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Soubrier, J.

Publications and source records attributed to Soubrier, J..

2 recordsLinked to original sources

Untangling the Evolutionary History of European Bison (Bison bonasus)

European bison (Bison bonasus) are the largest endemic vertebrates in Europe, and one of the few megafaunal species to have survived the mass megafaunal extinction during the Pleistocene/Holocene transition (12-9 thousand years ago). Untangling their evolutionary history would provide valuable information about the response of European megafauna to periods of rapid environmental change. However, a severe and recent population bottleneck obscures much of the population history that could be inferred from the genomes of modern individuals. While several studies have attempted to analyse ancient European bison populations directly using ancient DNA, their datasets were limited in temporal and geographic range. In this study we present the most comprehensive dataset of ancient European bison mitochondrial genomes to date, with 131 ancient bison samples from across the Eurasian continent covering over 50 thousand years. We reveal patterns of bison distribution and concurrent environmental changes across a broad geographical and temporal range. In particular, population expansions following periods of extensive forest reduction combined with a decrease in anthropogenic pressures suggest that European bison remain preferentially adapted to an open steppe environment through to the present day.

evolutionary biology↗

Population size history from short genomic scaffolds: how short is too short?

The Pairwise Sequentially Markov Coalescent (PSMC), and its extension PSMC', model past population sizes from a single diploid genome. Both models have been widely applied, even to organisms with scaffold-level genome reference assemblies of limited contiguity. However it is unclear how PSMC and PSMC' perform on short scaffolds. We evaluated psmc and msmc, implementations of the PSMC and PSMC' models respectively, on simulated genomes with low contiguity, and compared results to those from fully contiguous data. Simulations with scaffolds from 100 Mb to 10 kb revealed that psmc maintains high accuracy down to lengths of 100 kb, while msmc is accurate down to 1 Mb. The discrepancy is not due to differing models, but stems from an implementation detail of msmc--homozygous tracts at the ends of scaffolds are discarded, making msmc unreliable for low contiguity genomes. We recommend excluding data that are aligned to shorter scaffolds when undertaking demographic inference.

genetics↗