Nightmare or delight: taxonomic circumscription meets reticulate evolution in the phylogenomic era. Jin, Z., Hodel, R. G., Ma, D., Wang, H., Liu, G., Ren, C., Ge, B., Fan, Q., Jin, S., Xu, C., Wu, J., & Liu, B. Technical Report Evolutionary Biology, March, 2023.
Nightmare or delight: taxonomic circumscription meets reticulate evolution in the phylogenomic era [link]Paper  doi  abstract   bibtex   
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 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. The well-inferred phylogenetic backbone revealed an updated generic delimitation of Stranvaesia and 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.
@techreport{jin_nightmare_2023,
	type = {preprint},
	title = {Nightmare or delight: taxonomic circumscription meets reticulate evolution in the phylogenomic era},
	shorttitle = {Nightmare or delight},
	url = {http://biorxiv.org/lookup/doi/10.1101/2023.03.28.534649},
	abstract = {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 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. The well-inferred phylogenetic backbone revealed an updated generic delimitation of
            Stranvaesia
            and 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.},
	language = {en},
	urldate = {2023-04-12},
	institution = {Evolutionary Biology},
	author = {Jin, Ze-Tao and Hodel, Richard G.J. and Ma, Dai-Kun and Wang, Hui and Liu, Guang-Ning and Ren, Chen and Ge, Bin-Jie and Fan, Qiang and Jin, Shui-Hu and Xu, Chao and Wu, Jun and Liu, Bin-Bin},
	month = mar,
	year = {2023},
	doi = {10.1101/2023.03.28.534649},
	keywords = {PENDING TO READ},
}

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