Data from: Did geckos ride the Palawan raft to the Philippines?

AIM: We examine the genetic diversity within the lizard genus Gekko in the Philippine islands to understand the role of geography and geological history in shaping species diversity in this group. We test multiple biogeographical hypotheses of species relationships, including the recently proposed Palawan Ark hypothesis. LOCATION: Southeast Asia and the Philippines. METHODS: Samples of all island endemic and widespread Philippine Gekko species were collected and sequenced for one mitochondrial gene (NADH dehydrogenase subunit 2) and one nuclear gene (phosducin). We used maximum likelihood and Bayesian phylogenetic methods to derive the phylogeny. Divergence time analyses were used to estimate the time tree of Philippine Gekko to test biogeographical predictions of species relationships. The phylogenetic trees from the posterior distribution of the Bayesian analyses were used for testing biogeographical hypotheses. Haplotype networks were created for the widespread species Gekko mindorensis to explore genetic variation within recently divergent clades. RESULTS: Both maximum likelihood and Bayesian phylogenetic analyses indicated that Philippine Gekko species are a diverse clade with a long history in the archipelago. Ancestral range reconstruction and divergence time analyses suggest a Palawan microcontinental origin for this clade, coinciding with Palawan’s separation from Asia beginning 30 Ma, with subsequent diversification in the oceanic Philippine Islands. The widespread species G. mindorensis and G. monarchus diversified in the late Miocene/early Pliocene and are potentially complexes of numerous undescribed species. MAIN CONCLUSIONS: The view of the Philippine islands as a “fringing archipelago” does not explain the pattern of species diversity in the genus Gekko. Philippine Gekko species have diversified within the archipelago over millions of years of isolation, forming a large diverse group of endemic species. Furthermore, the Philippine radiation of gekkonid lizards demonstrates biogeographical patterns most consistent with stochastic colonization followed by in situ diversification. Our results reveal the need to consider deeper time geological processes and their potential role in the evolution of some Philippine terrestrial organisms.

研究目的：本研究以菲律宾群岛睑虎属（Gekko）类群为研究对象，解析其内部遗传多样性，旨在厘清地理因素与地质历史对该类群物种多样性形成的调控机制，并检验多项关于物种演化关系的生物地理学假说，其中包括新近提出的巴拉望方舟假说（Palawan Ark Hypothesis）。
研究区域：东南亚及菲律宾群岛。
研究方法：本研究采集了所有菲律宾特有及广布的睑虎属物种样本，对1个线粒体基因——烟酰胺腺嘌呤二核苷酸脱氢酶亚基2（NADH dehydrogenase subunit 2），以及1个核基因——磷脱蛋白（phosducin）进行了测序。我们采用最大似然法与贝叶斯系统发育分析方法构建系统发育树；通过分化时间分析估算菲律宾睑虎属的时间树，以验证物种演化关系的生物地理学预测；同时利用贝叶斯分析后验分布中的系统发育树开展生物地理学假说检验。针对广布物种明多罗睑虎（Gekko mindorensis）构建单倍型网络，以探究新近分化支系内的遗传变异情况。
研究结果：最大似然法与贝叶斯系统发育分析均显示，菲律宾睑虎属物种构成一个物种丰富的演化支系，在菲律宾群岛拥有悠久的演化历史。祖先分布区重建与分化时间分析表明，该支系起源于巴拉望微大陆，这与巴拉望自亚洲大陆分离的时间（约30 Ma）相吻合，随后在大洋型菲律宾群岛中发生了适应性分化。广布物种明多罗睑虎（G. mindorensis）与君主睑虎（G. monarchus）于中新世晚期/上新世早期发生分化，它们极有可能是包含多个未描述物种的复合群。
主要结论：将菲律宾群岛视为“边缘群岛”的传统观点无法解释睑虎属的物种多样性分布格局。菲律宾睑虎属类群在数百万年的隔离演化过程中于群岛内部发生分化，形成了一个物种丰富的特有类群。此外，菲律宾睑虎科蜥蜴的辐射演化所呈现的生物地理学模式，最符合“随机定植后原地分化”的假说。本研究结果表明，在探讨部分菲律宾陆生生物的演化历程时，需要考虑更深时间尺度的地质过程及其潜在作用。