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Phylogenomics and biogeography of Castanea (chestnut) and Hamamelis (witch-hazel): Choosing between RAD-seq and Hyb-Seq approaches

Zhou, Wenbin; Xiang, Qiu-yun (Jenny)


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  <identifier identifierType="DOI">10.5281/zenodo.6954327</identifier>
  <creators>
    <creator>
      <creatorName>Zhou, Wenbin</creatorName>
      <givenName>Wenbin</givenName>
      <familyName>Zhou</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-4413-2227</nameIdentifier>
      <affiliation>North Carolina State University</affiliation>
    </creator>
    <creator>
      <creatorName>Xiang, Qiu-yun (Jenny)</creatorName>
      <givenName>Qiu-yun (Jenny)</givenName>
      <familyName>Xiang</familyName>
      <affiliation>North Carolina State University</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Phylogenomics and biogeography of Castanea (chestnut) and Hamamelis (witch-hazel): Choosing between RAD-seq and Hyb-Seq approaches</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2022</publicationYear>
  <dates>
    <date dateType="Issued">2022-08-28</date>
  </dates>
  <resourceType resourceTypeGeneral="Other"/>
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    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/6954327</alternateIdentifier>
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  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsCitedBy">10.1016/j.ympev.2022.107592</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsDerivedFrom">10.5061/dryad.w9ghx3fps</relatedIdentifier>
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  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Target enrichment and RAD-seq are well-established high throughput sequencing technologies that have been increasingly used for phylogenomic studies. Each method has its own pros and cons. The choice between them is a practical issue for plant systematists studying the evolutionary histories of biodiversity of rela­tively recent origins. However, few studies have compared the congruence and conflict between results from the two methods within the same group of organisms in plants. In this study, we employed RAD-seq and Hyb-Seq of Angiosperm 353 genes in phylogenomic and biogeographic studies of &lt;em&gt;Hamamelis&lt;/em&gt; (the witch-hazels) and &lt;em&gt;Castanea &lt;/em&gt;(chestnuts), two classic examples exhibiting the well-known eastern Asian (EA)-eastern North American (ENA) disjunct distribution, and compared them side by side. Our results showed congruences in phylogenetic inference and divergence time dating between the two data sets obtained through our customized procedures of library preparation and sequence trimming, although they differed in the number of loci and informative sites, the amount of missing data, and sampling within species. We suggest the selection of the two methods based on fund availability and sampling scale. Our phylogenetic analyses of RAD-seq and Hyb-Seq data resulted in well-resolved species relationships, and ancient introgressions were revealed in both genera by D-statistic test and PhyloNet. Biogeographic analyses including fossil data using total evidence-based dated tree and DEC model, applying specific inter-area dispersal probabilities, revealed a complicated history for each genus, indicating multiple intercontinental dispersals and local extinctions in areas outside of the taxa's modern ranges in both the Paleogene and Neogene. The study demonstrates the importance of including fossil taxa for a more accurate reconstruction of biogeographic histories of taxa to understand the EA and ENA floristic disjunction. Our results support an "out of western North America" migration of &lt;em&gt;Castanea&lt;/em&gt; but an "out of Asia" migration of &lt;em&gt;Hamamelis&lt;/em&gt; during their initial diversification, and the origins of the EA-ENA disjunction in both genera were results of vicariance.&lt;/p&gt;</description>
    <description descriptionType="Other">&lt;p&gt;Funding provided by: National Science Foundation&lt;br&gt;Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001&lt;br&gt;Award Number: DEB – 1442161&lt;/p&gt;&lt;p&gt;Funding provided by: National Institute of Food and Agriculture&lt;br&gt;Crossref Funder Registry ID: http://dx.doi.org/10.13039/100005825&lt;br&gt;Award Number: Hatch project 02718&lt;/p&gt;&lt;p&gt;Funding provided by: Arnold Arboretum&lt;br&gt;Crossref Funder Registry ID: http://dx.doi.org/10.13039/100009403&lt;br&gt;Award Number: Shiu-Ying Hu Student/Post-Doctoral Exchange Award&lt;/p&gt;</description>
  </descriptions>
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