Intrabreed stratification related to divergent selection regimes in purebred dogs may affect the interpretation of genetic association studies

Journal of Heredity

Volumn 100, Issue , 2009, Pages S28-S36

  Chang, Melanie L ^a   Yokoyama, Jennifer S ^a   Branson, Nick ^b   Dyer, Donna J ^b   Hitte, Christophe ^c   Overall, Karen L ^b   Hamilton, Steven P ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c UNIVERSITÉ DE RENNES 1   (France)

Author keywords

Bayesian analysis; Canine genetics; Maximum parsimony; Phylogenetics; Population stratification; Purebred dogs

Indexed keywords

CANIS FAMILIARIS;

EID: 79952615664     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esp012     Document Type: Article

References (24)

1. Australian National Kennel Council (ANKC), 2005. The extended breed standard of the Border Collie. Victoria (Australia): The Border Collie Club of Victoria and the Australian National Kennel Council.
2. Björnerfeldt S, Hailer F, Nord M, Vilà C. 2008. Assortative mating and fragmentation within dog breeds. BMC Evol Biol. 8:28.
3. Calboli FC, Sampson J, Fretwell N, Balding DJ. 2008. Population structure and inbreeding from pedigree analysis of purebred dogs. Genetics. 179(1):593-601.
4. Chen D, Eulenstein O, Fernández-Baca D. 2004. Rainbow: A toolbox for phylogenetic supertree construction and analysis. Bioinformatics. 20(16): 2872-2873.
5. Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software structure: A simulation study. Mol Ecol. 14(8):2611-2620.
6. Falush D, Stephens M, Pritchard JK. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 164:1567-1587.
7. Falush D, Stephens M, Pritchard JK. 2007. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes. 7(4):574-578.
8. Felsenstein J. 1985. Phylogenies and the comparative method. Am Nat. 125:1-15.
9. Hennig W. 1966. Phylogenetic systematics. Urbana (IL): University of Illinois Press.
10. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 294:2310-2314.
11. Midford PE, Garland T Jr, Maddison WP. 2005. PDAP package of mesquite. Version 1.07. Available from: URL http://mesquiteproject.org/pdap-mesquite/index.html.
12. Overall KL, Hamilton SP, Chang ML. 2006. Understanding the genetic basis of canine anxiety: phenotyping dogs for behavioral, neurochemical, and genetic assessment. J Vet Behav: Clin Appl Res. 1(3):124-141.
13. Parker HG, Kim LV, Sutter NB, Carlson S, Lorentzen TD, Malek TB, Johnson GS, DeFrance HB, Ostrander EA, Kruglyak L. 2004. Genetic structure of the purebred domestic dog. Science. 304:1160-1164.
14. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. 2006. Principal components analysis corrects for stratification in genomewide association studies. Nat Genet. 38(8):904-909.
15. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics. 155:945-959.
16. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, et al. 2007. pLINK: A toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet. 81(3):559-575.
17. Quignon P, Herbin L, Cadieu E, Kirkness EF, Hédan B, Mosher DS, Galibert F, André C, Ostrander EA, Hitte C. 2007. Canine population structure: Assessment and impact of intra-breed stratification on SNP-based association studies. PLoS ONE. 2(12):e1324.
18. Rambaut A. 2008. FigTree v1.1.2. Edinburgh (UK): Institute of Evolutionary Biology, University of Edinburgh.
19. Ronquist F, Huelsenbeck JP. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572-1574.
20. Salmon Hillbertz NH, Isaksson M, Karlsson EK, Hellmén E, Pielberg GR, Savolainen P, Wade CM, von Euler H, Gustafson U, Hedhammar A, et al. 2007. Duplication of FGF3, FGF4, FGF19 and ORAOV1 causes hair ridge and predisposition to dermoid sinus in Ridgeback dogs. Nat Genet. 39(11):1318-1320.
21. Sikes DS, Lewis PS. 2001. Beta software, version 1. PAUPRat: PAUP implementation of the parsimony ratchet. Distributed by the authors. Storrs (CT): Department of Ecology and Evolutionary Biology, University of Connecticut.
22. Sorenson MD, Franzosa EA. 2007. TreeRot, version 3. Boston (MA): Boston University.
23. Sutter NB, Ostrander EA. 2004. Dog Star Rising: The canine genetic system. Nature Genetics. 5:900-910.
24. Swofford DL. 2003. PAUP∗. Phylogenetic analysis using parsimony (∗and other methods). Version 4. Sunderland (MA): Sinauer Associates.