ArticleGenome biology and evolution2017
Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity.
Article in Genome biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed.
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- Phylogenetic Inferences and Historical Biogeography of Onocleaceae.Plants (Basel, Switzerland) · 2025Article
- Comparative chloroplast genomes and phylogenetic analysis of theFrontiers in plant science · 2025Article
- Patterns in Genome-Wide Codon Usage Bias in Representative Species of Lycophytes and Ferns.Genes · 2024Article
- Comparative analysis ofPeerJ · 2024Article
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2024Article
- The complete chloroplast genome sequence and phylogenetic analysis ofMitochondrial DNA. Part B, Resources · 2024Article
- Chloroplast genome structure analysis ofFrontiers in plant science · 2024Article
- Evolution of the Araliaceae family involved rapid diversification of the Asian Palmate group and Hydrocotyle specific mutational pressure.Scientific reports · 2023Article
- Insights into cryptic speciation of quillworts in China.Plant diversity · 2023Article
- Analysis of the Chloroplast Genome ofCurrent issues in molecular biology · 2023Article
- Phylogeny ofFrontiers in plant science · 2023Article
- Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution.Frontiers in plant science · 2023Article
- The complete chloroplast genome and phylogenetic analysis ofMitochondrial DNA. Part B, Resources · 2023Article
- Complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2023Article
- The complete chloroplast genome and phylogenetic analysis ofMitochondrial DNA. Part B, Resources · 2023Article
- Article
- An open and continuously updated fern tree of life.Frontiers in plant science · 2022Article
- Structural Variation of Plastomes Provides Key Insight Into the Deep Phylogeny of Ferns.Frontiers in plant science · 2022Article
- Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns.Frontiers in plant science · 2022Article
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7 authors.
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Abstract
The eupolypods II ferns represent a classic case of evolutionary radiation and, simultaneously, exhibit high substitution rate heterogeneity. These factors have been proposed to contribute to the contentious resolutions among clades within this fern group in multilocus phylogenetic studies. We investigated the deep phylogenetic relationships of eupolypod II ferns by sampling all major families and using 40 plastid genomes, or plastomes, of which 33 were newly sequenced with next-generation sequencing technology. We performed model-based analyses to evaluate the diversity of molecular evolutionary rates for these ferns. Our plastome data, with more than 26,000 informative characters, yielded good resolution for deep relationships within eupolypods II and unambiguously clarified the position of Rhachidosoraceae and the monophyly of Athyriaceae. Results of rate heterogeneity analysis revealed approximately 33 significant rate shifts in eupolypod II ferns, with the most heterogeneous rates (both accelerations and decelerations) occurring in two phylogenetically difficult lineages, that is, the Rhachidosoraceae-Aspleniaceae and Athyriaceae clades. These observations support the hypothesis that rate heterogeneity has previously constrained the deep phylogenetic resolution in eupolypods II. According to the plastome data, we propose that 14 chloroplast markers are particularly phylogenetically informative for eupolypods II both at the familial and generic levels. Our study demonstrates the power of a character-rich plastome data set and high-throughput sequencing for resolving the recalcitrant lineages, which have undergone rapid evolutionary radiation and dramatic changes in substitution rates.
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