Ancient DNA evidence for the ecological globalization of cod fishing in medieval and post-medieval Europe.

Understanding the historical emergence and growth of long-range fisheries can provide fundamental insights into the timing of ecological impacts and the development of coastal communities during the last millennium. Whole-genome sequencing approaches can improve such understanding by determining the origin of archaeological fish specimens that may have been obtained from historic trade or distant water. Here, we used genome-wide data to individually infer the biological source of 37 ancient Atlantic cod specimens (ca 1050-1950 CE) from England and Spain. Our findings provide novel genetic evidence that eleventh- to twelfth-century specimens from London were predominantly obtained from nearby populations, while thirteenth- to fourteenth-century specimens were derived from distant sources. Our results further suggest that Icelandic cod was indeed exported to London earlier than previously reported. Our observations confirm the chronology and geography of the trans-Atlantic cod trade from Newfoundland to Spain starting by the early sixteenth century. Our findings demonstrate the utility of whole-genome sequencing and ancient DNA approaches to describe the globalization of marine fisheries and increase our understanding regarding the extent of the North Atlantic fish trade and long-range fisheries in medieval and early modern times.

The globalization of naval provisioning: ancient DNA and stable isotope analyses of stored cod from the wreck of the Mary Rose, AD 1545.

A comparison of ancient DNA (single-nucleotide polymorphisms) and carbon and nitrogen stable isotope evidence suggests that stored cod provisions recovered from the wreck of the Tudor warship Mary Rose, which sank in the Solent, southern England, in 1545, had been caught in northern and transatlantic waters such as the northern North Sea and the fishing grounds of Iceland and Newfoundland. This discovery, underpinned by control data from archaeological samples of cod bones from potential source regions, illuminates the role of naval provisioning in the early development of extensive sea fisheries, with their long-term economic and ecological impacts.

The dangers of ignoring stock complexity in fishery management: the case of the North Sea cod.

The plight of the marine fisheries is attracting increasing attention as unsustainably high exploitation levels, exacerbated by more extreme climatic conditions, are driving stocks to the point of collapse. The North Atlantic cod (Gadus morhua), a species which until recently formed a major component of the demersal fisheries, has undergone significant declines across its range. The North Sea stock is typical of many, with a spawning stock biomass that has remained below the safe biological limit since 2000 and recruitment levels near the lowest on record. Cod within the North Sea are currently managed as a single stock, and yet mounting empirical evidence supports the existence of a metapopulation of regionally variable, genetically distinct, sub-stocks. Applying the same management strategies to multiple stocks that differ in their resilience to exploitation inevitably results in the overfishing and likely collapse of the weaker components. Indeed, recent studies have identified two North Sea spawning stocks that have undergone disproportionally large collapses with very substantial reductions in egg production. Similarly affected cod stocks in the northwest Atlantic have shown little evidence of recovery, despite fishery closures. The possible implications of ignoring sub-structuring within management units for biocomplexity, local adaptation and ecosystem stability are considered.

Phylogeography of the rare Balkan endemic Martino's vole, Dinaromys bogdanovi, reveals strong differentiation within the western Balkan Peninsula.

The spatial genetic structure of Martino's vole, a rare palaeoendemic species of the western Balkans, was investigated using DNA isolated from archived museum samples. The study was based on partial sequencing (555 bp) of the mitochondrial cytochrome b gene for 63 specimens from 20 different localities throughout the species' range. Three highly divergent allopatric phylogenetic lineages (Northwestern, Central and Southeastern) were recognized among 47 haplotypes, suggesting three independent glacial differentiation centres within the western Balkans. The Northwestern lineage, which showed the highest divergence from all other samples (mean sequence divergence of 6.64% +/- 1.10), comprised samples collected from northwest of the Neretva River in Croatia, western Bosnia and Herzegovina. The Central and Southeastern lineages were separated by an average sequence divergence of 2.95% +/- 0.66 and were geographically divided by the Drim River (the Kosovo Basin in Serbia). Overall, haplotype diversity decreased from the Northwestern lineage to the Central and subsequently the Southeastern lineage, in a geographical pattern consistent with a stepping stone colonization. The observed distribution indicates a gradual southerly expansion with subsequent allopatry across the Neretva River and Drim River approximately 1 and 0.3 million years ago, respectively. Such a scenario is concordant with palaeontological evidence. Several highly divergent sublineages within the Northwestern and Central lineages showed no significant geographical structuring, suggesting secondary contact of allopatrically evolved lineages. We hypothesize that the topographical complexity of the Balkans promoted allopatry and isolation on a small geographical scale during interglacial periods, with secondary contact during glacial maxima. Furthermore, the three main lineages should be regarded as evolutionary significant units with important implications for conservation. Ecological data show that the Northwestern lineage in particular fulfils all criteria for a highly endangered, evolutionarily significant unit.

Biocomplexity in a highly migratory pelagic marine fish, Atlantic herring.

The existence of biologically differentiated populations has been credited with a major role in conferring sustainability and in buffering overall productivity of anadromous fish population complexes where evidence for spatial structure is uncontroversial. Here, we describe evidence of correlated genetic and life history (spawning season linked to spawning location) differentiation in an abundant and highly migratory pelagic fish, Atlantic herring, Clupea harengus, in the North Sea (NS) and adjacent areas. The existence of genetically and phenotypically diverse stocks in this region despite intense seasonal mixing strongly implicates natal homing in this species. Based on information from genetic markers and otolith morphology, we estimate the proportional contribution by NS, Skagerrak (SKG) and Kattegat and western Baltic (WBS) fish to mixed aggregations targeted by the NS fishery. We use these estimates to identify spatial and temporal differences in life history (migratory behaviour) and habitat use among genetically differentiated migratory populations that mix seasonally. Our study suggests the existence of more complex patterns of intraspecific diversity than was previously recognized. Sustainability may be compromised if such complex patterns are reduced through generalized management (e.g. area closures) that overlooks population differences in spatial use throughout the life cycle.

Temporal analysis of archived samples indicates marked genetic changes in declining North Sea cod (Gadus morhua).

Despite increasing evidence that current exploitation rates can contribute to shifts in life-history traits and the collapse of marine fish stocks, few empirical studies have investigated the likely evolutionary impacts. Here, we used DNA recovered from a temporal series of archived North Sea cod (Gadus morhua) otoliths, to investigate genetic diversity within the Flamborough Head population between 1954 and 1998, during which time the population underwent two successive declines. Microsatellite data indicated a significant reduction in genetic diversity between 1954 and 1970 (total number of alleles: 1954, 46; 1960, 42; 1970, 37), and a subsequent recovery between 1970 and 1998 (total number of alleles: 1970, 37; 1981, 42; 1998, 45). Furthermore, estimates of genetic differentiation (F(ST) and R(ST)) showed a significant divergence between 1998 and earlier samples. Data are consistent with a period of prolonged genetic drift, accompanied by a replacement of the Flamborough Head population through an increased effective migration rate that occurred during a period of high exploitation and appreciable demographic and phenotypic change. Other studies indicate that diversity at neutral microsatellite loci may be correlated with variability at selected genes, thus compromising a population's subsequent recovery and adaptive potential. Such effects are especially pertinent to North Sea cod, which are threatened by continuing exploitation and rising sea temperatures.