Approximating the coalescent with recombination

Philosophical Transactions of the Royal Society B: Biological Sciences - Tập 360 Số 1459 - Trang 1387-1393 - 2005
Gil McVean1,2,3,4, Niall J. Cardin1,2,4,5
1Department of Statistics, 1 South Parks Road, University of OxfordOxford, OX1 3TG, UK
2Find this author on PubMed
3Gilean A.T McVean
4Google Scholar
5Niall J Cardin

Tóm tắt

The coalescent with recombination describes the distribution of genealogical histories and resulting patterns of genetic variation in samples of DNA sequences from natural populations. However, using the model as the basis for inference is currently severely restricted by the computational challenge of estimating the likelihood. We discuss why the coalescent with recombination is so challenging to work with and explore whether simpler models, under which inference is more tractable, may prove useful for genealogy-based inference. We introduce a simplification of the coalescent process in which coalescence between lineages with no overlapping ancestral material is banned. The resulting process has a simple Markovian structure when generating genealogies sequentially along a sequence, yet has very similar properties to the full model, both in terms of describing patterns of genetic variation and as the basis for statistical inference.

Từ khóa


Tài liệu tham khảo

Beaumont M.A, 2002, Approximate Bayesian computation in population genetics, Genetics, 162, 2025, 10.1093/genetics/162.4.2025

10.1038/ng1376

Fearnhead P, 2001, Estimating recombination rates from population genetic data, Genetics, 159, 1299, 10.1093/genetics/159.3.1299

10.1111/1467-9868.00355

10.1534/genetics.103.021584

10.1006/tpbi.1998.1390

Griffiths R.C, 1996, IMA volume on mathematical population genetics, 257

10.1016/0040-5809(75)90028-3

10.1007/BF01245622

10.1016/0040-5809(83)90013-8

10.1017/S0016672300023776

Hudson R.R, 1990, Oxford surveys in evolutionary biology, 1

Hudson R.R, 2001, Two-locus sampling distributions and their application, Genetics, 159, 1805, 10.1093/genetics/159.4.1805

Hudson R.R, 1985, Statistical properties of the number of recombination events in the history of a sample of DNA sequences, Genetics, 111, 147, 10.1093/genetics/111.1.147

Kuhner M.K, 2000, Usefulness of single nucleotide polymorphism data for estimating population parameters, Genetics, 156, 439, 10.1093/genetics/156.1.439

Li N, 2003, Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data, Genetics, 165, 2213, 10.1093/genetics/165.4.2213

McVean G.A.T, 2002, A genealogical interpretation of linkage disequilibrium, Genetics, 162, 987, 10.1093/genetics/162.2.987

McVean G, 2002, A coalescent-based method for detecting and estimating recombination rates from gene sequences, Genetics, 160, 1231, 10.1093/genetics/160.3.1231

10.1126/science.1092500

Myers S.R, 2003, Bounds on the minimum number of recombination events in a sample history, Genetics, 163, 375, 10.1093/genetics/163.1.375

Nielsen R, 2000, Estimation of population parameters and recombination rates from single nucleotide polymorphisms, Genetics, 154, 931, 10.1093/genetics/154.2.931

Ohta T, 1971, Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population, Genetics, 68, 571, 10.1093/genetics/68.4.571

Pluzhnikov A, 1996, Optimal sequencing strategies for surveying molecular genetic diversity, Genetics, 144, 1247, 10.1093/genetics/144.3.1247

10.1038/nrg1227

10.1017/S0016672396002571

10.1093/oxfordjournals.molbev.a026228

Weir B.S, 1986, Nonuniform recombination within the human β-globin gene cluster, Am. J. Hum. Genet, 38, 776

10.1006/tpbi.1998.1403

10.1093/oxfordjournals.molbev.a003733

Thông tin
Thông tin xuất bản

Philosophical Transactions of the Royal Society B: Biological Sciences

Tập 360 Số 1459

1387-1393

Thông tin tác giả