ArticleGenetics2010
The effect of recombination on the reconstruction of ancestral sequences.
Article in Genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
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Who cites it
55 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Challenges in Elucidating HIV-1 Genetic Diversity in the Middle East and North Africa: A Review Based on a Systematic Search.Viruses · 2025Pooled it
- Global Population Structure and Dynamics of Wheat Powdery Mildew.Molecular ecology · 2026Article
- Concatenation, Conflict, and Complexity: Genealogical Heterogeneity Mimics Substitutional Heterogeneity for Nucleotide Model Selection.Journal of molecular evolution · 2026Article
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- Genomic characterization and pathogenicity assessment of a novel strain of duck reovirus identified in China.Frontiers in microbiology · 2026Article
- Evolutionary Dynamics and Transboundary Spread of Senecavirus A: The Role of Recombination and Global Swine Trade.Transboundary and emerging diseases · 2026Article
- Article
- Review
- Recombination Analysis of Geminiviruses Using Recombination Detection Program (RDP).Methods in molecular biology (Clifton, N.J.) · 2025Article
- Applications of ancestral sequence reconstruction for understanding the evolution of plant specialized metabolism.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Untangling lineage introductions, persistence and transmission drivers of HP-PRRSV sublineage 8.7.Nature communications · 2024Article
- Intra- and inter-host origin, evolution dynamics and spatial-temporal transmission characteristics of circoviruses.Frontiers in immunology · 2024Article
- Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation.BMC genomics · 2023Article
- Molecular evolution analysis of three species gyroviruses in China from 2018 to 2019.Virus research · 2023Article
- Review
- Consequences of Genetic Recombination on Protein Folding Stability.Journal of molecular evolution · 2023Article
- Article
- Newly Characterized Porcine Epidemic Diarrhea Virus GII Subtype Strain.Transboundary and emerging diseases · 2023Article
- Evaluation of recombination detection methods for viral sequencing.Virus evolution · 2023Article
- Molecular characterization of Infectious Bursal Disease Virus isolated in Chile reveals several mutations in VP2 coding region and a reassortment in its genome.Veterinary research communications · 2022Article
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Authors and funding
2 authors.
Funding
Abstract
While a variety of methods exist to reconstruct ancestral sequences, all of them assume that a single phylogeny underlies all the positions in the alignment and therefore that recombination has not taken place. Using computer simulations we show that recombination can severely bias ancestral sequence reconstruction (ASR), and quantify this effect. If recombination is ignored, the ancestral sequences recovered can be quite distinct from the grand most recent common ancestor (GMRCA) of the sample and better resemble the concatenate of partial most recent common ancestors (MRCAs) at each recombination fragment. When independent phylogenetic trees are assumed for the different recombinant segments, the estimation of the fragment MRCAs improves significantly. Importantly, we show that recombination can change the biological predictions derived from ASRs carried out with real data. Given that recombination is widespread on nuclear genes and in particular in RNA viruses and some bacteria, the reconstruction of ancestral sequences in these cases should consider the potential impact of recombination and ideally be carried out using approaches that accommodate recombination.
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