Skip to main content Skip to main navigation menu Skip to site footer
Responsive image
Issue: Vol. 7 No. 2: 15 December 2022
Type: Article
Published: 2022-12-15
DOI: 10.11646/megataxa.7.2.1
Page range: 113–311
Abstract views: 2392
PDF downloaded: 710

An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar

Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen Ø, Denmark
CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal, Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Hauptstr. 13, 82234 Weßling, Germany
Museo Regionale di Scienze Naturali, Via G. Giolitti, 36, 10123 Torino, Italy
Natural and Environmental Sciences, Regional University Centre of the SAVA Region (CURSA), Antalaha, Madagascar, Mention Zoologie et Biodiversité Animale, Université d’Antananarivo, BP 906, Antananarivo, 101 Madagascar
Senckenberg Forschungsinstitut und Naturmuseum, Senckenberganlage 25, D-60325, Frankfurt, Germany
Institute of Zoology, Ecology and Conservation, Biocentre Grindel, University of Hamburg, Martin-Luther-King-Platz 3, 29146 Hamburg, Germany
Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS, MNHN, Sorbonne Université, EPHE, Université des Antilles, Muséum National d'Histoire Naturelle, CP 51, 57 rue Cuvier, 75231 PARIS Cedex 05 France
Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
Mention Zoologie et Biodiversité Animale, Université d’Antananarivo, BP 906, Antananarivo, 101 Madagascar, School for International Training, VN 41A Bis Ankazolava Ambohitsoa, Antananarivo, 101 Madagascar
Zoologisches Institut, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany, Uppsala University, Department of Ecology and Genetics, Animal Ecology, Norbyvägen 18 D, 752 36 Uppsala, Sweden
Mention Zoologie et Biodiversité Animale, Université d’Antananarivo, BP 906, Antananarivo, 101 Madagascar, Association Vahatra, Lot V A 38 LBA Ter Ambohidempona Tsiadana, BP 3972, Antananarivo, 101 Madagascar
Institute of Zoology, Ecology and Conservation, Biocentre Grindel, University of Hamburg, Martin-Luther-King-Platz 3, 29146 Hamburg, Germany
Museum für Naturkunde—Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115 Berlin, Germany
Institute of Zoology, Zoological Society of London, London NW1 4RY, UK, Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
Department of Life Sciences, The Natural History Museum, Cromwell Road, London, UK
Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales—CSIC. Calle José Gutierrez Abascal 2, 28006, Madrid, Spain
Hessisches Landesmuseum Darmstadt, Friedensplatz 1, 64283 Darmstadt, Germany
Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstr. 21, 81247 München, Germany
Technische Universität Braunschweig, Zoological Institute, Mendelssohnstr. 4, 38106 Braunschweig
Amphibia Anura Mantellidae Madagascar FrogCap target enrichment museomics museum genomics phylogenomics ASAP integrative taxonomy

Abstract

Malagasy frogs of the subgenus Brygoomantis in the mantellid frog genus Mantidactylus currently comprise 14 described species of mostly brown, riparian frogs. Data from DNA barcoding suggested that the diversity of this subgenus is dramatically underestimated by current taxonomy. We here provide a comprehensive revision of this subgenus. We use hybrid-enrichment based DNA barcode fishing to obtain mitochondrial DNA fragments from the name-bearing type material of 16 of the 20 available names for members of this subgenus, and integrate these into a genetic dataset consisting of 1305 individuals sampled across Madagascar. By thus assigning the nomina to genetic lineages, we can confidently establish synonyms, revalidate old names, and describe the remaining diversity. We take an integrative approach to our descriptions, drawing together genetics, morphometrics and morphology, and bioacoustics for assignment. We also provide a robust phylogenomic hypothesis for the subgenus, based on 12,951 nuclear-encoded markers (almost 10 million base pairs) for 58 representative samples, sequenced using a hybrid-enrichment bait set for amphibians. Those data suggest a division of the subgenus into eight major clades and shows that morphological species complexes are often paraphyletic or polyphyletic. Lectotypes are designated for Rana betsileana Boulenger, 1882; Rana biporus Boulenger, 1889; Rana curta Boulenger, 1882; Mantidactylus ambohimitombi Boulenger, 1918; Mantidactylus tripunctatus Angel, 1930; and Rana inaudax Peracca, 1893. For several other nomina, previous authors had considered a certain syntype as holotype; this has been seen as lectotype designation by implication, which, however, is ambiguous according to the provisions of the International Code of Zoological Nomenclature. Hence, we validate a previous lectotype designation by implication for Limnodytes ulcerosus Boettger, 1880 by explicitly designating the same individual as lectotype. In one other such case, that of Mantidactylus brauni Ahl, 1929, we deviate from previous authors and designate a different specimen as lectotype. We revalidate Rana inaudax Peracca, 1893 as Mantidactylus inaudax (Peracca, 1893) bona species, and Mantidactylus tripunctatus Angel, 1930 bona species. The identities of three further species (M. ambohimitombi, M. biporus, M. tricinctus) are largely redefined based on new genetic data. By designating the lectotype of Rana aluta (MZUT An725.1) as the neotype of Mantidactylus laevis Angel, 1929 we also stabilize the latter nomen (as junior synonym of M. alutus) whose original type material is lost. Based on DNA sequences of its lectotype, we consider Mantidactylus brauni Ahl, 1929 as junior synonym of M. ulcerosus (rather than M. biporus). We formally name 20 new species and four new subspecies: M. ambohimitombi marefo ssp. nov., M. ambohimitombi miloko ssp. nov., M. mahery sp. nov., M. steinfartzi sp. nov., M. incognitus sp. nov., M. jonasi sp. nov., M. katae sp. nov., M. kortei sp. nov., M. riparius sp. nov., M. fergusoni sp. nov., M. georgei sp. nov., M. jahnarum sp. nov., M. marintsoai sp. nov., M. grubenmanni sp. nov., M. gudrunae sp. nov., M. augustini sp. nov., M. bletzae sp. nov., M. brevirostris sp. nov., M. eulenbergeri sp. nov., M. glosi sp. nov., M. stelliger sp. nov., M. manerana sp. nov., M. manerana fotaka ssp. nov., and M. manerana antsanga ssp. nov. Based on our taxonomic revision, we discuss (i) the importance of definitive assignment of historical names via archival DNA analysis; (ii) the relevance of the subspecies category to name geographic variation within species; (iii) the value of molecular characters in formal species diagnoses in taxa with substantial individual variation of morphology; (iv) the use of phylogenomic approaches for taxonomy, by confirming that some morphologically similar taxa are not each other’s closest relatives, and in several cases belong to entirely different major subclades within Brygoomantis, thus facilitating lineage diagnosis; and (v) the need to interpret genetic distances in a probabilistic framework rather than using fixed thresholds, where higher distances confer a higher likelihood of genetic incompatibilities across the genome and thus completion of speciation.

References

  1. Ahl, E. (1929 ‘1928’) Beschreibung neuer Frösche aus Madagascar. Mitteilungen aus dem Zoologischen Museum in Berlin, 14, 469–484.
  2. Ahrens, D., Ahyong, S.T., Ballerio, A., Barclay, M.V.L., Eberle, J., Espeland, M., Huber, B.A., Mengual, X., Pacheco, T.L., Peters, R.S., Rulik, B., Vaz-de-Mello, F., Wesener, T. & Krell, F.-T. (2021) Is it time to describe new species without diagnoses?—A comment on Sharkey et al. (2021). Zootaxa, 5027, 151–159. https://doi.org/10.11646/zootaxa.5027.2.1
  3. Alluaud, C.A. (1893) Correspondance. Compte rendu des Séances de la Societé de Géographie et de la Commission centrale, 14 (Numéro Supplémentaire), 355.
  4. AmphibiaWeb. (2022) AmphibiaWeb: Information on amphibian biology and conservation. Available at: http://amphibiaweb.org. Accessed 10 March 2022. https://amphibiaweb.org/, accessed: 10 March 2022.
  5. Andreone, F., Cadle, J.E., Cox, N., Glaw, F., Nussbaum, R.A., Raxworthy, C.J., Stuart, S.N., Vallan, D. & Vences, M. (2005) Species review of amphibian extinction risks in Madagascar: conclusions from the Global Amphibian Assessment. Conservation Biology, 19, 1790–1802. https://doi.org/10.1111/j.1523-1739.2005.00249.x
  6. Andreone, F., Crottini, A., Rabemananjara, F.C.E., Randrianirina, J.E., Razafindrabe, T. & Tessa, G. (2014) Age structure, population estimate and Bd-status of two Critically Endangered frogs from the Ankaratra Massif (Madagascar), Boophis willliamsi and Mantidactylus pauliani (Amphibia: Mantellidae). Scripta Herpetologica, Studies on Amphibians and Reptiles in honour of Benedetto Lanza, 17–29.
  7. Andreone, F., Dawson, J.S., Rabemananjara, F.C.E., Rabibisoa, N.H.C. & Rakotonanahary, T.F. (2016) New Sahonagasy Action Plan 2016–2020. Turin, Italy, Museo Regionale di Scienze Naturali & Amphibian Survival Alliance, 46 pp.
  8. Andreone, F., Glaw, F., Nussbaum, R.A., Raxworthy, C.J., Vences, M. & Randrianirina, J.E. (2003) The amphibians and reptiles of Nosy Be (NW Madagascar) and nearby islands: a case study of diversity and conservation of an insular fauna. Journal of Natural History, 37, 2119–2149. https://doi.org/10.1080/00222930210130357
  9. Angel, F. (1929) Matériaux de la Mission G. Petit à Madagascar. Description de trois Batraciens nouveaux appartenant aux genres Mantidactylus et Gephyromantis. Bulletin du Muséum National d’Histoire Naturelle, Paris, Serie 2, 1, 358–362.
  10. Angel, F. (1930) Description d’un Batracien nouveau de Madagascar, appartenant au genre Mantidactylus (Materiaux des Missions de M. R. Decary). Bulletin du Muséum National d’Histoire Naturelle, Paris, Serie 2, 2, 619–620.
  11. Avise, J.C. & Ball, R.M. (1990) Principles of genealogical concordance in species concepts and biological taxonomy. In: Futuyma, D. & Antonovics, J. (Eds.) Oxford Surveys in Evolutionary Biology. Oxford University Press, Oxford, UK, pp. 45–67.
  12. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Lesin, V.M., Nikolenko, S.I., Pham, S., Prjibelski, A.D. & Pyshkin, A.V. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19, 455–477. https://doi.org/10.1089/cmb.2012.0021
  13. Barbour, T. & Loveridge, A. (1929) Typical reptiles and amphibians in the Museum of Comparative Zoölogy. Bulletin of the Museum of Comparative Zoology, 69, 205–360.
  14. Barbour, T. & Loveridge, A. (1946) First supplement to typical reptiles and amphibians. Bulletin of the Museum of Comparative Zoology, 96, 59–214.
  15. Basler, N., Xenikoudakis, G., Westbury, M.V., Song, L., Sheng, G. & Barlow, A. (2017) Reduction of the contaminant fraction of DNA obtained from an ancient giant panda bone. BMC Research Notes, 10, 754. https://doi.org/10.1186/s13104-017-3061-3
  16. Bernal, M.H. & Clavijo, J.A. (2009) An essay on precision in morphometric measurements in anurans: inter-individual, intra-individual and temporal comparisons. Zootaxa, 2246, 32–44. https://doi.org/10.11646/zootaxa.2246.1.3
  17. Bletz, M.C., Rosa, G.M., Andreone, F., Courtois, E.A., Schmeller, D.S., Rabibisoa, N.H.C., Rabemananjara, F.C.E., Raharivololoniaina, L., Vences, M., Weldon, C., Edmonds, D., Raxworthy, C.J., Harris, R.N., Fisher, M.C. & Crottini, A. (2015) Widespread presence of the pathogenic fungus Batrachochytrium dendrobatidis in wild amphibian communities in Madagascar. Scientific Reports, 5, 1–10. https://doi.org/10.1038/srep08633
  18. Blommers-Schlösser, R.M.A. (1979) Biosystematics of the Malagasy frogs. I. Mantellinae (Ranidae). Beaufortia, 352, 1–77.
  19. Blommers-Schlösser, R.M.A. & Blanc, C.P. (1991) Amphibiens (première partie). Faune de Madagascar, 75, 1–397.
  20. Boettger, O. (1880) Diagnoses reptilium et batrachiorum novorum a Carolo Ebenau in insula Nossi-Bé madagascariensi lectorum. Zoologischer Anzeiger, 3, 279–283.
  21. Boettger, O. (1881) Diagnoses reptilium et batrachiorum novorum ab ill. Antonio Stumpff in insula Nossi-Bé Madagascariensi lectorum. Zoologischer Anzeiger, 4, 358–362.
  22. Boettger, O. (1913) Reptilien und Amphibien von Madagascar, den Inseln und dem Festland Ostafrikas. Reise in Ost-Afrika in den Jahren 1903–1905 mit Mitteln der Hermann und Elise geb. Heckmann-Wentzel-Stiftung. Wissenschaftliche Ergebnisse. Systematische Arbeiten., 3, 269–376.
  23. Bora, P., Otisitraka Randriambahiniarime, M., Rabemananjara, F.C.E., Ravoahangimalala Ramilijaona, O., Glaw, F. & Vences, M. (2007) A rapid assessment survey of the herpetofauna at Befotaka-Midongy National Park, south-eastern Madagascar. Mitteilungen aus dem Museum für Naturkunde in Berlin—Zoologische Reihe, 83, 170–178. https://doi.org/10.1002/mmnz.200700007
  24. Boulenger, G.A. (1882) Catalogue of the Batrachia Salientia s. Ecaudata in the Collection of the British Museum. Taylor and Francis, London, UK. 2nd Edition.
  25. Boulenger, G.A. (1889) Descriptions of new reptiles and batrachians from Madagascar. Annals and Magazine of Natural History, Series 6, 4, 244–248. https://doi.org/10.1080/00222938909460511
  26. Boulenger, G.A. (1895) On a genus of frog peculiar to Madagascar. Annals and Magazine of Natural History, Series 6, 15, 450. https://doi.org/10.1080/00222939508677910
  27. Boulenger, G.A. (1895 ‘1894’) Third report on additions to the batrachian collection in the Natural-History Museum. Proceedings of the Zoological Society of London, 1894, 640–646.
  28. Boulenger, G.A. (1919 ‘1918’) On the Madagascar frogs of the genus Mantidactylus. Proceedings of the Zoological Society of London, 1918, 257–261. https://doi.org/10.1111/j.1096-3642.1918.tb02096.x
  29. Boumans, L., Vieites, D.R., Glaw, F. & Vences, M. (2007) Geographical patterns of deep mitochondrial differentiation in widespread Malagasy reptiles. Molecular Phylogenetics and Evolution, 45, 822–839. https://doi.org/10.1016/j.ympev.2007.05.028
  30. Brown, J.L., Cameron, A., Yoder, A.D. & Vences, M. (2014) A necessarily complex model to explain the biogeography of the amphibians and reptiles of Madagascar. Nature Communications, 5, 5046. https://doi.org/10.1038/ncomms6046
  31. Brown, J.L., Sillero, N., Glaw, F., Bora, P., Vieites, D.R. & Vences, M. (2016) Spatial biodiversity patterns of Madagascar‘s amphibians and reptiles. PLoS One, 11, e0144076. https://doi.org/10.1371/journal.pone.0144076
  32. Brühl, C.A., Schmidt, T., Pieper, S. & Alscher, A. (2013) Terrestrial pesticide exposure of amphibians: An underestimated cause of global decline? Scientific Reports, 3, 1135. https://doi.org/10.1038/srep01135
  33. Buitrago Aristizábal, M.A., Oliveira Gouvêa De Figueiredo, F. & André, T. (2020) Accommodating trait overlap and individual variability in species diagnosis of Ischnosiphon (Marantaceae). Botanical Journal of the Linnean Society, 194, 469–479. https://doi.org/10.1093/botlinnean/boaa043
  34. Bushnell, B., Rood, J. & Singer, E. (2017) BBMerge—Accurate paired shotgun read merging via overlap. PLoS One, 12, e0185056. https://doi.org/10.1371/journal.pone.0185056
  35. Capella-Gutiérrez, S., Silla-Martínez, J.M. & Gabaldón, T. (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25, 1972–1973. https://doi.org/10.1093/bioinformatics/btp348
  36. Catenazzi, A. (2015) State of the world‘s amphibians. Annual Review of Environment and Resources, 40, 91–119. https://doi.org/10.1146/annurev-environ-102014-021358
  37. Chan, K.O., Hutter, C.R., Wood, P.L.J., Grismer, L.L., Das, I. & Brown, R.M. (2020) Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex. Molecular Ecology, 29, 3970–3987. https://doi.org/10.1111/mec.15603
  38. Chan, K.O., Hutter, C.R., Wood, P.L.J., Su, Y.-C. & Brown, R.M. (2022) Gene flow increases phylogenetic structure and inflates cryptic species estimations: a case study on widespread Philippine puddle frogs (Occidozyga laevis). Systematic Biology, 71, 40–57. https://doi.org/10.1093/sysbio/syab034
  39. Chen, S., Huang, T., Zhou, Y., Han, Y., Xu, M. & Gu, J. (2017) AfterQC: automatic filtering, trimming, error removing and quality control for fastq data. BMC Bioinformatics, 18, 80. https://doi.org/10.1186/s12859-017-1469-3
  40. Cocca, W., Rosa, G.M., Andreone, F., Aprea, G., Bergò, P.E., Mattioli, F., Mercurio, V., Randrianirina, J.E., Rosado, D., Vences, M. & Crottini, A. (2018) The herpetofauna (Amphibia, Crocodylia, Squamata, Testudines) of the Isalo Massif, Southwest Madagascar: combining morphological, molecular and museum data. Salamandra, 54, 178–200.
  41. Cook, L.G., Edwards, R.D., Crisp, M.D. & Hardy, N.B. (2010) Need morphology always be required for new species descriptions? Invertebrate Systematics, 24, 322–326. https://doi.org/10.1071/IS10011
  42. Crottini, A., Harris, D.J., Miralles, A., Glaw, F., Jenkins, R.K.B., Randrianantoandro, J.C., Bauer, A.M. & Vences, M. (2015) Morphology and molecules reveal two new species of the poorly studied gecko genus Paragehyra (Squamata: Gekkonidae) from Madagascar. Organisms Diversity & Evolution, 15, 175–198. https://doi.org/10.1007/s13127-014-0191-5
  43. Dabney, J., Knapp, M., Glock, I., Gansauge, M., Weihmann, A., Nickel, B., Valdioserad, C., García, N., Pääbo, S., Arsuag, J. & Meyer, M. (2013) Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proceedings of the National Academy of Sciences of the USA, 110, 15758–15763. https://doi.org/10.1073/pnas.1314445110
  44. Dayrat, B. (2005) Towards integrative taxonomy. Biological Journal of the Linnean Society, 85, 407–415. https://doi.org/10.1111/j.1095-8312.2005.00503.x
  45. de Queiroz, K. (1998) The General Lineage Concept of species, species criteria, and the process of speciation. In: Howard, D.J. & Berlocher, S.H. (Eds.) Endless Forms: Species and Speciation. Oxford University Press, Oxford, UK, pp. 57–75.
  46. de Queiroz, K. (2007) Species concepts and species delimitation. Systematic Biology, 56, 879–886. https://doi.org/10.1080/10635150701701083
  47. de Queiroz, K. (2020) An updated concept of subspecies resolves a dispute about the taxonomy of incompletely separated lineages. Herpetological Review, 51, 459–461.
  48. Dubois, A. (1992) Notes sur la classification des Ranidae (Amphibiens Anoures). Bulletin Mensuel de la Société Linnéenne de Lyon, 61, 305–352. https://doi.org/10.3406/linly.1992.11011
  49. Dufresnes, C., Brelsford, A., Jeffries, D.L., Mazepa, G., Suchan, T., Canestrelli, D., Nicieza, A., Fumagalli, L., Dubey, S., Martínez-Solano, I., Litvinchuk, S.N., Vences, M., Perrin, N. & Crochet, P.-A. (2021) Mass of genes rather than master genes underlie the genomic architecture of amphibian speciation. Proceedings of the National Academy of Sciences of the USA, 118, e2103963118. https://doi.org/10.1073/pnas.2103963118
  50. Edmonds, D., Kessler, E. & Bolte, L. (2019) How common is common? Rapidly assessing population size and structure of the frog Mantidactylus betsileanus at a site in east-central Madagascar. Austral Ecology, 44, 1196–1203. https://doi.org/10.1111/aec.12797
  51. Edmonds, D., Rakotoarisoa, J.C., Dolch, R., Pramuk, J., Gagliardo, R., Andreone, F., Rabibisoa, N., Rabemananjara, F., Rabesihanaka, S. & Robsomanitrandrasana, E. (2012) Building capacity to implement conservation breeding programs for frogs in Madagascar: Results from year one of Mitsinjo‘s amphibian husbandry research and captive breeding facility. Amphibian & Reptile Conservation, 5, 57–69.
  52. Endler, D., Klein, J., Antonelli, A. & Silvestro, D. (2020) raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML. Methods in Ecology and Evolution, 12, 373–377. https://doi.org/10.1111/2041-210X.13512
  53. Everson, K.M., Jansa, S.A., Goodman, S.M. & Olson, L.E. (2020) Montane regions shape patterns of diversification in small mammals and reptiles from Madagascar’s moist evergreen forest. Journal of Biogeography, 47, 2059–2072. https://doi.org/10.1111/jbi.13945
  54. Fedosov, A., Achaz, G. & Puillandre, N. (2019) Revisiting use of DNA characters in taxonomy with MolD - a tree independent algorithm to retrieve diagnostic nucleotide characters from monolocus datasets. bioRxiv, 838151. https://doi.org/10.1101/838151
  55. Feng, Y.-J., Blackburn, D.C., Liang, D., Hillis, D.M., Wake, D.B., Cannatella, D.C. & Zhang, P. (2017) Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary. Proceedings of the National Academy of Sciences of the USA, 114, E5864–E5870. https://doi.org/10.1073/pnas.1704632114
  56. Fernandez-Triana, J.L. (2022) Turbo taxonomy approaches: lessons from the past and recommendations for the future based on the experience with Braconidae (Hymenoptera) parasitoid wasps. ZooKeys, 1087, 199–220. https://doi.org/10.3897/zookeys.1087.76720
  57. Ficetola, G.F. & de Bernardi, F. (2006) Trade-off between larval development rate and post-metamorphic traits in the frog Rana latastei. Evolutionary Ecology, 20, 143–158. https://doi.org/10.1007/s10682-005-5508-6
  58. Forsman, A. (2015) Rethinking phenotypic plasticity and its consequences for individuals, populations and species. Heredity, 115, 276–284. https://doi.org/10.1038/hdy.2014.92
  59. Fouquet, A., Gilles, A., Vences, M., Marty, C., Blanc, M. & Gemmell, N.J. (2007) Underestimation of species richness in neotropical frogs revealed by mtDNA analyses. PLoS One, 2, e1109. https://doi.org/10.1371/journal.pone.0001109
  60. Frizzell, D.L. (1933) Terminology of types. The American Midland Naturalist, 14, 637–668. https://doi.org/10.2307/2420124
  61. Frost, D.R. (2021) Amphibian Species of the World: an Online Reference. Version 6.1 (Accessed 18 February 2021). Electronic Database accessible at http://research.amnh.org/herpetology/amphibia/index.html. American Museum of Natural History, New York, USA
  62. Gansauge, M.-T., Gerber, T., Glocke, I., Korlević, P., Lippik, L., Nagel, S., Riehl, L.M., Schmidt, A. & Meyer, M. (2017) Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Research, 45, e79. https://doi.org/10.1093/nar/gkx033
  63. Gansauge, M.-T. & Meyer, M. (2013) Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nature Methods, 8, 737–748. https://doi.org/10.1038/nprot.2013.038
  64. Ganzhorn, J.U., Lowry, P.P., Schatz, G.E. & Sommer, S. (2009) The biodiversity of Madagascar: one of the world‘s hottest hotspots on its way out. Oryx, 35, 346–348. https://doi.org/10.1046/j.1365-3008.2001.00201.x
  65. Gavetti, E. & Andreone, F. (1993) Revised catalogue of the herpetological collection in Turin University. 1. Amphibia. Cataloghi. Museo Regionale di Scienze Naturali. Torino 10: 1–187. Cataloghi X, Museo Regionale di Scienze Naturali, Torino, Italy.
  66. Glaw, F. & Vences, M. (1992a) A Fieldguide to the Amphibians and Reptiles of Madagascar. Vences & Glaw Verlags GbR, Cologne, Germany, 335 pp. First Edition.
  67. Glaw, F. & Vences, M. (1992b) Zur Kenntnis der Gattungen Boophis, Aglyptodactylus und Mantidactylus (Amphibia: Anura) aus Madagaskar, mit Beschreibung einer neuen Art. Bonner zoologische Beiträge, 43, 45–77.
  68. Glaw, F. & Vences, M. (1994) A Fieldguide to the Amphibians and Reptiles of Madagascar. Vences & Glaw Verlags GbR, Cologne, Germany, 478 pp. Second Edition.
  69. Glaw, F. & Vences, M. (1999) Resurrection and redescription of Mantidactylus tricinctus (Guibé, 1947) from eastern Madagascar (Anura: Ranidae: Mantellinae). Journal of Herpetology, 33, 639–647. https://doi.org/10.2307/1565581
  70. Glaw, F. & Vences, M. (2006) Phylogeny and genus-level classification of mantellid frogs (Amphibia, Anura). Organisms Diversity & Evolution, 6, 236–253. https://doi.org/10.1016/j.ode.2005.12.001
  71. Glaw, F. & Vences, M. (2007) A Field Guide to the Amphibians and Reptiles of Madagascar. Vences & Glaw Verlags GbR, Cologne, Germany, 496 pp. Third Edition.
  72. Glaw, F., Vences, M. & Gossmann, V. (2000) A new species of Mantidactylus (subgenus Guibemantis) from Madagascar, with a comparative survey of internal femoral gland structure in the genus (Amphibia: Ranidae: Mantellinae). Journal of Natural History, 34, 1135–1154. https://doi.org/10.1080/00222930050020140
  73. González Gutiérrez, P.A., Köhler, E. & Borsch, T. (2013) New species of Buxus (Buxaceae) from northeastern Cuba based on morphological and molecular characters, including some comments on molecular diagnosis [Novitiae florae cubensis 40]. Willdenowia, 43, 125–137. https://doi.org/10.3372/wi.43.43115
  74. Guibé, J. (1947) Trois Gephyromantis nouveaux de Madagascar (Batraciens). Bulletin du Muséum National d’Histoire Naturelle, Paris, Serie 2, 19, 151–155.
  75. Guibé, J. (1950) Catalogue des Types d’Amphibiens du Muséum National d’Histoire Naturelle. Imprimerie Nationale, Paris, France.
  76. Guibé, J. (1973a) Batraciens nouveaux de Madagascar. Bulletin du Muséum National d’Histoire Naturelle, Paris, Serie 3, 145, 1009–1017.
  77. Guibé, J. (1973b) Batraciens nouveaux de Madagascar. Bulletin du Muséum National d’Histoire Naturelle, Paris, Serie 3, 171, 1169–1192.
  78. Guibé, J. (1978) Les batraciens de Madagascar. Bonner zoologische Monographien, 11, 1–140.
  79. Habel, J.C., Rasche, L., Schneider, U.A., Engler, J.O., Schmid, E., Rödder, D., Meyer, S.T., Trapp, N., del Diego, R.S., Eggermont, H., Lens, L. & Stork, N.E. (2019) Final countdown for biodiversity hotspots. Conservation Letters, 12, e12668. https://doi.org/10.1111/conl.12668
  80. Härer, A., Torres-Dowdall, J. & Meyer, A. (2017) Rapid adaptation to a novel light environment: The importance of ontogeny and phenotypic plasticity in shaping the visual system of Nicaraguan Midas cichlid fish (Amphilophus citrinellus spp.). Molecular Ecology, 26, 5582–5593. https://doi.org/10.1111/mec.14289
  81. Hawlitschek, O., Nagy, Z.T. & Glaw, F. (2012) Island evolution and systematic revision of Comoran snakes: Why and when subspecies still make sense. PLoS One, 7, e42970. https://doi.org/10.1371/journal.pone.0042970
  82. Hillis, D.M. (2019) Species delimitation in herpetology. Journal of Herpetology, 53, 3–12. https://doi.org/10.1670/18-123
  83. Hillis, D.M. (2020) The detection and naming of geographic variation within species. Herpetological Review, 51, 52–56.
  84. Hillis, D.M. (2022) Species, clades, and their relationship to paraphyly and monophyly: examples from the Pantherophis obsoletus complex. Herpetological Review, 53, 47–53.
  85. Houlahan, J.E., Findlay, C.S., Schmidt, B.R., Meyer, A.H. & Kuzmin, S.L. (2000) Quantitative evidence for global amphibian population declines. Nature, 404, 752–755. https://doi.org/10.1038/35008052
  86. Hutter, C.R., Cobb, K.A., Portik, D.M., Travers, S.L., Wood Jr, P.L. & Brown, R.M. (2021) FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. Molecular Ecology Resources, 22, 1100–1119. https://doi.org/10.1111/1755-0998.13517
  87. Hütter, T., Ganser, M.H., Kocher, M., Halkic, M., Agatha, S. & Augsten, N. (2020) DeSignate: detecting signature characters in gene sequence alignments for taxon diagnoses. BMC Bioinformatics, 21, 151. https://doi.org/10.1186/s12859-020-3498-6
  88. Hyde Roberts, S. & Daly, C. (2014) A rapid herpetofaunal assessment of Nosy Komba Island, northwestern Madagascar, with new locality records for seventeen species. Salamandra, 50, 18–26.
  89. ICZN. (1999) International Code of Zoological Nomenclature. The International Trust for Zoological Nomenclature, London, 306 pp. 4th Edition.
  90. IUCN. (2012) IUCN Red List Categories and Criteria: Version 3.1. IUCN, Gland, Switzerland and Cambridge, UK. 2nd Edition.
  91. IUCN SSC Amphibian Specialist Group. (2016) Mantidactylus pauliani. The IUCN Red List of Threatened Species, 2016, e.T57509A84175039. https://doi.org/10.2305/IUCN.UK.2016-1.RLTS.T57509A8-4175039.en
  92. Jörger, K.M. & Schrödl, M. (2013) How to describe a cryptic species? Practical challenges of molecular taxonomy. Frontiers in Zoology, 10, 59. https://doi.org/10.1186/1742-9994-10-59
  93. Katoh, K. & Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution, 30, 772–780. https://doi.org/10.1093/molbev/mst010
  94. Knoll, A., Köhler, J., Glaw, F., Teschke, M. & Vences, M. (2007) Larval morphology in four species of Madagascan frogs of the subgenus Brygoomantis (Mantellidae: Mantidactylus). Zootaxa, 59, 49–59. https://doi.org/10.11646/zootaxa.1616.1.4
  95. Köhler, G. (2021) Taxonomy of horned lizards, genus Phrynosoma (Squamata, Phrynosomatidae). Taxonomy, 1, 83–115. https://doi.org/10.3390/taxonomy1020009
  96. Köhler, J., Jansen, M., Rodríguez, A., Kok, P.J.R., Toledo, L.F., Emmrich, M., Glaw, F., Haddad, C.F.B., Rödel, M.-O. & Vences, M. (2017) The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice. Zootaxa, 4251, 1–124. https://doi.org/10.11646/zootaxa.4251.1.1
  97. Kollár, J., Poulíčková, A. & Dvořák, P. (2022) On the relativity of species, or the probabilistic solution to the species problem. Molecular Ecology, 31, 411–418. https://doi.org/10.1111/mec.16218
  98. Kumar, S., Stecher, G. & Tamura, K. (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870–1874. https://doi.org/10.1093/molbev/msw054
  99. Kurabayashi, A., Usuki, C., Mikami, N., Fujii, T., Yonekawa, H., Sumida, M. & Hasegawa, M. (2006) Complete nucleotide sequence of the mitochondrial genome of a Malagasy poison frog Mantella madagascariensis: evolutionary implications on mitochondrial genomes of higher anuran groups. Molecular Phylogenetics and Evolution, 39, 223–236. https://doi.org/10.1016/j.ympev.2005.11.021
  100. Laurent, R. (1943) Sur la position systématique et l’ostéologie du genre Mantidactylus Boulenger. Bulletin du Musée royal d’Histoire naturelle de Belgique, 19, 1–8.
  101. Li, C., Corrigan, S., Yang, L., Straube, N., Harris, M., Hofreiter, M., White, W.T. & Naylor, G.J.P. (2015) DNA capture reveals transoceanic gene flow in endangered river sharks. Proceedings of the National Academy of Sciences of the USA, 112, 13302–13307. https://doi.org/10.1073/pnas.1508735112
  102. Librado, P. & Rozas, J. (2009) DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451–1452. https://doi.org/10.1093/bioinformatics/btp187
  103. Lötters, S., Rödder, D., Kielgast, J. & Glaw, F. (2011) Hotspots, conservation, and diseases: Madagascar’s megadiverse amphibians and the potential impact of chytridiomycosis. In: Zachos, F. & Habel, J. (Eds.) Biodiversity Hotspots. Springer Berlin, Germany, pp. 255–274. https://doi.org/10.1007/978-3-642-20992-5_14
  104. Malone, J.H. & Fontenot, B.E. (2008) Patterns of reproductive isolation in toads. PLoS One, 3, e3900. https://doi.org/10.1371/journal.pone.0003900
  105. Martinazzo, L.B., Basso, N.G. & Úbeda, C.A. (2011) The aquatic and littoral forms of the Patagonian frog Atelognathus patagonicus (Batrachylinae): new molecular evidence. Zootaxa, 3129, 62–68. https://doi.org/10.11646/zootaxa.3129.1.5
  106. Mayden, R.L. (1997) A hierarchy of species concepts: the denouement in the saga of the species problem. In: Claridge, M.F., Dawah, H.A. & Wilson, M.R. (Eds.) Species: The Units of Biodiversity. Chapman & Hall, London, UK, pp. 381–424.
  107. McCollum, S.A. & Van Buskirk, J. (1996) Costs and benefits of a predator-induced polyphenism in the gray treefrog Hyla chrysoscelis. Evolution, 50, 583–593. https://doi.org/10.1111/j.1558-5646.1996.tb03870.x
  108. Meierotto, S., Sharkey, M.J., Janzen, D.H., Hallwachs, W., Hebert, P.D.N., Chapman, E.G. & Smith, M.A. (2019) A revolutionary protocol to describe understudied hyperdiverse taxa and overcome the taxonomic impediment. Deutsche Entomologische Zeitschrift, 66, 119–145. https://doi.org/10.3897/dez.66.34683
  109. Merckelbach, L.M. & Borges, L.M.S. (2020) Make every species count: fastachar software for rapid determination of molecular diagnostic characters to describe species. Molecular Ecology Resources, 20, 1761–1768. https://doi.org/10.1111/1755-0998.13222
  110. Mercurio, V. & Andreone, F. (2007) Two new canyon-dwelling frogs from the arid sandstone Isalo Massif, central-southern Madagascar (Mantellidae, Mantellinae). Zootaxa, 1574, 31–47. https://doi.org/10.11646/zootaxa.1574.1.2
  111. Mertens, R. (1967) Die herpetologische Sektion des Natur-Museums und Forschungs-Institutes Senckenberg in Frankfurt a. M. nebst einem Verseichnis ihrer Typen. Senckenbergiana Biologica, 48, 1–106.
  112. Millot, J. & Guibé, J. (1950) Les batraciens du nord de l’Andringitra (Madagascar). Memoires de l’Institut Scientifique de Madagascar, 4, 197–206.
  113. Miralles, A., Bruy, T., Crottini, A., Rakotoarison, A., Ratsoavina, F.M., Scherz, M.D., Schmidt, R., Köhler, J., Glaw, F. & Vences, M. (2021) Completing a taxonomic puzzle: integrative review of geckos of the Paroedura bastardi species complex (Squamata, Gekkonidae). Vertebrate Zoology, 71, 27–48. https://doi.org/10.3897/vz.71.e59495
  114. Miralles, A. & Vences, M. (2013) New metrics for comparison of taxonomies reveal striking discrepancies among species delimitation methods in Madascincus lizards. PLoS One, 8, e68242. https://doi.org/10.1371/journal.pone.0068242
  115. Mocquard, F. (1895a) Sur les reptiles recueillis Madascar de 1867 a 1885 par M. Grandidier. Bulletin de la Société Philomathique de Paris, Huitième Série, 7, 93–111.
  116. Mocquard, M.F. (1895b) Sur une collection de reptiles recueillis a Madagascar par MM. Alluaud et Belly. Bulletin de la Société Philomathique de Paris, Huitième Série, 7, 112–136.
  117. Moen, D.S., Morlon, H. & Wiens, J.J. (2016) Testing convergence versus history: convergence dominates phenotypic evolution for over 150 million years in frogs. Systematic Biology, 65, 146–160. https://doi.org/10.1093/sysbio/syv073
  118. Muñoz, J. (2007) Biodiversity conservation including uncharismatic species. Biodiversity and Conservation, 16, 2233–2235. https://doi.org/10.1007/s10531-006-9147-1
  119. Muschick, M., Barluenga, M., Salzburger, W. & Meyer, A. (2011) Adaptive phenotypic plasticity in the Midas cichlid fish pharyngeal jaw and its relevance in adaptive radiation. BMC Evolutionary Biology, 11, 116. https://doi.org/10.1186/1471-2148-11-116
  120. Myers, N., Mittermeier, R.A., Mittermeier, C.G., da Fonseca, G.A.B. & Kent, J. (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853–858. https://doi.org/10.1038/35002501
  121. Ndriantsoa, S.H., Riemann, J.C., Raminosoa, N.R., Rödel, M.-O. & Glos, J. (2017) Amphibian diversity in the matrix of a fragmented landscape around Ranomafana in Madagascar depends on matrix quality. Tropical Conservation Science, 10, 1–16. https://doi.org/10.1177/1940082916686065
  122. Nikolenko, S.I., Korobeynikov, A.I. & Alekseyev, M.A. (2013) BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics, 14, S7. https://doi.org/10.1186/1471-2164-14-S1-S7
  123. Nosil, P. (2012) Ecological Speciation. Oxford University Press, Oxford, UK, 274 pp. https://doi.org/10.1093/acprof:osobl/9780199587100.001.0001
  124. Padial, J.M., Castroviejo-Fisher, S., Köhler, J., Vilà, C., Chaparro, J.C. & de la Riva, I. (2009) Deciphering the products of evolution at the species level: the need for an integrative taxonomy. Zoologica Scripta, 38, 431–447. https://doi.org/10.1111/j.1463-6409.2008.00381.x
  125. Padial, J.M., Miralles, A., De La Riva, I. & Vences, M. (2010) The integrative future of taxonomy. Frontiers in Zoology, 7, 16. https://doi.org/10.1186/1742-9994-7-16
  126. Paijmans, J.L.A., Baleka, S., Henneberger, K., Taron, U.H., Trinks, A., Westbury, M.V. & Barlow, A. (2017) Sequencing single-stranded libraries on the Illumina NextSeq 500 platform. arXiv, arXiv:1711.11004.
  127. Paijmans, J.L.A., Fickel, J., Courtiol, A., Hofreiter, M. & Förster, D.W. (2016) Impact of enrichment conditions on cross-species capture of fresh and degraded DNA. Molecular Ecology Resources, 16, 42–55. https://doi.org/10.1111/1755-0998.12420
  128. Paradis, E. & Schliep, K. (2019) ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35, 526–528. https://doi.org/10.1093/bioinformatics/bty633
  129. Penny, S.G., Crottini, A., Andreone, F., Bellati, A., Rakotozafy, L.M.S., Holderied, M.W., Schwitzer, C. & Rosa, G.M. (2017) Combining old and new evidence to increase the known biodiversity value of the Sahamalaza Peninsula, Northwest Madagascar. Contributions to Zoology, 86, 273–296. https://doi.org/10.1163/18759866-08604002
  130. Peracca, M.G. (1893) Descrizione di nuove specie di rettili e anfibi di Madagascar. Nota II (1). Bollettino dei Musei di Zoologia ed Anatomia comparata della R. Università di Torino, 8, 1–16. https://doi.org/10.5962/bhl.part.27224
  131. Perl, R.G.B., Nagy, Z.T., Sonet, G., Glaw, F., Wollenberg, K.C. & Vences, M. (2014) DNA barcoding Madagascar‘s amphibian fauna. Amphibia-Reptilia, 35, 197–206. https://doi.org/10.1163/15685381-00002942
  132. Pfennig, D. (1990) The adaptive significance of an environmentally-cued developmental switch in an anuran tadpole. Oecologia, 85, 101–107. https://doi.org/10.1007/BF00317349
  133. Piersma, T. & Drent, J. (2003) Phenotypic flexibility and the evolution of organismal design. Trends in Ecology and Evolution, 18, 228–233. https://doi.org/10.1016/S0169-5347(03)00036-3
  134. Poth, D., Peram, P.S., Vences, M. & Schulz, S. (2013) Macrolides and alcohols as scent gland constituents of the Madagascan frog Mantidactylus femoralis and their intraspecific diversity. Journal of Natural Products, 76, 1548–1558. https://doi.org/10.1021/np400131q
  135. Poth, D., Wollenberg, K.C., Vences, M. & Schulz, S. (2012) Volatile amphibian pheromones: macrolides of mantellid frogs from Madagascar. Angewandte Chemie International Edition, 51, 1–5. https://doi.org/10.1002/anie.201106592
  136. Price, S.J., Garner, T.W.J., Nichols, R.A., Balloux, F., Ayres, C., Mora-Cabello de Alba, A. & Bosch, J. (2014) Collapse of Amphibian Communities Due to an Introduced Ranavirus. Current Biology, 24, 2586–2591. https://doi.org/10.1016/j.cub.2014.09.028
  137. Prötzel, D., Scherz, M.D., Ratsoavina, F.M., Vences, M. & Glaw, F. (2020) Untangling the trees: Revision of the Calumma nasutum complex (Squamata: Chamaeleonidae). Vertebrate Zoology, 70, 23–59. https://doi.org/10.1093/zoolinnean/zlx112
  138. Prötzel, D., Vences, M., Hawlitschek, O., Scherz, M.D., Ratsoavina, F.M. & Glaw, F. (2018) Endangered beauties: micro-CT cranial osteology, molecular genetics and external morphology reveal three new species of chameleons in the Calumma boettgeri complex (Squamata: Chamaeleonidae). Zoological Journal of the Linnean Society, 184, 471–498. https://doi.org/10.1093/zoolinnean/zlx112
  139. Prötzel, D., Vences, M., Scherz, M.D., Vieites, D.R. & Glaw, F. (2017) Splitting and lumping: An integrative taxonomic assessment of Malagasy chameleons in the Calumma guibei complex results in the new species C. gehringi sp. nov. Vertebrate Zoology, 67, 231–249.
  140. Puillandre, N., Brouillet, S. & Achaz, G. (2021) ASAP: assemble species by automatic partitioning. Molecular Ecology Resources, 21, 609–620. https://doi.org/10.1111/1755-0998.13281
  141. QGIS Development Team. (2022) QGIS Geographic Information System. Open Source Geospatial Foundation Project. http://qgis.osgeo.org.
  142. R Core Team. (2020) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/.
  143. Rabemananjara, F., Randriamahazo, H., Rahantamalala, J., Rahantalisoa, H., Rakotoarisoa, J.M., Rabibisoa, N.H.C. & Andreone, F. (2012) The conservation effort for two critically endangered amphibian species of the Ankaratra Massif, Boophis williamsi and Mantidactylus pauliani. FrogLog, 20, 29–31.
  144. Rakotoarison, A., Scherz, M.D., Bletz, M.C., Razafindraibe, J.H., Glaw, F. & Vences, M. (2019) Diversity, elevational variation, and phylogenetic origin of stump-toed frogs (Microhylidae: Cophylinae: Stumpffia) on the Marojejy massif, northern Madagascar. Salamandra, 55, 115–123.
  145. Rakotoarison, A., Scherz, M.D., Glaw, F., Köhler, J., Andreone, F., Franzen, M., Glos, J., Hawlitschek, O., Jono, T., Mori, A., Ndriantsoa, S.H., Raminosoa Rasoamampionona, N., Riemann, J.C., Rödel, M.-O., Rosa, G.M., Vieites, D.R., Crottini, A. & Vences, M. (2017) Describing the smaller majority: Integrative taxonomy reveals twenty-six new species of tiny microhylid frogs (genus Stumpffia) from Madagascar. Vertebrate Zoology, 67, 271–398.
  146. Rakotondravony, H.A. & Goodman, S.M. (2011) Rapid herpetofaunal surveys within five isolated forests on sedimentary rock in western Madagascar. Herpetological Conservation and Biology, 6, 297–311.
  147. Rancilhac, L., Bruy, T., Scherz, M.D., Pereira, E.A., Preick, M., Straube, N., Lyra, M., Ohler, A., Streicher, J.W., Andreone, F., Crottini, A., Hutter, C.R., Randrianantoandro, J.C., Rakotoarison, A., Glaw, F., Hofreiter, M. & Vences, M. (2020) Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus). Journal of Natural History, 54, 87–118. https://doi.org/10.1080/00222933.2020.1748243
  148. Randrianiaina, R.-D., Strauß, A., Glos, J., Glaw, F. & Vences, M. (2011) Diversity, external morphology and ‘reverse taxonomy’ in the specialized tadpoles of Malagasy river bank frogs of the subgenus Ochthomantis (genus Mantidactylus). Contributions to Zoology, 80, 17–65. https://doi.org/10.1163/18759866-08001002
  149. Raselimanana, A.P. (2008) Herpétofaune des forêts sèches malgaches. Malagasy Nature, 1, 46–75.
  150. Raselimanana, A.P., Vences, M. & Glaw, F. (2018) Liste des amphibiens connus dans 98 aires protégées terrestres de Madagascar / List of the known amphibians in 98 protected areas of Madagascar. In: Goodman, S.M., Raherilalao, M.J. & Wohlhauser, S. (Eds.) Les aires protégées terrestres de Madagascar : Leur histoire, description et biote / The terrestrial protected areas of Madagascar: Their history, description, and biota. Association Vahatra, Antananarivo, Madagascar,
  151. Rasolonjatovo, S.M., Scherz, M.D., Rakotoarison, A., Glos, J., Raselimanana, A.P. & Vences, M. (2020) Field body temperatures in the rainforest frog Mantidactylus (Brygoomantis) bellyi from northern Madagascar: Variance and predictors. Malagasy Nature, 14, 57–68.
  152. Rasolonjatovo, S.M., Scherz, M.D., Raselimanana, A.P. & Vences, M. (2018) Tadpole predation by Mantidactylus bellyi Mocquard, 1895 with brief description of the site and morphological measurements of the specimen. Herpetology Notes, 11, 747–750.
  153. Rasolonjatovo, S.M., Scherz, M.D., Schmidt, R., Glos, J., Rakotoarison, A., Raselimanana, A.P. & Vences, M. (2022) Population diversification in the frog Mantidactylus bellyi on an isolated massif in northern Madagascar: genetic, morphological, bioacoustic and ecological evidence. PLoS One, 17, e0263764. https://doi.org/10.1371/journal.pone.0263764
  154. Ratsoavina, F.M., Gehring, P.-S., Scherz, M.D., Vieites, D.R., Glaw, F. & Vences, M. (2017) Two new species of leaf-tailed geckos (Uroplatus) from the Tsaratanana mountain massif in northern Madagascar. Zootaxa, 4347, 446–464. https://doi.org/10.11646/zootaxa.4347.3.2
  155. Ratsoavina, F.M., Glaw, F., Raselimanana, A.P., Rakotoarison, A., Vieites, D.R., Hawlitschek, O., Vences, M. & Scherz, M.D. (2020) Towards completion of the species inventory of small-sized leaf-tailed geckos: two new species of Uroplatus from northern Madagascar. Zootaxa, 4895, 251–271. https://doi.org/10.11646/zootaxa.4895.2.5
  156. Relyea, R.A. (2001) The lasting effects of adaptive plasticity: predator-induced tadpoles become long-legged frogs. Ecology, 82, 1947–1955. https://doi.org/10.1890/0012-9658(2001)082[1947:TLEOAP]2.0.CO;2
  157. Renner, S.S. (2016) A return to Linnaeus‘s focus on diagnosis, not description: the use of DNA characters in the formal naming of species. Systematic Biology, 65, 1085–1095. https://doi.org/10.1093/sysbio/syw032
  158. Riedel, A. & Narakusumo, R.P. (2019) One hundred and three new species of Trigonopterus weevils from Sulawesi. Zookeys, 828, 1–153. https://doi.org/10.3897/zookeys.828.32200
  159. Riedel, A., Sagata, K., Suhardjono, Y.R., Tänzler, R. & Balke, M. (2013) Integrative taxonomy on the fast track - towards more sustainability in biodiversity research. Frontiers in Zoology, 10, 15. https://doi.org/10.1186/1742-9994-10-15
  160. Riedel, A., Tänzler, R., Balke, M., Rahmadi, C. & Suhardjono, Y.R. (2014) Ninety-eight new species of Trigonopterus weevils from Sundaland and the Lesser Sunda Islands. Zookeys, 467, 1–162. https://doi.org/10.3897/zookeys.828.32200
  161. Riemann, J.C., Ndriantsoa, S.H., Raminosoa, N.R., Rödel, M.-O. & Glos, J. (2015) The value of forest fragments for maintaining amphibian diversity in Madagascar. Biological Conservation, 191, 707–715. https://doi.org/10.1016/j.biocon.2015.08.020
  162. Rohland, N., Siedel, H. & Hofreiter, M. (2004) Nondestructive DNA extraction method for mitochondrial DNA analyses of museum specimens. BioTechniques, 36, 814–821. https://doi.org/10.2144/04365ST05
  163. Rosa, G.M., Andreone, F., Crottini, A., Hauswaldt, J.S., Noël, J., Rabibisoa, N.H., Randriambahiniarime, M.O., Rebelo, R. & Raxworthy, C.J. (2012) The amphibians of the relict Betampona low-elevation rainforest, eastern Madagascar: an application of the integrative taxonomy approach to biodiversity assessments. Biodiversity and Conservation, 21, 1531–1559. https://doi.org/10.1007/s10531-012-0262-x
  164. Rosa, G.M., Marquez, R. & Andreone, F. (2011) The astonishing calls of the frogs of Betampona. Museo Regionale di Scienze Naturali and Fonoteca Zoológica, Torino, Italy.
  165. RStudio Team. (2019) RStudio: Integrated Development for R. RStudio, Inc., Boston, MA. http://www.rstudio.com/.
  166. Salzburger, W., Ewing, G.B. & Von Haeseler, A. (2011) The performance of phylogenetic algorithms in estimating haplotype genealogies with migration. Molecular Ecology, 20, 1952–1963. https://doi.org/10.1111/j.1365-294X.2011.05066.x
  167. Sanchez, E., Pröhl, H., Lüddecke, T., Schulz, S., Steinfartz, S. & Vences, M. (2019) The conspicuous postmetamorphic coloration of fire salamanders, but not their toxicity, is affected by larval background albedo. Journal of Experimental Zoology, 332, 26–35. https://doi.org/10.1002/jez.b.22845
  168. Santiago, J.R., de la Cruz-López, L.E., Kuzmina, M. & Vergara-Silva, F. (2020) Morphological and molecular diagnostic characters reveal a new species of Pachyphytum (Crassulaceae). Haseltonia, 2019, 14–22. https://doi.org/10.2985/026.026.0103
  169. Sarkar, I.N., Planet, P.J. & DeSalle, R. (2008) CAOS software for use in character-based DNA barcoding. Molecular Ecology Resources, 8, 1256–1259. https://doi.org/10.1111/j.1755-0998.2008.02235.x
  170. Scheld, S., Perl, R.G.B., Rauhaus, A., Karbe, D., van der Straeten, K., Hauswaldt, J.S., Randrianiaina, R.D., Gawor, A., Vences, M. & Ziegler, T. (2013) Larval morphology and development of the Malagasy frog Mantidactylus betsileanus. Salamandra, 49, 186–200.
  171. Scherz, M.D., Glaw, F., Hutter, C.R., Bletz, M.C., Rakotoarison, A., Köhler, J. & Vences, M. (2019) Species complexes and the importance of Data Deficient classification in Red List assessments: the case of Hylobatrachus frogs. PLoS One, 14, e0219437. https://doi.org/10.1371/journal.pone.0219437
  172. Scherz, M.D., Rakotoarison, A., Ratsoavina, F.M., Hawlitschek, O., Vences, M. & Glaw, F. (2018) Two new Madagascan frog species of the Gephyromantis (Duboimantis) tandroka complex from northern Madagascar. Alytes, 36, 130–158.
  173. Scherz, M.D., Rasolonjatovo, S.M., Köhler, J., Rancilhac, L., Rakotoarison, A., Raselimanana, A.P., Ohler, A., Preick, M., Hofreiter, M., Glaw, F. & Vences, M. (2020) ‘Barcode fishing’ for archival DNA from historical type material overcomes taxonomic hurdles, enabling the description of a new frog species. Scientific Reports, 10, 19109. https://doi.org/10.1038/s41598-020-75431-9
  174. Scherz, M.D., Schmidt, L., Crottini, A., Miralles, A., Rakotoarison, A., Raselimanana, A.P., Köhler, J., Glaw, F. & Vences, M. (2021) Into the Chamber of Horrors: A proposal for the resolution of nomenclatural chaos in the Scaphiophryne calcarata complex (Anura: Microhylidae), with a new species-level phylogenetic hypothesis for Scaphiophryninae. Zootaxa, 4938, 392–420. https://doi.org/10.11646/zootaxa.4938.4.2
  175. Scherz, M.D., Vences, M., Borrell, J., Ball, L., Nomenjanahary, D.H., Parker, D., Rakotondratsima, M., Razafimandimby, E., Starnes, T., Rabearivony, J. & Glaw, F. (2017a) A new frog species of the subgenus Asperomantis (Anura: Mantellidae: Gephyromantis) from the Bealanana District of northern Madagascar. Zoosystematics and Evolution, 93, 451–466. https://doi.org/10.3897/zse.93.14906
  176. Scherz, M.D., Vences, M., Rakotoarison, A., Andreone, F., Köhler, J., Glaw, F. & Crottini, A. (2017b) Lumping or splitting in the Cophylinae (Anura: Microhylidae) and the need for a parsimony of taxonomic changes: a response to Peloso et al. (2017). Salamandra, 53, 479–483.
  177. Schmidt, H., Strauß, A., Glaw, F., Teschke, M. & Vences, M. (2009) Description of tadpoles of five frog species in the subgenus Brygoomantis from Madagascar (Mantellidae: Mantidactylus). Zootaxa, 1988, 48–60. https://doi.org/10.11646/zootaxa.1988.1.4
  178. Schneider, R.F. & Meyer, A. (2017) How plasticity, genetic assimilation and cryptic genetic variation may contribute to adaptive radiations. Molecular Ecology, 26, 330–350. https://doi.org/10.1111/mec.13880
  179. Sharkey, M.J., Janzen, D.H., Hallwachs, W., Chapman, E.G., Smith, M.A., Dapkey, T., Brown, A., Ratnasingham, S., Naik, S., Manjunath, R., Perez, K., Milton, M., Hebert, P., Shaw, S.R., Kittel, R.N., Solis, M.A., Metz, M.A., Goldstein, P.Z., Brown, J.W., Quicke, D.L.J., van Achterberg, C., Brown, B.V. & Burns, J.M. (2021) Minimalist revision and description of 403 new species in 11 subfamilies of Costa Rican braconid parasitoid wasps, including host records for 219 species. ZooKeys, 1013, 1–665. https://doi.org/10.3897/zookeys.1013.55600
  180. Soamiarimampionona, J., Sam, D.S., Dolch, R., Klymus, K., Rabemananjara, F., Robsomanitrandrasana, E., Rakotoarisoa, J.C. & Edmonds, D. (2015) Effects of three diets on development of Mantidactylus betsileanus larvae in captivity. Alytes, 32, 7–15.
  181. Sofanova, Y., Bankevich, A. & Pevzner, P.A. (2015) dipSPAdes: assembler for highly polymorphic diploid genomes. Journal of Computational Biology, 22, 528–545. https://doi.org/10.1089/cmb.2014.0153
  182. Solís-Lemus, C. & Ané, C. (2016) Inferring phylogenetic networks with Maximum Pseudolikelihood under incomplete lineage sorting. PLoS Genetics, 12, e1005896. https://doi.org/10.1371/journal.pgen.1005896
  183. Solís-Lemus, C., Bastide, P. & Ané, C. (2017) PhyloNetworks: a package for phylogenetic networks. Molecular Biology and Evolution, 34, 3292–3298. https://doi.org/10.1093/molbev/msx235
  184. Solís-Lemus, C., Knowles, L.L. & Ané, C. (2015) Bayesian species delimitation combining multiple genes and traits in a unified framework. Evolution, 69, 492–507. https://doi.org/10.1111/evo.12582
  185. Stamatakis, A. (2014) RAxML Version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312–1313. https://doi.org/10.1093/bioinformatics/btu033
  186. Stamper, C.E., Stevens, D.J., Downie, J.R. & Monaghan, P. (2008) The effects of competition on pre- and post-metamorphic phenotypes in the common frog. The Herpetological Journal, 18, 187–195.
  187. Stephens, M., Smith, N.J. & Donnelly, P. (2001) A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978–989. https://doi.org/10.1086/319501
  188. Streicher, J.W., Miller, E.C., Guerrero, P.C., Correa, C., Ortiz, J.C., Crawford, A.J., Pie, M.R. & Wiens, J.J. (2018) Evaluating methods for phylogenomic analyses, and a new phylogeny for a major frog clade (Hyloidea) based on 2214 loci. Molecular Phylogenetics and Evolution, 119, 128–143. https://doi.org/10.1016/j.ympev.2017.10.013
  189. Stuart, S.N., Chanson, J.S., Cox, N.A., Young, B.E., Rodrigues, A.S.L., Fischman, D.L. & Waller, R.W. (2004) Status and trends of amphibian declines and extinction worldwide. Science, 306, 1783–1786. https://doi.org/10.1126/science.1103538
  190. Sun, Y.-B., Xiong, Z.-J., Xiang, X.-Y., Liu, S.-P., Zhou, W.-W., Tu, X.-L., Zhong, L., Wang, L., Wu, D.-D., Zhang, B.-L., Zhu, C.-L., Yang, M.-M., Chen, H.-M., Li, F., Zhou, L., Feng, S.-H., Huang, C., Zhang, G.-J., Irwin, D., Hillis, D.M., Murphy, R.W., Yang, H.-M., Che, J., Wang, J. & Zhang, Y.-P. (2015) Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes. Proceedings of the National Academy of Sciences of the USA, 112, E1257. https://doi.org/10.1073/pnas.1501764112
  191. Tessa, G., Crottini, A., Giacoma, C., Guarino, F.M., Randrianirina, J.E. & Andreone, F. (2017) Comparative longevity and age at sexual maturity in twelve rainforest frogs of the genera Boophis, Gephyromantis, and Mantidactylus (Anura: Mantellidae) from Madagascar. Phyllomedusa, 16, 13–21. https://doi.org/10.11606/issn.2316-9079.v16i1p13-21
  192. Thomas, M., Raharivololoniaina, L., Glaw, F., Vences, M. & Vieites, D.R. (2005) Montane tadpoles in Madagascar: molecular identification and description of the larval stages of Mantidactylus elegans, Mantidactylus madecassus, and Boophis laurenti from the Andringitra Massif. Copeia, 2005, 174–183. https://doi.org/10.1643/CH-03-293R2
  193. Vacher, J.-P., Chave, J., Ficetola, F.G., Sommeria-Klein, G., Tao, S., Thébaud, C., Blanc, M., Camacho, A., Cassimiro, J., Colston, T.J., Dewynter, M., Ernst, R., Gaucher, P., Gomes, J.O., Jairam, R., Kok, P.J.R., Lima, J.D., Martinez, Q., Marty, C., Noonan, B.P., Nunes, P.M.S., Ouboter, P., Recoder, R., Rodrigues, M.T., Snyder, A., Marques-Souza, S. & Fouquet, A. (2020) Large-scale DNA-based survey of frogs in Amazonia suggests a vast underestimation of species richness and endemism. Journal of Biogeography, 47, 1781–1791. https://doi.org/10.1111/jbi.13847
  194. Vences, M., Andreone, F., Glaw, F., Raminosoa, N., Randrianirina, J.E. & Vieites, D.R. (2002) Amphibians and reptiles of the Ankaratra Massif: reproductive diversity, biogeography and conservation of a montane fauna in Madagascar. Italian Journal of Zoology, 69, 263–284. https://doi.org/10.1080/11250000209356469
  195. Vences, M. & Glaw, F. (1999) Variation in Mantidactylus madecassus Millot & Guibé, 1950, a little known Malagasy frog, with resurrection of Mantidactylus pauliani Guibé, 1974. Herpetological Journal, 9, 101–110.
  196. Vences, M., Glaw, F. & Marquez, R. (2006) The Calls of the Frogs of Madagascar. 3 Audio CD’s and booklet. Madrid, Spain, Fonoteca Zoológica, 44 pp.
  197. Vences, M., Guayasamin, J.M., Miralles, A. & de la Riva, I. (2013) To name or not to name: Criteria to promote economy of change in Linnaean classification schemes. Zootaxa, 3636, 201–244. https://doi.org/10.11646/zootaxa.3636.2.1
  198. Vences, M., Hildenbrand, A., Warmuth, K.M., Andreone, F. & Glaw, F. (2018) A new riparian Mantidactylus (Brygoomantis) frog from the Tsaratanana and Manongarivo Massifs in northern Madagascar. Zootaxa, 4486, 575–588. https://doi.org/10.11646/zootaxa.4486.4.10
  199. Vences, M., Köhler, J., Pabijan, M., Bletz, M., Gehring, P.-S., Hawlitschek, O., Rakotoarison, A., Ratsoavina, F.M., Andreone, F., Crottini, A. & Glaw, F. (2017) Taxonomy and geographic distribution of Malagasy frogs of the Gephyromantis asper clade, with description of a new subgenus and revalidation of Gephyromantis ceratophrys. Salamandra, 53, 77–98.
  200. Vences, M., Kosuch, J., Glaw, F., Böhme, W. & Veith, M. (2003) Molecular phylogeny of hyperoliid treefrogs: biogeographic origin of Malagasy and Seychellean taxa and re-analysis of familial paraphyly. Journal of Zoological Systematics and Evolutionary Research, 41, 205–215. https://doi.org/10.1046/j.1439-0469.2003.00205.x
  201. Vences, M., Miralles, A., Brouillet, S., Ducasse, J., Fedosov, A., Kharchev, V., Kostadinov, I., Kumari, S., Patmanidis, S., Scherz, M.D., Puillandre, N. & Renner, S.S. (2021) iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists. Megataxa, 6, 77–92. https://doi.org/10.11646/megataxa.6.2.1
  202. Vences, M., Thomas, M., Bonett, R.M. & Vieites, D.R. (2005) Deciphering amphibian diversity through DNA barcoding: chances and challenges. Philosophical Transactions of the Royal Society B, 360, 1859–1868. https://doi.org/10.1098/rstb.2005.1717
  203. Vences, M., Wahl-Boos, G., Hoegg, S., Glaw, F., Oliveira, E.S., Meyer, A. & Perry, S. (2007) Molecular systematics of mantelline frogs from Madagascar and the evolution of their femoral glands. Biological Journal of the Linnean Society, 92, 529–539. https://doi.org/10.1111/j.1095-8312.2007.00859.x
  204. Vences, M., Wollenberg, K.C., Vieites, D.R. & Lees, D.C. (2009) Madagascar as a model region of species diversification. Trends in Ecology and Evolution, 24, 456–465. https://doi.org/10.1016/j.tree.2009.03.011
  205. Vieites, D.R., Wollenberg, K.C., Andreone, F., Köhler, J., Glaw, F. & Vences, M. (2009) Vast underestimation of Madagascar‘s biodiversity evidenced by an integrative amphibian inventory. Proceedings of the National Academy of Sciences of the USA, 106, 8267–8272. https://doi.org/10.1073/pnas.0810821106
  206. Vijayakumar, S.P., Dinesh, K.P., Prabhu, M.V. & Shanker, K. (2014) Lineage delimitation and description of nine new species of bush frogs (Anura: Raorchestes, Rhacophoridae) from the Western Ghats Escarpment. Zootaxa, 2893, 451–488. https://doi.org/10.11646/zootaxa.3893.4.1
  207. Watters, J.L., Cummings, S.T., Flanagan, R.L. & Siler, C.D. (2016) Review of morphometric measurements used in anuran species descriptions and recommendations for a standardized approach. Zootaxa, 4072, 477–495. https://doi.org/10.11646/zootaxa.4072.4.6
  208. Weisrock, D.W., Rasoloarison, R.M., Fiorentino, I., Ralison, J.M., Goodman, S.M., Kappeler, P.M. & Yoder, A.D. (2010) Delimiting species without nuclear monophyly in Madagascar‘s mouse lemurs. PLoS One, 5, e9883. https://doi.org/10.1371/journal.pone.0009883
  209. Wollenberg, K.C., Vieites, D.R., Glaw, F. & Vences, M. (2011) Speciation in little: the role of range and body size in the diversification of Malagasy mantellid frogs. BMC Evolutionary Biology, 11, 217. https://doi.org/10.1186/1471-2148-11-217
  210. Wollenberg Valero, K.C., Garcia-Porta, J., Rodríguez, A., Arias, M., Shah, A., Randrianiaina, R.D., Brown, J.L., Glaw, F., Amat, F., Künzel, S., Metzler, D., Isokpehi, R.D. & Vences, M. (2017) Transcriptomic and macroevolutionary evidence for phenotypic uncoupling between frog life history phases. Nature Communications, 8, 15213. https://doi.org/10.1038/ncomms15213
  211. World Bank. (2022) GDP per capita (current US$) - Madagascar. https://data.worldbank.org/indicator/NY.GDP.PCAP.CD?locations=MG, accessed: 2022-03-03.
  212. Zamani, A., Vahtera, V., Sääksjärvi, I.E. & Scherz, M.D. (2021) The omission of critical data in the pursuit of ‘revolutionary’ methods to accelerate the description of species. Systematic Entomology, 46, 1–4. https://doi.org/10.1111/syen.12444
  213. Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. (2018) ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics, 19, 153. https://doi.org/10.1186/s12859-018-2129-y
  214. Zuckerkandl, E. & Pauling, L.B. (1965) Evolutionary divergence and convergence in proteins. In: Bryson, V. & Vogel, H.J. (Eds.) Evolving Genes and Proteins. Academic Press, New York, NY USA, pp. 97–166. https://doi.org/10.1016/B978-1-4832-2734-4.50017-6