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      Phylogeny, biogeography and ecological diversification of New Caledonian palms (Arecaceae)

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          Abstract

          Background and Aims

          The geographical origin and evolutionary mechanisms underpinning the rich and distinctive New Caledonian flora remain poorly understood. This is attributable to the complex geological past of the island and to the scarcity of well-resolved species-level phylogenies. Here, we infer phylogenetic relationships and divergence times of New Caledonian palms, which comprise 40 species. We use this framework to elucidate the biogeography of New Caledonian palm lineages and to explore how extant species might have formed.

          Methods

          A phylogenetic tree including 37 New Caledonian palm species and 77 relatives from tribe Areceae was inferred from 151 nuclear genes obtained by targeted sequencing. Fossil-calibrated divergence times were estimated and ancestral ranges inferred. Ancestral and extant ecological preferences in terms of elevation, precipitation and substrate were compared between New Caledonian sister species to explore their possible roles as drivers of speciation.

          Key Results

          New Caledonian palms form four well-supported clades, inside which relationships are well resolved. Our results support the current classification but suggest that Veillonia and Campecarpus should be resurrected and fail to clarify whether Rhopalostylidinae is sister to or nested in Basseliniinae. New Caledonian palm lineages are derived from New Guinean and Australian ancestors, which reached the island through at least three independent dispersal events between the Eocene and Miocene. Palms then dispersed out of New Caledonia at least five times, mainly towards Pacific islands. Geographical and ecological transitions associated with speciation events differed across time and genera. Substrate transitions were more frequently associated with older events than with younger ones.

          Conclusions

          Neighbouring areas and a mosaic of local habitats shaped the palm flora of New Caledonia, and the island played a significant role in generating palm diversity across the Pacific region. This new spatio-temporal framework will enable population-level ecological and genetic studies to unpick the mechanisms underpinning New Caledonian palm endemism.

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          Most cited references111

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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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            Fast and accurate short read alignment with Burrows–Wheeler transform

            Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.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
                Journal
                Ann Bot
                Ann Bot
                annbot
                Annals of Botany
                Oxford University Press (US )
                0305-7364
                1095-8290
                03 July 2024
                25 March 2024
                25 March 2024
                : 134
                : 1
                : 85-100
                Affiliations
                Department of Biology, Memorial University of Newfoundland , St John’s, Newfoundland A1B 3X9, Canada
                Royal Botanic Gardens, Kew , Richmond TW9 3AE, UK
                Royal Botanic Gardens, Kew , Richmond TW9 3AE, UK
                DIADE, Univ Montpellier, CIRAD, IRD , Montpellier, France
                Royal Botanic Gardens, Kew , Richmond TW9 3AE, UK
                Royal Botanic Gardens, Kew , Richmond TW9 3AE, UK
                Royal Botanic Gardens, Kew , Richmond TW9 3AE, UK
                Author notes

                Victor Pérez-Calle and Sidonie Bellot equally contributed to the study.

                For correspondence. E-mail s.bellot@ 123456kew.org
                For correspondence. E-mail w.baker@ 123456kew.org
                Article
                mcae043
                10.1093/aob/mcae043
                11161567
                38527418
                2af606d7-daf9-4921-93f1-399263595066
                © The Author(s) 2024. Published by Oxford University Press on behalf of the Annals of Botany Company.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 27 November 2023
                : 05 March 2024
                : 24 March 2024
                : 11 March 2024
                : 01 April 2024
                Page count
                Pages: 16
                Funding
                Funded by: Garfield Weston Foundation, DOI 10.13039/100013999;
                Categories
                Original Articles
                AcademicSubjects/SCI01080
                AcademicSubjects/SCI01130
                AcademicSubjects/SCI01210

                Plant science & Botany
                arecaceae,areceae,biogeography,molecular dating,new caledonia,phylogeny,speciation,target sequence capture,ultramafic

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