Estimation of historical effective population size using linkage disequilibria with marker data

Journal of Animal Breeding and Genetics

Volumn 129, Issue 4, 2012, Pages 257-270

  Corbin, L J ^a   Liu, A Y H ^a   Bishop, S C ^a   Woolliams, J A ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Effective population size; Horse; Linkage disequilibrium; Method evaluation; Single nucleotide polymorphism

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC MARKER; GENETICS; GENOTYPING TECHNIQUE; HORSE; POPULATION DENSITY; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; GENE FREQUENCY; GENETIC MARKERS; GENOTYPING TECHNIQUES; HORSES; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION DENSITY;

EQUIDAE;

EID: 84863780681     PISSN: 09312668     EISSN: 14390388     Source Type: Journal    
DOI: 10.1111/j.1439-0388.2012.01003.x     Document Type: Article

References (30)

1. Cockerham C.C., Weir B.S. (1977) Digenic descent measures for finite populations. Genet. Res., 30, 121-147.
2. Corbin L.J., Blott S.C., Swinburne J.E., Vaudin M., Bishop S.C., Woolliams J.A. (2010) Linkage disequilibrium and historical effective population size in the Thoroughbred horse. Anim. Genet., 41, 8-15.
3. Cunningham E.P., Dooley J.J., Splan R.K., Bradley D.G. (2001) Microsatellite diversity, pedigree relatedness and the contributions of founder lineages to thoroughbred horses. Anim. Genet., 32, 360-364.
4. Falconer D.S., Mackay T.F.C. (1996) Introduction to Quantitative Genetics, 4th edn. Pearson Education Limited, Harlow, UK.
5. Frisse L., Hudson R.R., Bartoszewicz A., Wall J.D., Donfack J., Di Rienzo A. (2001) Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am. J. Hum. Genet., 69, 831-843.
6. Goddard K.A.B., Hopkins P.J., Hall J.M., Witte J.S. (2000) Linkage disequilibrium and allele-frequency distributions for 114 single-nucleotide polymorphisms in five populations. Am. J. Hum. Genet., 66, 216-234.
7. Hayes B.J., Visscher P.M., McPartlan H.C., Goddard M.E. (2003) Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res., 13, 635-643.
8. Hedrick P.W. (1987) Gametic disequilibrium measures: proceed with caution. Genetics, 117, 331-341.
9. Hill W.G. (1981) Estimation of effective population-size from data on linkage disequilibrium. Genet. Res., 38, 209-216.
10. Hill W.G., Robertson A. (1968) Linkage disequilibrium in finite populations. Theor. Appl. Genet., 38, 226-231.
11. Hudson R.R. (1985) The sampling distribution of linkage disequilibrium under an infinite allele model without selection. Genetics, 109, 611-631.
12. McEvoy B.P., Powell J.E., Goddard M.E., Visscher P.M. (2011) Human population dispersal "Out of Africa" estimated from linkage disequilibrium and allele frequencies of SNPs. Genome Res., 21, 821-829.
13. McVean G.A.T. (2002) A genealogical interpretation of linkage disequilibrium. Genetics, 162, 987-991.
14. Ohta T., Kimura M. (1969) Linkage disequilibrium at steady state determined by random genetic drift and recurrent mutation. Genetics, 63, 229-238.
15. Ohta T., Kimura M. (1971) Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population. Genetics, 68, 571-580.
16. Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M.A.R., Bender D., Maller J., Sklar P., de Bakker P.I.W., Daly M.J., Sham P.C. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet., 81, 559-575.
17. Qanbari S., Pimentel E.C.G., Tetens J., Thaller G., Lichtner P., Sharifi A.R., Simianer H. (2009) The pattern of linkage disequilibrium in German Holstein cattle. Anim. Genet., 41, 346-356.
18. Sved J.A. (1971) Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor. Popul. Biol., 2, 125-141.
19. Sved J.A., Feldman M.W. (1973) Correlation and probability methods for one and two loci. Theor. Popul. Biol., 4, 129-132.
20. Sved J.A., McRae A.F., Visscher P.M. (2008) Divergence between human populations estimated from linkage disequilibrium. Am. J. Hum. Genet., 83, 737-743.
21. Tenesa A., Navarro P., Hayes B.J., Duffy D.L., Clarke G.M., Goddard M.E., Visscher P.M. (2007) Recent human effective population size estimated from linkage disequilibrium. Genome Res., 17, 520-526.
22. Thévenon S., Dayo G.K., Sylla S., Sidibe I., Berthier D., Legros H., Boichard D., Eggen A., Gautier M. (2007) The extent of linkage disequilibrium in a large cattle population of western Africa and its consequences for association studies. Anim. Genet., 38, 277-286.
23. Toosi A., Fernando R.L., Dekkers J.C.M. (2010) Genomic selection in admixed and crossbred populations. J. Anim. Sci., 88, 32-46.
24. Uimari P., Tapio M. (2011) Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds. J. Anim. Sci., 89, 609-614.
25. Wang J.L. (2005) Estimation of effective population sizes from data on genetic markers. Philos. Trans. R. Soc. B-Biol. Sci., 360, 1395-1409.
26. Wang J., Wang W., Li R., Li Y., Tian G., Goodman L., Fan W., Zhang J., Li J., Zhang J., Guo Y., Feng B., Li H., Lu Y., Fang X., Liang H., Du Z., Li D., Zhao Y., Hu Y., Yang Z., Zheng H., Hellmann I., Inouye M., Pool J., Yi X., Zhao J., Duan J., Zhou Y., Qin J., Ma L., Li G., Yang Z., Zhang G., Yang B., Yu C., Liang F., Li W., Li S., Li D., Ni P., Ruan J., Li Q., Zhu H., Liu D., Lu Z., Li N., Guo G., Zhang J., Ye J., Fang L., Hao Q., Chen Q., Liang Y., Su Y., San A., Ping C., Yang S., Chen F., Li L., Zhou K., Zheng H., Ren Y., Yang L., Gao Y., Yang G., Li Z., Feng X., Kristiansen K., Wong G.K.-S., Nielsen R., Durbin R., Bolund L., Zhang X., Li S., Yang H., Wang J. (2008) The diploid genome sequence of an Asian individual. Nature, 456, 60-65.
27. Waples R.S. (2006) A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conserv. Genet., 7, 167-184.
28. Weir B.S. (1996) Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sinauer Associates, Inc., Sunderland, USA.
29. Weir B.S., Hill W.G. (1980) Effect of mating structure on variation in linkage disequilibrium. Genetics, 95, 477-488.
30. Woolliams J.A., Bijma P. (2000) Predicting rates of inbreeding in populations undergoing selection. Genetics, 154, 1851-1864.