Data from: Spatial patterns of AFLP diversity in Bulbophyllum occultum (Orchidaceae) indicate long-term refugial isolation in Madagascar and long-distance colonization effects in La Réunion

Bulbophyllum occultum, an epiphytic orchid mainly distributed in the rainforests of (north)eastern Madagascar and La Réunion, represents an interesting model case for testing the effects of anthropogenic vs historical (e.g., climate-induced) habitat isolation and long-distance colonization on the genetic structure of plant species with disjunct distributions in the Madagascan region. To this aim, we surveyed amplified fragment length polymorphisms (AFLPs) across 13 populations in Madagascar and nine in La Réunion (206 individuals in total). We found overall high levels of population subdivision (PT = 0.387) and low within-population diversity (HE, range: 0.026-0.124), indicating non-equilibrium conditions in a mainly selfing species. There was no impact of recent deforestation (Madagascar) or habitat disturbance (La Réunion) detectable on AFLP diversity. K-means clustering and BARRIER analyses identified multiple gene pools and several genetic breaks, both within and among islands. Inter-island levels of population genetic diversity and subdivision were similar, whereby inter-individual divergence in flower colour explained a significant part of gene pool divergence in La Réunion. Our results suggest that (i) B. occultum persisted across multiple isolated ('refugial') regions along the eastern rainforest corridor of Madagascar over recent climatic cycles; and (ii) populations in La Réunion arose from either single or few independent introductions from Madagascar. High selfing rates and sufficient time for genetic drift likely promoted unexpectedly high population genetic and phenotypic (flower colour) differentiation in La Réunion. Overall, this study highlights a strong imprint of history on the genetic structure of a low-gene-dispersing epiphytic orchid from the Madagascan region.隐序石豆兰（Bulbophyllum occultum）是一种附生兰，主要分布于马达加斯加东北部及留尼旺的热带雨林中，是探究人为与历史（如气候驱动的）生境隔离、长距离定植对马达加斯加地区间断分布植物物种遗传结构影响的理想模型体系。为此，本研究针对马达加斯加的13个种群与留尼旺的9个种群（总计206个个体）开展了扩增片段长度多态性（Amplified Fragment Length Polymorphisms, AFLPs）分析。研究发现，该物种整体种群分化程度较高（Φ_PT=0.387），种群内多样性偏低（期望杂合度H_E范围为0.026~0.124），表明这一主要自交物种处于遗传非平衡状态。近期的森林砍伐（马达加斯加）或生境干扰（留尼旺）未对AFLP多样性产生可检测的影响。K-means聚类与BARRIER分析鉴定出多个基因库，且在岛屿内部及岛屿之间均存在多处遗传断裂带。岛间种群的遗传多样性与分化水平相近，而留尼旺种群内花颜色的个体间差异可解释基因库分化的显著部分。本研究结果表明：（1）隐序石豆兰在近期的气候周期中，于马达加斯加东部雨林廊道沿线的多个隔离（‘避难所’）区域持续存续；（2）留尼旺的种群均源自马达加斯加的单次或少数几次独立定植事件。较高的自交率与充足的遗传漂变时间，可能推动了留尼旺种群出现意料之外的高水平种群遗传与表型（花颜色）分化。总体而言，本研究揭示了历史因素对马达加斯加地区低基因扩散能力附生兰遗传结构的强烈印记。