Publications

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Submitted or In Press

EL Jensen, DL Edwards, RC Garrick, JM Miller, JP Gibbs, LJ Cayot, W Tapia, A Caccone, MA Russello. Accepted “Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise”

EL Jensen, JM Miller, DL Edwards, RC Garrick, W Tapia, A Caccone, MA Russello. In press. “Temporal mitogenomics of Pinzón Galapagos tortoises reveals potential biases in population genetic inference” Journal of Heredity. doi: doi.org/10.1093/jhered/esy016

JM Miller*, MC Quinzin*, EH Scheibe, C Ciofi, F Villavla, W Tapia, A Caccone. In press. “Genetic pedigree analysis of the pilot breeding program for the rediscovered Galapagos giant tortoise from Floreana island.” Journal of Heredity. doi: doi.org/10.1093/jhered/esy010

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:doi.org/10.1111/eva.12551

JM Miller*, MC Quinzin*, DL Edwards, DAR Eaton, EL Jensen, MA Russello, JP Gibbs, W Tapia, D Rueda, A Caccone. In press. “Genome-wide assessment of diversity and divergence among extant Galapagos giant tortoise species.” Journal of Heredity. doi: doi.org/10.1093/jhered/esy031

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. In revision. “Giant tortoise genomes provide insights into longevity and cancer resistance mechanisms”

EA Hunter, JP Gibbs, LP Cayot, W Tapia, MC Quinzin, JM Miller, A Caccone, KT Shoemaker. Submitted. “Seeking compromise across competing goals in conservation translocations: The case of the “extinct” Floreana Island Galapagos giant tortoise”

MC Quinzin, J Sandoval-Castillo, JM Miller, LB Beheregaray, MA Russello, EA Hunter, JP Gibbs, W Tapia, F Villalva, A Caccone. Submitted. “Genetically informed captive breeding of hybrids with an extinct species of Galapagos giant tortoise”

2018

JA Hamilton, JM Miller. 2018. “From transects to transcripts: teasing apart the architecture of reproductive isolation.” Molecular Ecology. 27, 1339-1341. doi:doi.org/10.1111/mec.14516

  • Our perspective on the work of Rafati et al. (2018) who also got the cover

https://wol-prod-cdn.literatumonline.com/cms/attachment/a6882bd4-e604-4744-8696-bead5296c066/mec.2018.27.issue-6.cover.jpg

JM Miller, M Festa-Bianchet, DW Coltman.  2018. “Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium® HD SNP BeadChip.” PeerJ. 6, e4364. doi.org/10.7717/peerj.4364

2017

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

  • This paper was one of the 100 most read Ecology papers in Scientific Reports in 2017

https://i2.wp.com/fastart.nature.com/top100.jpg

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:doi.org/10.1111/mec.14187

2016

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:doi.org/10.1002/ece3.2563

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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: doi.org/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.

2015

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:doi.org/10.1002/ece3.1612

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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:doi.org/10.1186/s12864-015-1618-x.

2014

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.

2013

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.

2012

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.

2011

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

2010

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:doi.org/10.1186/1471-2164-11-524

*Denotes that these authors contributed equally to the manuscript

‡Denotes supervised undergraduate researcher

§Denotes supervised graduate researcher

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