Analyses of genome‐scale variation reveal divergence of two Sinalliaria species (Brassicaceae) with continuous but limited gene flow

Abstract

Numerous biogeographic studies have suggested that geographic isolations triggered by Quaternary climatic changes could have contributed greatly to the high species diversity of eastern Asia. However, little is known about how speciation proceeded during the evolutionary divergence of sister species in this region. In this study, we examined genomic divergence and investigated the speciation process of the two species in the genus Sinalliaria endemic to eastern China, S. limprichtiana (Pax) X. F. Jin, Y. Y. Zhou & H. W. Zhang and S. grandifolia (Z. X. An) Huan Hu, com. nov. (Basionym: Alliaria grandifolia Z. X. An (Acta Phytotax. Sin. 23: 396, 1985)). We sequenced the transcriptomes of seven and eight S. limprichtiana and S. grandifolia individuals, respectively. Analysis of transcriptome single nucleotide polymorphism data indicated that both species were well‐delineated with strong genetic differentiation (mean FST = 0.31). A total of 4000 genes showed differential expression between the two species. Based on these genome‐scale nucleotide variations, we used the allele frequency spectrum for modeling analysis with fastsimcoal to gain insights into the speciation process. Our results suggested divergence with continuous gene flow between the two species. These findings will add to our knowledge on the origin of species diversity in eastern Asia.

Genomic insight into “sky island” species diversification in a mountainous biodiversity hotspot

“…In order to distinguish between them, we designed alternative scenarios including bifurcating versus hybrid origin. Our statistical analyses based on allele frequencies supported that E. baimashanicum arose by a hybrid origin between E. heterophyllum and E. deltoideum because this model had a higher likelihood value than other alternative models, although we could not totally exclude incomplete lineage sorting because of the lack of de novo genomes of all species for statistical testing (Wang et al, ). This is also consistent with the recombination of the morphological traits of E. baimashanicum between the other two.…”

Phylotranscriptomics reveals extensive gene duplication in the subtribe Gentianinae (Gentianaceae)

“…In contrast, allopolyploidy arises through hybridization between closely related species, and is especially common among flowering plants (Estep et al, 2014). In addition, interspecific hybridization has been suggested as a major source of phylogenetic discordance between nuclear and organellar genomes (Pelser et al, 2010; Wallis et al, 2017; Lee‐Yaw et al, 2019; Wang et al, 2019; Zhang et al, 2019).…”

“…Although the monophyly of the major lineages in the subtribe Gentianinae (i.e., the six genera and several sections in the genus Gentiana ) has been established, phylogenetic relationships among these lineages remain poorly understood, mostly due to the lack of genome‐scale data and the increase of diversification rates in the subtribe Gentianinae associated with the extension of the QTP sl from the late Eocene to the present (Favre et al, 2016). In addition, natural hybridization is fairly common in the subtribe Gentianinae, especially in Gentiana sections Cruciata , Kudoa , and Pneumonanthe (Li et al, 2008; Struwe & Pringle, 2018), which could blur species boundaries (Vega et al, 2013; Wang et al, 2019) and further obscure phylogenetic inference based on relatively few genetic loci (Som, 2015; Zhang et al, 2019).…”

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

“…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.…”