Inference of historical migration rates via haplotype sharing

Bioinformatics

Volumn 29, Issue 13, 2013, Pages

  Palamara, Pier Francesco ^a   Pe'er, Itsik ^a  

^a Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; HAPLOTYPE; HAPLOTYPE MAP; HUMAN; MIGRATION;

HAPLOTYPES; HAPMAP PROJECT; HUMAN MIGRATION; HUMANS; MODELS, GENETIC;

EID: 84879911406     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt239     Document Type: Conference Paper

References (29)

1. Albrechtsen, A. et al. (2010) Natural selection and the distribution of identity-bydescent in the human genome. Genetics, 186, 295-308.
2. Atzmon, G. et al. (2010) Abraham's children in the genome era: Najor jewish diaspora populations comprise distinct genetic clusters with shared middle eastern ancestry. Am. J. Hum. Genet., 86, 850-859.
3. Brisbin, A. et al. (2012) Pcadmix: Principal components-based assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations. Hum. Biol., 84, 343-364.
4. Browning, B. and Browning, S. (2011) A fast, powerful method for detecting identity by descent. Am. J. Hum. Genet., 88, 173-182.
5. Browning, S. and Thompson, E. (2012) Detecting rare variant associations by identity-by-descent mapping in case-control studies. Genetics, 190, 1521-1531.
6. Browning, S.R. and Browning, B.L. (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet., 81, 1084.
7. Campbell, C.L. et al. (2012) North African Jewish and non-Jewish populations form distinctive, orthogonal clusters. Proc. Natl Acad. Sci., 109, 13865-13870.
8. Coast, E. (2001) Maasai demography. PhD thesis, University College London, London, UK.
9. Frazer, K.A. et al. (2007) A second generation human haplotype map of over 3.1 million snps. Nature, 449, 851-861.
10. Gravel, S. (2012) Population genetics models of local ancestry. Genetics, 191, 607-619.
11. Gusev, A. et al. (2009) Whole population, genome-wide mapping of hidden relatedness. Genome Res., 19, 318-326.
12. Gusev, A. et al. (2011) Dash: A method for identical-by-descent haplotype mapping uncovers association with recent variation. Am. J. Hum. Genet., 88, 706-717.
13. Gusev, A. et al. (2012) The architecture of long-range haplotypes shared within and across populations. Mol. Biol. Evol., 29, 473-486.
14. Han, L. and Abney, M. (2012) Using identity by descent estimation with dense genotype data to detect positive selection. Eur. J. Hum. Genet., 21, 205-211.
15. Henn, B. et al. (2010) Fine-scale population structure and the era of next-generation sequencing. Hum. Mol. Genet., 19, R221-R226.
16. Henn, B. et al. (2012) Genomic ancestry of North Africans supports back-to-Africa migrations. PLoS Genet., 8, e1002397.
17. Huff, C. et al. (2011) Maximum-likelihood estimation of recent shared ancestry (ERSA). Genome Res., 21, 768-774.
18. Kingman, J. (1982) The coalescent. Stoch. Process. Appl., 13, 235-248.
19. Kirkpatrick, B. et al. (2011) Pedigree reconstruction using identity by descent. J. Comput. Biol., 18, 1481-1493.
20. Lawson, D. and Falush, D. (2012) Population identification using genetic data. Annu. Rev. Genomics Hum. Genet., 13, 337-361.
21. Li, H. and Durbin, R. (2011) Inference of human population history from individual whole-genome sequences. Nature, 475, 493-496.
22. Liang, L. et al. (2007) Genome: A rapid coalescent-based whole genome simulator. Bioinformatics, 23, 1565-1567.
23. McVean, G.A. and Cardin, N.J. (2005) Approximating the coalescent with recombination. Philos. Trans. R. Soc. Lond. B Biol. Sci., 360, 1387-1393.
24. Palamara, P. et al. (2012) Length distributions of identity by descent reveal fine-scale demographic history. Am. J. Hum. Genet., 91, 809-822.
25. Pool, J. and Nielsen, R. (2009) Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics, 181, 711-719.
26. Ralph, P. and Coop, G. (2013) The geography of recent genetic ancestry across Europe. Plos Biol., 11, e1001555.
27. Roach, J.C. et al. (2010) Analysis of genetic inheritance in a family quartet by wholegenome sequencing. Science, 328, 636-639.
28. Sheehan, S. et al. (2013) Estimating variable effective population sizes from multiple genomes: A sequentially markov conditional sampling distribution approach. Genetics [Epub ahead of print, doi:10.1534/genetics.112.149096, April 22, 2013].
29. Velez, C. et al. (2012) The impact of converso jews on the genomes of modern latin americans. Hum. Genet., 131, 251-263.