Cao, YuAlmeida-Silva, FabricioZhang, Wei-PingDing, Ya-MeiBai, DanBai, Wei-NingZhang, Bo-WenVan de Peer, YvesZhang, Da-Yong2024-04-122024-04-122023-06Yu Cao, Fabricio Almeida-Silva, Wei-Ping Zhang, Ya-Mei Ding, Dan Bai, Wei-Ning Bai, Bo-Wen Zhang, Yves Van de Peer, Da-Yong Zhang, Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae), Molecular Biology and Evolution, Volume 40, Issue 6, June 2023, msad121, https://doi.org/10.1093/molbev/msad121.0737-4038 (print)1537-1719 (online)10.1093/molbev/msad121http://hdl.handle.net/2263/95491DATA AVAILABILITY : All sequencing data used in this study have been deposited at GenBank under the accession PRJNA356989. The reference genome and gene annotations have also been deposited on the website (http://cmb.bnu.edu.cn/juglans). All codes used for the main analyses in this paper are available for download from https://github.com/Caoyu819/protocols-for-karst-adaptation-of-Platycarya.git.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 Platycarya longipes and its only congeneric species, Platycarya strobilacea, 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 P. longipes and P. strobilacea 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 P. longipes, likely contributing to the incipient speciation of the genus Platycarya. Interestingly, our results unveil underlying karst adaptation in both copies of the calcium influx channel gene TPC1 in P. longipes. TPC1 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 TPC1 among karst endemics and the driving forces underneath the incipient speciation of the two Platycarya lineages.en© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This article is available under the Creative Commons CC-BY-NC license.Comparative genomicsEcological speciationGene flowMolecular convergencePositive selectionPopulation geneticsWalnut familyTPC1SDG-15: Life on landArticle