ArticleGenome biology and evolution2020
A Novel Approach to Investigate the Effect of Tree Reconstruction Artifacts in Single-Gene Analysis Clarifies Opsin Evolution in Nonbilaterian Metazoans.
Article in Genome biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed.
- G-protein-coupled receptor diversity and evolution in the closest living relatives of metazoa.eLife · 2025Article
- An Ocean of Opsins.Genome biology and evolution · 2025Article
- Genome assembly of Bougainvillia cf. muscus (Cnidaria: Hydrozoa).G3 (Bethesda, Md.) · 2025Article
- The origin, evolution, and molecular diversity of the chemokine system.Life science alliance · 2024Article
- The monoaminergic system is a bilaterian innovation.Nature communications · 2023Article
- Identifying and addressing methodological incongruence in phylogenomics: A review.Evolutionary applications · 2023Review
- nRCFV: a new, dataset-size-independent metric to quantify compositional heterogeneity in nucleotide and amino acid datasets.BMC bioinformatics · 2023Article
- Duplication and Losses of Opsin Genes in Lophotrochozoan Evolution.Molecular biology and evolution · 2023Article
- Deep Diversity: Extensive Variation in the Components of Complex Visual Systems across Animals.Cells · 2022Review
- Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering.Frontiers in chemistry · 2022Review
- Evolutionary Constraint on Visual and Nonvisual Mammalian Opsins.Journal of biological rhythms · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Our ability to correctly reconstruct a phylogenetic tree is strongly affected by both systematic errors and the amount of phylogenetic signal in the data. Current approaches to tackle tree reconstruction artifacts, such as the use of parameter-rich models, do not translate readily to single-gene alignments. This, coupled with the limited amount of phylogenetic information contained in single-gene alignments, makes gene trees particularly difficult to reconstruct. Opsin phylogeny illustrates this problem clearly. Opsins are G-protein coupled receptors utilized in photoreceptive processes across Metazoa and their protein sequences are roughly 300 amino acids long. A number of incongruent opsin phylogenies have been published and opsin evolution remains poorly understood. Here, we present a novel approach, the canary sequence approach, to investigate and potentially circumvent errors in single-gene phylogenies. First, we demonstrate our approach using two well-understood cases of long-branch attraction in single-gene data sets, and simulations. After that, we apply our approach to a large collection of well-characterized opsins to clarify the relationships of the three main opsin subfamilies.
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.