Data from: Long-term in situ persistence of biodiversity in tropical sky-islands revealed by landscape genomics

Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (1) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation, and; (2) the mountain areas may have allowed long-term population persistence during global climate fluctuations. These two phenomena have been studied using either species occurrence data or estimating species divergence times. However, only few studies have used intraspecific genetic data to analyse the mechanisms by which endemism may emerge at the microevolutionary scale. Here, we use landscape analysis of genomic SNP data sampled from two high-elevation plant species from an archipelago of tropical sky-islands (the Transmexican Volcanic Belt) to test for population genetic differentiation, synchronous demographic changes and habitat persistence. We show that genetic differentiation can be explained by the degree of glacial habitat connectivity among mountains, and that mountains have facilitated the persistence of populations throughout glacial/interglacial cycles. Our results support the ongoing role of tropical mountains as cradles for biodiversity by uncovering cryptic differentiation and limits to gene flow.

热带山地是物种丰富度与特有性（endemism）极高的区域。已有两类历史现象被证实促成了这一格局：其一，生境的碎片化与隔离化可能推动了种群的遗传分化，提升了种群异域分化（allopatric divergence）与物种形成（speciation）的发生可能性；其二，山地环境或可在全球气候波动期间为种群提供长期存续的条件。过往针对这两类现象的研究，多采用物种出现数据或物种分化时间估算的方法，但仅有少数研究借助种内遗传数据，解析特有性在微进化尺度下的形成机制。本研究针对热带天空群岛（sky-islands，跨墨西哥火山带（Transmexican Volcanic Belt））分布的两种高海拔植物类群，采集其基因组单核苷酸多态性（SNP）数据并开展景观遗传学分析，以此检验种群遗传分化、同步种群动态变化与生境存续性三个假说。研究结果表明，种群遗传分化可由山地间冰期生境连通程度予以解释，且山地环境助力种群在完整的冰期/间冰期循环中得以存续。本研究通过揭示隐秘分化（cryptic differentiation）与基因流（gene flow）限制，证实热带山地至今仍扮演着生物多样性摇篮的角色。