Data from: The role of geography in adaptive radiation

Although the importance of biogeography in the speciation process is well-recognized, the fundamental role of geographic diversification during adaptive radiations has not been studied to determine its importance during the adaptive radiation process. We examined the relationship between lineage and regional diversification patterns in the South American rodent subfamily Sigmodontinae, one of the best candidates for an adaptive radiation in mammals, to propose a conceptual framework for geographic transitions during adaptive radiations. We reconstructed a time-calibrated phylogeny from four nuclear and one mitochondrial gene for 77% of sigmodontine diversity. Historical biogeography was reconstructed among 14 regions, to which we applied a sliding-window approach to estimate regional transition rates through time. We compared these rate patterns and measured whether regions consisted of species that were more phylogenetically related than expected by chance. Following the initial South American colonization around 7 million years ago, multiple expansions from northern regions correlated with a burst of speciation. Subsequently, both diversification and regional transition rates decreased overall and within the majority of regions. Despite high regional transition rates, nearly all regional assemblages were phylogenetically clustered, indicating within-region diversification was common. We conclude that biogeographic complexity and partitioning played a profound role in the adaptive radiation of the South American Sigmodontinae (Oryzomyalia), the degree to which is determined by the relative scales of spatial variation and dispersal abilities.

尽管生物地理学在物种形成过程中的重要性已得到学界广泛认可，但适应辐射（adaptive radiation）进程中地理分化的核心作用，尚未有研究明确其在该辐射过程中的实际重要性。本研究以哺乳动物适应辐射的最佳候选类群之一——南美啮齿类棉鼠亚科（Sigmodontinae）为研究对象，分析支系分化与区域分化模式的关联，旨在提出适应辐射过程中地理转变的概念框架。我们针对覆盖77%棉鼠亚科物种多样性的类群，基于4个核基因与1个线粒体基因序列重建了时间校准的系统发育树（time-calibrated phylogeny）。研究选取14个区域开展历史生物地理学重建，并采用滑动窗口方法估算各区域随时间变化的物种转移速率。我们对比了这些速率模式，并检测各区域内的物种是否比随机预期的情况具有更近的系统发育亲缘关系。在约700万年前首次殖民南美之后，从北部区域发起的多次扩张与物种形成爆发存在显著相关性。后续研究发现，无论是整体还是多数区域内，物种分化与区域转移速率均整体呈下降趋势。尽管区域间转移速率较高，但几乎所有区域的物种组合均呈现系统发育聚集特征，表明区域内分化现象普遍存在。本研究得出结论：生物地理学复杂性与区域分化在南美棉鼠亚科（Sigmodontinae，Oryzomyalia）的适应辐射中发挥了深远作用，其影响程度由空间变异的相对尺度与物种扩散能力共同决定。