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Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants

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Abstract
The early diversification of angiosperms is thought to have been a rapid process, which may complicate phylogenetic analyses of early angiosperm relationships. Plastid and nuclear phylogenomic studies have raised several conflicting hypotheses regarding overall angiosperm phylogeny, but mitochondrial genomes have been largely ignored as a relevant source of information. Here we sequenced mitochondrial genomes from 18 angiosperms to fill taxon‐sampling gaps in Austrobaileyales, magnoliids, Chloranthales, Ceratophyllales, and major lineages of eudicots and monocots. We assembled a data matrix of 38 mitochondrial genes from 107 taxa to assess how well mitochondrial genomic data address current uncertainties in angiosperm relationships. Although we recovered conflicting phylogenies based on different datasets and analytical methods, we also observed congruence regarding deep relationships of several major angiosperm lineages: Chloranthales were always inferred to be the sister group of Ceratophyllales, Austrobaileyales to mesangiosperms, and the unplaced Dilleniales was consistently resolved as the sister to superasterids. Substitutional saturation, GC‐compositional heterogeneity, and codon‐usage bias are possible reasons for the noise/conflict that may impact phylogenetic reconstruction; and angiosperm mitochondrial genes may not be substantially affected by these factors. The third codon positions of the mitochondrial genes appear to contain more parsimony‐informative sites than the first and second codon positions, and therefore produced better resolved phylogenetic relationships with generally strong support. The relationships among these major lineages remain incompletely resolved, perhaps as a result of the rapidity of early radiations. Nevertheless, data from mitochondrial genomes provides additional evidence and alternative hypotheses for exploring the early evolution and diversification of the angiosperms.
Keywords
Plant Science, Ecology, Evolution, Behavior and Systematics, early angiosperm radiation, incongruence, mitochondrial genome, phylogenomics, systematic error

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MLA
Xue, Jia‐Yu, et al. “Mitochondrial Genes from 18 Angiosperms Fill Sampling Gaps for Phylogenomic Inferences of the Early Diversification of Flowering Plants.” JOURNAL OF SYSTEMATICS AND EVOLUTION, 2021, doi:10.1111/jse.12708.
APA
Xue, J., Dong, S., Wang, M., Song, T., Zhou, G., Li, Z., … Hang, Y. (2021). Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants. JOURNAL OF SYSTEMATICS AND EVOLUTION. https://doi.org/10.1111/jse.12708
Chicago author-date
Xue, Jia‐Yu, Shanshan Dong, Ming‐Qiang Wang, Tian‐Qiang Song, Guang‐Can Zhou, Zhen Li, Yves Van de Peer, et al. 2021. “Mitochondrial Genes from 18 Angiosperms Fill Sampling Gaps for Phylogenomic Inferences of the Early Diversification of Flowering Plants.” JOURNAL OF SYSTEMATICS AND EVOLUTION. https://doi.org/10.1111/jse.12708.
Chicago author-date (all authors)
Xue, Jia‐Yu, Shanshan Dong, Ming‐Qiang Wang, Tian‐Qiang Song, Guang‐Can Zhou, Zhen Li, Yves Van de Peer, Zhu‐Qing Shao, Wei Wang, Min Chen, Yan‐Mei Zhang, Xiao‐Qin Sun, Hongfeng Chen, Yong‐Xia Zhang, Shou‐Zhou Zhang, Fei Chen, Liangsheng Zhang, Cymon Cox, Yang Liu, Qiang Wang, and Yue‐Yu Hang. 2021. “Mitochondrial Genes from 18 Angiosperms Fill Sampling Gaps for Phylogenomic Inferences of the Early Diversification of Flowering Plants.” JOURNAL OF SYSTEMATICS AND EVOLUTION. doi:10.1111/jse.12708.
Vancouver
1.
Xue J, Dong S, Wang M, Song T, Zhou G, Li Z, et al. Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants. JOURNAL OF SYSTEMATICS AND EVOLUTION. 2021;
IEEE
[1]
J. Xue et al., “Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants,” JOURNAL OF SYSTEMATICS AND EVOLUTION, 2021.
@article{8682284,
  abstract     = {{The early diversification of angiosperms is thought to have been a rapid process, which may complicate phylogenetic analyses of early angiosperm relationships. Plastid and nuclear phylogenomic studies have raised several conflicting hypotheses regarding overall angiosperm phylogeny, but mitochondrial genomes have been largely ignored as a relevant source of information. Here we sequenced mitochondrial genomes from 18 angiosperms to fill taxon‐sampling gaps in Austrobaileyales, magnoliids, Chloranthales, Ceratophyllales, and major lineages of eudicots and monocots. We assembled a data matrix of 38 mitochondrial genes from 107 taxa to assess how well mitochondrial genomic data address current uncertainties in angiosperm relationships. Although we recovered conflicting phylogenies based on different datasets and analytical methods, we also observed congruence regarding deep relationships of several major angiosperm lineages: Chloranthales were always inferred to be the sister group of Ceratophyllales, Austrobaileyales to mesangiosperms, and the unplaced Dilleniales was consistently resolved as the sister to superasterids. Substitutional saturation, GC‐compositional heterogeneity, and codon‐usage bias are possible reasons for the noise/conflict that may impact phylogenetic reconstruction; and angiosperm mitochondrial genes may not be substantially affected by these factors. The third codon positions of the mitochondrial genes appear to contain more parsimony‐informative sites than the first and second codon positions, and therefore produced better resolved phylogenetic relationships with generally strong support. The relationships among these major lineages remain incompletely resolved, perhaps as a result of the rapidity of early radiations. Nevertheless, data from mitochondrial genomes provides additional evidence and alternative hypotheses for exploring the early evolution and diversification of the angiosperms.}},
  author       = {{Xue, Jia‐Yu and Dong, Shanshan and Wang, Ming‐Qiang and Song, Tian‐Qiang and Zhou, Guang‐Can and Li, Zhen and Van de Peer, Yves and Shao, Zhu‐Qing and Wang, Wei and Chen, Min and Zhang, Yan‐Mei and Sun, Xiao‐Qin and Chen, Hongfeng and Zhang, Yong‐Xia and Zhang, Shou‐Zhou and Chen, Fei and Zhang, Liangsheng and Cox, Cymon and Liu, Yang and Wang, Qiang and Hang, Yue‐Yu}},
  issn         = {{1674-4918}},
  journal      = {{JOURNAL OF SYSTEMATICS AND EVOLUTION}},
  keywords     = {{Plant Science,Ecology,Evolution,Behavior and Systematics,early angiosperm radiation,incongruence,mitochondrial genome,phylogenomics,systematic error}},
  language     = {{eng}},
  pages        = {{16}},
  title        = {{Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants}},
  url          = {{http://dx.doi.org/10.1111/jse.12708}},
  year         = {{2021}},
}

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