ArticlePloS one2013
Phylogenomics and coalescent analyses resolve extant seed plant relationships.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 77 citations in OpenAlex.
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- Specimen Identification Through Multilocus Species Tree Constructed From Single-Copy Orthologs (SCOs): A Case Study inEcology and evolution · 2025Article
- Global diversity of theIMA fungus · 2025Article
- The Systematics and Evolution of Gymnosperms with an Emphasis on a Few Problematic Taxa.Plants (Basel, Switzerland) · 2024Review
- African Mountain Thistles: Three New Genera in thePlants (Basel, Switzerland) · 2023Article
- HDR, the last enzyme in the MEP pathway, differently regulates isoprenoid biosynthesis in two woody plants.Plant physiology · 2023Article
- The Cycas genome and the early evolution of seed plants.Nature plants · 2022Article
- Reassessment ofPlants (Basel, Switzerland) · 2021Article
- The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence.The plant genome · 2021Article
- A new macrofossil ephedroid plant with unusual bract morphology from the Lower Cretaceous Jiufotang Formation of northeastern China.BMC evolutionary biology · 2020Article
- Reconstructing Krassilovia mongolica supports recognition of a new and unusual group of Mesozoic conifers.PloS one · 2020Article
- Reconstructing the phylogeny of new world monkeys (Current zoology · 2019Article
- Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms.Proceedings. Biological sciences · 2018Article
- Ginkgo biloba's footprint of dynamic Pleistocene history dates back only 390,000 years ago.BMC genomics · 2018Article
- Gymnosperms on the EDGE.Scientific reports · 2018Article
- Review
- The Evolution of Sexual Fluids in Gymnosperms From Pollination Drops to Nectar.Frontiers in plant science · 2018Review
- Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes.Frontiers in plant science · 2018Article
- Phylogenetic and functional signals in gymnosperm ovular secretions.Annals of botany · 2017Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The extant seed plants include more than 260,000 species that belong to five main lineages: angiosperms, conifers, cycads, Ginkgo, and gnetophytes. Despite tremendous effort using molecular data, phylogenetic relationships among these five lineages remain uncertain. Here, we provide the first broad coalescent-based species tree estimation of seed plants using genome-scale nuclear and plastid data By incorporating 305 nuclear genes and 47 plastid genes from 14 species, we identify that i) extant gymnosperms (i.e., conifers, cycads, Ginkgo, and gnetophytes) are monophyletic, ii) gnetophytes exhibit discordant placements within conifers between their nuclear and plastid genomes, and iii) cycads plus Ginkgo form a clade that is sister to all remaining extant gymnosperms. We additionally observe that the placement of Ginkgo inferred from coalescent analyses is congruent across different nucleotide rate partitions. In contrast, the standard concatenation method produces strongly supported, but incongruent placements of Ginkgo between slow- and fast-evolving sites. Specifically, fast-evolving sites yield relationships in conflict with coalescent analyses. We hypothesize that this incongruence may be related to the way in which concatenation methods treat sites with elevated nucleotide substitution rates. More empirical and simulation investigations are needed to understand this potential weakness of concatenation methods.
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