ArticleJournal of molecular evolution2007
Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches: case studies with diploblast LSU.
Article in Journal of molecular evolution, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 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
8 citing papers in PubMed.
- Ecological changes have driven biotic exchanges across the Indian Ocean.Scientific reports · 2021Article
- Sponge community of the western Black Sea shallow water caves: diversity and spatial distribution.PeerJ · 2018Article
- Phylogenomics of strongylocentrotid sea urchins.BMC evolutionary biology · 2013Article
- Article
- A rooted net of life.Biology direct · 2011Article
- Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: evidence from case studies in the Metazoa.BMC evolutionary biology · 2011Article
- An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models.BMC evolutionary biology · 2009Article
- Molecular evolution of rDNA in early diverging Metazoa: first comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera.BMC evolutionary biology · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many rDNA molecular phylogenetic studies result in trees that are incongruent to either alternative gene tree reconstructions and/or morphological assumptions. One reason for this outcome might be the application of suboptimal phylogenetic substitution models. While the most commonly implemented models describe the evolution of independently evolving characters fairly well, they do not account for character dependencies such as rRNA strands that form a helix in the ribosome. Such nonindependent sites require the use of models that take into account the coevolution of the complete nucleotide pair (doublet). We analyzed 28S rDNA (LSU) demosponge phylogenies using a "doublet" model for pairing sites (rRNA-helices) and compared our findings with the results of "standard" approaches using Bayes factors. We demonstrate that paired and unpaired sites of the same gene result in different reconstructions and that usage of a doublet model leads to more reliable demosponge trees. We show the influence of more sophisticated models on phylogenetic reconstructions of early-branching metazoans and the phylogenetic relationships of demosponge orders.
Indexed as
Identifiers
17460808What 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.