Data from: Nightmare or delight: taxonomic circumscription meets reticulate evolution in the phylogenomic era

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.