Publications

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Submitted or In Press

SJ Gaughran, R Gray, M Jones, N Fusco, A Ochoa, JM Miller, N Poulakakis, K de Queiroz, A Caccone, EL Jensen. Submitted. “Whole-genome sequencing confirms multiple species of Galapagos giant tortoises”. preprint doi: https://doi.org/10.1101/2023.04.05.535692

MC Quinzin, A Bishop‡, JM Miller, W Tapia, F Torres-Rojo‡, C Sevilla; A Caccone. In press. “Galapagos Giant tortoise trafficking case demonstrates the utility and applications of long-term comprehensive genetic monitoring”. Animal Conservation. doi: https://doi.org/10.1111/acv.12870

JM Miller, RM Malenfant, TC Atwood, EW Born, R Dietz, KL Laidre, J Pongracz, ES Richardson, Ø Wiig, CS Davis. In revision. “Development of an 8K SNP chip to assess adaptive diversity and hybridization in polar bears”.

RM Peery, CI Cullingham, JM Miller, CE Fortier, DW Coltman, K St. Onge, BM Sacchi, DPW Huber, BS Lindgren, JEK Cooke. In revision. “The effect of lodgepole pine genotype on survivorship following a mountain pine beetle epidemic”.

2023

CI Cullingham, R Peery, JM Miller. 2023. “A roadmap to robust Discriminant Analysis of Principal Components (DAPC)”. Molecular Ecology Resources. 23, 519-522. doi: 10.1111/1755-0998.13724

2022

R Gray, N Fusco, JM Miller, W Tapia, C Mariani, A Caccone, EL Jensen. 2022. “Temporal monitoring of the Floreana Island Galapagos giant tortoise captive breeding program”. Integrative and Comparative Biology. 62, 1864-1871. doi: https://doi.org/10.1093/icb/icac129

S Hoban, F Archer, L Bertola, J Bragg, M Breed, M Bruford, M Coleman, R Ekblom, WC Funk, C Grueber, B Hand, R Jaffé, EL Jensen, J Johnson, F Kershaw, L Liggins, A MacDonald, J Mergeay, JM Miller, F Muller-Karger, D O’Brien, I Paz-Vinas, K Potter, O Razgour, C Vernesi, M Hunter. 2022. “Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition”. Biological Reviews. 97, 1511-1538. doi: https://doi.org/10.1111/brv.12852

JM Miller, EO Campbell, JJ Rotella, KR Macdonald, TS Gelatt, CS Davis. 2022. “Evaluation of novel genomic markers for pedigree construction in an isolated population of Weddell seals (Leptonychotes weddellii) at White Island, Antarctica”. Conservation Genetics Resources. 14, 69–80. doi: https://doi.org/10.1007/s12686-021-01237-0

EL Jensen, MC Quinzin, JM Miller, MA Russello, RC Garrick, DL Edwards, S Glaberman, Y Chiari, N Poulakakis, W Tapia, JP Gibbs, A Caccone. 2022. “A new mitochondrial lineage of Galapagos giant tortoises identified from museum samples”. Heredity. 128, 261–270. doi: 10.1038/s41437-022-00510-8

S Deakin, M Festa-Bianchet, JM Miller, F Pelletier, DW Coltman. 2022. “Ewe are what you wear: bigger horns, better ewes, and the cross-sex fitness consequences of trophy hunting in bighorn sheep”. Proc. R. Soc. B. 289, 20212534. doi: https://doi.org/10.1098/rspb.2021.2534

  • Hear lead author Sam Deakin talk about this paper on CBC Edmonton’s Radio Active

JM Miller, D Garant, C Perrier, T Juette, JW Jameson, E Normandeau, L Bernatchez, Denis Réale. 2022. “When the island syndrome meets genomics: Linking genetic, morphological, and behavioural divergence between island and continental deer mice”. Heredity. 128, 97–106. doi: 10.1038/s41437-021-00492-z

2021

JR Reilly, JM Miller. 2021. “A phylogeographic contact zone for Arctic Grayling (Thymallus arcticus) in Alberta, Canada”. North American Journal of Fisheries Management. 41, 1619-1630. doi: doi.org/10.1002/nafm.10697

S Santos, RM Peery, JM Miller, A Dao, F Lyu, X Li, M Li, and DW Coltman. 2021. “Ancient hybridization patterns between bighorn and thinhorn sheep”. Molecular Ecology. 32, 6273-6288. doi: https://doi.org/10.1111/mec.16136

M Kardos, EE Armstrong, SW Fitzpatrick, S Hauser, PW Hedrick, JM Miller, DA Tallmon, WC Funk. 2021. “Genetic variation is crucial to the conservation of biodiversity”. PNAS. 118, e2104642118. Preprint doi: https://doi.org/10.1101/2021.07.05.451163

DM Leigh, CB Van Rees, KL Millette, MF Breed, C Schmidt, LD Bertola, BK Hand, ME Hunter, EL Jensen, F Kershaw, L Liggins, G Luikart, S Manel, J Mergeay, JM Miller, G Segelbacher, S Hoban, I Paz-Vinas. 2021. “Opportunities and challenges of macrogenetic studies”. Nature Reviews Genetics. 22, 791–807. doi: doi.org/10.1038/s41576-021-00394-0

I Paz-Vinas, EL Jensen, LD Bertola, MF Breed, BK Hand, ME Hunter, F Kershaw, DM Leigh, G Luikart, J Mergeay, JM Miller, CB van Rees, G Segelbacher, S Hoban. 2021. “Macro-genetic studies must not ignore limitations of genetic markers and scale”. Ecology Letters. 24, 1282-1284 (Preprint doi: 10.22541/au.161401200.09787142/v1)

Y Cao, S Xu, M Shen, Z Chen, L Gao, F Lv, X Xie, X Wang, H Yang, C Liu, P Zhou, P Wan, Y Zhang, J Yang, W Pi, H EEr, DP Berry, M Barbato, A Esmailizadeh, M Nosrati, H Salehian-Dehkordi, M Dehghani-Qanatqestani, AV Dotsev, TE Deniskova, NA Zinovieva, G Brem, O Štěpánek, E Ciani, C Weimann, G Erhardt, JM Mwacharo, A Ahbara, J Han, O Hanotte, JM Miller, Z Sim, DW Coltman, J Kantanen, MW Bruford, JA Lenstra, J Kijas, and M Li. In press. “Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep.” Molecular Biology and Evolution. 38, 838–855 doi: 10.1093/molbev/msaa236

2020

N Poulakakis*, JM Miller*, EL Jensen, LB Beheregaray, MA Russello, S Glaberman, J Boore, A Caccone. 2020. “Colonization history of Galapagos giant tortoises: Insights from mitogenomes support the progression rule”. Journal of Zoological Systematics and Evolutionary Research. 58, 1262-1275. doi: http://dx.doi.org/10.1111/jzs.12387

JM Miller, CI Cullingham, RM Peery. 2020. “The influence of a priori grouping on inference of genetic clusters: simulation study and literature review of the DAPC method”. Heredity. 125, 269–280. doi: doi.org/10.1038/s41437-020-0348-2

HR Taft, DN McCoskey, JM Miller, SK Pearson, MA Coleman, NK Fletcher, CS Mittan, MH Meek, S Barbosa. 2020. “Research-management partnerships: an opportunity to integrate genetics in conservation actions”. Conservation Science and Practice. 2, e218. doi: doi.org/10.1111/csp2.218

CM Bubac, JM Miller, DW Coltman. 2020. “The genetic basis of animal behavioural diversity in natural populations”. Molecular Ecology. 29, 1957-1971. doi: 10.1111/mec.15461

CI Cullingham, JM Miller, RM Peery, JR Dupuis, RM Malenfant, JC Gorrell,  JK Janes. 2020. “Confidently identifying the correct K value using the ΔK method: when does K = 2?”. Molecular Ecology. 29, 862-869. doi: 10.1111/mec.15374

EA Hunter, JP Gibbs, LP Cayot, W Tapia, MC Quinzin, JM Miller, A Caccone, KT Shoemaker. 2020. “Seeking compromise across competing goals in conservation translocations: The case of the “extinct” Floreana Island Galapagos giant tortoise”. Journal of Applied Ecology. 57, 136-148. doi: 10.1111/1365-2664.13516

2019

MC Quinzin, J Sandoval-Castillo, JM Miller, LB Beheregaray, MA Russello, EA Hunter, JP Gibbs, W Tapia, F Villalva, A Caccone. 2019. “Genetically informed captive breeding of hybrids with an extinct species of Galapagos giant tortoise”. Conservation Biology. 33, 1404-1414. doi: 10.1111/cobi.13319

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. 2019. “Giant tortoise genomes provide insights into longevity and cancer resistance mechanisms”. Nature Ecology & Evolution. 3, 87-95. doi: doi.org/10.1038/s41559-018-0733-x

2018

EL Jensen, DL Edwards, RC Garrick, JM Miller, JP Gibbs, LJ Cayot, W Tapia, A Caccone, MA Russello. 2018. “Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise”. Evolutionary Applications. 11, 1811-1821. doi: doi.org/10.1111/eva.12682

JM Miller*, MC Quinzin*, DL Edwards, DAR Eaton, EL Jensen, MA Russello, JP Gibbs, W Tapia, D Rueda, A Caccone. 2018. “Genome-wide assessment of diversity and divergence among extant Galapagos giant tortoise species”. Journal of Heredity. 109, 611–619. doi: doi.org/10.1093/jhered/esy031

  • Not only did we get the cover for our three tortoise papers in volume 109 of the Journal of Heredity, our genomic assessment of the species complex was the “Editor’s Choice”,  so enjoy it for free!

EL Jensen, JM Miller, DL Edwards, RC Garrick, W Tapia, A Caccone, MA Russello. 2018. “Temporal mitogenomics of Pinzón Galapagos tortoises reveals potential biases in population genetic inference“. Journal of Heredity. 63 doi: doi.org/10.1093/jhered/esy016

JM Miller*, MC Quinzin*, EH Scheibe‡, C Ciofi, F Villavla, W Tapia, A Caccone. 2018. “Genetic pedigree analysis of the pilot breeding program for the rediscovered Galapagos giant tortoise from Floreana island”. Journal of Heredity. 109, 620–630. 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. 2018. “Theory, practice and the conservation of Galápagos giant tortoises in the age of genomics”. Evolutionary Applications. 11, 1084-1093. doi:doi.org/10.1111/eva.12551

Evolutionary Applications cover featuring a collage of pictures including a Galapagos tortoise

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
Molecular Ecology cover featuring a rabbot

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
Banner commemorating that our paper was one of the 100 most read Ecology papers in Scientific Reports in 2017

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

  • Our paper was a #Top20article in Molecular Ecology with some of the highest downloads between July 2016 and December 2018!
Banner commemorating that our paper was one of the 20 most downloaded papers in Molecular Ecology Between July 2016 and December 2018

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

Ecology and Evolution cover featuring a polar bear

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, 839-851. doi:doi.org/10.1093/jmammal/gyw015

JM Miller and JA Hamilton. 2016. “Interspecies hybridization in the conservation toolbox: response to Kovach et al.”. Conservation Biology. 30, 431-433. doi: doi.org/10.1111/cobi.12677

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. doi:doi.org/10.1111/cobi.12574

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

Ecology and Evolution cover featuring a bighorn sheep

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. doi:doi.org/10.1111/mec.12707

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. doi:doi.org/10.1038/hdy.2013.99

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. doi:doi.org/10.1111/1755-0998.12142

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. doi:doi.org/10.1111/1755-0998.12017

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. doi:doi.org/10.1093/jhered/esr104

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. doi:doi.org/10.1111/j.1755-0998.2010.02918.x

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. doi:doi.org/10.1007/s10592-010-0149-x

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. doi:doi.org/10.1098/rspb.2010.1342

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