Demographic reconstruction from ancient DNA supports rapid extinction of the Great Auk

The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species’ geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation

Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum

PREMISE: Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger- sequencing approaches, the Lomatium packardiae/L. anomalum subcomplex within the larger Lomatium triternatum complex could not be resolved. Therefore, we attempt to resolve these boundaries here. METHODS: The Angiosperms353 probe set was employed to resolve the ambiguity within Lomatium triternatum species complex using 48 accessions assigned to L. packardiae, L. anomalum, or L. triternatum. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species boundaries: STACEY, a Bayesian coalescent- based species tree analysis that takes incomplete lineage sorting into account; ASTRAL- III, another coalescent- based species tree analysis; and a concatenated approach using MrBayes. Climatic factors, morphological characters, and soil variables were measured and analyzed to provide additional support for recovered groups. RESULTS: The STACEY analysis recovered three major clades and seven subclades, all of which are geographically structured, and some correspond to previously named taxa. No other analysis had full agreement between recovered clades and other parameters. Climatic niche and leaflet width and length provide some predictive ability for the major clades. CONCLUSIONS: The results suggest that these groups are in the process of incipient speciation and incomplete lineage sorting has been a major barrier to resolving boundaries within this lineage previously. These results are hypothesized through sequencing of multiple loci and analyzing data using coalescent- based processes

Crossing disciplinary lines: reconciling social and genomic perspectives on the histories and legacies of the transatlantic trade in enslaved Africans

Over the past two decades, advances in the field of genomics have presented new opportunities to shed light upon the origins of enslaved Africans and their contemporary descendants. While this possibility has caused enthusiasm among members of the public, it has provoked contention within the academic sphere. This paper represents an attempt to reconcile these opposing disciplinary divisions, by examining, explaining, and discussing the processes involved in the production of genetic “ancestry” estimates, in order to moderate the aura of absolute “truth” that is often associated with such techniques. Our discussion focuses on two case studies – the academic use of ancient DNA analyses to estimate the geographic origins of historically enslaved individuals, and the commercialization of DNA “ancestry” testing techniques aimed at African-American roots-seekers – and draws upon recent ethnographic data relating to the experiences of test creators and test-takers, in order to contribute to this debate.This work was supported by the EUROTAST project, a Marie Curie Actions Initial Training Network, funded by the European Union under the Seventh Framework Programme [grant number EUROTAST FP7-PEOPLE-2010]