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。已有两种历史现象或可促成这一特征：其一，生境破碎化与隔离可能推动种群产生遗传分化，提升了异域分化（allopatric divergence）与物种形成的可能性；其二，山地或可在全球气候波动期间为种群提供长期存续的环境。过往针对这两种现象的研究多采用物种分布数据或物种分化时间估算方法，但仅有少数研究借助种内遗传数据，在微观进化尺度上解析特有性的形成机制。本研究以位于跨墨西哥火山带（Transmexican Volcanic Belt）的热带天空岛（sky-islands）群岛中的两种高海拔植物为研究对象，通过其基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据的景观遗传学分析，检验种群遗传分化、同步种群动态变化与生境存续情况。研究结果表明，种群遗传分化程度可通过山地间的冰期生境连通性予以解释，且山地在冰期/间冰期循环中助力种群持续存续。本研究通过揭示隐存分化与基因流限制，佐证了热带山地作为生物多样性摇篮的持续作用。