Data_Sheet_1_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）区域作为地球上生物多样性热点之一，以其物种多样性和特有性而著称。与古环境动力学相关的因素，如植被避难所和流域的形成，对该区域内生物群落和生物多样性模式的形成产生不同的影响。在本研究中，我们从广泛分布的树蟾（Dendropsophus elegans）中采集了全基因组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性形成的影响。我们估计了与多斯河、帕拉伊巴河、伊瓜佩河和帕拉瓜苏河相关的遗传断裂处的分化时间以及迁移率，这些河流已知是其他大西洋森林特有物种基因流障碍，并测试了气候避难所的作用。最后，我们调查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群，分为两个地理上结构化的种群，分别对应大西洋森林的南北部。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域。我们的发现支持了一种隔离-距离模式，以及种群之间存在次级接触区的存在，这可能是种群扩张期间基因流促进的结果。进一步地，我们发现对于所有测试河流的迁移参数模型均得到了支持，这些河流具有不同的种群分化时间。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最近冰期最大值（LGM）之后种群扩张过程中对种群结构影响的角色。多斯河和帕拉伊巴河与主要的遗传断裂相吻合，表明它们可能在多样性形成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，但这种变异并不强烈，似乎与可能导致分类学变化的物种水平过程无关。这些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，在最近的时间内，由于时间不足和弱选择压力，尚未积累足够的表型差异。