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

Abstract

Having a comprehensive understanding of population structure, genetic differentiation and demographic history is important for the conservation and management of threatened species. High‐throughput sequencing (HTS) provides exciting opportunities to address a wide range of factors for conservation genetics. Here, we generated HTS data and identified 266,884 high‐quality single nucleotide polymorphisms from 82 individuals of Cupressus chengiana, to assess population genomics across the species' full range, comprising the Daduhe River (DDH), Minjiang River (MJR) and Bailongjiang River (BLJ) catchments in western China. admixture, principal components analysis and phylogenetic analyses indicated that each region contains a distinct lineage, with high levels of differentiation between them (DDH, MJR and BLJ lineages). MJR was newly distinguished compared to previous surveys, and evidence including coalescent simulations supported a hybrid origin of MJR during the Quaternary. Each of these three lineages should be recognized as an evolutionarily significant unit (ESU), due to isolation, differing genetic adaptations and different demographic history. Currently, each ESU faces distinct threats, and will require different conservation strategies. Our work shows that population genomic approaches using HTS can reconstruct the complex evolutionary history of threatened species in mountainous regions, and hence inform conservation efforts, and contribute to the understanding of high biodiversity in mountains.

Molecular Signatures of Reticulate Evolution within the Complex of European Pine Taxa

“…Additionally, coalescent estimations helped us infer both the magnitude and relative timing of gene flow between species, which suggests that secondary contact was possible long after species divergence. Similar findings in different conifer systems confirm that reproductive barriers between congeners in this group are weak and reticulate speciation is not only possible but often influences patterns of species diversity in this genus [25,77,78]. Our data indicate that the pattern of introgression is not symmetric between taxa, and in general, stronger gene flow was estimated from representatives of the P. mugo complex to P. sylvestris than in the opposite direction.…”

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).…”

Population Transcriptomics Reveals Gene Flow and Introgression Between Two Non-sister Alpine Gentians

“…In addition, such hybridizations might have also occurred between closely related species or intra-specific lineages of other genera in the QTPsl because of the Quaternary climatic oscillations (Liu et al, 2014). For example, hybridizations occurred and even one hybrid lineage originated in the genus Cupressus when two parental lineages overlapped their distributions during this stage (Li et al, 2020).…”

“…In addition, a few natural hybrids between G. siphonantha and G. straminea have been reported in their sympatric regions (Li et al, 2008). Population transcriptomics has been widely employed to infer the timing and prevalence of gene flow induced by interlineage hybridization (Ru et al, 2018;Ma et al, 2019;Wang et al, 2019;Li et al, 2020). Here, we aimed to address (i) whether gene flow between G. siphonantha and G. straminea can be detected using population transcriptomic data and (ii) whether gene flow between these two species is related to range expansion.…”