Tertiary Climate Change and the Diversification of the Amazonian Gecko Genus Gonatodes (Sphaerodactylidae, Squamata)

The genus Gonatodes is a monophyletic group of small-bodied, diurnal geckos distributed across northern South America, Central America, and the Caribbean. We used fragments of three nuclear genes (RAG2, ACM4, and c-mos) and one mitochondrial gene (16S) to estimate phylogenetic relationships among Amazonian species of Gonatodes. We used Penalized Likelihood to estimate timing of diversification in the genus. Most cladogenesis occurred in the Oligocene and early Miocene and coincided with a burst of diversification in other South American animal groups including mollusks, birds, and mammals. The Oligocene and early Miocene were periods dominated by dramatic climate change and Andean orogeny and we suggest that these factors drove the burst of cladogenesis in Gonatodes geckos as well as other taxa. A common pattern in Amazonian taxa is a biogeographic split between the eastern and western Amazon basin. We observed two clades with this spatial distribution, although large differences in timing of divergence between the east–west taxon pairs indicate that these divergences were not the result of a common vicariant event

A New Genus of Miniaturized and Pug-Nosed Gecko from South America (Sphaerodactylidae: Gekkota)

Sphaerodactyl geckos comprise five genera distributed across Central and South America and the Caribbean. We estimated phylogenetic relationships among sphaerodactyl genera using both separate and combined analyses of seven nuclear genes. Relationships among genera were incongruent at different loci and phylogenies were characterized by short, in some cases zero-length, internal branches and poor phylogenetic support at most nodes. We recovered a polyphyletic Coleodactylus, with Coleodactylus amazonicus being deeply divergent from the remaining Coleodactylus species sampled. The C. amazonicus lineage possessed unique codon deletions in the genes PTPN12 and RBMX while the remaining Coleodactylus species had unique codon deletions in RAG1. Topology tests could not reject a monophyletic Coleodactylus, but we show that short internal branch lengths decreased the accuracy of topology tests because there were not enough data along these short branches to support one phylogenetic hypothesis over another. Morphological data corroborated results of the molecular phylogeny, with Coleodactylus exhibiting substantial morphological heterogeneity. We identified a suite of unique craniofacial features that differentiate C. amazonicus not only from other Coleodactylus species, but also from all other geckos. We describe this novel sphaerodactyl lineage as a new genus, Chatogekko gen. nov. We present a detailed osteology of Chatogekko, characterizing osteological correlates of miniaturization that provide a framework for future studies in sphaerodactyl systematics and biology

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

The demography of the lizard Tropidurus torquatus (Squamata, Tropiduridae) in a highly seasonal Neotropical savanna

The demography of a population of Tropidurus torquatus was studied from March 1996 until December 1998, in the Cerrado biome of the Central Brazil, using the method of capture and recapture. Population size, number of incoming individuals in the population, and age structure varied seasonally, reflecting the reproductive cycle of the species. The instantaneous rate of population increase did not differ from zero throughout the study. In general, the permanence rate of juveniles and adults were low, indicating a large turnover of individuals in the population, with a maximum life expectancy of three years. The sex-ratio among adults was biased toward females. Since no bias was observed among juveniles and there was no difference in adults permanence between sexes, we suggestet that the biased adult sex-ratio resulted from a lower permanence of males during a short ontogenetic period, when secondary sexual characteristics develop. When compared to T. itambere, the studied population of T. torquatus attained a higher density and a greater female bias in the sex-ratio. In general, the studied population presented characteristics that, according to life history theory, should be associated with early age at maturity and polyginy: short life expectancy, high population turnover, and female biased sex-ratios

Cryptic, sympatric diversity in Tegu lizards of the Tupinambis teguixin Group (Squamata, Sauria, Teiidae) and the description of three new species

Tegus of the genera Tupinambis and Salvator are the largest Neotropical lizards and the most exploited clade of Neotropical reptiles. For three decades more than 34 million tegu skins were in trade, about 1.02 million per year. The genus Tupinambis is distributed in South America east of the Andes, and currently contains four recognized species, three of which are found only in Brazil. However, the type species of the genus, T. teguixin, is known from Bolivia, Brazil, Colombia, Ecuador, French Guyana, Guyana, Peru, Suriname, Trinidad and Tobago, and Venezuela (including the Isla de Margarita). Here we present molecular and morphological evidence that this species is genetically divergent across its range and identify four distinct clades some of which are sympatric. The occurrence of cryptic sympatric species undoubtedly exacerbated the nomenclatural problems of the past. We discuss the species supported by molecular and morphological evidence and increase the number of species in the genus Tupinambis to seven. The four members of the T. teguixin group continue to be confused with Salvator merianae, despite having a distinctly different morphology and reproductive mode. All members of the genus Tupinambis are CITES Appendix II. Yet, they continue to be heavily exploited, under studied, and confused in the minds of the public, conservationists, and scientists

Taxonomic Review of South American Butter Frogs: Phylogeny, Geographic Patterns, and Species Delimitation in the Leptodactylus latrans Species Group (Anura: Leptodactylidae)

The Leptodactylus latrans species group currently comprises eight medium- to large-sized frog species with a convoluted taxonomic history, particularly related to the specific limits of the L. latrans complex, and the species pair Leptodactylus chaquensis–Leptodactylus macrosternum. Their homogeneous external morphology and continental geographic distribution in South America have posed severe limitations to a comprehensive review, such that taxonomic consensus and species limits remain uncertain. This is further worsened by the presence of chromatic polymorphism among coexisting species that can hardly be distinguished by external morphology. Based on a large-scale geographic sampling including multilocus DNA analyses, and acoustic and morphological data, we provide a comprehensive evaluation of the taxonomic status and species limits of the L. latrans group, focusing on the resolution of the L. latranscomplex and the species pair L. chaquensis–L. macrosternum. We gathered 728 mitochondrial sequences from 429 localities, encompassing the entire geographic distribution of the group. Both generalized mixed Yule coalescent and automatic barcode gap discovery species delimitation methods recovered four major mitochondrial evolutionary lineages within the L. latrans complex, also supported by distribution patterns, multilocus molecular, morphological and/or bioacoustic data. One lineage is linked to nominal L. latrans,one revalidated as Leptodactylus luctator, and the other two are formally named and described. Another lineage encompasses all specimens previously assigned to the species pair L. chaquensis–L. macrosternum, clustered as a single evolutionary entity and is now regarded as L. macrosternum. We provide a revised diagnosis for these species based on acoustic data, morphological/chromatic variation, and phylogenetic relationships of all species currently included in the L. latrans group. Our findings reinforce the view that Neotropical diversity is highly underestimated and stress that appropriate geographic sampling in an integrative framework is crucial for the establishment of specific limits among broadly distributed and morphologically cryptic Neotropical frogs

Multilocus environmental adaptation and population structure in the Cerrado gecko Gymnodactylus amarali (Sauria, Phyllodactylidae) from Serra da Mesa Hydroelectric Plant, Central Brazil

Contrasting environmental conditions across geographic space might promote divergent selection, making adaptation to local biotic and abiotic conditions necessary for populations to survive. In order to understand how populations adapt to different environmental conditions, studies of local adaptation have been largely used as an interface to address ecological and evolutionary questions. Here, we studied populations of Gymnodactylus amarali (Phyllodactylidae) isolated in rapidly created artificial islands. We combined a genotyping-by-sequence (GBS) survey and redundancy analyses (RDA) to investigate genotype–environment associations (GEA), while DAPC, Fst, and Admixture analyses were used to determine genetic structure. Our hypothesis is that G. amarali populations on the islands are going through a local adaptation process and consequently becoming genetically different from the populations on the mainland. Our results indicate that geographic and environmental differences are related to genetic variation, as we detected the presence of two or three distinct genetic lineages in Serra da Mesa, Minaçu, and Colinas do Sul. Fst analysis shows moderate isolation between Serra da Mesa and Minaçu (0.082). The RDA pointed out potential local genetic signal correlated with temperature and precipitation. We identified 230 candidate loci associated with the environment and at least two locally structured subpopulations (Serra da Mesa and Minaçu) show significant association with environmental variation

Out of the deep: Cryptic speciation in a Neotropical gecko (Squamata, Phyllodactylidae) revealed by species delimitation methods

Levels of biodiversity in the Neotropics are largely underestimated despite centuries of research interest in this region. This is particularly true for the Cerrado, the largest Neotropical savanna and a formally recognized biodiversity hotspot. Molecular species delimitation methods have become essential tools to uncover cryptic species and can be notably robust when coupled with morphological information. We present the first evaluation of the monophyly and cryptic speciation of a widespread Cerrado endemic lizard, Gymnodactylus amarali, using phylogenetic and species-trees methods, as well as a coalescent-based Bayesian species delimitation method. We tested whether lineages resulting from the analyses of molecular data are morphologically diagnosed by traditional meristic scale characters. We recovered eight deeply divergent molecular clades within G. amarali, and two additional ones from seasonally dry tropical forest enclaves between the Cerrado and the Caatinga biomes. Analysis of morphological data statistically corroborated the molecular delimitation for all groups, in a pioneering example of the use of support vector machines to investigate morphological differences in animals. The eight G. amarali clades appear monophyletic and endemic to the Cerrado. They display several different properties used by biologists to delineate species and are therefore considered here as candidates for formal taxonomic description. We also present a preliminary account of the biogeographic history of these lineages in the Cerrado, evidence for speciation of sister lineages in the Cerrado–Caatinga contact, and highlight the need for further morphological and genetic studies to assess cryptic diversity in this biodiversity hotspot.FMCBD was supported by scholarships from ‘Coordenação de Aperfeiçoamento de Pessoal de Nível Superior’ (CAPES) and ‘Conselho Nacional de Desenvolvimento Científico e Tecnológico’ (CNPq). This work was funded by CAPES, CNPq, ‘Fundação de Apoio à Pesquisa do Distrito Federal’ (FAPDF), ‘GENPAC15’ and ‘Rede de Pesquisa Biota do Cerrado’, coordinated by GRC. MTR and JC acknowledge ‘Fundação de Amparo à Pesquisa do Estado de São Paulo’ (FAPESP) for funding and D. Pavan, F. Curcio, M. Dixo, M. Teixeira Jr., N. Silva P. Nunes and, T. Mott for collecting tissues and help in field. LBB thanks additional support provided by the Australian Research Council (ARC DP0556496). We are grateful to Fernanda Werneck for collecting the Gymnodactylus specimens of Manga and Matias Cardoso. We also acknowledge two anonymous reviewers for comments that improved the quality of the manuscript. FMCBD is also grateful to Marina Scalon for commenting on early drafts of the manuscript

Out of the deep: Cryptic speciation in a Neotropical gecko (Squamata, Phyllodactylidae) revealed by species delimitation methods

Levels of biodiversity in the Neotropics are largely underestimated despite centuries of research interest in this region. This is particularly true for the Cerrado, the largest Neotropical savanna and a formally recognized biodiversity hotspot. Molecular species delimitation methods have become essential tools to uncover cryptic species and can be notably robust when coupled with morphological information. We present the first evaluation of the monophyly and cryptic speciation of a widespread Cerrado endemic lizard, Gymnodactylus amarali, using phylogenetic and species-trees methods, as well as a coalescent-based Bayesian species delimitation method. We tested whether lineages resulting from the analyses of molecular data are morphologically diagnosed by traditional meristic scale characters. We recovered eight deeply divergent molecular clades within G. amarali, and two additional ones from seasonally dry tropical forest enclaves between the Cerrado and the Caatinga biomes. Analysis of morphological data statistically corroborated the molecular delimitation for all groups, in a pioneering example of the use of support vector machines to investigate morphological differences in animals. The eight G. amarali clades appear monophyletic and endemic to the Cerrado. They display several different properties used by biologists to delineate species and are therefore considered here as candidates for formal taxonomic description. We also present a preliminary account of the biogeographic history of these lineages in the Cerrado, evidence for speciation of sister lineages in the Cerrado–Caatinga contact, and highlight the need for further morphological and genetic studies to assess cryptic diversity in this biodiversity hotspot.FMCBD was supported by scholarships from ‘Coordenação de Aperfeiçoamento de Pessoal de Nível Superior’ (CAPES) and ‘Conselho Nacional de Desenvolvimento Científico e Tecnológico’ (CNPq). This work was funded by CAPES, CNPq, ‘Fundação de Apoio à Pesquisa do Distrito Federal’ (FAPDF), ‘GENPAC15’ and ‘Rede de Pesquisa Biota do Cerrado’, coordinated by GRC. MTR and JC acknowledge ‘Fundação de Amparo à Pesquisa do Estado de São Paulo’ (FAPESP) for funding and D. Pavan, F. Curcio, M. Dixo, M. Teixeira Jr., N. Silva P. Nunes and, T. Mott for collecting tissues and help in field. LBB thanks additional support provided by the Australian Research Council (ARC DP0556496). We are grateful to Fernanda Werneck for collecting the Gymnodactylus specimens of Manga and Matias Cardoso. We also acknowledge two anonymous reviewers for comments that improved the quality of the manuscript. FMCBD is also grateful to Marina Scalon for commenting on early drafts of the manuscript