ArticleGenome biology and evolution2013
Chloroplast phylogenomics indicates that Ginkgo biloba is sister to cycads.
Article in Genome biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed.
- The complete mitochondrial genome ofFrontiers in plant science · 2026Article
- Phylogenomic Inference Suggests Differential Deep Time Phylogenetic Signals from Nuclear and Organellar Genomes in Gymnosperms.Plants (Basel, Switzerland) · 2025Article
- The Systematics and Evolution of Gymnosperms with an Emphasis on a Few Problematic Taxa.Plants (Basel, Switzerland) · 2024Review
- Increasing Information Content and Diagnosability in Family-Level Classifications.Systematic biology · 2023Article
- Species delimitation and coexistence in an ancient, depauperate vertebrate clade.BMC ecology and evolution · 2022Article
- Recent advances on phylogenomics of gymnosperms and a new classification.Plant diversity · 2022Article
- A revised view on the evolution of glutamine synthetase isoenzymes in plants.The Plant journal : for cell and molecular biology · 2022Article
- The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence.The plant genome · 2021Article
- Species Identification of Oaks (International journal of molecular sciences · 2019Article
- Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics.Botanical studies · 2019Article
- Perspectives on Endosymbiosis in Coralloid Roots: Association of Cycads and Cyanobacteria.Frontiers in microbiology · 2019Review
- 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
- Comparative Genomics and Phylogenetic Analysis Revealed the Chloroplast Genome Variation and Interspecific Relationships ofFrontiers in plant science · 2018Article
- Plastome Evolution in the Sole Hemiparasitic Genus Laurel Dodder (Cassytha) and Insights into the Plastid Phylogenomics of Lauraceae.Genome biology and evolution · 2017Article
- Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots.Scientific reports · 2017Article
- Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants.Genome biology and evolution · 2017Article
- Article
- The Complete Plastome Sequences of Four Orchid Species: Insights into the Evolution of the Orchidaceae and the Utility of Plastomic Mutational Hotspots.Frontiers in plant science · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular phylogenetic studies have not yet reached a consensus on the placement of Ginkgoales, which is represented by the only living species, Ginkgo biloba (common name: ginkgo). At least six discrepant placements of ginkgo have been proposed. This study aimed to use the chloroplast phylogenomic approach to examine possible factors that lead to such disagreeing placements. We found the sequence types used in the analyses as the most critical factor in the conflicting placements of ginkgo. In addition, the placement of ginkgo varied in the trees inferred from nucleotide (NU) sequences, which notably depended on breadth of taxon sampling, tree-building methods, codon positions, positions of Gnetopsida (common name: gnetophytes), and including or excluding gnetophytes in data sets. In contrast, the trees inferred from amino acid (AA) sequences congruently supported the monophyly of a ginkgo and Cycadales (common name: cycads) clade, regardless of which factors were examined. Our site-stripping analysis further revealed that the high substitution saturation of NU sequences mainly derived from the third codon positions and contributed to the variable placements of ginkgo. In summary, the factors we surveyed did not affect results inferred from analyses of AA sequences. Congruent topologies in our AA trees give more confidence in supporting the ginkgo-cycad sister-group hypothesis.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.