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

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

doi:10.1016/j.ympev.2023.107914

Cited by 10 publications

(1 citation statement)

References 108 publications

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“…This assembly method has been successfully employed in a series of studies, encompassing various angiosperm lineages, such as Amaryllidaceae (Lou & al., 2022b), Araliaceae (J. Jin & al., 2023;, Fabaceae (C. Su & al., 2019Su & al., , 2020, Magnoliaceae (G.N. , Rosaceae (B.B.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

Phylogenomic analyses support a new infrageneric classification of Pourthiaea (Maleae, Rosaceae) using multiple inference methods and extensive taxon sampling

Liu,

Ma,

Zhang

et al. 2023

TAXON

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In this comprehensive study, based on extensive taxon sampling, we performed phylogenomic analyses of plastome and nuclear ribosomal DNA (nrDNA) datasets. We employed multiple inference methods, including concatenated and coalescent‐based strategies, to generate an accurate phylogeny of the woody Rosaceae genus Pourthiaea. The nrDNA phylogeny of Pourthiaea strongly supports three major clades, which are consistent with morphology. However, the plastid tree provides an alternative phylogenetic topology, indicating cytonuclear discordance which could be explained by frequent hybridizations between and among the species of Pourthiaea. Considering evidence from morphology and phylogenomic data, we propose a new infrageneric classification for Pourthiaea, consisting of three sections: P. sect. Pourthiaea, P. sect. Amphidoxae sect. nov., and P. sect. Impressivenae sect. nov.

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Section: ■ Materials and Methodsmentioning

confidence: 99%

Phylogenomic analyses support a new infrageneric classification of Pourthiaea (Maleae, Rosaceae) using multiple inference methods and extensive taxon sampling

Liu,

Ma,

Zhang

et al. 2023

TAXON

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AdvancingPyrusphylogeny: Deep genome skimming‐based inference coupled with paralogy analysis yields a robust phylogenetic backbone and an updated infrageneric classification of the pear genus (Maleae, Rosaceae)

Jin,

Ma,

Liu

et al. 2024

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The lack of a robust phylogenetic backbone has posed significant challenges to proposing an infrageneric taxonomic classification of the pear genus, Pyrus, a widely distributed Eurasian lineage of Rosaceae. This issue has been exacerbated by limited informative loci and inaccessible taxon sampling. To address these limitations, we conducted extensive taxon sampling, encompassing 78 Pyrus ingroup individuals representing 32 species, along with 4 outgroup species. This comprehensive sampling strategy covers a wide range of morphological and geographical variations. To enable accurate phylogenomic inference, we assembled 801 single‐copy nuclear genes and 72 plastid coding sequences from deep genome skimming (DGS) data. Additionally, we employed a tree‐based method for nuclear orthology inference, which led to the generation of three orthologous datasets: one‐to‐one orthologs (1to1), monophyletic outgroups (MO), and rooted ingroups (RT). The results yielded from both nuclear and plastid analyses consistently support the monophyly of Pyrus, and two well‐supported clades, the Occidental and Oriental clades, were recovered in nine nuclear and three plastid trees. Integrating evidence from morphology and phylogenomics, we propose an updated infrageneric classification of Pyrus, which consists of two subgenera: P. subg. Pyrus and P. subg. Pashia stat. nov. This revised classification provides a more robust framework for understanding the evolutionary relationships within the pear genus.

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Phylogenomics and morphology of Celmisiinae (Asteraceae: Astereae): Taxonomic and evolutionary implications

Nicol,

Saldivia,

Summerfield

et al. 2024

Molecular Phylogenetics and Evolution

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

Cited by 10 publications

References 108 publications

Phylogenomic analyses support a new infrageneric classification of Pourthiaea (Maleae, Rosaceae) using multiple inference methods and extensive taxon sampling

Phylogenomic analyses support a new infrageneric classification of Pourthiaea (Maleae, Rosaceae) using multiple inference methods and extensive taxon sampling

AdvancingPyrusphylogeny: Deep genome skimming‐based inference coupled with paralogy analysis yields a robust phylogenetic backbone and an updated infrageneric classification of the pear genus (Maleae, Rosaceae)

Phylogenomics and morphology of Celmisiinae (Asteraceae: Astereae): Taxonomic and evolutionary implications

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