Loter: A software package to infer local ancestry for a wide range of species

Molecular Biology and Evolution

Volumn 35, Issue 9, 2018, Pages 2318-2326

  Dias Alves, Thomas ^a   Mairal, Julien ^b   Blum, Michael G B ^a  

^a UNIV GRENOBLE ALPES   (France)

^b UNIV GRENOBLE ALPES   (France)

Author keywords

Admixture; Local ancestry; Optimization; Population genetics

Indexed keywords

AFRICAN; ANCESTRY GROUP; ARTICLE; EUROPEAN; GENOTYPE; HAPLOTYPE; HUMAN; NONHUMAN; PHENOTYPIC VARIATION; POPULATION GENETICS; POPULUS BALSAMIFERA; POPULUS TRICHOCARPA; SIMULATION; SOFTWARE; SPECIES; COMPARATIVE STUDY; GENETIC PROCEDURES; GENETICS; POPULUS;

GENETIC TECHNIQUES; HAPLOTYPES; HUMANS; POPULUS; SOFTWARE;

EID: 85055347062     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msy126     Document Type: Article

References (34)

1. Baran Y, Pasaniuc B, Sankararaman S, Torgerson DG, Gignoux C, Eng C, Rodriguez-Cintron W, Chapela R, Ford JG, Avila PC. 2012. Fast and accurate inference of local ancestry in Latino populations. Bioinformatics 28(10):1359-1367.
2. Bhatia G, Patterson N, Sankararaman S, Price AL. 2013. Estimating and interpreting FST: the impact of rare variants. Genome Res. 23(9):1514-1521.
3. Brandvain Y, Kenney AM, Flagel L, Coop G, Sweigart AL. 2014. Speciation and Introgression between Mimulus nasutus and Mimulus guttatus. PLoS Genet. 10(6):e1004410.
4. Breiman L. 1996. Bagging predictors. Mach Learn. 24(2):123-140.
5. Browning SR, Browning BL. 2007. Rapid and accurate haplotype phasing andmissing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 81(5):1084-1097.
6. Browning SR, Browning BL. 2011. Haplotype phasing: existing methods and new developments. Nat Rev Genet. 12(10):703-714.
7. Bryc K, Durand E, Macpherson JM, Reich D, Mountain J. 2015. The genetic ancestry of African, Latino, and European Americans across the United States. Am J Hum Genet. 96(1):37-53.
8. Buerkle CA, Lexer C. 2008. Admixture as the basis for genetic mapping. Trends Ecol Evol. 23(12):686-694.
9. Corbett-Detig R, Nielsen R. 2017. A hidden Markov model approach for simultaneously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy. PLoS Genet. 13:e1006529.
10. Gravel S. 2012. Population genetics models of local ancestry. Genetics 191(2):607-619.
11. Hufford MB, Lubinksy P, Pyhäjärvi T, Devengenzo MT, Ellstrand NC, Ross-Ibarra J. 2013. The genomic signature of crop-wild introgression in maize. PLoS Genet. 9(5):e1003477.
12. International HapMap 3 Consortium 2010. Integrating common and rare genetic variation in diverse human populations. Nature 467(7311):52-58.
13. Kimmel G, Sharan R, Shamir R. 2003. Identifying blocks and subpopulations in noisy snp data. International Workshop on Algorithms in Bioinformatics. Berlin, Heidelberg: Springer. p. 303-319.
14. Li N, Stephens M. 2003. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165:2213-2233.
15. Lindtke D, Gonzalez-Martinez S, Macaya-Sanz D, Lexer C. 2013. Admixture mapping of quantitative traits in Populus hybrid zones: power and limitations. Heredity 111(6):474-485.
16. Liu S, Lorenzen ED, Fumagalli M, Li B, Harris K, Xiong Z, Zhou L, Korneliussen TS, Somel M, Babbitt C. 2014. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell 157(4):785-794.
17. Malinsky M, Svardal H, Tyers AM, Miska EA, Genner MJ, Turner GF, Durbin R. 2017. Whole genome sequences of malawi cichlids reveal multiple radiations interconnected by gene flow. BioRxiv 143859.
18. Maples BK, Gravel S, Kenny EE, Bustamante CD. 2013. RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference. Am J Hum Genet. 93(2):278-288.
19. Medugorac I, Graf A, Grohs C, Rothammer S, Zagdsuren Y, Gladyr E, Zinovieva N, Barbieri J, Seichter D, Russ I, et al. 2017. Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks. Nat Genet. 49(3):470-475.
20. Ni X, Yang X, Guo W, Yuan K, Zhou Y, Ma Z, Xu S. 2016. Length distribution of ancestral tracks under a general admixture model and its applications in population history inference. Sci Rep. 6:20048.
21. Pasaniuc B, Sankararaman S, Kimmel G, Halperin E. 2009. Inference of locus-specific ancestry in closely related populations. Bioinformatics 25(12):i213-i221.
22. Patin E, Siddle KJ, Laval G, Quach H, Harmant C, Becker N, Froment A, Régnault B, Lemée L, Gravel S, et al. 2014. The impact of agricultural emergence on the genetic history of African rainforest huntergatherers and agriculturalists. Nat Commun. 5(1):3163.
23. Patterson N, Hattangadi N, Lane B, Lohmueller KE, Hafler DA, Oksenberg JR, Hauser SL, Smith MW, O'Brien SJ, Altshuler D, et al. 2004. Methods for high-density admixture mapping of disease genes. Am J Hum Genet. 74(5):979-1000.
24. Payseur BA, Rieseberg LH. 2016. A genomic perspective on hybridization and speciation. Mol Ecol. 25(11):2337-2360.
25. Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, Ruczinski I, Beaty TH, Mathias R, Reich D, Myers S. 2009. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 5(6):e1000519.
26. Sankararaman S, Kimmel G, Halperin E, Jordan MI. 2008. On the inference of ancestries in admixed populations. Genome Res. 18(4):668-675.
27. Sankararaman S, Sridhar S, Kimmel G, Halperin E. 2008. Estimating local ancestry in admixed populations. Am J Hum Genet. 82(2):290-303.
28. Scheet P, Stephens M. 2006. A fast and flexible statisticalmodel for largescale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet. 78(4):629-644.
29. Seldin MF, Pasaniuc B, Price AL. 2011. New approaches to disease mapping in admixed populations. Nat Rev Genet. 12(8):523-528.
30. Suarez-Gonzalez A, Hefer CA, Christe C, Corea O, Lexer C, Cronk QC, Douglas CJ. 2016. Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood). Mol Ecol. 25(11):2427-2442.
31. vonHoldt BM, Kays R, Pollinger JP, Wayne RK. 2016. Admixture mapping identifies introgressed genomic regions in North American canids. Mol Ecol. 25(11):2443-2453.
32. Xue J, Lencz T, Darvasi A, Pe'er I, Carmi S. 2017. The time and place of European admixture in Ashkenazi Jewish history. PLoS Genet. 13(4):e1006644.
33. Zhang K, Deng M, Chen T, Waterman MS, Sun F. 2002. A dynamic programming algorithm for haplotype block partitioning. Proc Natl Acad Sci U S A 99(11):7335-7339.
34. Zhou Q, Zhao L, Guan Y. 2016. Strong selection at MHC in Mexicans since admixture. PLoS Genet. 12(2):e1005847.