Skip to main content Skip to main navigation menu Skip to site footer
Responsive image
Issue: Vol. 5665 No. 3: 23 Jul. 2025
Type: Article
Published: 2025-07-23
DOI: 10.11646/zootaxa.5665.3.1
Page range: 301-328
Abstract views: 112
PDF downloaded: 6

Revision of the Lygodactylus tolampyae complex, with descriptions of three additional new dwarf gecko species from Madagascar’s North West

Zoologisches Institut; Technische Universität Braunschweig; Mendelssohnstr. 4; 38106 Braunschweig; Germany
Zoologisches Institut; Technische Universität Braunschweig; Mendelssohnstr. 4; 38106 Braunschweig; Germany
Zoologisches Institut; Technische Universität Braunschweig; Mendelssohnstr. 4; 38106 Braunschweig; Germany
Zoologisches Institut; Technische Universität Braunschweig; Mendelssohnstr. 4; 38106 Braunschweig; Germany
Mention Environnement; Université de l’Itasy; Faliarivo Ambohidanerana; 118 Soavinandriana Itasy; Madagascar
Mention Zoologie et Biodiversité Animale; Université d’Antananarivo; BP 906; Antananarivo; 101 Madagascar
Mention Zoologie et Biodiversité Animale; Université d’Antananarivo; BP 906; Antananarivo; 101 Madagascar
Mention Environnement; Université de l’Itasy; Faliarivo Ambohidanerana; 118 Soavinandriana Itasy; Madagascar; School for International Training; VN 41A Bis Ambohitsoa; 101 Antananarivo; Madagascar
Zoologische Staatssammlung München (ZSM-SNSB); Münchhausenstr. 21; 81247 München; Germany
Institut de Systématique; Évolution; Biodiversité (ISYEB); Muséum National d’Histoire Naturelle; CNRS; Sorbonne Université; EPHE; Université des Antilles; 57 rue Cuvier; 75231 Paris cedex; France
Reptilia Squamata gekkonidae tsingy de Namoroka integrative taxonomy karst adaptation microendemism Lygodactylus andavambato sp. nov. Lygodactylus arnei sp. nov. Lygodactylus anjajavy sp. nov.

Abstract

The Lygodactylus tolampyae complex currently contains four nominal species of dwarf geckos from the North West and West of Madagascar. These four species are genetically distinct but have been flagged as morphologically cryptic, with only very subtle differences in scale counts between them. Based on new collections and extended molecular datasets, we here investigate the genetic and morphological differentiation of this species complex. We find seven deeply divergent mitochondrial lineages separated by 9.7–18.0% uncorrected pairwise distance in the 16S rRNA gene which correspond to the four recognized species and three further candidate species. Not a single instance of haplotype sharing between any of these lineages was found in four nuclear-encoded gene fragments, despite several of these lineages occurring in close geographic proximity or even syntopy. A Principal Component Analysis of morphometric measurements and meristic characters confirmed a wide overlap of most species in morphospace, but the new data also confirm statistically significant differences between numerous lineages in scale counts and morphometric ratios. We conclude that the three candidate species previously known only from very limited material and named Lygodactylus sp. 25, L. sp. 28 and L. sp. 29 correspond to distinct species which we formally name as L. andavambato sp. nov., L. anjajavy sp. nov., and L. arnei sp. nov. One of the new species, L. andavambato sp. nov. from the limestone karst of the Tsingy de Namoroka, has a peculiar phenotype with slender body and legs, and regular dark crossbands on the tail, differing from all other species in the L. tolampyae complex while superficially reminding L. rarus, a species from the limestone karst massif of Ankarana but belonging to another species group in Lygodactylus. The taxonomic progress, in only a few years, from a single species L. tolampyae to now seven species in this complex calls for further revisionary work, including more fieldwork to survey forest fragments and rocky outcrops across Madagascar which may host yet unknown locally endemic species of dwarf geckos.

 

References

  1. 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, pp. 45–67. https://doi.org/10.1073/pnas.94.15.7748
  2. Avise, J. & Wollenberg, K. (1997) Phylogenetics and the origin of species. Proceedings of the National Academy of Sciences of the United States of America, 94, 7748–7755.
  3. Bell, J. (2008) A simple way to treat PCR products prior to sequencing using ExoSAP-IT. Biotechniques, 44, 834. https://doi.org/10.2144/000112890
  4. 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
  5. 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, e5046. https://doi.org/10.1038/ncomms6046
  6. 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
  7. Bruford, M.W., Hanotte, O., Brookfield, J.F.Y. & Burke, T. (1992) Single-locus and multilocus DNA fingerprint. In: Hoelzel, A.R. (Ed.), Molecular Genetic Analysis of Populations: A Practical Approach. IRL Press, Oxford, pp. 225–270.
  8. Brygoo, E.R. (1990) Les types de Gekkonidés (Reptiles, Sauriens) du Muséum national d’Histoire naturelle. Catalogue critique. Bulletin Museum National d’Histoire Naturelle, Série 4, Section A (Zoologie, Biologie Écologie Animale), 3–4 (Supplement), 19–141. https://doi.org/10.5962/p.289594
  9. Chan, K.O. & Grismer, L.L. (2021) A standardized and statistically defensible framework for quantitative morphological analyses in taxonomic studies. Zootaxa, 5023 (2), 293–300. https://doi.org/10.11646/zootaxa.5023.2.9
  10. 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, pp. 49–89.
  11. de Queiroz, K. (2007) Species concepts and species delimitation. Systematic Biology, 56, 879–886. https://doi.org/10.1080/10635150701701083
  12. Edler, 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
  13. Fedosov, A., Achaz, G., Gontchar, A. & Puillandre, N. (2022) Mold, a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions. Molecular Ecology Resources, 22, 2038–2053. https://doi.org/10.1111/1755-0998.13590
  14. Gamble, T., Bauer, A.M., Colli, G.R., Greenbaum, E., Jackman, T.R., Vitt, L.J. & Simons, A.M. (2011) Coming to America: Multiple origins of New World geckos. Journal of Evolutionary Biology, 24, 231–244. https://doi.org/10.1111/j.1420-9101.2010.02184.x
  15. Gaston, K.J. & Blackburn, T.M. (1996) Range size-body size relationships: evidence of scale dependence. Oikos, 75, 479–485. https://doi.org/10.2307/3545889
  16. Gippner, S., Travers, S.L., Scherz, M.D., Colston, T.J., Lyra, M.L., Mohan, A.V., Multzsch, M., Nielsen, S.V., Rancilhac, L., Glaw, F., Bauer, A.M. & Vences, M. (2021) A comprehensive phylogeny of dwarf geckos of the genus Lygodactylus, with insights into their systematics and morphological variation. Molecular Phylogenetics and Evolution, 165, 107311. https://doi.org/10.1016/j.ympev.2021.107311
  17. Glaw, F., Köhler, J. & Vences, M. (2018) Three new species of nocturnal geckos of the Paroedura oviceps clade from xeric environments of Madagascar (Squamata: Gekkonidae). Zootaxa, 4433 (2), 305–324. https://doi.org/10.11646/zootaxa.4433.2.4
  18. Glaw, F., Prötzel, D., Eckhardt, F., Raharinoro, N.A., Ravelojaona, R.N., Glaw, T., Glaw, K., Forster, J. & Vences, M. (2020) Rediscovery, conservation status and genetic relationships of the Malagasy chameleon Furcifer voeltzkowi. Salamandra, 56, 342–354.
  19. Glaw, F., Raharinoro, N.A., Ravelojaona, R.N., Prötzel, D. & Vences, M. (2022) New records of threatened leaf chameleons highlight unexpected genetic diversity of the Brookesia decaryi/B. bonsi species complex in western Madagascar. Der Zoologische Garten, 90, 71–80.
  20. Grandidier, A. (1872) Quelque reptiles nouveaux découverts à Madagascar en 1870. Annales des Sciences Naturelles, Zoologie, 15 (5), 6–11.
  21. Grandidier, A. (1893) Les voyageurs français à Madagascar pendant les trente dernières années. Bulletin de la Société Géographie, 14, 289–300.
  22. Grismer, L., Perry, L.W., Quah, E.S.H. & Thura, M.K. (2020a) Origin, diversity, and conservation of karst-associated Bent-toed Geckos (genus Cyrtodactylus) in Myanmar (Burma). Israel Journal of Ecology and Evolution, 66, 202–208. https://doi.org/10.1163/22244662-20191094
  23. Grismer, L.L., Wood Jr., P.L., Le, M.D., Quah, E.S.H. & Grismer, J.L. (2020b) Evolution of habitat preference in 243 species of Bent-toed geckos (genus Cyrtodactylus Gray, 1827) with a discussion of karst habitat conservation. Ecology and Evolution, 10, 13717–13730. https://doi.org/10.1002/ece3.6961
  24. IUCN (2012) IUCN Red List Categories and Criteria. Version 3.1. IUCN, Gland and Cambridge. [program]
  25. Jenkins, R.K.B., Andreone, F., Andriamazava, A., Anjeriniaina, M., Glaw, F., Rabibisoa, N., Rakotomalala, D., Randrianantoandro, J.C., Randrianiriana, J., Randrianizahana, H., Raselimanana, A., Ratsoavina, F., Raxworthy, C.J. & Robsomanitrandrasana, E. (2011) Brookesia bonsi. The IUCN Red List of Threatened Species, 2011, e.T172878A6934200. Available from: https://doi.org/ 10.2305/IUCN.UK.2011-2.RLTS.T172878A6934200.en (accessed 7 December 2024)
  26. Jono, T., Bauer, A.M., Brennan, I. & Mori, A. (2015) New species of Blaesodactylus (Squamata: Gekkonidae) from Tsingy karstic outcrops in Ankarana National Park, northern Madagascar. Zootaxa, 3980 (3), 406–416. https://doi.org/10.11646/zootaxa.3980.3.4
  27. Josse, J. & Husson, F. (2016) missMDA: A package for handling missing values in multivariate data analysis. Journal of Statistical Software, 70, 1–31. https://doi.org/10.18637/jss.v070.i01
  28. Kaatz, A., Grismer, J.L. & Grismer, L.L. (2021) Convergent evolution of karst habitat preference and its ecomorphological correlation in three species of Bent-toed Geckos (Cyrtodactylus) from Peninsular Malaysia. Vertebrate Zoology, 71, 367–386. https://doi.org/10.3897/vz.71.e66871
  29. Köhler, J., Vences, M., Scherz, M.D. & Glaw, F. (2019) A new species of nocturnal gecko, genus Paroedura, from the karstic Tsingy de Bemaraha formation in western Madagascar. Salamandra, 55, 73–81.
  30. 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
  31. Kumazawa, Y., Miura, S., Yamada, C. & Hashiguchi, Y. (2014) Gene rearrangements in gekkonid mitochondrial genomes with shuffling, loss, and reassignment of tRNA genes. BMC Genomics, 15, 930. https://doi.org/10.1186/1471-2164-15-930
  32. Lanna, F.M., Werneck, F.P., Gehara, M., Fonseca, E.M., Colli, G.R., Sites Jr., J.W., Rodrigues, M.T. & Garda, A.A. (2018) The evolutionary history of Lygodactylus lizards in the South American open diagonal. Molecular Phylogenetics and Evolution, 127, 638–645. https://doi.org/10.1016/j.ympev.2018.06.010
  33. Lobón-Rovira, J., Bauer, A.M., Vaz Pinto, P., Trape, J.F., Conradie, W., Kusamba, C., Júlio, T., Cael, G., Stanley, E.L., Hughes, D.F., Behangana, M., Masudi, F.M., Pauwels, O.S.G. & Greenbaum, E. (2023) Integrative revision of the Lygodactylus gutturalis (Bocage, 1873) complex unveils extensive cryptic diversity and traces its evolutionary history. Zoological Journal of the Linnean Society, zlad123. [published online] https://doi.org/10.1093/zoolinnean/zlad123
  34. Matschiner, M. (2015) Fitchi: Haplotype genealogy graphs based on the Fitch algorithm. Bioinformatics, 32, 1250–1252. https://doi.org/10.1093/bioinformatics/btv717
  35. Mertens, R. (1922) Verzeichnis der Typen in der herpetologischen Sammlung des senckenbergischen Museums. Senckenbergiana, 4, 162–183.
  36. Mertens, R. (1965) Über Lygodactylus tuberifer und seinen Lectotypus. Senckenbergiana biologica, 46, 467–469.
  37. Miralles, A., Hipsley, C.A., Erens, J., Gehara, M., Rakotoarison, A., Glaw, F., Müller, J. & Vences, M. (2015) Distinct patterns of desynchronized limb regression in Malagasy scincine lizards (Squamata, Scincidae). PLoS ONE, 10, e0126074. https://doi.org/10.1371/journal.pone.0126074
  38. Moat, J. & Smith, P. (Eds.) (2007) Atlas of the vegetation of Madagascar. Kew Publishing, Kew, 124 pp.
  39. Padial, J.M., Miralles, A., De la Riva, I. & Vences, M. (2010) The integrative future of taxonomy. Frontiers in Zoology, 7, e16. https://doi.org/10.1186/1742-9994-7-16
  40. Puente, M., Glaw, F., Vieites, D.R. & Vences, M. (2009) Review of the systematics, morphology and distribution of Malagasy dwarf geckos, genera Lygodactylus and Microscalabotes (Squamata: Gekkonidae). Zootaxa, 2103 (1), 1–76. https://doi.org/10.11646/zootaxa.2103.1.1
  41. 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
  42. R Core Team (2022) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. Available from: https://www.R-project.org/ (accessed 9 June 2025)
  43. Rafanoharana, S.C., Andrianambinina, F.O.D., Rasamuel, H.A., Rakotoarijaona, M.A., Ganzhorn, J.U., Waeber, P.O. & Wilmé, L. (2021) Exemplifying stratified deforestation in four protected areas in Madagascar. Forests, 12, 1143. https://doi.org/10.3390/f12091143
  44. Rakotoarison, A., Gippner, S., Multzsch, M., Miralles, A., Razafimanafo, D., Hasiniaina, A. & Glaw, F. & Vences, M. (2025) Molecular systematics of the enigmatic dwarf gecko Lygodactylus ornatus and description of a new species of the L. verticillatus group from the North West of Madagascar. Zootaxa, 5621 (4), 420–436. https://doi.org/10.11646/zootaxa.5621.4.2
  45. Röll, B., Pinto, P.V. & Lobón-Rovira, J. (2024) A new species of African diurnal dwarf geckos (Gekkonidae: Lygodactylus) from the Lower Guinea rainforest. Zootaxa, 5538 (6), 561–574. https://doi.org/10.11646/zootaxa.5538.6.3
  46. Röll, B., Pröhl, H. & Hoffmann, K.-P. (2010) Multigene phylogenetic analysis of Lygodactylus dwarf geckos (Squamata: Gekkonidae). Molecular Phylogenetics and Evolution, 56, 327–335. https://doi.org/10.1016/j.ympev.2010.02.002
  47. Röll, B., Sanchez, M., Gippner, S., Bauer, A.M., Travers, S.L., Glaw, F., Hawlitschek, O. & Vences, M. (2023) Phylogeny of dwarf geckos of the genus Lygodactylus (Gekkonidae) in the Western Indian Ocean. Zootaxa, 5311 (2), 232–250. https://doi.org/10.11646/zootaxa.5311.2.4
  48. 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
  49. Scarpetta, S., Gray, L., Nieto Montes de Oca, A., del Rosario Castañeda, M., Herrel, A., Losos, J., Luna-Reyes, R., Jiménez Lang, N. & Poe, S. (2015) Morphology and ecology of the Mexican cave anole Anolis alvarezdeltoroi. Mesoamerican Herpetology, 2, 261–270.
  50. Signorell, A. (2024) DescTools: Tools for Descriptive Statistics. R Package Version 0.99.55. Available from: https://github.com/AndriSignorell/DescTools/ (accessed 9 June 2025)
  51. Speybroeck, J., Beukema, W., Dufresnes, C., Fritz, U., Jablonski, D., Lymberakis, P., Martinez-Solano, I., Razzettis, E., Vamberger, M., Vences, M., Vörös, J. & Crochet, P.-A. (2020) Species list of the European herpetofauna – 2020 update by the Taxonomic Committee of the Societas Europaea Herpetologica. Amphibia-Reptilia, 41, 139–189. https://doi.org/10.1163/15685381-bja10010
  52. 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
  53. 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
  54. Suzzi-Simmons, A. (2023) Status of deforestation of Madagascar. Global Ecology and Conservation, 42, e02389. https://doi.org/10.1016/j.gecco.2023.e02389
  55. Uetz, P., Freed, P., Aguilar, R. & Hošek, J. (Eds.) (2024) The Reptile Database. Available from: http://www.reptile-database.org (accessed 7 December 2024)
  56. 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 (2), 77–92. https://doi.org/10.11646/megataxa.6.2.1
  57. Vences, M., Multzsch, M., Gippner, S., Miralles, A., Crottini, A., Gehring, P.-S., Rakotoarison, A., Ratsoavina, F.M., Glaw, F. & Scherz, M.D. (2022) Integrative revision of the Lygodactylus madagascariensis group reveals an unexpected diversity of little brown geckos in Madagascar’s rainforest. Zootaxa, 5179 (1), 1–61. https://doi.org/10.11646/zootaxa.5179.1.1
  58. Vences, M., Multzsch, M., Zerbe, M., Gippner, S., Andreone, F., Crottini, A., Glaw, F., Köhler, J., Rakotomanga, S., Rasamison, S. & Raselimanana, A.P. (2024a) Taxonomizing a truly morphologically cryptic complex of dwarf geckos from Madagascar: molecular evidence for new species-level lineages within the Lygodactylus tolampyae complex. Zootaxa, 5468 (3), 416–448. https://doi.org/10.11646/zootaxa.5468.3.2
  59. Vences, M., Patmanidis, S., Schmidt, J.-C., Matschiner, M., Miralles, A. & Renner, S.S. (2024b) Hapsolutely: a user-friendly tool integrating haplotype phasing, network construction and haploweb calculation. Bioinformatics Advances, vbae083. [published online] https://doi.org/10.1093/bioadv/vbae083
  60. Vieilledent, G., Nourtier, M., Grinand, C., Pedrono, M., Clausen, A., Rabetrano, T., Rakotoarijaona, J.R., Rakotoarivelo, B., Rakotomalala, F.A., Rakotomalala, L., Razafimpahanana, A., Ralison, J.R. & Achard, F. (2020) It’s not just poverty: Unregulated global market and bad governance explain unceasing deforestation in Western Madagascar. bioRxiv, 2020.07.30.229104. https://doi.org/10.1101/2020.07.30.229104
  61. Waeber, P.O., Wilmé, L., Ramamonjisoa, C., Garcia, C., Rakotomalala, D., Rabemananjara, Z.H., Kull, C.A., Ganzhorn, J.U. & Sorg, J.P. (2015) Dry forests in Madagascar: Neglected and under pressure. International Forestry Review, 17 (S2), 127–148. https://doi.org/10.1505/146554815815834822
  62. Wilmé, L., Goodman, S.M. & Ganzhorn, J.U. (2006) Biogeographic evolution of Madagascar’s microendemic biota. Science, 312, 1063–1065. https://doi.org/10.1126/science.1122806

How to Cite

Vences, M., Herrmann, C., Multzsch, M., Gippner, S., Razafimanafo, D., Rahagalala, N.A., Rakotomanga, S., Rakotoarison, A., Glaw, F. & Miralles, A. (2025) Revision of the Lygodactylus tolampyae complex, with descriptions of three additional new dwarf gecko species from Madagascar’s North West. Zootaxa, 5665 (3), 301–328. https://doi.org/10.11646/zootaxa.5665.3.1