ArticleTheoretical population biology2009
An approximate likelihood for genetic data under a model with recombination and population splitting.
Article in Theoretical population biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Inference of population history using coalescent HMMs: review and outlook.Current opinion in genetics & development · 2018Review
- Theory and applications of a deterministic approximation to the coalescent model.Theoretical population biology · 2014Article
- Distinguishing migration from isolation using genes with intragenic recombination: detecting introgression in the Drosophila simulans species complex.BMC evolutionary biology · 2014Article
- A sequentially Markov conditional sampling distribution for structured populations with migration and recombination.Theoretical population biology · 2013Article
- Article
- Blockwise HMM computation for large-scale population genomic inference.Bioinformatics (Oxford, England) · 2012Article
- An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination.Genetics · 2011Article
- To pool, or not to pool?Genetics · 2010Article
- A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination.Genetics · 2010Article
- Population genetic inference from genomic sequence variation.Genome research · 2010Review
- Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species.Heredity · 2009Review
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3 authors.
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Abstract
We describe a new approximate likelihood for population genetic data under a model in which a single ancestral population has split into two daughter populations. The approximate likelihood is based on the 'Product of Approximate Conditionals' likelihood and 'copying model' of Li and Stephens [Li, N., Stephens, M., 2003. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165 (4), 2213-2233]. The approach developed here may be used for efficient approximate likelihood-based analyses of unlinked data. However our copying model also considers the effects of recombination. Hence, a more important application is to loosely-linked haplotype data, for which efficient statistical models explicitly featuring non-equilibrium population structure have so far been unavailable. Thus, in addition to the information in allele frequency differences about the timing of the population split, the method can also extract information from the lengths of haplotypes shared between the populations. There are a number of challenges posed by extracting such information, which makes parameter estimation difficult. We discuss how the approach could be extended to identify haplotypes introduced by migrants.
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