Data from: Evolutionary history of Lost World frogs (Ph.D. thesis)

The Lost World of South America is a unique landscape of flattop mountains that are home to hundreds of endemic species. These flattop mountains, or tepuis, were formed after millions of years of erosion of the high-altitude Guiana Shield plateau. The tepui summits, isolated by their surrounding cliffs that can be up to 1000 m tall, are thought of as “islands in the sky,” harboring relict flora and fauna that underwent vicariant speciation due to plateau fragmentation. High endemicity atop tepui summits supports the idea of an ancient “Lost World” biota. However, recent work suggests dispersal between lowlands and summits occurred long after tepui formation, but neither view (i.e., ancient vicariance vs. recent dispersal) has strong empirical support owing to a lack of studies. I tested diversification hypotheses of the Guiana Shield highlands by estimating divergence times of Tepuihyla, a Guiana Shield endemic genus. Diversification among the different species did not support the Lost World Hypothesis of summit diversification, but rather recent dispersal approximately 50 million years after tepuis formed. This study was the first to explicitly test these hypotheses with a tepui endemic vertebrate, and as such a significant contribution to our understanding of the evolutionary history of this region. After increasing sampling, I focused on three of the most recently diverged lineages of Tepuihyla, in order to examine population genetics, phylogeography, and species delimitation atop these summits. I found high levels of lineage sorting in spite of low divergences in both nuclear and mitochondrial genes. I also found an unexpected pattern of nuclear versus mitochondrial diversity, suggesting the possibility of a recent mitochondrial selective sweep. Species delimitation analyses support the existence of a cryptic, undescribed summit species. Finally, I obtained a Single Nucleotide Polymorphism matrix with next-generation sequencing in order to observe more fine-scale population structure atop the Chimantá massif, a formation composed of ten tepui summits and intermediate altitudes separating them. I found high levels of population structure and assignment atop different tepui summits on the massif, indicating that even at extremely low levels of divergence the landscape complexity may be fomenting population isolation even at the smaller scale of within-massif divergences.“南美失落世界”是一片独特的平顶山地貌，栖息着数百种特有物种。这些平顶山，或称特普伊山（tepui），是经数百万年对高海拔圭亚那地盾（Guiana Shield）高原的侵蚀作用形成的。特普伊山顶被最高可达1000米的周边悬崖所隔绝，被视作“天空中的岛屿”，承载着因高原破碎而发生异域成种（vicariant speciation）的孑遗动植物。特普伊山顶极高的特有性支持了“失落世界”古生物区系的假说。然而，近期研究表明，低地与山顶之间的扩散发生在特普伊山形成之后很久，但由于相关研究匮乏，两种观点（即古老异域成种与近期扩散）均缺乏强有力的实证支持。 本研究通过估算圭亚那地盾特有属——特普伊雨蛙属（Tepuihyla）的分化时间，检验了圭亚那高地的多样化演化假说。不同物种间的多样化结果并不支持山顶多样化的“失落世界假说”，而是支持特普伊山形成约5000万年后发生的近期扩散事件。本研究首次以特普伊特有脊椎动物为对象，明确检验了上述假说，因此为理解该区域的演化历史做出了重要贡献。 在扩大采样规模后，本研究聚焦于特普伊雨蛙属中三个最近分化的支系，以探究这些山顶的种群遗传学、系统地理学（phylogeography）及物种界定问题。研究发现，尽管核基因与线粒体基因的分化程度较低，但支系分选（lineage sorting）水平较高。同时还观察到核基因与线粒体多样性间的异常模式，提示存在近期线粒体选择性清除（selective sweep）的可能性。物种界定分析支持存在一种隐秘的、尚未被描述的山顶物种。 最后，本研究通过下一代测序获得了单核苷酸多态性（Single Nucleotide Polymorphism, SNP）矩阵，以更精细地观察钦坦萨山块（Chimantá massif）的种群结构。该山块由10座特普伊山顶及其间的过渡海拔区域构成。研究发现，该山块内不同特普伊山顶的种群结构与个体归属均呈现高度分化，表明即便在极低的遗传分化水平下，景观复杂性也可能在山块内部的小尺度范围内推动种群隔离。