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We assessed population structure and the spatio‐temporal pattern of diversification in the Glossy AntshrikeSakesphorus luctuosus(Aves, Thamnophilidae) to understand the processes shaping the evolutionary history of Amazonian floodplains and address unresolved taxonomic controversies surrounding its species limits. By targeting ultraconserved elements (UCEs) from 32 specimens ofS.luctuosus, we identified independent lineages and estimated their differentiation, divergence times, and migration rates. We also estimated current and past demographic histories for each recovered lineage. We found evidence confirming thatS.luctuosusconsists of a single species, comprising at least four populations, with some highly admixed individuals and overall similar levels of migration between populations. We confirmed the differentiation of the Araguaia River basin population (S. l.araguayae) and gathered circumstantial evidence indicating that the taxonS.hagmannimay represent a highly introgressed population between three distinct phylogroups ofS.luctuosus. Divergences between populations occurred during the last 1.2 mya. Signs of population expansions were detected for populations attributed to subspeciesS. l.luctuosus, but not for theS. l.araguayaepopulation. Our results support thatS.luctuosushas had a complex population history, resulting from a high dependence on southeastern “clear water” seasonally flooded habitats and their availability through time. Spatial and demographic expansions toward the western “white water” flooded forests might be related to recent changes in connectivity and availability of these habitats. Our study reinforces the view that isolation due to absence of suitable habitat has been an important driver of population differentiation within Amazonian flooded forests, but also that differences betweenvárzeas(“white water” floodplains, mostly in southwestern Amazonia) andigapós(“clear water” floodplains, especially located in the east) should be further explored as drivers of micro‐evolution for terrestrial species.

Hylexetasteswoodcreepers are endemic to theterra firmeforests of the Amazon basin. Currently, most taxonomic sources recognize two species ofHylexetastes(H. perrotiiandH. stresemanni), each divided into three subspecies. Some authors maintain that theH. perrotiisubspecies should be elevated to full species status. In particular,Hylexetastes perrotii brigidaiis endemic to the eastern Amazon, the second Amazonian area of endemism (Xingu) most affected by deforestation and habitat degradation. Consequently, the taxonomic status ofH. p. brigidaiis of particular concern for conservation. Thus far, only morphological characters have been evaluated for the taxonomic delimitation of species and subspecies ofHylexetastes. We present a molecular phylogenetic analysis of all subspecies to help delimitHylexetastesinterspecific limits. Fragments of two mitochondrial (CytbandND2) and three nuclear genes (FGB5, G3PDHandMUSK) from 57Hylexetastesspecimens were sequenced. An ecological niche model was estimated to describe more accurately the potential distributions of taxa and to evaluate their vulnerability to ongoing deforestation. Phylogenetic analyses support the paraphyly of the polytypicH. perrotiias currently delimited and the elevation ofHylexetastes perrotii uniformisto full species rank, as well as the presence of three evolutionary significant units (ESUs) within this newly delimited species, including one grouping allH. p. brigidaispecimens. Alternatively, under lineage‐based species concepts, our results support at least five evolutionary species inHylexetastes:H. stresemanni,H. undulatus,H. perrotii,H. uniformisandH. brigidai. Each of these taxa andESUs are distributed in different interfluvial areas of the Amazon basin, which have different degrees of disturbance. Because they occupy the most heavily impacted region among allHylexetastesESUs, regular assessments of the conservation statuses ofH. p. brigidaiand bothH. uniformisESUs are paramount.