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Resolving Recent Plant Radiations: Power and Robustness of Genotyping-by-Sequencing.

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cam.issuedOnline2017-07-11
dc.contributor.authorFernández-Mazuecos, Mario
dc.contributor.authorMellers, Greg
dc.contributor.authorVigalondo, Beatriz
dc.contributor.authorSáez, Llorenç
dc.contributor.authorVargas, Pablo
dc.contributor.authorGlover, Beverley J
dc.contributor.orcidGlover, Beverley [0000-0002-6393-819X]
dc.date.accessioned2018-03-29T13:01:14Z
dc.date.available2018-03-29T13:01:14Z
dc.date.issued2018-03-01
dc.description.abstractDisentangling species boundaries and phylogenetic relationships within recent evolutionary radiations is a challenge due to the poor morphological differentiation and low genetic divergence between species, frequently accompanied by phenotypic convergence, interspecific gene flow and incomplete lineage sorting. Here we employed a genotyping-by-sequencing (GBS) approach, in combination with morphometric analyses, to investigate a small western Mediterranean clade in the flowering plant genus Linaria that radiated in the Quaternary. After confirming the morphological and genetic distinctness of eight species, we evaluated the relative performances of concatenation and coalescent methods to resolve phylogenetic relationships. Specifically, we focused on assessing the robustness of both approaches to variations in the parameter used to estimate sequence homology (clustering threshold). Concatenation analyses suffered from strong systematic bias, as revealed by the high statistical support for multiple alternative topologies depending on clustering threshold values. By contrast, topologies produced by two coalescent-based methods (NJ$_{\mathrm{st}}$, SVDquartets) were robust to variations in the clustering threshold. Reticulate evolution may partly explain incongruences between NJ$_{\mathrm{st}}$, SVDquartets and concatenated trees. Integration of morphometric and coalescent-based phylogenetic results revealed (i) extensive morphological divergence associated with recent splits between geographically close or sympatric sister species and (ii) morphological convergence in geographically disjunct species. These patterns are particularly true for floral traits related to pollinator specialization, including nectar spur length, tube width and corolla color, suggesting pollinator-driven diversification. Given its relatively simple and inexpensive implementation, GBS is a promising technique for the phylogenetic and systematic study of recent radiations, but care must be taken to evaluate the robustness of results to variation of data assembly parameters.
dc.format.mediumPrint
dc.identifier.doi10.17863/CAM.12037
dc.identifier.eissn1076-836X
dc.identifier.issn1063-5157
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/274497
dc.languageeng
dc.language.isoeng
dc.publisherOxford University Press (OUP)
dc.publisher.urlhttp://dx.doi.org/10.1093/sysbio/syx062
dc.subjectClassification
dc.subjectGenotype
dc.subjectLinaria
dc.subjectPlant Dispersal
dc.subjectSequence Analysis, DNA
dc.titleResolving Recent Plant Radiations: Power and Robustness of Genotyping-by-Sequencing.
dc.typeArticle
dcterms.dateAccepted2017-06-30
prism.endingPage268
prism.issueIdentifier2
prism.publicationDate2018
prism.publicationNameSyst Biol
prism.startingPage250
prism.volume67
pubs.funder-project-idEuropean Commission (624396)
pubs.funder-project-idIsaac Newton Trust (Minute 1423 (u))
rioxxterms.licenseref.startdate2018-03
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.typeJournal Article/Review
rioxxterms.versionAM
rioxxterms.versionofrecord10.1093/sysbio/syx062

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