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      Testing the potential contribution of Wolbachia to speciation when cytoplasmic incompatibility becomes associated with host‐related reproductive isolation

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          Abstract

          Endosymbiont‐induced cytoplasmic incompatibility (CI) may play an important role in arthropod speciation. However, whether CI consistently becomes associated or coupled with other host‐related forms of reproductive isolation (RI) to impede the transfer of endosymbionts between hybridizing populations and further the divergence process remains an open question. Here, we show that varying degrees of pre‐ and postmating RI exist among allopatric populations of two interbreeding cherry‐infesting tephritid fruit flies ( Rhagoletis cingulata and R. indifferens) across North America. These flies display allochronic and sexual isolation among populations, as well as unidirectional reductions in egg hatch in hybrid crosses involving southwestern USA males. All populations are infected by a Wolbachia strain, wCin2, whereas a second strain, wCin3, only co‐infects flies from the southwest USA and Mexico. Strain wCin3 is associated with a unique mitochondrial DNA haplotype and unidirectional postmating RI, implicating the strain as the cause of CI. When coupled with nonendosymbiont RI barriers, we estimate the strength of CI associated with wCin3 would not prevent the strain from introgressing from infected southwestern to uninfected populations elsewhere in the USA if populations were to come into secondary contact and hybridize. In contrast, cytoplasmic–nuclear coupling may impede the transfer of wCin3 if Mexican and USA populations were to come into contact. We discuss our results in the context of the general paucity of examples demonstrating stable Wolbachia hybrid zones and whether the spread of Wolbachia among taxa can be constrained in natural hybrid zones long enough for the endosymbiont to participate in speciation.

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          DADA2: High resolution sample inference from Illumina amplicon data

          We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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            Cutadapt removes adapter sequences from high-throughput sequencing reads

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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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                Author and article information

                Contributors
                dbruzzes@nd.edu
                Journal
                Mol Ecol
                Mol Ecol
                10.1111/(ISSN)1365-294X
                MEC
                Molecular Ecology
                John Wiley and Sons Inc. (Hoboken )
                0962-1083
                1365-294X
                16 September 2021
                May 2022
                : 31
                : 10 ( doiID: 10.1111/mec.v31.10 )
                : 2935-2950
                Affiliations
                [ 1 ] Department of Biological Sciences University of Notre Dame Notre Dame IN USA
                [ 2 ] Faculty of Science and Technology Free University of Bozen‐Bolzano Bozen‐Bolzano Italy
                [ 3 ] Competence Centre for Plant Health Free University of Bozen‐Bolzano Bozen‐Bolzano Italy
                [ 4 ] Department of Forest and Soil Sciences Boku, University of Natural Resources and Life Sciences Vienna Austria
                [ 5 ] United States Department of Agriculture Temperate Tree Fruit & Vegetable Research Unit Agricultural Research Service Wapato WA USA
                [ 6 ] Instituto de Ecología A.C. Xalapa México
                [ 7 ] LIEMEN‐División Control Biológico de Plagas PROIMI Biotecnología‐CONICET Tucumán Argentina
                [ 8 ] Department of Biological Sciences Wayne State University Detroit MI USA
                [ 9 ] Washington State University Extension Vancouver WA USA
                [ 10 ] CEFE University Montpellier CNRS EPHE IRD University Paul Valéry Montpellier 3 Montpellier France
                [ 11 ] Department of Biology Utah State University UT USA
                Author notes
                [*] [* ] Correspondence

                Daniel J. Bruzzese, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.

                Email: dbruzzes@ 123456nd.edu

                Author information
                https://orcid.org/0000-0002-3115-6599
                https://orcid.org/0000-0001-8307-9831
                https://orcid.org/0000-0002-1509-0147
                https://orcid.org/0000-0002-0903-6590
                https://orcid.org/0000-0002-1851-8911
                https://orcid.org/0000-0002-9301-6153
                https://orcid.org/0000-0002-2985-8911
                https://orcid.org/0000-0002-8271-9005
                Article
                MEC16157
                10.1111/mec.16157
                9290789
                34455644
                765a78dd-32da-4b1b-af60-44052f355077
                © 2021 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
                : 18 August 2021
                : 16 April 2021
                : 25 August 2021
                Page count
                Figures: 5, Tables: 0, Pages: 16, Words: 11889
                Funding
                Funded by: National Institute of Food and Agriculture , doi 10.13039/100005825;
                Award ID: 2015‐67013‐23289
                Funded by: Austrian Science Fund , doi 10.13039/501100002428;
                Award ID: J3527
                Award ID: P31441
                Funded by: National Science Foundation , doi 10.13039/100000001;
                Award ID: DEB‐1638997
                Funded by: Province of Bozen‐Bolzano
                Categories
                Original Article
                ORIGINAL ARTICLES
                Speciation and Hybridization
                Custom metadata
                2.0
                May 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.1.7 mode:remove_FC converted:18.07.2022

                Ecology
                cytoplasmic incompatibility,postmating isolation,premating isolation,rhagoletis cingulata,rhagoletis indifferens,wolbachia

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