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

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 identified to have pervasive reticulate evolution. The red-fruit genus,Stranvaesia, provides an ideal model for testing the effect of reticulation on generic circumscription when hybridization and allopolyploidy define a group's evolutionary history. Here, 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 ofStranvaesiaand 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 theStranvaesiaclade, a conclusion further bolstered by cytonuclear and gene tree discordance. The well-inferred phylogenetic backbone revealed an updated generic delimitation ofStranvaesiaand a new genus,Weniomeles, characterized by purple-black fruits, trunk and/or branches with thorns, and fruit core with multilocular separated by a layer of sclereids and a cluster of sclereids at the top of the locules. Here, we highlight a broadly-applicable workflow for inferring how analyses of reticulate evolution in phylogenomic data can directly shape taxonomic revisions.

Malus includes Docynia (Maleae, Rosaceae): evidence from phylogenomics and morphology

“…Docyniopsis C.K.Schneid.) based on the plastomes and the nuclear sequences (Lo and Donoghue 2012;Liu et al 2019Liu et al , 2020aLiu et al , 2020bLiu et al , 2022Jin et al 2023). Several shared morphological characteristics have also supported their close relationship, i.e., cone-shaped non-adnate part of the ovaries, fully connate carpels, incurved and persistent calyx, numerous scattered sclereids throughout the flesh, juvenile leaves deeply lobed, and similar flavonoid chemistry (Williams 1982;Robertson et al 1991;Kalkman 2004).…”

Malus includes Docynia (Maleae, Rosaceae): evidence from phylogenomics and morphology

“… Docyniopsis C.K.Schneid. ), based on the plastomes and the nuclear sequences ( Lo and Donoghue 2012 ; Liu et al 2019 , 2020a , 2020b , 2022 ; Jin et al 2023 ). Several shared morphological characteristics have also supported their close relationship, i.e.…”