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This Week in PNAS: Aug 8, 2017

In the early, online version of the Proceedings of the National Academy of Sciences, researchers from the University of Utah and the MD Anderson Cancer Center explore the early history of ancient hominins using a new statistical approach for inferring admixture based on allele sharing patterns between samples. Based on sequence data from African, Eurasian, Neanderthal, and Denisovan representatives, for example, the team estimated that Neanderthals and Denisovans diverged from one in the wake of an ancestral population decline that followed a split with the lineage leading to modern humans. The Neanderthal population subsequent grew and diverged, the authors say, leading to disjointed local groups.

An international team led by investigators in Norway and the UK examines DNA sequences from ancient fish bones to get a glimpse at the fish trade for populations living long ago. The researchers did SNP genotyping and whole-genome reconstructions on 15 Viking Age fish bone samples believed to be roughly 950 years to more than 1,200 years old, along with dozens of more recent medieval cod bone samples, collected at sites in present-day Norway, the UK, Iceland, and Germany. From genetic features in these samples, they were able to retrace fish sources and identify mixed cod ancestry marking sites with a robust fish trading tradition. Moreover, the authors say, the findings "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."

Finally, investigators in Belgium tally up the inactivating changes to protein-coding sequences in three dozen inbred mouse strains that are frequently used in the lab with their newly developed bioinformatics tool. With the help of publicly available genome sequence, SNP, and structural variant data generated for the Sanger Institute's Mouse Genomes Project, the team searched for premature stop codons, in-frame insertions and deletions, and other inactivating alterations and attempted to predict their protein consequences relative to the mouse reference genome. The resulting database "makes the enormous richness of variant alleles present in these 36 inbred strains visible, accessible, and useful to the whole mouse research community," the authors write.