ArticleNucleic acids research2009
Accurate and efficient reconstruction of deep phylogenies from structured RNAs.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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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.
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Who cites it
33 citing papers in PubMed, 115 citations in OpenAlex.
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- Molecular Apomorphies in the Secondary and Tertiary Structures of Length-Variable Regions (LVRs) of 18S rRNA Shed Light on the Systematic Position of the Family Thaumastellidae (Hemiptera: Heteroptera: Pentatomoidea).International journal of molecular sciences · 2023Article
- Phylogenomic Analyses of the Tenthredinoidea Support the Familial Rank of Athaliidae (Insecta, Tenthredinoidea).Insects · 2022Article
- 18S rRNA variability maps reveal three highly divergent, conserved motifs within Rotifera.BMC ecology and evolution · 2021Article
- Phylogenomics of the Hyalella amphipod species-flock of the Andean Altiplano.Scientific reports · 2021Article
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- Phylogeny of spiny frogsEcology and evolution · 2019Article
- Climate and host-plant associations shaped the evolution of ceutorhynch weevils throughout the Cenozoic.Evolution; international journal of organic evolution · 2018Article
- A mega-cryptic species complex hidden among one of the most common annelids in the North East Atlantic.PloS one · 2018Article
- Molecular phylogeny of Oncaeidae (Copepoda) using nuclear ribosomal internal transcribed spacer (ITS rDNA).PloS one · 2017Article
- Progress, pitfalls and parallel universes: a history of insect phylogenetics.Journal of the Royal Society, Interface · 2016Review
- Origin and higher-level diversification of acariform mites - evidence from nuclear ribosomal genes, extensive taxon sampling, and secondary structure alignment.BMC evolutionary biology · 2015Article
- Five new cryptic freshwater gastropod species from New Caledonia (Caenogastropoda, Truncatelloidea, Tateidae).ZooKeys · 2015Article
- Next-generation sequencing, phylogenetic signal and comparative mitogenomic analyses in Metacrangonyctidae (Amphipoda: Crustacea).BMC genomics · 2014Article
- Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes.Molecular phylogenetics and evolution · 2014Article
- Disparate molecular evolution of two types of repetitive DNAs in the genome of the grasshopper Eyprepocnemis plorans.Heredity · 2014Article
- Stereopsidales--a new order of mushroom-forming fungi.PloS one · 2014Article
- Comparative analysis of mitochondrial genomes in Diplura (hexapoda, arthropoda): taxon sampling is crucial for phylogenetic inferences.Genome biology and evolution · 2014Article
- Fast-evolving mitochondrial DNA in Ceriantharia: a reflection of hexacorallia paraphyly?PloS one · 2014Article
- Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ribosomal RNA (rRNA) genes are probably the most frequently used data source in phylogenetic reconstruction. Individual columns of rRNA alignments are not independent as a consequence of their highly conserved secondary structures. Unless explicitly taken into account, these correlation can distort the phylogenetic signal and/or lead to gross overestimates of tree stability. Maximum likelihood and Bayesian approaches are of course amenable to using RNA-specific substitution models that treat conserved base pairs appropriately, but require accurate secondary structure models as input. So far, however, no accurate and easy-to-use tool has been available for computing structure-aware alignments and consensus structures that can deal with the large rRNAs. The RNAsalsa approach is designed to fill this gap. Capitalizing on the improved accuracy of pairwise consensus structures and informed by a priori knowledge of group-specific structural constraints, the tool provides both alignments and consensus structures that are of sufficient accuracy for routine phylogenetic analysis based on RNA-specific substitution models. The power of the approach is demonstrated using two rRNA data sets: a mitochondrial rRNA set of 26 Mammalia, and a collection of 28S nuclear rRNAs representative of the five major echinoderm groups.
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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.