Ancient hybridization patterns between bighorn and thinhorn sheep

Abstract

Vertical transmission of genomic information does not always offer a complete picture of the evolutionary history of species.Gene trees are often discordant from species trees, and mechanisms leading to discordance, such as hybridization and incomplete lineage sorting (ILS), are missed due to a lack of comprehensive genomic sequences (Bravo et al., 2019;Payseur & Rieseberg, 2016).The advancement of high-throughput whole-genome sequencing technologies and computation efficiency has brought new opportunities for understanding how speciation has happened through-

Development of a high-density sub-species-specific targeted SNP assay for Rocky Mountain bighorn sheep (Ovis canadensis canadensis)

“…The development of this assay was facilitated by the cross-species application of the domestic sheep genome ( Bunch et al, 2006 ) to Rocky Mountain bighorn sheep, further exemplifying the utility of genomic resources for studies of closely related wild species ( Li et al, 2019 ; Santos et al, 2021 ; Sim & Coltman, 2019 ). Additionally, our study contributes to the growing number of successful applications of ATG and SPET in non-human mammals ( Andrews et al, 2021 ; Gavriliuc et al, 2022 ) and other species ( Saber et al, 2017 ; Scaglione et al, 2019 ; Vu et al, 2023 ), proving to be a viable option for low-cost, high-throughput, high-density SNP genotyping.…”

“…However, for some non-model species genomic information from other closely related species can be used. For example, genomic resources developed for the domestic cat and sheep have been applied to their wild counterparts ( Li et al, 2019 ; Santos et al, 2021 ; Sim & Coltman, 2019 ). Thus, for wild species for which a genome of a closely related species and SNP or genomic regions of interest are known for the target species or closely related species, targeted-GBS is a viable high-density SNP genotyping technology.…”

Seeing the whole picture: What molecular ecology is gaining from whole genomes

“…Whole genome sequencing of different host species of Rhagoletis fruit flies highlighted the horizontal transfer of Wolbachia strains between hosts (Wolfe et al, 2021). Lastly, Santos et al (2021) uncover a robust species tree between bighorn and thinhorn sheep, however the use of whole genomes demonstrated genealogical discordance throughout their genomes and evidence of ancient hybridization with implications for adaptation. WGS data is increasingly painting a complex picture of evolution that challenges basic bifurcating tree models.…”

Editorial 2022

“…These papers demonstrate that, even with samples from just a few individuals, WGS can be used to detect shifts in historical effective population size along with signatures of gene flow and isolation (Foote et al, 2021; Sarabia et al, 2021; Taylor, Manseau, et al, 2021; Torres Vilaça et al, 2021; Vershinina et al, 2021). At shallower timescales, WGS data can also be used to disentangle complex evolutionary processes such as the adaptive roles of introgression (Comeault et al, 2021; Errbii et al, 2021), hybridization (Santos et al, 2021), horizontal gene transfer (Wolfe et al 2021), and low recombining regions (Purcell et al, 2021) such as inversions (Owens et al, 2021). A final manuscript on this topic provides a comprehensive review of how the particular advantages of WGS compared to RRL allow for a fine‐scale picture of the evolutionary history of invasive species (North et al, 2021).…”