Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process

Abstract

An increasing number of species are thought to have originated by homoploid hybrid speciation (HHS), but in only a handful of cases are details of the process known. A previous study indicated that Picea purpurea, a conifer in the Qinghai–Tibet Plateau (QTP), originated through HHS from P. likiangensis and P. wilsonii. To investigate this origin in more detail, we analysed transcriptome data for 114 individuals collected from 34 populations of the three Picea species from their core distributions in the QTP. Phylogenetic, principal component and admixture analyses of nuclear SNPs showed the species to be delimited genetically and that P. purpurea was admixed with approximately 60% of its ancestry derived from P. wilsonii and 40% from P. likiangensis. Coalescent simulations revealed the best‐fitting model of origin involved formation of an intermediate hybrid lineage between P. likiangensis and P. wilsonii approximately 6 million years ago (mya), which backcrossed to P. wilsonii to form P. purpurea approximately one mya. The intermediate hybrid lineage no longer exists and is referred to as a “ghost” lineage. Our study emphasizes the power of population genomic analysis combined with coalescent analysis for reconstructing the stages involved in the origin of a homoploid hybrid species over an extended period. In contrast to other studies, we show that these stages can in some instances span a relatively long period of evolutionary time.

Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut

“…Today, Persian walnut can readily hybridize with both black walnut and butternuts (Xu et al 2007;Woeste and Michler 2011;Shu et al 2016), suggesting no inherent reproductive barriers with congeners. Although the number of cases of homoploid hybrid speciation is increasing (Sun et al 2014;Elgvin et al 2017;Lamichhaney et al 2018;Ru et al 2018), information is still lacking that would link the presence of hybrid ancestry in the genome to the process of speciation by hybridization (Schumer et al 2014). Perhaps the criteria for homoploid hybrid speciation are too stringent, causing researchers to overlook important contributions of hybridization to evolution and speciation (Nieto Feliner et al 2017).…”

Allopatric divergence and hybridization withinCupressus chengiana(Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China

“…We used vcftools (Danecek et al, 2011) and a perl script (Ru et al, 2018) to estimate the value of Tajima's D , population genetic differentiation ( F ST ), absolute differentiation ( D XY ) and nucleotide diversity ( π , for all callable sites). To keep rare variants, the MAF control was not performed for the data set that was used to calculate Tajima's D and π .…”

Genomic insights into adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis (Circaeasteraceae, Ranunculales)

“…Hence, the absolute differentiations ( D XY ) among genetic groups also were measured using a Perl script provided by Ru et al . (2018) (Li et al ., 2020). Finally, we assessed the contemporary effective population sizes ( N e ) for each population and group using NeEstimator v.2.1 (Do et al ., 2014).…”

“…Table S1 1 Paired mean D XY among genetic groups using a Perl script provided by Ru et al . (2018). Table S1 2 Detailed annotation information of 16 genes under potential divergent selection.…”