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 SNP s 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.

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