ArticleBMC genomics2012
Controversies in modern evolutionary biology: the imperative for error detection and quality control.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 47 citations in OpenAlex.
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- Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes.BMC bioinformatics · 2020Article
- Comparative genomic analysis of eutherian fibroblast growth factor genes.BMC genomics · 2020Article
- The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses.Life (Basel, Switzerland) · 2020Article
- Reconstruction of the Carbohydrate 6-O Sulfotransferase Gene Family Evolution in Vertebrates Reveals Novel Member, CHST16, Lost in Amniotes.Genome biology and evolution · 2020Article
- Comparative analysis of corrected tiger genome provides clues to its neuronal evolution.Scientific reports · 2019Article
- Repertoire-wide gene structure analyses: a case study comparing automatically predicted and manually annotated gene models.BMC genomics · 2019Article
- Referee: Reference Assembly Quality Scores.Genome biology and evolution · 2019Article
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- LEON-BIS: multiple alignment evaluation of sequence neighbours using a Bayesian inference system.BMC bioinformatics · 2016Article
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- Tex19 and Sectm1 concordant molecular phylogenies support co-evolution of both eutherian-specific genes.BMC evolutionary biology · 2015Article
- FixPred: a resource for correction of erroneous protein sequences.Database : the journal of biological databases and curation · 2014Article
- MisPred: a resource for identification of erroneous protein sequences in public databases.Database : the journal of biological databases and curation · 2013Article
- Evaluating the Evolutionary Origins of Unexpected Character Distributions within the Bacterial Planctomycetes-Verrucomicrobia-Chlamydiae Superphylum.Frontiers in microbiology · 2012Article
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe data from high throughput genomics technologies provide unique opportunities for studies of complex biological systems, but also pose many new challenges. The shift to the genome scale in evolutionary biology, for example, has led to many interesting, but often controversial studies. It has been suggested that part of the conflict may be due to errors in the initial sequences. Most gene sequences are predicted by bioinformatics programs and a number of quality issues have been raised, concerning DNA sequencing errors or badly predicted coding regions, particularly in eukaryotes.
resultsWe investigated the impact of these errors on evolutionary studies and specifically on the identification of important genetic events. We focused on the detection of asymmetric evolution after duplication, which has been the subject of controversy recently. Using the human genome as a reference, we established a reliable set of 688 duplicated genes in 13 complete vertebrate genomes, where significantly different evolutionary rates are observed. We estimated the rates at which protein sequence errors occur and are accumulated in the higher-level analyses. We showed that the majority of the detected events (57%) are in fact artifacts due to the putative erroneous sequences and that these artifacts are sufficient to mask the true functional significance of the events.
conclusionsInitial errors are accumulated throughout the evolutionary analysis, generating artificially high rates of event predictions and leading to substantial uncertainty in the conclusions. This study emphasizes the urgent need for error detection and quality control strategies in order to efficiently extract knowledge from the new genome data.
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