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      Rapid Evolution of Host Repertoire and Geographic Range in a Young and Diverse Genus of Montane Butterflies

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          Abstract

          Evolutionary changes in geographic distribution and larval host plants may promote the rapid diversification of montane insects, but this scenario has been rarely investigated. We studied the rapid radiation of the butterfly genus Colias, which has diversified in mountain ecosystems in Eurasia, Africa, and the Americas. Based on a data set of 150 nuclear protein-coding genetic loci and mitochondrial genomes, we constructed a time-calibrated phylogenetic tree of Colias species with broad taxon sampling. We then inferred their ancestral geographic ranges, historical diversification rates, and the evolution of host use. We found that the most recent common ancestor of Colias was likely geographically widespread and originated ~3.5 Ma. The group subsequently diversified in different regions across the world, often in tandem with geographic expansion events. No aspect of elevation was found to have a direct effect on diversification. The genus underwent a burst of diversification soon after the divergence of the Neotropical lineage, followed by an exponential decline in diversification rate toward the present. The ancestral host repertoire included the legume genera Astragalus and Trifolium but later expanded to include a wide range of Fabaceae genera and plants in more distantly related families, punctuated with periods of host range expansion and contraction. We suggest that the widespread distribution of the ancestor of all extant Colias lineages set the stage for diversification by isolation of populations that locally adapted to the various different environments they encountered, including different host plants. In this scenario, elevation is not the main driver but might have accelerated diversification by isolating populations.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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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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              MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

              We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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                Author and article information

                Contributors
                Role: Associate Editor
                Journal
                Syst Biol
                Syst Biol
                sysbio
                Systematic Biology
                Oxford University Press (US )
                1063-5157
                1076-836X
                January 2025
                01 November 2024
                01 November 2024
                : 74
                : 1
                : 141-157
                Affiliations
                Department of Entomology, College of Plant Protection, South China Agricultural University , 483 Wushan Road, Tianhe District, Guangzhou, 510000, China
                State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University , 135 Xingangxi Road, Haizhu District, Guangzhou, 510275, China
                Department of Ecology, Swedish University of Agricultural Sciences , Ulls väg 16 Uppsala, 75649, Sweden
                Department of Biology, City College of New York, City University of New York , 160 Convent Ave., New York, NY 10031, USA
                PhD Program in Biology, Graduate Center, City University of New York , 365 5th Ave., New York, NY 10016, USA
                Entomology Section, National Museum of Natural History , Rizal Park, T.W. Kalaw St., Manila, 1000, Philippines
                Department of Zoology, Svante Arrhenius väg 18B, Stockholm University , Stockholm, SE-10691, Sweden
                Department of Biology, City College of New York, City University of New York , 160 Convent Ave., New York, NY 10031, USA
                Department of Zoology, Svante Arrhenius väg 18B, Stockholm University , Stockholm, SE-10691, Sweden
                Department of Biology, Kontaktvägen 10, Lund University , Lund, SWE-22362, Sweden
                Department of Entomology, College of Plant Protection, South China Agricultural University , 483 Wushan Road, Tianhe District, Guangzhou, 510000, China
                Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China , 8 Jiangwangmiao Road, Xuanwu District, Nanjing, 210000, China
                State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University , 135 Xingangxi Road, Haizhu District, Guangzhou, 510275, China
                Department of Entomology, College of Plant Protection, South China Agricultural University , 483 Wushan Road, Tianhe District, Guangzhou, 510000, China
                Author notes
                Correspondence to be sent to: Fangzhou Ma, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210000, China; E-mail: mfz@ 123456nies.org
                Peng Zhang, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; E-mail: zhangp35@ 123456mail.sysu.edu.cn
                Houshuai Wang, Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510000, China; E-mail: houshuaiwang@ 123456scau.edu.cn

                Shifang Mo, Yaowei Zhu, and Mariana P. Braga contributed equally to this article and shoud be considered as joint first authors.

                Author information
                https://orcid.org/0000-0002-1253-2536
                https://orcid.org/0000-0003-4195-8920
                https://orcid.org/0000-0003-1863-2340
                https://orcid.org/0000-0002-1259-3363
                Article
                syae061
                10.1093/sysbio/syae061
                11809587
                39484941
                5ce819b0-1d9f-46ec-8a48-1470fe6f7bf6
                © The Author(s) 2024. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.

                History
                : 22 October 2022
                : 14 October 2024
                : 05 November 2024
                : 29 November 2024
                Page count
                Pages: 17
                Funding
                Funded by: National Natural Science Foundation of China, DOI 10.13039/501100001809;
                Award ID: 32070469
                Award ID: 32270478
                Award ID: 32071611
                Funded by: Swedish Research Council, DOI 10.13039/501100004359;
                Award ID: 2020-06422
                Award ID: 2019-03441
                Funded by: US National Science Foundation;
                Award ID: DEB-1541557
                Funded by: China Biodiversity Observation Networks for Butterflies;
                Award ID: China BON-Butterfly
                Categories
                Regular Manuscripts
                AcademicSubjects/SCI00960
                AcademicSubjects/SCI01130
                AcademicSubjects/SCI01130

                Animal science & Zoology
                biogeography,host use,montane species,rapid diversification,target capture

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