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

Abstract

“Sky island” species diversification contributes greatly to mountainous biodiversity. However, the underlying genomic divergence and the inferred drivers remain largely unknown. In this study, we examined the diversification history of five diploid species with three exclusively endemic to the sky islands (mountains) of the Himalaya–Hengduan Mountains biodiversity hotspot. All of them together comprise a clade of the genus Eutrema (Brassicaceae). We resequenced genomes of multiple individuals of the found populations for each species. We recovered the inconsistent phylogenetic relationships between plastome and nuclear‐genome trees for one species. Based on nuclear population genomic data, we detected high genetic divergence between five species with limited gene flow. Four species seemed to diverge mainly through geographical isolation, whereas one arose through hybrid origin. The origins of the sampled five species were dated to within the late Miocene when mountains were uplifted and climates oscillated. All species decreased their population sizes since the inferred origin of each species initially, but only two of them expanded after the Last Glacial Maximum. Together, these findings suggest that geographic isolation plays an important role in driving the sky island species diversification of the sampled species in addition to the occasional gene flow that might have led to the hybrid origin of some sky island species, similar to the species diversification of sea islands.

Evaluating species origins within tropical sky‐islands arthropod communities

“…The present study presents a potential strategy to overcome these challenges, by first delimiting OTUs from mtDNA data, which allowed us to compare diversity patterns among communities without previous taxonomic information, and using a methodology that can be repeated without introducing potential human error from taxonomic assignment of specimens (Emerson et al, 2011). A caveat of generating OTUs from only mtDNA is that with this data it is not possible to detect interspecific hybridization, which may cause inconsistent phylogenetic relationships between plastome and nuclear-genome trees, and is a potential source of new species in sky-islands (Zhang et al, 2019). However, delimiting OTUs based on molecular data allowed us to perform diversity analyses at the 'species' and haplotype levels.…”

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).…”

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

“…A previous research showed that the individuals of Gentiana siphonantha and G. straminea occurred sympatrically or parapatrically might have experienced historical hybridization and gene flow, which could have resulted in genetic homogenization at ITS (Internal Transcribed Spacer DNA) loci and shared cpDNA haplotypes despite well morphological delimitations (Hu et al, 2016). Except for hybridization after speciation due to the second contact, incomplete lineage sorting could also explain these observed genetic variations between and within each morphological units (Wang et al, 2018;Zhang et al, 2019). If hybridization did occur in the contact zone in the current or past of the two species, such introgressions could be clearly detected by population genomic data.…”