New species of Melanophryniscus.

31 p. : ill. (some col.) ; 26 cm.We describe a new species of bufonid from a lowland, sandy soil, restinga habitat in the state of Espírito Santo, southeastern Brazil. Based on the shared occurrence of putative morphological synapomorphies of Melanophryniscus and the results of a phylogenetic analysis of DNA sequences of a broad sample of bufonids, and other anurans, we assign the new species to Melanophryniscus. The new species possesses several peculiar character states that distinguish it from all other Melanophryniscus including, but not limited to: fingers II, III, and V much reduced; nuptial pad with few enlarged, brown-colored spines on medial margin of finger II; seven presacral vertebrae, the last fused with the sacrum; and ventral humeral crest prominent, forming a spinelike projection

New genus and species of Gymnophthalmidae.

24 p. : ill., map ; 26 cm. "May 9, 2011."Marinussaurus curupira, a new genus and species of Gymnophthalmidae lizard is described from Iranduba, state of Amazonas, Brazil. The genus is characterized by an elongate body; short and stout pentadactyl limbs; all digits clawed; single frontonasal; two prefrontals; absence of frontoparietals; interparietal and parietals forming a straight posterior margin, with interparietal shorter than parietals; distinctive ear opening and eyelid; few temporals; three pairs of chin shields; nasal divided; a distinct collar; smooth, mainly hexagonal, dorsal scales; smooth quadrangular ventral scales; two precloacal and three femoral pores on each side in males; pores between three or four scales. Parsimony (PAR) and partitioned Bayesian (BA) phylogenetic analyses with morphological and molecular data recovered the new genus as a member of the Ecpleopodini radiation of the Cercosaurinae. A close relationship of the new genus with Arthrosaura is postulated

A new “Bat-Voiced” species of Dendropsophus Fitzinger, 1843 (Anura, Hylidae) from the Amazon Basin, Brazil

We describe Dendropsophus ozzyi sp. nov., a new species of treefrog, tentatively included in the Dendropsophus microcephalus Group and most notably diagnosed by the presence of pointed fingers and an advertisement call with a very high dominant frequency. The new species is known from three localities in the Brazilian Amazon forest, two on western State of Pará and one (the type locality) in eastern State of Amazonas (03°56’50”S and 58°26’36”W, 45 m a.s.l.).Fil: Orrico, Victor G. D.. Universidade Estadual de Santa Cruz; BrasilFil: Peloso, Pedro L. V.. American Museum Of Natural History; Estados Unidos. Museu Paraense Emílio Goeldi; BrasilFil: Sturaro, Marcelo J.. Museu Paraense Emílio Goeldi; Brasil. Universidade Federal Do Pará; BrasilFil: Silva Filho, Heriberto F. Da. Universidade Federal Do Pará; BrasilFil: Neckel Oliveira, Selvino. Universidade Federal Da Santa Catarina; BrasilFil: Gordo, Marcelo. Universidade Federal do Amazonas; BrasilFil: Faivovich, Julián. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; ArgentinaFil: Haddad, Celio F. B.. Universidade Estadual Paulista Julio de Mesquita Filho; Brasi

Species diversity and biogeography of an ancient frog clade from the Guiana Shield (Anura: Microhylidae: Adelastes, Otophryne, Synapturanus) exhibiting spectacular phenotypic diversification

The outstanding biodiversity of the Guiana Shield has raised many questions about its origins and evolution. Frogs of the genera Adelastes, Otophryne and Synapturanus form an ancient lineage distributed mostly across this region. These genera display strikingly disparate morphologies and life-history traits. Notably, Synapturanus is conspicuously adapted to fossoriality and is the only genus within this group to have dispersed further into Amazonia. Moreover, morphological differences among Synapturanus species suggest different degrees of fossoriality that might be linked to their biogeographical history. Through integrative analysis of genetic, morphometric and acoustic data, we delimited 25 species in this clade, representing a fourfold increase. We found that the entire clade started to diversify ~55 Mya and Synapturanus ~30 Mya. Members of this genus probably dispersed three times out of the Guiana Shield both before and after the Pebas system, a wetland ecosystem occupying most of Western Amazonia during the Miocene. Using a three-dimensional osteological dataset, we characterized a high morphological disparity across the three genera. Within Synapturanus, we further characterized distinct phenotypes that emerged concomitantly with dispersals during the Miocene and possibly represent adaptations to different habitats, such as soils with different physical properties.Peer reviewe

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

The Author(s) 2020. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.].This work was supported by grants from a graduate student research award from the Society of Systematic Biologists and the University of Kentucky G.F. Ribble Endowment (to P.M.H.), by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES/BEX 2806/09-6 to P.L.V.P.), and by the National Science Foundation (DEB-0949532 and DEB-1355000 to D.W.W., DEB-1120516 to E.M.L., IIP-1313554 to A.R.L. and E.M.L, DEB-1355071 to J.M.B., DEB-1441719 to R.A.P., DEB-1311442 to P.L.V.P., DEB-1354506 to R.C.T., DEB-1021247 to E.P. and C.J.R., DEB-1021299 to K.M. Kjer, and DEB-1257610, DEB-0641023, DEB-0423286, and DEB-9984496 to C.J.R.), and the Australian Research Council (DP120104146 to J.S.K. and S.C.D.). S.R.R. thanks SENESCYT (Arca de Noé Initiative; SRR and O. Torres-Carvajal principal investigators) for funding for tissue collection. J.L. was supported by the Systematics Association and the Linnean Society Systematics Research Fund. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program (DGE-3048109801 to P.M.H.) and by the National Science Foundation-supported National Center for Supercomputing Applications Blue Waters Graduate Research Fellowship Program (under Grant No. 0725070, subaward 15836, to P.M.H.). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Abstract Background Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Funding GMP, PN, and CW are supported by NHLBI R01HL127564. GMP and PN are supported by R01HL142711. AG acknowledge support from the Wellcome Trust (201543/B/16/Z), European Union Seventh Framework Programme FP7/2007–2013 under grant agreement no. HEALTH-F2-2013–601456 (CVGenes@Target) & the TriPartite Immunometabolism Consortium [TrIC]-Novo Nordisk Foundation’s Grant number NNF15CC0018486. JMM is supported by American Diabetes Association Innovative and Clinical Translational Award 1–19-ICTS-068. SR was supported by the Academy of Finland Center of Excellence in Complex Disease Genetics (Grant No 312062), the Finnish Foundation for Cardiovascular Research, the Sigrid Juselius Foundation, and University of Helsinki HiLIFE Fellow and Grand Challenge grants. EW was supported by the Finnish innovation fund Sitra (EW) and Finska Läkaresällskapet. CNS was supported by American Heart Association Postdoctoral Fellowships 15POST24470131 and 17POST33650016. Charles N Rotimi is supported by Z01HG200362. Zhe Wang, Michael H Preuss, and Ruth JF Loos are supported by R01HL142302. NJT is a Wellcome Trust Investigator (202802/Z/16/Z), is the PI of the Avon Longitudinal Study of Parents and Children (MRC & WT 217065/Z/19/Z), is supported by the University of Bristol NIHR Biomedical Research Centre (BRC-1215–2001) and the MRC Integrative Epidemiology Unit (MC_UU_00011), and works within the CRUK Integrative Cancer Epidemiology Programme (C18281/A19169). Ruth E Mitchell is a member of the MRC Integrative Epidemiology Unit at the University of Bristol funded by the MRC (MC_UU_00011/1). Simon Haworth is supported by the UK National Institute for Health Research Academic Clinical Fellowship. Paul S. de Vries was supported by American Heart Association grant number 18CDA34110116. Julia Ramierz acknowledges support by the People Programme of the European Union’s Seventh Framework Programme grant n° 608765 and Marie Sklodowska-Curie grant n° 786833. Maria Sabater-Lleal is supported by a Miguel Servet contract from the ISCIII Spanish Health Institute (CP17/00142) and co-financed by the European Social Fund. Jian Yang is funded by the Westlake Education Foundation. Olga Giannakopoulou has received funding from the British Heart Foundation (BHF) (FS/14/66/3129). CHARGE Consortium cohorts were supported by R01HL105756. Study-specific acknowledgements are available in the Additional file 32: Supplementary Note. The views expressed in this manuscript are those of the authors and do not necessarily represent the views of the National Heart, Lung, and Blood Institute; the National Institutes of Health; or the U.S. Department of Health and Human Services.Peer reviewedPublisher PD

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Publisher Copyright: © 2022, The Author(s).Background: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results: To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions: Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.Peer reviewe