Skip to main content Skip to main navigation menu Skip to site footer
Responsive image
Issue: Vol. 5538 No. 4: 18 Nov. 2024
Type: Article
Published: 2024-11-18
DOI: 10.11646/zootaxa.5538.4.1
Page range: 301-321
Abstract views: 2298
PDF downloaded: 25

A new species of giant gecko of the genus Rhacodactylus from New Caledonia (Squamata, Gekkota, Diplodactylidae)

Senckenberg Forschungsinstitut und Naturmuseum; Senckenberganlage 25; 60325 Frankfurt a.M.; Germany
Alfred-Döblin-Str. 68; 59192 Bergkamen; Germany
Alt Praunheim 45; 60488 Frankfurt a.M.; Germany
Senckenberg Forschungsinstitut und Naturmuseum; Senckenberganlage 25; 60325 Frankfurt a.M.; Germany
Reptilia Cryptic species diversity Rhacodactylus willihenkeli sp. nov.

Abstract

We describe a new species of giant gecko, Rhacodactylus willihenkeli sp. nov. from New Caledonia. The new species is most similar in external appearance and molecular data (16S and ND2 sequences) with R. leachianus from which it differs in coloration as well as having a genetic distance of 5.0% in the 16S gene fragment and 8.5% in the ND2 fragment, respectively.

 

References

  1. Andrews, S. (2010) FastQC: A Quality Control Tool for High Throughput Sequence Data. Available from: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (accessed 21 October 2024)
  2. Bauer, A.M. & Jackman, T.R. (2006) Phylogeny and microendemism of the New Caledonian lizard fauna. In: Vences, M., Köhler, J., Ziegler, T. & Böhme, W. (Eds.), Herpetologia Bonnensis II. Proceedings of the 13th Congress of the Societas Europaea Herpetologica, Bonn, 2006, pp. 9–13.
  3. Bauer, A.M., Jackmann, T.R., Sadlier, R.A. & Whitaker, A.H. (2012a) Revision of the giant geckos of New Caledonia (Reptilia: Diplodactylidae: Rhacodactylus). Zootaxa, 3404 (1), 1–52. https://doi.org/10.11646/zootaxa.3404.1.1
  4. Bauer, A.M., Sadlier, R.A., Jackman, T.R. & Shea, G. (2012b) A New Member of the Bavayia cyclura Species Group (Reptilia: Squamata: Diplodactylidae) from the Southern Ranges of New Caledonia. Pacific Science, 66, 239–247. https://doi.org/10.2984/66.2.10
  5. Bolger, A.M., Lohse, M. & Usadel, B. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, Oxford, England, 30, 2114–2120. https://doi.org/10.1093/bioinformatics/btu170
  6. Burbrink, F.T., Lawson, R. & Slowinski, J.B. (2000) Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): a critique of the subspecies concept. Evolution, 54, 2107–2118. https://doi.org/10.1111/j.0014-3820.2000.tb01253.x
  7. Chikhi, R. & Medvedev, P. (2014) Informed and automated k-mer size selection for genome assembly. Bioinformatics, 30, 31–37. https://doi.org/10.1093/bioinformatics/btt310
  8. Danecek, P., Bonfield, J.K., Liddle, J., Marshall, J., Ohan, V., Pollard, M.O., Whitwham, A., Keane, T., McCarthy, S.A., Davies, R.M. & Li, H. (2021) Twelve years of SAMtools and BCFtools. GigaScience, 10, giab008. https://doi.org/10.1093/gigascience/giab008
  9. de Queiroz, K. (2020) An updated concept of subspecies resolves a dispute about the taxonomy of incompletely separated lineages. Herpetological Review, 51, 459–461.
  10. Dierckxsens, N., Mardulyn, P. & Smits, G. (2017) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Research, 45, e18. https://doi.org/10.1093/nar/gkw955
  11. Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC bioinformatics, 5, 1–19. https://doi.org/10.1186/1471-2105-5-113
  12. Ewels, P., Magnusson, M., Lundin, S. & Käller, M. (2016) MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32, 3047–3048. https://doi.org/10.1093/bioinformatics/btw354
  13. Gelman, A. & Rubin, D.B. (1992) Inference from iterative simulation using multiple sequences. Statistical Science, 7, 457–472. https://doi.org/10.1214/ss/1177011136
  14. Glez-Peña, D., Gómez-Blanco, D., Reboiro-Jato, M., Fdez-Riverola, F. & Posada, D. (2010) ALTER: program-oriented conversion of DNA and protein alignments. Nucleic Acids Research, 38, 14–18. https://doi.org/10.1093/nar/gkq321
  15. Good, D.A., Bauer, A. & Sadlier, R.A. (1997) Allozyme evidence for the phylogeny of giant New Caledonain geckos (Squamata: Diplodactylidae: Rhacodactylus), with comments on the status of R. leachianus henkeli. Australian Journal of Zoology, 45 (3), 317–330. https://doi.org/10.1071/ZO96036
  16. Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W. & Gascuel, O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology, 59, 307–321. https://doi.org/10.1093/sysbio/syq010
  17. 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
  18. Henkel, F.-W. (2009) Beobachtungen an Neukaledonischen Riesengeckos in der Natur. Draco, 9, 14–22.
  19. Hillis, D.M. (2020) The detection and naming of geographic variation within species. Herpetological Review, 51, 52–56.
  20. Huelsenbeck, J.P. & Ronquist, F. (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, Oxford, England, 17, 754–755. https://doi.org/10.1093/bioinformatics/17.8.754
  21. Ivanova, N.V., Waard, J. de & Hebert, P.D. (2006) An inexpensive, automation-friendly protocol for recovering high-quality DNA. Molecular Ecology Notes, 6, 998–1002. https://doi.org/10.1111/j.1471-8286.2006.01428.x
  22. Jackman, S.D., Vandervalk, B.P., Mohamadi, H., Chu, J., Yeo, S., Hammond, S.A., Jahesh, G., Khan, H., Coombe, L., Warren, R.L. & Birol, I. (2017) ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter. Genome Research, 27, 768–777. https://doi.org/10.1101/gr.214346.116
  23. 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
  24. Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P. & Drummond, A. (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28, 1647–1649. https://doi.org/10.1093/bioinformatics/bts199
  25. Kehlmaier, C., Albury, N.A., Steadman, D.W., Graciá, E., Franz, R. & Fritz, U. (2021) Ancient mitogenomics elucidates diversity of extinct West Indian tortoises. Scientific Reports, 11, 3224. https://doi.org/10.1038/s41598-021-82299-w
  26. Kekkonen, M., Mutanen, M., Kaila, L., Nieminen, M. & Hebert, P.D.N. (2015) Delineating species with DNA Barcodes: A case of taxon dependent method performance in moths. PLoS ONE, 10 (4), e0122481. https://doi.org/10.1371/journal.pone.0122481
  27. Köhler, G. (2012) Color Catalogue for Field Biologists. Herpeton, Offenbach.
  28. Köhler, G. (2021) Taxonomy of horned lizards, genus Phrynosoma (Squamata, Phrynosomatidae). Taxonomy, 1, 83–115. https://doi.org/10.3390/taxonomy1020009
  29. Kueck, P. & Longo, G.C. (2014) FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies. Frontiers in Zoology, 11, 81. https://doi.org/10.1186/s12983-014-0081-x
  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. Laetsch, D.R. & Blaxter, M.L. (2017) BlobTools: Interrogation of genome assemblies. F1000Research, 6, 1287. https://doi.org/10.12688/f1000research.12232.1
  32. Lanfear, R., Frandsen, P.B., Wright, A.M., Senfeld, T. & Calcott, B. (2017) PartitionFinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution, 34, 772–773. https://doi.org/10.1093/molbev/msw260
  33. Langmead, B. & Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357–359. https://doi.org/10.1038/nmeth.1923
  34. Li, H. (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics, Oxford, England, 27, 2987–2993. https://doi.org/10.1093/bioinformatics/btr509
  35. Li, H. (2013a) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXi, 1303.3997v2. [q-bio.GN]
  36. Li, H. (2013b) Seqtk: a fast and lightweight tool for processing FASTA or FASTQ sequences. Available from: https://github.com/lh3/seqtk (accessed 21 October 2024)
  37. Manier, M.K. (2004) Geographic variation in the long-nosed snake, Rhinocheilus lecontei (Colubridae): beyond the subspecies debate. Biological Journal of the Linnean Society, 83, 65–85. https://doi.org/10.1111/j.1095-8312.2004.00373.x
  38. Manni, M., Berkeley, M.R., Seppey, M. & Zdobnov, E.M. (2021) BUSCO: Assessing Genomic Data Quality and Beyond. Current Protocols, 1 (12), e323. https://doi.org/10.1002/cpz1.323
  39. Marçais, G. & Kingsford, C. (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics, 27, 764–770. https://doi.org/10.1093/bioinformatics/btr011
  40. Meng, G., Li, Y., Yang, C. & Liu, S. (2019) MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Research, 47, e63. https://doi.org/10.1093/nar/gkz173
  41. Mikheenko, A., Prjibelski, A., Saveliev, V., Antipov, D. & Gurevich, A. (2018) Versatile genome assembly evaluation with QUAST-LG. Bioinformatics, 34, i142–i150. https://doi.org/10.1093/bioinformatics/bty266
  42. Minh, B.Q., Nguyen, M.A.T. & Haeseler, A. von (2013) Ultrafast approximation for phylogenetic bootstrap. Molecular Biology and Evolution, 30, 1188–1195. https://doi.org/10.1093/molbev/mst024
  43. Mittermeier, R.A. (2004) Hotspots revisited. Earth’s biologically richest and most endangered terrestrial ecoregions. CEMEX, Mexico City, 390 pp.
  44. 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
  45. Puillandre, N., Lambert, A., Brouillet, S. & Achaz, G. (2012) ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular ecology, 21, 1864–1877. https://doi.org/10.1111/j.1365-294X.2011.05239.x
  46. Ranallo-Benavidez, T.R., Jaron, K.S. & Schatz, M.C. (2020) GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nature Communications, 11, 1432. https://doi.org/10.1038/s41467-020-14998-3
  47. Ronquist, F. & Huelsenbeck, J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, Oxford, England, 19, 1572–1574. https://doi.org/10.1093/bioinformatics/btg180
  48. Ronquist, F., Teslenko, M., Mark, P., Ayres, D., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. & Huelsenbeck, J. (2012) MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Systematic Biology, 61, 539–542. https://doi.org/10.1093/sysbio/sys029
  49. Schneider, C., Woehle, C., Greve, C., D’Haese, C.A., Wolf, M., Hiller, M., Janke, A., Bálint, M. & Huettel, B. (2021) Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola). GigaScience, 10 (5), jiab035. https://doi.org/10.1093/gigascience/giab035
  50. Seipp, R. & Henkel, F.-W. (2011) Rhacodactylus: Biology, Natural History and Husbandry. Edition Chimaira, Frankfurt, 173 pp.
  51. Seipp, R. & Obst, F.J. (1994) Beschreibung einer neuen Unterart des neukaledonischen Rhacodactylus leachianus Cuvier, 1829 (Reptilia: Sauria: Gekkonidae). Senckenbergiana Biologica, 74, 205–211.
  52. Shen, W., Le, S., Li, Y. & Hu, F. (2016) SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS ONE, 11, e0163962. https://doi.org/10.1371/journal.pone.0163962
  53. Simpson, G.G. (1951) The species concept. Evolution, 285–298. https://doi.org/10.2307/2405675
  54. Steenwyk, J.L., Buida, T.J., Li, Y., Shen, X.-X. & Rokas, A. (2020) ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference. PLOS Biology, 18, e3001007. https://doi.org/10.1371/journal.pbio.3001007
  55. Tamura, K., Stecher, G. & Kumar, S. (2021) MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution, 38, 3022–3027. https://doi.org/10.1093/molbev/msab120
  56. Trifinopoulos, J., Nguyen, L.-T., Haeseler, A. von & Minh, B.Q. (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research, 44, W232–W235. https://doi.org/10.1093/nar/gkw256
  57. Vences, M., Henkel, F.-W. & Seipp, R. (2001) Molekulare Untersuchungen zur Phylogenie und Taxonomie der Neukaledonischen Geckos der Gattung Rhacodactylus (Reptilia: Gekkonidae). Salamandra, 37, 73–82.
  58. Vurture, G.W., Sedlazeck, F.J., Nattestad, M., Underwood, C.J., Fang, H., Gurtowski, J. & Schatz, M.C. (2017) GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics, 33, 2202–2204. https://doi.org/10.1093/bioinformatics/btx153
  59. Wiley, E.O. (1978) The Evolutionary Species Concept Reconsidered. Systematic Biology, 27, 17–26. https://doi.org/10.2307/2412809
  60. Wright, J.L., Bauer, A.M. & Sadlier, R.A. (2000) Two new gecko species allied to Bavayia sauvagii and Bavayia cyclura (Reptilia: Squamata: Diplodactylidae) from New Caledonia. Pacific Science, 54, 39–55.
  61. Yang, Z., Landry, J.-F. & Hebert, P.D.N. (2016) A DNA barcode library for North American Pyraustinae (Lepidoptera: Pyraloidea: Crambidae). PLoS ONE, 11, e0161449. https://doi.org/10.1371/journal.pone.0161449
  62. Zhang, Z., Schwartz, S., Wagner, L. & Miller, W. (2000) A Greedy Algorithm for Aligning DNA Sequences. Journal of computational biology, 7, 203–214. https://doi.org/10.1089/10665270050081478