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

Liu, Guang-Ning; Ma, Dai-Kun; Xu, Chao; Huang, Jian; Ge, Bin‐Jie; Qiang, Luo; Yu, Wei; Liu, Bin‐Bin

doi:10.3897/phytokeys.229.103888

Cited by 6 publications

(2 citation statements)

References 32 publications

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“…exhibits significant cytonuclear discordance, sister to either Malus in the nuclear phylogenies (B.B. Liu & al., 2022;Ufimov & al., 2022;G.N. Liu & al., 2023a) or to Cormus in the plastid phylogenies (B.B.…”

Section: ■ Discussionmentioning

confidence: 99%

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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

TAXON

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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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Section: ■ Discussionmentioning

confidence: 99%

“…1A2,B2) (G.N. Liu & al., 2023a), fruits with dense sclereids (Fig. 1C3,D3; as opposed to few sclereids under the skin in Malus, Fig.…”

Section: ■ Discussionmentioning

confidence: 99%

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

TAXON

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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

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

Liu,

Ma,

Zhang

et al. 2023

Preprint

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In this comprehensive study, we conducted extensive taxon sampling and performed phylogenomic analyses based on 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 genusPourthiaea. The nrDNA phylogeny ofPourthiaeastrongly supported three major clades, which were consistent with morphology. However, the plastid tree provided an alternative phylogenetic topology, indicating cytonuclear discordance. Frequent hybridizations between and among the species ofPourthiaeacould explain the cytonuclear discordance. Considering the evidence from morphology and phylogenomic data, we propose a new infrageneric classification forPourthiaea, consisting of three sections:P. sect.Pourthiaea,P. sect.AmphidoxaeB.B.Liu, andP. sect.ImpressivenaeB.B.Liu.

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

Cited by 6 publications

References 32 publications

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)

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)

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 ofPourthiaea(Maleae, Rosaceae) using multiple inference methods and extensive taxon sampling

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

Cited by 6 publications

References 32 publications

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)

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)

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 ofPourthiaea(Maleae, Rosaceae) using multiple inference methods and extensive taxon sampling

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