How species evolve reproductive isolation in the species-rich Amazon basin is poorly understood in vertebrates. Here, we sequenced a reference genome and used a genome-wide sample of SNPs to analyze a hybrid zone between two highly cryptic species of Hypocnemis warbling-antbirds-the Rondonia warbling-antbird (H. ochrogyna) and Spix's warbling-antbird (H. striata)-in a headwater region of southern Amazonia. We found that both species commonly hybridize, producing F 1 s and a variety of backcrosses with each species but we detected only one F 2-like hybrid. Patterns of heterozygosity, hybrid index, and interchromosomal linkage disequilibrium in hybrid populations closely match expectations under strong postzygotic isolation. Hybrid zone width (15.4 km) was much narrower than expected (211 km) indicating strong selection against hybrids. A remarkably high degree of concordance in cline centers and widths across loci, and a lack of reduced interspecific F st between populations close to versus far from the contact zone, suggest that genetic incompatibilities have rendered most of the genome immune to introgression. These results support intrinsic postzygotic isolation as a driver of speciation in a moderately young cryptic species pair from the Amazon and suggest that species richness of the Amazon may be grossly underestimated.

The genus Willisornis is endemic to the Amazon Basin, inhabiting upland terra firme forest, with two species and seven subspecies currently recognized. Despite numerous systematic studies, a taxonomically-dense sampled phylogeny for Willisornis is still lacking, which, combined with evidence of paraphyly and gene flow between its recognized species, underscores the uncertainty concerning species limits and evolutionary history of the genus. Here we present phylogenies and population genetic analyses, including all currently recognized Willisornis taxa, relating them to patterns of plumage variation, and reconstructing the spatiotemporal context of diversification in the genus. Our analyses have uncovered 13 independent genetic lineages in the genus, and the monophyly of all currently named taxa, which also showed robust plumage diagnoses. However, deeply coalesced genetic lineages were also found within most Willisornis taxa, for which no consistent variation in plumage was found. The diversification of the genus Willisornis is related to hydrographic and climate change cycles across Amazonia since the Plio-Pleistocene, with most genetic lineages originating in the past one million years. Based on our findings, we recommend the recognition of a total of six species in Willisornis (one of which polytypic) based on the congruency between deeply coalesced lineages and consistent plumage diagnoses.

Few data are available on the morphology of the hemipenis of teiid lizards, especially those of the recently-defined genus Tupinambis, a widely-distributed group of large-bodied lizards. This study provides an illustrated description of the hemipenis of Tupinambis quadrilineatus, which is similar to that of other representatives of the Tupinambinae subfamily. New records of the species from the state of Piauí, in northeastern Brazil, are also presented.

The formation of the Amazon drainage basin has been considered an important driver of speciation of several taxa, promoting vicariant events or reinforcement of barriers that restrict gene flow between opposite river margins. Several recent studies reported a set of miscellaneous events involving climatic fluctuations, geomorphological changes, and dispersal mechanisms as propellers of diversification of Amazonian rainforest taxa. Here, we show the results of dated phylogenetic, biogeographic, and populational analyses to investigate which events could better explain the current distribution of a heliothermic, active foraging lizard in the central and eastern portions of the Amazonian rainforest (besides a disjunct distribution in part of the Atlantic Forest). We sampled Kentropyx calcarata from most of its area of occurrence in Amazonia and used mitochondrial and nuclear markers to evaluate if the genetic structure agrees with evolutionary scenarios previously proposed for Amazonia. We performed phylogenetic and populational analyses to better understand the dynamics of this species in the Amazonia rainforest over time. Phylogenetic inference recovered ten K. calcarata structured lineages in eastern Amazonia, some of them limited by the Amazon River and its southern tributaries (Tapajós, Xingu, and Tocantins), although we detected occasional haplotype sharing across some of the river banks. According to molecular dating, K. calcarata diversified since Miocene–Pliocene, and some of the lineages presented signs of demographic expansion during the Pleistocene, supposedly triggered by climatic dynamics. The putative ancestral lineage of K. calcarata was distributed on the Guiana Shield, later spreading south and southeastward by dispersion. Our results indicate that Amazonian rivers acted as barriers to the dispersal of Kentropyx calcarata, but they were not the sole drivers of diversification.