Biology subjects

Lucotte, E.

Publications and source records attributed to Lucotte, E..

3 recordsLinked to original sources

bioRxiv2025

EASYstrata: a new workflow to infer evolutionary strata along sex chromosomes and other supergenes

New reference genomes and transcriptomes are increasingly available across the tree of life, opening new avenues to tackle exciting questions. However, there are still challenges associated with annotating genomes and inferring evolutionary processes and with a lack of methodological standardisation. Here, we propose a new workflow designed for evolutionary analyses to overcome these challenges, facilitating the detection of recombination suppression and its consequences in terms of rearrangements and transposable element accumulation. To do so, we assemble multiple bioinformatic steps in a single easy-to-use workflow. We combine state-of-the-art tools to detect transposable elements, annotate genomes, infer gene orthology relationships, compute divergence between sequences, infer evolutionary strata (i.e., footprints of stepwise extension of recombination suppression) and their structural rearrangements, and visualise the results. This workflow, called EASYstrata, was applied to reannotate 42 published genomes from Microbotryum fungi. We show in further case examples from a plant and an animal that we recover the same strata as previously described. While this tool was developed with the goal to infer divergence between sex or mating-type chromosomes, it can be applied to any pair of haplotypes whose patteern of divergence is of interest. This workflow will facilitate the study of non-model species for which newly sequenced phased diploid genomes are becoming available. Contactquentinrougemont@orange.fr

genomics↗

bioRxiv2022

Extraordinary selection on the human X chromosome associated with archaic admixture

The X chromosome in non-African human populations shows less diversity and less Neanderthal introgression than expected under the standard neutral model. We analyzed 162 X chromosomes from human males worldwide and discovered 14 chromosomal regions where haplotypes of several hundred kilobases rapidly rose to high frequencies in non-Africans. These observations cannot be explained by neutral genetic drift in realistic demographic scenarios and are only consistent with partial selective sweeps produced by strong selection. Using an approach for inferring individual Neanderthal-derived haplotypes, which do not rely on an archaic reference genome, we further discover that the swept haplotypes are devoid of the archaic ancestry otherwise typical of the affected chromosomal regions. The ancient Ust-Ishim male carries its expected proportion of these haplotypes, implying that the sweeps must have occurred between 45,000 and 55,000 years ago. Finally, we find that the chromosomal positions of sweeps overlap previously reported hotspots of selection in great ape evolution. We propose that this puzzling combination of observations points to a general mechanism of positive selection unique to the X chromosome.

evolutionary biology↗

bioRxiv2018

Strong selective sweeps before 45,000BP displaced archaic admixture across the human X chromosome

The X chromosome in non-African populations has less diversity and less Neanderthal introgression than expected. We analyzed X chromosome diversity across the globe and discovered seventeen chromosomal regions, where haplotypes of several hundred kilobases have recently reached high frequencies in non-African populations only. The selective sweeps must have occurred more than 45,000 years ago because the ancient Ust-Ishim male also carries its expected proportion of these haplotypes. Surprisingly, the swept haplotypes are entirely devoid of Neanderthal introgression, which implies that a population without Neanderthal admixture contributed the swept haplotypes. It also implies that the sweeps must have happened after the main interbreeding event with Neanderthals about 55,000 BP. These swept haplotypes may thus be the only genetic remnants of an earlier out-of-Africa event.\n\nOne Sentence SummaryAfter humans expanded out of Africa, the X chromosome experienced a burst of extreme natural selection that removed Neanderthal admixture.

genomics↗