High Levels of Diversity Uncovered in a Widespread Nominal Taxon: Continental Phylogeography of the Neotropical Tree Frog

Species distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and closely related species distributed across eleven countries, effectively comprising the entire range of the group. We performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of eight mtDNA lineages have ranges >100,000 km2. One of them occupies an area of almost one million km2 encompassing multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered

The First Bromeligenous Species of Dendropsophus (Anura: Hylidae) from Brazil\u27s Atlantic Forest

We describe a new treefrog species of Dendropsophus collected on rocky outcrops in the Brazilian Atlantic Forest. Ecologically, the new species can be distinguished from all known congeners by having a larval phase associated with rainwater accumulated in bromeliad phytotelms instead of temporary or lentic water bodies. Phylogenetic analysis based on molecular data confirms that the new species is a member of Dendropsophus; our analysis does not assign it to any recognized species group in the genus. Morphologically, based on comparison with the 96 known congeners, the new species is diagnosed by its small size, framed dorsal color pattern, and short webbing between toes IV-V. The advertisement call is composed of a moderate-pitched two-note call (~5 kHz). The territorial call contains more notes and pulses than the advertisement call. Field observations suggest that this new bromeligenous species uses a variety of bromeliad species to breed in, and may be both territorial and exhibit male parental care

Demographic histories and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history

A central paradigm in conservation biology is that population bottlenecks reduce genetic diversity and population viability. In an era of biodiversity loss and climate change, understanding the determinants and consequences of bottlenecks is therefore an important challenge. However, as most studies focus on single species, the multitude of potential drivers and the consequences of bottlenecks remain elusive. Here, we combined genetic data from over 11,000 individuals of 30 pinniped species with demographic, ecological and life history data to evaluate the consequences of commercial exploitation by 18th and 19th century sealers. We show that around one third of these species exhibit strong signatures of recent population declines. Bottleneck strength is associated with breeding habitat and mating system variation, and together with global abundance explains much of the variation in genetic diversity across species. Overall, bottleneck intensity is unrelated to IUCN status, although the three most heavily bottlenecked species are endangered. Our study reveals an unforeseen interplay between human exploitation, animal biology, demographic declines and genetic diversity

Genetic divergence in tropical anurans : deeper phylogeographic structure in forest specialists and in topographically complex regions

Made available in DSpace on 2018-11-26T16:16:25Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-09-01Deutsche ForschungsgemeinschaftHumboldt FoundationKatholischer Akademischer AustauschdienstFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Many tropical organisms show large genetic differences among populations, yet the prevalent drivers of the underlying divergence processes are incompletely understood. We explored the effect of several habitat and natural history features (body size, macrohabitat, microhabitat, reproduction site, climatic heterogeneity, and topography) on population genetic divergence in tropical amphibians, based on a data set of 2680 DNA sequences of the mitochondrial cytochrome b gene in 39 widely distributed frog species from Brazil, Central America, Cuba, and Madagascar. Generalized linear models were implemented in an information-theoretic framework to evaluate the effects of the six predictors on genetic divergence among populations, measured as spatially corrected pairwise distances. Results indicate that topographic complexity and macrohabitat preferences have a strong effect on population divergence with species specialized to forest habitat and/or from topographically complex regions showing higher phylogeographic structure. This relationship changed after accounting for phylogenetic relatedness among taxa rendering macrohabitat preferences as the most important feature shaping genetic divergence. The remaining predictors showed negligible effects on the observed genetic divergence. A similar analysis performed using the population-scaled mutation rate (I similar to) as response variable showed little effect of the predictors. Our results demonstrate greater evolutionary independence among populations of anurans from forested regions versus species from open habitats. This pattern may result from lower vagility and stringency in reproductive requirements of rainforest species. Conversely, open landscapes may offer ephemeral and unstable breeding sites suitable for vagile generalist species, resulting in reduced intraspecific divergence. Our results predict that, for a given period of time, there should be a higher chance of speciation in tropical anurans living in forests than in species adapted to open habitats.Tech Univ Carolo Wilhelmina Braunschweig, Inst Zool, Div Evolutionary Biol, D-38106 Braunschweig, GermanyJagiellonian Univ, Inst Zool, Dept Comparat Anat, PL-30387 Krakow, PolandJagiellonian Univ, Inst Environm Sci, PL-30387 Krakow, PolandUniv Fed Rio Grande do Norte, DBEZ, Ctr Biociencias, BR-59078900 Natal, RN, BrazilUniv Estadual Paulista, Inst Biociencias, Dept Zool, BR-13506900 Rio Claro, SP, BrazilUniv Estadual Paulista, Inst Biociencias, Dept Zool, BR-13506900 Rio Claro, SP, BrazilDeutsche Forschungsgemeinschaft: VE247/7-1FAPESP: 2008/50928-1FAPESP: 2013/50741-7CNPq: 302518/2013-

Dwarf geckos and giant rivers: The role of the São Francisco River in the evolution of Lygodactylus klugei (Squamata: Gekkonidae) in the semi-arid Caatinga of north-eastern Brazil

Species diversification can be strongly influenced by geomorphological features, such as mountains, valleys and rivers. Rivers can act as hard or soft barriers to gene flow depending on their size, speed of flow, historical dynamics and regional topographical characteristics. The São Francisco River (SFR) is the largest perennial river in the Caatinga biome in north-eastern Brazil and has been considered a barrier to gene flow and dispersal. Herein, we evaluated the role of the SFR on the evolution of Lygodactylus klugei, a small gecko from the Caatinga. Using a single-locus species delimitation method (generalized mixed Yule coalescent), we defined lineages (haploclades). Subsequently, we evaluated the role of the SFR in structuring genetic diversity in this species using a multilocus approach to quantify migration across margins. We also evaluated genetic structure based on nuclear markers, testing the number of populations found through an assignment test (STRUCTURE) across the species distribution. We recovered two mitochondrial lineages structured with respect to the SFR, but only a single population was inferred from nuclear markers. Given that we detected an influence of the SFR only on mitochondrial markers, we suggest that the current river course has acted as a relatively recent geographical barrier for L. klugei, for ~450 000 years. © 2019 The Linnean Society of London, Biological Journal of the Linnean Society

Diversification with gene flow and niche divergence in a lizard species along the South American “diagonal of open formations”

Aim: To assess the effects of historical events on the tempo and mode of diversification of the lizard Polychrus acutirostris along the South American diagonal of open formations (DOF). Location: Caatinga and Cerrado biomes in Brazil. Methods: We sequenced fragments of one mtDNA and three nuDNA genes of 68 individuals from 33 localities. We used population assignment methods to access genetic structure and estimate lineage boundaries. Next, we estimated lineage relationships, intraspecific diversity, environmental niche similarity and demographic history. Finally, we tested 12 diversification scenarios using an approximate Bayesian computation (ABC) approach. Results: We recovered three non-overlapping, geographically structured lineages corresponding to Caatinga, north-east Cerrado and south-west Cerrado, with the major divergence event dating to the Late Neogene. We also recovered a complex scenario of divergence associated with gene flow and niche divergence. Main conclusions: We show a complex history of diversification along the South American DOF. Our findings support the role of environmental features as the likely drivers of P. acutirostris intraspecific diversification during the Late Neogene. © 2018 John Wiley & Sons Lt

The evolutionary history of Lygodactylus lizards in the South American open diagonal

The Pleistocenic Arc Hypothesis (PAH) posits that South American Seasonally Dry Tropical Forests (SDTF) were interconnected during Pleistocene glacial periods, enabling the expansion of species ranges that were subsequently fragmented in interglacial periods, promoting speciation. The lizard genus Lygodactylus occurs in Africa, Madagascar, and South America. Compared to the high diversity of African Lygodactylus, only two species are known to occur in South America, L. klugei and L. wetzeli, distributed in SDTFs and the Chaco, respectively. We use a phylogenetic approach based on mitochondrial (ND2) and nuclear (RAG-1) markers covering the known range of South American Lygodactylus to investigate (i) if they are monophyletic relative to their African congeners, (ii) if their divergence is congruent with the fragmentation of the PAH, and (iii) if cryptic diversity exists within currently recognized species. Maximum likelihood and Bayesian phylogenetic analyses recovered a well-supported monophyletic South American Lygodactylus, presumably resulting from a single trans-Atlantic dispersal event 29 Mya. Species delimitation analyses supported the existence of five putative species, three of them undescribed. Divergence times among L. klugei and the three putative undescribed species, all endemic to the SDTFs, are not congruent with the fragmentation of the PAH. However, fragmentation of the once broader and continuous SDTFs likely influenced the divergence of L. wetzeli in the Chaco and Lygodactylus sp. 3 (in a SDTF enclave in the Cerrado). © 2018 Elsevier Inc

Data from: Climatic suitability, isolation by distance and river resistance explain genetic variation in a Brazilian whiptail lizard

Spatial patterns of genetic variation can help understand how environmental factors either permit or restrict gene flow and create opportunities for regional adaptations. Organisms from harsh environments such as the Brazilian semiarid Caatinga biome may reveal how severe climate conditions may affect patterns of genetic variation. Herein we combine information from mitochondrial DNA with physical and environmental features to study the association between different aspects of the Caatinga landscape and spatial genetic variation in the whiptail lizard Ameivula ocellifera. We investigated which of the climatic, environmental, geographical and/or historical components best predict: (1) the spatial distribution of genetic diversity, and (2) the genetic differentiation among populations. We found that genetic variation in A. ocellifera has been influenced mainly by temperature variability, which modulates connectivity among populations. Past climate conditions were important for shaping current genetic diversity, suggesting a time lag in genetic responses. Population structure in A. ocellifera was best explained by both isolation by distance and isolation by resistance (main rivers). Our findings indicate that both physical and climatic features are important for explaining the observed patterns of genetic variation across the xeric Caatinga biome

The riverine thruway hypothesis: rivers as a key mediator of gene flow for the aquatic paradoxical frog Pseudis tocantins (Anura, Hylidae)

Context: Rivers, landscape, and climate can alter patterns of gene flow and consequently, shape intraspecific genetic variation. While rivers are predicted to halt gene flow in terrestrial species, they may facilitate migration for aquatic species. Amphibians are usually seen as water-dependent, yet multiple studies have indicated that rivers exert a barrier effect on these organisms. Objectives: In this study, we investigated the effects of rivers and other abiotic factors, such as climate and geography on genetic variation of a highly aquatic frog (Pseudis tocantins) inhabiting central Brazil. Methods: We sequenced fragments of one mitochondrial and two nuclear genes of 179 individuals of P. tocantins from 19 localities along the Tocantins-Araguaia Basin in Brazil and used Generalized Dissimilarity Modeling (GDM) to test the role of rivers, landscape, and climate features on its genetic differentiation. Next, we tested three scenarios of migration along the Tocantins-Araguaia Basin using approximate Bayesian computation (ABC). Results: We found that genetic differentiation among localities is mostly explained by the influence of river connectivity. Conversely, elevation, slope, and past and current climate have little or no impact on genetic differentiation. Furthermore, our results show that patterns of migration took place directionally, from upstream to downstream sites. Conclusions: Rivers have shaped patterns of intraspecific diversity in P. tocantins by acting as the most important facilitator of gene flow. Therefore, we suggest that future research should include the role of rivers as a facilitator of gene flow, especially for those species that are associated with aquatic environments.Fil: Fonseca, Emanuel M.. Ohio State University; Estados UnidosFil: Garda, Adrian A.. Universidade Federal do Rio Grande do Norte; BrasilFil: Oliveira, Eliana F.. Universidade Federal do Mato Grosso do Sul; BrasilFil: Camurugi, Felipe. Universidade Federal do Mato Grosso do Sul; BrasilFil: Magalhães, Felipe de M.. Universidade Estadual da Paraiba; BrasilFil: Lanna, Flávia M.. Ohio State University; Estados UnidosFil: Zurano, Juan Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú; ArgentinaFil: Marques, Ricardo. Universidade Estadual da Paraiba; BrasilFil: Vences, Miguel. Universidad Técnica de Brunswick; AlemaniaFil: Gehara, Marcelo. Rutgers University newark; Estados Unido

The role of strict nature reserves in protecting genetic diversity in a semiarid vegetation in Brazil

Genetic diversity is an important component of biodiversity, providing the means for species to evolve and adapt in changing environments. Although regions that retain high genetic diversity provide ideal targets for conservation due to their evolutionary potential, they have been poorly mapped in the Neotropics. Here, we mapped genetic diversity, expressed in this study by nucleotide diversity, for five lizards, four amphibians, and one spider widely distributed in the Brazilian Caatinga, a semiarid vegetation. We identified areas that contain higher genetic diversity, which may be used to establish conservation priorities for the region, and evaluated their representativeness within strict nature reserves. Our results show that only 1.5% of the areas holding higher genetic diversity are within strict nature reserves. However, we show that very high genetic diversity regions are overrepresented inside strict nature reserves and encompass areas such as “Brejo Paraibano”, Catimbau National Park, and part of the Borborema plateau. Thus, the maintenance of biota’s evolutionary potential relies upon the inclusion of areas with higher genetic diversity in future conservation planning. © 2019, Springer Nature B.V