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      Mountaintops phylogeography: A case study using small mammals from the Andes and the coast of central Chile

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          Abstract

          We evaluated if two sigmodontine rodent taxa ( Abrothrix olivacea and Phyllotis darwini) from the Andes and Coastal mountaintops of central Chile, experienced distributional shifts due to altitudinal movements of habitat and climate change during and after the Last Glacial Maximum (LGM). We tested the hypothesis that during LGM populations of both species experienced altitudinal shifts from the Andes to the lowlands and the coastal Cordillera, and then range retractions during interglacial towards higher elevations in the Andes. These distributional shifts may have left remnants populations on the mountaintops. We evaluated the occurrence of intraspecific lineages for each species, to construct distribution models at LGM and at present, as extreme climatic conditions for each lineage. Differences in distribution between extreme climatic conditions were interpreted as post-glacial distributional shifts. Abrothrix olivacea displayed a lineage with shared sequences between both mountain systems, whereas a second lineage was restricted to the Andes. A similar scenario of panmictic unit in the past was recovered for A. olivacea in the Andes, along with an additional unit that included localities from the rest of its distribution. For P. darwini, both lineages recovered were distributed in coastal and Andean mountain ranges at present as well, and structuring analyses for this species recovered coastal and Andean localities as panmictic units in the past. Niche modeling depicted differential postglacial expansions in the recovered lineages. Results suggest that historical events such as LGM triggered the descending of populations to Andean refuge areas (one of the A. olivacea’s lineages), to the lowlands, and to the coastal Cordillera. Backward movements of populations after glacial retreats may have left isolates on mountaintops of the coastal Cordillera, suggesting that current species distribution would be the outcome of climate change and habitat reconfiguration after LGM.

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          MRBAYES: Bayesian inference of phylogenetic trees.

          The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
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            Neighbor-net: an agglomerative method for the construction of phylogenetic networks.

            We present Neighbor-Net, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei. Neighbor-Net provides a snapshot of the data that can guide more detailed analysis. Unlike split decomposition, Neighbor-Net scales well and can quickly produce detailed and informative networks for several hundred taxa. We illustrate the method by reanalyzing three published data sets: a collection of 110 highly recombinant Salmonella multi-locus sequence typing sequences, the 135 "African Eve" human mitochondrial sequences published by Vigilant et al., and a collection of 12 Archeal chaperonin sequences demonstrating strong evidence for gene conversion. Neighbor-Net is available as part of the SplitsTree4 software package.
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              The general stochastic model of nucleotide substitution.

              DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                3 July 2017
                2017
                : 12
                : 7
                : e0180231
                Affiliations
                [1 ]Departamento de Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile
                [2 ]Laboratorio de Ecología y Biodiversidad, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
                [3 ]Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
                National Cheng Kung University, TAIWAN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: REP PGT.

                • Formal analysis: REP PGT JFG DBB.

                • Funding acquisition: REP FTP.

                • Investigation: REP PGT FTP.

                • Methodology: REP PGT JFG DBB.

                • Project administration: REP.

                • Resources: REP FTP PGT.

                • Supervision: REP.

                • Writing – original draft: REP PGT.

                • Writing – review & editing: REP PGT.

                Author information
                http://orcid.org/0000-0002-0806-1268
                Article
                PONE-D-16-45302
                10.1371/journal.pone.0180231
                5495339
                28672032
                a424e1bc-8ec5-4712-aa1f-3a604cb0b24c
                © 2017 Palma et al

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

                History
                : 14 November 2016
                : 12 June 2017
                Page count
                Figures: 6, Tables: 3, Pages: 21
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100002850, Fondo Nacional de Desarrollo Científico y Tecnológico;
                Award ID: 1140929
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100007194, Universidad de Santiago de Chile;
                Award ID: USA 1555.48
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100002850, Fondo Nacional de Desarrollo Científico y Tecnológico;
                Award ID: 1100558
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100002850, Fondo Nacional de Desarrollo Científico y Tecnológico;
                Award ID: 1130467
                Award Recipient :
                Funded by: Postdoctoral Project
                Award ID: 2015-2016 VRIEA PUCV
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100002850, Fondo Nacional de Desarrollo Científico y Tecnológico;
                Award ID: 1170761
                Award Recipient :
                This work was supported by Grants 1100558 and 1040929 from Fondo Nacional de Ciencia y Tecnología (FONDECYT, Chile) funded to REP and FTP, respectively, url: http://www.conicyt.cl/fondecyt/; Grant USA 1555. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Earth Sciences
                Geomorphology
                Topography
                Landforms
                Mountains
                Ecology and Environmental Sciences
                Terrestrial Environments
                Mountains
                Biology and Life Sciences
                Genetics
                Heredity
                Genetic Mapping
                Haplotypes
                People and places
                Geographical locations
                South America
                Chile (Country)
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Earth Sciences
                Atmospheric Science
                Climatology
                Paleoclimatology
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                Biogeography
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                Ecology and Environmental Sciences
                Biogeography
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                Earth Sciences
                Geography
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                Evolutionary Biology
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Genetics
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                Phylogeography
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Evolutionary Biology
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                Population Biology
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                Custom metadata
                All the data (nucleotide sequences) have been entered into the GenBank and accession numbers are provided in the Supporting Information file ( S1 Table). At the same file a detailed list of specimens captured per species, localities, geographic coordinates and altitude (in some cases) is provided.

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