportunity. This represents a clear example of a natural long-range dispersal event in A. thaliana . Long-term effective population size on the island, rather than the founder effect, had the greatest impact on levels of diversity, and rates of coalescence. Our results uncover a selective sweep signature on the ancestral haplotype of a known translocation in Eurasia, as well as the possible importance of the low phosphorous availability in volcanic soils, and altitude, in shaping early adaptations to the island conditions. Madeiran genomes, sheltered from the complexities of continental demography, help illuminate ancient demographic events in Eurasia. Our data support a model in which two separate lineages of A. thaliana , one originating in Africa and the other from the Caucasus expanded and met in Iberia, resulting in a secondary contact zone there. Although previous studies inferred that the westward expansion of A. thaliana coincided with the spread of human agriculture, our results suggest that it happened much earlier (20–40 ka).

Beschreibung: The Shine–Dalgarno (SD) sequence motif is frequently found upstream of protein coding genes and is thought to be the dominant mechanism of translation initiation used by bacteria. Experimental studies have shown that the SD sequence facilitates start codon recognition and enhances translation initiation by directly interacting with the highly conserved anti-SD sequence on the 30S ribosomal subunit. However, the proportion of SD-led genes within a genome varies across species and the factors governing this variation in translation initiation mechanisms remain largely unknown. Here, we conduct a phylogenetically informed analysis and find that species capable of rapid growth contain a higher proportion of SD-led genes throughout their genomes. We show that SD sequence utilization covaries with a suite of genomic features that are important for efficient translation initiation and elongation. In addition to these endogenous genomic factors, we further show that exogenous environmental factors may influence the evolution of translation initiation mechanisms by finding that thermophilic species contain significantly more SD-led genes than mesophiles. Our results demonstrate that variation in translation initiation mechanisms across bacterial species is predictable and is a consequence of differential life-history strategies related to maximum growth rate and environmental-specific constraints.

Beschreibung: Although any genotype–phenotype relationships are a result of evolution, little is known about how natural selection and neutral drift, two distinct driving forces of evolution, operate to shape the relationships. By analyzing ∼500 yeast quantitative traits, we reveal a basic “supervisor–worker” gene architecture underlying a trait. Supervisors are often identified by “perturbational” approaches (such as gene deletion), whereas workers, which usually show small and statistically insignificant deletion effects, are tracked primarily by “observational” approaches that examine the correlation between gene activity and trait value across a number of conditions. Accordingly, supervisors provide most of the genetic understandings of the trait whereas workers provide rich mechanistic understandings. Further analyses suggest that most observed supervisor–worker interactions may evolve largely neutrally, resulting in pervasive between-worker epistasis that suppresses the tractability of workers. In contrast, a fraction of supervisors are recruited/maintained by natural selection to build worker co-expression, boosting the tractability of workers. Thus, by revealing a supervisor–worker gene architecture underlying complex traits, the opposite roles of natural selection versus neutral drift in shaping the gene architecture, and the complementary strengths of the perturbational and observational research strategies in characterizing the gene architecture, this study may lay a new conceptual foundation for understanding the molecular basis of complex traits.

Beschreibung: Insects are an important food resource for many primates, but the chitinous exoskeletons of arthropods have long been considered to be indigestible by the digestive enzymes of most mammals. However, recently mice and insectivorous bats were found to produce the enzyme acidic mammalian chitinase (AMCase) to digest insect exoskeletons. Here, we report on the gene CHIA and its paralogs, which encode AMCase, in a comparative sample of nonhuman primates. Our results show that early primates likely had three CHIA genes, suggesting that insects were an important component of the ancestral primate diet. With some exceptions, most extant primate species retain only one functional CHIA paralog. The exceptions include two colobine species, in which all CHIA genes have premature stop codons, and several New World monkey species that retain two functional genes. The most insectivorous species in our sample also have the largest number of functional CHIA genes. Tupaia chinensis and Otolemur garnettii retain three functional CHIA paralogs, whereas Tarsius syrichta has a total of five, two of which may be duplications specific to the tarsier lineage. Selection analyses indicate that CHIA genes are under more intense selection in species with higher insect consumption, as well as in smaller-bodied species (〈500 g), providing molecular support for Kay’s Threshold, a well-established component of primatological theory which proposes that only small primates can be primarily insectivorous. These findings suggest that primates, like mice and insectivorous bats, may use the enzyme AMCase to digest the chitin in insect exoskeletons, providing potentially significant nutritional benefits.

Beschreibung: New genes can arise through duplication of a pre-existing gene or de novo from non-coding DNA, providing raw material for evolution of new functions in response to a changing environment. A prime example is the independent evolution of antifreeze glycoprotein genes ( afgp s) in the Arctic codfishes and Antarctic notothenioids to prevent freezing. However, the highly repetitive nature of these genes complicates studies of their organization. In notothenioids, afgp s evolved from an extant gene, yet the evolutionary origin of afgp s in codfishes is unknown. Here, we demonstrate that afgp s in codfishes have evolved de novo from non-coding DNA 13–18 Ma, coinciding with the cooling of the Northern Hemisphere. Using whole-genome sequence data from several codfishes and notothenioids, we find higher copy number of afgp in species exposed to more severe freezing suggesting a gene dosage effect. Notably, antifreeze function is lost in one lineage of codfishes analogous to the afgp losses in non-Antarctic notothenioids. This indicates that selection can eliminate the antifreeze function when freezing is no longer imminent. In addition, we show that evolution of afgp -assisting antifreeze potentiating protein genes ( afpp s) in notothenioids coincides with origin and lineage-specific losses of afgp . The origin of afgp s in codfishes is one of the first examples of an essential gene born from non-coding DNA in a non-model species. Our study underlines the power of comparative genomics to uncover past molecular signatures of genome evolution, and further highlights the impact of de novo gene origin in response to a changing selection regime.

Beschreibung: Experimental evolution is a powerful tool to understand the adaptive potential of populations under environmental change. Here, we study the importance of the historical genetic background in the outcome of evolution at the genome-wide level. Using the natural clinal variation of Drosophila subobscura , we sampled populations from two contrasting latitudes (Adraga, Portugal and Groningen, Netherlands) and introduced them in a new common environment in the laboratory. We characterized the genome-wide temporal changes underlying the evolutionary dynamics of these populations, which had previously shown fast convergence at the phenotypic level, but not at chromosomal inversion frequencies. We found that initially differentiated populations did not converge either at genome-wide level or at candidate SNPs with signs of selection. In contrast, populations from Portugal showed convergence to the control population that derived from the same geographical origin and had been long-established in the laboratory. Candidate SNPs showed a variety of different allele frequency change patterns across generations, indicative of an underlying polygenic basis. We did not detect strong linkage around candidate SNPs, but rather a small but long-ranging effect. In conclusion, we found that history played a major role in genomic variation and evolution, with initially differentiated populations reaching the same adaptive outcome through different genetic routes.

Beschreibung: Fatty acids (FAs) were analysed in Baltic herring ( Clupea harengus membras ) stored in the Swedish Environmental Specimen Bank for up to 40 years. The purpose was to evaluate the retrospective use of FA signatures to detect temporal and spatial changes in the Baltic ecosystem. Fish from northern and central Baltic captured in the 1970s, the 1980s, in 1990, 2000, and 2009 and stored at − 25 °C were analysed. From the 1980s and onward herring from the south Baltic were included. A total of 55 FA and 4 alkenyl chains (detected as dimethyl acetals) were identified, and 28 of these (present at 〉 0.5% by weight) were used in evaluation of the data. The amount of some 20–22 carbon polyunsaturated fatty acids (PUFA) was related to time with lower amounts in older samples while other PUFAs were not related to time. Principal component analysis with saturated FAs and monounsaturated FAs showed similar sample groupings as the one obtained by including the PUFAs. The differences found in herring FA in this longitudinal study could be attributed to location of sampling, year of collection and storage time. However, the clearly distinguishable pattern in the FA composition in herrings from different locations in the Baltic Sea seen at all decades indicate that this technique can be used retrospectively.

Beschreibung: Ecosystem structure and function in the eastern Bering Sea are impacted by seasonal, interannual, and spatial variation of the zooplankton community. Zooplankton abundance, community composition and individual responses of key taxa, in spring, summer, and fall were evaluated across ecoregions during three years with high sea-ice, 2008–2010 (cold years). Interannual variations were greatest in spring, but less pronounced compared with intra-annual variations. Intra-annual variations were greatest in the south middle domain in spring and the north middle domain in all seasons. Models using environmental variables were able to explain 69–77% of zooplankton community variation within each season. Among individual taxa, Calanus marshallae/glacialis had delayed stage progression in spring 2009 compared with 2008 and 2010 on the south middle shelf, likely due to late ice retreat and cold temperatures that increased development times. In contrast, stage progression was fastest in summer 2008 likely due to warmer temperatures. Our findings indicate that intra-annual variation of zooplankton community composition, life history stage, and abundance within a cold period may affect the amount of high–lipid zooplankton prey (e.g. Neocalanus and Calanus spp. copepods and euphausiids) available seasonally for forage fish (e.g. age-0 walleye pollock) to grow to a sufficient size (to avoid size-dependent predation) and have sufficient lipid stores (to avoid starvation) to survive the first winter at sea.

Beschreibung: Indices of annual growth variation are not routinely incorporated into fisheries stock assessment models, due to a lack of a general framework for deciding when to include these indices, and of a mechanistic understanding about growth drivers. Such incorporation may also not necessarily lead to improved estimation or management performance. We demonstrate a way to incorporate such an index into an assessment model (Stock Synthesis), and use risk analysis to evaluate its management-related advantages and shortcomings. We applied this method to splitnose rockfish ( Sebastes diploproa ), where a previously developed growth index is highly correlated with decadal-scale climate indices. We find that including a similar index in the simulated assessment increases precision and reduces bias of parameter estimates. However, not including an index or including a completely erroneous index led to highly imprecise estimates when growth was strongly climate-driven. Including this growth index when individual growth was actually constant did not lead to poorer estimation performance. The risk analysis approach can be applied to other stocks to evaluate the consequences of including an index of growth variation.

Beschreibung: Establishing a network of marine-protected areas (MPAs) in areas beyond national jurisdiction (ABNJ) is viewed as an important measure to protect marine biodiversity. To date 12 MPAs have been established: two in the Southern Ocean and 10 in the North-East Atlantic region, and more are proposed. The Southern Ocean MPAs were adopted by Members of the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) in a complex, slow and challenging process. The North-East Atlantic MPAs were established under the OSPAR Convention and although the MPA network was established swiftly, doubts remain about whether it was a successful institutional development for the protection of marine biodiversity or just a network of ‘paper parks’. This article analyses the planning and negotiation processes that took place in establishing the 12 current MPAs to identify lessons useful for establishing MPAs in ABNJ in the future.

Beschreibung: Refugia can facilitate the persistence of biodiversity under changing environmental conditions, such as anthropogenic climate change, and therefore constitute the best chance of survival for many coral species in the wild. Despite an increasing amount of literature, the concept of coral reef refugia remains poorly defined; so that climate change refugia have been confused with other phenomena, including temporal refuges, pristine habitats and physiological processes such as adaptation and acclimatization. We propose six criteria that determine the capacity of refugia to facilitate species persistence, including long-term buffering, protection from multiple climatic stressors, accessibility, microclimatic heterogeneity, size, and low exposure to non-climate disturbances. Any effective, high-capacity coral reef refugium should be characterized by long-term buffering of environmental conditions (for several decades) and multi-stressor buffering (provision of suitable environmental conditions with respect to climatic change, particularly ocean warming and acidification). Although not always essential, the remaining criteria are important for quantifying the capacity of potential refugia.

Beschreibung: Marine ecosystems have been heavily impacted by fishing pressure, which can cause major changes in the structure of communities. Fishing directly removes biomass and causes secondary effects such as changing predatory and competitive interactions and altering energy pathways, all of which affect the functional groups and size distributions of marine ecosystems. We conducted a meta-analysis of eighteen trawl surveys from around the world to identify if there have been consistent changes in size-structure and life history groups across ecosystems. Declining biomass trends for larger fish and invertebrates were present in nine systems, all in the North Atlantic, while seven ecosystems did not exhibit consistent declining trends in larger organisms. Two systems had alternative patterns. Smaller taxa, across all ecosystems, had biomass trends with time that were typically flat or slightly increasing. Changes in the ratio of pelagic taxa to demersal taxa were variable across the surveys. Pelagic species were not uniformly increasing, but did show periods of increase in certain regions. In the western Atlantic, the pelagic-to-demersal ratio increased across a number of surveys in the 1990s and declined in the mid 2000s. The trawl survey data suggest there have been considerable structural changes over time and region, but the patterns are not consistent across all ecosystems.

Beschreibung: Science diplomacy is lauded as a catalyst for cooperation in international spaces. International science cooperation is a duty under international law and a necessity in reality. With the international community poised to begin historic negotiations to develop a new international legally binding instrument for the conservation and sustainable use of biodiversity in areas beyond national jurisdiction, it is timely to consider what role science diplomacy could play in advancing governance of this vast international space encompassing 64% of the ocean’s surface. In this article, three forms of science diplomacy are examined: how international science collaboration could provide a unifying focus in the development of the new instrument (science for diplomacy), what opportunities and challenges this could pose for global ocean science (diplomacy for science), and how scientists, as stakeholders, could help to identify and overcome obstacles (science in diplomacy). Learning from past examples of science diplomacy in international spaces and engaging a diverse group of scientific stakeholders to look to the future would enable ocean science to be a unifying focus for this new agreement.

Beschreibung: As with many other regions in the world, more complete information on the distribution of marine habitats in the Gulf is required to inform environmental policy, and spatial management of fisheries resources will require better understanding of the relationships between habitat and fish communities. Towed cameras and sediment grabs were used to investigate benthic habitats and associated epifauna, infauna and fish communities in the central Gulf, offshore from the east coast of Qatar, in water depths of between 12 and 52 m. Six different habitats were identified: (i) soft sediment habitats of mud and (ii) sand, and structured habitats of (iii) macro-algal reef, (iv) coral reef, (v) mixed reef, and (vi) oyster bed. The epibenthic community assemblage of the mud habitat was significantly different to that of sand, which in turn differed from the structured habitats of coral reef, mixed reef and oyster bed, with the macroalgal assemblage having similarities to both sand and the other structured habitats. Fish assemblages derived from video data did not differ between habitats, although certain species were only associated with particular habitats. Epibenthic diversity indices were significantly lower in mud, sand and macro-algal habitats, with no differences recorded for fish diversity. Soft sediment grab samples indicated that mud habitats had the highest benthic diversity, with Shannon-Weiner values of 〉4, and were more diverse than sand with values of 3.3. The study demonstrates high biodiversity in benthic habitats in the central and southwestern Gulf, which may in part be due to the absence of trawling activity in Qatari waters. There is a strong influence of depth on benthic habitat type, so that depth can be used to predict habitat distribution with a high level of accuracy. The presence of outcrops of hard substrata creates a mosaic of patchy shallow structured benthic habitat across extensive areas of the offshore seabed. Such heterogeneity, and the association of commercially exploited fish species with specific habitats, indicates that this region is well suited to a spatial approach to fisheries management.

Beschreibung: A new EU Common Fisheries Policy (CFP) came into force on 1 January 2014. Article 15 of the new CFP basic regulation introduced a discard ban or landing obligation (LO) in EU fisheries whereby the discarding of quota species is prohibited. There is an urgent need to understand the impact of this new regulation on the UK fishing industry and fishing industries elsewhere in Europe. This study conducted a discard ban trial to provide an opportunity for the fishing industry to demonstrate what a LO would mean for them. The results are mostly illustrative and qualitative, designed to inform policy decisions and identify areas of future work to assist in the implementation of the discard ban. Five recommendations are made, which if adopted, would significantly improve the prospects of a smooth transition to a largely discard-free EU fishery.

Beschreibung: Unmanned aerial vehicles (UAVs) are increasingly used in marine wildlife research. As technological developments rapidly advance the versatility and functionality of affordable UAVs, their potential as a marine aerial survey tool is quickly gaining attention. Currently, there is significant interest in whether cost-effective UAVs can outperform manned aircraft in aerial surveys of marine fauna at sea, although few empirical studies have compared relative sampling efficiency, accuracy and precision. Civil aviation restrictions, and subsequent available civilian technologies, make it unlikely that UAVs will currently be more effective than manned aircraft for large area marine surveys. UAVs do, however, have the capacity to fill a niche for intensive smaller spatial scale sampling and for undertaking aerial surveys in isolated locations. Improvements in UAV sensor resolutions and alternative sensor types, such as multispectral cameras, may increase area coverage, reduce perception error, and increase water penetration for sightability. Additionally, the further development of auto-detection software will rapidly improve image processing and further reduce human observer error inherent in manned aerial surveys. As UAV technologies and associated methodology is further developed and becomes more affordable, these aircraft will be increasingly adopted as a marine aerial survey tool in place of traditional methods using manned aircraft.

Beschreibung: Climate-mediated oceanographic changes have led to protracted periods of above- or below-average water temperatures over the eastern Bering Sea shelf since the early 2000s. Ecosystem components, from phytoplankton to marine birds, have shown dichotomous responses to these temperature stanzas. Understanding within-stanza responses is fundamental to modelling efforts that project ecosystem responses under future climate scenarios. This study describes fish communities associated with Walleye Pollock during the age-0 period and also examines within-stanza homogeneity of assemblages. Spatial patterns of assemblage structure are compared with pre-defined ecoregions and environmental indices are assessed to determine potential mechanisms that delineate species assemblages. Walleye Pollock, rockfishes, Sand Lance, and Northern Rock Sole contributed to spring assemblages in every year. Assemblages were delineated by across-shelf gradients in 2008 and 2010 while 2009 assemblages showed less spatial structure. In summer, the diversity of fish assemblages increased across years but early-stage juvenile Walleye Pollock represented a small portion of the total abundance in 2009. Environmental gradients were related to fish assemblages, but patterns were along-shelf in 2008 and across-shelf in 2010. In fall, late-stage juvenile Walleye Pollock dominated the catch in 2008, but did not typify any assemblage in 2009. Overall, patterns of assemblage structure were not consistent with pre-defined ecoregions. Assemblage structure in 2009 was unique and indicates that within-stanza variability may complicate modelling projections based on ecosystem-level responses to climate changes.

Beschreibung: Ecosystem-based fisheries-management (EBFM) is increasingly used in the United States (U.S.), including in the Gulf of Mexico (GOM). Producing distribution maps for marine organisms is a critical step in the implementation of EBFM. In particular, distribution maps are important inputs for many spatially-explicit ecosystem models, such as OSMOSE models, as well as for biophysical models used to predict annual recruitment anomalies due to oceanographic factors. In this study, we applied a recently proposed statistical modelling framework to produce distribution maps for: (i) younger juveniles (ages 0–1) of red snapper ( Lutjanus campechanus ), red grouper ( Epinephelus morio ), and gag ( Mycteroperca microlepis ), so as to be able to define the potential larval settlement areas of the three species in a biophysical model; and (ii) the functional groups and life stages represented in the OSMOSE model of the West Florida Shelf (“OSMOSE-WFS”). This statistical modelling framework consists of: (i) compiling a large database blending all of the encounter/non-encounter data of the GOM collected by the fisheries-independent and fisheries-dependent surveys using random sampling schemes, referred to as the “comprehensive survey database;” (ii) employing the comprehensive survey database to fit spatio-temporal binomial generalized linear mixed models (GLMMs) that integrate the confounding effects of survey and year; and (iii) using the predictions of the fitted spatio-temporal binomial GLMMs to generate distribution maps. This large endeavour allowed us to produce distribution maps for younger juveniles of red snapper, red grouper and gag and nearly all of the other functional groups and life stages represented in OSMOSE-WFS, at different seasons. Using Pearson residuals, the probabilities of encounter predicted by all spatio-temporal binomial GLMMs were demonstrated to be reasonable. Moreover, the results obtained for younger juvenile fish concur with the literature, provide additional insights into the spatial distribution patterns of these life stages, and highlight important future research avenues.

Beschreibung: In 2015 the United Nations General Assembly decided to develop an international legally binding instrument (ILBI) under the United Nations Convention on the Law of the Sea (UNCLOS) on the conservation and sustainable use of marine biological diversity of areas beyond national jurisdiction. To that end, it established a Preparatory Committee (PrepCom), to make substantive recommendations to the General Assembly on the elements of a draft text of an ILBI. The PrepCom has identified the tension between the principle of the common heritage of mankind and high seas freedoms embodied in UNCLOS as one of the issues which must be addressed in such an international agreement. Some participants in the process have proposed a sui generis regime as a way of resolving any apparent clash of these international legal principles, particularly as it relates to marine genetic resources and their access and benefit sharing. This article argues that environmental stewardship may provide the framework for such a sui generis regime. For it to do so, however, it must be grounded in international legal principles and act as a balance between competing values, perspectives and interests in the conservation and sustainable use of marine biodiversity beyond national jurisdiction. If appropriately redefined in this way, environmental stewardship can deliver a governance framework which addresses some of the central issues with which the PrepCom will have to deal. These include the practical problems of access and benefit sharing of the marine genetic resources of areas beyond national jurisdiction, and reconciling the conflicting pressure for international decision-making for the conservation and sustainable use of marine biological diversity on the one hand, and the maintenance of existing regional and sectoral frameworks on the other. Environmental stewardship, redefined, can provide an intellectual framework for an ILBI under UNCLOS on marine biodiversity beyond national jurisdiction.

Beschreibung: We gratefully acknowledge the following reviewers for their contributions during 2017.

Beschreibung: United Nations General Assembly resolution 69/292 provides that in developing an internationally legally binding instrument on the conservation and sustainable use of marine biological diversity in areas beyond national jurisdiction, the process should “not undermine” relevant existing legal instruments and frameworks and relevant global, regional, and sectoral bodies. An analysis of the varied interpretations of this ambiguous expression and its surrounding language raises questions about the role envisaged for such existing architecture. This article considers the practice of regional fisheries management organizations as an illustration of the possibilities and potential for improved practices generated from within existing architecture. It reviews measures taken to protect biodiversity and innovative applications of international law that have improved the ability of RFMOs to take such environmental measures. It seeks to highlight the importance of avoiding too narrow an interpretation of the notion of “not undermining”, and of recognizing the potential in existing architecture when designing an improved regime for the protection of biodiversity beyond national jurisdiction.

Beschreibung: Prior experience is as much an eye opener in science as it is in life, and often results in increased efficiency, greater productivity and reduced stress. While some actions and behaviours must be experienced first-hand to be appreciated, there are some behavioural patterns that can be readily absorbed from others, allowing the learning curve to be shortened and the professional career enhanced. After nearly 40 years of scientific research in otolith and shark science, it is clear that some strategies and tactics worked well at advancing my career, while others were ineffective or even counterproductive. Targeted mainly at graduate students and early-to-mid-career scientists, this somewhat philosophical essay identifies 12 easily adopted scientific behaviour patterns that would have had a hugely positive effect on my career, if only I had known about them early on. My hope is that early-career scientists can take advantage of some of the hard lessons that I have learned along the way, thus avoiding needless mistakes in the process of becoming the best scientist that they can be.

Beschreibung: Similar to many diadromous fish species, dramatic declines were observed for Allis shad, an anadromous Clupeidae, since the beginning of the 2000s. The knowledge of population and metapopulation dynamics is a key issue for the management of migratory species. Although homing behaviour is dominant in Allis shad, staying causes exchanges between populations of each river catchment. Currently, the management of Allis shad is applied at the population scale, without accounting for a potential metapopulation structure. Herein we propose a method to estimate the exchanges flux between rivers and a method to identify source and sink rivers. We used otolith microchemistry within a Bayesian model of reallocation coupled with abundance estimates of spawners per watershed. Results showed a metapopulation dynamic with several rivers acting as sources and other as sinks. However, the lack of precision and homogeneity in abundance data resulted in large credibility intervals, which calls for a better standardization in the acquisition of abundance data. Nevertheless, this method should provide an overview of the metapopulation dynamics of other anadromous species with management concerns.

Beschreibung: In laboratory studies, shellfish larvae often respond negatively to augmented [CO 2 ], but no prior tests have related wild bivalve larval performance and carbonate chemistry spatiotemporally. The geography of Willapa Bay (Washington, USA) naturally generates two distinct regions of carbonate chemistry where non-native Pacific oysters ( Crassostrea gigas ) dominate the intertidal fauna and successfully reproduce. On the river-influenced east side, pCO 2 is higher and alkalinity lower, which both contribute to reduced aragonite saturation state (Ω aragonite 1.3–1.5) relative to the west side receiving low watershed inputs (Ω aragonite 1.8–1.9). pH sws is also 〉0.1 lower on the east vs. west sides. Despite this difference in field conditions, no biological signal related to carbonate chemistry was apparent in oyster reproduction based on coupled chemical–biological comparisons over three summers. Instead, survival was equal between the two sides of the bay, and settlement was equal or higher on the low-Ω aragonite , low-pH east side. In a temporal comparison of four larval cohorts, settlement differed by two orders of magnitude and increased with water temperature. These field data on oyster reproduction illustrate that population-level effects may not emerge in higher mean [CO 2 ] conditions, with possible decoupling due to local adaptation, spatio-temporal heterogeneity, or higher sensitivity to other axes of environmental variability such as temperature.

Beschreibung: This “Food for Thought” article examines the potential uses of several novel scientific and technological developments, which are currently available or being developed, to significantly advance or supplement existing experimental approaches to study water-column biogeochemical processes (WCB-processes). After examining the complementary roles of observation, experiments and numerical models to study WCB-processes, we focus on the main experimental approaches of free-water in situ experiments, and at-sea and on-land meso- and macrocosms. We identify some of the incompletely resolved aspects of marine WCB-processes, and explore advanced experimental approaches that could be used to reduce their uncertainties. We examine three such approaches: free-water experiments of lengthened duration using bioArgo floats and gliders, at-sea mesocosms deployed several 100s m below the sea-surface using new biogeochemical sensors, and 50 m-tall on-land macrocosms. These approaches could lead to significant progress in concepts related to marine WCB-processes.

Beschreibung: Fisheries management is mainly conducted via single-stock assessment models assuming that fish stocks do not interact, except through assumed natural mortalities. Currently, the main alternative is complex ecosystem models which require extensive data, are difficult to calibrate, and have long run times. We propose a simple alternative. In three case studies each with two stocks, we improve the single-stock models, as measured by Akaike information criterion, by adding correlation in the cohort survival. To limit the number of parameters, the correlations are parameterized through the corresponding partial correlations. We consider six models where the partial correlation matrix between stocks follows a band structure ranging from independent assessments to complex correlation structures. Further, a simulation study illustrates the importance of handling correlated data sufficiently by investigating the coverage of confidence intervals for estimated fishing mortality. The results presented will allow managers to evaluate stock statuses based on a more accurate evaluation of model output uncertainty. The methods are directly implementable for stocks with an analytical assessment and do not require any new data sources.

Beschreibung: In the deep sea trawl fishery targeting shrimp ( Pandalus borealis ) and other cold-water shrimp species, fishers often use a Nordmöre sorting grid ahead of a small mesh codend to avoid bycatch. However, small fish can pass through the grid and are subsequently retained in the codend. This makes shrimp size selection complex and the size-dependent curve for both the shrimp and the bycatch species often exhibits a bell-shaped signature. In this study we developed a new model and method to estimate size selection in this fishery, conducted fishing trials in the Northeast Barents Sea, and applied the new method to quantify the individual and combined size selection of the Nordmöre grid and codend for deep water shrimp and two bycatch species. The size selectivity for both bycatch species showed the expected bell-shaped signature with low retention probability of very small and larger fish. The Nordmöre grid had high passage probability for all sizes, although it decreased slightly for the largest shrimps. The smallest shrimps were released by the codend.

Beschreibung: There is a need for automatic systems that can reliably detect, track and classify fish and other marine species in underwater videos without human intervention. Conventional computer vision techniques do not perform well in underwater conditions where the background is complex and the shape and textural features of fish are subtle. Data-driven classification models like neural networks require a huge amount of labelled data, otherwise they tend to over-fit to the training data and fail on unseen test data which is not involved in training. We present a state-of-the-art computer vision method for fine-grained fish species classification based on deep learning techniques. A cross-layer pooling algorithm using a pre-trained Convolutional Neural Network as a generalized feature detector is proposed, thus avoiding the need for a large amount of training data. Classification on test data is performed by a SVM on the features computed through the proposed method, resulting in classification accuracy of 94.3% for fish species from typical underwater video imagery captured off the coast of Western Australia. This research advocates that the development of automated classification systems which can identify fish from underwater video imagery is feasible and a cost-effective alternative to manual identification by humans.

Beschreibung: Characterizing migratory behaviours contributes to the sustainable management of marine fishes by resolving stock structure and identifying the timing and locations of events within fish life cycles. The migratory behaviour of Atlantic halibut ( Hippoglossus hippoglossus ) in the Gulf of St. Lawrence (GSL), Canada was characterized over an annual cycle using pop-up satellite archival tags ( n  = 15). Daily probability density functions of individual halibut positions were estimated using a geolocation model specifically developed to track demersal fish species in the GSL. Reconstructed migration routes ( n  = 8) revealed that Atlantic halibut displayed seasonal migrations, moving from deeper offshore waters in the winter to shallower nearshore waters in the summer. Variability in migratory behaviours was observed among individuals tagged at the same location and time. One individual resided year round in the vicinity of the tagging site, three individuals displayed homing behaviour, and four individuals did not return to the tagging site. The identification of presumed spawning rises for two individuals suggested that spawning of Atlantic halibut occurred in the GSL. Although based on a limited number of individuals, these results suggest that Atlantic halibut in the GSL forms a philopatric population, supporting the current separate management of this stock from the adjacent Scotian Shelf and southern Grand Banks stock.

Beschreibung: Life-history strategies often vary within motile marine species, affecting morphometry, growth, diet, and fecundity. Atlantic cod ( Gadus morhua ) in the Gulf of Maine display marked variation in a number of life-history traits, exemplified by differences in body colour. Migratory behaviours are suspected to differ among these colour types, but have yet to be shown definitively. Here, we used the combination of an acoustic telemetry system and fine-scale benthic habitat maps to reveal that the red phenotype cod adhered to an isolated kelp forest covering 〈2 km 2 of a seamount in the central Gulf of Maine. Meanwhile, the olive phenotype cod adopted diel vertical migratory behaviour, possibly in response to a temperature gradient. Use of shallow, structured habitat was influenced by temperature and may be enabled by dynamic conditions related to internal waves that persist throughout the summer and early fall. Detections decreased in response to changing thermal conditions, although phenotypes reacted to these changes in distinct ways: the olive phenotype abandoned shallow habitat prior to peak summer temperatures, while the red phenotype remained until mid-fall when temperatures and temperature variability declined. Our findings support a link between morphometry, colour, behavioural strategies, and habitat preferences that may be widespread in Atlantic cod.

Beschreibung: Toxic pollutants such as crude oil have direct negative effects for a wide array of marine life. While mortality from acute exposure to oil is obvious, sub-lethal consequences of exposure to petroleum derivatives for growth and reproduction are less evident and sub-lethal effects in fish populations are obscured by natural environmental variation, fishing, and measurement error. We use fisheries independent surveys in the Gulf of Alaska to examine the consequences of the 1989 Exxon Valdez oil spill (EVOS) for demersal fish. We delineate areas across a range of exposure to EVOS and use spatio-temporal models to quantify the abundance of 53 species-groups over 31 years. We compare multiple community metrics for demersal fish in EVOS and Control areas. We find that areas more exposed to EVOS have more negative trends in total groundfish biomass than non-EVOS areas, and that this change is driven primarily by reductions in the abundance of the apex predator guild. We show no signature of increased variability or increased levels of synchrony within EVOS areas. Our analysis supports mild consequences of EVOS for groundfish communities, but suggests that long time-series and assessments of changes at the community level may reveal sub-lethal effects in marine communities.

Beschreibung: Real-time spatial management in fisheries, a type of dynamic ocean management, uses nearly real-time data collection and dissemination to reduce susceptibility of certain species or age classes to being caught in mixed fisheries. However, as with many fisheries regulations, it is difficult to assess whether such a regulation can produce tangible results on population dynamics. In this study, we take advantage of a rare opportunity in which data regarding real-time closures (RTCs) are available for 1990–2014 alongside annual estimates of fishing mortality for three species (Atlantic cod, haddock, and herring) and catch for four species (all plus saithe) in Icelandic fisheries management. We use time series analyses to assess whether RTCs work as expected and yield a lower susceptibility of small fish to being caught, indicated by lower catch levels and selectivities (as estimated from fishing mortalities) in years with more closures. Results indicate that haddock and herring followed this pattern, but only under conditions of generally high fishing mortality. This study represents the first time evidence has been presented that real-time fishery closures can have a beneficial effect on population dynamics, but also suggests that results differ among species.

Beschreibung: The location and intensity of small-scale fishing is dynamic over time, greatly shaping ecosystems. However, historical information about fishing effort and fishing gear-use are often unavailable. Within a marine biodiversity hotspot in the Philippines, we characterized spatio-temporal dynamics of fishing (1960–2010) using participatory mapping. First, we compared non-spatial and spatial estimates of total fishing effort. Our non-spatial estimate indicated that fishing increased 2.5 fold, reaching 1.3 million fishing days per year in 2010. Yet, spatial estimates showed fishing effort increased 〉20 fold, with the highest effort in 1990. Second, we evaluated how spatial characteristics of fishing changed over time. We introduced a method to estimate the sample size of fishers needed to accurately map the extent of fishing. By 2000, fishing extent grew 50% and small-scale fisheries affected over 90% of the coastal ocean. The expanded fishing area coincided with a greater spatial overlap among fishing gears and a proliferation of intensive fishing gears (destructive, active, non-selective). The expansion and intensification of fishing shown here emphasize the need for spatial approaches to management that focus on intensive, and often illegal, fishing gears. Such approaches are critical in targeting conservation actions (e.g. gear restrictions) in the most vulnerable areas.

Beschreibung: This article presents a non-invasive fully automatic procedure for Bluefin Tuna sizing, based on a stereoscopic vision system and a deformable model of the fish ventral silhouette. An image processing procedure is performed on each video frame to extract individual fish, followed by a fitting procedure to adjust the fish model to the extracted targets, adapting it to the bending movements of the fish. The proposed system is able to give accurate measurements of tuna snout fork length (SFL) and widths at five predefined silhouette points without manual intervention. In this work, the system is used to study size evolution in adult Atlantic Bluefin Tuna ( Thunnus Thynnus ) over time in a growing farm. The dataset is composed of 12 pairs of videos, which were acquired once a month in 2015, between July and October, in three grow-out cages of tuna aquaculture facilities on the west Mediterranean coast. Each grow out cage contains between 300 and 650 fish on an approximate volume of 20 000 m 3 . Measurements were automatically obtained for the 4 consecutive months after caging and suggest a fattening process: SFL shows an increase of just a few centimetres (2%) while the maximum width ( A1 ) shows a relative increase of more than 20%, mostly in the first 2 months in farm. Moreover, a linear relation (with coefficient of determination R 2 〉 0.98) between SFL and widths for each month is deduced, and a fattening factor ( F ) is introduced. The validity of the measurements is proved by comparing 15 780 SFL measurements, obtained with our automatic system in the last month, versus ground truth data of a high percentage of the stock under study (1143 out of 1579), obtaining no statistically significant difference. This procedure could be extended to other species to assess the size distribution of stocks, as discussed in the article.

Beschreibung: On 24 February 2017, a workshop entitled “Law Beyond Boundaries: innovative mechanisms for the integrated management of biodiversity beyond national jurisdiction” was held in Wollongong, Australia hosted by the Oceans and International Environmental Law Interest Group of the Australian and New Zealand Society of International Law, in association with the Australian National Centre for Ocean Resources and Security at the University of Wollongong. The aim of the workshop was to address the question, how can international law be used in innovative ways to effectively conserve and sustainably manage marine biological diversity in areas beyond national jurisdiction (ABNJ)? In this introduction, we briefly summarize five of the papers developed for the workshop, highlighting the way in which they address three important themes: the promise and limits of existing institutional mechanisms governing activities in ABNJ; interactions between established principles and regimes for ABNJ; and the lessons that can be drawn from existing global and regional approaches to ABNJ. We hope that the ideas developed in this article theme set will contribute to the ongoing discussions at the United Nations General Assembly, as the international community works toward the development of an international legally binding instrument to govern activities in ABNJ.

Beschreibung: When it comes to rats, even scientists can get caught up in the blame game.

Beschreibung: It is well known that cancer incidence is increasing worldwide, with pockets of human populations and geographical locations seemingly at higher risk than others.

Beschreibung: Protein structures strongly influence molecular evolution. In particular, the evolutionary rate of a protein site depends on the number of its native contacts. Stability-constrained models of protein evolution consider this influence of protein structure on evolution by predicting the effect of mutations on the stability of the native state, but they currently neglect how mutations affect the protein structure. These models predict that buried protein sites with more native contacts are more constrained by natural selection and less variable, as observed. Nevertheless, previous work did not consider the stability against compact misfolded conformations, although it is known that the negative design that destabilizes these misfolded conformations influences protein evolution significantly. Here, we show that stability-constrained models that consider misfolding predict that site-specific sequence entropy and substitution rate peak at amphiphilic sites with an intermediate number of contacts, as these sites are less constrained than exposed sites with few contacts whose hydrophobicity must be limited. This result holds both for a mean-field model with independent sites and for a pairwise model that takes as a reference the wild-type sequence, but it contrasts with the observations that indicate that the entropy and the substitution rate decrease monotonically with the number of contacts. Our work suggests that stability-constrained models overestimate the tolerance of amphiphilic sites against mutations, either because of the limits of the free energy function or, more importantly in our opinion, because they do not consider how mutations perturb the native protein structure.

Beschreibung: The bovine genetic resources in China are diverse, but their value and potential are yet to be discovered. To determine the genetic diversity and population structure of Chinese cattle, we analyzed the whole genomes of 46 cattle from six phenotypically and geographically representative Chinese cattle breeds, together with 18 Red Angus cattle genomes, 11 Japanese black cattle genomes and taurine and indicine genomes available from previous studies. Our results showed that Chinese cattle originated from hybridization between Bos taurus and Bos indicus . Moreover, we found that the level of genetic variation in Chinese cattle depends upon the degree of indicine content. We also discovered many potential selective sweep regions associated with domestication related to breed-specific characteristics, with selective sweep regions including genes associated with coat color ( ERCC2 , MC1R , ZBTB17 , and MAP2K1 ), dairy traits ( NCAPG , MAPK7 , FST, ITFG1 , SETMAR , PAG1 , CSN3 , and RPL37A ), and meat production/quality traits (such as BB S2, R3HDM1, IGFBP2 , IGFBP5 , MYH9 , MYH4 , and MC5R ). These findings substantially expand the catalogue of genetic variants in cattle and reveal new insights into the evolutionary history and domestication traits of Chinese cattle.

Beschreibung: The avoidance of cytotoxic effects associated with protein misfolding has been proposed as a dominant constraint on the sequence evolution and molecular clock of highly expressed proteins. Recently, Leuenberger et al. developed an elegant experimental approach to measure protein thermal stability at the proteome scale. The collected data allow us to rigorously test the predictions of the misfolding avoidance hypothesis that highly expressed proteins have evolved to be more stable, and that maintaining thermodynamic stability significantly constrains their evolution. Notably, reanalysis of the Leuenberger et al. data across four different organisms reveals no substantial correlation between protein stability and protein abundance. Therefore, the key predictions of the misfolding toxicity and related hypotheses are not supported by available empirical data. The data also suggest that, regardless of protein expression, protein stability does not substantially affect the protein molecular clock across organisms.

Beschreibung: Simple satellites are tandemly repeating short DNA motifs that can span megabases in eukaryotic genomes. Because they can cause genomic instability through nonallelic homologous exchange, they are primarily found in the repressive heterochromatin near centromeres and telomeres where recombination is minimal, and on the Y chromosome, where they accumulate as the chromosome degenerates. Interestingly, the types and abundances of simple satellites often vary dramatically between closely related species, suggesting that they turn over rapidly. However, limited sampling has prevented detailed understanding of their evolutionary dynamics. Here, we characterize simple satellites from whole-genome sequences generated from males and females of nine Drosophila species, spanning 40 Ma of evolution. We show that PCR-free library preparation and postsequencing GC-correction better capture satellite quantities than conventional methods. We find that over half of the 207 simple satellites identified are species-specific, consistent with previous descriptions of their rapid evolution. Based on a maximum parsimony framework, we determined that most interspecific differences are due to lineage-specific gains. Simple satellites gained within a species are typically a single mutation away from abundant existing satellites, suggesting that they likely emerge from existing satellites, especially in the genomes of satellite-rich species. Interestingly, unlike most of the other lineages which experience various degrees of gains, the lineage leading up to the satellite-poor D. pseudoobscura and D. persimilis appears to be recalcitrant to gains, providing a counterpoint to the notion that simple satellites are universally rapidly evolving.

Beschreibung: Animal and plant centromeres are embedded in repetitive “satellite” DNA, but are thought to be epigenetically specified. To define genetic characteristics of centromeres, we surveyed satellite DNA from diverse eukaryotes and identified variation in