Genomic consequences of a recent three‐way admixture in supplemented wild brown trout populations revealed by local ancestry tracts

Abstract

Understanding the evolutionary consequences of human-mediated introductions of domesticated strains into the wild and their subsequent admixture with natural populations is of major concern in conservation biology. However, the genomic impacts of stocking from distinct sources (locally derived vs. divergent) on the genetic integrity of wild populations remain poorly understood. We designed an approach based on estimating local ancestry along individual chromosomes to provide a detailed picture of genomic admixture in supplemented populations. We used this approach to document admixture consequences in the brown trout Salmo trutta, for which decades of stocking practices have profoundly impacted the genetic make-up of wild populations. In southern France, small local Mediterranean populations have been subject to successive introductions of domestic strains derived from the Atlantic and Mediterranean lineages. To address the impact of stocking, we evaluate the extent of admixture from both domestic strains within populations, using 75,684 mapped SNPs obtained from double-digested restriction site-associated DNA sequencing. Then, the chromosomal ancestry profiles of admixed individuals reveal a wider diversity of hybrid and introgressed genotypes than estimated using classical methods for inferring ancestry and hybrid pedigrees. In addition, the length distribution of introgressed tracts retained different timings of introgression between the two domestic strains. We finally reveal opposite consequences of admixture on the level of polymorphism of the recipient populations between domestic strains. Our study illustrates the potential of using the information contained in the genomic mosaic of ancestry tracts in combination with classical methods based on allele frequencies for analysing multiple-way admixture with population genomic data.

Identifying hybrids & the genomics of hybridization: Mallards & American black ducks of Eastern North America

“…First, ADMIXTURE simulations were only able to resolve up to F3/F4 generation as compared to junction simulations that resolved hybrid status up to F9. These results confirm that traditional population assignment programs are reliable in determining several generations of hybrids but can miss‐assign late generational hybrids as parental (Leitwein et al, ). Conversely, junction simulations were unable to detect early hybrids (i.e., F1 hybrids) and were biased toward F3 hybrid status.…”

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

“…Consistent with theoretical predictions (Racimo et al, ), we observed an increase in the number of domestic ancestry haplotypes and a decrease in the mean domestic haplotype length as a function of the number of years since the main stocking event. This corroborates findings by Leitwein et al () who suggested that the mean length of foreign ancestry could be used as a proxy to retrieve the history of stocking practice. We indeed observed a higher number of smaller introgressed domestic haplotypes for the lakes where stocking has stopped earlier in the past.…”

“…Our method may help to consider the potential evolutionary consequences of hybridization in the short and possibly long terms in order to take sound management decisions. Moreover, evaluating the length and distribution of introgressed haplotypes allows determination of the approximate time since hybridization (Duranton, Bonhomme, & Gagnaire, ; Leitwein et al, ) and hybrid categories, which can influence management practices and conservation decisions (Allendorf, Leary, Spruell, & Wenburg, ). Indeed, a population carrying a small proportion of domestic ancestry might be of more interest from a conservation standpoint than a population carrying a stronger one.…”

“…Moreover, evaluating the length and distribution of introgressed haplotypes allows determination of the approximate time since hybridization (Duranton, Bonhomme, & Gagnaire, 2019;Leitwein et al, 2018) and hybrid categories, which can influence management practices and conservation decisions (Allendorf, Leary, Spruell, & Wenburg, 2001).…”

“…Because recombination is expected to progressively reduce the length of introgressed haplotypes across generations following initial admixture (Racimo et al, 2015), the length of introgressed haplotypes can be used as a proxy to estimate the time since hybridization (Gravel, 2012;Racimo et al, 2015). Thus, longer admixture tracts are expected in early hybrids while later hybrid generations tend to display shorter tracts (Leitwein, Gagnaire, Desmarais, Berrebi, & Guinand, 2018;Racimo et al, 2015). Additionally, the local variation in the recombination rate is also expected to affect the introgressed haplotype length with longer and shorter haplotypes expected in lower and higher recombining regions, respectively (Martin & Jiggins, 2017;Racimo et al, 2015).…”