Tracking footprints of artificial selection in the dog genome

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

Volumn 107, Issue 3, 2010, Pages 1160-1165

  Akey, Joshua M ^a   Ruhe, Alison L ^b   Akey, Dayna T ^a   Wong, Aaron K ^b   Connelly, Caitlin F ^a   Madeoy, Jennifer ^a   Nicholas, Thomas J ^a   Neff, Mark W ^b,c,d  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

^d VAN ANDEL RESEARCH INSTITUTE   (United States)

Author keywords

Canis lupis; Evolution

Indexed keywords

ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; DNA FOOTPRINTING; DOG; GENE IDENTIFICATION; GENOME; NONHUMAN; PHENOTYPE; PHENOTYPIC VARIATION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; WRINKLE;

ANIMALS; DOGS; GENOME; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC; SPECIES SPECIFICITY;

CANIS; CANIS FAMILIARIS;

EID: 75749154475     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0909918107     Document Type: Article

References (42)

1. American Kennel Club (1998) in The Complete Dog Book, eds American Kennel Club Staff (Howell Book House, Foster City).
2. Sutter NB, Ostrander EA (2004) Dog star rising: the canine genetic system. Nat Rev Genet 5:900-910.
3. Neff MW, Rine J (2006) A fetching model organism. Cell 124:229-231.
4. Vilà C, et al. (1997) Multiple and ancient origins of the domestic dog. Science 276: 1687-1689.
5. Leonard JA, et al. (2002) Ancient DNA evidence for Old World origin of New World dogs. Science 298:1613-1616.
6. Darwin C (1859) On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. (John Murray, London) 1st Ed.
7. Sutter NB, et al. (2007) A single IGF1 allele is a major determinant of small size in dogs. Science 316:112-115.
8. Parker HG, et al. (2009) An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs. Science 325:995-998.
9. Cadieu E, et al. (2009) Coat variation in the domestic dog is governed by variants in three genes. Science 326:150-153.
10. Akey JM (2009) Constructing genomic maps of positive selection in humans: where do we go from here? Genome Res 19:711-722.
11. Pollinger JP, et al. (2005) Selective sweep mapping of genes with large phenotypic effects. Genome Res 15:1809-1819.
12. Lindblad-Toh K, et al. (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438:803-819.
13. Karlsson EK, et al. (2007) Efficient mapping of mendelian traits in dogs through genome-wide association. Nat Genet 39:1321-1328.
14. Innan H, Kim Y (2008) Detecting local adaptation using the joint sampling of polymorphism data in the parental and derived populations. Genetics 179:1713-1720.
15. Weir BS (1996) Genetic Data Analysis II (Sinauer Associates, Inc. Publishers, Sunderland).
16. Shriver MD, et al. (2004) The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs. Hum Genomics 1:274-286.
17. Weir BS, Cardon LR, Anderson AD, Nielsen DM, Hill WG (2005) Measures of human population structure show heterogeneity among genomic regions. Genome Res 15: 1468-1476.
18. Kelley JL, Madeoy J, Calhoun JC, Swanson W, Akey JM (2006) Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Res 16: 980-989.
19. Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A map of recent positive selection in the human genome. PLoS Biol 4:e72.
20. Grosschedl R, Giese K, Pagel J (1994) HMG domain proteins: architectural elements in the assembly of nucleoprotein structures. Trends Genet 10:94-100.
21. Zhou X, Benson KF, Ashar HR, Chada K (1995) Mutation responsible for the mouse pygmy phenotype in the developmentally regulated factor HMGI-C. Nature 377: 771-774.
22. Dhoot GK, et al. (2001) Regulation of Wnt signaling and embryo patterning by an extracellular sulfatase. Science 293:1663-1668.
23. Kosiol C, et al. (2008) Patterns of positive selection in six Mammalian genomes. PLoS Genet 4:e1000144.
24. Ye YH, Chenoweth SF, McGraw EA (2009) Effective but costly, evolved mechanisms of defense against a virulent opportunistic pathogen in Drosophila melanogaster. PLoS Pathog 5:e1000385.
25. Hoekstra HE, Coyne JA (2007) The locus of evolution: evo devo and the genetics of adaptation. Evolution 61:995-1016.
26. Wray GA (2007) The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 8:206-216.
27. Wang RL, Stec A, Hey J, Lukens L, Doebley J (1999) The limits of selection during maize domestication. Nature 398:236-239.
28. Cong B, Barrero LS, Tanksley SD (2008) Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nat Genet 40:800-804.
29. Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309-1321.
30. Jacob F (1977) Evolution and tinkering. Science 196:1161-1166.
31. Zanna G, et al. (2008) Cutaneous mucinosis in Shar-Pei dogs is due to hyaluronic acid deposition and is associated with high levels of hyaluronic acid in serum. Vet Dermatol 19:314-318.
32. Ramsden CA, et al. (2000) A new disorder of hyaluronan metabolism associated with generalized folding and thickening of the skin. J Pediatr 136:62-68.
33. Agresti A (2002) Categorical Data Analysis, eds Agresti A, David HA (Wiley, New Jersey), 2nd Ed, pp 165-196.
34. Harr B, Kauer M, Schlötterer C (2002) Hitchhiking mapping: a population-based finemapping strategy for adaptive mutations in Drosophila melanogaster. Proc Natl Acad Sci USA 99:12949-12954.
35. Frayling TM, et al. (2007) A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science 316:889-894.
36. Bell GI, Karam JH, RutterWJ (1981) Polymorphic DNA region adjacent to the 5′ end of the human insulin gene. Proc Natl Acad Sci USA 78:5759-5763.
37. Oberbauer AM, et al. (2003) Alternatives to blood as a source of DNA for large-scale scanning studies of canine genome linkages. Vet Res Commun 27:27-38.
38. Epstein MP, Duren WL, BoehnkeM(2000) Improved inference of relationship for pairs of individuals. Am J Hum Genet 67:1219-1231.
39. Wigginton JE, Cutler DJ, Abecasis GR (2005) A note on exact tests of Hardy-Weinberg equilibrium. Am J Hum Genet 76:887-893.
40. Biswas S, Scheinfeldt LB, Akey JM (2009) Genome-wide insights into the patterns and determinants of fine-scale population structure in humans. Am J Hum Genet 84: 641-650.
41. Hudson RR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18:337-338.
42. Guedj M, Wojcik J, Della-Chiesa E, Nuel G, Forner K (2006) A fast, unbiased and exact allelic test for case-control association studies. Hum Hered 61:210-221.