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. 2021 Jul;108(7):1143-1165.
doi: 10.1002/ajb2.1697. Epub 2021 Jul 13.

Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes

Alexandre Antonelli  1   2   3 , James J Clarkson  1 , Kent Kainulainen  4 , Olivier Maurin  1 , Grace E Brewer  1 , Aaron P Davis  1 , Niroshini Epitawalage  1 , David J Goyder  1 , Tatyana Livshultz  5 , Claes Persson  2 , Lisa Pokorny  1 , Shannon C K Straub  6 , Lena Struwe  7 , Alexandre R Zuntini  1 , Félix Forest  1 , William J Baker  1
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Free article

Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes

Alexandre Antonelli et al. Am J Bot. 2021 Jul.
Free article

Erratum in

  • Corrigendum.
    [No authors listed] [No authors listed] Am J Bot. 2022 Aug;109(8):1326-1327. doi: 10.1002/ajb2.16049. Epub 2022 Aug 26. Am J Bot. 2022. PMID: 36017873 Free PMC article. No abstract available.

Abstract

Premise: Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family-level relationships within Gentianales have been presented in previous studies.

Methods: Here we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off-target reads for most taxa and infer phylogenetic trees for comparison with the nuclear-derived trees.

Results: We recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order's classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae).

Conclusions: The higher-level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.

Keywords: Angiosperms353; Hyb-Seq; asterids; molecular phylogenetics; museomics; target sequence capture; tree of life.

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References

LITERATURE CITED

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    1. Backlund, M., B. Oxelman, and B. Bremer. 2000. Phylogenetic relationships within the Gentianales based on ndhF and rbcL sequences, with particular reference to Loganiaceae. American Journal of Botany 87: 1029-1043.

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