Biology subjects

Pompanon, F.

Publications and source records attributed to Pompanon, F..

5 recordsLinked to original sources

bioRxiv2025

Inferring domestic goat demographic history through ancient genome imputation

Goats were among the earliest managed animals, making them a natural model to explore the genetic consequences of domestication. However, a challenge in ancient genomic analysis is the relatively low genome coverage for most samples, limiting analysis to pseudohaploid genotypes. Genotype imputation offers potential to alleviate this limitation by improving information content and accuracy in low coverage genomes. To test this we used published high coverage (>8x) goat palaeogenomes, imputing downsampled genomes using the VarGoats dataset (1,372 individuals) as a reference panel. Measuring concordance between imputed and high coverage genotypes, we find high concordance after filtering for common (>5%), high confidence variants, with 0.5x genomes reaching >0.97 concordance. There is a trade-off between coverage, genotype probability (GP) thresholds, and genotype recovery, where higher coverage and more lenient GP thresholds result in higher recovery, and a reduction in heterozygous false-positive rates with stricter thresholds. We then imputed 36 goat palaeogenomes with [≥]0.5x coverage to examine runs-of-homozygosity (ROH) and identity-by-descent (IBD) patterns. Using a novel approach combining ROH profiles across tools, we find that among Neolithic goats, ROH increases with distance from the Zagros Mountains, suggesting a large effect of the initial dispersal of managed herds. Inbreeding levels decrease across Southwest Asia in more recent periods. IBD mirrored this pattern, with less relatedness in the early herding site of Ganj Dareh compared to higher relatedness in goats from later in the dispersal process. These findings provide insights into the genetic consequences of early goat management on demography, and confirm the utility of imputation in leveraging low coverage palaeogenomes. SignificancePaleogenomics offers crucial insight into how animals were domesticated, but poor DNA preservation in ancient remains often limits the reach of genetic analyses. We utilise a cutting-edge technique, genotype imputation, to recover missing genetic information from ancient low coverage goat genomes and shine light on their domestication process. Early domestic goats showed low overall runs-of-homozygosity (ROH) and relatedness. We find that during the Neolithic, runs-of-homozygosity (ROH) and relatedness among goats increased, likely a consequence of the movement of herds beyond their natural range by humans. Inbreeding levels decline in more recent periods, potentially due to expanded herd sizes, animal trade networks, or improved husbandry practices. These findings challenge long-standing assumptions about domestication bottlenecks and highlight how ancient DNA can be used to uncover complex evolutionary histories, even from low coverage ancient samples.

genomics↗

bioRxiv2021

Multiple adaptive solutions to face climatic constraints: novel insights in the debate over the role of convergence in local adaptation

The extent to which genomic convergence shapes locally adapted phenotypes in different species remains a fundamental question in evolutionary biology. To bring new insights to this debate we set up a framework which aimed to compare the adaptive trajectories of two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the more than 430 adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different adaptive mechanisms in these two closely related species. Such diversity of adaptive pathways may result from a high number of biological functions involved in adaptation to multiple eco-climatic gradients, and provides more arguments for the role of contingency and stochasticity in adaptation rather than repeatability.

evolutionary biology↗

bioRxiv2021

Local adaptations of Mediterranean sheep and goats through an integrative approach

In a context of climate change, identifying the genes underlying adaptations to extreme environments is essential. Small ruminants are adapted to a wide variety of habitats and thus, are promising study models. Here, we considered 17 goat and 25 sheep local Mediterranean breeds, in Italy, France and Spain. We proposed, and empirically tested a new methodology to highlight selection signatures in relation to the environments. Based on historical archives, we selected the breeds potentially most linked to a territory and defined their original geographical cradle, including transhumant pastoral areas. For both species, the cradles were arranged along latitudinal gradient of aridity and altitude. Then we used the programs PCAdapt and LFMM. Considering cradles, instead of current GPS coordinates, markedly improved the sensitivity of the LFMM analyses. All the results combined with a systematic literature review, revealed a set of genes with potentially key adaptive roles. Some of these genes, have been found implicated in lipid metabolism (SUCLG2, BMP2), hypoxia/heat stress (UBE2R2/UBAP2), lung function (BMPR2), seasonal patterns (SOX2, DPH6) or neuronal function (TRPC4, TRPC6). For the intergenic region between PCDH9 and KLH1, as well as NBEA, identified in both species, the adaptive role could be strong. We found for RXFP2, associated with sheep horn development, and MSRB3 and SLC26A4, both associated with hearing of sheep, a strong association with the environment gradient. We conclude that our new methodology, which considers breeds in their historical, environmental and anthropological context, provides novel and essential information on local breeds and their unique adaptations.

evolutionary biology↗

bioRxiv2020

BAdabouM: a genomic structural variations discovery tool for polymorphism analyses

Genomic Structural Variations (SVs) are known to impact the evolution of genomes and to have consequences on individuals fitness. Nevertheless, they remain challenging to detect in whole genome re-sequencing (WGS) data. Lots of methods detecting SVs are described in the literature but they might be hard to install, have non-trivial settings, do not detect all SVs categories and have generally high levels of false positive. Here we introduce BAdabouM, a fast (C written) and easy to install SVs discovery tool. BAdabouM auto evaluates read length, library size and mean coverage to set thresholds specific to each experiment. BAdabouM interprets multiple SVs signatures (reads aligned with a split, non-concordant mapped pairs or uneven coverage) to detect insertions, deletions, copy number variations, inversions, and translocations at single-nucleotide resolution. When compared with two widely used methods on simulated and real datasets, BAdabouM was faster, exhibited a similar accuracy with a good concordance on SVs detected, and detected significantly more insertions. BAdabouM was more reproducible to detect independently SVs across individuals, which is a clear advantage when characterizing population polymorphism. Furthermore, BAdabouM demonstrated a superior ability to detect breakpoints with a base pair resolution. BAdabouM proved to be efficient, fast and accurate to detect SVs, and handle. BAdabouM is a complementary method to be used for a more comprehensive detection of SVs, and is especially suited for studying polymorphism for all types of SVs with a high accuracy.

bioinformatics↗

bioRxiv2020

Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats

The male-specific part of the Y-chromosome is in mammalian and many other species the longest haplotype that is inherited without recombination. By its paternal transmission it has a small effective population size in species with dominant males. In several species, Y-chromosomal haplotypes are sensitive markers of population history and introgression. Previous studies have identified in domestic goats four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic differentiation and several regional variants. In this study we used published whole-genome sequences of 70 male goats from 16 modern breeds, 11 ancient-DNA samples and 29 samples from seven wild goat species. We identified single-copy male-specific SNPs in four scaffolds, containing SRY, ZFY, DBY with SSX3Y and UTY, and USP9Y with UMN2001, respectively. Phylogenetic analyses indicated haplogroups corresponding to the haplotypes Y1B, Y2A and Y2B, respectively, but Y1A was split into Y1AA and Y1AB. All haplogroups were detected in ancient DNA samples from southeast Europe and, with the exception of Y1AB, in the bezoar goat, which is the wild ancestor of the domestic goats. Combining these data with those of previous studies and with genotypes obtained by Sanger sequencing or the KASP assay yielded haplogroup distributions for 132 domestic breeds or populations. The phylogeographic differentiation indicated paternal population bottlenecks on all three continents. This possibly occurred during the Neolithic introductions of domestic goats to those continents with a particularly strong influence in Europe along the Danubian route. This study illustrates the power of the Y-chromosomal haplotype for the reconstructing the history of mammalian species with a wide geographic range.

genetics↗