Genomic insights into differentiation and adaptation of Amorphophallus yunnanensis in the mountainous region of Southwest China

Abstract

The role of geographical isolation and environmental adaptation in driving the differentiation and radiation of species has been a hotspot in evolutionary biology. The extremely complicated and fragmented geography of the mountainous region of Southwest China provides an excellent system for investigating the process of species divergence in heterogeneous habitats. Amorphophallus yunnanensis is a species of extreme habitat preference that resides mainly in the mountainous region of Southwest China. Here, we used restriction site‐associated DNA sequencing (RAD‐seq) to characterize the geographic pattern of genetic variation among 19 populations of A. yunnanensis as well as the genomic basis of environmental adaptation. A pattern of low population genetic diversity and high level of genetic differentiation was observed. The genomic data revealed a clear east–west genetic differentiation, with two distinct genetic lineages corresponding to the Guizhou plateau and Yunnan plateau, respectively. However, we discovered demographic expansion of the Guizhou Plateau lineage and recent hybridization in populations at the contact region. Significant levels of isolation by distance along with isolation by environment were detected. Outlier tests and genome–environment association analyses identified 89 putatively adaptive loci that might play a role in environmental adaptation. Our results suggest that the genetic divergence of A. yunnanensis is attributed to geographical isolation together with divergent selection in the mountainous region of Southwest China.

Phylogeography of Morella nana: The Wumeng Mountains as a natural geographical isolation boundary on the Yunnan‐Guizhou Plateau

“…Some nrDNA chlorotypes occurred across the Wumeng Mts, where the east–west genetic differences became smaller. This phylogeographic pattern may be due to pollen‐mediated high gene flow and secondary contact between east and west groups, which has been reported in other species on YGP and in the mountainous region of Southwest China (Gao et al., 2024 ; Ma et al., 2021 ). However, chlorotype h1 (13 individual plants) was mainly distributed in the east of the Wumeng Mts, and h3 (56 individual plants) exhibited a frequency of 68% and was mainly distributed in the west of the Wumeng Mts.…”

“…Notably, the H d value for M. nana is higher than that of some plants on the YGP Such as, Juglans regia subsp. sigillata (0.203), Amorphophallus yunnanensis (0.341), and Urophysa rockii (0.742; Gao et al., 2024 ; Sun et al., 2019 ; Xie et al., 2017 ). Low chloroplast gene diversity in general shows that species have a relatively short evolutionary history and significant effects of the ice age (Ge, 2001 ; Hewitt, 2000 ).…”

“…The latest research reveals an obvious east–west divergence in genetic structure for Amorphophallus yunnanensis , Juglans regia subsp. Sigillata and Urophysa rockii and found that outliers are significantly related to environmental factors (e.g., altitudes) between east and west on the YGP and adjacent areas (Gao et al., 2024 ; Sun et al., 2019 ; Xie et al., 2017 ). The regional isolation and differences are significant, forming a unique topographic and ecological environment whose evolution has specific regional characteristics as well as global significance on the YGP (Tong et al., 1994 ; Xue et al., 2010 ).…”

“…The obvious spatial and ecological isolation of the YGP makes it an ideal region to study genetic variations and phylogeographical patterns in plants, and researchers have previously identified an east–west divergence in the phylogeographical pattern for some species, such as Juglans regia subsp. sigillata , Urophysa rockii , and Amorphophallus yunnanensis (Gao et al., 2024 ; Sun et al., 2019 ; Xie et al., 2017 ). Despite this, studies on the YGP remain sparse, and little is known about the effects of the geographic isolation caused by the Wumeng Mts on the phylogeographic patterns and genetic structure of plants in this area.…”