Description and Phylogenetic Relationships of a New Genus and Two New Species of Lizards from Brazilian Amazonia, with Nomenclat
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Zootaxa 4000 (4): 401–427 ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ Article ZOOTAXA Copyright © 2015 Magnolia Press ISSN 1175-5334 (online edition) http://dx.doi.org/10.11646/zootaxa.4000.4.1 http://zoobank.org/urn:lsid:zoobank.org:pub:9D8F0DD1-B28B-4E43-8817-0E165467D68B 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) GUARINO R. COLLI1,8, MARINUS S. HOOGMOED2, DAVID C. CANNATELLA3, JOSÉ CASSIMIRO4, JERRIANE OLIVEIRA GOMES2, JOSÉ MÁRIO GHELLERE4, PEDRO M. SALES NUNES5, KÁTIA C. M. PELLEGRINO6, PATRICIA SALERNO7, SERGIO MARQUES DE SOUZA4 & MIGUEL TREFAUT RODRIGUES4 1Departamento de Zoologia, Universidade de Brasília, 70910-900 Brasília, DF, Brazil 2Museu Paraense Emílio Goeldi/CZO, Caixa Postal 399, 66017-970 Belém, PA, Brazil 3The University of Texas at Austin, Section of Integrative Biology, 1 University Station C0930, 78712, Austin, Texas, USA 4Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, Caixa Postal 11.461, 05422-970, São Paulo, SP, Brazil 5Universidade Federal de Pernambuco, Centro de Ciências Biológicas, Departamento de Zoologia, Av. Professor Moraes Rego, s/n. Cidade Universitária CEP 50670-901, Recife, PE, Brazil 6Universidade Federal de São Paulo, Departamento de Ciências Biológicas, Rua Prof. Artur Riedel, 275, 09972-270, Diadema, SP, Brazil 7Department of Biology, Colorado State University, 80523, Fort Collins, CO, USA 8Corresponding author. E-mail: [email protected] Abstract We describe a new genus and two new species of gymnophthalmid lizards based on specimens collected from Brazilian Amazonia, mostly in the "arc of deforestation". The new genus is easily distinguished from other Gymnophthalmidae by having very wide, smooth, and imbricate nuchals, arranged in two longitudinal and 6–10 transverse rows from nape to brachium level, followed by much narrower, strongly keeled, lanceolate, and mucronate scales. It also differs from all oth- er Gymnophthalmidae, except Iphisa, by the presence of two longitudinal rows of ventrals. The new genus differs from Iphisa by having two pairs of enlarged chinshields (one in Iphisa); posterior dorsal scales lanceolate, strongly keeled and not arranged in longitudinal rows (dorsals broad, smooth and forming two longitudinal rows), and lateral scales keeled (smooth). Maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses based on morphological and molecular data indicate the new species form a clade that is most closely related to Iphisa. We also address several no- menclatural issues and present a revised classification of Gymnophthalmidae. Key words: Reptiles, phylogeny, biodiversity, forest, Conservation, Amazon, South America Introduction The ongoing biodiversity crisis, primarily driven by human activities, could lead to a mass extinction event comparable to the "Big Five" (Bambach 2006; Benton 1995; Raup & Sepkoski 1982) in just a few centuries (Barnosky et al. 2011; Glavin 2007; Leakey & Lewin 1995). Even worse, current estimates of extinction rates may well be seriously biased because a large number of species still awaits formal description (Costello et al. 2013; Dirzo & Raven 2003; May 2011). Therefore, discovering and describing species is a fundamental and necessary step towards biodiversity conservation. Previous analyses indicate that most undescribed species are likely cryptozoic, small-bodied, with small geographic ranges, lower abundance and from less-explored regions, including threatened biodiversity hotspots (Mora et al. 2011; Scheffers et al. 2012). Gymnophthalmid lizards are an exemplary case of a group that may harbour many undescribed species. They Accepted by A. Bauer: 23 Jun. 2015; published: 18 Aug. 2015 401 are often cryptic, with many species having fossorial or semi-fossorial habits (Colli et al. 1998; Mesquita et al. 2006; Vitt et al. 2003). All species are small-bodied (e.g., Avila-Pires 1995; Vitt & Caldwell 2009) and many have small geographic ranges, such as the sand dunes in the São Francisco Basin in Brazil (Rodrigues 1996). Finally, several species have recently been described from the Atlantic Forest (Rodrigues & Borges 1997; Rodrigues et al. 2005, 2009b, 2013) and Cerrado biodiversity hotspots (Rodrigues et al. 2007a, 2008, 2009a; Teixeira et al. 2013b), as well as from the Amazon basin (Peloso et al. 2011; Rodrigues & Avila-Pires 2005; Teixeira et al. 2013a). Among the 246 recognized species of Gymnophthalmidae, 63 (26%) were described since 2000 (Uetz et al. 2007). Furthermore, additional undetected diversity should be described in the near future, as revealed by recent studies evidencing deep divergences in single widespread species (Nunes et al. 2012; Pellegrino et al. 2011). Herein we describe a new genus and two new species of gymnophthalmid lizards from Brazilian Amazonia. We assess their phylogenetic relationships with other gymnophthalmid genera based on morphological and molecular characters and examine distribution records in light of current trends of deforestation in Brazilian Amazonia. We also address several nomenclatural issues to correct misuses of family-group names within Gymnophthalmidae. Material and methods Morphological data. All specimens we examined are deposited in CHUNB (Coleção Herpetológica da Universidade de Brasília), MPEG (Museu Paraense Emílio Goeldi, Belém), and MZUSP (Museu de Zoologia da Universidade de São Paulo). We recorded the snout-vent length (SVL) and tail length of all specimens with a ruler (1 mm precision). We also recorded 77 morphological characters (Appendix S1) pertaining to external morphology, scalation, hemipenis morphology, and osteology following Rodrigues et al. (2005, 2007b, 2009b). We obtained hemipenial characters from the left hemipenis of CHUNB 18738 and CHUNB 50548 and osteological characters from CHUNB 23454 (cleared-and-stained). We prepared the hemipenis following the procedures described by Manzani & Abe (1988), modified by Pesantes (1994) and Zaher (1999). We manually severed the retractor muscle and filled the everted organ with stained petroleum jelly. We stained calcareous hemipenial structures in an alcoholic solution of alizarin red following Uzzell (1973) and Nunes et al. (2012). Terminology of hemipenial morphology follows Dowling & Savage (1960), Savage (1997) and Nunes et al. (2012). We determined the sex of all individuals based on the presence of femoral pores. DNA extraction, amplification and sequencing. We obtained sequence data for one nuclear (c-mos) and three mitochondrial (12S, 16S, ND4) genes of four specimens of the first newly described species (below), from two different localities (CHUNB 18738–18739, 50568–50569). Tissue samples of the second newly described species were not available. We extracted genomic DNA of liver samples with the Viogene Blood and Tissue Genomic DNA Extraction Kit. We used primers and polymerase chain reaction protocols for all genes following Pellegrino et al. (2001). We purified products using the Viogene Gel-M Extraction Kit and performed sequencing in the Core Sequencing Facility at the University of Texas at Austin. We edited sequences using Sequencher 4.8, constructed initial alignments with MUSCLE 3.5 (Edgar 2004) and slightly manually adjusted alignments with MacClade 4.08 (Maddison & Maddison 2005). We excluded 26 bases from the alignment due to homology uncertainty, and after trimming sequence ends used 1884 bases for the combined DNA dataset. Phylogenetic analyses. We downloaded sequences of 69 gymnophthalmids from GenBank representing all major lineages of Gymnophthalmidae (Appendix S2). We chose sequences so as to minimize missing data and selected loci that had been found useful in previous studies (e.g., Castoe et al. 2004; Pellegrino et al. 2001). The ingroup consisted of Gymnophthalminae and the outgroup taxa consisted of Alopoglossus atriventris and Ptychoglossus (Alopoglossinae), following Pellegrino et al. (2001). We used morphological data (77 characters) from Rodrigues et al. (2005; 2007b; 2009b) and collected data from the new genus. This dataset included ingroup taxa only from Gymnophthalminae. The outgroup taxa were Alopoglossus atriventris and Rhachisaurus brachylepis. We performed phylogenetic analyses on three datasets: DNA only, morphology only, and a pruned DNA matrix plus morphology. In the last dataset, we pruned the DNA matrix to retain only taxa for which morphological data were available. The best-fitting model of evolution for the DNA dataset was inferred under the Akaike Information Criterion (AIC) in MrModeltest (Nylander 2004): GTR+I+G for each mitochondrial gene and GTR+G 402 · Zootaxa 4000 (4) © 2015 Magnolia Press COLLI ET AL. for the nuclear gene. We analysed the DNA dataset under five different partitioning schemes: single partition, partition by gene, partition by gene and codon position for ND4 only, partition by gene and codon position for c- mos only, partition by gene and by codon position for both ND4 and c-mos. Using MrBayes 3.1 (Ronquist & Huelsenbeck 2003), we obtained the highest Bayes factor for the partition by gene and codon position for both ND4 and c-mos, and subsequently used it in all analyses (including the combined DNA/morphology datasets). The Bayesian phylogenetic analysis of the DNA dataset was performed using MrBayes 3.1 (10 million generations, sampled every 1,000, with burn-in of 1,000 samples); the partitions and models of evolution were as described