Data_Sheet_2_Deep Genomic Divergence and Phenotypic Admixture of the Treefrog Dendropsophus elegans (Hylidae: Amphibia) Coincide With Riverine Boundaries at the Brazilian Atlantic Forest.docx

The Atlantic Forest (AF) domain is one of the Earth’s biodiversity hotspots, known for its high levels of species diversity and endemism. Factors related to palaeoenvironmental dynamics, such as the establishment of vegetational refugia and river basins, have different impacts on biological communities and biodiversity patterns in this domain. Here, we sample genome-wide RADseq data from a widespread treefrog (Dendropsophus elegans), inhabiting natural and human-impacted ecosystems at the Brazilian AF to test the impact of riverine boundaries and climatic refugia on population structure and diversification. We estimate divergence times and migration rate across identified genetic breaks related to the rivers Doce, Paraíba do Sul, Ribeira de Iguape, and Paraguaçu, known to represent barriers to gene flow for other AF endemic species, and test the role of climatic refugia. Finally, we investigate the impact of spatio-temporal population history on morphological variation in this species. We recovered a phylogeographic history supporting three distinct clades separated into two geographically structured populations, corresponding to the north and south of AF. In addition, we identified an admixture zone between north and south populations in the latitude close to the Doce River. Our findings support a pattern of isolation-by-distance and the existence of a secondary contact zone between populations, which might have been promoted by gene flow during population expansion. Further, we found support for models considering migration parameters for all the tested rivers with different population divergence times. Based on the species history and the AF palaeoenvironmental dynamics, we corroborate the role of forest refugia impacting population structure for this species through recent range expansion after the Last Glacial Maximum (LGM). The Doce and Paraíba do Sul Rivers coincide with the main genetic breaks, suggesting they might also have played a role in the diversification processes. Finally, despite finding subtle correlations for phenotypic data among different populations, variation is not strongly detectable and does not seem associated with speciation-level processes that could warrant taxonomic changes. Such results can be explained by phenotypic plasticity of the evaluated traits and by recent divergence times, where there has been insufficient time and weak selective pressures to accumulate enough phenotypic differences.

大西洋森林（AF）区域是全球生物多样性热点之一，以其物种多样性和特有性而闻名。与古环境动力学相关的因素，例如植被避难所和流域的形成，对这一区域生物群落和生物多样性模式产生不同的影响。在本研究中，我们从广泛分布的树蟾（Dendropsophus elegans）中采集全基因组RADseq数据，该树蟾栖息于巴西大西洋森林的自然和受人类影响生态系统中，以检验河流边界和气候避难所对种群结构和多样化的影响。我们估计了与多斯河、帕拉伊巴河、里贝拉伊瓜佩河和巴拉瓜苏河相关的遗传断裂处的分化时间以及迁移率，这些河流被认为是其他AF特有物种基因流障碍，并测试了气候避难所的作用。最后，我们研究了时空种群历史对该物种形态变异的影响。我们恢复了一个系统发育地理历史，支持三个不同的谱系分支，分别对应大西洋森林的北部和南部两个地理结构化的种群。此外，我们在多斯河附近的纬度上识别了南北种群之间的混合区。我们的发现支持了隔离-距离模式的存在，以及种群之间可能由种群扩张期间的基因流促进的次级接触区的存在。进一步地，我们发现所有测试河流的迁移参数模型都得到了支持，不同种群之间的分化时间不同。基于物种历史和AF的古环境动力学，我们证实了森林避难所在该物种通过末次冰期后的最近范围扩张影响种群结构的作用。多斯河和帕拉伊巴河与主要遗传断裂相吻合，表明它们可能在多样化过程中也发挥了作用。最后，尽管在不同种群之间发现了表型数据的微妙相关性，但变异并不强烈，且似乎与可能导致分类学变化的物种水平过程无关。这样的结果可以通过评估特征的表型可塑性以及最近的分化时间来解释，在最近的分化时间中，存在不足的时间和较弱的自然选择压力，无法积累足够的表型差异。