Nightmare or delight: Taxonomic circumscription meets reticulate evolution in the phylogenomic era

Ze Tao Jin, Richard G.J. Hodel, Dai Kun Ma, Hui Wang, Guang Ning Liu, Chen Ren, Bin Jie Ge, Qiang Fan, Shui Hu Jin, Chao Xu, Jun Wu, Bin Bin Liu

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments. However, the systematics community lacks a broadly applicable strategy for taxonomic delimitation in groups characterized by pervasive reticulate evolution. The red-fruit genus, Stranvaesia, provides an ideal model to examine the influence of reticulation on generic circumscription, particularly where hybridization and allopolyploidy dominate the evolutionary history. In this study, we conducted phylogenomic analyses integrating data from hundreds of single-copy nuclear (SCN) genes and plastomes, and interrogated nuclear paralogs to clarify the inter/intra-generic relationship of Stranvaesia and its allies in the framework of Maleae. Analyses of phylogenomic discord and phylogenetic networks showed that allopolyploidization and introgression promoted the origin and diversification of the Stranvaesia clade, a conclusion further bolstered by cytonuclear and gene tree discordance. With a well-inferred phylogenetic backbone, we propose an updated generic delimitation of Stranvaesia and introduce a new genus, Weniomeles. This new genus is distinguished by its purple-black fruits, thorns trunk and/or branches, and a distinctive fruit core anatomy characterized by multilocular separated by a layer of sclereids and a cluster of sclereids at the top of the locules. Through this study, we highlight a broadly-applicable workflow that underscores the significance of reticulate evolution analyses in shaping taxonomic revisions from phylogenomic data.

Original languageEnglish (US)
Article number107914
JournalMolecular Phylogenetics and Evolution
Volume189
DOIs
StatePublished - Dec 2023
Externally publishedYes

Keywords

  • Allopolyploidization
  • Ancient hybridization
  • Paralogs
  • Rosaceae
  • Stranvaesia
  • Weniomeles

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

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