Methods for exploring the plant tree of life

Gitzendanner, Matthew A.; Yang, Ya; Wickett, Norman J.; McKain, Michael R.; Beaulieu, Jeremy M.

doi:10.1002/aps3.1039

Cited by 2 publications

(1 citation statement)

References 17 publications

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“…Genome skimming via shotgun sequencing of total genomic DNA at relatively low coverage is an efficient approach to recover entire plastomes and nrDNA [47]. Recently, genome skimming has been widely employed to reconstruct the evolutionary relationship at lower taxonomic levels and among closely related species [51][52][53][54][55], as well as to investigate reticulate evolution in diverse plant clades [52,[56][57][58]. In this study, we generated plastome and nrDNA sequences from all currently recognized Paris species using genome skimming method.…”

Section: Introductionmentioning

confidence: 99%

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

Yang

Chase

et al. 2019

Preprint

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Background: Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus.Results: All 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary.Conclusions: Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris. Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris. Our findings challenge the theoretical prediction that large genome sizes may limit speciation.

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Section: Introductionmentioning

confidence: 99%

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

Yang

Chase

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

Yang

Chase

et al. 2019

BMC Plant Biol

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BackgroundParis (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus.ResultsAll 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary.ConclusionsOur results provide important insights for clarifying some of the long-standing taxonomic debates in Paris. Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris. Our findings challenge the theoretical prediction that large genome sizes may limit speciation.

show abstract

Methods for exploring the plant tree of life

Cited by 2 publications

References 17 publications

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

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