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      The dual role of Amazonian rivers in the generation and maintenance of avian diversity

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      1 , 2 , * , 2
      Science Advances
      American Association for the Advancement of Science

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          Abstract

          We use comparative phylogeography to investigate the role of Amazonian rivers in the origin and maintenance of avian diversity.

          Abstract

          The Amazon River and its major tributaries delimit the distributions of hundreds of terrestrial taxa. It remains unclear whether river-bounded distributions and taxon replacements reflect the historical role of rivers in generating species diversity as vicariant forces, or are the result of their role as secondary barriers, maintaining current levels of species diversity by inhibiting gene flow and population introgression. We use a community-wide comparative phylogeographic and phylogenetic approach to address the roles that the Rio Negro and the Rio Branco play in the avian speciation process in the Guiana Shield. Examining 74 pairs of ecologically similar geographic replacements that turn over across the lower Negro, we found substantial variation in the levels of genetic divergence and the inferred timing of diversification among pairs, ranging from ~0.24 to over 8 million years (Ma ago). The breadth of this variation is inconsistent with a single, shared speciation event. Coalescent simulations also rejected a simultaneous divergence scenario for pairs divided by the Rio Branco but could not reject a single diversification pulse for a subset of 12 pairs of taxa divided by the upper Negro. These results are consistent with recent geomorphological hypotheses regarding the origins of these rivers. Phylogenetically, taxon pairs represent a blend of sister (~40%) and nonsister taxa (~60%), consistent with river-associated allopatric or peripatric speciation and secondary contact, respectively. Our data provide compelling evidence that species turnover across the Rio Negro basin encompasses a mixture of histories, supporting a dual role for Amazonian rivers in the generation and maintenance of biological diversity.

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          Most cited references78

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          Speciation in amazonian forest birds.

          J Haffer (1969)
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            MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity

            Background MTML-msBayes uses hierarchical approximate Bayesian computation (HABC) under a coalescent model to infer temporal patterns of divergence and gene flow across codistributed taxon-pairs. Under a model of multiple codistributed taxa that diverge into taxon-pairs with subsequent gene flow or isolation, one can estimate hyper-parameters that quantify the mean and variability in divergence times or test models of migration and isolation. The software uses multi-locus DNA sequence data collected from multiple taxon-pairs and allows variation across taxa in demographic parameters as well as heterogeneity in DNA mutation rates across loci. The method also allows a flexible sampling scheme: different numbers of loci of varying length can be sampled from different taxon-pairs. Results Simulation tests reveal increasing power with increasing numbers of loci when attempting to distinguish temporal congruence from incongruence in divergence times across taxon-pairs. These results are robust to DNA mutation rate heterogeneity. Estimating mean divergence times and testing simultaneous divergence was less accurate with migration, but improved if one specified the correct migration model. Simulation validation tests demonstrated that one can detect the correct migration or isolation model with high probability, and that this HABC model testing procedure was greatly improved by incorporating a summary statistic originally developed for this task (Wakeley's ΨW ). The method is applied to an empirical data set of three Australian avian taxon-pairs and a result of simultaneous divergence with some subsequent gene flow is inferred. Conclusions To retain flexibility and compatibility with existing bioinformatics tools, MTML-msBayes is a pipeline software package consisting of Perl, C and R programs that are executed via the command line. Source code and binaries are available for download at http://msbayes.sourceforge.net/ under an open source license (GNU Public License).
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              Tracing the peopling of the world through genomics

              Advances in the sequencing and the analysis of the genomes of both modern and ancient peoples have facilitated a number of breakthroughs in our understanding of human evolutionary history. These include the discovery of interbreeding between anatomically modern humans and extinct hominins; the development of
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                Author and article information

                Journal
                Sci Adv
                Sci Adv
                SciAdv
                advances
                Science Advances
                American Association for the Advancement of Science
                2375-2548
                August 2018
                01 August 2018
                : 4
                : 8
                Affiliations
                [1 ]Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil.
                [2 ]Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA.
                Author notes
                [* ]Corresponding author. Email: lnaka1@ 123456lsu.edu
                Article
                aar8575
                10.1126/sciadv.aar8575
                6070317
                5612d5a4-d069-46d9-b238-2291dcc695aa
                Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

                This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

                Funding
                Funded by: doi http://dx.doi.org/10.13039/100000179, NSF Office of the Director;
                Award ID: DEB-1011512
                Funded by: doi http://dx.doi.org/10.13039/100000179, NSF Office of the Director;
                Award ID: DEB-0400797
                Funded by: doi http://dx.doi.org/10.13039/100000179, NSF Office of the Director;
                Award ID: DEB-0841739
                Funded by: Frank Chapman Memorial Fund;
                Funded by: American Ornithologists’ Union;
                Funded by: Brazilian National Council for Scientific and Technological Development (;
                Award ID: 486253/2006-6
                Funded by: The Brazilian National Council for Scientific and Technological Development (;
                Award ID: 202131/2006-8
                Categories
                Research Article
                Research Articles
                SciAdv r-articles
                Evolutionary Biology
                Evolutionary Biology
                Custom metadata
                Judith Urtula

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