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Submitted or In Press

JA Hamilton, JM Miller. Submitted. “From transects to transcripts: teasing apart the architecture of reproductive isolation”

V Quesada*, S Freitas-Rodríguez*, JM Miller*, JG Pérez-Silva*, Z Jiang, W Tapia, O Santiago-Fernández, D Campos-Iglesias, LFK Kuderna, MC Quinzin, MG Álvarez, D Carrero, LB Beheregaray, JP Gibbs, Y Chiari, S Glaberman, C Ciofi, M Araujo-Voces, P Mayoral, JR Arango, I Tamargo-Gómez, D Roiz-Valle, BR Evans, DL Edwards, RC Garrick, MA Russello, N Poulakakis, SJ Gaughran, DO Rueda, G Bretones, T Marquès-Bonet, KP White, A Caccone, C López-Otín. Submitted. “Giant tortoise genomes provide insights into longevity and cancer resistance mechanisms”

EL Jensen, JM Miller, DL Edwards, RC Garrick, W Tapia, A Caccone, MA Russello. Submitted. “Temporal mitogenomics of Pinzón Galapagos tortoises reveals potential biases in population genetic inference”

JM Miller*, MC Quinzin*, EH Scheibe, C Ciofi, FGV Sanchez, W Tapia, A Caccone. Submitted. “Genetic pedigree analysis of pilot breeding program for the rediscovered Galapagos giant tortoise from Floreana island”

EL Jensen, DL Edwards, RC Garrick, JM Miller, JP Gibbs, LJ Cayot, W Tapia, A Caccone, MA Russello. Submitted “Population genomics through time corroborates bottleneck theory in Pinzón Galápagos giant tortoises”

JM Miller*, MC Quinzin*, DL Edwards, DAR Eaton, EL Jensen, MA Russello, JP Gibbs, W Tapia, D Rueda, A Caccone. In revision. “SNP loci for genome-wide assessment of diversity and divergence among extant Galapagos giant tortoise species”

JM Miller, M Festa-Bianchet, DW Coltman. In revision. “Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium® HD SNP BeadChip”

SJ Gaughran§, MC Quinzin, JM Miller, DL Edwards, LB Beheregaray, RC Garrick, MA Russello, C Ciofi, N Poulakakis, A Caccone. In press. “Theory, practice and the conservation of Galápagos giant tortoises in the age of genomics.” Evolutionary Applications. doi:10.1111/eva.12551


JM Miller*, MC Quinzin*, N Poulakakis, JP Gibbs, LB Beheregaray, RC Garrick, MA Russello, C Ciofi, DL Edwards, EA Hunter, W Tapia, DO Rueda, J Carrión, AA Valdivieso, A Caccone. 2017. “Identification of genetically important individuals of the rediscovered Floreana Galápagos giant tortoise (Chelonoidis elephantopus) provide founders for species restoration program.” Scientific Reports. doi:10.1038/s41598-017-11516-2

JK Janes, JM Miller, JR Dupuis, RM Malenfant, JC Gorrell, CI Cullingham, RL Andrew. 2017. “The K=2 conundrum.” Molecular Ecology. 14, 3594–3602. doi:10.1111/mec.14187


M Viengkone, AE Derocher, E Richardson, RM Malenfant, JM Miller, M Obbard, M Dyck, V Sahanatien, N Lunn, CS Davis. 2016. “Assessing polar bear (Ursus maritimus) population structure in the Hudson Bay region.” Ecology and Evolution. 6, 8474–8484. doi:10.1002/ece3.2563


CI Cullingham, CD Thiessen, AE Derocher, PC Paquet, JM Miller, JA Hamilton, DW Coltman. 2016. “Population structure and dispersal of wolves in the Canadian Rocky Mountains.” Journal of Mammology. 97, .

JM Miller and JA Hamilton. 2016. “Interspecies hybridization merits consideration in the conservation toolbox: response to Kovach et al.” Conservation Biology. 30, 431-433. 

ABA Shafer, JM Miller, MD Kardos. 2016. “Cross-species application of SNP chips is not suitable for identifying runs of homozygosity.” Journal of Heredity. 107: 193-195. doi: 10.1093/jhered/esv137

JA Hamilton and JM Miller. 2016. “Adaptive introgression: a resource for management and genetic conservation in a changing climate.” Conservation Biology. 30, 33–414.


JM Miller*, J Poissant*, RM Malenfant, JT Hogg, DW Coltman. 2015. “Temporal dynamics of linkage disequilibrium in two populations of bighorn sheep.” Ecology & Evolution. 5, 3401–3412. doi:10.1002/ece3.1612


JM Miller, SS Moore, P Stothard, X Liao, DW Coltman. 2015. “Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis).” BMC Genomics 16:397. doi:10.1186/s12864-015-1618-x.


JM Miller and DW Coltman. 2014. “Assessment of identity disequilibrium and its relation to empirical heterozygosity fitness correlations: a meta-analysis.” Molecular Ecology. 23, 1899-1909.

JM Miller, RM Malenfant, P David, CS Davis, J Poissant, JT Hogg, M Festa-Bianchet, DW Coltman. 2014. “Estimating genome-wide heterozygosity: effects of demographic history and marker type.” Heredity 112, 240-247.


JM Miller, JT Hogg, DW Coltman. 2013. “RAD sequencing for SNP discovery in two populations of bighorn sheep (Ovis canadensis).” In Genomic Resources Notes accepted 1 April 2013–31 May 2013, Molecular Ecology Resources 13, 965.


JM Miller, JW Kijas, MP Heaton, JC McEwan, and DW Coltman. 2012. “Consistent divergence times and allele sharing measured from cross-species application of SNP chips developed for three domestic species.” Molecular Ecology Resources 12, 1145–1150.

JM Miller, J Poissant, JT Hogg, and DW Coltman. 2012. “Genomic consequences of genetic rescue in an insular population of bighorn sheep (Ovis canadensis).” Molecular Ecology 21, 1583–1596.

JM Miller, RM Malenfant, SS Moore, and DW Coltman. 2012. “Short reads, circular genome: skimming SOLiD sequence to construct the bighorn sheep mitochondrial genome.” Journal of Heredity 103, 140-146.


JM Miller, J Poissant, JW Kijas, the International Sheep Genomics Consortium, and DW Coltman. 2011. “A genome wide set of SNPs detects population substructure and long range linkage disequilibrium in wild sheep.” Molecular Ecology Resources 11, 314-322.

JM Miller, S Hallager, S Monfort, J Newby, K Bishop, S Tidmus, P Black, B Houston, C Matthee, J Robinson, and RC Fleischer. 2011. “Phylogeographic analysis of nuclear and mtDNA supports subspecies designations in the ostrich (Struthio camelus).” Conservation Genetics 12, 423-431.

F Hailer, EA Schreiber, JM Miller, II Levin, PG Parker, RT Chesser, RC Fleischer. 2011. “Long-term isolation of a highly mobile seabird on the Galapagos.” Proc. R. Soc. B. 278, 817-825


J Poissant, JT Hogg, CS Davis, JM Miller, JF Maddox, and DW Coltman. 2010. “Genetic linkage map of a wild genome: genomic structure, recombination and sexual dimorphism in bighorn sheep.” BMC Genomics, 11:524. doi:10.1186/1471-2164-11-524

*Denotes that these authors contributed equally to the manuscript

‡Denotes supervised undergraduate researcher

§Denotes supervised graduate researcher