Mechanisms and consequences of life cycle diversity of beaked redfish, Sebastes mentella

Recent genetic research, supported by life history information, indicates that there are three biological stocks of S. mentella in the Irminger Sea and adjacent waters: a ‘Deep Pelagic’ stock (>500m), a ‘Shallow Pelagic’ stock (<500m), and an ‘Icelandic Slope’ stock. Throughout their range, Sebastes species are adapted to a diversity of ecological niches, with overlapping spatial distributions of different species that have little or no morphological differences. Divergence of behavioral groups into depth-defined adult habitats has led to reproductive isolation, adaptive radiation and speciation of several Sebastes species. Congruent differences in fatty acid composition and parasites suggests that the three genetically distinct populations of S. mentella are adapted to disparate trophic habitats in pelagic waters (shallower and deeper than the deep-scattering layer), and in demersal habitats on the continental slope. Patterns of morphology are also consistent with adaptation to different habitats, because pelagic forms are more streamlined. Although genetic differences and evidence for reproductive isolation are clear, these populations appear to share common nursery habitats on the Greenlandic Shelf. Spatial overlap at early life stages and depth-defined adult populations present challenges for stock identification and fishery management. Effective resource monitoring, conservation and fishery management requires that the spatial definition of management units reflects biological stock structure. We describe a proposal for a redefinition of practical management units that are based on geographic proxies for biological stocks which minimizes mixed-stock catches according to spatial patterns of the recent fishery

Archived DNA reveals fisheries and climate induced collapse of a major fishery

Fishing and climate change impact the demography of marine fishes, but it is generally ignored that many species are made up of genetically distinct locally adapted populations that may show idiosyncratic responses to environmental and anthropogenic pressures. Here, we track 80 years of Atlantic cod (Gadus morhua) population dynamics in West Greenland using DNA from archived otoliths in combination with fish population and niche based modeling. We document how the interacting effects of climate change and high fishing pressure lead to dramatic spatiotemporal changes in the proportions and abundance of different genetic populations, and eventually drove the cod fishery to a collapse in the early 1970s. Our results highlight the relevance of fisheries management at the level of genetic populations under future scenarios of climate change

Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany.

Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15-46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800-1066 CE) and subsequent medieval (1066-1280 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.Leverhulme Trust (MRF-2013-065

Exploitation shifted trophic ecology and habitat preferences of Mediterranean and Black Sea bluefin tuna over centuries

During recent decades, the health of ocean ecosystems and fish populations has been threatened by overexploitation, pollution and anthropogenic-driven climate change. Due to a lack of long-term ecological data, we have a poor grasp of the true impact on the diet and habitat use of fishes. This information is vital if we are to recover depleted fish populations and predict their future dynamics. Here, we trace the long-term diet and habitat use of Atlantic bluefin tuna (BFT), Thunnus thynnus, a species that has had one of the longest and most intense exploitation histories, owing to its tremendous cultural and economic importance. Using carbon, nitrogen and sulphur stable isotope analyses of modern and ancient BFT including 98 archaeological and archival bones from 11 Mediterranean locations ca. 1st century to 1941 CE, we infer a shift to increased pelagic foraging around the 16th century in Mediterranean BFT. This likely reflects the early anthropogenic exploitation of inshore coastal ecosystems, as attested by historical literature sources. Further, we reveal that BFT which migrated to the Black Sea–and that disappeared during a period of intense exploitation and ecosystem changes in the 1980s–represented a unique component, isotopically distinct from BFT of NE Atlantic and Mediterranean locations. These data suggest that anthropogenic activities had the ability to alter the diet and habitat use of fishes in conditions prior to those of recent decades. Consequently, long-term data provide novel perspectives on when marine ecosystem modification began and the responses of marine populations, with which to guide conservation policy

Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly

The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 380 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively 'trivial' aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic

Evidence of unidirectional hybridization and second‐generation adult hybrid between the two largest animals on Earth, the fin and blue whales

Biodiversity in the oceans has dramatically declined since the beginning of the industrial era, with accelerated loss of marine biodiversity impairing the ocean's capacity to maintain vital ecosystem services. A few organisms epitomize the damaging and long‐lasting effects of anthropogenic exploitation: some whale species, for instance, were brought to the brink of extinction, with their population sizes reduced to such low levels that may have cause a significant disruption to their reproductive dynamics and facilitated hybridization events. The incidence of hybridization is nevertheless believed to be rare and very little information exist on its directionality. Here, using genetic markers, we show that all but one whale hybrid sample collected in Icelandic waters originated from the successful mating of male fin whale and female blue whale, thus suggesting unidirectional hybridization. We also demonstrate for the first time the existence of a second‐generation adult (male) hybrid resulting from a backcross between a female hybrid and a pure male fin whale. The incidence of hybridization events between fin and blue whales is likely underestimated and the observed unidirectional hybridization (for F1 and F2 hybrids) is likely to induce a reproductive loss in blue whale, which may represent an additional challenge to its recovery in the Atlantic Ocean compared to other rorquals

The era of reference genomes in conservation genomics

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics