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Published July 22, 2021 | Version v1
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Taxonomic inflation due to inadequate sampling: are girdled lizards (Cordylus minor species complex) from the Great Karoo one and the same?

Creators

  • 1. School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, P.O. Wits 2050, Johannesburg, South Africa
  • 2. Division of Herpetology, Department of Animal and Plant Systematics, National Museum, P.O. Box 266, Bloemfontein 9300, South Africa & Department of Zoology & Entomology, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
  • 3. Port Elizabeth Museum (Bayworld), Gqeberha 6013, South Africa
  • 4. Division of Herpetology, Department of Animal and Plant Systematics, National Museum, P.O. Box 266, Bloemfontein 9300, South Africa

Description

Tolley, Krystal A., Telford, Nicolas S., Taft, Jody M., Bates, Michael F., Conradie, Werner, Makhubo, Buyisile G., Alexander, Graham J. (2022): Taxonomic inflation due to inadequate sampling: are girdled lizards (Cordylus minor species complex) from the Great Karoo one and the same? Biological Journal of the Linnean Society 135: 1-24, DOI: 10.1093/biolinnean/blab119

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Identifiers

LSID
urn:lsid:plazi.org:pub:6526FF874B78FFD14D3FAE4A5461FFCA

Has part
Figure: 10.5281/zenodo.7849463 (DOI)
Figure: 10.5281/zenodo.7849465 (DOI)
Dataset: http://table.plazi.org/id/45C966614B7DFFD44DB0AFE1554DFD9E (URL)
Figure: 10.5281/zenodo.7849469 (DOI)
Figure: 10.5281/zenodo.7849471 (DOI)
Figure: 10.5281/zenodo.7849473 (DOI)
Figure: 10.5281/zenodo.7849475 (DOI)
Figure: 10.5281/zenodo.7849477 (DOI)
Dataset: http://table.plazi.org/id/45C966614B6AFFC34DACAE8E57EDFEA6 (URL)

References

  • Adams DC, Berns CM, Kozak KH, Wiens JJ. 2009. Are rates of species diversification correlated with rates of morphological evolution? Proceedings of the Royal Society B: Biological Sciences 276: 2729-2738.
  • Aiello-Lammens ME, Boria RA, Radosavljevic A, Vilela B, Anderson RP. 2015. spThin: an R package for spatial thinning of species occurrence records for use in ecological niche models. Ecography 38: 541-545.
  • Aljanabi SM, Martinez I. 1997. Universal and rapid saltextraction of high quality genomic DNA for PCR based techniques. Nucleic Acids Research 25: 4692-4693.
  • Anderson RP, Gonzalez JI. 2011. Species-specific tuning increases robustness to sampling bias in models of species distributions: an implementation with Maxent. Ecological Modelling 222: 2796-2811.
  • Bates MF, Branch WR, Bauer AM, Burger M, Marais J, Alexander GJ, de Villiers MS. 2014. Atlas and Red List of the reptiles of South Africa, Lesotho and Swaziland. Suricata 1. Pretoria: South African National Biodiversity Institute.
  • Bouckaert R, Heled J, Kuhnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10: e1003537.
  • Braconnot P, Otto-Bliesner B, Harrison S, Joussaume S, Peterchmitt JY, Abe-Ouchi A, Crucifix M, Fichefet T, Hewitt CD, Kageyama M, Kitoh A, Loutre MF, Marti O, Merkel U, Ramstein G, Valdes P, Weber L, Yu Y, Zhao Y. 2007. Coupled simulations of the mid-Holocene and Last Glacial Maximum: new results from PMIP2. Climate of the Past Discussions 2: 1293-1346.
  • Brown JL, Knowles LL. 2012. Spatially explicit models of dynamic histories: examination of the genetic consequences of Pleistocene glaciation and recent climate change on the American pika. Molecular Ecology 21: 3757-3775.
  • Carstens BC, Pelletier TA, Reid NM, Satler JD. 2013. How to fail at species delimitation. Molecular Ecology 22: 4369-4383.
  • Chambers EA, Hillis DM. 2020. The multispecies coalescent over-splits species in the case of geographically widespread taxa. Systematic Biology 69: 184-193.
  • Cicero C, Mason NA, Jimenez RA, Wait DR, Wang- Claypool CY, Bowie RC. 2021. Integrative taxonomy and geographic sampling underlie successful species delimitation. The Auk 138: ukab009.
  • Clement M, Posada D, Crandall KA. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1659.
  • Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772.
  • De la Riva I, Chaparro JC, Castroviejo-Fisher S, Padial JM. 2018. Underestimated anuran radiations in the high Andes: five new species and a new genus of Holoadeninae, and their phylogenetic relationships (Anura: Craugastoridae). Zoological Journal of the Linnean Society 182: 129-172.
  • Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 1-8.
  • Elith J, Graham CH, Anderson RP, Dudik M, Ferrier S, Guisan A, Hijmans RJ, Huettmann F, Leathwick JR, Lehmann A, Li J, Lohmann LG, Loiselle BA , Manion G, Moritz C, Nakamura M, Nakazawa Y, Overton JM, Peterson AT, Phillips SJ, Richardson KS, Scachetti-Pereira R, Schapire RE, Soberon J, Williams S, Wisz MS, Zimmermann NE. 2006. Novel methods improve prediction of species' distributions from occurrence data. Ecography 29: 129-151.
  • Elith J, Phillips SJ, Hastie T, Dudik M, Chee YE, Yates CJ. 2011. A statistical explanation of MaxEnt for ecologists. Diversity and Distributions 17: 43-57.
  • Engelbrecht HM, Branch WR, Greenbaum E, Alexander GJ, Jackson K, Burger M, Conradie W, Kusamba C, Zassi- Boulou AG, Tolley KA. 2019. Diversifying into the branches: species boundaries in African green and bush snakes, Philothamnus (Serpentes: Colubridae). Molecular Phylogenetics and Evolution 130: 357-365.
  • Fick SE, Hijmans RJ. 2017. WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas. International Journal of Climatology 37: 4302-4315.
  • FitzSimons VF. 1943. The lizards of South Africa. Transvaal Museum Memoirs 1: 1-528.
  • Freitas I, Ursenbacher S, Mebert K, Zinenko O, Schweiger S , Wuster W, Brito JC, Crnobrnja- Isailovic J , Halpern B , Fahd S , Santos X , Pleguezuelos JM, Joger U, Orlov N, Mizsei E, Lourdais P , Zuffi MAL , Strugariu A , Zamfirescu SR, Martinez-Solano I, Velo-Anton G, Kaliontzopoulou A , Martinez-Freiria F. 2020. Evaluating taxonomic inflation: towards evidence-based species delimitation in Eurasian vipers (Serpentes: Viperinae). Amphibia-Reptilia 41: 285-311.
  • Gaston KJ. 2003. The Structure and dynamics of geographic ranges. Oxford: Oxford University Press.
  • Goldstein PZ, De Salle R. 2011. Integrating DNA barcode data and taxonomic practice: determination, discovery, and description. Bioessays 33: 135-147.
  • Gorodkov KB. 1986. Three-dimensional climatic model of the potential range and some of its characteristics.Entomological Review 65: 1-18.
  • Guindon S, Gascuel O. 2003. A simple, fast and accurate method to estimate large phylogenies by maximumlikelihood. Systematic Biology 52: 696-704.
  • Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A. 2005. Very high-resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25: 1965-1978.
  • Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
  • Ikeda DH, Max TL, Allan GJ, Lau MK, Shuster SM, Whitham TG. 2016. Genetically informed ecological niche models improve climate change predictions. Global Change Biology 23: 164-176.
  • Isaac NJB, Mallet J, Mace GM. 2004. Taxonomic inflation: its influence on the macroecology and conservation. Trends in Ecology and Evolution 19: 464-469.
  • 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.
  • 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.
  • Lefebure T, Douady C, Gouy M, Gibert J. 2006. Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation. Molecular Phylogenetics and Evolution 40: 435-477.
  • Leigh JW, Bryant D. 2015. PopART: full-feature software for haplotype network construction. Methods in Ecology and Evolution 6: 1110-1116.
  • Luo A, Ling C, Ho SY, Zhu CD. 2018. Comparison of methods for molecular species delimitation across a range of speciation scenarios. Systematic Biology 67: 830-846.
  • Macey JR, Larson A, Ananjeva NB, Fang Z, Papenfuss TJ. 1997. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Molecular Biology and Evolution 14: 91-104.
  • McCarthy T, Rubridge B. 2005. The story of earth and life: a Southern African perspective on a 4.6-billion-year journey. Cape Town: Struik Publishers.
  • Meier R, Dikow T. 2004. Significance of specimen databases from taxonomic revisions for estimating and mapping the global species diversity of invertebrates and repatriating reliable specimen data. Conservation Biology 18: 478-488.
  • Meier R, Shiyang K, Vaidya G, Ng P. 2006. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology 55: 715-728.
  • Miller MA, Pfeiffer W, Schwartz T. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments workshop (GCE). San Diego Supercomputer Center, New Orleans, LA, 14 November 2010, 1-8.
  • Miller MP. 2005. Alleles in space (AIS): computer software for the joint analysis of interindividual spatial and genetic information. Journal of Heredity 96: 722-724.
  • Mora C, Tittensor DP, Adl S, Simpson AG, Worm B. 2011. How many species are there on Earth and in the ocean? PLoS Biology 9: e1001127.
  • Mouton PLF, van Wyk JH. 1989. Cordylus minor: a valid species of South African lizard (Reptilia: Cordylidae). African Zoology 24: 322-328.
  • Mouton PLF, van Wyk JH. 1994. Taxonomic status of geographical isolates in the Cordylus minor complex (Reptilia: Cordylidae): a description of three new species. Journal of the Herpetological Association of Africa 43: 6-18.
  • Muscarella R, Galante PJ, Soley-Guardia M, Boria RA, Kass JM, Uriarte M, Anderson RP. 2014. ENMeval: an R package for conducting spatially independent evaluations and estimating optimal model complexity for Maxent ecological niche models. Methods in Ecology and Evolution 5: 1198-1205.
  • Padial JM, Miralles A, De la Riva I, Vences M. 2010. The integrative future of taxonomy. Frontiers in Zoology 7: 1-14.
  • Palumbi S, Martin A, Romano S, McMillan WO, Stice L, Grabowski G. 1991. Simple fool's guide to PCR. Honolulu: Department of Zoology and Kewalo Marine Laboratory.
  • Paterson HEH. 1985. The recognition concept of species. In: Vrba ES, ed. Species and speciation. Pretoria: Transvaal Museum, 21-29.
  • Perez-Ponce de Leon G, Poulin R. 2016. Taxonomic distribution of cryptic diversity among metazoans: not so homogeneous after all. Biology Letters 12: 20160371.
  • Phillips SJ, Anderson RP, Schapire RE. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling 190: 231-259.
  • QGIS.org. 2021. QGIS Geographic Information System. QGIS Association. Available at: http://www.qgis.org
  • de Queiroz K. 1998. The general lineage concept of species, species criteria, and the process of speciation: a conceptual unification and terminological recommendations. In: Howard DJ, Berlocher SH, eds. Endless forms: species and speciation. Oxford: Oxford University Press, 57-75.
  • de Queiroz K. 2007. Species concepts and species delimitation. Systematic Biology 56: 879-886.
  • R Core Team. 2013. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing. Available at: http://www.R-project.org/
  • Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. 2018. Posterior summarisation in Bayesian phylogenetics using Tracer 1.7. Systematic Biology 67: 901.
  • Reid NM, Carstens BC. 2012. Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evolutionary Biology 12: 196.
  • Reissig J. 2014. Girdled lizards and their relatives: natural history, captive care and breeding. Frankfurt am Main: Edition Chimaira.
  • Riley SJ, DeGloria SD, Elliot R . 1999. A terrain ruggedness index that quantifies topographic heterogeneity. Intermountain Journal of Sciences 5: 23-27.
  • Rosenzweig C, Karoly D, Vicarelli M, Neofotis P, Wu Q, Casassa G, Menzel A, Root TL, Estrella N, Seguin B, Tryjanowski P, Liu C, Rawlins S, Imeson A. 2008. Attributing physical and biological impacts to anthropogenic climate change. Nature 453: 353-357.
  • Satler JD, Carstens BC, Hedin M. 2013. Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus). Systematic Biology 62: 805-823.
  • Stamatakis A. 2014 . RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313.
  • Stanley EL, Bauer AM, Jackman TR, Branch WR, Mouton PLFN. 2011. Between a rock and a hard polytomy: rapid radiation in the rupicolous girdled lizards (Squamata: Cordylidae). Molecular Phylogenetics and Evolution 58: 53-70.
  • Tabachnick BG, Fidell LS. 1996. Using multivariate statistics, 3rd edn. New York: HarperCollins College Publishers.
  • Taylor KE, Stouffer RJ, Meehl GA. 2012. An overview of CMIP5 and the experiment design. Bulletin of the American Meteorological Society 93: 485-498.
  • Telford NS, Alexander GJ, Becker FS, Conradie W, Jordaan A, Kemp L, le Grange A, Rebelo AD, Strauss P, Taft JM, Weeber J, Tolley KA. In press. Extensions to the known Geographic distributions of reptiles in the Karoo, South Africa. Amphibian and Reptile Conservation.
  • Tolley KA, Bowie RCK, Price BW, Measey GJ, Forest F. 2014. The shifting landscape of genes since the Pliocene: terrestrial phylogeography in the Greater Cape Floristic Region. In: Allsopp N, Colville JF, Verboom T, eds. Ecology and evolution of fynbos understanding megadiversity. Oxford: Oxford University Press, 142-163.
  • Townsend TM, Alegre RE, Kelley ST, Wiens JJ, Reeder TW. 2008. Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: an example from squamate reptiles. Molecular Phylogenetics and Evolution 47: 129-142.
  • Vacher JP, Chave J, Ficetola FG, Sommeria-Klein G, Tao S, Thebaud C,Blanc M,Camacho A, Cassimiro J,Colston TJ, Dewynter M. 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.
  • Warren DL, Glor RE, Turelli M. 2010. ENMTools: a toolbox for comparative studies of environmental niche models. Ecography 33: 607-611.
  • Warren DL, Seifert SN. 2011. Ecological niche modeling in Maxent: the importance of model complexity and the performance of model selection criteria. Ecological Applications 21: 335-342.
  • Wiemers M, Fiedler K. 2007. Does the DNA barcoding gap exist? - a case study in blue butterflies (Lepidoptera: Lycaenidae). Frontiers in Zoology 4: 8.
  • Zheng Y, Wiens JJ. 2016. Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species.Molecular Phylogenetics and Evolution 94: 537-547.