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
- 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)
- 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.
- 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
- 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
- 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
- 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
- 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
- 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
- de Queiroz, K. (2020) An updated concept of subspecies resolves a dispute about the taxonomy of incompletely separated lineages. Herpetological Review, 51, 459–461.
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Henkel, F.-W. (2009) Beobachtungen an Neukaledonischen Riesengeckos in der Natur. Draco, 9, 14–22.
- Hillis, D.M. (2020) The detection and naming of geographic variation within species. Herpetological Review, 51, 52–56.
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Köhler, G. (2012) Color Catalogue for Field Biologists. Herpeton, Offenbach.
- Köhler, G. (2021) Taxonomy of horned lizards, genus Phrynosoma (Squamata, Phrynosomatidae). Taxonomy, 1, 83–115. https://doi.org/10.3390/taxonomy1020009
- 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
- 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
- Laetsch, D.R. & Blaxter, M.L. (2017) BlobTools: Interrogation of genome assemblies. F1000Research, 6, 1287. https://doi.org/10.12688/f1000research.12232.1
- 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
- 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
- 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
- Li, H. (2013a) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXi, 1303.3997v2. [q-bio.GN]
- 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)
- 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
- 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
- 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
- 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
- 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
- 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
- Mittermeier, R.A. (2004) Hotspots revisited. Earth’s biologically richest and most endangered terrestrial ecoregions. CEMEX, Mexico City, 390 pp.
- 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
- 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
- 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
- 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
- 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
- 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
- Seipp, R. & Henkel, F.-W. (2011) Rhacodactylus: Biology, Natural History and Husbandry. Edition Chimaira, Frankfurt, 173 pp.
- Seipp, R. & Obst, F.J. (1994) Beschreibung einer neuen Unterart des neukaledonischen Rhacodactylus leachianus Cuvier, 1829 (Reptilia: Sauria: Gekkonidae). Senckenbergiana Biologica, 74, 205–211.
- 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
- Simpson, G.G. (1951) The species concept. Evolution, 285–298. https://doi.org/10.2307/2405675
- 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
- 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
- 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
- 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.
- 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
- Wiley, E.O. (1978) The Evolutionary Species Concept Reconsidered. Systematic Biology, 27, 17–26. https://doi.org/10.2307/2412809
- 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.
- 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
- 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