The role of recombination on genome‐wide patterns of local ancestry exemplified by supplemented brook charr populations

Abstract

Assessing the immediate and long‐term evolutionary consequences of human‐mediated hybridization is of major concern for conservation biology. Several studies have documented how selection in interaction with recombination modulates introgression at a genome‐wide scale, but few have considered the dynamics of this process within and among chromosomes. Here, we used an exploited freshwater fish, the brook charr (Salvelinus fontinalis), for which decades of stocking practices have resulted in admixture between wild populations and an introduced domestic strain, to assess both the temporal dynamics and local chromosomal variation in domestic ancestry. We provide a detailed picture of the domestic ancestry patterns across the genome using about 33,000 mapped single nucleotide polymorphisms genotyped in 611 individuals from 24 supplemented populations. For each lake, we distinguished early‐ and late‐generation hybrids using information regarding admixture tracts. To assess the selective outcomes following admixture we then evaluated the relationship between recombination and admixture proportions at three different scales: the whole genome, chromosomes and within 2‐Mb windows. This allowed us to detect a wide range of evolutionary mechanisms varying along the genome, as reflected by the finding of favoured or disfavoured introgression of domestic haplotypes. Among these, the main factor modulating local ancestry was probably the presence of deleterious recessive mutations in the wild populations, which can be efficiently hidden to selection in the presence of long admixture tracts. Overall, our results emphasize the relevance of taking into consideration local ancestry information to assess both the temporal and the chromosomal variation in local admixture ancestry toward better understanding post‐hybridization evolutionary outcomes.

Hybridization underlies localized trait evolution in cavefish

“…Hybrid genomes exhibit a mosaic of ancestry from their parental populations. A number of recent studies have shown that hybridization interacts with recombination and selection to shape patterns of local ancestry along chromosomes ( Hohenlohe et al., 2012 ; Wang et al., 2016 ; Janzen et al., 2018 ; Schumer et al., 2018 ; Leitwein et al., 2019 ). Non-random distributions of local ancestry in hybrid populations can indicate selection.…”

Population genomics for wildlife conservation and management

“…Additionally, mapping genomic data onto a reference genome assembly can identify chromosomal tracts of ancestry. Because these blocks of ancestry break down through recombination following a hybridization event, the distribution of their sizes can be used to infer the history of hybridization and admixture in wildlife species, as well as evidence for selection in admixed genomes (e.g., Leitwein et al, 2018Leitwein et al, , 2019. long-term viability, potential for increases in distribution or population size, and extinction probability.…”

Hybridization underlies localized trait evolution in cavefish

“…Hybrid genomes exhibit a mosaic of ancestry from their parental populations. A number of recent studies have shown that hybridization interacts with recombination and selection to shape patterns of local ancestry along chromosomes [83][84][85][86][87] . Non-random distributions of local ancestry in hybrid populations can indicate selection.…”