Journal Articles

Articles published since 2003.

Dudek SM, Phoenix AN, Scappini E, Shepeleva DV, Herbeck YE, Trut LN, Farris S, Kukekova AV. Defining hippocampal Area CA2 in the fox (Vulpes vulpes) brain. 2023 May 9. doi: 10.1002/hipo.23546. Online ahead of print. PMID: 37159095

Rogers Flattery CN, Abdulla M, Barton SA, Michlich JM, Trut LN, Kukekova AV, Hecht EE. Histological and MRI atlas of the silver fox (Vulpes vulpes). Brain Structure and Function. 2023 May 9. doi: 10.1007/s00429-023-02648-5. Online ahead of print. PMID: 37160458

Kukekova AV, Trut LN, Acland GM. Genetics of Domesticated Behavior in Dogs and Foxes. Genetics and the Behavior of Domestic Animals. 3rd Edition. Edited by: Temple Grandin. Elsevier Academic Press. 2022. Chapter 8: 275-323 pp.

Hecht EE, Kukekova AV, Gutman DA, Acland GM, Preuss TM, Trut LN. Neuromorphological changes following selection for tameness and aggression in the Russian fox-farm experiment. J Neurosci. 2021 Jun 14;41(28):6144-6156. doi: 10.1523/JNEUROSCI.3114-20.2021.

Sacks BN, Lounsberry ZT, Rando HM, Kluepfel K, Fain SR, Brown SK, Kukekova AV. Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography. Genes (Basel). 2021 Jan 14;12(1):97. doi: 10.3390/genes12010097. PMID: 33466657

Rosenfeld CS, Hekman JP, Johnson JL, Lyu Z, Ortega MT, Joshi T, Mao J, Vladimirova AV, Gulevich RG, Kharlamova AV, Acland GM, Hecht EE, Wang X, Clark AG, Trut LN, Behura SK, Kukekova AV. Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions. Genes Brain Behav. 2020 Jan;19(1):e12614. doi: 10.1111/gbb.12614. PMID: 31605445

Rando HM, Wadlington WH, Johnson JL, Stutchman JT, Trut LN, Farré M, Kukekova AV. (2019). The red fox Y-chromosome in comparative context. Genes, 10, 409.

Farré M, Kim J, Proskuryakova AA, Zhang Y, Kulemzina AI, Li Q, Zhou Y, Xiong Y, Johnson JL, Perelman P, Johnson WE, Warren WC, Kukekova AV, Zhang G, O’Brien SJ, Ryder OA, Graphodatsky AS, Ma J, Lewin HA, Larkin DM. (2019). Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. Genome Research. Feb 13. doi: 10.1101/gr.239863.118. [Epub ahead of print]

Bastounes ER, Rando HM, Johnson JL, Trut LN, Sacks BN, Driscoll CA, vonHoldt B, Kukekova AV. (2019). Four structural variants associated with human-directed sociability in dogs are not found in tame red foxes (Vulpes vulpes). Animal Genetics, 50(1), 116-118. Available online at DOI: 10.1111/age.12755.

Wang X, Pipes L, Trut LN, Herbeck Y, Vladimirova AV, Gulevich RG, Kharlamova AV, Johnson JL, Acland GM, Kukekova AV, Clark AG. (2018). Genomic responses to selection for tame/aggressive behaviors in the silver fox (Vulpes vulpes). Proceedings of the National Academy of Sciences. PNAS published ahead of print September 18, 2018.

Kukekova AV, Johnson JL, Xiang X, Feng S, Liu S, Rando HM, Kharlamova AV, Herbeck Y, Serdyukova NA, Xiong Z, Beklemischeva V, Koepfli KP, Gulevich RG, Vladimirova AV, Hekman JP, Perelman PL, Graphodatsky AS, O’Brien SJ, Wang X, Clark AG, Acland GM, Trut LN, Zhang G. (2018). Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviors. Nature Ecology & Evolution. 2(9):1479-1491.

Makunin AI, Romanenko SA, Beklemisheva VB, Perelman PL, Druzhkova AS, Petrova KO, Dmitry Yu. Prokopov DYu, Chernyaeva EN, Johnson JL, Kukekova AV, Yang F, Ferguson-Smith MA, Alexander S. Graphodatsky AS, Trifonov AV. (2018). Sequencing of Supernumerary Chromosomes of Red Fox and Raccoon Dog Confirms a Non-Random Gene Acquisition by B Chromosomes. Genes, 9, 405.

Rando HM, Farré M, Robson MP, Won NB, Johnson JL, Buch R, Bastounes ER, Xiang X, Feng S, Liu S, Xiong Z, Kim J, Zhang G, Trut LN, Larkin DM, Kukekova AV. (2018). Construction of red fox chromosomal fragments from the short-read genome assembly. Genes, 9, 308.

Hekman JP, Johnson JL, Edwards W, Vladimirova AV, Gulevich RG, Ford AL, Kharlamova AV, Herbeck Y, Acland GM, Raetzman LT, Trut LN, Kukekova AV. (2018). Anterior Pituitary Transcriptome Suggests Differences in ACTH Release in Tame and Aggressive Foxes. G3: Genes, Genomes, Genetics (Bethesda). 8(3): 858-873.

Donaldson ME, Rico Y, Hueffer K, Rando HM, Kukekova AV, Kyle CJ. (2018). Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure. Ecology and Evolution, 8, 572–583.

Proskuryakova A, Kulemzina A, Perelman P, Makunin A, Larkin D, Farré M, Kukekova A, Johnson JL, Lemskaya N, Beklemisheva V, Roelke-Parker ME, Bellizzi J, Ryder OA, O’Brien S, Graphodatsky A. (2017). X chromosome evolution in Cetartiodactyla. Genes (Basel). 8(9), pii: E216.

Rando HM, Stutchman JT, Bastounes ER, Johnson JL, Driscoll CA, Barr CS, Trut LN, Sacks BN, Kukekova AV. (2017). Y-chromosome markers for the red fox. Journal of Heredity, 108(6), 678–685.

Nelson RM, Temnykh SV, Johnson JL, Kharlamova AV, Vladimirova AV, Gulevich RG, Shepeleva DV, Oskina IN, Acland GM, Rönnegård L, Trut LN, Carlborg Ö, Kukekova AV. (2017). Genetics of interactive behavior in silver foxes (Vulpes vulpes). Behavior Genetics. 47(1), 88-101.

Kukekova AV, Johnson JL, Kharlamova AV, Vladimirova AV, Shepeleva DV, Gulevich RG, Trut LN. (2016). Georgian white coat color of red fox (Vulpes vulpes) maps to fox chromosome 2 in the region containing KIT gene. Animal Genetics. 47(4):514-5.

Hekman JP, Johnson JL, Kukekova AV (2016). Transcriptome analysis in domesticated species: challenges and strategies. Bioinformatics and Biology Insights. 9(Suppl 4):21-31.

Johnson JL, Wittgenstein H, Mitchell SE, Hyma KE, Temnykh SV, Kharlamova AV, Gulevich RG, Vladimirova AV, Fong HWF, Acland GM, Trut LN, Kukekova AV (2015). Genotyping-by-sequencing (GBS) detects genetic structure and confirms behavioral QTL in tame and aggressive foxes (Vulpes vulpes). PLoS One. 10(6):e0127013. PMID: 26061395.

Johnson JL, Kozysa A, Kharlamova AV, Gulevich RG, Perelman P, Fong HWF, Vladimirova AV, Oskina IN, Trut LN, Kukekova AV (2015). Platinum coat color in red fox (Vulpes vulpes) is caused by a mutation in an autosomal copy of KIT. Animal Genetics. 46(2):190-9. PMID: 25662789.

Makunin AI, Dementyeva PV, Graphodatsky AS, Volobouev VT, Kukekova AV, Trifonov VA. (2014). Genes on B chromosomes of vertebrates. Molecular Cytogenetics. 7(1):99. PMID: 25538793.

Yeh CY, Goldstein O, Kukekova AV, Holley D, Knollinger AM, Huson HJ, Pearce-Kelling SE, Acland GM, Komaromy AM. (2013). Genomic deletion of CNGB3 is identical by descent in multiple canine breeds and causes achromatopsia. BMC Genetics. 14:27. PMCID: PMC3639114.

Kukekova AV, Temnykh SV, Johnson JL, Trut LN, Acland GM. (2012). Genetics of behavior in the silver fox. Mammalian Genome. 23(1-2):164-77 PMID: 22108806.

Statham MJ, Trut LN, Sacks BN, Kharlamova AV, Oskina IN, Gulevich RG, Johnson JL, Temnykh SV, Acland GM, Kukekova AV. (2011). On the origin of a domesticated species: Identifying the parent population of Russian silver foxes (Vulpes vulpes). Biological Journal of the Linnean Society. 103(1):168-75. PMCID: PMC3101803.

Kukekova AV, Trut LN, Chase K, Kharlamova AV, Johnson JL, Temnykh SV, Oskina IN, Gulevich RG, Vladimirova AV, Klebanov S, Shepeleva DV, Shikhevich SG, Acland GM, Lark KG. (2011). Mapping Loci for fox domestication: deconstruction/reconstruction of a behavioral phenotype. Behavior Genetics. 41(4):593-606. PMCID: PMC3076541.

Kukekova AV, Johnson JL, Teiling C, Li L, Oskina IN, Kharlamova AV, Gulevich RG, Padte R, Dubreuil MM, Vladimirova AV, Shepeleva DV, Shikhevich SG, Sun Q, Ponnala L, Temnykh SV, Trut LN, Acland GM. (2011). Sequence comparison of prefrontal cortical brain transcriptome from a tame and an aggressive silver fox (Vulpes vulpes). BMC Genomics. 12:482. PMCID: PMC3199282.

Kharlamova AV, Trut LN, Chase K, Kukekova AV, Lark KG. (2010). Directional asymmetry in the limbs, skull and pelvis of the silver fox (V. vulpes). Journal of morphology. 271(12):1501-8. PMCID: PMC3057660.

Goldstein O, Kukekova AV, Aguirre GD, Acland GM. (2010). Exonic SINE insertion in STK38L causes canine early retinal degeneration (erd). Genomics. 96(6):362-8. PMCID: PMC2996878.

Goldstein O, Guyon R, Kukekova A, Kuznetsova TN, Pearce-Kelling SE, Johnson J, Aguirre GD, Acland GM. (2010). COL9A2 and COL9A3 mutations in canine autosomal recessive oculoskeletal dysplasia. Mammalian Genome. 21(7-8):398-408. PMCID: PMC2954766.

Kukekova AV, Vorobieva NV, Beklemisheva VR, Johnson JL, Temnykh SV, Yudkin DV, Trut LN, Andre C, Galibert F, Aguirre GD, Acland GM, Graphodatsky AS. (2009). Chromosomal mapping of canine-derived BAC clones to the red fox and American mink genomes. Journal of Heredity. 100 Suppl 1:S42-53. PMCID: PMC3139363.

Kukekova AV, Goldstein O, Johnson JL, Richardson MA, Pearce-Kelling SE, Swaroop A, Friedman JS, Aguirre GD, Acland GM. (2009). Canine RD3 mutation establishes rod-cone dysplasia type 2 (rcd2) as ortholog of human and murine rd3. Mammalian Genome. 20(2):109-23. PMCID: PMC2652121.

Kukekova AV, Trut LN, Chase K, Shepeleva DV, Vladimirova AV, Kharlamova AV, Oskina IN, Stepika A, Klebanov S, Erb HN, Acland GM. (2008). Measurement of segregating behaviors in experimental silver fox pedigrees. Behavior Genetics. 38(2):185-94. PMCID: PMC2374754

Kukekova A, Oskina I, Kharlamova AV, Chase K, Temnykh SV, Johnson JL, Pivovarova IV, Shepeleva DV, Vladimirova A, Semenova TI, Gulievich RG, Schikhevich SG, Graphodatsky AS, Aguirre GD, Erb HN, Lark KG, Acland GM, Trut LN. (2008). Fox Farm Experiment: Hunting For Behavioral Genes. The Herald of Vavilov Society for Genetics and Breeding Scientists. 12(1/2):50-62.

Zangerl B, Johnson JL, Acland GM, Aguirre GD. (2007). Independent origin and restricted distribution of RPGR deletions causing XLPRA. Journal of Heredity. 98(5):526-30. PMCID: PMCPMC2647561.

Parker HG, Kukekova AV, Akey DT, Goldstein O, Kirkness EF, Baysac KC, Mosher DS, Aguirre GD, Acland GM, Ostrander EA. (2007). Breed relationships facilitate fine-mapping studies: a 7.8-kb deletion cosegregates with Collie eye anomaly across multiple dog breeds. Genome Research. 17(11):1562-71. PMCID: PMC2045139.

Kukekova AV, Trut LN, Oskina IN, Johnson JL, Temnykh SV, Kharlamova AV, Shepeleva DV, Gulievich RG, Shikhevich SG, Graphodatsky AS, Aguirre GD, Acland GM. (2007). A meiotic linkage map of the silver fox, aligned and compared to the canine genome. Genome Research. 17(3):387-99. PMCID: PMC1800930.

Hunter LS, Sidjanin DJ, Hijar MV, Johnson JL, Kirkness E, Acland GM, Aguirre GD. (2007). Cloning and characterization of canine PAX6 and evaluation as a candidate gene in a canine model of aniridia. Molecular Vision. 13(43-46):431-42. PMCID: PMC2647561

Zangerl B, Sun Q, Pillardy J, Johnson JL, Schweitzer PA, Hernandez AG, Liu L, Acland GM, Aguirre GD. (2006). Development and characterization of a normalized canine retinal cDNA library for genomic and expression studies. Investigative Ophthalmology & Visual Science. 47(6):2632-8 PMID: 16723480.

Kukekova AV, Nelson J, Kuchtey RW, Lowe JK, Johnson JL, Ostrander EA, Aguirre GD, Acland GM. (2006). Linkage mapping of canine rod cone dysplasia type 2 (rcd2) to CFA7, the canine orthologue of human 1q32. Investigative Ophthalmology & Visual Science. 47(3):1210-5. PMCID: PMC1509099.

Hunter LS, Sidjanin DJ, Johnson JL, Zangerl B, Galibert F, Andre C, Kirkness E, Talamas E, Acland GM, Aguirre GD. (2006). Radiation hybrid mapping of cataract genes in the dog. Molecular Vision. 12:588-96. PMCID: PMC1509099.

Graphodatsky AS, Kukekova AV, Yudkin DV, Trifonov VA, Vorobieva NV, Beklemisheva VR, Perelman PL, Graphodatskaya DA, Trut LN, Yang F, Ferguson-Smith MA, Acland GM, Aguirre GD. (2005). The proto-oncogene C-KIT maps to canid B-chromosomes. Chromosome Research. 13(2):113-22 PMID: 15861301.

Kukekova AV, Trut LN, Oskina IN, Kharlamova AV, Shikhevich SG, Kirkness EF, Aguirre GD, Acland GM. (2004). A marker set for construction of a genetic map of the silver fox (Vulpes vulpes). Journal of Heredity. 95(3):185-94 PMID: 15220384.

Kukekova AV, Aguirre GD, Acland GM. (2003). Cloning and characterization of canine SHARP1 and its evaluation as a positional candidate for canine early retinal degeneration (erd). Gene. 312:335-43. PMID: 12909371.

Lowe JK, Kukekova AV, Kirkness EF, Langlois MC, Aguirre GD, Acland GM, Ostrander EA. (2003). Linkage mapping of the primary disease locus for collie eye anomaly. Genomics. 82(1):86-95. PMID: 12809679.

Li K, Zhang Q, Johnson JL, Aguirre GD. (2003). Comparative analysis, gene organization and expression of canine TCTE1L. Gene. 303:207-12 PMID: 12559582.

Zhang Q, Beltran WA, Mao Z, Li K, Johnson JL, Acland GM, Aguirre GD. (2003). Comparative analysis and expression of CLUL1, a cone photoreceptor-specific gene. Investigative Ophthalmology & Visual Science. 44(10):4542-9 PMID: 14507903.

Book Chapters

Kukekova AV. Genetics of Aggression in Nonhuman Animals. In: The Wiley Handbook of Aggression and Violence. Editor-in-Chief: Peter Sturmey. John Wiley & Sons Ltd. 2017. 11 pages.

Kukekova AV, Trut LN, Acland GM. (2013). Genetics of Domesticated Behavior in Dogs and Foxes. Chapter 10. In: Genetics and the Behavior of Domestic Animals, 2nd Edition (ed Grandin T, Deesing M). Elsevier; p. 361-396.

Trut LN, Kharlamova AV, Kukekova AV, Acland GM, Carrier DR, Chase K, Lark KG. (2006). Morphology and Behavior: Are They Coupled at the Genome Level? In: The Dog and its Genome. Ostrander E, Giger U, Lindblad-Toh K, editors. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press; p. 81-96.

Kukekova AV, Acland GM, Oskina IN, Kharlamova AV, Trut LN, Chase K, Lark KG, Erb HN, Aguirre GD. (2006). The Genetics of Domesticated Behavior in Canids: What Can Dogs and Silver Foxes Tell Us about Each Other? In: The Dog and its Genome. Ostrander EA, Giger U, Lindblad-Toh K, editors. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory Press; p. 515-37.