ArticleGenetics2010
A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination.
Article in Genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Recent advances in methods to characterize archaic introgression in modern humans.Genome research · 2026Review
- Not Just Ne Ne-More: New Applications for SMC from Ecology to Phylogenies.Genome biology and evolution · 2026Review
- The Promise of Inferring the Past Using the Ancestral Recombination Graph.Genome biology and evolution · 2024Article
- Exact Decoding of a Sequentially Markov Coalescent Model in Genetics.Journal of the American Statistical Association · 2024Article
- The solution surface of the Li-Stephens haplotype copying model.Algorithms for molecular biology : AMB · 2023Article
- Creating artificial human genomes using generative neural networks.PLoS genetics · 2021Article
- Inference of population history using coalescent HMMs: review and outlook.Current opinion in genetics & development · 2018Review
- Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans.Molecular ecology · 2018Article
- Article
- Detecting hybridization using ancient DNA.Molecular ecology · 2016Review
- Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intrahost HIV Infection.Genetics · 2016Article
- POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.Science (New York, N.Y.) · 2015Article
- Footprints of ancient-balanced polymorphisms in genetic variation data from closely related species.Evolution; international journal of organic evolution · 2015Article
- Theory and applications of a deterministic approximation to the coalescent model.Theoretical population biology · 2014Article
- Detecting structure of haplotypes and local ancestry.Genetics · 2014Article
- Genome-wide inference of ancestral recombination graphs.PLoS genetics · 2014Article
- A sequentially Markov conditional sampling distribution for structured populations with migration and recombination.Theoretical population biology · 2013Article
- Estimating variable effective population sizes from multiple genomes: a sequentially markov conditional sampling distribution approach.Genetics · 2013Article
- Blockwise HMM computation for large-scale population genomic inference.Bioinformatics (Oxford, England) · 2012Article
- Stopping-time resampling and population genetic inference under coalescent models.Statistical applications in genetics and molecular biology · 2012Article
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2 authors.
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Abstract
The multilocus conditional sampling distribution (CSD) describes the probability that an additionally sampled DNA sequence is of a certain type, given that a collection of sequences has already been observed. The CSD has a wide range of applications in both computational biology and population genomics analysis, including phasing genotype data into haplotype data, imputing missing data, estimating recombination rates, inferring local ancestry in admixed populations, and importance sampling of coalescent genealogies. Unfortunately, the true CSD under the coalescent with recombination is not known, so approximations, formulated as hidden Markov models, have been proposed in the past. These approximations have led to a number of useful statistical tools, but it is important to recognize that they were not derived from, though were certainly motivated by, principles underlying the coalescent process. The goal of this article is to develop a principled approach to derive improved CSDs directly from the underlying population genetics model. Our approach is based on the diffusion process approximation and the resulting mathematical expressions admit intuitive genealogical interpretations, which we utilize to introduce further approximations and make our method scalable in the number of loci. The general algorithm presented here applies to an arbitrary number of loci and an arbitrary finite-alleles recurrent mutation model. Empirical results are provided to demonstrate that our new CSDs are in general substantially more accurate than previously proposed approximations.
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