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      Genetic variability and the ecology of geographic range: A test of the central‐marginal hypothesis in Australian scincid lizards

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          Abstract

          For many species, both local abundance and regional occupancy are highest near the centre of their geographic distributions. One hypothesis for this pattern is that niche suitability declines with increasing distance from a species geographic centre, such that populations near range margins are characterized by reduced density and increased patchiness. In these smaller edge populations, genetic drift is more powerful, leading to the loss of genetic diversity. This simple verbal model has been formalized as the central‐marginal hypothesis, which predicts that core populations should have greater genetic diversity than edge populations. Here, we tested the central‐marginal hypothesis using a genomic data set of 25 species‐level taxa of Australian scincid lizards in the genera Ctenotus and Lerista. A majority of taxa in our data set showed range‐wide patterns of genetic variation consistent with central‐marginal hypothesis, and eight of 25 taxa showed significantly greater genetic diversity in the centre of their range. We then explored biological, historical, and methodological factors that might predict which taxa support the central‐marginal hypothesis. We found that taxa with the strongest evidence for range expansion were the least likely to follow predictions of the central‐marginal hypothesis. The majority of these taxa had range expansions that originated at the range edge, which led to a gradient of decreasing genetic diversity from the range edge to the core, contrary to the central‐marginal hypothesis.

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

            Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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              WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas

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                Author and article information

                Contributors
                sonal.singhal1@gmail.com
                Journal
                Mol Ecol
                Mol Ecol
                10.1111/(ISSN)1365-294X
                MEC
                Molecular Ecology
                John Wiley and Sons Inc. (Hoboken )
                0962-1083
                1365-294X
                14 July 2022
                August 2022
                : 31
                : 16 ( doiID: 10.1111/mec.v31.16 )
                : 4242-4253
                Affiliations
                [ 1 ] Department of Biology CSU Dominguez Hills Carson California USA
                [ 2 ] Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan USA
                [ 3 ] Museum of Zoology University of Michigan Ann Arbor Michigan USA
                Author notes
                [*] [* ] Correspondence

                Sonal Singhal, Department of Biology, CSU Dominguez Hills, Carson, CA 90747, USA.

                Email: sonal.singhal1@ 123456gmail.com

                Author information
                https://orcid.org/0000-0001-5407-5567
                Article
                MEC16589 MEC-21-1380.R2
                10.1111/mec.16589
                9545263
                35779002
                339bb6db-3611-48be-9ff3-16a16f69f0d4
                © 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

                History
                : 23 June 2022
                : 19 November 2021
                : 27 June 2022
                Page count
                Figures: 6, Tables: 0, Pages: 12, Words: 8882
                Funding
                Funded by: CSUDH Graduate Writing Institute for Excellence Fellowship
                Funded by: CSUDH Research, Scholarship and Creative Activity Grant
                Funded by: National Science Foundation , doi 10.13039/100000001;
                Award ID: DEB‐1754398
                Categories
                Original Article
                ORIGINAL ARTICLES
                Population and Conservation Genetics
                Custom metadata
                2.0
                August 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.2.0 mode:remove_FC converted:07.10.2022

                Ecology
                australia,central‐marginal hypothesis,ddrad,genetic variation,historical demography,lizards
                Ecology
                australia, central‐marginal hypothesis, ddrad, genetic variation, historical demography, lizards

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