ReviewPhilosophical transactions of the Royal Society of London. Series B, Biological sciences2006
From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction.
Review in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Inferring complex evolutionary history of the closely related East Asian wild roses in Rosa sect. Synstylae (Rosaceae) based on genomic evidence from conserved orthologues.Annals of botany · 2025Article
- Skmer approach improves species discrimination in taxonomically problematic genusPlant diversity · 2024Article
- Lack of ITS sequence homogenization in Erysimum species (Brassicaceae) with different ploidy levels.Scientific reports · 2022Article
- Organization, Phylogenetic Marker Exploitation, and Gene Evolution in the Plastome ofFrontiers in plant science · 2022Article
- Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae).BMC evolutionary biology · 2019Article
- Plastomes of nine hornbeams and phylogenetic implications.Ecology and evolution · 2018Article
- Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics.Applications in plant sciences · 2018Article
- The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks.Frontiers in plant science · 2018Article
- From Genomes to GENE-omes: Exome Sequencing Concept and Applications in Crop Improvement.Frontiers in plant science · 2017Review
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- Molecular phylogeny and evolutionary history of the Eurasiatic orchid genus Himantoglossum s.l. (Orchidaceae).Annals of botany · 2014Article
- Biological pattern and transcriptomic exploration and phylogenetic analysis in the odd floral architecture tree: Helwingia willd.BMC research notes · 2014Article
- Limited genetic divergence among Australian alpine Poa tussock grasses coupled with regional structuring points to ongoing gene flow and taxonomic challenges.Annals of botany · 2014Article
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- Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars.Frontiers in plant science · 2014Article
- Predicting plastid marker variation: can complete plastid genomes from closely related species help?PloS one · 2013Article
- Phylogeny of the genus Chrysanthemum L.: evidence from single-copy nuclear gene and chloroplast DNA sequences.PloS one · 2012Article
- Chasing the hare - evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level within the species rich group Peperomia (Piperaceae).BMC evolutionary biology · 2011Article
- Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels.BMC evolutionary biology · 2010Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phylogenetic analyses of DNA sequences have prompted spectacular progress in assembling the Tree of Life. However, progress in constructing phylogenies among closely related species, at least for plants, has been less encouraging. We show that for plants, the rapid accumulation of DNA characters at higher taxonomic levels has not been matched by conventional sequence loci at the species level, leaving a lack of well-resolved gene trees that is hindering investigations of many fundamental questions in plant evolutionary biology. The most popular approach to address this problem has been to use low-copy nuclear genes as a source of DNA sequence data. However, this has had limited success because levels of variation among nuclear intron sequences across groups of closely related species are extremely variable and generally lower than conventionally used loci, and because no universally useful low-copy nuclear DNA sequence loci have been developed. This suggests that solutions will, for the most part, be lineage-specific, prompting a move away from 'universal' gene thinking for species-level phylogenetics. The benefits and limitations of alternative approaches to locate more variable nuclear loci are discussed and the potential of anonymous nongenic nuclear loci is highlighted. Given the virtually unlimited number of loci that can be generated using these new approaches, it is clear that effective screening will be critical for efficient selection of the most informative loci. Strategies for screening are outlined.
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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.