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Nečas T, Kielgast J, Nagy ZT, Kusamba Chifundera Z, Gvoždík V. Systematic position of the Clicking Frog (Kassinula Laurent, 1940), the problem of chimeric sequences and the revised classification of the family Hyperoliidae. Mol Phylogenet Evol 2022; 174:107514. [PMID: 35589055 DOI: 10.1016/j.ympev.2022.107514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 04/26/2022] [Accepted: 05/07/2022] [Indexed: 11/18/2022]
Abstract
The systematics of the African frog family Hyperoliidae has undergone turbulent changes in last decades. Representatives of several genera have not been genetically investigated or with only limited data, and their phylogenetic positions are thus still not reliably known. This is the case of the De Witte's Clicking Frog (Kassinula wittei) which belongs to a monotypic genus. This miniature frog occurs in a poorly studied region, southeastern Democratic Republic of the Congo, northern Zambia, Angola. So far it is not settled whether this genus belongs to the subfamily Kassininae as a relative of the genus Kassina, or to the subfamily Hyperoliinae as a relative of the genus Afrixalus. Here we present for the first time a multilocus phylogenetic reconstruction (using five nuclear and one mitochondrial marker) of the family Hyperoliidae, including Kassinula. We demonstrate with high confidence that Kassinula is a member of Hyperoliinae belonging to a clade also containing Afrixalus (sub-Saharan Africa), Heterixalus (Madagascar) and Tachycnemis (Seychelles). We find that Kassinula represents a divergent lineage (17-25 Mya), which supports its separate genus-level status, but its exact systematic position remains uncertain. We propose to name the clade to which the above four genera belong as the tribe Tachycnemini Channing, 1989. A new taxonomy of the family Hyperoliidae was recently proposed by Dubois et al. (2021: Megataxa 5, 1-738). We demonstrate here that the new taxonomy was based on a partially erroneous phylogenetic reconstruction resulting from a supermatrix analysis of chimeric DNA sequences combining data from two families, Hyperoliidae and Arthroleptidae (the case of Cryptothylax). We therefore correct the erroneous part and propose a new, revised suprageneric taxonomy of the family Hyperoliidae. We also emphasize the importance of inspecting individual genetic markers before their concatenation or coalescent-based tree reconstructions to avoid analyses of chimeric DNA sequences producing incorrect phylogenetic reconstructions. Especially when phylogenetic reconstructions are used to propose taxonomies and systematic classifications.
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Affiliation(s)
- Tadeáš Nečas
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Jos Kielgast
- Section for Freshwater Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark
| | | | - Zacharie Kusamba Chifundera
- Laboratory of Herpetology, Department of Biology, Natural Science Research Centre, Lwiro, Democratic Republic of the Congo; National Pedagogical University, Kinshasa, Democratic Republic of the Congo
| | - Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; National Museum, Department of Zoology, Prague, Czech Republic.
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2
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Greener MS, Hutton E, Pollock CJ, Wilson A, Lam CY, Nokhbatolfoghahai M, Jowers MJ, Downie JR. Sexual dichromatism in the neotropical genus Mannophryne (Anura: Aromobatidae). PLoS One 2020; 15:e0223080. [PMID: 32639962 PMCID: PMC7343140 DOI: 10.1371/journal.pone.0223080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 05/30/2020] [Indexed: 11/18/2022] Open
Abstract
Recent reviews on sexual dichromatism in frogs included Mannophryne trinitatis as the only example they could find of dynamic dichromatism (males turn black when calling) within the family Aromobatidae and found no example of ontogenetic dichromatism in this group. We demonstrate ontogenetic dichromatism in M. trinitatis by rearing post-metamorphic froglets to near maturity: the throats of all individuals started as grey coloured; at around seven weeks, the throat became pale yellow in some, and more strongly yellow as development proceeded; the throats of adults are grey in males and variably bright yellow in females, backed by a dark collar. We demonstrated the degree of throat colour variability by analysing a large sample of females. The red: green (R:G) ratio ranged from ~1.1 to 1.4, reflecting variation from yellow to yellow/orange, and there was also variation in the tone and width of the dark collar, and in the extent to which the yellow colouration occurred posterior to the collar. Female M. trinitatis are known to be territorial in behaviour. We show a positive relationship between throat colour (R:G ratio) and escape performance, as a proxy for quality. Our field observations on Tobago’s M. olmonae showed variability in female throat colour and confirmed that males in this species also turn black when calling. Our literature review of the 20 Mannophryne species so far named showed that all females have yellow throats with dark collars, and that male colour change to black when calling has been reported in eight species; in the remaining 12 species, descriptions of males calling are usually lacking so far. We predict that both dynamic and ontogenetic sexual dichromatism are universal in this genus and provide discussion of the ecological role of dichromatism in this genus of predominantly diurnal, non-toxic frogs, with strong paternal care of offspring.
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Affiliation(s)
- Mark S. Greener
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
- * E-mail:
| | - Emily Hutton
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Christopher J. Pollock
- School of Biology, Faculty of Biological sciences, University of Leeds, Leeds, United Kingdom
| | - Annabeth Wilson
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Chun Yin Lam
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Michael J. Jowers
- CIBIO/InBIO (Centro de Investigacao em Biodiversidade e Recursos Genticos), Universide do Porto, Vairao, Portugal
| | - J. Roger Downie
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
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3
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Portik DM, Bell RC, Blackburn DC, Bauer AM, Barratt CD, Branch WR, Burger M, Channing A, Colston TJ, Conradie W, Dehling JM, Drewes RC, Ernst R, Greenbaum E, Gvoždík V, Harvey J, Hillers A, Hirschfeld M, Jongsma GFM, Kielgast J, Kouete MT, Lawson LP, Leaché AD, Loader SP, Lötters S, Meijden AVD, Menegon M, Müller S, Nagy ZT, Ofori-Boateng C, Ohler A, Papenfuss TJ, Rößler D, Sinsch U, Rödel MO, Veith M, Vindum J, Zassi-Boulou AG, McGuire JA. Sexual Dichromatism Drives Diversification within a Major Radiation of African Amphibians. Syst Biol 2020; 68:859-875. [PMID: 31140573 DOI: 10.1093/sysbio/syz023] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 02/15/2019] [Accepted: 04/09/2019] [Indexed: 01/11/2023] Open
Abstract
Theory predicts that sexually dimorphic traits under strong sexual selection, particularly those involved with intersexual signaling, can accelerate speciation and produce bursts of diversification. Sexual dichromatism (sexual dimorphism in color) is widely used as a proxy for sexual selection and is associated with rapid diversification in several animal groups, yet studies using phylogenetic comparative methods to explicitly test for an association between sexual dichromatism and diversification have produced conflicting results. Sexual dichromatism is rare in frogs, but it is both striking and prevalent in African reed frogs, a major component of the diverse frog radiation termed Afrobatrachia. In contrast to most other vertebrates, reed frogs display female-biased dichromatism in which females undergo color transformation, often resulting in more ornate coloration in females than in males. We produce a robust phylogeny of Afrobatrachia to investigate the evolutionary origins of sexual dichromatism in this radiation and examine whether the presence of dichromatism is associated with increased rates of net diversification. We find that sexual dichromatism evolved once within hyperoliids and was followed by numerous independent reversals to monochromatism. We detect significant diversification rate heterogeneity in Afrobatrachia and find that sexually dichromatic lineages have double the average net diversification rate of monochromatic lineages. By conducting trait simulations on our empirical phylogeny, we demonstrate that our inference of trait-dependent diversification is robust. Although sexual dichromatism in hyperoliid frogs is linked to their rapid diversification and supports macroevolutionary predictions of speciation by sexual selection, the function of dichromatism in reed frogs remains unclear. We propose that reed frogs are a compelling system for studying the roles of natural and sexual selection on the evolution of sexual dichromatism across micro- and macroevolutionary timescales.
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Affiliation(s)
- Daniel M Portik
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Rayna C Bell
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0162, USA
| | - David C Blackburn
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Aaron M Bauer
- Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA
| | - Christopher D Barratt
- Department of Environmental Sciences, University of Basel, Basel 4056, Switzerland.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig 0413, Germany.,Max Planck Institute for Evolutionary Anthropology, Leipzig 0413, Germany
| | - William R Branch
- Port Elizabeth Museum, P.O. Box 11347, Humewood 6013, South Africa.,Department of Zoology, Nelson Mandela Metropolitan University, P.O. Box 77000, Port Elizabeth 6031, South Africa
| | - Marius Burger
- African Amphibian Conservation Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa.,Flora Fauna & Man, Ecological Services Ltd. Tortola, British Virgin, Island
| | - Alan Channing
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
| | - Timothy J Colston
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA.,Zoological Natural History Museum, Addis Ababa University, Arat Kilo, Addis Ababa, Ethiopia
| | - Werner Conradie
- Port Elizabeth Museum, P.O. Box 11347, Humewood 6013, South Africa.,School of Natural Resource Management, Nelson Mandela University, George Campus, George 6530, South Africa
| | - J Maximilian Dehling
- Department of Biology, Institute of Sciences, University of Koblenz-Landau, Universitätsstr. 1, D-56070 Koblenz, Germany
| | - Robert C Drewes
- California Academy of Sciences, San Francisco, CA 94118, USA
| | - Raffael Ernst
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Königsbrücker Landstr. 159, Dresden 01109, Germany.,Department of Ecology, Technische Universität Berlin, Rothenburgstr. 12, Berlin 12165, Germany
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Václav Gvoždík
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech Republic.,Department of Zoology, National Museum, Prague, Czech Republic
| | | | - Annika Hillers
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Biodiversity Dynamics, Invalidenstr. 43, Berlin 10115, Germany.,Across the River - A Transboundary Peace Park for Sierra Leone and Liberia, The Royal Society for the Protection of Birds, 164 Dama Road, Kenema, Sierra Leone
| | - Mareike Hirschfeld
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Biodiversity Dynamics, Invalidenstr. 43, Berlin 10115, Germany
| | - Gregory F M Jongsma
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Jos Kielgast
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, Copenhagen 2100, Denmark
| | - Marcel T Kouete
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Lucinda P Lawson
- Department of Biological Sciences, University of Cincinnati, 614 Rieveschl Hall, Cincinnati, OH 45220, USA.,Life Sciences, Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA
| | - Adam D Leaché
- Department of Biology, Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
| | - Simon P Loader
- Life Sciences Department, Natural History Museum, London SW7 5BD, UK
| | - Stefan Lötters
- Biogeography Department, Trier University, Universitätsring 15, Trier 54296, Germany
| | - Arie Van Der Meijden
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrario de Vairão, Rua Padre Armando Quintas, No. 7, 4485-661 Vairão, Vila do Conde, Portugal
| | - Michele Menegon
- Tropical Biodiversity Section, Science Museum of Trento, Corso del lavoro e della Scienza 3, Trento 38122, Italy
| | - Susanne Müller
- Biogeography Department, Trier University, Universitätsring 15, Trier 54296, Germany
| | - Zoltán T Nagy
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, Rue Vautier 29, B-1000 Brussels, Belgium
| | | | - Annemarie Ohler
- Département Origines et Evolution, Muséum National d'Histoire Naturelle, UMR 7205 ISYEB, 25 rue Cuvier, Paris 75005, France
| | | | - Daniela Rößler
- Biogeography Department, Trier University, Universitätsring 15, Trier 54296, Germany
| | - Ulrich Sinsch
- Department of Biology, Institute of Sciences, University of Koblenz-Landau, Universitätsstr. 1, D-56070 Koblenz, Germany
| | - Mark-Oliver Rödel
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Biodiversity Dynamics, Invalidenstr. 43, Berlin 10115, Germany
| | - Michael Veith
- Biogeography Department, Trier University, Universitätsring 15, Trier 54296, Germany
| | - Jens Vindum
- California Academy of Sciences, San Francisco, CA 94118, USA
| | - Ange-Ghislain Zassi-Boulou
- Institut National de Recherche en Sciences Exactes et Naturelles, Brazzaville BP 2400, République du Congo
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
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Deichmann JL, Mulcahy DG, Vanthomme H, Tobi E, Wynn AH, Zimkus BM, McDiarmid RW. How many species and under what names? Using DNA barcoding and GenBank data for west Central African amphibian conservation. PLoS One 2017; 12:e0187283. [PMID: 29131846 PMCID: PMC5683629 DOI: 10.1371/journal.pone.0187283] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 09/06/2017] [Indexed: 11/19/2022] Open
Abstract
Development projects in west Central Africa are proceeding at an unprecedented rate, often with little concern for their effects on biodiversity. In an attempt to better understand potential impacts of a road development project on the anuran amphibian community, we conducted a biodiversity assessment employing multiple methodologies (visual encounter transects, auditory surveys, leaf litter plots and pitfall traps) to inventory species prior to construction of a new road within the buffer zone of Moukalaba-Doudou National Park, Gabon. Because of difficulties in morphological identification and taxonomic uncertainty of amphibian species observed in the area, we integrated a DNA barcoding analysis into the project to improve the overall quality and accuracy of the species inventory. Based on morphology alone, 48 species were recognized in the field and voucher specimens of each were collected. We used tissue samples from specimens collected at our field site, material available from amphibians collected in other parts of Gabon and the Republic of Congo to initiate a DNA barcode library for west Central African amphibians. We then compared our sequences with material in GenBank for the genera recorded at the study site to assist in identifications. The resulting COI and 16S barcode library allowed us to update the number of species documented at the study site to 28, thereby providing a more accurate assessment of diversity and distributions. We caution that because sequence data maintained in GenBank are often poorly curated by the original submitters and cannot be amended by third-parties, these data have limited utility for identification purposes. Nevertheless, the use of DNA barcoding is likely to benefit biodiversity inventories and long-term monitoring, particularly for taxa that can be difficult to identify based on morphology alone; likewise, inventory and monitoring programs can contribute invaluable data to the DNA barcode library and the taxonomy of complex groups. Our methods provide an example of how non-taxonomists and parataxonomists working in understudied parts of the world with limited geographic sampling and comparative morphological material can use DNA barcoding and publicly available sequence data (GenBank) to rapidly identify the number of species and assign tentative names to aid in urgent conservation management actions and contribute to taxonomic resolution.
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Affiliation(s)
- Jessica L. Deichmann
- Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States of America
| | - Daniel G. Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Hadrien Vanthomme
- Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States of America
| | - Elie Tobi
- Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States of America
| | - Addison H. Wynn
- Department of Vertebrate Zoology, Division of Amphibians and Reptiles, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Breda M. Zimkus
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America
| | - Roy W. McDiarmid
- USGS, Patuxent Wildlife Research Center, National Museum of Natural History, Washington DC, United States of America
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