Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae)

• Published in: Molecular biology and evolution Vol. 40; no. 6; p. msad121
• Main Authors: Cao, Yu, Almeida-Silva, Fabricio, Zhang, Wei-Ping, Ding, Ya-Mei, Bai, Dan, Bai, Wei-Ning, Zhang, Bo-Wen, Van de Peer, Yves, Zhang, Da-Yong
• Format: Journal Article
• Language: English
• Published: United States 22.05.2023
• Subjects: Calcium; Calcium Carbonate; Genetic Speciation; Genomics; Juglandaceae; gene flow; population genetics; molecular convergence; ecological speciation; Comparative genomics; walnut family; positive selection; TPC1

When challenged by similar environmental conditions, phylogenetically distant taxa often independently evolve similar traits (convergent evolution). Meanwhile, adaptation to extreme habitats might lead to divergence between taxa that are otherwise closely related. These processes have long existed in the conceptual sphere, yet molecular evidence, especially for woody perennials, is scarce. The karst endemic , and its only congeneric species, . , which is widely distributed in the mountains in East Asia, provide an ideal model for examining the molecular basis of both convergent evolution and speciation. Using chromosome-level genome assemblies of both species, and whole genome resequencing data from 207 individuals spanning their entire distribution range, we demonstrate that . and . form two species-specific clades, which diverged around 2.09 million years ago. We find an excess of genomic regions exhibiting extreme interspecific differentiation, potentially due to long-term selection in . , likely contributing to the incipient speciation of the genus . Interestingly, our results unveil underlying karst adaptation in both copies of the calcium influx channel gene in . . has previously been identified as a selective target in certain karst-endemic herbs, indicating a convergent adaptation to high calcium stress among karst-endemic species. Our study reveals the genic convergence of among karst endemics, and the driving forces underneath the incipient speciation of the two lineages.