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      Cryptic Diversity in the Neotropical Gecko Genus Phyllopezus Peters, 1878 (Reptilia: Squamata: Phyllodactylidae): A New Species from Paraguay

      1 , 2 , 3 , 1 , 4 , 5 , 1 , 2
      International Journal of Zoology
      Hindawi Limited

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          Abstract

          The gecko genus Phyllopezus is distributed mainly along South America’s “Dry Diagonal” (Caatinga, Cerrado, and Chaco). The genus has been the subject of recent taxonomic analyses and includes four described species and seven candidate species referred to here as Phyllopezus pollicaris sensu lato. In Paraguay, Phyllopezus is known from the Chaco and Cerrado where it is abundant, and also from a small isolated population from a rocky hill formation named “Cordillera de Los Altos” (Los Altos mountain range). Here we analyzed genetic samples from across its range, including new samples from Paraguay, using DNA barcoding analysis of the mitochondrial 16S gene and phylogenetic analyses using both Bayesian and Maximum Likelihood methods. We found genetic and morphological differences among geckos from the Los Altos mountain range and the remaining Phyllopezus populations. Using both molecular and morphological evidence we describe a new Phyllopezus species, sister to P. przewalskii. Genetic differentiation among described and putative Phyllopezus species is greater than their morphological differences, which likely accounts for these cryptic taxa remaining undescribed for so long.

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          Inference from Iterative Simulation Using Multiple Sequences

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            An inexpensive, automation-friendly protocol for recovering high-quality DNA

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              Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

              Background Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized. Results We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1) pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2) a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage. Conclusion The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS) criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.
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                Author and article information

                Journal
                International Journal of Zoology
                International Journal of Zoology
                Hindawi Limited
                1687-8477
                1687-8485
                July 16 2018
                July 16 2018
                : 2018
                : 1-14
                Affiliations
                [1 ]Senckenberg Forschungsinstitut und Naturmuseum Frankfurt, Senckenberganlage 25, 60325 Frankfurt a.M., Germany
                [2 ]Johann Wolfgang Goethe University, Institute for Ecology, Evolution & Diversity, Biologicum, Building C, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany
                [3 ]Instituto de Investigación Biológica del Paraguay, Del Escudo 1607, 1425 Asunción, Paraguay
                [4 ]Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
                [5 ]Bell Museum of Natural History, University of Minnesota, St. Paul, MN 55108, USA
                Article
                10.1155/2018/3958327
                93d550ff-f278-4c3a-8d84-92ebe585efc4
                © 2018

                http://creativecommons.org/licenses/by/4.0/

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