Data from: Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica

Background. Cloud forest, characterized by a persistent, frequent or seasonal low-level cloud cover and a fragmented distribution, is one of the most threatened habitats especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remained in situ or expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials. Although the observed genetic signals of population size changes of cloud forest-adapted species including tree ferns correspond to predicted changes by Pleistocene climate change dynamics, the observed patterns of intraspecific lineage divergence showed temporal incongruence. Methods. Here we combined phylogenetic analyses, ancestral area reconstruction, and divergence time estimates with climatic and altitudinal data (environmental space) for phenotypic traits of tree fern species to make inferences about evolutionary processes in deep time. We used phylogenetic Bayesian inference and geographic and altitudinal distribution of tree ferns to investigate the ancestral area and elevation and environmental preferences of Mesoamerican tree ferns. The phylogeny was then used to estimate divergence times and ask whether the ancestral area and elevation and environmental shifts were linked to climatic events and historical climatic preferences. Results. Bayesian trees retrieved Cyathea, Alsophila, Gymnosphaera and Sphaeropteris in monophyletic clades. Splits for species in these genera found in the Mesoamerican cloud forests are recent, from the Neogene to the Quaternary. Australia was identified as the ancestral area for the clades of these genera, except for Gymnosphaera that was Mesoamerica. Climate tolerance was not divergent from hypothesized ancestors for the four most significant variables or elevation. For elevational shifts we found repeated changes from low to high elevations. Conclusions. Our data suggest that representatives of Cyatheaceae main lineages migrated from Australia to Mesoamerican cloud forests in different times and have persisted in these environmentally unstable areas but extant species diverged recently from their ancestors.背景： 云雾林以持续、频繁或季节性的低层云覆盖以及碎片化分布为典型特征，是受威胁程度最高的生境类型之一，在新热带区（Neotropics）尤为突出。树蕨是这类森林中最为醒目的组成部分之一，而蕨类植物仅能存活于最低气温极少低于冰点、全年降水充足且分布均匀的区域。当前的系统地理学（phylogeographic）数据显示，部分适应云雾林的物种在冰期阶段可维持原地分布或向低地扩张，而在间冰期则发生异域分布收缩。尽管包括树蕨在内的适应云雾林物种所观测到的种群规模变化遗传信号，符合更新世（Pleistocene）气候变化动力学的预测结果，但所观测到的种内谱系分化模式却呈现出时间上的不一致性。 方法： 本研究将系统发育分析、祖先区域重建、分化时间估算，与树蕨物种表型性状的气候及海拔数据（环境空间）相结合，以推演深时尺度下的演化过程。我们采用系统发育贝叶斯推断方法，结合树蕨的地理与海拔分布特征，探究中美洲树蕨的祖先区域、海拔偏好与环境偏好。随后利用该系统发育树估算分化时间，并探讨祖先区域、海拔与环境的转变是否与气候事件及历史气候偏好存在关联。 结果： 贝叶斯系统发育树显示，桫椤属（Cyathea）、白桫椤属（Alsophila）、黑桫椤属（Gymnosphaera）以及笔筒树属（Sphaeropteris）均形成单系支。分布于中美洲云雾林的上述各属物种的分化事件均较为新近，发生于新近纪（Neogene）至第四纪（Quaternary）期间。除黑桫椤属支系的祖先区域为中美洲外，其余各属支系的祖先区域均被推断为澳大利亚。针对四个最具显著性的环境变量及海拔而言，其气候耐受性与推测的祖先类群并无显著差异。在海拔转变模式方面，我们发现存在多次从低海拔向高海拔的转变事件。 结论： 本研究数据表明，桫椤科（Cyatheaceae）主要支系的类群曾在不同时期从澳大利亚迁移至中美洲云雾林，并在这些环境不稳定的区域持续存续，但现存物种与其祖先的分化时间均较晚。