Population genetic structure and species delimitation of a widespread, Neotropical dwarf gecko.

Amazonia harbors the greatest biological diversity on Earth. One trend that spans Amazonian taxa is that most taxonomic groups either exhibit broad geographic ranges or small restricted ranges. This is likely because many traits that determine a species range size, such as dispersal ability or body size, are autocorrelated. As such, it is rare to find groups that exhibit both large and small ranges. Once identified, however, these groups provide a powerful system for isolating specific traits that influence species distributions. One group of terrestrial vertebrates, gecko lizards, tends to exhibit small geographic ranges. Despite one exception, this applies to the Neotropical dwarf geckos of the genus Gonatodes. This exception, Gonatodes humeralis, has a geographic distribution almost 1,000,000 km2 larger than the combined ranges of its 30 congeners. As the smallest member of its genus and a gecko lizard more generally, G. humeralis is an unlikely candidate to be a wide-ranged Amazonian taxon. To test whether or not G. humeralis is one or more species, we generated molecular genetic data using restriction-site associated sequencing (RADseq) and traditional Sanger methods for samples from across its range and conducted a phylogeographic study. We conclude that G. humeralis is, in fact, a single species across its contiguous range in South America. Thus, Gonatodes is a unique clade among Neotropical taxa, containing both wide-ranged and range-restricted taxa, which provides empiricists with a powerful model system to correlate complex species traits and distributions. Additionally, we provide evidence to support species-level divergence of the allopatric population from Trinidad and we resurrect the name Gonatodes ferrugineus from synonymy for this population.

Recent chapters of Neotropical history overlooked in phylogeography: Shallow divergence explains phenotype and genotype uncoupling in Antilophia manakins.

Establishing links between phenotypic and genotypic variation is a central goal of evolutionary biology, as they might provide important insights into evolutionary processes shaping genetic and species diversity in nature. One of the more intriguing possibilities is when no genetic divergence is found to be associated with conspicuous phenotypic divergence. In that case, speciation theory predicts that phenotypic divergence may still occur in the presence of significant gene flow-thereby resulting in little genomic divergence-when genetic loci underpinning phenotypes are under strong divergent selection. However, a finding of phenotypic distinctiveness with weak or no population genetic structure may simply result from low statistical power to detect shallow genetic divergences when small data sets are used. Here, we used a subgenomic data set of 2,386 ultraconserved elements to explore genomewide divergence between two species of Antilophia manakins, which are phenotypically distinct yet evidently lack strong genetic differentiation according to previous studies based on a limited number of loci. Our results revealed clear population structure that matches the two phenotypes, supporting the idea that smaller data sets lacked the power to detect this recent divergence event (likely <100 k ya). Indeed, we found little or no introgression between the species, as well as evidence of genomewide divergence. One implication of our study is that the Araripe plateau may be a hot spot of cryptic-diverging forest Cerrado populations. Besides their use in biogeography, subgenomic data sets may help redefine local conservation programmes by revealing cryptic population structure that may be key to population management.