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      A new frog of the Leptodactylus fuscus species group (Anura: Leptodactylidae), endemic from the South American Gran Chaco

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          Abstract

          A new species of Leptodactylus frog (Anura: Leptodactylidae) from the South American Gran Chaco, morphologically similar and previously confused with the widespread Leptodactylus mystacinus, is described through the use of multiple sources of evidence (molecular, external morphology, coloration, osteology, bioacoustics, and behavior). The phylogenetic analysis with partial sequences of mitochondrial rDNA genes (12S and 16S) recovered the new species within the L. fuscus group, being highly divergent (>3% genetic distance in 16S). The new species was recovered as sister taxa of L. mystacinus, from which it is distinguished by tympanum coloration, cephalic index, dorsum and legs coloration, and some osteological differences in nasals and prevomers. This new frog is characterized by a moderate body size (SVL 46.80–66.21 mm), distinctive color pattern (reddish dorsal surfaces of body with noticeable black stripes in the dorsolateral folds), a circular and dark tympanum with dark tympanic annuli, and behavior of males that call on top of fallen logs and tree branches close to the ground.

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          SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

          We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases ("Ns"), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/. © The Willi Hennig Society 2010.
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            Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques.

            A very simple, fast, universally applicable and reproducible method to extract high quality megabase genomic DNA from different organisms is described. We applied the same method to extract high quality complex genomic DNA from different tissues (wheat, barley, potato, beans, pear and almond leaves as well as fungi, insects and shrimps' fresh tissue) without any modification. The method does not require expensive and environmentally hazardous reagents and equipment. It can be performed even in low technology laboratories. The amount of tissue required by this method is approximately 50-100 mg. The quantity and the quality of the DNA extracted by this method is high enough to perform hundreds of PCR-based reactions and also to be used in other DNA manipulation techniques such as restriction digestion, Southern blot and cloning.
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              Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers.

              With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research.
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                Author and article information

                Contributors
                Journal
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ Inc. (San Diego, USA )
                2167-8359
                11 October 2019
                2019
                : 7
                : e7869
                Affiliations
                [1 ]Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (CONICET-UNaM), Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones , Posadas, Misiones, Argentina
                [2 ]Instituto de Investigación Biológica del Paraguay , Asunción, Paraguay
                [3 ]Sección Herpetología, Museo Nacional de Historia Natural , Montevideo, Uruguay
                [4 ]Departamento de Zoologia, Instituto de Biociências e Centro de Aquicultura (CAUNESP). Universidade Estadual Paulista (UNESP) , Rio Claro, São Paulo, Brazil
                [5 ]Instituto de Diversidad y Evolución Austral (IDEAUS-CONICET) , Puerto Madryn, Chubut, Argentina
                Author information
                http://orcid.org/0000-0001-9245-6512
                http://orcid.org/0000-0003-0612-2458
                http://orcid.org/0000-0002-9985-3630
                Article
                7869
                10.7717/peerj.7869
                6791353
                912dcab0-9db6-404e-9a3b-3d29ea5f15e1
                © 2019 Schneider et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                : 10 July 2019
                : 11 September 2019
                Funding
                Funded by: Agencia Nacional de Promoción Científica y Tecnológica
                Award ID: PICTs 2381/2015, 2437/2017
                Funded by: São Paulo Research Foundation
                Award ID: FAPESP Procs. # 2013/50741-7, # 2014/50342-8
                Funded by: Conselho Nacional de Desenvolvimento Científico e Tecnológico, the Consejo Nacional de Ciencia y Tecnología (PRONII, CONACYT, Paraguay)
                Funded by: Agencia Nacional de Investigación e Innovación (ANII/SNI, Uruguay)
                This work was supported by the Agencia Nacional de Promoción Científica y Tecnológica (PICTs 2381/2015, 2437/2017), the São Paulo Research Foundation (FAPESP Procs. # 2013/50741-7, # 2014/50342-8), the Conselho Nacional de Desenvolvimento Científico e Tecnológico, the Consejo Nacional de Ciencia y Tecnología (PRONII, CONACYT, Paraguay), and the Agencia Nacional de Investigación e Innovación (ANII/SNI, Uruguay). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Biodiversity
                Taxonomy
                Zoology

                taxonomy,molecular systematics,morphology,bioacoustics,leptodactylinae

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