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Oval frogs (Elachistocleis) have a broad geographic distribution covering nearly all of South America and parts of Central America. They also have a large inter- and intraspecific variation of the few morphological characters commonly used as diagnostic traits among species of the genus. Based on molecular data, we provide the most complete phylogeny of Elachistocleis to date, and explore its genetic diversity using distance-based and tree-based methods for putative species delimitation. Our results show that at least two of the most relevant traditional characters used in the taxonomy of this group (belly pattern and dorsal median white line) carry less phylogenetic information than previously thought. Based on our results, we propose some synonymizations and some candidate new species. This study is a first major step in disentangling the current systematics of Elachistocleis. Yet, a comprehensive review of morphological data is needed before any new species descriptions can be properly made.

Made available in DSpace on 2022-04-29T08:34:55Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-03-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) The molecular bases for the symbiosis of the amphibian skin microbiome with its host are poorly understood. Here, we used the odor-producer Pseudomonas sp. MPFS and the treefrog Boana prasina as a model to explore bacterial genome determinants and the resulting mechanisms facilitating symbiosis. Pseudomonas sp. MPFS and its closest relatives, within a new clade of the P. fluoresens Group, have large genomes and were isolated from fishes and plants, suggesting environmental plasticity. We annotated 16 biosynthetic gene clusters from the complete genome sequence of this strain, including those encoding the synthesis of compounds with known antifungal activity and of odorous methoxypyrazines that likely mediate sexual interactions in Boana prasina. Comparative genomics of Pseudomonas also revealed that Pseudomonas sp. MPFS and its closest relatives have acquired specific resistance mechanisms against host antimicrobial peptides (AMPs), specifically two extra copies of a multidrug efflux pump and the same two-component regulatory systems known to trigger adaptive resistance to AMPs in P. aeruginosa. Subsequent molecular modeling indicated that these regulatory systems interact with an AMP identified in Boana prasina through the highly acidic surfaces of the proteins comprising their sensory domains. In agreement with a symbiotic relationship and a highly selective antibacterial function, this AMP did not inhibit the growth of Pseudomonas sp. MPFS but inhibited the growth of another Pseudomonas species and Escherichia coli in laboratory tests. This study provides deeper insights into the molecular interaction of the bacteria-amphibian symbiosis and highlights the role of specific adaptive resistance toward AMPs of the hosts. Departamento de Ciências Biomoleculares Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo, SP Laboratorio de Genética Evolutiva Instituto de Biología Subtropical (CONICET – UNaM) Facultad de Ciencias Exactas Universidad Nacional de Misiones Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Departamento de Biodiversidade e Centro de Aquicultura Instituto de Biociências Universidade Estadual Paulista, SP Departamento de Análises Clínicas Toxicológicas e Bromatológicas Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo, SP IPEEC-CONICET Instituto Patagónico para el Estudio de los Ecosistemas Continentales Consejo Nacional de Investigaciones Científicas y Técnicas Mikrobiologie Technische Universität Braunschweig Departamento de Biodiversidade e Centro de Aquicultura Instituto de Biociências Universidade Estadual Paulista, SP FAPESP: 2013/50741-7 FAPESP: 2013/50954-0 FAPESP: 2014/20915-6 FAPESP: 2014/50265-3 FAPESP: 2017/23725-1 FAPESP: 2017/26162-8 CAPES: 88881.062205/2014-01 CAPES: 88887.464731/2019-00

Microbial diversity positively influences community resilience of the host microbiome. However, extinction risk factors such as habitat specialization, narrow environmental tolerances, and exposure to anthropogenic disturbance may homogenize host-associated microbial communities critical for stress responses including disease defense. In a dataset containing 43 threatened and 90 non-threatened amphibian species across two biodiversity hotspots (Brazil’s Atlantic Forest and Madagascar), we found that threatened host species carried lower skin bacterial diversity, after accounting for key environmental and host factors. The consistency of our findings across continents suggests the broad scale at which low bacteriome diversity may compromise pathogen defenses in species already burdened with the threat of extinction.

Anthropogenic habitat disturbance is fundamentally altering patterns of disease transmission and immunity across the vertebrate tree of life. Most studies linking anthropogenic habitat change and disease focus on habitat loss and fragmentation, but these processes often lead to a third process that is equally important: habitat split. Defined as spatial separation between the multiple classes of natural habitat that many vertebrate species require to complete their life cycles, habitat split has been linked to population declines in vertebrates, e.g. amphibians breeding in lowland aquatic habitats and overwintering in fragments of upland terrestrial vegetation. Here, we link habitat split to enhanced disease risk in amphibians (i) by reviewing the biotic and abiotic forces shaping elements of immunity and (ii) through a spatially oriented field study focused on tropical frogs. We propose a framework to investigate mechanisms by which habitat split influences disease risk in amphibians, focusing on three broad host factors linked to immunity: (i) composition of symbiotic microbial communities, (ii) immunogenetic variation, and (iii) stress hormone levels. Our review highlights the potential for habitat split to contribute to host-associated microbiome dysbiosis, reductions in immunogenetic repertoire, and chronic stress, that often facilitate pathogenic infections and disease in amphibians and other classes of vertebrates. We highlight that targeted habitat-restoration strategies aiming to connect multiple classes of natural habitats (e.g. terrestrial-freshwater, terrestrial-marine, marine-freshwater) could enhance priming of the vertebrate immune system through repeated low-load exposure to enzootic pathogens and reduced stress-induced immunosuppression.

Amphibians are increasingly threatened worldwide, but the availability of genomic resources that could be crucial for implementing informed conservation practices lags well behind that for other vertebrate groups. Here, we describe draft de novo genome, mitogenome, and transcriptome assemblies for the Neotropical leaf-frog Phyllomedusa bahiana native to the Brazilian Atlantic Forest and Caatinga. We used a combination of PacBio long reads and Illumina sequencing to produce a 4.74-Gbp contig-level genome assembly, which has a contiguity comparable to other recent nonchromosome level assemblies. The assembled mitogenome comprises 16,239 bp and the gene content and arrangement are similar to other Neobratrachia. RNA-sequencing from 8 tissues resulted in a highly complete (86.3%) reference transcriptome. We further use whole-genome resequencing data from P. bahiana and from its sister species Phyllomedusa burmeisteri, to demonstrate how our assembly can be used as a backbone for population genomics studies within the P. burmeisteri species group. Our assemblies thus represent important additions to the catalog of genomic resources available from amphibians.

The host‐associated microbiome plays a significant role in health. However, the roles of factors such as host genetics and microbial interactions in determining microbiome diversity remain unclear. We examined these factors using amplicon‐based sequencing of 175 Thoropa taophora frog skin swabs collected from a naturally fragmented landscape in southeastern Brazil. Specifically, we examined (1) the effects of geography and host genetics on microbiome diversity and structure; (2) the structure of microbial eukaryotic and bacterial co‐occurrence networks; and (3) co‐occurrence between microeukaryotes with bacterial OTUs known to affect growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). While bacterial alpha diversity varied by both site type and host MHC IIB genotype, microeukaryotic alpha diversity varied only by site type. However, bacteria and microeukaryote composition showed variation according to both site type and host MHC IIB genotype. Our network analysis showed the highest connectivity when both eukaryotes and bacteria were included, implying that ecological interactions may occur among domains. Lastly, anti‐Bd bacteria were not broadly negatively co‐associated with the fungal microbiome and were positively associated with potential amphibian parasites. Our findings emphasize the importance of considering both domains in microbiome research and suggest that for effective probiotic strategies for amphibian disease management, considering potential interactions among all members of the microbiome is crucial., We use a natural laboratory to examine the relationship between host genetic diversity, bacterial diversity, and microeukaryote diversity in the skin microbiome of a Brazilian frog. We find that host immunogenetic diversity is associated with variation in microbiome diversity and structure, and present results that support novel associations between microeukaryotes and bacteria on frog skin. Our results have implications for the relationships between host genetics and health mediated through microbiome diversity and structure. ​

Made available in DSpace on 2021-06-25T11:01:27Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-01 Aim: To test the importance of evolutionary and biogeographical processes in shaping the assembly of local frog communities in two adjacent regions (hereafter, coastal and inland regions) with different historical signatures. We asked two main questions: (1) why does the coastal region harbour more frog species than the inland region? and (2) how do these processes affect the spatial variation in taxonomic, phylogenetic and functional diversities within and across these regions?. Location: southeastern Brazil. Taxon: Anurans. Methods: We generated time-calibrated phylogenies to estimate the relative timing of colonization, rates of speciation, extinction and dispersal between regions. We tested the phylogenetic signal in reproductive modes. These traits were also used to examine variation in functional composition across sites. We calculated metrics of phylogenetic community structure that capture the relationships near the root and tips of the tree. Finally, we tested the relationships between the spatial variation of multiple diversity dimensions and topographic complexity, Pleistocene and contemporary climate gradients for three spatial extents: (1) only coastal sites; (2) only inland sites; and (3) the two regions combined. Results: The structure of communities was related to the region in which they are located, with regional pool size being two times greater for the coastal than inland region. This pattern seems to reflect both a higher speciation rate and earlier colonization time in the coastal than in the inland region. Reproductive modes within frog genera were less variable than among families, indicating phylogenetic signal. This pattern influenced local community assembly within the inland region due to the absence of species with direct development, tadpoles in bromeliads or eggs and tadpoles in streams in this region. Main conclusions: Macroevolutionary dynamics, such as colonization time, differences in speciation rates and niche conservatism generate the disparity in species richness and assembly patterns of local communities between regions, but not within regions, in which local communities were more similar to each other. Programa de Pós-Graduação em Ecologia e Recursos Naturais Universidade Federal de São Carlos Laboratório de Herpetologia Universidade Federal do Ceará Instituto de Biociências Universidade Federal de Mato Grosso do Sul Mato Grosso do Sul Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP) Instituto de Biociências Universidade Estadual Paulista Finnish Environment Institute Freshwater Centre Departamento de Zoologia e Botânica Universidade Estadual Paulista (UNESP) São José do Rio Preto Laboratório de Ecologia Teórica: Integrando Tempo Biologia e Espaço (LET.IT.BE) Departamento de Ciências Ambientais Universidade Federal de São Carlos Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP) Instituto de Biociências Universidade Estadual Paulista Departamento de Zoologia e Botânica Universidade Estadual Paulista (UNESP) São José do Rio Preto

Made available in DSpace on 2020-12-12T02:22:14Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-01-01 In recent years, the taxonomic knowledge of Pseudopaludicola has increased and it is currently possible to elucidate aspects of the species within this genus such as their geographic distributions. Here we accessed new data on geographic distribution of P. boliviana and three long-legged species of the P. saltica group (P. saltica, P. murundu, and P. jaredi). Based on morphometric, acoustic and genetic data, we accessed the specific status of long-legged specimens from Chapada dos Veadeiros highlands and attributed them to the P. murundu. We also performed a phylogenetic analysis including several populations of the three species. Based on this novel dataset, we discussed the geographical distributions of P. saltica, P. murundu, and P. jaredi, providing new records for them. Pseudopaludicola boliviana is one of the five species of the P. pusilla group and it is thought to be a widely distributed species based on its morphology. Hence, we evaluated the geographic distribution of P. boliviana, using novel acoustic data of specimens from Argentina, Northern Brazil, and Bolivia. Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB) Departamento de Biologia Animal Instituto de Biologia Universidade Estadual de Campinas (UNICAMP Laboratório de Taxonomia e Sistemática de Anuros Neotropicais (LTSAN) Instituto de Ciências Exatas e Naturais do Pontal Universidade Federal de Uberlândia (UFU) Instituto de Biologia Universidade Estadual de Campinas (UNICAMP Laboratório de Herpetologia Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP) Instituto de Biociências Universidade Estadual Paulista (UNESP, Rio Claro Laboratório de Citogenética Animal Departamento de Biologia Instituto de Biociências Universidade Estadual Paulista (UNESP, Rio Claro Laboratorio de Herpetología Universidad Nacional del Nordeste Laboratório de Herpetologia Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP) Instituto de Biociências Universidade Estadual Paulista (UNESP, Rio Claro Laboratório de Citogenética Animal Departamento de Biologia Instituto de Biociências Universidade Estadual Paulista (UNESP, Rio Claro

Made available in DSpace on 2022-04-29T08:46:48Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-02-22 Pristimantis is the most diverse Neotropical genus of terrestrial vertebrates and is distributed from Central America to Argentina. The last few years have seen the description of several new species of the genus, suggesting that its diversity is still underestimated. After decades of uncertainties about the taxonomic status of populations of Pristimantis from the Brejos de Altitude of the state of Cear, Northeast Brazil, we finally found morphological, acoustic and molecular evidence confirming their distinctiveness from other Atlantic Forest species. The new species is characterized by the following: shagreen dorsal skin with small-scattered tubercles, absence of dorsolateral fold, presence of tarsal fold, advertisement call composed of 18 pulsed notes, (25 pulses per note), and dominant frequency located in the second energy band, ranging from 36174220 Hz. Phylogenetic analysis placed the new species in the Pristimantis conspicillatus species group and the sister lineage of the Atlantic Forest clade comprising P. ramagii, P. paulodutrai and the P. vinhai species complex. Departamento de Biologia Universidade Federal do Cear, Centro de Cincias ,Campus do Pici Laboratrio de Vertebrados, Instituto de Cincias Biolgicas, Universidade Federal do Rio Grande, Av. Itlia, Km 8, 96203-900, Rio Grande, Rio Grande do Sul, Brazil. pinguimfiel@yahoo.com.br Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Instituto de Biocincias, Universidade Estadual Paulista (UNESP), Av. 24A, 1515, Rio Claro, So Paulo, CEP 13506-900, Brazil

Ants have long been known for their associations with other taxa, including macroscopic fungi and symbiotic bacteria. Recently, many ant species have had the composition and function of their bacterial communities investigated. Due to its behavioral and ecological diversity, the subfamily Ponerinae deserves more attention regarding its associated microbiota. Here, we used the V4 region of the 16S rRNA gene to characterize the bacterial communities of Odontomachus chelifer (ground-nesting) and Odontomachus hastatus (arboreal), two ponerine trap-jaw species commonly found in the Brazilian savanna ("Cerrado") and Atlantic rainforest. We investigated habitat effects (O. chelifer in the Cerrado and the Atlantic rainforest) and species-specific effects (both species in the Atlantic rainforest) on the bacterial communities' structure (composition and abundance) in two different body parts: cuticle and gaster. Bacterial communities differed in all populations studied. Cuticular communities were more diverse, while gaster communities presented variants common to other ants, including Wolbachia and Candidatus Tokpelaia hoelldoblerii. Odontomachus chelifer populations presented different communities in both body parts, highlighting the influence of habitat type. In the Atlantic rainforest, the outcome depended on the body part targeted. Cuticular communities were similar between species, reinforcing the habitat effect on bacterial communities, which are mainly composed of environmentally acquired taxa. Gaster communities, however, differed between the two Odontomachus species, suggesting species-specific effects and selective filters. Unclassified Firmicutes and uncultured Rhizobiales variants are the main components accounting for the observed differences. Our study indicates that both host species and habitat act synergistically, but to different degrees, to shape the bacterial communities in these Odontomachus species.

Here, we summarize examples of significant advances in amphibian research supported by the São Paulo Research Foundation (FAPESP), focusing on recent discoveries in the fields of community ecology, habitat change, infection diseases, and multipurpose DNA sequencing. We demonstrated that FAPESP has been fundamental not only by directly funding research projects and scholarships, but also through its science training policy, fostering international collaborations with world-class research institutions, improving and consolidating new lines of research that often depended on a synergetic combination of different knowledge and complex tools. We emphasized that future studies will continue to focus on basic questions, such as description of new species, as well as taxonomic and systematic corrections. Furthermore, we also expect that there will be a strong integration among different disciplines using novel bioinformatics tools and modeling approaches, such as machine learning. These new approaches will be critical to further develop our understanding of foundational questions of amphibian life-history trait variation, disease transmission, community assembly, biogeography, and population forecasts under different global change scenarios such as agricultural expansion, agrochemical use, habitat loss, and climate change.

Background Host microbiomes may differ under the same environmental conditions and these differences may influence susceptibility to infection. Amphibians are ideal for comparing microbiomes in the context of disease defense because hundreds of species face infection with the skin-invading microbe Batrachochytrium dendrobatidis (Bd), and species richness of host communities, including their skin bacteria (bacteriome), may be exceptionally high. We conducted a landscape-scale Bd survey of six co-occurring amphibian species in Brazil’s Atlantic Forest. To test the bacteriome as a driver of differential Bd prevalence, we compared bacteriome composition and co-occurrence network structure among the six focal host species. Results Intensive sampling yielded divergent Bd prevalence in two ecologically similar terrestrial-breeding species, a group with historically low Bd resistance. Specifically, we detected the highest Bd prevalence in Ischnocnema henselii but no Bd detections in Haddadus binotatus. Haddadus binotatus carried the highest bacteriome alpha and common core diversity, and a modular network partitioned by negative co-occurrences, characteristics associated with community stability and competitive interactions that could inhibit Bd colonization. Conclusions Our findings suggest that community structure of the bacteriome might drive Bd resistance in H. binotatus, which could guide microbiome manipulation as a conservation strategy to protect diverse radiations of direct-developing species from Bd-induced population collapses.

Temperature-induced developmental plasticity could allow amphibian larvae to complete metamorphosis successfully despite new thermal challenges and increased desiccation risk due to climate change. Here we investigated how the capacity for temperature-induced developmental plasticity varies with latitude and whether population-specific biogeographic background accounts for the different degree of plastic responses to temperature. We carried out a combined analysis based on the data from 150 studies (93 articles) performed on 64 amphibian species. We collected empirical data for age and size at metamorphosis in amphibian larvae acclimated to different temperatures during development and found that all larvae from all populations in these studies revealed a change in metamorphic traits with a given change in temperature and thus, were able to exhibit temperature-induced developmental plasticity. Age at metamorphosis was more affected by temperature than size at metamorphosis. Age and size at the onset of metamorphosis were generally lowest at warmest temperatures during development. Furthermore, populations from tropical latitudes were less sensitive to a change in developmental temperature compared to populations from higher latitudes. Accordingly, we suggest tropical populations to be the most vulnerable to increasing temperatures during metamorphosis. Our analyses reveal biases with respect to taxonomy, biogeographic distribution of species, and study design. Data from tropical populations are underrepresented and thus, the capacity for developmental plasticity of the most threatened species probably remains poorly understood. Future studies should focus on under-represented regions, most threatened species, and include a broader range of temperatures during development in order to make robust projections on future sensitivity of populations to climate change.

Made available in DSpace on 2022-04-29T08:38:53Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-04-01 ASCRS Research Foundation Phylogeographic studies primarily focus on the major role of landscape topography in driving lineage diversification. However, populational phylogeographic breaks may also occur as a result of either niche conservatism or divergence, in the absence of geographic barriers to gene flow. Furthermore, these two factors are not mutually exclusive and can act in concert, making it challenging to evaluate their relative importances on explaining genetic variation in nature. Herein, we use sequences of two mitochondrial and four nuclear genes to investigate the timing and diversification patterns of species pertaining to the Leptodactylus latrans complex, which harbors four morphologically cryptic species with broad distributions across environmental gradients in eastern South America. The origin of this species complex dates back to the late Miocene (ca. 5.5 Mya), but most diversification events occurred synchronically during the late Pleistocene likely as the result of ecological divergence driven by Quaternary climatic oscillations. Further, significant patterns of environmental niche divergences among species in the L. latrans complex imply that ecological isolation is the primary mode of genetic diversification, mostly because phylogenetic breaks are associated with environmental transitions rather than topographic barriers at both species and populational scales. We provided new insights about diversification patterns and processes within a species complex of broadly and continuously distributed group of frogs along South America. Programa de Pós-Graduação em Ciências Biológicas Universidade Federal da Paraíba–UFPB Centro de Ciências Exatas e da Natureza, Cidade Universitária Paraiba Earth and Environmental Sciences Ecology and Evolution Rutgers University-Newark, 195 University Ave Instituto de Biociências Universidade Federal de Mato Grosso do Sul, Cidade Universitária Instituto de Biociências Universidade Estadual Paulista Campus Rio Claro Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP) Laboratório de Herpetologia, Cx. Postal 199 São Paulo Instituto de Biología Subtropical (IBS CONICET-UNaM) Laboratorio de Genética Evolutiva Facultad de Ciencias Exactas Universidad Nacional de Misiones, Félix de Azara 1552 Misiones Laboratório de Anfíbios e Répteis (LAR) Departamento de Botânica e Zoologia da Universidade Federal do Rio Grande do Norte, Campus Universitário. Lagoa Nova Rio Grande do Norte Instituto de Biociências Universidade Estadual Paulista Campus Rio Claro Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP) Laboratório de Herpetologia, Cx. Postal 199 São Paulo

Amphibians are known to possess a wide variety of compounds stored in their skin glands. While significant progress has been made in understanding the chemical diversity and biological relevance of alkaloids, amines, steroids, and peptides, most aspects of the odorous secretions are completely unknown. In this study, we examined sexual variations in the volatile profile from the skin of the tree frog Boana prasina and combined culture and culture-independent methods to investigate if microorganisms might be a source of these compounds. We found that sesquiterpenes, thioethers, and methoxypyrazines are major contributors to the observed sex differences. We also observed that each sex has a distinct profile of methoxypyrazines, and that the chemical origin of these compounds can be traced to a Pseudomonas sp. strain isolated from the frog´s skin. This symbiotic bacterium was present in almost all individuals examined from different sites and was maintained in captive conditions, supporting its significance as the source of methoxypyrazines in these frogs. Our results highlight the potential relevance of bacteria as a source of chemical signals in amphibians and contribute to increasing our understanding of the role that symbiotic associations have in animals. Fil: Brunetti, Andrés Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentina. Universidade de Sao Paulo; Brasil Fil: Lucio Lyra, Mariana. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil Fil: Melo, Weilan G. P.. Universidade de Sao Paulo; Brasil Fil: Andrade, Laura Elena. Universidade de Sao Paulo; Brasil Fil: Palacios Rodríguez, Pablo. Universidad de los Andes; Colombia Fil: Prado, Bárbara M.. Universidade de Sao Paulo; Brasil Fil: Baptista Haddad, Célio Fernando. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil Fil: Tallarico Pupo, Monica. Universidade de Sao Paulo; Brasil Fil: Peporine Lopes, Norberto. Universidade de Sao Paulo; Brasil

We reconstructed nearly complete mitogenomes for three species of poison frogs, Dendrobates auratus, D. leucomelas, and D. tinctorius, from RNAseq data. We recovered the 13 protein-coding genes, 22 tRNA genes (except tRNA-Val for D. leucomelas), and two rRNA genes for all three species, plus partial sequences of the control region. The order of genes agrees with that known from a previously sequenced D. auratus, being the most commonly found for neobatrachian frogs. Based on full-sibling comparisons we estimate the probable error rate of Illumina-RNAseq reconstructed mitogenomes of up to 0.15%.

Made available in DSpace on 2021-06-25T10:55:53Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-01 Aim: There is little consensus on which environmental variables are best at predicting multiple dimensions of diversity. We ask whether there are common environmental correlates of diversity, despite ecological differences, across nine clades of plants and animals distributed along a single rainforest domain. For that, we compare the environmental correlates of species richness, phylogenetic diversity, and phylogenetic endemism. Location: Brazilian Atlantic Forest. Taxon:Five clades of plants (Bromelioideae, Miconieae, Bertolonia, Cambessedesieae, and the Fridericia and allies) and four clades of animals (butterlies in the tribe Ithomiini, frogs in the genera Boana and Proceratophrys, and birds in the subfamily Thraupinae). Methods: Using curated occurrence localities and phylogenetic data, we generated maps of (a) species richness, (b) phylogenetic diversity, (c) residuals of phylogenetic diversity regressed on species richness, and (d) phylogenetic endemism for all groups. We also compiled a set of 30 environmental descriptors, including records of current temperature and precipitation, climatic stability over time, and topography. Through a machine learning framework, we explored the environmental correlates of each of these diversity measures for each group. Results: The environmental variables used here were strong predictors of diversity for all studied groups. However, models for phylogenetic endemism had lower predictive power. Although patterns of diversity are different among groups, correlates of diversity are consistent across taxa. For both species richness and phylogenetic diversity, current precipitation and precipitation stability over time were consistently ranked among the variables that strongly correlate with diversity patterns. The correlates of phylogenetic endemism were less homogeneous across groups. The results suggest that including climate stability over time is important when predicting diversity measures that reflect historical components. Main conclusions: Investigating environmental correlates of diversity for multiple clades and diversity measures in a single geographic area allows for a better understanding of common patterns across taxa. This study shows that environmental conditions, particularly precipitation, are good predictors of the patterns of species richness and phylogenetic diversity-but not phylogenetic endemism-across different Atlantic Forest groups. Department of Biology City College of New York Ph.D. Program in Biology Graduate Center City University of New York Department of Zoology School of Biological Sciences Southern Illinois University Instituto de Geociências e Ciências Exatas UNESP-Universidade Estadual Paulista Departamento de Geografia Observatório de Dinâmicas Ecossistêmicas Instituto de Ciencias Naturales Universidad Nacional de Colombia Instituto de Biociências Universidade de São Paulo Departamento de Ecologia e Biologia Evolutiva Universidade Federal de São Paulo Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Universidade Federal de Santa Catarina Departamento de Biodiversidade & Centro de Aquicultura (CAUNESP) Instituto de Biociências Universidade Estadual Paulista Institute of Energy and Environment Universidade de São Paulo Departamento de Botânica Universidade Federal do Rio Grande do Sul Universidade Federal do ABC Santo André UFABC Departamento de Biologia Animal & Museu da Biodiversidade Instituto de Biologia Unicamp Universidade Federal do Paraná Institute of Systematic Botany The New York Botanical Garden Departamento de Genética e Biologia Evolutiva Instituto de Biociências Universidade de São Paulo Biological and Environmental Sciences Faculty of Natural Sciences University of Stirling Instituto de Geociências e Ciências Exatas UNESP-Universidade Estadual Paulista Departamento de Geografia Observatório de Dinâmicas Ecossistêmicas Departamento de Biodiversidade & Centro de Aquicultura (CAUNESP) Instituto de Biociências Universidade Estadual Paulista

Made available in DSpace on 2022-04-29T08:30:43Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-01 The mitogenome of the South American parthenogenetic lizard Loxopholis percarinatum Müller, 1923 (Squamata: Gymnophthalmidae), a uni-bisexual species complex, was recovered for three individuals from Rio Negro region, Amazonas, Brazil. The content and order of genes are typical for vertebrate mitochondrial genomes, and we recovered 13 protein-coding genes, 22 tRNA, and two rRNA (12S and 16S), in addition to partial fragments of the Control Region. A maximum likelihood phylogenetic analysis with mitogenomes of selected lizard families recovered L. percarinatum with Iphisa elegans Gray, 1851, the only other Gymnophthalmidae species available in GenBank. Departamento de Zoologia Instituto de Biociências Universidade de São Paulo Departamento de Biodiversidade e Centro de Aquicultura Instituto de Biociências Universidade Estadual Paulista (UNESP) Amphibian and Reptile Diversity Research Center and Department of Biology University of Texas at Arlington Departamento de Ecologia e Biologia Evolutiva Universidade Federal de São Paulo Departamento de Biodiversidade e Centro de Aquicultura Instituto de Biociências Universidade Estadual Paulista (UNESP)

Declines and extinctions are increasing globally and challenge conservationists to keep pace with biodiversity monitoring. Organisms leave DNA traces in the environment, e.g., in soil, water, and air. These DNA traces are referred to as environmental DNA (eDNA). The analysis of eDNA is a highly sensitive method with the potential to rapidly assess local diversity and the status of threatened species. We searched for DNA traces of 30 target amphibian species of conservation concern, at different levels of threat, using an environmental DNA metabarcoding approach, together with an extensive sequence reference database to analyse water samples from six montane sites in the Atlantic Coastal Forest and adjacent Cerrado grasslands of Brazil. We successfully detected DNA traces of four declined species (Hylodes ornatus, Hylodes regius, Crossodactylus timbuhy, and Vitreorana eurygnatha); two locally disappeared (Phasmahyla exilis and Phasmahyla guttata); and one species that has not been seen since 1968 (putatively assigned to Megaelosia bocainensis). We confirm the presence of species undetected by traditional methods, underscoring the efficacy of eDNA metabarcoding for biodiversity monitoring at low population densities, especially in megadiverse tropical sites. Our results support the potential application of eDNA in conservation biology, to evaluate persistence and distribution of threatened species in surveyed habitats or sites, and improve accuracy of red lists, especially for species undetected over long periods.

Made available in DSpace on 2020-12-12T02:22:06Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-01-01 The Neotropical frog genus Pseudopaludicola includes 25 species distributed throughout South America. Herein we review the taxonomic status of P. parnaiba relative to P. canga and the specific identity of the population treated in previous studies as Pseudopaludicola sp. 3 from Barreirinhas in the Brazilian state of Maranhão. The lack of differentiation in advertisement call, morphology, and mitochondrial markers from topotypes and different populations rejects the status of P. parnaiba and Pseudopaludicola sp. 3 from Barreirinhas as distinct species. For these reasons, we suggest to formally consider P. parnaiba as a junior synonym of P. canga. We also found that a population previously reported as P. facureae from central Brazil (Palmeiras de Goiás, Goiás) corresponds to a cryptic species that we describe here as a new species. Lastly, we provide for the first time the phylogenetic positions of P. giarettai, P. llanera and P. pusilla. Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB) Departamento de Biologia Animal Instituto de Biologia Universidade Estadual de Campinas (UNICAMP) Laboratório de Taxonomia e Sistemática de Anuros Neotropicais (LTSAN) Instituto de Ciências Exatas e Naturais do Pontal (ICENP) Universidade Federal de Uberlândia (UFU) Instituto de Biologia Universidade Estadual de Campinas (UNICAMP) Laboratório de Herpetologia Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP) Instituto de Biociências Universidade Estadual Paulista (UNESP) Laboratório de Herpetologia Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP) Instituto de Biociências Universidade Estadual Paulista (UNESP)

The host-associated microbiome plays a significant role in health. However, the roles of factors such as host genetics and microbial interactions in determining microbiome diversity remain unclear. We examined these factors using amplicon-based sequencing of 175 Thoropa taophora frog skin swabs collected from a naturally fragmented landscape in southeastern Brazil. Specifically, we examined (1) the effects of geography and host genetics on microbiome diversity and structure; (2) the structure of microbial eukaryotic and bacterial co-occurrence networks; and (3) co-occurrence between microeukaryotes with bacterial OTUs known to affect growth of the fungal frog pathogen Batrachochytrium dendrobatidis (including anti-Bd bacteria commonly referred to as “antifungal”). Microbiome structure correlated with geographic distance, and microbiome diversity varied with both overall host genetic diversity and diversity at the frog MHC IIB immunity locus. Our network analysis showed the highest connectivity when both eukaryotes and bacteria were included, implying that ecological interactions occur among Domains. Lastly, anti-Bd bacteria did not demonstrate broad negative co-occurrence with fungal OTUs in the microbiome, indicating that these bacteria are unlikely to be broadly antifungal. Our findings emphasize the importance of considering both Domains in microbiome research, and suggest that probiotic strategies for amphibian disease management should be considered with caution.

Made available in DSpace on 2020-12-12T01:22:39Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-01-17 The subgenus Mantidactylus is a group of frogs endemic to Madagascar, including the largest anuran species on the island. Although these frogs are common and widely distributed, their taxonomy remains unclear. Two species are currently recognised, M. grandidieri and M. guttulatus, with another available name, Rana pigra, considered to be a synonym of M. grandidieri. However, molecular studies have suggested the presence of several cryptic species within the group. Additionally, due to the lack of prominent morphological features, allocating the available names to evolutionary lineages has proven challenging. In the present study, we take a first step towards solving these problems by using fragments of the 16S mitochondrial gene and RAG1 nuclear gene from all over the range of the subgenus to describe its genetic diversity. We also use a newly designed target enrichment laboratory protocol to sequence three mitochondrial fragments from five name-holding museum specimens (as old as 120 years) in order to determine to which lineages the existing names should be applied. The study of the 16S mitochondrial gene revealed 7 geographically separated lineages, distinct enough to be considered candidate species. Out of the five museum specimens analysed, four successfully yielded DNA sequences and could be attributed to one of the aforementioned lineages. Therefore, the name Mantidactylus grandidieri should be applied to the populations from North-Eastern Madagascar, while M. guttulatus refers to populations from inland localities along the Eastern coast of the island. On the other hand, the holotype of Rana pigra did not yield enough genetic material to allow definitive identification. While our data were not sufficient to assess the status of the four lineages distributed along the Eastern coast, the populations from North-Western Madagascar were highly distinct on both the mitochondrial and nuclear markers. We thus describe them as a new species, M. radaka sp. nov. http://www.zoobank.org/urn:lsid:zoobank.org:pub:1EDDAF0D-FE37-490A-B09E-E136A0C5CB35. Zoological Institute Braunschweig University of Technology Sektion Herpetologie Zoologische Staatssammlung München (ZSM-SNSB) Institut de Systématique Biodiversité (ISYEB) Sorbonne Université Programa de Pós-Graduação em Biologia Animal Departamento de Biologia Animal Laboratório de Herpetologia Universidade Federal Rural do Rio de Janeiro Faculty of Mathematics and Natural Sciences Institute for Biochemistry and Biology University of Potsdam Department of Natural History University Museum of Bergen Depto de Zoologia Instituto de Biologia Universidade Estadual Paulista - UNESP Department of Life Sciences The Natural History Museum, Cromwell Road Museo Regionale di Scienze Naturali Research Centre in Biodiversity Genetics and Evolution Universidade do Porto Biodiversity Institute and Department of Ecology and Evolutionary Biology University of Kansas Mention Zoologie et Biodiversité Animale Faculté des Sciences Université d’Antananarivo Depto de Zoologia Instituto de Biologia Universidade Estadual Paulista - UNESP

Made available in DSpace on 2020-12-10T17:36:29Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-07-07 Aim We combine phylogenetic and point locality data from selected lineages of the Atlantic Forest flora and fauna to compare spatial patterns of biodiversity sustained by the current configuration of forest remnants to a scenario of complete forest preservation. We then ask the question how much biodiversity is likely lost, already? Specifically, we assess how habitat loss likely impacted the climatic spaces occupied by the local species, the inferred composition of local communities and the spatial distribution of phylogenetic diversity and endemism. Location Atlantic Forest, Brazil. Methods Using carefully curated point localities, phylogenetic data and parameterized models of species distributions, we generate maps of phylogenetic diversity, phylogenetic endemism and phylogenetic turnover for the entire Atlantic Forest. We map patterns of clade-specific diversity under complete preservation of forest and then incorporate present-day deforestation patterns to provide a more realistic scenario. Results Instead of a singular pattern, three different reoccurring syndromes described the flora and fauna of the Atlantic Forest. These patterns emerged irrespectively of clade age and life history traits. General turnover patterns were highly consistent with previous analyses of species composition and panbiogeographical studies. Deforestation has altered the availability of climatic spaces in the Atlantic Forest, its biological communities and the distribution of evolutionary lineages in space. However, approximately 60% of the pre-Columbian climatic space persists in forest remnants, and today's biological communities are estimated to be 45% similar to pre-deforestation times. Main conclusions The Atlantic Forest has been reduced to 8% of its once largely continuous range. However, the disproportionately large amounts of climate, community and lineage diversity that persist in remnants provide hope and support for conservation efforts that combine species occurrence and phylogenetic data. Inclusion of evolutionary thinking into strategic approaches to restoring Brazilian ecosystems could further conservation effectiveness by incorporating the adaptive potential of local assemblages in the face of further environmental shifts. Southern Illinois Univ, Sch Biol Sci, Carbondale, IL 62901 USA CUNY, Grad Ctr, City Coll New York Biol Program 1, Biol Dept, New York, NY USA Univ Fed Rio Grande do Sul, Dept Bot, Porto Alegre, RS, Brazil Univ Fed Sao Paulo, Campus Diadema, Diadema, Brazil Univ Sao Paulo, Inst Biociencias, Sao Paulo, Brazil Univ Estadual Paulista, Campus Rio Claro, Rio Claro, Brazil Univ Fed Santa Catarina, Dept Bot, Florianopolis, SC, Brazil Univ Nacl Colombia, Inst Ciencias Nat, Bogota, Colombia Inst Nacl de Pesquisas da Amazonia, Manaus, Amazonas, Brazil Univ Fed Parana, Curitiba, Parana, Brazil Univ Fed ABC, Ctr Ciencias Nat & Humanas, Santo Andre, SP, Brazil Univ Estadual Campinas, Campinas, Brazil New York Bot Garden, Bronx, NY 10458 USA Univ Estadual Paulista, Campus Rio Claro, Rio Claro, Brazil

Made available in DSpace on 2022-04-29T08:33:20Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-01-01 Species delimitation can be challenging and affected by subjectivity. Sibling lineages that occur in sympatry constitute good candidates for species delimitation regardless of the adopted species concept. The Thoropa miliaris + T. taophora species complex exhibits high genetic diversity distributed in several lineages that occur sympatrically in the southeastern Atlantic Forest of Brazil. We used 414 loci obtained by anchored hybrid enrichment to characterize genetic variation in the Thoropa miliaris species group (T. saxatilis, T megatympanum, T. miliaris, and T. taophora), combining assignment analyses with traditional and coalescent phylogeny reconstruction. We also investigated evolutionary independence in co-occurring lineages by estimating gene flow, and validated lineages under the multispecies coalescent. We recovered most previously described lineages as unique populations in assignment analyses; exceptions include two lineages within T. miliaris that are further substructured, and the merging of all T. taophora lineages. We found very low probabilities of gene flow between sympatric lineages, suggesting independent evolution. Species tree inferences and species delimitation yielded resolved relationships and indicate that all lineages constitute putative species that diverged during the Pliocene and Pleistocene, later than previously estimated. Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP) Instituto de Biociências Universidade Estadual Paulista - UNESP Departamento de Ecologia e Biologia Evolutiva Universidade Federal de São Paulo, 09972-270 Diadema Department of Biological Sciences Florida State University Department of Scientific Computing Florida State University Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP) Instituto de Biociências Universidade Estadual Paulista - UNESP

Made available in DSpace on 2019-10-04T12:30:57Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-10-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) The New World screwworm fly Cochliomyia hominivorax (Coquerel, 1858) (Diptera: Calliphoridae) is an important livestock pest endemic to the Americas that has been eradicated from North and continental Central America with a control program based on the Sterile Insect Technique (SIT). The establishment of target management units is a strategic step in the implementation of new control programs, which can be achieved using genetic studies of natural populations. Previous studies of New World screwworm fly populations were conducted on the continental scale and identified four main groups: two in South America and two in the Caribbean. However, studies within these groups are needed to determine which smaller geographic areas can be treated as management units. Here, we analyze the genetic variability distribution and the population demographic signals of the New World screwworm fly in a 6,000 km(2) area located along the border of Brazil and Uruguay.This area was the subject of the first control pilot program conducted in South America. We studied eight microsatellite loci and sequences from two mitochondrial DNA regions in individuals sampled at 20-25 livestock breeding farms. We observed no population structure and found high genetic variability on the geographical scale sampled for both molecular markers. Our microsatellite data suggest that these populations are not in equilibrium, and demographic analyses based on mitochondrial data indicate population expansion.These results suggest that this geographic scale is not adequate for future New World screwworm fly management in South America. Univ Estadual Campinas, UNICAMP, Inst Biol, Dept Genet Evolucao Microbiol & Imunol, BR-13083970 Campinas, SP, Brazil Univ Estadual Campinas, UNICAMP, Programa Posgrad Genet & Biol Mol, BR-13083970 Campinas, SP, Brazil Univ Estadual Campinas, UNICAMP, Ctr Biol Mol & Engn Genet, Av Candido Rondon 400, BR-13083875 Campinas, SP, Brazil Inst Pasteur Montevideo, Unidad Bioinformat, Montevideo 11400, Uruguay Univ Estadual Paulista, Inst Biociencias, Dept Zool, BR-13506900 Rio Claro, SP, Brazil Univ Estadual Paulista, Inst Biociencias, Dept Zool, BR-13506900 Rio Claro, SP, Brazil CNPq: 578231/2008-5 MAPA CNPq: 141777/2014-1

Made available in DSpace on 2018-11-26T17:48:23Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-05-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) The Brazilian Atlantic coastal forest is one of the most heterogeneous morphoclimatic domains on earth and is thus an excellent region in which to examine the role that habitat heterogeneity plays in shaping diversification of lineages and species. Here we present a molecular phylogeny of the rock frogs of the genus Thoropa Cope, 1865, native to the Atlantic forest and extending to adjacent campo rupestre of Brazil. The goal of this study is to reconstruct the evolutionary history of the genus using multilocus molecular phylogenetic analyses. Our topology reveals 12 highly supported lineages among the four nominal species included in the study. Species T. saxatilis and T. megatympanum are monophyletic. Thoropa taophora is also monophyletic, but nested within T. miliaris. Populations of T. miliaris cluster in five geographically distinct lineages, with low support for relationships among them. Although all 12 lineages are geographically structured, some T. miliaris lineages have syntopic distributions with others, likely reflecting a secondary contact zone between divergent lineages. We discuss a biogeographic scenario that best explains the order of divergence and the distribution of species in Atlantic forest and adjacent areas, and outline the implications of our findings for the taxonomy of Thoropa. Univ Estadual Paulista, Inst Biociencias, Dept Zool, BR-13506900 Sao Paulo, Brazil Univ Estadual Paulista, Ctr Aquicultura CAUNESP, BR-13506900 Sao Paulo, Brazil Cornell Univ, Dept Ecol & Evolutionary Biol, Ithaca, NY 14853 USA Univ Fed Vicosa, Dept Biol Anim, Museu Zool Joao Moojen, Ctr Ciencias Biol & Saude, BR-36571000 Vicosa, MG, Brazil Univ Fed Vicosa, Inst Ciencias Biol & Saude, BR-35690000 Florestal, MG, Brazil Univ Fed Espirito Santo, Lab Vertebrados Terr, BR-29932540 Sao Mateus, ES, Brazil Univ Estadual Campinas, Inst Biociencias, Grp Hist Nat Vertebrados, BR-13083970 Campinas, SP, Brazil Univ Fed Sao Paulo, Dept Ecol & Biol Evolut, BR-09972270 Sao Paulo, Brazil Univ Estadual Paulista, Inst Biociencias, Dept Zool, BR-13506900 Sao Paulo, Brazil Univ Estadual Paulista, Ctr Aquicultura CAUNESP, BR-13506900 Sao Paulo, Brazil FAPESP: 08/50928-1 FAPESP: 13/50741-7 FAPESP: 2014/50342-8 CNPq: 564955/2010-8 CNPq: 302518/2013-4

Made available in DSpace on 2018-12-11T17:17:26Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-06-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Heteromorphic sex chromosomes are common in eukaryotes and largely ubiquitous in birds and mammals. The largest number of multiple sex chromosomes in vertebrates known today is found in the monotreme platypus (Ornithorhynchus anatinus, 2n = 52) which exhibits precisely 10 sex chromosomes. Interestingly, fish, amphibians, and reptiles have sex determination mechanisms that do or do not involve morphologically differentiated sex chromosomes. Relatively few amphibian species carry heteromorphic sex chromosomes, and when present, they are frequently represented by only one pair, either XX:XY or ZZ:ZW types. Here, in contrast, with several evidences, from classical and molecular cytogenetic analyses, we found 12 sex chromosomes in a Brazilian population of the smoky jungle frog, designated as Leptodactylus pentadactylus Laurenti, 1768 (Leptodactylinae), which has a karyotype with 2n = 22 chromosomes. Males exhibited an astonishing stable ring-shaped meiotic chain composed of six X and six Y chromosomes. The number of sex chromosomes is larger than the number of autosomes found, and these data represent the largest number of multiple sex chromosomes ever found among vertebrate species. Additionally, sequence and karyotype variation data suggest that this species may represent a complex of species, in which the chromosomal rearrangements may possibly have played an important role in the evolution process. Departamento de Biologia Instituto de Biociências UNESP – Universidade Estadual Paulista, Campus de Rio Claro Departamento de Zoologia and Centro de Aquicultura (CAUNESP) Instituto de Biociências UNESP – Universidade Estadual Paulista, Campus de Rio Claro Departamento de Biologia Instituto de Biociências UNESP – Universidade Estadual Paulista, Campus de Rio Claro Departamento de Zoologia and Centro de Aquicultura (CAUNESP) Instituto de Biociências UNESP – Universidade Estadual Paulista, Campus de Rio Claro FAPESP: 2013/50741-7 CNPq: 473264/212-9

Made available in DSpace on 2022-04-28T19:44:50Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-12-01 The 71 currently known species of dwarf geckos of the genus Lygodactylus are a clade of biogeographic interest due to their occurrence in continental Africa, Madagascar, and South America. Furthermore, because many species are morphologically cryptic, our knowledge of species-level diversity within this genus is incomplete, as indicated by numerous unnamed genetic lineages revealed in previous molecular studies. Here we provide an extensive multigene phylogeny covering 56 of the named Lygodactylus species, four named subspecies, and 34 candidate species of which 19 are newly identified in this study. Phylogenetic analyses, based on ∼10.1 kbp concatenated sequences of eight nuclear-encoded and five mitochondrial gene fragments, confirm the monophyly of 14 Lygodactylus species groups, arranged in four major clades. We recover two clades splitting from basal nodes, one comprising exclusively Malagasy species groups, and the other containing three clades. In the latter, there is a clade with only Madagascar species, which is followed by a clade containing three African and one South American species groups, and its sister clade containing six African and two Malagasy species groups. Relationships among species groups within these latter clades remain weakly supported. We reconstruct a Lygodactylus timetree based on a novel fossil-dated phylotranscriptomic tree of squamates, in which we included data from two newly sequenced Lygodactylus transcriptomes. We estimate the crown diversification of Lygodactylus started at 46 mya, and the dispersal of Lygodactylus among the main landmasses in the Oligocene and Miocene, 35–22 mya, but emphasize the wide confidence intervals of these estimates. The phylogeny suggests an initial out-of-Madagascar dispersal as most parsimonious, but accounting for poorly resolved nodes, an out-of-Africa scenario may only require one extra dispersal step. More accurate inferences into the biogeographic history of these geckos will likely require broader sampling of related genera and phylogenomic approaches to provide better topological support. A survey of morphological characters revealed that most of the major clades and species groups within Lygodactylus cannot be unambiguously characterized by external morphology alone, neither by unique character states nor by a diagnostic combination of character states. Thus, any future taxonomic work will likely benefit from integrative, phylogenomic approaches. Zoological Institute Technical University of Braunschweig, Mendelssohnstr. 4 State Natural History Museum of Braunschweig, Pockelsstr. 10 Department of Biological Sciences Rutgers University-Newark, 195 University Avenue Faculty of Mathematics and Natural Sciences Institute for Biochemistry and Biology University of Potsdam Department of Biology University of Florida, 220 Bartram Hall Departamento de Biodiversidade Instituto de Biociências Universidade Estadual Paulista (UNESP), Campus Rio Claro, Avenida 24A, N 1515 Bela Vista Santa Fe College, 3000 NW 83rd St. Florida Museum of Natural History Division of Herpetology, 1659 Museum Road – Dickinson Hall Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21 Department of Biology and Center for Biodiversity and Ecosystem Stewardship Villanova University, 800 Lancaster Avenue Departamento de Biodiversidade Instituto de Biociências Universidade Estadual Paulista (UNESP), Campus Rio Claro, Avenida 24A, N 1515 Bela Vista

Made available in DSpace on 2021-06-25T10:56:14Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-07-01 We evaluated the role of Quaternary climatic fluctuations on the demographic history and population structure of amphibian species endemic to the ‘campo rupestre’ in the Neotropics, evaluating their distributional shifts, demographic changes, and lineage formation from the end of Pleistocene to present. We chose two anurans endemic to the high-elevation ‘campo rupestre’ in the Espinhaço Range (ER) in northeastern and southeastern Brazil (Bokermannohyla alvarengai and Bokermannohyla oxente), as models to test the role of Quaternary climatic fluctuations over their distribution range in this region. We collected tissue samples throughout their distribution range and used statistical phylogeography to examine processes of divergence and population demography. We generated spatial–temporal reconstructions using Bayesian inference in a coalescent framework in combination with hind-cast projections of species distribution models (SDMs). We also used the results and literature information to test alternative diversification scenarios via approximate Bayesian computation (ABC). Our results show that Quaternary climatic fluctuations influenced the geographic ranges of both species showing population expansion during the last glacial maximum (LGM) and range contraction during interglacial periods, as inferred from selected ABC models and from past projections of SDMs. We recovered Pleistocene diversification for both species occuring in distinctly unique periods for each taxon. An older and range-restricted lineage was recovered in a geographically isolated geological massif, deserving conservation and further taxonomic study. The diversification and distribution of these amphibian species endemic to the Neotropical ‘campo rupestre’ were influenced by Quaternary climatic fluctuations. The expansion of cold adapted species restricted to higher elevations during glacial periods and their concomitant retraction during interglacial periods may have been crucial for producing patterns of species richness and endemism along elevation gradients in tropical and subtropical domains. Such processes may influence the evolution of the biota distributed in heterogeneous landscapes with varied topography. Programa de Pós-graduação em Ecologia e Conservação da Biodiversidade Universidade Estadual de Santa Cruz Department of Herpetology American Museum of Natural History Herpetology Section Zoologisches Forschungsmuseum Alexander Koenig Instituto Federal Goiano – IF Goiano Departamento de Biologia Departamento de Ciências Naturais Campus Dom Bosco Universidade Federal de São João del-Rei Laboratório Sagarana Instituto de Ciências Biológicas e da Saúde Universidade Federal de Viçosa – UFV Department of Earth and Environmental Sciences Rutgers University - Newark Universidade Estadual Paulista (UNESP) Departamento de Biodiversidade Instituto de Biociências and Centro de Aquicultura (CAUNESP), Campus Rio Claro Universidade Estadual Paulista (UNESP) Departamento de Biodiversidade Instituto de Biociências and Centro de Aquicultura (CAUNESP), Campus Rio Claro

Made available in DSpace on 2018-12-11T17:23:22Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-04-03 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Physalaemus centralis is distributed over open areas of eastern South America. Herein, we perform an extensive review of occurrence records and propose a potential distribution based on ecological niche modeling. In order to confirm species identification, as well taxonomic status along its distribution, we provide morphological and molecular data from analysed specimens. To reach our goals, we compiled data available in the literature and from scientific collections, as well as unpublished data. We identified records of P. centralis in 123 localities, 86 of those records remain unpublished. Consequently, it is possible to extend its range of distribution to the state of Rondônia, Brazil, and also to the Caatinga formation. The Maxent algorithm provided a model of potential distribution consistent with the distribution proposed here. Results indicate that P. centralis has a large distribution associated to open areas of South America (Cerrado, Caatinga and Pantanal), with no evidence that this is a case of species complex. The multiple approach proposed herein, that combines occurrence data from different sources and molecular data to confirm species identification, provided consistent results. Therefore, we recommend that this framework be used as a protocol to assess species distribution in future studies, especially in the case of widely distributed species. Laboratório de Vertebrados. Av. Itália Instituto de Ciências Biológicas Universidade Federal do Rio Grande, km 8, Vila Carreiros Laboratório de Herpetologia Departamento de Zoologia Instituto de Biociências Universidade Estadual Paulista (UNESP), Av 24 A, 1515, Bela Vista, Caixa Postal 199 Laboratório de Ecologia e Sistemática Departamento de Ciências Biológicas Instituto de Ciências Ambientais Químicas e Farmacêuticas Universidade Federal de São Paulo, Rua Prof. Artur Riedel, 275, Eldorado Laboratório de Herpetologia Departamento de Zoologia Instituto de Biociências Universidade Estadual Paulista (UNESP), Av 24 A, 1515, Bela Vista, Caixa Postal 199

Made available in DSpace on 2020-12-10T19:54:02Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-03-27 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Rede Baiana de Pesquisa sobre Anfibios (RBPA) Fundacao O Boticario de Protecao a Natureza Fundacao de Amparo a Pesquisa da Bahia (FAPESB) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Mohamed bin Zayed Species Conservation Fund Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) Smithsonian Institution (USA) Agencia Nacional de Promocion Cientifica y Tecnologica (ANPCyT) The South American and West Indian Casque-headed Treefrogs (Hylidae: Hylinae: Lophyohylini) include 85 species. These are notably diverse in morphology (e.g. disparate levels of cranial hyperossification) and life history (e.g. different reproductive modes, chemical defences), have a wide distribution, and occupy habitats from the tropical rainforests to semiarid scrubland. In this paper, we present a phylogenetic analysis of this hylid tribe based on sequence fragments of up to five mitochondrial (12S, 16S, ND1, COI, Cytb) and six nuclear genes (POMC, RAG-1, RHOD, SIAH, TNS3, TYR). We included most of its species (> 96%), in addition to a number of new species. Our results indicate: (i) the paraphyly of Trachycephalus with respect to Aparasphenodon venezolanus; (ii) the nonmonophyly of Aparasphenodon, with Argenteohyla siemersi, Corythomantis galeata and Nyctimantis rugiceps nested within it, and Ap. venezolanus nested within Trachycephalus; (iii) the polyphyly of Corythomantis; (iv) the nonmonophyly of the recognized species groups of Phyllodytes; and (v) a pervasive low support for the deep relationships among the major clades of Lophyohylini, including C. greeningi and the monotypic genera Itapotihyla and Phytotriades. To remedy the nonmonophyly of Aparasphenodon, Corythomantis, and Trachycephalus, we redefined Nyctimantis to include Aparasphenodon (with the exception of Ap. venezolanus, which we transferred to Trachycephalus), Argenteohyla, and C. galeata. Additionally, our results indicate the need for taxonomic work in the following clades: (i) Trachycephalus dibernardoi and Tr. imitatrix; (ii) Tr. atlas, Tr. mambaiensis and Tr. nigromaculatus; and (iii) Phyllodytes. On the basis of our phylogenetic results, we analyzed the evolution of skull hyperossification and reproductive biology, with emphasis on the multiple independent origins of phytotelm breeding, in the context of Anura. We also analyzed the inter-related aspects of chemical defences, venom delivery, phragmotic behaviour, co-ossification, and prevention of evaporative water loss. Univ Estadual Paulista, Inst Biociencias, Dept Biodiversidade, Av 24A 1515, BR-13506900 Rio Claro, SP, Brazil Univ Estadual Paulista, Inst Biociencias, Ctr Aquicultura, Av 24A 1515, BR-13506900 Rio Claro, SP, Brazil Univ Sao Paulo, Inst Biociencias, Dept Zool, BR-05508090 Sao Paulo, SP, Brazil Univ Fed Rio de Janeiro, Museu Nacl, Dept Vertebrados, Setor Herpetol, BR-20940040 Rio De Janeiro, RJ, Brazil Univ Estadual Santa Cruz, Dept Ciencias Biol, Trop Herpetol Lab, Rodovia Jorge Amado,Km 16, BR-45662900 Ilheus, BA, Brazil Univ Brasilia, Dept Engn Florestal, Lab Fauna & Unidades Conservacao, BR-70910900 Brasilia, DF, Brazil Univ Fed Vicosa, Dept Biol Anim, Museu Zool Joao Moojen, BR-36570900 Vicosa, MG, Brazil Univ West Indies, Zool Museum, Dept Life Sci, St Augustine, Trinidad Tobago Pontificia Univ Catolica Rio Grande do Sul, Lab Sistemat Vertebrados, Av Ipiranga 6681,Predio 40,Sala 110, BR-90619900 Porto Alegre, RS, Brazil Consejo Nacl Invest Cient & Tecn, UNaM, Inst Biol Subtrop, Lab Genet Evolut Claudio Juan Bidau, Felix Azara 1552,CPA N3300LQF Posadas, Misiones, Argentina Univ Estadual Paulista, Inst Biociencias, Lab Herpetol, Campus Litoral Paulista, BR-11330900 Sao Vicente, SP, Brazil Univ Nacl Nordeste, CONICET, Fac Ciencias Exactas & Nat & Agrimensura, Lab Herpetol,Dept Biol, Av Libertad 5470, RA-3400 Corrientes, Argentina Consejo Nacl Invest Cient & Tecn, Fdn Miguel Lillo, Unidad Ejecutora Lillo, Miguel Lillo 251, RA-4000 San Miguel De Tucuman, Tucuman, Argentina Univ Koblenz Landau, Inst Integrated Sci, Dept Biol, Univ Str 1, D-56070 Koblenz, Germany Univ Fed Rural Rio De Janeiro, Inst Biol, Dept Biol Anim, Caixa Postal 74524, BR-23851970 Seropedica, RJ, Brazil Consejo Nacl Invest Cient & Tecn, Museo Argentino Ciencias Nat Bernardino Rivadavia, Div Herpetol, Angel Gallardo 470,C1405DJR, Buenos Aires, DF, Argentina Univ Buenos Aires, Fac Ciencias Exactas & Nat, Dept Biodiversidad & Biol Expt, Buenos Aires, DF, Argentina Univ Estadual Paulista, Inst Biociencias, Dept Biodiversidade, Av 24A 1515, BR-13506900 Rio Claro, SP, Brazil Univ Estadual Paulista, Inst Biociencias, Ctr Aquicultura, Av 24A 1515, BR-13506900 Rio Claro, SP, Brazil Univ Estadual Paulista, Inst Biociencias, Lab Herpetol, Campus Litoral Paulista, BR-11330900 Sao Vicente, SP, Brazil FAPESP: 2013/20423-3 FAPESP: 2017/26162-8 FAPESP: 2003/10335-8 FAPESP: 2011/50146-6 FAPESP: 2018/15425-0 FAPESP: 2012/10000-5 FAPESP: 2013/50741-7 FAPESP: 2007/57067-9 FAPESP: 2012/12500-5 CNPq: 167387/20170 CNPq: 155198/2018-1 CNPq: 476789/2009-5 CNPq: 306823/2017-9 CNPq: 140412/2008-5 CNPq: 150377/2012-6 CNPq: 150122/2014-4 Fundacao O Boticario de Protecao a Natureza: 0991_20132 Fundacao de Amparo a Pesquisa da Bahia (FAPESB): 8951/2014 CAPES: 001 CAPES: 88881.133927/2016-01 CNPq: 140716/2016-5 FAPESP: 2014/50342-8 Agencia Nacional de Promocion Cientifica y Tecnologica (ANPCyT): PICT 2013-404 Agencia Nacional de Promocion Cientifica y Tecnologica (ANPCyT): 2015-820

Made available in DSpace on 2019-10-04T12:39:13Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-06-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) The host-associated microbiome is vital to host immunity and pathogen defense. In aquatic ecosystems, organisms may interact with environmental bacteria to influence the pool of potential symbionts, but the effects of these interactions on host microbiome assembly and pathogen resistance are unresolved. We used replicated bromeliad microecosystems to test for indirect effects of arthropod-bacteria interactions on host microbiome assembly and pathogen burden, using tadpoles and the fungal amphibian pathogen Batrachochytrium dendrobatidis as a model host-pathogen system. Arthropods influenced host microbiome assembly by altering the pool of environmental bacteria, with arthropod-bacteria interactions specifically reducing host colonization by transient bacteria and promoting antimicrobial components of aquatic bacterial communities. Arthropods also reduced fungal zoospores in the environment, but fungal infection burdens in tadpoles corresponded most closely with arthropod-mediated patterns in microbiome assembly. This result indicates that the cascading effects of arthropods on the maintenance of a protective host microbiome may be more strongly linked to host health than negative effects of arthropods on pools of pathogenic zoospores. Our work reveals tight links between healthy ecosystem dynamics and the functioning of host microbiomes, suggesting that ecosystem disturbances such as loss of arthropods may have downstream effects on host-associated microbial pathogen defenses and host fitness. Univ Alabama, Dept Biol Sci, Tuscaloosa, AL 35487 USA Univ Estadual Paulista, Dept Zool, BR-13506900 Rio Claro, SP, Brazil Univ Estadual Paulista, Aquaculture Ctr CAUNESP, BR-13506900 Rio Claro, SP, Brazil Univ Estadual Paulista, Programa Posgrad Biol Anim, BR-15054000 Sao Jose Do Rio Preto, SP, Brazil Univ Massachusetts, Dept Biol, Boston, MA 02125 USA Fundacao Parque Zool Sao Paulo, BR-04301905 Sao Paulo, SP, Brazil Univ Estadual Campinas, Inst Biol, Programa Posgrad Ecol, BR-13083862 Campinas, SP, Brazil Univ Estadual Campinas, Dept Biol Anim, BR-13083862 Campinas, SP, Brazil Univ Estadual Campinas, Dept Biol Anim, Lab Hist Nat Anfibios Brasileiros LaHNAB, BR-13083862 Campinas, SP, Brazil Univ Estadual Paulista, Dept Zool, BR-13506900 Rio Claro, SP, Brazil Univ Estadual Paulista, Aquaculture Ctr CAUNESP, BR-13506900 Rio Claro, SP, Brazil Univ Estadual Paulista, Programa Posgrad Biol Anim, BR-15054000 Sao Jose Do Rio Preto, SP, Brazil FAPESP: 2014/23388-7 FAPESP: 2013/50741-7 FAPESP: 2014/50342-8 FAPESP: 2017/26162-8 FAPESP: 2016/03344-0 CNPq: 312895/2014-3 CNPq: 300896/2016-6 CNPq: 302518/2013-4 CAPES: 001

WOS: 000484779500005, PubMed ID: 31501432, Climatic conditions changing over time and space shape the evolution of organisms at multiple levels, including temperate lizards in the family Lacertidae. Here we reconstruct a dated phylogenetic tree of 262 lacertid species based on a supermatrix relying on novel phylogenomic datasets and fossil calibrations. Diversification of lacertids was accompanied by an increasing disparity among occupied bioclimatic niches, especially in the last 10 Ma, during a period of progressive global cooling. Temperate species also underwent a genomewide slowdown in molecular substitution rates compared to tropical and desert-adapted lacertids. Evaporative water loss and preferred temperature are correlated with bioclimatic parameters, indicating physiological adaptations to climate. Tropical, but also some populations of cool-adapted species experience maximum temperatures close to their preferred temperatures. We hypothesize these species-specific physiological preferences may constitute a handicap to prevail under rapid global warming, and contribute to explaining local lizard extinctions in cool and humid climates., Deutsche Forschungsgemeinschaft (DFG)German Research Foundation (DFG) [VE 247/11-1/MU 1760/9-1, VE 247/16-1-HO3492/6-1]; Juan de la Cierva fellowships from the Spanish 'Ministerio de Economia y Competitividad' [FJCI-2014-20380, IJCI-2016-29566]; 'Rita Levi Montalcini' program for recruitment of young researchers at the University of L'Aquila; US-National Science Foundation Emerging Frontiers program [EF-1241848]; Hassan II Academy of Sciences and Technologies (ICGVSA Project); Slovenian Research Agency Research Program [P1-0255]; Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) [SNIC 2017/7-275]; [NORTE-01-0145-FEDER-000007]; [ON173025 MESTD RS], We are grateful to numerous students, field assistants and technicians who supported field and laboratory work, and to G. Jones for useful comments on the manuscript. This study was supported by the Deutsche Forschungsgemeinschaft (DFG) to M.V. and J.M. (VE 247/11-1/MU 1760/9-1), and to L.R. in the framework of the "TaxonOmics" priority program (VE 247/16-1-HO3492/6-1). J.G.-P. and I. I. were supported by Juan de la Cierva fellowships from the Spanish 'Ministerio de Economia y Competitividad' (FJCI-2014-20380 and IJCI-2016-29566), D.S. by the 'Rita Levi Montalcini' program for recruitment of young researchers at the University of L'Aquila, M.A.C. by project NORTE-01-0145-FEDER-000007, B.S. and D.B.M. by the US-National Science Foundation Emerging Frontiers program (EF-1241848), J.C.I. by project ON173025 MESTD RS, T.S., A.F., and A.S. by the Hassan II Academy of Sciences and Technologies (ICGVSA Project), A.Z. by the Slovenian Research Agency Research Program P1-0255. The computations were in part performed on the Altamira supercomputer at the Institute of Physics of Cantabria (IFCA-CSIC), Spain; the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) under Project SNIC 2017/7-275; as well as the Zentraler Informations-und Datenverarbeitungsservice of the Tierarztliche Hochschule Hannover (IDS-TiHo). Further, we acknowledge the Viper High Performance Computing facility of the University of Hull and its support team, especially Ahmed Elnawasany, for facilitating computational analyses.

Made available in DSpace on 2018-11-26T17:44:50Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-01-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) We reconstructed nearly complete mitogenomes for three species of poison frogs, Dendrobates auratus, D. leucomelas, and D. tinctorius, from RNAseq data. We recovered the 13 protein-coding genes, 22 tRNA genes (except tRNA-Val for D. leucomelas), and two rRNA genes for all three species, plus partial sequences of the control region. The order of genes agrees with that known from a previously sequenced D. auratus, being the most commonly found for neobatrachian frogs. Based on full-sibling comparisons we estimate the probable error rate of Illumina-RNAseq reconstructed mitogenomes of up to 0.15%. Sao Paulo State Univ UNESP, Biosci Inst, Dept Zool, Campus Rio Claro, Rio Claro, SP, Brazil Sao Paulo State Univ UNESP, Biosci Inst, Aquiculture Ctr CAUNESP, Campus Rio Claro, Rio Claro, SP, Brazil Tech Univ Carolo Wilhelmina Braunschweig, Zool Inst, Braunschweig, Germany Max Planck Inst Evolutionary Biol, Dept Evolutionary Genet, Plon, Germany Trier Univ, Biogeog Dept, Trier, Germany Sao Paulo State Univ UNESP, Biosci Inst, Dept Zool, Campus Rio Claro, Rio Claro, SP, Brazil Sao Paulo State Univ UNESP, Biosci Inst, Aquiculture Ctr CAUNESP, Campus Rio Claro, Rio Claro, SP, Brazil FAPESP: 2013/50741-7 CAPES: 88881.062205/2014-01

Chironius bicarinatus is a conspicuous colubrid snake species, widely distributed in northeastern, southeastern, central-western, and southern Brazil, as well as Paraguay, Argentina, and Uruguay. On the basis of new morphological data of individuals from previously unsampled regions and deoxyribonucleic acid sequences, we reviewed the taxonomy of populations previously referred to as C. bicarinatus, revisiting the species definition with an updated diagnosis, inferring its phylogenetic relationships with closely related lineages in southern Brazil, herein described as a new species restricted to Pampa forests or grasslands and Atlantic Forest semidecidual forests in southern Brazil. The new species can be readily diagnosed from C. bicarinatus and all other congeners on the basis of internal (hemipenis unilobed, unicalyculate, cylindrical, apex with smooth calyces, with spinules restricted to proximal portion, near the medial area; lacrimal foramen with small projection on the anteroventral margin) and external morphology (ventrals 153–165 [153–165 in males, 155–164 in females]; subcaudals 103–146 pairs [129–142 in males, 103–146 in females]; adult dorsal pattern with dark green background, scales sometimes with light blue margin, two conspicuous black dorsal stripes with light green vertebral stripe between them that gradually dissipates to the tail, ventrals with black margin on its edges) and molecular evidence.

The genus of Neotropical frogs Pseudopaludicola Miranda-Ribeiro, 1926 includes 23 species, which occur throughout South America. Herein we describe a new species of Pseudopaludicola from the central region of the state of Minas Gerais (southeastern Brazil). This new species is distinguished by the adult morphology, the advertisement call, and molecular data. It is diagnosed mainly by its small size, terminal phalanges knobbed (lack of any expansion of the digital tips), proportionally short hind limbs, and its advertisement call composed of series of two-pulsed notes, emitted at a high repetition rate. In addition, we report the occurrence of the new species in the southern foothills of the Serra do Cipó National Park, at elevations lower than 800 m above sea level (a.s.l). The sister species of this new taxon is P. mineira Lobo, 1994, which occurs in rupestrian grasslands above 1200 m a.s.l. at the Serra do Cipó National Park and in Serra do Cabral, both in the state of Minas Gerais, Brazil. We also redescribe the advertisement call of P. mineira based on recordings from topotypical males and compare it to calls of related species.

Made available in DSpace on 2020-12-12T02:04:27Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-05-01 National Science Foundation Rufford Foundation Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Ecologists studying emerging wildlife diseases need to confront the realism of imperfect pathogen detection across heterogeneous habitats to aid in conservation decisions. For example, spatial risk assessments of amphibian disease caused by Batrachochytrium dendrobatidis (Bd) has largely ignored imperfect pathogen detection across sampling sites. Because changes in pathogenicity and host susceptibility could trigger recurrent population declines, it is imperative to understand how pathogen prevalence and occupancy vary across environmental gradients. Here, we assessed how Bd occurrence, prevalence, and infection intensity in a diverse Neotropical landscape vary across streams in relation to abiotic and biotic predictors using a hierarchical Bayesian model that accounts for imperfect Bd detection caused by qPCR error. Our model indicated that the number of streams harboring Bd-infected frogs is higher than observed, with Bd likely being present at ~ 43% more streams than it was detected. We found that terrestrial-breeders captured along streams had higher Bd prevalence, but lower infection intensity, than aquatic-breeding species. We found a positive relationship between Bd occupancy probability and stream density, and a negative relationship between Bd occupancy probability and amphibian local richness. Forest cover was a weak predictor of Bd occurrence and infection intensity. Finally, we provide estimates for the minimum number of amphibian captures needed to determine the presence of Bd at a given site where Bd occurs, thus, providing guidence for cost-effective disease risk monitoring programs. Instituto de Biociências Universidade Estadual Paulista (Unesp), Av. 24A 1515 Department of Ecology Evolution and Marine Biology University of California Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB) Departamento de Biologia Animal Instituto de Biologia Universidade Estadual de Campinas Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP) Instituto de Biociências Universidade Estadual Paulista (Unesp) Department of Biological Sciences The University of Alabama Instituto de Biociências Universidade Estadual Paulista (Unesp), Av. 24A 1515 Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP) Instituto de Biociências Universidade Estadual Paulista (Unesp) National Science Foundation: 1611692 Rufford Foundation: 16419-1 FAPESP: 2013/50424-1 FAPESP: 2014/07113-8 FAPESP: 2016/07469-2 FAPESP: 2016/25358-3 CNPq: 300896/2016-6

The Neotropical genus Pseudopaludicola includes 21 species, which occur throughout South America. Recent studies suggested that the population of Andaraí, in the state of Bahia, is an undescribed species, related to P. pocoto. Herein we formally describe this new species from lowlands of eastern Brazil. Recognition of this new species is supported by adult morphology, advertisement call, karyotype, and molecular data. It is diagnosed mainly by its small size, terminal phalanges knobbed (lack any expansion of the digital tips), proportionally short hindlimbs, 11 pairs of chromosomes, and advertisement call composed of series of three-pulsed notes, emitted at a high rate. In addition, we report for the first time the presence of P. pocoto in the campo rupestre (rupestrian grasslands) of Chapada Diamantina, a population with a much darker dorsal coloration than the population from the type locality. We also redescribed the advertisement call of P. falcipes based on recordings from topotypic males.

Recent advances in the field of landscape genetics provide ways to jointly analyze the role of present-day climate and landscape configuration in current biodiversity patterns. Expanding this framework into a phylogeographic study, we incorporate information on historical climatic shifts, tied to descriptions of the local topography and river configuration, to explore the processes that underlie genetic diversity patterns in the Atlantic Forest hotspot. We study two montane, stream-associated species of glassfrogs: Vitreorana eurygnatha and V. uranoscopa. By integrating species distribution modeling with geographic information systems and molecular data, we find that regional patterns of molecular diversity are jointly explained by geographic distance, historical (last 120 ky) climatic stability, and (in one species) river configuration. Mitochondrial DNA genealogies recover significant regional structure in both species, matching previous classifications of the northern and southern forests in the Atlantic Forest, and are consistent with patterns reported in other taxa. Yet, these spatial patterns of genetic diversity are only partially supported by nuclear data. Contrary to data from lowland taxa, historical climate projections suggest that these montane species were able to persist in the southern Atlantic Forest during glacial periods, particularly during the Last Glacial Maximum. These results support generally differential responses to climatic cycling by northern (lowland) and southern (montane) Atlantic Forest species, triggered by the joint impact of regional landscape configuration and climate change.

Made available in DSpace on 2018-11-26T17:49:07Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-06-01 Fundacao Grupo Boticario de Protecao a Natureza Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) The genus Fritziana (Anura: Hemiphractidae) comprises six described species (F. goeldii, F. ohausi, F. fissilis, F. ulei, F. tonimi, and F. izecksohni) that are endemic to the Brazilian Atlantic Forest. Although the genus has been the subject of studies dealing with its taxonomy, phylogeny, and systematics, there is considerable evidence for cryptic diversity hidden among the species. The present study aims to understand the genetic diversity and phylogenetic relationships among the species of Fritziana, as well as the relationships among populations within species. We analyzed 107 individuals throughout the distribution of the genus using three mitochondrial gene fragments (12S, 16S, and COI) and two nuclear genes (RAG1 and SLC8A3). Our data indicated that the species diversity in the genus Fritziana is underestimated by the existence of at least three candidate species hidden amongst the group of species with a closed dorsal pouch (i.e. F. fissilis and F. ulei). We also found four species presenting geographical population structures and high genetic diversity, and thus require further investigations. In addition, we found that two candidate species show a new arrangement for the tRNA-Phe gene, unique in Anura so far. Based on our results, we suggest that the conservation status of the species, as well as the species diversity in the genus Fritziana, needs to be reviewed. Univ Estadual Paulista, Inst Biociencias, Dept Zool, Campus Rio Claro,Av 24A,1515, BR-13506900 Rio Claro, SP, Brazil Ctr Aquicultura CAUNESP, Campus Rio Claro,Av 24A,1515, BR-13506900 Rio Claro, SP, Brazil Univ Estadual Paulista, Inst Biociencias, Dept Zool, Campus Rio Claro,Av 24A,1515, BR-13506900 Rio Claro, SP, Brazil Ctr Aquicultura CAUNESP, Campus Rio Claro,Av 24A,1515, BR-13506900 Rio Claro, SP, Brazil FAPESP: 2008/50928-1 FAPESP: 2010/50124-0 FAPESP: 2013/50741-7 FAPESP: 2014/50342-8

Made available in DSpace on 2018-12-11T17:16:38Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-12-01 Host-generalist pathogens sporadically infect naive hosts, potentially triggering epizootics. The waterborne fungus Batrachochytrium dendrobatidis (Bd) is linked to declines of hundreds of amphibian species with aquatic larvae. Although several population declines and extinctions attributed to Bd have been reported among cryptic species undergoing direct development away from water, epidemiological studies focused on these terrestrial frogs are lacking. Our field data support that terrestrial direct-developing hosts are less exposed to Bd during their ontogeny than species with aquatic larvae, and thus they might lack adaptive responses against waterborne chytrids. Using controlled laboratory experiments, we exposed wild-caught amphibian species with terrestrial and aquatic life histories to Bd and found that direct developers showed more rapid increases in infection loads and experienced higher mortality rates than species with aquatic larvae. Our findings provide novel information about host responses to generalist pathogens and specifically show that our focal direct developing species have low resistance to Bd infections. Finally, our results underscore that we should not ignore Bd as a potential threat to direct developing species simply because they are less exposed to Bd in nature; instead future amphibian conservation plans should include efforts to safeguard hundreds of direct-developing amphibian species globally. Universidade Estadual Paulista (UNESP) Instituto de Biociências Departamento de Zoologia Centro de Aquicultura (CAUNESP) Departamento de Biologia Animal I.B. Universidade Estadual de Campinas Department of Ecology and Evolutionary Biology University of Michigan Department of Biological Sciences University of Alabama Universidade Estadual Paulista (UNESP) Instituto de Biociências Departamento de Zoologia Centro de Aquicultura (CAUNESP)

Made available in DSpace on 2018-12-11T17:16:08Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-07-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Bacterial communities associated to eukaryotes play important roles in the physiology, development, and health of their hosts. Here, we examine the intestinal microbiota in tadpoles and aquatic invertebrates (insects and gastropods) to better understand the degree of specialization in the tadpole microbiotas. Samples were collected at the same time in one pond, and the V4 region of the bacterial 16S rRNA gene was sequenced with Illumina amplicon sequencing. We found that bacterial richness and diversity were highest in two studied snail individuals, intermediate in tadpoles, and lowest in the four groups of aquatic insects. All groups had substantial numbers of exclusive bacterial operational taxonomic units (OTUs) in their guts, but also shared a high proportion of OTUs, probably corresponding to transient environmental bacteria. Significant differences were found for all pairwise comparisons of tadpoles and snails with the major groups of insects, but not among insect groups or between snails and tadpoles. The similarity between tadpoles and snails may be related to similar feeding mode as both snails and tadpoles scratch biofilms and algae from surfaces; however, this requires confirmation due to low sample sizes. Overall, the gut microbiota differences found among syntopic aquatic animals are likely shaped by both food preferences and host identity. Departamento de Zoologia Universidade Estadual Paulista (UNESP) Instituto de Biociências Campus Rio Claro, Avenida 24A, N 1515 Bela Vista Zoological Institute Technische Universität Braunschweig, Mendelssohnstr. 4 Centro de Aquicultura (CAUNESP) Universidade Estadual Paulista (UNESP) Instituto de Biociências Campus Rio Claro, Avenida 24A, N 1515 Bela Vista Departamento de Zoologia Universidade Estadual Paulista (UNESP) Instituto de Biociências Campus Rio Claro, Avenida 24A, N 1515 Bela Vista Centro de Aquicultura (CAUNESP) Universidade Estadual Paulista (UNESP) Instituto de Biociências Campus Rio Claro, Avenida 24A, N 1515 Bela Vista FAPESP: 2013/50741-7 CAPES: 88881.062205/2014-01

Cochliomyia hominivorax (Coquerel) is a myiasis fly that causes economic losses to livestock farmers in warmer American regions. Previous studies of this pest had found population structure at north and south of the Amazon Basin, which was considered to be a barrier to dispersal. The present study analyzed three mitochondrial DNA (mtDNA) markers and eight nuclear microsatellite loci to investigate for the first time the genetic diversity and population structure across the Brazilian Amazon region (Amazonia). Both mtDNA and microsatellite data supported the existence of much diversity and significant population structure among nine regional populations of C. hominivorax, which was found to be surprisingly common in Amazonia. Forty-six mtDNA haplotypes were identified, of which 39 were novel and seven had previously been found only at south of Amazonia. Seventy microsatellite alleles were identified by size, moderate to high values of heterozygosity were discovered in all regions, and a Bayesian clustering analysis identified four genetic groups that were not geographically distributed. Reproductive compatibility was also investigated by laboratory crossing, but no evidence of hybrid dysgenesis was found between an Amazonian colony and one each of from Northeast and Southeast Brazil. The results have important implications for area-wide control by the Sterile Insect Technique.

Made available in DSpace on 2020-12-12T01:53:39Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-10-01 We describe the larval external morphology and internal oral features of Crossodactylus caramaschii sampled in protected areas of the Atlantic Forest in southeastern Brazil. The tadpoles of C. caramaschii (Gosner stage 38) have an ovoid body in dorsal view and globular in lateral view, dorsal eyes, a ventral oral disc bordered by a single row of marginal papillae, with a wide gap on the anterior labium, and few and scattered submarginal papillae. The labial tooth row formula is 2(2)/3(1), with A-1 shorter than A-2, and P-3 shorter than P-1 and P-2. This is the first description of the larval morphology of this species and may help future studies on the intrageneric relationships of Crossodactylus. Laboratório de Ecologia Teórica: Integrando Tempo Biologia e Espaço (LET.IT.BE) Departamento de Ciências Ambientais Universidade Federal de Sao Carlos Campus Sorocaba Instituto de Biociências Universidade Federal de Mato Grosso Do sul Campo Grande Departamento de Zoologia e Centro de Aquicultura da UNESP (CAUNESP) Instituto de Biociências Universidade Estadual Paulista Júlio de Mesquita Filho Campus Rio Claro Departamento de Zoologia e Botânica Universidade Estadual Paulista Júlio de Mesquita Filho-UNESP Campus de Sao José Do Rio Preto Departamento de Zoologia e Centro de Aquicultura da UNESP (CAUNESP) Instituto de Biociências Universidade Estadual Paulista Júlio de Mesquita Filho Campus Rio Claro Departamento de Zoologia e Botânica Universidade Estadual Paulista Júlio de Mesquita Filho-UNESP Campus de Sao José Do Rio Preto

The main goal of this manuscript is the reevaluation of the taxonomic status of the teiid lizard Contomastix charrua, known only from Cabo Polonio, a small coastal rocky outcrop in southeastern Uruguay. This species was erected on the basis of the presence of a second pair of ceratobranchials and longer cornua in the hyoid bone, in addition to a reduced expression of the pattern of coloration as compared with C. lacertoides. Nevertheless, we found that both species have indistinguishable hyoid morphology, bearing C. lacertoides a noticeable second pair of ceratobranchials. Besides, we realized that the pattern of coloration in this species is more variable than previously considered. As a result of the present work, C. charrua is included in the synonymy of C. lacertoides. In addition, we provide some observations on the holotype of Cnemidophorus grandensis, a junior synonym of C. lacertoides.

Spiroplasma endosymbionts are maternally transmitted bacteria that may kill infected sons resulting in the production of female-biased broods. The prevalence of male killers varies considerably both between and within species. Here, we evaluate the spatial and temporal status of male-killing and non-male-killing Spiroplasma infection in three Brazilian populations of Drosophila melanogaster, nearly a decade after the first occurrence report for this species. The incidence of the male-killing Spiroplasma ranged from close to 0 to 17.7 % (so far the highest estimate for a Drosophila species) with a suggestion of temporal decline in a population. We also found non-male-killing Spiroplasma coexisting in one population at lower prevalence (3-5 %), and we did not detect it in the other two. This may be taken as a suggestion of a spreading advantage conferred by the male-killing strategy. Sequencing two loci, we identified the phylogenetic position of Spiroplasma strains from the three localities, showing that all strains group closely in the poulsonii clade. Due to intensive sampling effort, we were able to test the association between Spiroplasma infections and another widespread endosymbiont, Wolbachia, whose prevalence ranged from 81.8 to 100 %. The prevalence of Wolbachia did not differ between Spiroplasma-infected and uninfected strains in our largest sample nor were the prevalences of the two endosymbionts associated across localities.

The phylogeographical history of the pest fly screwworm, Cochliomyia hominivorax (Coquerel), was studied using partial mitochondrial DNA sequences of the control region, Cytochrome c oxidase (CO) subunit I and CO subunit II from 361 individuals collected across its current geographic range. Analyses showed marked genetic differentiation on a macrogeographic scale. The genetic diversity in the species is structured into four main "regional groups," corresponding to Cuba, the Dominican Republic, and the North and South Amazon region. Results indicated that the distribution of screwworm genetic diversity was mainly shaped by historical events, i.e., colonization of Caribbean islands, vicariance in the Amazon region and population expansion. Demographic history analyses revealed that the population expansion started approximately 20-25,000 yr ago and recently increased exponentially. We hypothesized that the initial period of expansion was probably associated with environmental amelioration in the late Pleistocene and the exponential increase with resource availability in recent times. The population expansion is probably responsible for the low divergence and the lack of genetic and geographic correlation in the South Amazon region but did not erase the genetic structure pattern on a continental scale. The screwworm is one of the most damaging livestock pests in South and Central America, and the pattern of genetic variability distribution reported here suggests that the Caribbean area and the North and South Amazon regions could be considered as independent units for future pest control programs.

Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae), the New World screwworm fly, is an important agent of traumatic myiasis, which is endemic in the Neotropical region and which has great economic impact on the development of the livestock industry. International efforts have been aimed at designing programmes to control and eradicate this species from endemic areas. Thorough knowledge of the population genetics of an insect pest is a fundamental component to ensuring the success of a pest management strategy because it enables the determination of an appropriate geographic scale for carrying out effective treatments. This study undertook an analysis of mtDNA polymerase chain reaction-restricted fragment length polymorphism (PCR-RFLP) in 34 populations of C. hominivorax from 10 countries, encompassing almost all the current distribution of the species. Results showed high levels of mitochondrial DNA variability (π= 2.9%) and a complex pattern of population genetic structure for this species. Significant population structure (>st= 0.5234) and low variability were found in Caribbean populations, suggesting that, in general, islands constitute independent evolutionary entities connected by restricted gene flow. By contrast, high variability and low, but significant, differentiation was found among mainland populations (>st= 0.0483), which could not be attributed to geographic distance. Several processes may be acting to maintain the observed patterns, with different implications for establishing control programmes.

Cochliomyia hominivoraxandCochliomyia macellariaare endemic Neotropical Calliphoridae species. The former causes severe myiasis in hosts while the latter is Sarcosaprophagous, but commonly found as a second invader in wounds. Due to the morphological similarity between them and the potential losses thatC. hominivoraxrepresents for cattle breeders, the rapid and correct identification of these two species is very important. In addition to a correct identification of these species, a good knowledge ofC. hominivoraxbiology can be helpful for designing control programs. We applied geometric morphometric methods to assess wing differences betweenC. hominivoraxandC. macellariaand conduct a preliminary analysis of wing morphological variation inC. hominivoraxpopulations. Canonical variate analysis, using wing shape data, correctly classified 100% of the individuals analyzed according to sex and species. This result demonstrates that wing morphometry is a simple and reliable method for identifyingC. hominivoraxandC. macellariasamples and can be used to monitorC. hominivorax. Both species show sexual dimorphism, but inC. hominivoraxit is magnified. We suggest that this may reflect different histories of selection pressures operating on males and females. Significant differences in wing size and shape were obtained amongC. hominivoraxpopulations, with little correlation with latitude. This result suggests that wing variation is also a good morphological marker for studying population variation inC. hominivorax.

Amphibians are one of the most threatened vertebrate classes, yet at the same time new species are being described every year, demonstrating that the number of existing species is grossly underestimated. In groups such as amphibians, with high extinction rates and poorly known species boundaries, DNA barcoding is a tool that can rapidly assess genetic diversity and estimate species richness for prioritizing conservation decisions. However, reliable recovery of the 5′ region of the cytochrome c oxidase subunit 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all amphibian species. Here we provide new PCR conditions and tested new primers that increase the efficiency of barcode recovery in amphibians. We found that a low extension temperature for PCR cycles significantly improves the efficiency of amplification for all combinations of primers. Combining low PCR extension temperature and primers AnF1 + AnR1 we were able to recover COI sequences for 100% of the species analyzed (N=161), encompassing ~15% of the species known from Brazil (representing 77 genera and 23 families), which is an important improvement over previous studies. The preliminary assessment of species diversity suggested that number of species might be underestimated by about 25%. We conclude that DNA barcoding is an efficient, simple, and standardized protocol for identifying cryptic diversity in amphibians and advocate for its use in biodiversity inventories and across widespread populations within known species. This article is protected by copyright. All rights reserved.