Biology subjects

Mathieu Gautier

Publications and source records attributed to Mathieu Gautier.

2 recordsLinked to original sources

bioRxiv2016

rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure.

Identifying genomic regions with unusually high local haplotype homozygosity represents a powerful strategy to characterize candidate genes responding to natural or artificial positive selection. To that end, statistics measuring the extent of haplotype homozygosity within (e.g., EHH, iHS) and between (Rsb or XP-EHH) populations have been proposed in the literature. The O_SCPLOWREHHC_SCPLOW package for R was previously developed to facilitate genome-wide scans of selection, based on the analysis of long-range haplotypes. However, its performance wasnt sufficient to cope with the growing size of available data sets. Here we propose a major upgrade of the O_SCPLOWREHHC_SCPLOW package, which includes an improved processing of the input files, a faster algorithm to enumerate haplotypes, as well as multi-threading. As illustrated with the analysis of large human haplotype data sets, these improvements decrease the computation time by more than an order of magnitude. This new version of O_SCPLOWREHHC_SCPLOW will thus allow performing iHS-, Rsb- or XP-EHH-based scans on large data sets. The package O_SCPLOWREHHC_SCPLOW 2.0 is available from the CRAN repository (http://cran.r-project.org/web/packages/rehh/index.html) together with help files and a detailed manual.

Evolutionary Biology↗

bioRxiv2016

Deciphering the wisent demographic and adaptive histories from individual whole-genome sequences

As the largest European herbivore, the wisent (Bison bonasus) is emblematic of the continent wildlife but has unclear origins. Here, we infer its demographic and adaptive histories from two individual whole genome sequences via a detailed comparative analysis with bovine genomes. We estimate that the wisent and bovine species diverged from 1.7x106 to 850,000 YBP through a speciation process involving an extended period of limited gene flow. Our data further support the occurrence of more recent secondary contacts, posterior to the Bos taurus and Bos indicus divergence (ca. 150,000 YBP), between the wisent and (European) taurine cattle lineages. Although the wisent and bovine population sizes experienced a similar sharp decline since the Last Glacial Maximum, we find that the wisent demography remained more fluctuating during the Pleistocene. This is in agreement with a scenario in which wisents responded to successive glaciations by habitat fragmentation rather than southward and eastward migration as for the bovine ancestors.\n\nWe finally detect 423 genes under positive selection between the wisent and bovine lineages, which shed a new light on the genome response to different living conditions (temperature, available food resource and pathogen exposure) and on the key gene functions altered by the domestication process.

Evolutionary Biology↗