Abstract
Cryptic species have been detected in many groups of organisms and must be assumed to make up a significant portion of global biodiversity. We study geckos of the Ebenavia inunguis complex from Madagascar and surrounding islands and use species delimitation algorithms (GMYC, BOLD, BPP), COI barcode divergence, diagnostic codon indels in the nuclear marker PRLR, diagnostic categorical morphological characters, and significant differences in continuous morphological characters for its taxonomic revision. BPP yielded ≥ 10 operational taxonomic units, whereas GMYC (≥ 27) and BOLD (26) suggested substantial oversplitting. In consequnce, we resurrect Ebenavia boettgeri Boulenger 1885 and describe Ebenavia tuelinae sp. nov., Ebenavia safari sp. nov., and Ebenavia robusta sp. nov., increasing the number of recognised species in Ebenavia from two to six. Further lineages of Ebenavia retrieved by BPP may warrant species or subspecies status, but further taxonomic conclusions are postponed until more data become available. Finally, we present an identification key to the genus Ebenavia, provide an updated distribution map, and discuss the diagnostic values of computational species delimitation as well as morphological and molecular diagnostic characters.
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References
Adams M, Raadik TA, Burridge CP, Georges A (2014) Global biodiversity assessment and hyper-cryptic species complexes: more than one species of elephant in the room? Syst Biol 63:518–533
Andreone F, Glaw F, Nussbaum RA, Raxworthy CJ, Vences M, Randrianirina JE (2003) The amphibians and reptiles of Nosy Be (NW Madagascar) and nearby islands: a case study of diversity and conservation of an insular fauna. J Nat Hist 37:2119–2149
Angel F (1942) Les lézards de Madagascar. Mém Acad Malgache 36:1–139
Babb PL, McIntosh AM, Fernandez-Duque E, Schurr TG (2014) Prolactin receptor gene diversity in Azara’s owl monkeys (Aotus azarai) and humans (Homo sapiens) suggests a non-neutral evolutionary history among primates. Int J Primatol 35:129–155. https://doi.org/10.1007/s10764-013-9721-9
Bellati A, Scherz MD, Megson S, Hyde Roberts S, Andreone F, Rosa GM, Noël J, Randrianirina JE, Fasola M, Glaw F, Crottini A (2018) Resurrection and re-description of Plethodontohyla laevis (Boettger, 1913) and transfer of Rhombophryne alluaudi (Mocquard, 1901) to the genus Plethodontohyla (Amphibia, Microhylidae, Cophylinae). Zoosystematics Evol 94:109–135
Bickford D, Lohman DJ, Sodhi NS, Ng PKL, Meier R, Winker K, Ingram KK, Das I (2007) Cryptic species as a window on diversity and conservation. Trends Ecol Evol 22:148–155
Blanc CP (1971) Les reptiles de Madagascar et des îles voisines. Ann Univ Mada 8:95–178
Blanc CP (1972) Les reptiles de Madagascar et des îles voisines. In: Battistini R, Richard-Vindard G (eds) Biogeography and ecology in Madagascar. Springer, pp 501–614
Blumgart D, Dolheim J, Raxworthy CJ (2017) Herpetological diversity across intact and modified habitats of Nosy Komba Island. Madagascar. J Nat Hist 51:1–18
Boettger O (1878) Die Reptilien und Amphibien von Madagascar. Erster Nachtrag. Abh Senckenb naturforsch Ges 11:1–56
Boettger O (1893) Katalog der Reptilien-Sammlung im Museum der Senckenbergischen Naturforschenden Gesellschaft in Frankfurt am Main. I. Teil (Rhynchocephalen, Schildkröten, Krokodile, Eidechsen, Chamäleons). Gebrüder Knauer, Frankfurt a. M.
Boulenger GA (1885) Catalogue of the lizards in the British Museum (Nat. Hist.) I. Geckonidae, Eublepharidae, Uroplatidae, Pygopodidae, Agamidae. British Museum of Natural History, London
Boulenger GA (1887) Catalogue of the lizards in the British Museum (Nat. Hist.) III. Lacertidae, Gerrhosauridae, Soinidae, Anclytropidae, Dibamidae, Chamaeleontidae. Taylor & Francis, London
Boumans L, Vieites DR, Glaw F, Vences M (2007) Geographical patterns of deep mitochondrial differentiation in widespread Malagasy reptiles. Mol Phylogenet Evol 45:822–839
Carstens BC, Pelletier TA, Reid NM, Satler JD (2013) How to fail at species delimitation. Mol Ecol 22:4369–4383
de Queiroz K (1998) The general lineage concept of species, species criteria, and the process of speciation. In: Howard DJ, Berlocher SH (eds) Endless forms. Species and speciation. Oxford University Press, Oxford, pp 49–89
Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969–1973
Edwards DL, Keogh JS, Knowles LL (2012) Effects of vicariant barriers, habitat stability, population isolation and environmental features on species divergence in the south-western Australian coastal reptile community. Mol Ecol 21:3809–3822
Garcia-Porta J, Simó-Riudalbas M, Robinson M, Carranza S (2017) Diversification in arid mountains: biogeography and cryptic diversity of Pristurus rupestris rupestris in Arabia. J Biogeogr 44:1694–1704. https://doi.org/10.1111/jbi.12929
Gehring P-S, Tolley KA, Eckhardt FS, Townsend TM, Ziegler T, Ratsoavina F, Glaw F, Vences M (2012) Hiding deep in the trees: discovery of divergent mitochondrial lineages in Malagasy chameleons of the Calumma nasutum group. Ecol Evol 2:1468–1479
Giam X, Scheffers BR, Sodhi NS, Wilcove DS, Ceballos G, Ehrlich PR (2012) Reservoirs of richness: least disturbed tropical forests are centres of undescribed species diversity. Proc R Soc B Biol Sci 279:67–76
Glaw F, Vences M (2007) A fieldguide to the amphibians and reptiles of Madagascar, 3rd edn. Vences & Glaw Verlag, Cologne
Glaw K (2016) Pinselschwanzgecko Ebenavia inunguis: Ein interessanter Zwerggecko aus deutscher Nachzucht. Zool Zent Anz 2:30–32
Gvoždík V, Jandzik D, Lymberakis P, Jablonski D, Moravec J (2010) Slow worm, Anguis fragilis (Reptilia: Anguidae) as a species complex: genetic structure reveals deep divergences. Mol Phylogenet Evol 55:460–472
Gvoždík V, Benkovský N, Crottini A, Bellati A, Moravec J, Romano A, Sacchi R, Jandzik D (2013) An ancient lineage of slow worms, genus Anguis (Squamata: Anguidae), survived in the Italian Peninsula. Mol Phylogenet Evol 69:1077–1092
Hawlitschek O, Brückmann B, Berger J, Green K, Glaw F (2011) Integrating field surveys and remote sensing data to study distribution, habitat use and conservation status of the herpetofauna of the Comoro Islands. Zookeys 144:21–79
Hawlitschek O, Nagy ZT, Glaw F (2012) Island evolution and systematic revision of Comoran snakes: why and when subspecies still make sense. PLoS One 7:e42970
Hawlitschek O, Nagy ZT, Berger J, Glaw F (2013) Reliable DNA barcoding performance proved for species and island populations of Comoran squamate reptiles. PLoS One 8:e73368
Hawlitschek O, Glaw F (2014) Determinant species of reptiles and amphibians for the delimitation of ZNIEFF zones in Mayotte. Direction de l'Environnement de l'Aménagement et du Logement (DEAL), Mayotte, France
Hawlitschek O, Ramírez-Garrído S, Glaw F (2017a) How marine currents influenced the widespread natural overseas dispersal of reptiles in the Western Indian Ocean region. J Biogeogr 44:1435–1440
Hawlitschek O, Toussaint EFAT, Gehring PS, Ratsoavina FM, Cole N, Crottini A, Nopper J, Lam AW, Vences M, Glaw F (2017b) Gecko phylogeography in the Western Indian Ocean region: the oldest clade of Ebenavia inunguis lives on the youngest island. J Biogeogr 44:409–420
Hazkani-Covo E, Zeller RM, Martin W (2010) Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet 6:e1000834
Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc B Biol Sci 270:313–321
Hebert PDN, Penton EH, Burns JM, Hanzen DH, Hallwachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci U S A 101:14812–14817
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
International Commission on Zoological Nomenclature (1999) International code of zoological nomenclature, 4th edn. International Trust for Zoological Nomenclature, London
Jackman TR, Bauer AM, Greenbaum E, Glaw F, Vences M (2008) Molecular phylogenetic relationships among species of the Malagasy-Comoran gecko genus Paroedura (Squamata: Gekkonidae). Mol Phylogenet Evol 46:74–81
Kato K, Ikemoto T, Park MK (2005) Identification of the reptilian prolactin and its receptor cDNAs in the leopard gecko, Eublepharis macularius. Gene 346:267–276
Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
Lemme I, Erbacher M, Kaffenberger N, Vences M, Köhler J (2013) Molecules and morphology suggest cryptic species diversity and an overall complex taxonomy of fish scale geckos, genus Geckolepis. Org Divers Evol 13:87–95
Marotta R, Crottini A, Raimondi E, Fondello C, Ferraguti M (2014) Alike but different: the evolution of the Tubifex tubifex species complex (Annelida, Clitellata) through polyploidization. BMC Evol Biol 14:73
Meirte D (1999) Reptiles. In: Louette M (Ed) La faune terrestre de Mayotte. Annales du Musée royal de l'Afrique Centrale, Sciences zoologique 284:114–135
Meirte D (2004) Reptiles. In: Louette M, Meirte D, Jocqué R (Eds) La faune terrestre de l'archipel des Comores. Studies in Afrotropical Zoology 293:199–220
Mertens R (1967) Die herpetologische Sektion des Naturmuseums und Forschungsinstitutes Senckenberg in Frankfurt a. M. nebst einem Verzeichnis ihrer Typen. Senckenb Biol 48:1–106
Metcalf CJE, Hampson K, Gray A, Andrianirina R (2007) Herpetofaunal assemblages on seven offshore islands of northwestern Madagascar. Trop Zool 20:151–161
Miralles A, Köhler J, Glaw F, Vences M (2016) Species delimitation methods put into taxonomic practice: two new Madascincus species formerly allocated to historical species names (Squamata, Scincidae). Zoosystematics Evol 92:257–275
Miralles A, Vasconcelos R, Perera A, Harris DJ, Carranza S (2011) An integrative taxonomic revision of the Cape Verdean skinks (Squamata, Scincidae). Zool Scr 40:16–44
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
Mocquard F (1909) Synopsis des familles, genres et espèces des reptiles éscailleux et des batraciens de Madagascar. Nouv Arch MusHist Nat 5:1–110
Nagy ZT, Sonet G, Glaw F, Vences M (2012) First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers. PLoS One 7:e34506
Nussbaum RA, Raxworthy CJ (1993) A new Madagascan Phelsuma, with a review of Phelsuma trilineata and comments on Phelsuma cepediana in Madagascar (Squamata: Gekkonidae). Herpetologica 49:342–349
Nussbaum RA, Raxworthy CJ (1998) Revision of the genus Ebenavia Boettger (Reptilia: Squamata: Gekkonidae). Herpetologica 54:18–34
Padial JM, Miralles A, De la Riva I, Vences M (2010) The integrative future of taxonomy. Front Zool 7:16
Pakenham RHW (1983) The reptiles and amphibians of Zanzibar and Pemba Islands (with a note on the freshwater fishes). J East Africa Nat Soc Natl Mus 177:1–43
Penny SG, Andreone F, Crottini A, Holderied MW, Rakotozafy LS, Schwitzer C, Rosa GM (2014) A new species of the Boophis rappiodes group (Anura, Mantellidae) from the Sahamalaza Peninsula, Northwest Madagascar, with acoustic monitoring of its nocturnal calling activity. Zookeys:111–132
Penny SG, Andreone F, Crottini A, Holderied MW, Rosa GM, Schwitzer C (2016) The amphibians of the Sahamalaza Peninsula, Northwest Madagascar—actions for their conservation. Bristol Zoological Society, Bristol
Penny SG, Crottini A, Andreone F, Bellati A, Rakotozafy LS, Holderied MW, Schwitzer C, Rosa GM (2018) Combining old and new evidence to increase the known biodiversity value of the Sahamalaza Peninsula, Northwest Madagascar. Contrib Zool 86:273–296
Pfenninger M, Schwenk K (2007) Cryptic animal species are homogeneously distributed among taxa and biogeographical regions. BMC Evol Biol 7:121. https://doi.org/10.1186/1471-2148-7-121
Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, Hazell S, Kamoun S, Sumlin WD, Vogler AP (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst Biol 55:595–609
Rabearivony J, Rasamoelina M, Raveloson J, Rakotomanana HV, Raselimanana AP, Raminosoa NR, Zaonarivelo JR (2015) Roles of a forest corridor between Marojejy, Anjanaharibe-Sud and Tsaratanana protected areas, northern Madagascar, in maintaining endemic and threatened Malagasy taxa. Madagascar Conserv Dev 10:85–92
R Core Team (2014) R: a language and environment for statistical computing. R Development Core Team, Vienna
Rakotomalala D, Raselimanana AP (2003) Les amphibiens et les reptiles des massifs de Marojejy, d'Anjanaharibe-Sud et du couloir forestier de Betaolana. In: Goodman SM, Wilmé L (eds) Nouveaux résultats d'inventaires biologiques faisant référence à l'altitude dans la région des massifs montagneux de Marojejy et d'Anjanaharibe-Sud. Rech Dévelop, Sér Sci Biol 19:147–202
Rakotondravony HA (2006) Patterns de la diversité des reptiles et amphibiens de la région de Loky-Manambato. In: Goodman SM, Wilmé L (Eds) Inventaires de la faune et de la flore du nord de Madagascar dans la région Loky-Manambato, Analamerana et Andavakoera. Rech Dévelop Sér Sci Biol 23:101–148
Ratnasingham S, Hebert PDN (2007) BOLD: the Barcode Of Life Data system (www.barcodinglife.org). Mol Ecol Notes 7:355–364
Ratnasingham S, Hebert PDN (2013) A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS One 8:e66213
Ratsoavina FM, Raminosoa EEL, Raselimanana AP, Glaw F, Vences M (2013) An overview of Madagascar's leaf tailed geckos (genus Uroplatus): species boundaries, candidate species and review of geographical distribution based on molecular data. Salamandra 49:115–148
Raxworthy CJ, Andreone F, Nussbaum RA, Rabibisoa N, Randriamahazo H (1998) Amphibians and reptiles of the Anjanaharibe-Sud Massif, Madagascar: elevational distribution and regional endemicity. Fieldiana Zool 90:79–92
Raxworthy CJ, Pearson RG, Zimkus BM, Reddy S, Deo AJ, Nussbaum RA, Ingram CM (2008) Continental speciation in the tropics: contrasting biogeographic patterns of divergence in the Uroplatus leaf-tailed gecko radiation of Madagascar. J Zool 275:423–440
Renner SS (2016) A return to Linnaeus’s focus on diagnosis, not description: the use of DNA characters in the formal naming of species. Syst Biol 65:1085–1095
Rodda GH, Campbell EW (2002) Distance sampling of forest snakes and lizards. Herpetol Rev 33:271–274
Scherz MD, Daza JD, Köhler J, Vences M, Glaw F (2017) Off the scale: a new species of fish-scale gecko (Squamata: Gekkonidae: Geckolepis) with exceptionally large scales. PeerJ 5:e2955
Schwitzer N, Randriatahina GH, Kaumanns W, Hoffmeister D, Schwitzer C (2007) Habitat utilization of blue-eyed black lemurs, Eulemur macaco flavifrons (Gray, 1867), in primary and altered forest fragments. Primate Conserv 22:79–87
Seiler M, Randriatahina GH, Schwitzer C (2017) The rapid boost of forest destruction and poaching of lemurs inside the Sahamalaza—Iles Radama National Park. Lemur News 16:28–30
Spawls S, Howell K, Hinkel H, Menegon M (2018) Field guide to East African reptiles. Bloomsbury Natural History, London
Sukumaran J, Knowles LL (2017) Multispecies coalescent delimits structure, not species. Proc Natl Acad Sci U S A 114:1607–1612
Talavera G, Dincă V, Vila R (2013) Factors affecting species delimitations with the GMYC model: insights from a butterfly survey. Methods Ecol Evol 4:1101–1110
Vences M, Lima A, Miralles A, Glaw F (2014) DNA barcoding assessment of genetic variation in two widespread skinks from Madagascar, Trachylepis elegans and T. gravenhorstii (Squamata: Scincidae). Zootaxa 3755:477–484
Volampeno, MSN (2009) Reproductive behaviour and habitat use in the blue-eyed black lemur (Eulemur flavifrons, Gray, 1867) at the Sahamalaza Peninsula, National Park Madagascar. University of Kwa-Zulu Natal, Pietermaritzburg
Wang C, Scherz MD, Montfort L, Hawlitschek O (2015) Complementary herpetological surveys to complete the ZNIEFF database of Mayotte: results. Direction de l'Environnement de l'Aménagement et du Logement (DEAL), Mayotte, France
Yang Z (2015) The BPP program for species tree estimation and species delimitation. Curr Zool 61:854–865
Yang Z, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. Proc Natl Acad Sci U S A 107:9264–9269
Yang Z, Rannala B (2017) Bayesian species identification under the multispecies coalescent provides significant improvements to DNA barcoding analyses. Mol Ecol 26:3028–3036
Acknowledgements
We thank F. Andreone, J. Berger, H.-P. Berghof, M. Bletz, P. Bora, B. Brückmann, N. Cole, S. Faravelli, J. Forster, K. Freeman, P.-S. Gehring, George, K. Glaw, T. Glaw, D.J. Harris, S. Hyde Roberts, J. Köhler, H. Lava, K. Mebert, L. Montfort, J. Noel, M. Pabijan, S. Penny, I. Porton, D. Prötzel, M. Puente, L. Raharivololoniaina, E. Rajeriarison, T. Rajoafiarison, A. Rakotoarison, L. Randriamanana, M. Randriamialisoa, F. Randrianasolo, R.D. Randrianiaina, S. Rasamison, F.M. Ratsoavina, A. Razafimanantsoa, J. H. Razafindraibe, D. Rödder, G.M. Rosa, D. Salvi, E. Scanarini, V. Tatayah, M. Thomas, J.H. Velo, M. Vences, D.R. Vieites, and C.Y.H. Wang-Claypool, as well as the teams from the CNDRS and Dahari, Comoros, the DEAL and Naturalistes, Mayotte, and Frontier, Nosy Be, Madagascar, for contributing specimens, pictures and observational data, and support in the field. Furthermore, we thank C.J. McCarthy and P. Campbell (BMNH, London), G. Köhler and L. Mogk (SMF, Frankfurt), W. Böhme (ZFMK, Bonn), and D. Langer (ZMB, Berlin) for granting us access to their collections and M. Franzen (ZSM, Munich) and F. Tillack (ZMB, Berlin) for general collection-based support. Authorities at Antananarivo (Madagascar), Zanzibar (Tanzania, for Pemba), Mamoudzou (Mayotte, France), Moroni (Comoros), and Port Louis (Mauritius) are acknowledged for issuing collection and export permits. Finally, we thank M. Balke, Munich, and K. Tamar, Barcelona, for providing computational and lab infrastructure, A.W. Lam for the technical support in the lab, M. Spies for nomenclatural advice, and three anonymous referees for providing very thorough and competent reviews of the manuscript of this paper.
Funding
The research was financially supported by the Volkswagen Foundation, the Mohamed bin Zayed Species Conservation Fund (projects 0925157 and 11253064) to FG and OH, by DAAD grant D/09/49634 to OH, the Deutsche Forschungsgemeinschaft DFG (GL 314/1) to FG, DFG (BA2152/7-1) to M. Balke, and DFG (HA 7255/2-1) to OH, by the Portuguese National Funds through FCT–Foundation for Science and Technology under the IF/00209/2014/CP1256/CT0011 Exploratory Research Project, the Investigador FCT (IF) grant (IF/00209/2014) and by the Saint Louis Zoo’s Field Research for Conservation programme (FRC# 12-12) of the Wildcare Institute and Gondwana Conservation and Research to AC. The ‘Freunde der Zoologischen Staatssammlung München’, the Society of the University of Munich, and EES funding programme of the University of Munich provided additional financial support.
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Communicated by: Sven Thatje
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ESM 1
: Morphological counts and measurements of all specimens examined, including the ANOVA results. (XLSX 58 kb)
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: Micro-CT scans of the skulls of Ebenavia inunguis, E. boettgeri, E. tuelinae sp. nov., E. safari sp. nov., and E. robusta sp. nov. in dorsal and lateral view. Length of scale bars = 1 mm. (PNG 9619 kb)
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Hawlitschek, O., Scherz, M.D., Ruthensteiner, B. et al. Computational molecular species delimitation and taxonomic revision of the gecko genus Ebenavia Boettger, 1878. Sci Nat 105, 49 (2018). https://doi.org/10.1007/s00114-018-1574-9
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DOI: https://doi.org/10.1007/s00114-018-1574-9