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      Systematics of Pholidobolus lizards (Squamata, Gymnophthalmidae) from southern Ecuador, with descriptions of four new species

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          Abstract

          Four new species of Pholidobolus lizards are described from poorly explored areas in the Andes of southern Ecuador based on morphological and genetic evidence. Among other morphological characters, Pholidobolus samek sp. nov. and P. condor sp. nov. differ from their congeners in having green dorsolateral stripes on head. Males of P. condor sp. nov. differ from those of P. samek sp. nov. in having reddish flanks and venter. P. dolichoderes sp. nov. is distinguished by having a long neck, with more scales between orbit and tympanum, whereas P. fascinatus sp. nov. is distinguished by lacking enlarged medial scales on collar and a conspicuous vertebral stripe. In addition, the phylogenetic position of the new species is inferred using DNA sequences of mitochondrial and nuclear genes. The phylogeny supports strongly monophyly of each of the new species and renders P. macbrydei paraphyletic and split into six subclades. Available data suggest that the new species have restricted distribution ranges (< 100 km 2 each), and it is proposed that their classification be as Data Deficient or Critically Endangered species. The results reveal unexpected levels of diversity within Pholidobolus in the Andes of southern Ecuador and highlight the importance of improving scientific collections and conservation efforts in this area.

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          Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: an example from squamate reptiles.

          Recently, as genome-scale data have become available for more organisms, the development of phylogenetic markers from nuclear protein-coding loci (NPCL) has become more tractable. However, new methods are needed to efficiently sort the large number of genes from genomic databases into more limited sets appropriate for particular phylogenetic questions, while avoiding introns and paralogs. Here we describe a general methodology for identifying candidate single-copy NPCL from genomic databases. Our method uses information from reference genomes to identify genes with relatively large continuous protein-coding regions (i.e., 700bp). BLAST comparisons are used to help avoid genes with paralogous copies or close relatives (i.e., gene families) that might confound phylogenetic analyses. Exon boundary information is used to identify appropriately spaced potential priming sites. Using this method, we have developed over 25 novel NPCL, which span a variety of desirable evolutionary rates for phylogenetic analyses. Although targeted for higher-level phylogenetics of squamate reptiles, many of these loci appear to be useful across and within other vertebrate clades (e.g., amphibians), and some are relatively rapidly evolving and may be useful for closely-related species (e.g., within genera). This general method can be used whenever large-scale genomic data are available for an appropriate reference species (not necessarily within the focal clade). The method is also well suited for the development of intron regions for lower-level phylogenetic and phylogeographic studies. We provide an online database of alignments and suggested primers for approximately 85 NPCL that should be useful across vertebrates.
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              Data partitions and complex models in Bayesian analysis: the phylogeny of Gymnophthalmid lizards.

              Phylogenetic studies incorporating multiple loci, and multiple genomes, are becoming increasingly common. Coincident with this trend in genetic sampling, model-based likelihood techniques including Bayesian phylogenetic methods continue to gain popularity. Few studies, however, have examined model fit and sensitivity to such potentially heterogeneous data partitions within combined data analyses using empirical data. Here we investigate the relative model fit and sensitivity of Bayesian phylogenetic methods when alternative site-specific partitions of among-site rate variation (with and without autocorrelated rates) are considered. Our primary goal in choosing a best-fit model was to employ the simplest model that was a good fit to the data while optimizing topology and/or Bayesian posterior probabilities. Thus, we were not interested in complex models that did not practically affect our interpretation of the topology under study. We applied these alternative models to a four-gene data set including one protein-coding nuclear gene (c-mos), one protein-coding mitochondrial gene (ND4), and two mitochondrial rRNA genes (12S and 16S) for the diverse yet poorly known lizard family Gymnophthalmidae. Our results suggest that the best-fit model partitioned among-site rate variation separately among the c-mos, ND4, and 12S + 16S gene regions. We found this model yielded identical topologies to those from analyses based on the GTR+I+G model, but significantly changed posterior probability estimates of clade support. This partitioned model also produced more precise (less variable) estimates of posterior probabilities across generations of long Bayesian runs, compared to runs employing a GTR+I+G model estimated for the combined data. We use this three-way gamma partitioning in Bayesian analyses to reconstruct a robust phylogenetic hypothesis for the relationships of genera within the lizard family Gymnophthalmidae. We then reevaluate the higher-level taxonomic arrangement of the Gymnophthalmidae. Based on our findings, we discuss the utility of nontraditional parameters for modeling among-site rate variation and the implications and future directions for complex model building and testing.
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                Author and article information

                Contributors
                Journal
                Zookeys
                Zookeys
                2
                urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2020
                29 July 2020
                : 954
                : 109-156
                Affiliations
                [1 ] Museo de Zoología, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Avenida 12 de Octubre 1076 y Roca, Quito, Ecuador Pontificia Universidad Católica del Ecuador Quito Ecuador
                [2 ] Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Avenida Professor Moraes Rego, s/n. Cidade Universitária CEP 50670-901, Recife, PE, Brazil Universidade Federal de Pernambuco Recife Brazil
                Author notes
                Corresponding author: Omar Torres-Carvajal ( omartorcar@ 123456gmail.com )

                Academic editor: Anthony Herrel

                Author information
                https://orcid.org/0000-0003-0041-9250
                Article
                50667
                10.3897/zookeys.954.50667
                7406543
                32821208
                b75b8ec5-1a79-4576-a676-dbd58962d0e4
                Vanessa Parra, Pedro M. Sales Nunes, Omar Torres-Carvajal

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 30 January 2020
                : 28 May 2020
                Funding
                Funded by: Secretaría de Educación Superior, Ciencia, Tecnología e Innovación 501100004299 http://doi.org/10.13039/501100004299
                Categories
                Research Article
                Gymnophthalmidae
                Squamata
                Biodiversity &amp; Conservation
                Systematics
                Neogene
                South America

                Animal science & Zoology
                andes,cordillera del cóndor,diversity,phylogeny,taxonomy,animalia,squamata ,gymnophthalmidae

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