6
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      The role of Central American barriers in shaping the evolutionary history of the northernmost glassfrog, Hyalinobatrachium fleischmanni (Anura: Centrolenidae)

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The complex geological history of Central America has been useful for understanding the processes influencing the distribution and diversity of multiple groups of organisms. Anurans are an excellent choice for such studies because they typically exhibit site fidelity and reduced movement. The objective of this work was to identify the impact of recognized geographic barriers on the genetic structure, phylogeographic patterns and divergence times of a wide-ranging amphibian species, Hyalinobatrachium fleischmanni. We amplified three mitochondrial regions, two coding (COI and ND1) and one ribosomal (16S), in samples collected from the coasts of Veracruz and Guerrero in Mexico to the humid forests of Chocó in Ecuador. We examined the biogeographic history of the species through spatial clustering analyses (Geneland and sPCA), Bayesian and maximum likelihood reconstructions, and spatiotemporal diffusion analysis. Our data suggest a Central American origin of H. fleischmanni and two posterior independent dispersals towards North and South American regions. The first clade comprises individuals from Colombia, Ecuador, Panama and the sister species Hyalinobatrachium tatayoi; this clade shows little structure, despite the presence of the Andes mountain range and the long distances between sampling sites. The second clade consists of individuals from Costa Rica, Nicaragua, and eastern Honduras with no apparent structure. The third clade includes individuals from western Honduras, Guatemala, and Mexico and displays deep population structure. Herein, we synthesize the impact of known geographic areas that act as barriers to glassfrog dispersal and demonstrated their effect of differentiating H. fleischmanni into three markedly isolated clades. The observed genetic structure is associated with an initial dispersal event from Central America followed by vicariance that likely occurred during the Pliocene. The southern samples are characterized by a very recent population expansion, likely related to sea-level and climatic oscillations during the Pleistocene, whereas the structure of the northern clade has probably been driven by dispersal through the Isthmus of Tehuantepec and isolation by the Motagua–Polochic–Jocotán fault system and the Mexican highlands.

          Related collections

          Most cited references76

          • Record: found
          • Abstract: found
          • Article: not found

          Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences.

          Although phylogenetic inference of protein-coding sequences continues to dominate the literature, few analyses incorporate evolutionary models that consider the genetic code. This problem is exacerbated by the exclusion of codon-based models from commonly employed model selection techniques, presumably due to the computational cost associated with codon models. We investigated an efficient alternative to standard nucleotide substitution models, in which codon position (CP) is incorporated into the model. We determined the most appropriate model for alignments of 177 RNA virus genes and 106 yeast genes, using 11 substitution models including one codon model and four CP models. The majority of analyzed gene alignments are best described by CP substitution models, rather than by standard nucleotide models, and without the computational cost of full codon models. These results have significant implications for phylogenetic inference of coding sequences as they make it clear that substitution models incorporating CPs not only are a computationally realistic alternative to standard models but may also frequently be statistically superior.
            Bookmark
            • Record: found
            • Abstract: not found
            • Article: not found

            Purification of nucleic acids by extraction with phenol:chloroform.

              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes.

              Model-based phylogenetic reconstructions increasingly consider spatial or phenotypic traits in conjunction with sequence data to study evolutionary processes. Alongside parameter estimation, visualization of ancestral reconstructions represents an integral part of these analyses. Here, we present a complete overhaul of the spatial phylogenetic reconstruction of evolutionary dynamics software, now called SpreaD3 to emphasize the use of data-driven documents, as an analysis and visualization package that primarily complements Bayesian inference in BEAST (http://beast.bio.ed.ac.uk, last accessed 9 May 2016). The integration of JavaScript D3 libraries (www.d3.org, last accessed 9 May 2016) offers novel interactive web-based visualization capacities that are not restricted to spatial traits and extend to any discrete or continuously valued trait for any organism of interest.
                Bookmark

                Author and article information

                Contributors
                Journal
                PeerJ
                PeerJ
                peerj
                peerj
                PeerJ
                PeerJ Inc. (San Diego, USA )
                2167-8359
                3 January 2019
                2019
                : 7
                : e6115
                Affiliations
                [1 ]Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México , Mexico city, México
                [2 ]Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México , Mexico City, Mexico
                [3 ]Departamento de Biología, Grupo de Investigación en Ecología Animal, Universidad del Valle , Cali, Colombia
                [4 ]Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México , Mexico City, México
                [5 ]Departamento de Zoología, Smithsonian Tropical Research Institute , Balboa, Panamá
                [6 ]Universidad de Panamá , Panamá
                [7 ]Sistema Nacional de Investigación , Panamá
                Article
                6115
                10.7717/peerj.6115
                6321759
                00626bdf-58ec-4d2f-bd96-d8c99b484d70
                ©2019 Mendoza 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
                : 31 July 2018
                : 15 November 2018
                Funding
                Funded by: PAPIIT-DGAPA (UNAM) project
                Award ID: IN203617
                Funded by: Rufford Foundation (Rufford Small Grant)
                Award ID: 18423-1
                This project was supported by PAPIIT-DGAPA (UNAM) project IN203617 and the Rufford Foundation (Rufford Small Grant reference 18423-1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Biogeography
                Zoology

                amphibian,biogeography,hyalinobatrachium,pliocene,centrolenidae,pleistocene,central america

                Comments

                Comment on this article