Complex population structure in African village dogs and its implications for inferring dog domestication history

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 33, 2009, Pages 13903-13908

  Boyko, Adam R ^a   Boyko, Ryan H ^b   Boyko, Corin M ^b   Parker, Heidi G ^c   Castelhano, Marta ^d   Corey, Liz ^d   Degenhardt, Jeremiah D ^a   Auton, Adam ^a   Hedimbi, Marius ^e   Kityo, Robert ^f   Ostrander, Elaine A ^c   Schoenebeck, Jeffrey ^c   Todhunter, Rory J ^d   Jones, Paul ^g   Bustamante, Carlos D ^a  

^a Plant Breeding and Genetics Section in the School of Integrative Plant Science   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^d Department of Obstetrics Gynecology   (United States)

^e UNIVERSITY OF NAMIBIA   (Namibia)

^f MAKERERE UNIVERSITY   (Uganda)

^g WALTHAM CENTRE FOR PET NUTRITION   (United Kingdom)

Author keywords

Canis familiaris; Microsatellites; Principal component analysis; Single nucleotide polymorphisms

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; BREED DIFFERENCE; CONTROLLED STUDY; DOG; DOMESTICATION; GENETIC VARIABILITY; HAPLOTYPE; MEASUREMENT; MICROSATELLITE MARKER; NONHUMAN; POPULATION GENETIC STRUCTURE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

AFRICA; ANIMALS; ANIMALS, DOMESTIC; BREEDING; DNA, MITOCHONDRIAL; DOGS; GENETIC VARIATION; GENETICS, POPULATION; MICROSATELLITE REPEATS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS;

CANIS FAMILIARIS;

EID: 69549122686     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0902129106     Document Type: Article

References (29)

1. Wayne R (2001) Consequences of domestication: Morphological diversity of the dog. In The Genetics of the Dog, eds Ruvinsky A, Sampson J (CABI Publishing, Oxon, UK), pp43-60.
2. Clutton-Brock J (1995) Origins of the dog: Domestication and early history. In The Domestic Dog, Its Evolution, Behavior and Interactions with People, ed Serpell J CUP, Cambridge), pp 7-20.
3. Vilà C, Maldonado J, Wayne R (1999) Phylogenetic relationships, evolution, and genetic diversity of the domestic dog. J Hered 90:71-77. (Pubitemid 29067904)
4. Germonpré M, et al. (2009) Fossil dogs and wolves from Palaeolithic sites in Belgium, the Ukraine and Russia: Osteometry, ancient DNA and stable isotopes. J Arch Sci 36:473-490.
5. Vilà C, et al. (1997) Multiple and ancient origins of the domestic dog. Science 276:1687-1689. (Pubitemid 27421973)
6. Savolainen P, Zhang Y, Luo J, Lundeberg J, Leitner T (2002) Genetic evidence for an East Asian origin of domestic dogs. Science 298:1610-1613. (Pubitemid 35387197)
7. Coppinger R, Coppinger L (2001) in Dogs: A Startling New Understanding of Canine Origin, Behavior and Evolution (Scribner, New York).
8. Dobney K, Larson G (2006) Genetics and animal domestication: New windows on an elusive process. J Zool 269:261-271. (Pubitemid 43780607)
9. Miklosi A (2008) in Dog Behaviour, Evolution, and Cognition (Oxford Univ Press, Oxford), p 304.
10. Pires A, et al. (2006) Mitochondrial DNA sequence variation in Portuguese native breed dogs: diversity and phylogenetic affinities. J Hered 97:318-330. (Pubitemid 44313648)
11. Irion D, Schaffer A, Grant S, Wilton A, Pedersen N (2005) Genetic variation analysis of the Bali street dog using microsatellites. BMC Genet 6:6. (Pubitemid 41363925)
12. Runstadler J, Angles J, Pedersen N (2006) Dog leucocyte antigen class II diversity and relationships among indigenous dogs of the island nations of Indonesia (Bali). Australia and New Guinea Tissue Antigens 68:418-426. (Pubitemid 44707053)
13. (2008) Police Zone. Encyclopædia Britannica. Online Ed.
14. Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945-949. (Pubitemid 30397141)
15. Parker HG, et al. (2004) Genetic structure of the purebred domestic dog. Science 304:1160-1164.
16. Parker H, et al. (2007) Breed relationships facilitate fine-mapping studies: A 7.8-kb deletion cosegregates with Collie eye anomaly across multiple dog breeds. Genome Res 2007:1562-1571. (Pubitemid 350074852)
17. Gundry R, et al. (2007) Mitochondrial DNA analysis of the domestic dog: Control region variation within and among breeds. J Forensic Sci 52:562-572. (Pubitemid 46646779)
18. Savolainen P, Leitner T, Wilton A, Matisoo-Smith E, Lundeberg J (2004) A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA. Proc Natl Acad Sci USA 101:12387-12390. (Pubitemid 39145453)
19. Björnerfeldt S, Webster M, Vilà C (2006) Relaxation of selective constraint on dog mitochondrial DNA following domestication. Genome Res 16:990-994.
20. Jones P, et al. (2008) Single-nucleotide-polymorphism-based association mapping of dog stereotypes. Genetics 179:1033-1044.
21. Purcell S, et al. (2007) PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559-575. (Pubitemid 47330214)
22. Patterson N, Price A, Reich D (2006) Population structure and eigenanalysis. PLoS Genet 2:e190.
23. Kaeuffer R, Ré ale D, Coltman D, Pontier D (2007) Detecting population structure using STRUCTURE software: Effect of background linkage disequilibrium. J Hered 99:374-380.
24. Excoffier L, Schneider S (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol Bioinform Online 1:47-50.
25. Jakobsson M, Rosenberg N (2007) CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801-1806. (Pubitemid 47250313)
26. Weir B, Cockerman C (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370. (Pubitemid 16277759)
27. R Development Core Team (2008) in R: A language and environment for statistical computing (R Foundation for Statistical Computing, Vienna, Austria).
28. Rosenberg N (2004) DISTRUCT: A program for the graphical display of population structure. Mol Ecol Notes 4:137-138.
29. Ewens W (1972) The sampling theory of selectively neutral alleles. Theor Pop Biol 3:87-112.