New tales for the Amazonian biogeography: overlooked flooodplain forest birds support climatic oscillation in pleistocene as driver for speciation in the Amazon

The majority of the bird phylogeographic studies in the Amazonian region has focused on organisms of non flooded ombrophilous forests (“terra-firme”). However, this biome is an intricate mosaic of several distinct environments with endemic fauna and flora, such as floodplain forest habitats of “varzea” and “igapo”. Organisms from these environments tend to respond differently from those of terra-firme even when affected by the same historical events. In this study we perform a comparative phylogenomic analysis of floodplain forest birds, testing diversification hypotheses regarding the potential effects of past changes in this environment. We selected three widely distributed species complexes of Antbirds comprising 12 subspecific taxa (Myrmoborus lugubris, Myrmotherula assimilis and Thamnophilus nigrocinereus/cryptoleucus) with similar geographic distributions. We sequenced ~2,300 Ultra Conserved Elements and applied coalescent and model-based methods to test alternative hypotheses concerning divergence time, population size change, and gene flow. Our findings support a similar pattern of diversification for these species complexes starting at Mid- and Late-Pleistocene and gene flow mainly between populations occurring at white water rivers. This supports the central portion of the Amazon Basin, in the confluence of Solimões and Negro rivers, as a suture zone for these taxa. These results indicate that historical processes affecting the level of Amazonian rivers related to climatic oscillations during the Pleistocene promoted cladogenetic events along the Amazon floodplains.