ArticleGenetics2021
Estimating divergence times from DNA sequences.
Article in Genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
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- Tracing the evolutionary histories of ultra-rare variants using variational dating of large ancestral recombination graphs.bioRxiv : the preprint server for biology · 2026Article
- Muscle AMP deaminase activity was lower in Neandertals than in modern humans.Nature communications · 2025Article
- The impact of ancestral, genetic, and environmental influences on germline de novo mutation rates and spectra.Nature communications · 2025Article
- Persistent Gene Flow Suggests an Absence of Reproductive Isolation in an African Antelope Speciation Model.Systematic biology · 2024Article
- Genetic and evolutionary divergence of harbour seals (Biology letters · 2024Article
- African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival.Nature communications · 2024Article
- Inclusion of highly admixed genotypes in grapevine genomic analyses leads to an equivocal reconstruction of its domestication history.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Major Genetic Risk Factors for Dupuytren's Disease Are Inherited From Neandertals.Molecular biology and evolution · 2023Article
- Warthog Genomes Resolve an Evolutionary Conundrum and Reveal Introgression of Disease Resistance Genes.Molecular biology and evolution · 2022Article
- Philippine Ayta possess the highest level of Denisovan ancestry in the world.Current biology : CB · 2021Article
- The deep population history in Africa.Human molecular genetics · 2021Review
- Multiple migrations to the Philippines during the last 50,000 years.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
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3 authors.
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Abstract
The patterns of genetic variation within and among individuals and populations can be used to make inferences about the evolutionary forces that generated those patterns. Numerous population genetic approaches have been developed in order to infer evolutionary history. Here, we present the "Two-Two (TT)" and the "Two-Two-outgroup (TTo)" methods; two closely related approaches for estimating divergence time based in coalescent theory. They rely on sequence data from two haploid genomes (or a single diploid individual) from each of two populations. Under a simple population-divergence model, we derive the probabilities of the possible sample configurations. These probabilities form a set of equations that can be solved to obtain estimates of the model parameters, including population split times, directly from the sequence data. This transparent and computationally efficient approach to infer population divergence time makes it possible to estimate time scaled in generations (assuming a mutation rate), and not as a compound parameter of genetic drift. Using simulations under a range of demographic scenarios, we show that the method is relatively robust to migration and that the TTo method can alleviate biases that can appear from drastic ancestral population size changes. We illustrate the utility of the approaches with some examples, including estimating split times for pairs of human populations as well as providing further evidence for the complex relationship among Neandertals and Denisovans and their ancestors.
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