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      Phylogenomic inference and demographic model selection suggest peripatric separation of the cryptic steppe ant species Plagiolepis pyrenaica stat. rev.

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          Abstract

          The ant Plagiolepis taurica Santschi, 1920 (Hymenoptera, Formicidae) is a typical species of the Eurasian steppes, a large grassland dominated biome that stretches continuously from Central Asia to Eastern Europe and is represented by disjunct outposts also in Central and Western Europe. The extent of this biome has been influenced by the Pleistocene climate, and steppes expanded recurrently during cold stages and contracted in warm stages. Consequently, stenotopic steppe species such as P. taurica repeatedly went through periods of demographic expansion and severe isolation. Here, we explore the impact of these dynamics on the genetic diversification within P. taurica. Delimitation of P. taurica from other Plagiolepis species has been unclear since its initial description, which raised questions on both its classification and its spatiotemporal diversification early on. We re‐evaluate species limits and explore underlying mechanisms driving speciation by using an integrative approach based on genomic and morphometric data. We found large intraspecific divergence within P. taurica and resolved geographically coherent western and eastern genetic groups, which likewise differed morphologically. A morphometric survey of type material showed that Plagiolepis from the western group were more similar to P. barbara pyrenaica Emery, 1921 than to P. taurica; we thus lift the former from synonymy and establish it as separate species, P. pyrenaica stat. rev. Explicit evolutionary model testing based on genomic data supported a peripatric speciation for the species pair, probably as a consequence of steppe contraction and isolation during the mid‐Pleistocene. We speculate that this scenario could be exemplary for many stenotopic steppe species, given the emphasized dynamics of Eurasian steppes.

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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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            The variant call format and VCFtools

            Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. Availability: http://vcftools.sourceforge.net Contact: rd@sanger.ac.uk
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              Inference of Population Structure Using Multilocus Genotype Data

              We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
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                Author and article information

                Contributors
                philipp.kirschner@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
                20 January 2023
                March 2023
                : 32
                : 5 ( doiID: 10.1111/mec.v32.5 )
                : 1149-1168
                Affiliations
                [ 1 ] Department of Ecology University of Innsbruck Innsbruck Austria
                [ 2 ] Department of Botany University of Innsbruck Innsbruck Austria
                [ 3 ] Senckenberg Museum of Natural History Görlitz Germany
                Author notes
                [*] [* ] Correspondence

                Philipp Kirschner, Department of Ecology, University of Innsbruck, Innsbruck, Austria.

                Email: philipp.kirschner@ 123456gmail.com

                Author information
                https://orcid.org/0000-0002-9263-5112
                https://orcid.org/0000-0003-2414-4650
                Article
                MEC16828 MEC-22-0901.R1
                10.1111/mec.16828
                10946478
                36530155
                464b7e46-c399-4f64-99c9-f40cf2456bd3
                © 2023 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/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 24 November 2022
                : 11 October 2021
                : 29 November 2022
                Page count
                Figures: 5, Tables: 1, Pages: 20, Words: 15035
                Funding
                Funded by: Austrian Science Fund , doi 10.13039/501100002428;
                Award ID: P 25955
                Categories
                Original Article
                Original Articles
                Phylogeography
                Custom metadata
                2.0
                March 2023
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.3.9 mode:remove_FC converted:18.03.2024

                Ecology
                demographic inference,eurasian steppe,integrative species delimitation,morphometrics,pleistocene speciation

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