ArticleGenetics2018
Inferring the Probability of the Derived
Article in Genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers, 1 of them a synthesis that pooled it.
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Who cites it
84 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Multi-ancestry sequencing-based genome-wide association study of C-reactive protein in 513,273 genomes.Nature communications · 2025Pooled it
- Gene-level complexity explains genome-wide variation in the distribution of fitness effects.Molecular biology and evolution · 2026Article
- Local Trade-Offs Shape Flower Size Evolution Across Arabidopsis thaliana Distribution.Molecular ecology · 2026Article
- Estimating the evolutionary fitness of specific synonymous codon changes.Molecular biology and evolution · 2026Article
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- Population history rather than tree age contributes to the evolutionary importance of ancient trees in an endangered conifer.Nature plants · 2026Article
- Sequence context and methylation interact to shape germline mutation rate variation at CpG sites.PLoS genetics · 2026Article
- Interpreting GC content differences across populations at polymorphic sites.bioRxiv : the preprint server for biology · 2026Article
- Sequence context and methylation interact to shape germline mutation rate variation at CpG sites.bioRxiv : the preprint server for biology · 2026Article
- Identification of Genetic Variation Associated With Heat Tolerance in Cowpea (Vigna unguiculata L. Walp.).Molecular ecology · 2026Article
- Natural selection and recombination interact to structure genome-wide variation in pines.The Plant journal : for cell and molecular biology · 2026Article
- The distribution of fitness effects of new mutations in regulatory regions of thebioRxiv : the preprint server for biology · 2026Article
- Genomic consequences of residual recombination in a hybrid apomictic hickory complex.Nature communications · 2026Article
- Evolutionary history and genomic consequences of polyploidization in natural populations ofHorticulture research · 2026Article
- Polarising SNPs Without Outgroup.Molecular ecology resources · 2026Article
- A Test of the Long-Term Efficiency of Genetic Rescue With Drosophila melanogaster.Molecular ecology · 2025Article
- Whole-Genome Duplication Reshapes Adaptation: Autotetraploid Arabidopsis arenosa Leverages its High Genetic Variation to Compensate for Selection Constraints.Molecular biology and evolution · 2025Article
- Heterogeneous constraint and adaptation across the malaria parasite life cycle.Proceedings. Biological sciences · 2025Article
- Whole-genome duplication increases genetic diversity and load in outcrossingProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Population Genomic Analysis Provides Insights Into the Evolution and Conservation of Two Critically Endangered Musk Deer Species.Evolutionary applications · 2025Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is known that the allele ancestral to the variation at a polymorphic site cannot be assigned with certainty, and that the most frequently used method to assign the ancestral state-maximum parsimony-is prone to misinference. Estimates of counts of sites that have a certain number of copies of the derived allele in a sample (the unfolded site frequency spectrum, uSFS) made by parsimony are therefore also biased. We previously developed a maximum likelihood method to estimate the uSFS for a focal species using information from two outgroups while assuming simple models of nucleotide substitution. Here, we extend this approach to allow multiple outgroups (implemented for three outgroups), potentially any phylogenetic tree topology, and more complex models of nucleotide substitution. We find, however, that two outgroups and the Kimura two-parameter model are adequate for uSFS inference in most cases. We show that using parsimony to infer the ancestral state at a specific site seriously breaks down in two situations. The first is where the outgroups provide no information about the ancestral state of variation in the focal species. In this case, nucleotide variation will be underestimated if such sites are excluded. The second is where the minor allele in the focal species agrees with the allelic state of the outgroups. In this situation, parsimony tends to overestimate the probability of the major allele being derived, because it fails to account for the fact that sites with a high frequency of the derived allele tend to be rare. We present a method that corrects this deficiency and is capable of providing nearly unbiased estimates of ancestral state probabilities on a site-by-site basis and the uSFS.
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