Canine genetics

• PhD, Biology, Purdue University, 2005
• MS, Computer Science, Purdue University, 2004
• BS, Ecology, Ethology & Evolution, University of Illinois at Urbana-Champaign, 1999
• BS, Computer Science, University of Illinois at Urbana-Champaign, 1999

Adam Boyko is an assistant professor in Biomedical Sciences at the Cornell University College of Veterinary Medicine. His research focuses on genomic investigation of dogs as a model of genetic disease and evolutionary genetics. One aspect of this work is understanding the evolution and genetics of village dogs, the semi-feral pariah dogs found in much of the world today. Dr. Boyko is a graduate of the University of Illinois, Urbana-Champaign and received an MS in Computer Science and a PhD in Biology from Purdue University before his postdoctoral research in the Department of Biological Statistics and Computational Biology at Cornell University. He served as a Research Associate in the Genetics Department at the Stanford School of Medicine before beginning his faculty appointment at Cornell in 2011.

Dr. Boyko is a member of Cornell's Center for Vertebrate Genomics, the Center for Comparative and Population Genomics, and the fields of Comparative Biomedical Sciences; Computational Biology; Genetics, Genomics and Development; Molecular and Integrative Physiology and Zoology and Wildlife Conservation. He also serves as Founder and Chief Science Officer of Embark Veterinary, a canine genetic testing company.

1. Hernandez, I, JJ Hayward, JA Brockman, ME White, L Mouttham, EA Wilcox, S Garrison, MG Castelhano, JP Loftus, FE Gomes, C Balkman, MB Brooks, N Fiani, M Forman, T Kern, B Kornreich, E Ledbetter, S Perealta, AM Struble, L Caligiuri, E Corey, L Lin, J Jordan, D Sack, AR Boyko, LA Lyons and RJ Todhunter. 2022. Complex feline disease mapping using a dense genotyping array.
   Front Vet Sci, in press.
2. Kawakami, T, V Raghavan, AL Ruhe, MK Jensen, A Milano, TC Nelson and AR Boyko. 2022. Early onset adult deafness in the Rhodesian Ridgeback dog is associated with an in-frame deletion in the EPS8L2 gene. PLOS One, 17, e0264365.
3. Neradilová, S, AM Schauer, JJ Hayward, MAT Brunner, M Bohutínská, V Jagannathan, LB Connell, AR Boyko, MM Welle and BˆC Bolfíková. 2022. Genomic and transcriptomic characterization of atypical recurrent flank alopecia in the Cesky Fousek. Genes, 13, 650.
4. Slavney, AJ, T Kawakami, MK Jensen, TC Nelson, AJ Sams and AR Boyko. 2021. Five genetic variants explain over 70% of the hair coat pheomelanin intensity variation in purebred and mixed breed domestic dogs. PLOS One, 16, e0250579.
5. Lyons, LA, RM Buckley, RJ Harvey, the 99 Lives Cat Genome Consortium, D Aberdein, AO Andersson,TE Bergström, AR Boyko, ML Casal, BW Davis, O Distl, NM Ellinwood, OP Forman, EI Ginns, D Hasegawa, V Jagannathan, I Hernandez, M Kaukonen, E Leclerc, T Leeb, H Lohi, MA Magnuson, SP Mane, JS Munday, AN Myres, SM Peterson-Jones, C Rusbridge, B Shapiro, WF Swanson, RJ Todhunter, EA Wilcox and Y Yu. 2021. Mining the 99 Lives Cat Genome Sequencing Consortium database implicates genes and variants for the Ticked locus in domestic cats (Felis catus). Anim Genet, 51, 321–332.
6. Kawakami, T, MK Jensen, A Slavney, PE Dean, A Milano, V Raghavan, B Ford, ET Chu, AJ Sams and AR Boyko. 2021. R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting. PLOS One, 16, e0248233.
7. Halo, JV, AL Pendleton, FC Shen, AJ Doucet, T Derrien, C Hitte, LE Kirby, B Myers, E Sliwerska, S Emery, JV Moran, AR Boyko and JM Kidd. 2021. Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes. Proc Natl Acad Sci U S A, 118, e2016274118.
8. Sams, AJ, B Ford, A Gardner and AR Boyko. 2020. Examination of the efficacy of small genetic panels in genomic conservation of companion animal populations. Evol Appl, 13, 2555–2565.
9. Hayward, JJ, M Kelly-Smith, AR Boyko, L Burmeister, L De Risio, C Mellersh, J Freeman and GM Strain. 2020. A genome-wide association study of deafness in three canine breeds. PLOS One, 15, e0232900.
10. Yordy, J, C Kraus, JJ Hayward, ME White, LM Shannon, KE Creevy, DEL Promislow and AR Boyko. 2019. Body size, inbreeding, and lifespan in domestic dogs. Conserv Genet, 21, 137–148.
11. Hayward, JJ, ME White, M Boyle, LM Shannon, ML Casal, MG Castelhano, SA Center, VN Meyers-Wallen, KW Simpson, NB Sutter, RJ Todhunter and AR Boyko. 2019. Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association. PLOS Genet, 15, e1008003.
12. Chu, ET, MJ Simpson, K Diehl, RL Page, AJ Sams and AR Boyko. 2019. Inbreeding depression causes reduced fecundity in Golden Retrievers. Mamm Genom, 30, 166–172.
13. Sams, AJ and AR Boyko. 2019. Fine-scale runs of homozygosity reveal patterns of inbreeding and substantial overlap with recessive disease genotypes in domestic dogs. G3, 9, 117–123.
14. Deane-Coe, PE, ET Chu, A Slavney, AR Boyko* and AJ Sams*. 2018. Direct-To-Consumer DNA testing of 6,000 dogs reveals 98.6-kb duplication associated with blue eyes and heterochromia in Siberian Huskies. PLOS Genet, 14, e1007648.
15. Leathlobhair, MN, AR Perri, EK Irving-Pease, KE Witt, A Linderholm, J Haile, O Lebasseur, C Ameen, J Blick, AR Boyko, S Brace, YN Cortes, SJ Crockford, EA Dimopoulos, M Eldridge, S Gopalakrishnan, K Gori, V Grimes, E Guiry, AJ Hansen, A Hulme-Beaman, J Johnson, A Kitchen, AK Kasparov, Y-M Kwon, PA Nikolskiy, CP Lope, A Manin, T Martin, M Meyer, KN Myers, M Omura, JM Rouillard, EY Pavolva, P Sciulli, MHS Sinding, A Strakova, VV Ivanova, C Widga, E Willerslev, VV Pitulko, I Barnes, MTP Gilbert, KM Dobney, RS Malhi, EP Murchinson, G Larson and LAF Frantz. 2018. The evolutionary history of dogs in the Americas. Science, 361, 81–85.
16. Pendelton, AL, FC Shen, AM Taravella, S Emery, KR Veeramah, AR Boyko and JM Kidd. 2018. Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication. BMC Genom, 16, 64.
17. Cairns, KM, LM Shannon, J Koler-Matznick, JWO Ballard and AR Boyko. 2018. Elucidating biogeographical patterns in Australian native candis using genome wid SNPs. PLOS One, 13, e0198754.
18. Meyers-Wallen, VN, AR Boyko, CG Danko, JK Grenier, JG Mezey, JJ Hayward, LM Shannon, C Gao, A Shafquat, EJ Rice, S Pujar, S Eggers, T Ohnesorg and AH Sinclair. 2017. XX disorder of sex development is associated with an insertion on chromosome 9 and downregulation of RSPO1 in dogs (Canis lupus familiaris). PLOS One, 12, e0186331.
19. Huang, M, J Hayward, E Corey, S Garrison, G Wagner, U Krotscheck, K Hayashi, P Schweitzer, G Lust, AR Boyko and R Todhunter. 2017. A novel iterative mixed model to remap three complex orthopedic traits in dogs. PLOS One, 12, e0176932.
20. Campbell, CL, C Bhérer, BE Morrow, AR Boyko and A Auton. 2016. A pedigree-based map of recombination in the domestic dog genome. G3, 6, 3517–3524.
21. Shannon, LM, RH Boyko, MG Castelhano, E Corey, JJ Hayward, C McLean, ME White, M Abi Said, BA Anita, NB Ikombe, J Calero, A Galov, M Hedimbi, B Imam, R Khalap, D Lally, A Masta, KC Oliveira, J Randall, NM Tam, C Valeriano, FJT Cornejo, L Pérez, NB Sutter, RJ Todhunter, CD Bustamante and AR Boyko. 2016. Reply to Wang et al.: Sequencing datasets do not refute Central Asian domestication origin of dogs. Proc Natl Acad Sci U S A, 113, E2556–E2557.
22. Adam H. Freedman, AH, RM Schweizer, DO Vecchyo, E Han, B Davis, I Gronau, PM Silva, M Galaverni, Z Fan, P Marx, B Lorente-Galdos, O Ramirez, F Hormozdiari, C Alkan, C Vilà, K Squire, E Geffen, J Kusak, AR Boyko, HG Parker, C Lee, V Tadigotla, A Siepel, CD Bustamante, TT Harkins, SF Nelson, T Marques-Bonet, EA Ostrander, RK Wayne and J Novembre. 2016. Demographically based evaluation of genomic regions under selection in domestic dogs. PLOS Genet, 12, e1005851.
23. Hayward, JJ, MG Castelhano, KC Oliveira, E Corey, C Balkman, TL Baxter, ML Casal, SA Center, M Fang, SJ Garrison, SE Kalla, P Korniliev, MI Kotlikoff, NS Moise, LM Shannon, KW Simpson, NB Sutter, RJ Todhunter and AR Boyko. 2016. Complex disease and phenotype mapping in the domestic dog. Nat Comm, 7, 10460.
24. Schlamp, F, J van der Made, R Stambler, L Chesebrough, AR Boyko* and PW Messer*. 2016. Evaluating the performance of selection scans to detect selective sweeps in domestic dogs. Mol Ecol, 25, 342–356.
25. White, ME, JJ Hayward, T Stokol, AR Boyko. 2015 Genetic mapping of novel loci affecting canine blood phenotypes. PLOS One, 10, e0145199.
26. Shannon, LM, RH Boyko, MG Castelhano, E Corey, JJ Hayward, C McLean, ME White, M Abi Said, BA Anita, NB Ikombe, J Calero, A Galov, M Hedimbi, B Imam, R Khalap, D Lally, A Masta, KC Oliveira, J Randall, NM Tam, C Valeriano, FJT Cornejo, L Pérez, NB Sutter, RJ Todhunter, CD Bustamante and AR Boyko. 2015. Genetic structure in village dogs reveals a Central Asian domestication origin. Proc Natl Acad Sci U S A, 112, 13639–13644.
27. Li, Y, D Wu, AR Boyko, G Wang, S Wu, DM Irwin and Y-P Zhang. 2014. Population variation revealed high altitude adaptation of Tibetan Mastiffs. Mol Biol Evol, 31, 1200-1205.
28. Boyko, AR, SA Brooks, AL Behan, E Corey, KC Oliveira, RJ Todhunter, Z Zhang, MG Castelhano, DM Ainsworth and NE Robinson. 2014. Genomic analysis establishes correlation between growth and laryngeal neuropathy in Thoroughbreds. BMC Genom, 15, 259.
29. Freedman, HA, RM Schweizer, I Gronau, E Han, DO Vecchyo, PM Silva, M Galavemi, Z Fan, P Marx, B Lorente-Galdos, H Beale, O Ramierz, F Hormozdiari, C Alkan, C Vilà, K Squire, E Geffen, J Kusak, AR Boyko, H Parker, C Lee, V Tadigotla, A Siepel, CD Bustamante, TT Harkins, SF Nelson, EA Ostrander, T Marques-Bonet, RK Wayne and J Novembre. 2014. Genome sequencing highlights the dynamic early history of dogs. PLOS Genet, 10, e1004016.
30. Tang, R, HJ Noh, D Wang, S Sigurdsson, R Swofford, M Perloski, M Duxbury, EE Pettersson, J Albright, M Castelhano, A Auton, AR Boyko, G Feng, K Lindblad-Toh and EK Karlsson. 2014. Candidate genes and functional noncoding variants identified in a canine model of obsessive-compulsive disorder. Genom Biol, 15, R25.
31. Auton, A, Y Rui Li, J Kidd, K Oliveira, J Nadel, JK Holloway, JJ Hayward, PE Cohen, JM Greally, J Wang, CD Bustamante and AR Boyko. 2013. Genetic recombination is targeted towards gene promoter regions in dogs. PLOS Genet, 9, e1003984.
32. Goldstein, O, J Mezey, P Schweitzer, AR Boyko, C Gao, C Bustamante, J Jordan, G Aguirre and G Acland. 2013. IQCB1 and PDE6B mutations cause similar early onset retinal degenerations in two closely related terrier dog breeds. Invest Ophthalmol Vis Sci, 54, 7005–7019.
33. Li, Y, BM vonHoldt, GWang, A Reynolds, AR Boyko, RKWayne, DWu and Y Zhang. 2013. Artificial selection on brain expressed genes during the domestication of dog. Mol Biol Evol, 30, 1867–1876.
34. Schoenebeck, JJ, SA Hutchinson, A Byers, HC Beale, B Carrington, DL Faden, M Rimbault, B Decker, JM Kidd, R Sood, AR Boyko, JW Fondon III, RK Wayne, CD Bustamante, B Ciruna and EA Ostrander. 2012. Variation of BMP3 contributes to dog breed skull diversity. PLOS Genet, 8, e1002849.
35. Xie, X, J Molina, R Hernandez, A Reynolds, AR Boyko, CD Bustamante and MD Purugganan. 2011. Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection. PLOS One, 6, e20670.
36. Molina, J, M Sikora, N Garud, JM Flowers, S Rubinstein, A Reynolds, P Huang, SA Jackson, BA Schaal, CD Bustamante, AR Boyko and MD Purugganan. 2011. Reply to Ge and Sang: A single origin of domesticated rice. Proc Natl Acad Sci U S A, 108, e756.
37. vonHoldt, BM, JP Pollinger, DA Earl, JC Knowles, AR Boyko, H Parker, E Geffen, M Pilot, W Jedrzejewski, B Jedrzejewska, V Sidorovich, C Greco, E Randi, M Musiani, R Kays, CD Bustamante, EA Ostrander, J Novembre and RK Wayne. 2011. A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genom Res, 21, 1294–1305.
38. Molina, J, M Sikora, N Garud, JM Flowers, S Rubinstein, A Reynolds, P Huang, SA Jackson, BA Schaal, CD Bustamante, AR Boyko and MD Purugganan. 2011. Molecular evidence for a single origin of rice. Proc Natl Acad Sci U S A, 108, 8351–8356.
39. Boyko, AR. 2011. The domestic dog: man’s best friend in the genomic era. Genom Biol, 12, 216.
40. Myers, RA, F Casals, J Gauthier, FF Hamdan, J Keebler, AR Boyko, CD Bustamante, AM Piton, D Spiegelman, E Henrion, M Zilversmit, J Hussin, J Quinlan, Y Yang, RG Lafrenière, AR Griffing, EA Stone, GA Rouleau and P Awadalla. 2011. A population genetic approach to mapping neurological disorder genes using deep resequencing. PLOS Genetics, 7, e1001318.
41. Myles, S, AR Boyko, C Owens, PJ Brown, F Grassi, MK Aradhya, B Prins, A Reynolds, J Chia, D Ware, CD Bustamante and ES Buckler. 2011. Genetic structure and domestication history of the grape. Proc Natl Acad Sci U S A, 108, 3530–3535.
42. Boyko, AR*, P Quignon*, L Li*, JJ Schoenebeck, JD Degenhardt, KE Lohmueller, K Zhao, A Brisbin, HG Parker, BM vonHoldt, M Cargill, A Auton, A Reynolds, AG Elkahloun, M Castelhano, DS Mosher, NB Sutter, GS Johnson, J Novembre, MJ Hubisz, A Siepel, RK Wayne, CD Bustamante and EA Ostrander. 2010. A simple genetic architecture underlies morphological variation in dogs. PLOS
    Biol, 8, e1000451.
43. Awadalla, P, J Gauthier, RA Myers, F Casals, FF Hamdan, AR Griffing, M Côté, E Henrion, D Spiegelman, J Tarabeux, A Piton, Y Yang, AR Boyko, CD Bustamante, L Xiong, É Fombonne, L Mottron, M Zilversmit, J Keebler, H Daoud, C Marineau, MH Roy-Gagnon, MP Dubé, A Eyre-Walker, P Drapeau, EA Stone, RG Lafrenière, GA Rouleau. 2010. Direct measure of the de novo mutation rate in autism and schizophrenia cohorts. Amer J Hum Genet, 87, 316–324.
44. Goldstein, O, JG Mezey, AR Boyko, C Gao, W Wang, CD Bustamante, LJ Anguish, JA Jordan, SE Pearce-Kelling, GD Aguirre and GM Acland. 2010. An ADAM9 mutation in canine cone-rod dystrophy 3 establishes homology with human cone-rod dystrophy 9. Mol Vision, 16, 1549–1569.
45. Williams, LM, X Ma, AR Boyko, CD Bustamante and MF Oleksiak. 2010. SNP identification, verification, and utility for population genetics in a non-model genus. BMC Genet, 11, 32.
46. vonHoldt, BM, JP Pollinger, KE Lohmueller, E Han, HG Parker, P Quignon, JD Degenhardt, AR Boyko, DA Earl, A Auton, A Reynolds, K Bryc, A Brisbin, JC Knowles, DS Mosher, TC Spady, A Elkahloun, E Geffen, M Pilot, W Jedrzejewski, C Greco, E Randi, D Bannasch, A Wilton, J Shearman, M Musiani, M Cargill, PG PG Jones, Z Qian, W Huang, Z Ding, Y Zhang, CD Bustamante, EA Ostrander, J Novembre and RK Wayne. 2010. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature, 464, 898–902.
47. Andrés, AM, MJ Hubisz, A Indap, DG Torgerson, JD Degenhardt, AR Boyko, RN Gutenkunst, TJ White, ED Green, CD Bustamante, AG Clark and R Nielsen. 2009. Targets of balancing selection in the human genome. Mol Biol Evol, 26, 2755–2764.
48. Cadieu, E, M Neff, P Quignon, K Walsh, K Chase, HG Parker, BM vonHoldt, A Rhue, AR Boyko, A Byers, A Wong, DS Mosher, A Elkahoun, TC Spady, C André, KG Lark, M Cargill, CD Bustamante, RK Wayne and EA Ostrander. 2009. Coat variation in the domestic dog is governed by variants in three genes. Science, 326, 150–153.
49. Torgerson, DG, AR Boyko, RD Hernandez, A Indap, X Hu, TJ White, JJ Sninsky, M Cargill, CD Bustamante and AG Clark. 2009. Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLOS Genet, 5, e1000592.
50. Boyko, AR, RH Boyko, CM Boyko, P Jones, HG Parker, M Castelhano, L Corey, J Degenhardt, A Auton, M Hedimbi, R Kityo, EA Ostrander, J Schoenebeck, RJ Todhunter and CD Bustamante. 2009. Complex population structure in African village dogs and its implications for inferring dog domestication history. Proc Natl Acad Sci U S A, 106, 13903–13908.
51. Gray, MM, JM Granka, CD Bustamante, NB Sutter, AR Boyko, L Zhu, EA Ostrander and RK Wayne. 2009. Linkage disequilibrium and demographic history of wild and domestic canids. Genetics, 181, 1493–1505.
52. Auton, A, K Bryc, AR Boyko, KE Lohmueller, J Novembre, A Reynolds, A Indap, MH Wright, J Degenhardt, RN Gutenkunst, KS King, MR Nelson and CD Bustamante. 2009. Global distribution of genomic diversity underscores rich complex history of continental human populations. Genom Res, 19, 795–803.
53. Nielsen, R, MJ Hubisz, I Hellmann, D Torgerson, AM Andrés, A Albrechtsen, R Gutenkunst, MD Adams, M Cargill, AR Boyko, A Indap, CD Bustamante and AG Clark. 2009. Darwinian and demographic forces affecting human protein coding genes. Genom Res, 19, 838–849.
54. Novembre, J, T Johnson, K Bryc, Z Kutalik, AR Boyko, A Auton, A Indap, KS King, S Bergmann,MR Nelson, M Stephens and CD Bustamante. 2008. Genes mirror geography within Europe. Nature,
    456, 98–101.
55. Nelson, MR, K Bryc, KS King, A Indap, AR Boyko, J Novembre, LP Briley, Y Maruyama, DM Waterworth, G Waeber, P Vollenweider, JR Oksenberg, SL Hauser, HA Stirnadel, JS Kooner, JCChambers, B Jones, V Mooser, CD Bustamante, AD Roses, DK Burns, MG Ehm and EH Lai. 2008.The population reference sample (POPRES): a resource for population, disease, and pharmacological genetics research. Amer J Hum Genet, 83, 347–358.
56. Blekhman, R, M Oma, L Hermann, AR Boyko, A Indap, C Koisol, CD Bustamante, KM Teshima and M Przeworski. 2008. Natural selection on genes that underlie human disease susceptibility. Curr Biol, 18, 883–889.
57. Boyko, AR, SH Williamson, AR Indap, JD Degenhardt, RD Hernandez, KE Lohmueller, MD Adams, S Schmidt, JJ Sninsky, SR Sunyaev, TJ White, R Nielsen, AG Clark and CD Bustamante. 2008.Assessing the evolutionary impact of amino acid mutations in the human genome. PLOS  Genet, 4, e1000083.
58. Lohmueller, KE, AR Indap, S Schmidt, AR Boyko, RD Hernandez, MJ Hubisz, JJ Sninsky, TJ White, SR Sunyaev, R Nielsen, AG Clark and CD Bustamante. 2008. Proportionally more deleterious genetic variation in European than in African populations. Nature, 451, 994–998.
59. Boyko, AR. 2008. Optimal age difference cannot differ between monogamous males and females: a comment on Fieder and Huber. Biol Let, 4, 82.
60. Caicedo, AL, SH Williamson, RD Hernandez, AR Boyko, A Fledel-Anon, TL York, NR Polato, KM Olsen, R Nielsen, SR McCouch, CD Bustamante and MD Purugganan. 2007. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLOS Genet, 3, 1745–1756.
61. Boyko, RH, AR Boyko and MG Boyko. 2007. Referee bias contributes to home-field advantage in English premiership football. J Sports Sci, 25, 1185–1194.
62. Boyko, AR, RM Gibson and JR Lucas. 2004. How predation risk affects the temporal dynamics of avian leks: sage grouse vs. golden eagles. Am Nat, 163, 154–165.

Browse PubMed for a complete listing of Dr. Boyko's publications

• Zoetis Award for Veterinary Research Excellence (2015)
• Genome Technology magazine Young Investigator award (2010)
• Walter M. Fitch finalist, Society for Molecular Biology and Evolution (2006)
• H. E. Umbarger Outstanding Graduate Student in Research, Purdue University (2005)
• Graduate Student Award for Outstanding Teaching, Purdue University (2005)
• Andrews Fellowship, Purdue University (1999)
• Chancellor’s Scholar, Campus Honor Program, University of Illinois (1995–1999)
• James Scholar, College of Engineering, University of Illinois (1995–1999)

• 2011-present, Assistant Professor, Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
• 2015-present, Co-founder and Chief Science Officer, Embark Veterinary, Inc., Ithaca, NY
• 2009-2011, Research Associate, Genetics, Stanford University School of Medicine, Stanford, CA
• 2008-2009, Research Associate, Biological Statistics & Computational Biology, Cornell University, Ithaca, NY
• 2005-2008, Postdoctoral Researcher, Biological Statistics & Computational Biology