Published September 11, 2023
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Integrative taxonomy of the Iphisa elegans Gray, 1851 species complex (Squamata: Gymnophthalmidae) leads to the description of five new species
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- 1. Programa de Pós-Graduação em Biologia Animal, Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, CEP 50740-570, Recife, PE, Brazil
- 2. Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Caixa Postal 11.461, CEP 05422-970, São Paulo, SP, Brazil
- 3. Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, Université Paul Sabatier, 118 Rte de Narbonne, 31062 cedex 9, Toulouse, France
Description
Albano, Anna V., Mello, Recoder, Renato S., Fouquet, Antoine, Rodrigues, Miguel T., Nunes, Pedro M. S. (2024): Integrative taxonomy of the Iphisa elegans Gray, 1851 species complex (Squamata: Gymnophthalmidae) leads to the description of five new species. Zoological Journal of the Linnean Society 200 (2): 477-504, DOI: 10.1093/zoolinnean/zlad073, URL: http://dx.doi.org/10.1093/zoolinnean/zlad073
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References
- Amaral AD. Check-list of the 'Lacertilia' of Brazil. Comptes Rendus XII Congres International de Zoologie (Lisbonne 1935) 1937a:1733-43.
- Amaral AD. Estudos sobre lacertilios do neotropico.4.Lista remissiva dos lacertilios do Brazil. Memorias do Instituto Butantan 1937b;11:167- 204 + i-ix.
- Arnold EN. The hemipenis of lacertid lizards (Reptilia: Lacertidae): structure, variation and systematic implications. Journal of Natural History 1986;20:1221-57.
- Avila-Pires TC. Lizards of Brazilian Amazonia (Reptilia: Squamata). Zoologische Verhandelingen 1995;299:1-706.
- Bouckaert R, Heled J, Kuhnert D et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology 2014;10:e1003537.
- Boulenger GA. Catalogue of the Lizards in the British Museum (Natural History), Vol. 2, 2nd ed. London: Taylor and Francis, 1885, 423-425.
- Boulenger GA.Description of a new genus of lizards of the family Teiidae. Proceedings of the Zoological Society of London 1887;55:640-42.
- Braune P, Schmidt S, Zimmermann E. Acoustic divergence in the communication of cryptic species of nocturnal primates (Microcebus ssp.). BMC Biology 2008;6:19.
- Burt CE, Burt MD. The South American lizards in the collection of the United States National Museum. Proceedings of the United States National Museum 1930;78:1-52.
- Byers JR, Struble DL.Identification of sex pheromones of two sibling species in dingy cutworm complex, Feltia jaculifera (GN.) (Lepidoptera: Noctuidae). Journal of Chemical Ecology 1990;16:2981-92.
- Carstens BC, Pelletier TA, Reid NM et al. How to fail at species delimitation. Molecular Ecology 2013;22:4369-83.
- Clarke BC, Shelton PR, Mani GS. Frequency-dependent selection, metrical characters and molecular evolution. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 1988;319:631-40.
- Clement M, Posada D, Crandall D. TCS: a computer program to estimate gene genealogies. Molecular Ecology 2000;9:1657-9.
- Colli GR, Hoogmoed MS, Cannatella DC et al. Description and phylogenetic relationships of a new genus and two new species of lizards from Brazilian Amazonia, with nomenclatural comments on the taxonomy of Gymnophthalmidae (Reptilia: Squamata). Zootaxa 2015;4000:401-27.
- Cunha OR. Lacertilios da Amazonia II. Os lagartos da Amazonia brasileira, com especial referencia aos representantes na colecao do Museu Goeldi. Boletim do Museu Paraense Emilio Goeldi serie zoologia 1961;39:1-189.
- D'Angiolella AB, Klaczko J, Rodrigues MT et al. Hemipenial morphology and diversity in South American anoles (Squamata: Dactyloidae). Canadian Journal of Zoology 2016;94:251-6.
- Dirksen L, De la Riva I. The lizards and amphisbaenians of Bolivia (Reptilia, Squamata): checklist, localities, and bibliography. Graellsia 1999;55:199-215.
- Dixon JR. Systematic review of the lizard genus Anotosaura (Teiidae). Herpetologica 1974;30:13-8.
- Duellman WE. The biology of an Equatorial Herpetofauna in Amazonian Ecuador. Miscellaneous Publication (University of Kansas, Museum of Natural History) 1978;65:1-352.
- Fetzner JW. Extracting high-quality DNA from shed reptile skins: a simplified method. Biotechniques 1999;26:1052-4.
- Fitch HS. Temperature and behaviour of some Equatorial lizards. Herpetologica 1968;24:35-8.
- Fouquet A, Gilles A, Vences M et al. Underestimation of species richness in neotropical frogs revealed by mtDNA analyses. PLoS One 2007;2:e1109.
- Fujisawa T, Barraclough TG. Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets. Systematic Biology 2013;62:707-24.
- Gamble T, Colli GR, Rodrigues MT et al. Phylogeny and cryptic diversity in geckos (Phyllopezus; Phyllodactylidae; Gekkota) from South America's open biomes. Molecular Phylogenetics and Evolution 2012;62:943-53.
- Garcia-Porta J,Simo-Riudalbas M,Robinson M et al. Diversification in arid mountains: biogeography and cryptic diversity of Pristurus rupestris rupestris in Arabia. Journal of Biogeography 2017;44:1694-704.
- Geurgas SR, Rodrigues MT. The hidden diversity of Coleodactylus amazonicus (Sphaerodactylinae, Gekkota) revealed by molecular data. Molecular Phylogenetics and Evolution 2010;54:583-93.
- Goicoechea N, Frost DR, De la Riva I et al. Molecular systematics of teioid lizards (Teioidea/Gymnophthalmoidea: Squamata) based on the analysis of 48 loci under tree-alignment and similarity-alignment. Cladistics 2016;32:624-71.
- Gray JE. Description of a new genus and family of cyclosaurian lizards, from Para. Proceedings of the Zoological Society of London 1851;19:38-9.
- Harvey MB, Aparicio J, Cortez C et al. Reptiles and amphibians of Parque Nacional Noel Kempff Mercado. In: Killen TJ, Schulenberg TS, (ed). A biological assessment of Parque Nacional Noel Kempff Mercado, Bolivia. Washington (DC): RAP Working Papers 10, Conservation International, 1998;348-355.
- Harvey MB, Embert D. Review of Bolivian Dipsas (Serpentes: Colubridae), with comments on other South American species. Herpetological Monographs 2008;22:54-105.
- Hill EC, Fraser CJ, Gao DF et al. Resolving the deep phylogeny: implications for early adaptive radiation, cryptic, and present-day ecological diversity of Papuan microhylid frogs. Molecular Phylogenetics and Evolution 2022;177:107618.
- Hofmann EP, Nicholson KE, Luque-Montes IR et al. Cryptic diversity, but to what extent? Discordance between single-locus species delimitation methods within mainland anoles (Squamata: Dactyloidae) of northern central America. Frontiers in Genetics 2019;10:11.
- Hoogmoed MS. Notes on the herpetofauna of Surinam IV. The lizards and amphisbaenians of Surinam. Biogeographica 1973;4:i-ix + 1-419.
- Hoogmoed MS. The Herpetofauna of the Guiana region. In: Duellman WE (ed.), The South American Herpetofauna: its Origin, Evolution, and Dispersal. Lawrence: Museum of Natural History. University of Kansas Monographs. 1979;7:241-79.
- Hoogmoed MS, Avila-Pires TCS. Observations on the nocturnal activity of lizards in a marshy area in Serra do Navio, Brazil. Tropical Zoology 1989;2:165-73.
- Hoogmoed MS, Lescure J. An annotated checklist of the lizards of French Guiana, mainly based on two recent collections. Zoologische Mededelingen 1975;49:141-71.
- Hurtado-Gomez JP, Arredondo JC, Nunes PMS et al. A new species of Pholidobolus (Squamata: Gymnophthalmidae) from the Paramo ecosystem in the Northern Andes of Colombia. South American Journal of Herpetology 2018;13:271.
- Kapli P, Lutteropp S, Zhang J et al. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 2017;33:1630-8.
- Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution 2013;30:772-80.
- Klaczko J, Ingram T, Losos J. Genitals evolve faster than other traits in Anolis lizards. Journal of Zoology 2015;295:44-8.
- Kearse M, Moir R, Wilson A et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012;28:1647-9. http://www. geneious.com
- Kumar S, Stecher G, Li M et al. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution 2018;35:1547-9.
- Lanna FM, Gehara M, Werneck FP et al. Dwarf geckos and giant rivers:the role of the Sao Francisco River in the evolution of Lygodactylus klugei (Squamata: Gekkonidae) in the semi-arid Caatinga of north-eastern Brazil. Biological Journal of the Linnean Society 2020;129:88-98.
- Leigh JW, Bryant D. PopART: full-feature software for haplotype network construction. Methods in Ecology and Evolution 2015;6:1110-6.
- Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009;25:1451-2.
- Lima AP, Ferrao M, Lacerda da Silva D. Not as widespread as thought: integrative taxonomy reveals cryptic diversity in the Amazonian nurse frog Allobates tinae Melo-Sampaio, Oliveira and Prates, 2018 and description of a new species. Journal of Zoological Systematics and Evolutionary Research 2020;58:1173-94.
- Luo A, Ling C, Ho SY et al. Comparison of methods for molecular species delimitation across a range of speciation scenarios. Systematic Biology 2018;67:830-46.
- Mani GS, Clarke BC. Mutational order: a major stochastic process in evolution. Proceedings of the Royal Society B: Biological Sciences 1990;240:29-37.
- Manzani PR, Abe AS. Sobre dois novos metodos de preparo do hemipenis de serpentes. Memorias do Instituto Butantan (Sao Paulo) 1988;50:15-20.
- Marques-Souza S, Pellegrino KCM, Brunes TO et al. Hidden in the DNA: how multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf-litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae). Journal of Biogeography 2020;47:501-15.
- Mendelson TC, Shaw KL. Genetic and behavioral components of the cryptic species boundary between Laupala cerasina and L. kohalensis (Orthoptera: Gryllidae). Genetica 2002;116:301-10.
- Mendes J, Salvi D, Harris DJ et al. Hidden in the Arabian Mountains: multilocus phylogeny reveals cryptic diversity in the endemic Omanosaura lizards. Journal of Zoological Systematics and Evolutionary Research 2018;56:395-407.
- Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE). New Orleans: IEEE; 2010:1-8.
- Miralles A, Geniez P, Beddek M et al. Morphology and multilocus phylogeny of the spiny-footed lizard (Acanthodactylus erythrurus) complex reveal two new mountain species from the Moroccan Atlas. Zootaxa 2020;4747:zootaxa4747.2.4.
- Nunes PMS, Fouquet A, Curcio FF et al. Cryptic species in Iphisa elegans Gray, 1851 (Squamata: Gymnophthalmidae) revealed by hemipenial morphology and molecular data. Zoological Journal of the Linnean Society 2012;166:361-76.
- Padial JM, De la Riva I. Integrative taxonomy reveals cryptic Amazonian species of Pristimantis (Anura: Strabomantidae). Zoological Journal of the Linnean Society 2009;155:97-122.
- Padial JM, Miralles A, De la Riva I et al. The integrative future of taxonomy. Frontiers in Zoology 2010;7:16.
- Pesantes OS. A method for preparing the hemipenis of preserved snakes. Journal of Herpetology 1994;28:93-5.
- Peters JA, Donoso-Barros R. Catalogue of the Neotropical Squamata pt. II: lizards and amphisbaenians. Bulletin of the United States National Museum 1970;297:1-293.
- Pinho C, Hey J. Divergence with gene flow: models and data. Annual Review of Ecology, Evolution, and Systematics 2010;41:215-30.
- Pons J, Barraclough TG, Gomez-Zurita J et al. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology 2006;55:595-609.
- Pope CH. Copulatory adjustment in snakes. Field Museum of Natural History, Zoological Series 1941;24:249-52.
- Puillandre N, Brouillet S, Achaz G. ASAP: assemble species by automatic partitioning. Molecular Ecology Resources 2021;21:609-20.
- Psonis N, Antoniou A, Kukushkin O et al. Hidden diversity in the Podarcis tauricus (Sauria, Lacertidae) species subgroup in the light of multilocus phylogeny and species delimitation. Molecular Phylogenetics and Evolution 2017;106:6-17.
- R Development Core Team. R: a Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing, 2022. https://www.R-project.org/
- RambautA,DrummondAJ,XieD etal. PosteriorsummarizationinBayesian phylogenetics using Tracer 1.7.Systematic Biology 2018;67:901-4.
- Ratnasingham S, Hebert PD. A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS One 2013;8:e66213.
- Reid NM, Carstens BC. Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evolutionary Biology 2012;12:196-11.
- Ribeiro-Junior MA, Amaral S. Catalogue of distribution of lizards (Reptilia:Squamata) fromtheBrazilianAmazonia.IV.Alopoglossidae, Gymnophthalmidae. Zootaxa 2017;4269:151-96.
- Rodrigues MT, Cassimiro J, De Freitas MA et al. A new microteiid lizard of the genus Acratosaura (Squamata: Gymnophthalmidae) from Serra do Sincora, State of Bahia, Brazil. Zootaxa 2009b;2013:17-29.
- Rodrigues MT, Cassimiro J, Pavan D et al. A new genus of microteiid lizard from the Caparao Mountains, southeastern Brazil, with a discussion of relationships among Gymnophthalminae (Squamata). American Museum Novitates 2009a;2009:1-27.
- Rodrigues MT, Pellegrino KCM, Dixo M et al. A new genus of microteiid lizard from the Atlantic Forests of state of Bahia, Brazil, with a new generic name for Colobosaura mentalis, and a discussion of relationships among the Heterodactylini (Squamata, Gymnophthalmidae). American Museum Novitates 2007;2007:1-27.
- Rojas RR, Chaparro JC, De Carvalho VT et al. Uncovering the diversity in the Amazophrynella minuta complex: integrative taxonomy reveals a new species of Amazophrynella (Anura, Bufonidae) from southern Peru.ZooKeys 2016;563:43-71.
- Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014;30:1312-3.
- Stephens M, Smith NJ, Donnelly P. A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics 2001;68:978-89.
- Sturaro MJ, Avila-Pires TC, Rodrigues MT. Molecular phylogenetic diversity inthewidespreadlizard Cercosauraocellata(Reptilia:Gymnophthalmidae) in South America.Systematics and Biodiversity 2017;15:532-40.
- Sturaro MJ, Rodrigues MT, Colli GR et al. Integrative taxonomy of the lizards Cercosaura ocellata species complex (Reptilia: Gymnophthalmidae). Zoologischer Anzeiger 2018;275:37-65.
- Uzzell T. A revision of lizards of the genus Prionodactylus, with a new genus for P. leucostictus and notes on the genus Euspondylus (Sauria, Teiidae). Postilla 1973;159:1-67.
- Vacher JP, Chave J, Ficetola FG et al. Large-scale DNA-based survey of frogs in Amazonia suggests a vast underestimation of species richness and endemism. Journal of Biogeography 2020;47:1781-91.
- Vacher JP, Kok PJ, Rodrigues MT et al. Cryptic diversity in Amazonian frogs: Integrative taxonomy of the genus Anomaloglossus (Amphibia: Anura: Aromobatidae) reveals a unique case of diversification within the Guiana Shield. Molecular Phylogenetics and Evolution 2017;112:158-73.
- Vaidya G, Lohman DJ, Meier R. SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics 2011;27:171-80.
- Vanzolini PE. Miscellaneous notes on the ecology of some Brasilian lizards (Sauria). Papeis Avulsos de Zoologia 1972;26:83-115.
- VasconcelosR,Montero-MendietaS,Simo-RiudalbasM etal.Unexpectedly high levels of cryptic diversity uncovered by a complete DNA barcoding of reptiles of the Socotra archipelago. PLoS One 2016;11:e0149985.
- Wallace AR. A Narrative of Travels on the Amazon and Rio Negro: with an Account of the Native Tribes, and Observations of the Climate, Geology, and Natural History of the Amazon Valley. London and New York: Ward, Lock, 1889.
- Werneck FP, Gamble T, Colli GR et al. Deep diversification and long-term persistence in the South American 'dry diagonal': integrating continent-wide phylogeography and distribution modeling of geckos. Evolution 2012;66:3014-34.
- Zaher H, Prudente ALC. Hemipenes of Siphlophis (Serpentes, Xenodontinae) and techniques of hemipenial preparation in snakes: a response to Dowling. Herpetological Review 2003;34:302.