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

      Mitochondrial DNA indicates paraphyletic relationships of disjunct populations in the Neotoma mexicana species group

      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

          Abstract: Woodrats (genus Neotoma) comprise 24 species found primarily in the United States and México. The Neotoma mexicana species group reaches its southernmost distribution in the highlands of southern México and Central America. Previous research suggested that N. mexicana has a discontinuous distribution, whereas N. ferruginea and N. picta have allopatric distributions around the lowlands of the Isthmus of Tehuantepec. However, these hypotheses were suggested with incomplete subspecific sampling near the isthmus. We used samples of N. m. parvidens from the Sierra Sur de Oaxaca and N. m. tropicalis from the Sierra Norte de Oaxaca to assess their taxonomic affinity. Our phylogenetic analyses of the mitochondrial cytochrome-b gene place both subspecies in N. ferruginea. Therefore, we suggest that N. mexicana is continuously distributed from the United States to the Transmexican Volcanic Belt, N. picta inhabits the Guerreran Sierra Madre del Sur, and N. ferruginea ranges from the Oaxacan Sierra Madre del Sur to Central America. Our findings also indicate that the Isthmus of Tehuantepec did not promote speciation in these woodrats.

          Translated abstract

          Resumen: Las ratas de campo (género Neotoma) incluyen 24 especies que principalmente habitan en Estados Unidos de América y México. El grupo de especies Neotoma mexicana alcanza su distribución más sureña en las zonas montañosas del sureste de México y Centro América. Previas investigaciones sugirieron que N. mexicana presenta una distribución discontinua, mientras que N. ferruginea y N. picta tienen distribuciones alopátricas alrededor de las tierras bajas del Istmo de Tehuantepec. Sin embargo, estas hipótesis fueron sugeridas con un muestreo sub-específico incompleto cerca del istmo. Utilizamos muestras de N. m. parvidens de la Sierra Sur de Oaxaca y N. m. tropicalis de la Sierra Norte de Oaxaca para evaluar su afinidad taxonómica. Nuestros análisis filogenéticos del gen mitocondrial citocromo b revelaron que ambas subespecies pertenecen a N. ferruginea. Por lo tanto, sugerimos que N. mexicana se distribuye de manera continua desde Estados Unidos hasta la Faja Volcánica Transmexicana, N. picta habita en la Sierra Madre del Sur en Guerrero, y N. ferruginea se distribuye desde la Sierra Madre del Sur en Oaxaca hasta Centro América. Nuestros resultados también indican que el Istmo de Tehuantepec no promovió procesos de especiación en estas ratas de campo.

          Related collections

          Most cited references64

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

          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

              Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
                Bookmark

                Author and article information

                Journal
                therya
                Therya
                Therya
                Asociación Mexicana de Mastozoología A.C. (La Paz, Baja California Sur, Mexico )
                2007-3364
                2021
                : 12
                : 3
                : 411-421
                Affiliations
                [2] Ciudad de México orgnameUniversidad Nacional Autónoma de México orgdiv1Departamento de Biología Evolutiva, Facultad de Ciencias Mexico llp@ 123456ciencias.unam.mx
                [1] Baton Rouge orgnameLouisiana State University orgdiv1Museum of Natural Science United States canchola@ 123456lsu.edu
                [3] Baton Rouge orgnameLouisiana State University orgdiv1Department of Biological Sciences United States
                Article
                S2007-33642021000300411 S2007-3364(21)01200300411
                10.12933/therya-21-1082
                1c22bae5-7cab-44cd-b4c4-6de15638003f

                This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

                History
                : 02 October 2020
                : 02 February 2021
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 64, Pages: 11
                Product

                SciELO Mexico

                Categories
                Articles

                molecular phylogeny,Neotoma ferruginea,Sierra Madre del Sur,Cytochrome b,Isthmus of Tehuantepec

                Comments

                Comment on this article