Deciphering the Origin of Dogs: From Fossils to Genomes

Literature Cited

1. 1. Am. Kennel Club. 1992. The Complete Dog Book: The Photograph, History, and Official Standard of Every Breed Admitted to AKC Registration, and the Selection, Training, Breeding, Care, and Feeding of Pure-Bred Dogs New York/Toronto: Howell Book House
2. Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB. 2.  et al. 2005. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438:803–19 [Google Scholar]
3. Drake AG, Klingenberg CP, Heard AESB, McPeek EMA. 3.  2010. Large‐scale diversification of skull shape in domestic dogs: disparity and modularity. Am. Nat. 175:289–301 [Google Scholar]
4. Wayne RK. 4.  1986. Limb morphology of domestic and wild canids: the influence of development on morphologic change. J. Morphol. 187:301–19 [Google Scholar]
5. Wayne RK. 5.  1986. Cranial morphology of domestic and wild canids: the influence of development on morphological change. Evolution 40:243–61 [Google Scholar]
6. Cadieu E, Neff MW, Quignon P, Walsh K, Chase K. 6.  et al. 2009. Coat variation in the domestic dog is governed by variants in three genes. Science 326:150–53 [Google Scholar]
7. Sutter NB, Bustamante CD, Chase K, Gray MM, Zhao K. 7.  et al. 2007. A single IGF1 allele is a major determinant of small size in dogs. Science 316:112–15 [Google Scholar]
8. Boyko AR, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD. 8.  et al. 2010. A simple genetic architecture underlies morphological variation in dogs. PLOS Biol 8:e1000451 [Google Scholar]
9. Hayward JJ, Castelhano MG, Oliveira KC, Corey E, Balkman C. 9.  et al. 2016. Complex disease and phenotype mapping in the domestic dog. Nat. Commun. 7:10460 [Google Scholar]
10. Rimbault M, Ostrander EA. 10.  2012. So many doggone traits: mapping genetics of multiple phenotypes in the domestic dog. Hum. Mol. Genet. 21:R52–57 [Google Scholar]
11. Vaysse A, Ratnakumar A, Derrien T, Axelsson E, Rosengren Pielberg G. 11.  et al. 2011. Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLOS Genet 7:e1002316 [Google Scholar]
12. Schoenebeck JJ, Hutchinson SA, Byers A, Beale HC, Carrington B. 12.  et al. 2012. Variation of BMP3 contributes to dog breed skull diversity. PLOS Genet 8:e1002849 [Google Scholar]
13. Parker HG, vonHoldt BM, Quignon P, Margulies EH, Shao S. 13.  et al. 2009. An expressed Fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs. Science 325:995–98 [Google Scholar]
14. Larson G, Karlsson EK, Perri A, Webster MT, Ho SYW. 14.  et al. 2012. Rethinking dog domestication by integrating genetics, archeology, and biogeography. PNAS 109:8878–83 [Google Scholar]
15. Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E. 15.  et al. 2014. Genome sequencing highlights the dynamic early history of dogs. PLOS Genet 10:e1004016 [Google Scholar]
16. Maddison WP. 16.  1997. Gene trees in species trees. Syst. Biol. 46:523–36 [Google Scholar]
17. Degnan JH, Rosenberg NA. 17.  2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 24:332–40 [Google Scholar]
18. Rogers J, Gibbs RA. 18.  2014. Comparative primate genomics: emerging patterns of genome content and dynamics. Nat. Rev. Genet. 15:347–59 [Google Scholar]
19. Thalmann O, Shapiro B, Cui P, Schuenemann VJ, Sawyer SK. 19.  et al. 2013. Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Science 342:871–74 [Google Scholar]
20. Fan Z, Silva P, Gronau I, Wang S, Armero AS. 20.  et al. 2016. Worldwide patterns of genomic variation and admixture in gray wolves. Genome Res 26:163–73 [Google Scholar]
21. Vilà C, Savolainen P, Maldonado JE, Amorim IR, Rice JE. 21.  et al. 1997. Multiple and ancient origins of the domestic dog. Science 276:1687–89 [Google Scholar]
22. vonHoldt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG. 22.  et al. 2010. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464:898–902 [Google Scholar]
23. Shipman P. 23.  2015. How do you kill 86 mammoths? Taphonomic investigations of mammoth megasites. Quat. Int. 359–360:38–46 [Google Scholar]
24. Shipman P. 24.  2015. The Invaders: How Humans and Their Dogs Drove Neanderthals to Extinction Cambridge, MA: Belknap288, 3rd ed..
25. Clutton-Brock J. 25.  1995. Origins of the dog: domestication and early history. The Domestic Dog: Its Evolution, Behaviour and Interactions with People J Serpell 7–20 Cambridge, UK: Cambridge Univ. Press [Google Scholar]
26. Thurston ME. 26.  1996. The Lost History of the Canine Race: Our 15,000-Year Love Affair With Dogs Kansas City, MO: Andrews & McMeel301 pp.
27. Germonpré M, Lázničková-Galetová M, Sablin MV. 27.  2012. Palaeolithic dog skulls at the Gravettian Předmostí site, the Czech Republic. J. Archaeol. Sci. 39:184–202 [Google Scholar]
28. Germonpré M, Sablin MV, Stevens RE, Hedges REM, Hofreiter M. 28.  et al. 2009. Fossil dogs and wolves from Palaeolithic sites in Belgium, the Ukraine and Russia: osteometry, ancient DNA and stable isotopes. J. Archaeol. Sci. 36:473–90 [Google Scholar]
29. Zeder MA. 29.  2012. Pathways to animal domestication. Biodiversity in Agriculture: Domestication, Evolution, and Sustainability P Gepts, TR Famula, RL Bettinger, SB Brush, AB Damania et al.227–58 Cambridge, MA: Cambridge Univ. Press [Google Scholar]
30. Ovodov ND, Crockford SJ, Kuzmin YV, Higham TFG, Hodgins GWL. 30.  et al. 2011. A 33,000-year-old incipient dog from the Altai mountains of Siberia: evidence of the earliest domestication disrupted by the last glacial maximum. PLOS ONE 6:e22821 [Google Scholar]
31. Leonard JA, Wayne RK, Wheeler J, Valadez R, Guillen S, Vilà C. 31.  2002. Ancient DNA evidence for Old World origin of New World dogs. Science 298:1613–16 [Google Scholar]
32. Frantz LAF, Mullin VE, Pionner-Capitan M, Lebrasseur O, Ollivier M. 32.  et al. 2016. Genomic and archaeological evidence suggest a dual origin of domestic dogs. Science 352:1228–31 [Google Scholar]
33. Crockford SJ, Kuzmin YV. 33.  2012. Comments on Germonpré et al., Journal of Archaeological Science 36, 2009 “Fossil dogs and wolves from Palaeolithic sites in Belgium, the Ukraine and Russia: osteometry, ancient DNA and stable isotopes,” and Germonpré, Lázničková-Galetová, and Sablin, Journal of Archaeological Science 39, 2012 “Palaeolithic dog skulls at the Gravettian Předmostí site, the Czech Republic.”. J. Archaeol. Sci. 39:2797–801 [Google Scholar]
34. Morey DF. 34.  2014. In search of Paleolithic dogs: a quest with mixed results. J. Archaeol. Sci. 52:300–7 [Google Scholar]
35. Germonpré M, Sablin MV, Després V, Hofreiter M, Lázničková-Galetová M. 35.  et al. 2013. Palaeolithic dogs and the early domestication of the wolf: a reply to the comments of Crockford and Kuzmin 2012. J. Archaeol. Sci. 40:786–92 [Google Scholar]
36. Germonpré M, Sablin MV, Lázničková-Galetová M, Després V, Stevens RE. 36.  et al. 2015. Palaeolithic dogs and Pleistocene wolves revisited: a reply to Morey 2014. J. Archaeol. Sci. 54:210–16 [Google Scholar]
37. Drake AG, Coquerelle M, Colombeau G. 37.  2015. 3D morphometric analysis of fossil canid skulls contradicts the suggested domestication of dogs during the Late Paleolithic. Sci. Rep. 5:8299 [Google Scholar]
38. Perri A. 38.  2016. A wolf in dog's clothing: initial dog domestication and Pleistocene wolf variation. J. Archaeol. Sci. 68:1–4 [Google Scholar]
39. Druzhkova AS, Thalmann O, Trifonov VA, Leonard JA, Vorobieva NV. 39.  et al. 2013. Ancient DNA analysis affirms the canid from Altai as a primitive dog. PLOS ONE 8:e57754 [Google Scholar]
40. Savolainen P, Zhang Y, Luo J, Lundeberg J, Leitner T. 40.  2002. Genetic evidence for an East Asian origin of domestic dogs. Science 298:1610–13 [Google Scholar]
41. Pang J-F, Kluetsch C, Zou X-J, Zhang A, Luo L-Y. 41.  et al. 2009. MtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves. Mol. Biol. Evol. 26:2849–64 [Google Scholar]
42. Brown SK, Pedersen NC, Jafarishorijeh S, Bannasch DL, Ahrens KD. 42.  et al. 2011. Phylogenetic distinctiveness of Middle Eastern and Southeast Asian village dog Y chromosomes illuminates dog origins. PLOS ONE 6:e28496 [Google Scholar]
43. Ding Z-L, Oskarsson M, Ardalan A, Angleby H, Dahlgren L-G. 43.  et al. 2012. Origins of domestic dog in southern East Asia is supported by analysis of Y-chromosome DNA. Heredity 108:507–14 [Google Scholar]
44. Boyko AR, Boyko RH, Boyko CM, Parker HG, Castelhano M. 44.  et al. 2009. Complex population structure in African village dogs and its implications for inferring dog domestication history. PNAS 106:13903–8 [Google Scholar]
45. Gray MM, Sutter NB, Ostrander EA, Wayne RK. 45.  2010. The IGF1 small dog haplotype is derived from Middle Eastern grey wolves. BMC Biol 8:16 [Google Scholar]
46. Wang GD, Zhai W, Yang HC, Fan RX, Cao X. 46.  et al. 2013. The genomics of selection in dogs and the parallel evolution between dogs and humans. Nat. Commun. 4:1860 [Google Scholar]
47. Durand EY, Patterson N, Reich D, Slatkin M. 47.  2011. Testing for ancient admixture between closely related populations. Mol. Biol. Evol. 28:2239–52 [Google Scholar]
48. Wang G-D, Zhai W, Yang H-C, Wang L, Zhong L. 48.  et al. 2016. Out of southern East Asia: the natural history of domestic dogs across the world. Cell Res 26:21–33 [Google Scholar]
49. Shannon LM, Boyko RH, Castelhano M, Corey E, Hayward JJ. 49.  et al. 2015. Genetic structure in village dogs reveals a Central Asian domestication origin. PNAS 112:13639–44 [Google Scholar]
50. Wang G-D, Peng M-S, Yang H-C, Savolainen P, Zhang Y-P. 50.  2016. Questioning the evidence for a Central Asian domestication origin of dogs. PNAS 113:E2554–55 [Google Scholar]
51. Shannon LM, Boyko RH, Castelhano M, Corey E, Hayward JJ. 51.  et al. 2016. Reply to Wang et al.: Sequencing datasets do not refute Central Asian domestication origin of dogs. PNAS 113:E2556–57 [Google Scholar]
52. Leonard JA, Vilà C, Fox-Dobbs K, Koch PL, Wayne RK, Van Valkenburgh B. 52.  2007. Megafaunal extinctions and the disappearance of a specialized wolf ecomorph. Curr. Biol. 17:1146–50 [Google Scholar]
53. Skoglund P, Ersmark E, Palkopoulou E, Dalén L. 53.  2015. Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds. Curr. Biol. 25:1515–19 [Google Scholar]
54. Schiffels S, Durbin R. 54.  2014. Inferring human population size and separation history from multiple genome sequences. Nat. Genet. 46:919–25 [Google Scholar]
55. Wayne RK, Van Valkenburgh B, O'Brien SJ. 55.  1991. Molecular distance and divergence time in carnivores and primates. Mol. Biol. Evol. 8:297–319 [Google Scholar]
56. vonHoldt BM, Cahill J, Fan Z, Gronau I, Robinson J. 56.  et al. 2016. Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf. Sci. Adv. 2:7e1501714 [Google Scholar]
57. Meachen JA, Samuels JX. 57.  2012. Evolution in coyotes (Canis latrans) in response to the megafaunal extinctions. PNAS 109:4191–96 [Google Scholar]
58. Li H, Durbin R. 58.  2011. Inference of human population history from individual whole-genome sequences. Nature 475:493–96 [Google Scholar]
59. Anderson TM, vonHoldt BM, Candille SI, Musiani M, Greco C. 59.  et al. 2009. Molecular and evolutionary history of melanism in North American gray wolves. Science 323:1339–43 [Google Scholar]
60. vonHoldt BM, Pollinger JP, Earl DA, Knowles JC, Boyko AR. 60.  et al. 2011. A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Res 21:1294–305 [Google Scholar]
61. Sacks BN, Brown SK, Stephens D, Pedersen NC, Wu J-T, Berry O. 61.  2013. Y chromosome analysis of dingoes and Southeast Asian village dogs suggests a Neolithic continental expansion from Southeast Asia followed by multiple Austronesian dispersals. Mol. Biol. Evol. 30:1103–18 [Google Scholar]
62. Schraiber JG, Akey JM. 62.  2015. Methods and models for unravelling human evolutionary history. Nat. Rev. Genet. 16:727–40 [Google Scholar]
63. Le Corre V, Kremer A. 63.  1998. Cumulative effects of founding events during colonisation on genetic diversity and differentiation in an island and stepping-stone model. J. Evol. Biol. 11:495–512 [Google Scholar]
64. Excoffier L, Ray N. 64.  2008. Surfing during population expansions promotes genetic revolutions and structuration. Trends Ecol. Evol. 23:347–51 [Google Scholar]
65. Tajima F. 65.  1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–95 [Google Scholar]
66. Fu YX, Li WH. 66.  1993. Statistical tests of neutrality of mutations. Genetics 133:693–709 [Google Scholar]
67. Gray MM, Granka JM, Bustamante CD, Sutter NB, Boyko AR. 67.  et al. 2009. Linkage disequilibrium and demographic history of wild and domestic canids. Genetics 181:1493–505 [Google Scholar]
68. Marsden CD, Ortega-Del Vecchyo D, O'Brien DP, Taylor JF, Ramírez O. 68.  et al. 2016. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs. PNAS 113:152–57 [Google Scholar]
69. Scally A, Durbin R. 69.  2012. Revising the human mutation rate: implications for understanding human evolution. Nat. Rev. Genet. 13:745–53 [Google Scholar]
70. Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I. 70.  et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483:169–75 [Google Scholar]
71. Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW. 71.  et al. 2016. Demographically-based evaluation of genomic regions under selection in domestic dogs. PLOS Genet 12:e1005851 [Google Scholar]
72. Axelsson E, Ratnakumar A, Arendt M-L, Maqbool K, Webster MT. 72.  et al. 2013. The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature 495:360–64 [Google Scholar]
73. Grimm D. 73.  2015. How the wolf became the dog. Science 348:277 [Google Scholar]