Total evidence phylogenetic analysis of Leiosauridae (Squamata) with focus on the ‘para-anoles’ and description of a new Urostrophus species from the Bolivian Andes

References

• Abdala, V., Manzano, A., Nieto, L., & Diogo, R. (2009). Comparative myology of Leiosauridae (Squamata) and its bearing on their phylogenetic relationships. Belgian Journal of Zoology, 139, 109–123.
   Web of Science ®Google Scholar
• Aberer, A. J., Krompass, D., & Stamatakis, A. (2013). Pruning rogue taxa improves phylogenetic accuracy: An efficient algorithm and webservice. Systematic Biology, 62, 162–166. https://doi.org/10.1093/sysbio/sys078
   PubMed Web of Science ®Google Scholar
• Aberer, A. J., & Stamatakis, A. (2011). A simple and accurate method for rogue taxon identification. In F. X. Wu, M. J. Zaki, S. Morishita, Y. Pan, S. Wong, A. Christianson, & X. Hu (Eds.), IEEE International Conference on Bioinformatics and Biomedicine. Atlanta, GA, 12–15 November, 2011 (pp. 118–122) IEEE Computer Society.
   Google Scholar
• Alonso, L. E., Deichmann, J. L., McKenna, S. A., Naskrecki, P., & Richards, S. J. (2011). Still counting…: biodiversity exploration for conservation—The first 20 years of the Rapid Assessment Program. Conservation International.
   Google Scholar
• Bell, T. (1843). Reptiles. In C. Darwin (Ed.), The zoology of the voyage of the H.M.S. Beagle, under the command of Captain Fitzroy, R.N., during the years 1832 to 1836 (Vol. 5, pp. 1–51) Smith, Elder and Co.
   Google Scholar
• Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120. https://doi.org/10.1093/bioinformatics/btu170
   PubMed Web of Science ®Google Scholar
• Boulenger, G. A. (1885). A list of reptiles and batrachians from the Province Rio Grande do Sul, Brazil, sent to the Natural-History Museum by Dr. H. von Ihering. Annals and Magazine of Natural History Series 5, 15, 191–196. https://doi.org/10.1080/00222938509459318
   Google Scholar
• Boulenger, G. A. (1885). Second list of reptiles and batrachians from the province Rio Grande do Sul, sent to the Natural History Museum by Dr. H. van Ihering. Annals and Magazine of Natural History Series 5, 16, 85–88. https://doi.org/10.1080/00222938509459848
   Google Scholar
• Boulenger, G. A. (1885). Catalogue of the lizards in the British Museum (Natural History). Iguanidae, Xenosauridae, Zonuridae, Anguidae, Anniellidae, Helodermatidae, Varanidae, Xantusiidae, Teiidae, Amphisbaenidae (2nd ed., Vol. 2). Taylor and Francis.
   Google Scholar
• Boulenger, G. A. (1891a). Description of a new genus of Iguanoid lizards. Annals and Magazine of Natural History, Series 6, 8, 85–86. https://doi.org/10.1080/00222939109460394
   Google Scholar
• Boulenger, G. A. (1891b). Description of a new Iguanoid lizard of the genus Anisolepis. Annali Del Museo Civico di Storia Naturale di Genova Series 2, 10, 909.
   Google Scholar
• Breitman, M. F., Domingos, F. M., Bagley, J. C., Wiederhecker, H. C., Ferrari, T. B., Cavalcante, V. H., Pereira, A. C., Abreu, T. L., De-Lima, A. K. S., Morais, C. J., Prette, A. C. D., Silva, I. P., Mello, R. D., Carvalho, G., Lima, T. M., Silva, A. A., Matias, C. A., Carvalho, G. C., Pantoja, J. A., … Colli, G. R. (2018). A new species of Enyalius (Squamata, Leiosauridae) endemic to the Brazilian Cerrado. Herpetologica, 74, 355–369. https://doi.org/10.1655/0018-0831.355
   Web of Science ®Google Scholar
• Britten, R. J., Rowen, L., Williams, J., & Cameron, R. A. (2003). Majority of divergence between closely related DNA samples is due to indels. Proceedings of the National Academy of Sciences of the United States of America, 100, 4661–4665. https://doi.org/10.1073/pnas.0330964100
   PubMed Web of Science ®Google Scholar
• Burmeister, H. (1861). Reise durch die La Plata-Staaten mit besonderer Rücksicht auf die Physische Beschaffenheit und den Culturzustand der Argentinische Republik. Ausgefuhrt in den Jahren 1857, 1858, 1859 und 1860 (Vol. 2). H.W. Schmidt.
   Google Scholar
• Callender-Crowe, L. M., & Sansom, R. (2022). Osteological characters of birds and reptiles are more congruent with molecular phylogenies than soft characters are. Zoological Journal of the Linnean Society, 194, 1–13. https://doi.org/10.1093/zoolinnean/zlaa136
   Web of Science ®Google Scholar
• Carvalho, A. L. G., Sena, M. A., Peloso, P. L. V., Machado, F. A., Montesinos, R., Silva, H. R., Campbell, G., & Rodrigues, M. T. (2016). A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: Evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstructions of South American collared lizards. American Museum Novitates, 3852, 1–68. https://doi.org/10.1206/3852.1
   Google Scholar
• Carvalho, A. L. G., Rivas, L. R., Céspedes, R., & Rodrigues, M. T. (2018). A new collared lizard (Tropidurus: Tropiduridae) endemic to the Western Bolivian Andes and its implications for seasonally dry tropical forests. American Museum Novitates, 3896, 1–56. https://doi.org/10.1206/3896.1
   Google Scholar
• Cei, J. M. (1993). Reptiles del noroeste, nordeste y este de la Argentina. Monografia XIV. Museo Regionale di Scienze Naturale.
   Google Scholar
• Cei, J. M., Scolaro, J. A., & Videla, F. (2001). The present status of Argentinean polychrotid species of the genus Pristidactylus and description of its southernmost taxon as a new species. Journal of Herpetology, 35, 597–605. https://doi.org/10.2307/1565897
   Web of Science ®Google Scholar
• Cei, J. M., Scolaro, J. A., & Videla, F. (2003). A taxonomic revision of recognized Argentine species of the leiosaurid genus Diplolaemus (Reptilia, Squamata, Leiosauridae). Facena, 19, 137–155.
   Google Scholar
• Cei, J. M., Scolaro, J. A., & Videla, F. (2004). An updated biosystematics approach to the leiosaurid genus Pristidactylus. Bollettino Museo Regionale di Scienze Naturale, Torino, 21, 159–192.
   Google Scholar
• Chifman, J., & Kubatko, L. (2014). Quartet inference from SNP data under the coalescent model. Bioinformatics (Oxford, England), 30, 3317–3324. https://doi.org/10.1093/bioinformatics/btu530
   PubMed Web of Science ®Google Scholar
• Chifman, J., & Kubatko, L. (2015). Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites. Journal of Theoretical Biology, 374, 35–47. https://doi.org/10.1016/j.jtbi.2015.03.006
   PubMed Web of Science ®Google Scholar
• Cope, E. D. (1864). On the characters of the higher groups of Reptilia Squamata—and especially of the Diploglossa. Proceedings of the Academy of Natural Sciences of Philadelphia, 16, 224–231.
   Google Scholar
• Crispieri, G. A. G., Fontúrbel, F. E., & Richard, E. (2009). Plan de manejo del Área Natural de Manejo Integrado Torotoro 2006–2016. Ecodreams Multimedia – Fundación Emegece.
   Google Scholar
• Cuvier, L. C. F. D. G. (1817). Le règne animal, distribué d‘après son organisation, pour servir de base a l‘histoire naturelle des animaux et d‘introduction a l‘anatomie comparee. Chez Déterville.
   Google Scholar
• Daudin, F. M. (1802). Histoire naturelle, générale et particulière des reptiles (Vol. 4). F. Dufart.
   Google Scholar
• D’Angiolella, A. B., Klaczko, J., Rodrigues, M. T., & Ávila-Pires, T. C. S. (2016). Hemipenial morphology and diversity in South American anoles (Squamata: Dactyloidae). Canadian Journal of Zoology, 94, 251–256. https://doi.org/10.1139/cjz-2015-0194
   Google Scholar
• Denton, J. S. S., & Wheeler, W. C. (2012). Indel information eliminates trivial sequence alignment in maximum likelihood phylogenetic analysis. Cladistics: The International Journal of the Willi Hennig Society, 28, 514–528. https://doi.org/10.1111/j.1096-0031.2012.00402.x
   PubMed Web of Science ®Google Scholar
• de Queiroz, K., & Gauthier, J. (1992). Phylogenetic taxonomy. Annual Review of Ecology and Systematics, 23, 449–480. https://doi.org/10.1146/annurev.es.23.110192.002313
   Google Scholar
• de Queiroz, A., & Gatesy, J. (2007). The supermatrix approach to systematics. Trends in Ecology & Evolution, 22, 34–41. https://doi.org/10.1016/j.tree.2006.10.002
   PubMed Web of Science ®Google Scholar
• de Queiroz, K., & Poe, S. (2001). Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper’s writings on corroboration. Systematic Biology, 50, 305–321. https://doi.org/10.1080/106351501300317941
   PubMed Web of Science ®Google Scholar
• Donoso-Barros, R. (1966). Reptiles de Chile. Ediciones de la Universidad de Chile Santiago.
   Google Scholar
• Donoso-Barros, R. (1975). Nuevos reptiles y anfibios de Chile. Boletin de la Sociedad de Biología de Concepción, 48, 217–229.
   Google Scholar
• d’Orbigny, A. (1937). Leiosaurus fasciatus. In A. M. C. Duméril & G. Bibron (Eds.), Erpétologie genérale ou histoire naturelle complète des reptiles. Histoire de quarante-six genres et de cent quarante-six espèces de la famille des Iguaniens, de l‘ordre des sauriens (Vol. 4, pp. 244–246.) Librarie Enclyclopedique de Roret.
   Google Scholar
• Duméril, A. M. C., & Bibron, G. (1837). Erpétologie genérale ou histoire naturelle complète des reptiles. Histoire de quarante-six genres et de cent quarante-six espèces de la famille des Iguaniens, de l‘ordre des sauriens (Vol. 4). Librarie Enclyclopedique de Roret.
   Google Scholar
• Echevarría, L. Y., De la Riva, I., Venegas, P. J., Rojas-Runjaic, F. J. M., Dias, I. R., & Castroviejo-Fisher, S. (2021). Total evidence and sensitivity phylogenetic analyses of egg-brooding frogs (Anura: Hemiphractidae). Cladistics: The International Journal of the Willi Hennig Society, 37, 375–401. https://doi.org/10.1111/cla.12447
   PubMed Web of Science ®Google Scholar
• Edwards, S. V., Xi, Z., Janke, A., Faircloth, B. C., McCormack, J. E., Glenn, T. C., Zhong, B., Wu, S., Lemmon, E. M., Lemmon, A. R., Leaché, A. D., Liu, L., & Davis, C. C. (2016). Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. Molecular Phylogenetics and Evolution, 94, 447–462. https://doi.org/10.1016/j.ympev.2015.10.027
   PubMed Web of Science ®Google Scholar
• Eernisse, D. J., & Kluge, A. G. (1993). Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Molecular Biology and Evolution, 10, 1170–1195.
   PubMed Web of Science ®Google Scholar
• Eriksson, N. (2005). Tree construction using singular value decomposition. In L. Pachter & B. Sturmfels (Eds.), Algebraic statistics for computational biology (pp. 347–358). Cambridge University Press.
   Google Scholar
• Etheridge, R. (1969). A review of the iguanid lizard genus Enyalius. Bulletin of the British Museum (Natural History), 18, 233–260. https://doi.org/10.5962/bhl.part.18421
   Google Scholar
• Etheridge, R. E. (1993). Lizards of the Liolaemus darwinii complex (Squamata: Iguania: Tropiduridae) in Northern Argentina. Bollettino Museo Regionale di Scienze Naturale, Torino, 11, 137–199.
   Google Scholar
• Etheridge, R. E., & de Queiroz, K. (1988). A phylogeny of Iguanidae. In R. D. Estes RD & G. K. Pregill (Eds.), Phylogenetic relationships of the lizard families: Essays commemorating Charles L. Camp (pp. 631–631). Stanford University Press.
   Google Scholar
• Etheridge, R. E., & Williams, E. E. (1985). Notes on Pristidactylus (Squamata: Iguanidae). Breviora, 483, 1–18.
   Google Scholar
• Etheridge, R. E., & Williams, E. E. (1991). A review of the South American lizard genera Urostrophus and Anisolepis (Squamata: Iguania: Polychridae). Bulletin of the Museum of Comparative Zoology, 152, 317–361.
   Google Scholar
• Faircloth, B. C. (2013). Illumiprocessor: A Trimmomatic wrapper for parallel adapter and quality trimming [Computer software]. Retreived 2020–2021 from https://doi.org/10.6079/J9ILL.
   Google Scholar
• Faircloth, B. C. (2016). PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics (Oxford, England), 32, 786–788. https://doi.org/10.1093/bioinformatics/btv646
   PubMed Web of Science ®Google Scholar
• Farris, J. S. (2008). Parsimony and explanatory power. Cladistics, 24, 825–847. https://doi.org/10.1111/j.1096-0031.2008.00214.x
   Web of Science ®Google Scholar
• Felsenstein, J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution; International Journal of Organic Evolution, 39, 783–791. https://doi.org/10.2307/2408678
   PubMed Web of Science ®Google Scholar
• Felsenstein, J. (2004). Inferring phylogenies. Sinauer Associates.
   Google Scholar
• Femenias, M. M., Avila, L. J., Sites, J. W., Jr., & Morando, M. (2020). The enigmatic Leiosaurae clade: Phylogeography, species delimitation, phylogeny and historical biogeography of its southernmost species. Molecular Phylogenetics and Evolution, 144, 106725. https://doi.org/10.1016/j.ympev.2019.106725
   PubMed Web of Science ®Google Scholar
• Fitzhugh, K. (2012). The limits of understanding in biological systematics. Zootaxa, 3435, 40–67. https://doi.org/10.11646/zootaxa.3435.1.2
   Google Scholar
• Fitzinger, L. J. F. J. (1843). Systema Reptilium. Fasciculus Primus. Braumüller et Seidel.
   Google Scholar
• Frost, D. R., & Etheridge, R. E. (1989). A phylogenetic analysis and taxonomy of Iguanian lizards (Reptilia: Squamata). Miscellaneous Publication – University of Kansas, Natural History Museum, 81, 1–65.
   Google Scholar
• Frost, D. R., Etheridge, R. E., Janies, D., & Titus, T. A. (2001). Total evidence, sequence alignment, evolution of polychrotid lizards, and a reclassification of the Iguania (Squamata: Iguania). American Museum Novitates, 3343, 1–39. https://doi.org/10.1206/0003-0082(2001)343<0001:TESAEO>2.0.CO;2
   Google Scholar
• Gallardo, J. M. (1964). Los géneros Urostrophus D. et B. y Cupriguanus gen. nov. (Sauria, Iguanidae) y sus especies. Neotropica, 10, 125–136.
   Google Scholar
• Gallardo, J. M. (1968). Dos nuevas especies de Iguanidae (Sauria) de la Argentina. Neotropica, 14, 1–8.
   Google Scholar
• Gasparini, J. L., Koski, D. A., & Peloso, P. L. V. (2010). Reptilia, Squamata, Leiosauridae, Urostrophus vautieri Duméril and Bibron, 1837: Distribution extension, new state record, and geographic distribution map. Check List, 6, 432–433. https://doi.org/10.15560/6.3.432
   Google Scholar
• Giribet, G., & Wheeler, W. (1999). On gaps. Molecular Phylogenetics and Evolution, 13, 132–143. https://doi.org/10.1006/mpev.1999.0643
   PubMed Web of Science ®Google Scholar
• Goloboff, P. A. (1999). Analyzing large data sets in reasonable times: Solutions for composite optima. Cladistics : The International Journal of the Willi Hennig Society, 15, 415–428. https://doi.org/10.1111/j.1096-0031.1999.tb00278.x
   PubMed Web of Science ®Google Scholar
• Goloboff, P. A., Farris, S., Nixon, K. (2000). TNT (Tree analysis using New Technology) (BETA) [Computer software]. http://www.lillo.org.ar/phylogeny/tnt/ Published by the authors.
   Google Scholar
• Goloboff, P. A., Farris, J. S., & Nixon, K. C. (2008). TNT, a free program for phylogenetic analysis. Cladistics, 24, 774–786. https://doi.org/10.1111/j.1096-0031.2008.00217.x
   Web of Science ®Google Scholar
• Goloboff, P. A., Mattoni, C. I., & Quinteros, A. S. (2006). Continuous characters analyzed as such. Cladistics: The International Journal of the Willi Hennig Society, 22, 589–601. https://doi.org/10.1111/j.1096-0031.2006.00122.x
   PubMed Web of Science ®Google Scholar
• Gonzales, L., Embert, D., & Montaño, R. R. (2004). Reptiles. In H. Azurduy, J. L. Aramayo, & M. J. Ledezma (Eds.), Historia natural del Municipio de Pampagrande. Una localidad típica de los valles interandinos de Bolivia (pp. 173–183). Museo de Historia Natural Noel Kempff Mercado, Universidad Autónoma Gabriel René Moren.
   Google Scholar
• Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B. W., Nusbaum, C., Lindblad-Toh, K., Friedman, N., & Regev, A. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29, 644–652. https://doi.org/10.1038/nbt.1883
   PubMed Web of Science ®Google Scholar
• Grant, T. (2019). Outgroup sampling in phylogenetics: severity of test and successive outgroup expansion. Journal of Zoological Systematics and Evolutionary Research, 57, 748–763. https://doi.org/10.1111/jzs.12317
   Web of Science ®Google Scholar
• Grant, T. (2002). Testing methods: The evaluation of discovery operations in evolutionary biology. Cladistics, 18, 94–111. https://doi.org/10.1111/j.1096-0031.2002.tb00142.x
   Web of Science ®Google Scholar
• Gray, J. E. (1831). A synopsis of the species of the Class Reptilia. In E. Griffith (Ed.), The Animal Kingdom arranged in conformity with its organization, by the Baron Cuvier, with additional descriptions of all the species hitherto named, and of many not before noticed by Edward Griffith (Vol. 9, pp. 1–110). Treacher, and Co.
   Google Scholar
• Green, M. R., & Sambrook, J. (2017). Isolation of high-molecular-weight DNA using organic solvents. Cold Spring Harbor Protocols, 4, pdb.prot093450.
   Google Scholar
• Guichenot, A. (1855). Reptiles. In F. de Castelnau (Ed.), Animaux nouveaux ou rares recueillis pendant l‘expédition dans les parties centrales de l‘Amérique du Sud, de Rio de Janeiro à Lima, et de Lima au Para; Exécutée par ordre du Gouvernement Français pendant les années 1843 à 1847, sous la direction de Francis de Castelnau (Part VII, Vol. 2). P. Bertrand.
   Google Scholar
• Hinchliff, C. E., & Smith, S. A. (2014). Some limitations of public sequence data for phylogenetic inference (in Plants). Public Library of Science One, 9, e98986. https://doi.org/10.1371/journal.pone.0098986
   Google Scholar
• Hołyński, R. B. (2005). Philosophy of science from a taxonomist’s perspective. Genus, 16, 469–502.
   Google Scholar
• IUCN. (2012). IUCN red list categories and criteria (Version 3.1, 2nd ed.). International Union for Conservation of Nature.
   Google Scholar
• Jackson, J. F. (1978). Differentiation in the genera Enyalius and Strobilurus (Iguanidae): Implications for Pleistocene climatic changes in eastern Brazil. Arquivos de Zoologia, 30, 1–79.
   Google Scholar
• Jiang, T., Kearney, P. E., & Li, M. (2001). A polynomial time approximation scheme for inferring evolutionary trees from quartet topologies and its application. SIAM Journal on Computing, 30, 1942–1961. https://doi.org/10.1137/S0097539799361683
   Web of Science ®Google Scholar
• Katoh, K., & Toh, H. (2008). Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics, 9, 286–298. https://doi.org/10.1093/bib/bbn013
   PubMed Web of Science ®Google Scholar
• Kluge, A. G. (1989). A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Systematic Zoology, 38, 7–25. https://doi.org/10.2307/2992432
   Google Scholar
• Kluge, A. G. (1997). Testability and the refutation and corroboration of cladistics hypothesis. Cladistics: The International Journal of the Willi Hennig Society, 13, 81–96. https://doi.org/10.1111/j.1096-0031.1997.tb00242.x
   PubMed Web of Science ®Google Scholar
• Kluge, A. G. (1998). Total evidence or taxonomic congruence: cladistics or consensus classification. Cladistics: The International Journal of the Willi Hennig Society, 14, 151–158. https://doi.org/10.1111/j.1096-0031.1998.tb00328.x
   PubMed Web of Science ®Google Scholar
• Kluge, A. G., & Grant, T. (2006). From conviction to anti-superfluity: old and new justifications of parsimony in phylogenetic inference. Cladistics, 22, 276–288. https://doi.org/10.1111/j.1096-0031.2006.00100.x
   Web of Science ®Google Scholar
• Koslowsky, J. (1898). Enumeración sistemática y distribución geográfica de los reptiles argentinos. Revista Del Museo de La Plata, 8, 161–200.
   Google Scholar
• Kozlov, A. M., Darriba, D., Flouri, T., Morel, B., & Stamatakis, A. (2019). RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics (Oxford, England), 35, 4453–4455. https://doi.org/10.1093/bioinformatics/btz305
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Labra, M. A., & Rosenmann, M. (1994). Energy metabolism and evaporative water loss of Pristidactylus lizards. Comparative Biochemistry and Physiology Part A: Physiology, 109, 369–376. https://doi.org/10.1016/0300-9629(94)90140-6
   Web of Science ®Google Scholar
• Lamborot, M., & Díaz, N. F. (1987). A new species of Pristidactylus (Sauria: Iguanidae) from central Chile and comments on the speciation in the genus. Journal of Herpetology, 21, 29–37. https://doi.org/10.2307/1564374
   Web of Science ®Google Scholar
• Lanfear, R., Calcott, B., Ho, S. Y. W., & Guindon, S. (2012). PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution, 29, 1695–1701. https://doi.org/10.1093/molbev/mss020
   PubMed Web of Science ®Google Scholar
• Langmead, B., & Salzberg, S. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357–359. https://doi.org/10.1038/nmeth.1923
   PubMed Web of Science ®Google Scholar
• Langstroth, R. P. (2005). Adiciones probables y confirmadas para la saurofauna boliviana. Kempffiana, 1, 101–128.
   Google Scholar
• Laspiur, J. A. (2016). Sistemática de las lagartijas de la subfamilia Leiosaurinae: Filogenia y biogeografía histórica. [Unpublished doctoral dissertation]. Universidad Nacional de Río Cuarto.
   Google Scholar
• Laspiur, A., Acosta, J. C., & Abdala, C. S. (2007). A new species of Leiosaurus (Iguania: Leiosauridae) from central-western Argentina. Zootaxa, 1470, 47–57. https://doi.org/10.11646/zootaxa.1470.1.3
   Google Scholar
• Lesson, R.-P. (1830). Observations générales sur les reptiles recueillis dan la voyage de la corvette La Coquille. In L. I. Duperrey (Ed.), Voyage autour du Monde, exécuté par Ordre du Roi, sur la Corvette de sa Majesté, La Coquille, pendant les années 1822, 1823, 1824, 1825 (Vol. 2, Tome 2, Partie 1, Chapt. 9, Livraison 17, pp. 1–66). Arthur Bertrand.
   Google Scholar
• Linnaeus, C. (1758). Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis (Tomus I, Editio decima, reformata). Laurentii Salvii.
   Google Scholar
• Long, C. L., & Kubatko, L. S. (2019). Identifiability and reconstructibility of species phylogenies under a modified coalescent. Bulletin of Mathematical Biology, 81, 408–430. https://doi.org/10.1007/s11538-018-0456-9
   PubMed Web of Science ®Google Scholar
• Maiolo, M., Zhang, X., Gil, M., & Anisimova, M. (2018). Progressive multiple sequence alignment with indel evolution. BioMedCentral Bioinformatics, 19, 331. https://doi.org/10.1186/s12859-018-2357-1
   PubMed Web of Science ®Google Scholar
• Morando, M., Olave, M., Avila, L. J., Baker, E., & Sites, J. W. Jr. (2015). Molecular phylogeny of the lizard clade Leiosaurae endemic to Southern South America. Herpetologica, 71, 322–331. https://doi.org/10.1655/HERPETOLOGICA-D-14-00067
   Web of Science ®Google Scholar
• Navarro, G. (2011). Clasificación de la vegetación en Bolivia. Centro de Ecología Difusión, Fundación Simón I. Patiño.
   Google Scholar
• Navarro, G., & Maldonado, M. (2002). Geografía ecológica de Bolivia: Vegetación y ambientes acuáticos. Centro de Ecología Difusión, Fundación Simón I. Patiño.
   Google Scholar
• Nixon, K. C. (1999). The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics : The International Journal of the Willi Hennig Society, 15, 407–414. https://doi.org/10.1111/j.1096-0031.1999.tb00277.x
   PubMed Web of Science ®Google Scholar
• Nixon, K. C., & Carpenter, J. M. (1993). On outgroups. Cladistics : The International Journal of the Willi Hennig Society, 9, 413–426. https://doi.org/10.1111/j.1096-0031.1993.tb00234.x
   PubMed Web of Science ®Google Scholar
• Nute, M., Chou, J., Molloy, E. K., & Warnow, T. (2018). The performance of coalescent-based species tree estimation methods under models of missing data. BioMedCentral Genomics, 19, 286. https://doi.org/10.1186/s12864-018-4619-8
   PubMed Web of Science ®Google Scholar
• Olson, D. M., Dinerstein, E., Wikramanayake, E. D., Burgess, N. D., Powell, G. V. N., Underwood, E. C., D’Amico, J. A., Itoua, I., Strand, H. E., Morrison, J. C., Loucks, C. J., Allnutt, T. F., Ricketts, T. H., Kura, Y., Lamoreux, J. F., Wettengel, W. W., Hedao, P., & Kassem, K. R. (2001). Terrestrial ecoregions of the world: a new map of life on Earth: A new global map of terrestrial ecoregions provides an innovative tool for conserving biodiversity. BioScience, 51, 933–938. https://doi.org/10.1641/0006-3568(2001)051[0933:TEOTWA2.0.CO;2]
   Web of Science ®Google Scholar
• Padial, J. M., Grant, T., & Frost, D. R. (2014). Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria. Zootaxa, 3825, 1–132. https://doi.org/10.11646/zootaxa.3825.1.1
   PubMed Web of Science ®Google Scholar
• Pattengale, N. D., Aberer, A. J., Swenson, K. M., Stamatakis, A., & Moret, B. M. (2011). Uncovering hidden phylogenetic consensus in large data sets. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8, 902–911. https://doi.org/10.1109/TCBB.2011.28
   PubMed Web of Science ®Google Scholar
• Pease, J. B., Brown, J. W., Walker, J. F., Hinchliff, C. E., & Smith, S. A. (2018). Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life. American Journal of Botany, 105, 385–403. https://doi.org/10.1002/ajb2.1016
   PubMed Web of Science ®Google Scholar
• Peloso, P. L. V., Frost, D. R., Richards, S. J., Rodrigues, M. T., Donnellan, S., Matsui, M., Raxworthy, C. J., Biju, S. D., Lemmon, E. M., Lemmon, A. R., & Wheeler, W. (2016). The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow-mouthed frogs (Anura, Microhylidae). Cladistics: The International Journal of the Willi Hennig Society, 32, 113–140. https://doi.org/10.1111/cla.12118
   PubMed Web of Science ®Google Scholar
• Peracca, M. G. (1897). Intorno ad un nuovo genere di Iguanide del Brasil. Bollettino Dei Musei di Zoologia ed Anatomia Comparata Della R. Università di Torino, 12, 1–20. https://doi.org/10.5962/bhl.part.4563
   Google Scholar
• Peters, W. C. H. (1854). Diagnosen neuer Batrachier, welche zusammen mit der früher (24. Juli und 17. August) gegebenen Übersicht der Schlangen und Eidechsen mitgetheilt weden. Monatsberichte Der Königlichen Preussische Akademie Des Wissenschaften zu Berlin, 1854, 614–628.
   Google Scholar
• Philippe, H., Brinkmann, H., Lavrov, D. V., Littlewood, D. T. J., Manuel, M., Wörheide, G., & Baurain, D. (2011). Resolving difficult phylogenetic questions: why more sequences are not enough. Public Library of Science Biology, 9, e1000602. https://doi.org/10.1371/journal.pbio.1000602
   Google Scholar
• Philippi, R. A., & Landbeck, L. (1861). Neue Wirbthiere von Chile. Archiv Für Naturgeschichte, 27, 289–301. https://doi.org/10.5962/bhl.part.19153
   Google Scholar
• Pyron, R. A., Burbrink, F. T., & Wiens, J. J. (2013). A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BioMedCentral Evolutionary Biology, 13, 93. https://doi.org/10.1186/1471-2148-13-93
   Google Scholar
• Rannala, B., Edwards, S., Leaché, A., & Yang, Z. (2020). The multi-species coalescent model and species tree inference. In C. Scornavacca, F. Delsuc, & N. Galtier (Eds.), Phylogenetics in the genomic era. No commercial publisher. Authors open access book. 3.3:1–3.3:21.
   Google Scholar
• Reaz, R., Bayzid, M. S., & Rahman, M. S. (2014). Accurate phylogenetic tree reconstruction from quartets: A heuristic approach. Public Library of Science One, 9, e104008. https://doi.org/10.1371/journal.pone.0104008
   Google Scholar
• Reeder, T. W., Townsend, T. M., Mulcahy, D. G., Noonan, B. P., Wood, P. L., Sites, J. W., Jr., & Wiens, J. J. (2015). Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa. Public Library of Science One, 10, e0118199–22. https://doi.org/10.1371/journal.pone.0118199
   Google Scholar
• Rivas, L. R., Mendoza-Miranda, P., & Muñoz-Saravia, A. (2018). Lista preliminar de la herpetofauna del Parque Nacional Torotoro, Potosí, Bolivia. Cuadernos de Herpetología, 32, 41–46. https://doi.org/10.31017/CdH.2018.(2017-23)
   Google Scholar
• Rieppel, O. (2008). Hypothetico-deductivism in systematics: fact or fiction? Papéis Avulsos de Zoologia, 48, 263–273. https://doi.org/10.1590/S0031-10492008002300001
   Google Scholar
• Rodrigues, M. T., Bertolotto, C. E. V., Amaro, R. C., Yonenaga-Yassuda, Y., Freire, E. M. X., & Pellegrino, K. C. M. (2014). Molecular phylogeny, species limits, and biogeography of the Brazilian endemic lizard genus Enyalius (Squamata: Leiosauridae): An example of the historical relationship between Atlantic Forests and Amazonia. Molecular Phylogenetics and Evolution, 81, 137–146. https://doi.org/10.1016/j.ympev.2014.07.019
   PubMed Web of Science ®Google Scholar
• Rodrigues, M. T., Freitas, M. A., Silva, T. F. S., & Bertolotto, C. E. V. (2006). A new species of lizard genus Enyalius (Squamata, Leiosauridae) from the highlands of Chapada Diamantina, State of Bahia, Brazil, with a key to species. Phyllomedusa: Journal of Herpetology, 5, 11–24. https://doi.org/10.11606/issn.2316-9079.v5i1p11-24
   Google Scholar
• Santos, R. C., Lucas, P. S., Sousa, B. M., & Novelli, I. A. (2009). Reptilia, Squamata, Leiosauridae, Urostrophus vautieri: distribution extension and geographic distribution map. Check List, 5, 533–536. https://doi.org/10.15560/5.3.533
   Google Scholar
• Schinz, H. R. (1822). Das Thierreich eingetheilt nach dem Bau der Thiere als Grundlage ihrer Naturgeschichte und der vergleichenden Anatomie von dem Herrn Ritter von Cuvier (Vol. 2). J.G. Cotta.
   Google Scholar
• Schmidt, K. P. (1921). Notes on the herpetology of Santo Domingo. Bulletin of the American Museum of Natural History, 44, 7–20.
   Google Scholar
• Schulte, J. A., II., & Cartwright, E. M. (2009). Phylogenetic relationships among iguanian lizards using alternative partitioning methods and TSHZ1: A new phylogenetic marker for reptiles. Molecular Phylogenetics and Evolution, 50, 391–396. https://doi.org/10.1016/j.ympev.2008.10.018
   PubMed Web of Science ®Google Scholar
• Schulte, J. A., II., Valladares, J. P., & Larson, A. (2003). Phylogenetic relationships within Iguanidae inferred using molecular and morphological data and a phylogenetic taxonomy of Iguanid lizards. Herpetologica, 59, 399–419. https://doi.org/10.1655/02-48
   Web of Science ®Google Scholar
• Siddall, M. E., & Kluge, A. G. (1997). Probabilism and Phylogenetic Inference. Cladistics: The International Journal of the Willi Hennig Society, 13, 313–336. https://doi.org/10.1111/j.1096-0031.1997.tb00322.x
   PubMed Web of Science ®Google Scholar
• Simmons, M. P., & Goloboff, P. A. (2014). Dubious resolution and support from published sparse supermatrices: The importance of through tree searches. Molecular Phylogenetics and Evolution, 78, 334–348. https://doi.org/10.1016/j.ympev.2014.06.002
   PubMed Web of Science ®Google Scholar
• Simmons, M. P., & Ochoterena, H. (2000). Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology, 49, 369–381. https://doi.org/10.1093/sysbio/49.2.369
   PubMed Web of Science ®Google Scholar
• Sober, E. (2004). The contest between parsimony and likelihood. Systematic Biology, 53, 644–653. https://doi.org/10.1080/10635150490468657
   PubMed Web of Science ®Google Scholar
• Spix, J. v. (1825). Animalia nova sive species nova lacertarum quas in itinere per Brasiliam annis MDCCCXVII-MDCCCXX jussu et auspicius Maximiliani Josephi I Bavariae Regis suscepto collegit et descripsit Dr. J. B. de Spix. Typis Franc. Seraph. Hübschmanni.
   Google Scholar
• Streicher, J. W., Schulte, J. A., II., & Wiens, J. J. (2016). How should genes and taxa be sampled for phylogenomic analyses with missing data? An empirical study in Iguanian lizards. Systematic Biology, 65, 128–145. https://doi.org/10.1093/sysbio/syv058
   PubMed Web of Science ®Google Scholar
• Sukumaran, J., & Holder, M. T. (2010). DendroPy: A Python library for phylogenetic computing. Bioinformatics, 26, 1569–1571. https://doi.org/10.1093/bioinformatics/btq228
   PubMed Web of Science ®Google Scholar
• Swofford, D. L. (2003). PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates.
   Google Scholar
• Swofford, D. L., Olsen, G. J., Waddell, P. J., & Hillis, D. M. (1996). Phylogenetic inference. In D. M. Hillis, C. Moritz, & B. K. Mable (Eds.), Molecular systematics (2nd ed., pp. 407–514). Sinauer Associates.
   Google Scholar
• Tedesco, M. E., Hernando, A., & Álvarez, B. B. (1992). Urostrophus gallardoi (Iguania, Polychridae). Nuevas localidades para Argentina. Facena, 9, 111–115.
   Google Scholar
• Townsend, T. M., Mulcahy, D. G., Noonan, B. P., Sites, J. W., Jr., Kuczynski, C. A., Wiens, J. J., & Reeder, T. W. (2011). Phylogeny of Iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation. Molecular Phylogenetics and Evolution, 61, 363–380. https://doi.org/10.1016/j.ympev.2011.07.008
   PubMed Web of Science ®Google Scholar
• Vaidya, G., Lohman, D. J., & Meier, R. (2011). SequenceMatrix: concatenation software for the fast assembly of multi-gene dataset with character set and codon information. Cladistics: The International Journal of the Willi Hennig Society, 27, 171–180. https://doi.org/10.1111/j.1096-0031.2010.00329.x
   PubMed Web of Science ®Google Scholar
• Vargas, S. M., Santos, M. D. O., Novelli, I. A., Varela-Rios, C. H., Lima, L. M. C., Lucas, P. D. S., Cozendey, P., Paiva, R. M., Gomides, S. C., Malaguti, S., & Sousa, B. M. (2015). Genetic diversity and structure of two species of Enyalius (Squamata: Leiosauridae) from Neotropical biodiversity hotspots. Phyllomedusa: Journal of Herpetology, 14, 99–111. https://doi.org/10.11606/issn.2316-9079.v14i2p99-111
   Google Scholar
• Vences, M., Guayasamin, J. M., Miralles, A., & De la Riva, I. (2013). To name or not to name: Criteria to promote economy of change in Linnaean classification schemes. Zootaxa, 3636, 201–244. https://doi.org/10.11646/zootaxa.3636.2.1
   PubMed Web of Science ®Google Scholar
• Xia, X. (2009). Assessing substitution saturation with DAMBE. In P. Lemey, M. Salemi, A-M. Vandamme (Eds.), The Phylogenetic Handbook. A practical approach to phylogenetic analysis and hypothesis testing (2nd ed., pp. 615–623). Cambridge University Press.
   Google Scholar
• Wagler, J. (1830). Natürliches System der Amphibien, mit vorangehender Classification der Säugthiere und Vogel. Ein Beitrag zur vergleichenden Zoologie. J. G. Cotta.
   Google Scholar
• Werner, F. (1898). Die Reptilien und Batrachier der Sammlung Plate. Zoologische Jahrbücher. Abteilung Für Systematik, Geographie Und Biologie Der Tiere, 4, 244–278.
   Google Scholar
• Wied, M. A. P. p v N. (1821). Reise nach Brasilien in den Jahren 1815 bis 1817. (Vol. 2). Henrich Ludwig Brönner.
   Google Scholar
• Wiegmann, A. F. A. (1834). Herpetologica Mexicana seu descriptio amphibiorum Novae Hispaniae quae itineribus comitis de Sack. Ferdinandi Deppe et Chr. Guil. Schiede in Museum Zoologicum Berolinense pervenerunt. Pars prima, Saurorum species amplectens, adiecto Systematis Saurorum Prodromo, additisque multis in hunc amphibiorum ordinem observationibus. Lüderitz.
   Google Scholar
• Wiens, J. J., Hutter, C. R., Mulcahy, D. G., Noonan, B. P., Townsend, T. M., Sites, J. W., Jr., & Reeder, T. W. (2012). Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species. Biology Letters, 8, 1043–1046. https://doi.org/10.1098/rsbl.2012.0703
   PubMed Web of Science ®Google Scholar
• Wilkinson, M. (1996). Majority rule reduced consensus and their use in bootstrapping. Molecular Biology and Evolution, 13, 437–444. https://doi.org/10.1093/oxfordjournals.molbev.a025604
   PubMed Web of Science ®Google Scholar
• Wilkinson, M., Thorley, J. L., & Upchurch, P. (2000). A chain is no stronger than its weakest link: double decay analysis of phylogenetic hypotheses. Systematic Biology, 49, 754–776. https://doi.org/10.1080/106351500750049815
   PubMed Web of Science ®Google Scholar
• Yang, Z. (2014). Molecular evolution: A statistical approach. Oxford University Press.
   Google Scholar
• Zwickl, D. J. (2006). Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. [Unpublished doctoral dissertation]. University of Texas at Austin.
   Google Scholar