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      Conservative plumage masks extraordinary phylogenetic diversity in the Grallaria rufula (Rufous Antpitta) complex of the humid Andes

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          Abstract

          The Grallaria rufula complex is currently considered to consist of 2 species, G. rufula (Rufous Antpitta) and G. blakei (Chestnut Antpitta). However, it has been suggested that the complex, populations of which occur in humid montane forests from Venezuela to Bolivia, comprises a suite of vocally distinct yet morphologically cryptic species. We sequenced nuclear and mitochondrial DNA for 80 individuals from across the distribution of the complex to determine the extent of genetic variation between and within described taxa. Our results revealed 18 geographically coherent clades separated by substantial genetic divergence: 14 within rufula, 3 within blakei, and 1 corresponding to G. rufocinerea (Bicolored Antpitta), a species with distinctive plumage found to be nested within the complex. Neither G. rufula nor G. blakei as presently defined was monophyletic. Although 6 of the 7 recognized subspecies of G. rufula were monophyletic, several subspecies contained substantial genetic differentiation. Genetic variation was largely partitioned across recognized geographic barriers, especially across deep river valleys in Peru and Colombia. Coalescent modeling identified 17 of the 18 clades as significantly differentiated lineages, whereas analyses of vocalizations delineated 16 biological species within the complex. The G. rufula complex seems unusually diverse even among birds of the humid Andes, a prime location for cryptic speciation; however, the extent to which other dispersal-limited Andean species groups exhibit similar degrees of cryptic differentiation awaits further study.

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          Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

          Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com
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            Biodiversity hotspots for conservation priorities.

            Conservationists are far from able to assist all species under threat, if only for lack of funding. This places a premium on priorities: how can we support the most species at the least cost? One way is to identify 'biodiversity hotspots' where exceptional concentrations of endemic species are undergoing exceptional loss of habitat. As many as 44% of all species of vascular plants and 35% of all species in four vertebrate groups are confined to 25 hotspots comprising only 1.4% of the land surface of the Earth. This opens the way for a 'silver bullet' strategy on the part of conservation planners, focusing on these hotspots in proportion to their share of the world's species at risk.
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              BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

              We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.
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                Author and article information

                Journal
                The Auk
                Oxford University Press (OUP)
                0004-8038
                1938-4254
                July 01 2020
                July 24 2020
                July 01 2020
                July 24 2020
                July 21 2020
                : 137
                : 3
                Affiliations
                [1 ]U.S. Geological Survey, Patuxent Wildlife Research Center, Laurel, Maryland, USA
                [2 ]Division of Birds, Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., USA
                [3 ]Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia
                [4 ]Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, USA
                [5 ]Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
                [6 ]Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, D.C., USA
                [7 ]Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
                [8 ]University of Kansas Biodiversity Institute, Lawrence, Kansas, USA
                [9 ]Department of Biology, University of Florida, Gainesville, Florida, USA
                Article
                10.1093/auk/ukaa009
                30f547bc-3c8f-4aaa-97ca-b4d11aea02d3
                © 2020
                History

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