Publications

** Check out Population Genomics: Wildlife, edited by Paul A. Hohenlohe and Om P. Rajora **
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2025

van Elst T, Schüßler D, Rafamantanantsoa SM, Radriarimanga T, Rabemananjara NR, Rasolofoson DW, Randimbiharinirina RD, Hohenlohe PA, Radespiel U. 2025. Species-specific responses to paleoclimatic changes and landscape barriers drive contrasting phylogeography of co-distributed lemur species in northeastern Madagascar. Molecular Ecology in press. [pdf]

Cheek RG, Hohenlohe PA, Sillett TS, Morrison SA, Funk WC, Ghalambor CK. 2025. Genetic parallelism underlying repeated bill divergence in the Island Scrub-jay (Aphelocoma insularis) increases at higher genetic levels of organization. Evolution in press.

Nerkowski SA, Hohenlohe PA, Rachlow JL, Warheit KI, Gallie JA, Waits LP. 2025. Long-term noninvasive genetic monitoring guides recovery of the endangered Columbia Basin pygmy rabbits. Genes 16: 956. [pdf]

Garrett MJ, Conway CJ, Waits LP, Hohenlohe PA. 2025. Genetic variation and metapopulation structure inform recovery goals in a threatened species. Genes 16: 694. [pdf]

Strickland K, Jones M, Lachish S, Comte S, Hamede Ross R, Hohenlohe PA, McCallum H, Storfer A, Kruuk LEB. 2025. Life-history trade-offs and reproductive strategies in Tasmanian devils following disease-induced population decline. Proceedings B 292: 20250697. [pdf]

Flores A-M, Christensen KA, Godin T, Palti Y, Campbell MR, Waldbieser GC, Simpson SA, Scheffler BE, Smith SR, Whiteley AR, Kovach RP, Luikart G, Boyer MC, Kardos M, Relyea S, Wells C, Koop BF. 2025. The genome assembly of the westslope cutthroat trout, Oncorhynchus lewisii, reveals interspecific chromosomal rearrangements with the rainbow trout, Oncorhynchus mykiss. G3 Genes Genomes Genetics jkaf064. [pdf]

Clark EI, Bean DW, Bitume EV, Stahlke AR, Hohenlohe PA, Hufbauer RA. 2025. Heritability of body size matches trait evolution in the range expansion of a biological control agent. Current Research in Insect Science 7: 100112. [pdf]

Egan JP, Ma J, Myrsell VL, Chen Z, Masingale J, Caudill CC, Boyle T, Browning J, Narum SR, Cain KD, Hohenlohe PA. 2025. Temperature-related effects on disease susceptibility and immune response in redband trout (Oncorhynchus mykiss gairdneri) following challenge with Flavobacterium columnare. Journal of Fish Diseases 48: e14046. [pdf]

Stacy EM, Robards MD, Jung TS, Kukka PM, Sullivan J, Hohenlohe PA, Waits LP. 2025. Comparing microsatellites and single nucleotide polymorphisms to evaluate genetic structure and diversity in wolverines (Gulo gulo) across Alaska and western Canada. Journal of Mammalogy 106: 561-575. [pdf]

van Elst T, Sgarlata GM, Schüßler D, Tiley GP, Poelstra JW, Scheumann, M, Blanco MB, Aleixo-Pais IG, Evasoa MR, Ganzhorn JU, Goodman SM, Hasiniaina AF, Hending D, Hohenlohe PA, Ibouroi MT, Iribar A, Jan F, Kappeler PM, LePors B, Manzi S, Olivieri G, Rakotonanahary AN, Rakotondranary SJ, Rakotondravony R, Ralison JM, Ranaivoarisoa JF, Randrianambinina B, Rasoloarison RM, Rasoloharijaona S, Rasolondraibe E, Teixeira H, Zaonarivelo JR, Louis EE Jr., Yoder AD, Chikhi L, Radespiel U, Salmona J. 2025. Integrative taxonomy clarifies the evolution of a cryptic primate clade. Nature Ecology & Evolution 9: 57-72. [pdf]

2024

Strickland K, Jones ME, Storfer A, Hamede RK, Hohenlohe PA, Margres MJ, McCallum HI, Comte S, Lachish S, Kruuk LEB. 2024. Adaptive potential in the face of a transmissible cancer in Tasmanian devils. Molecular Ecology 33: e17531. [pdf]

Beer MA, Trumbo DR, Rautsaw RM, Kozakiewicz CP, Epstein B, Hohenlohe PA, Alford RA, Schwarzkopf L, Storfer A. 2024. Spatial variation in genomic signatures of local adaptation during the cane toad invasion of Australia. Molecular Ecology 2024: e17464. [pdf]

Garrett MJ, Nerkowski SA, Kieran S, Campbell NR, Barbosa S, Conway CJ, Hohenlohe PA, Waits LP. 2024. Development and validation of a GT-seq panel for genetic monitoring in a threatened species using minimally invasive sampling. Ecology and Evolution 14: e11321. [pdf]

Lukaszewicz M, Issaka Salia O, Hohenlohe PA, Buzbas EO. 2024. Approximate Bayesian computational methods to estimate the strength of divergent selection in population genomics models. Journal of Computational Mathematics and Data Science 10: 100091. [pdf]

Clancey E, MacPherson A, Cheek RG, Mouton JC, Sillett TS, Ghalambor CK, Funk WC, Hohenlohe PA. 2024. Unraveling adaptive evolutionary divergence at microgeographic scales. American Naturalist 203: E35-E49. [pdf]

Beer MA, Proft KM, Veillet A, Kozakiewicz CP, Hamilton DG, Hamede R, McCallum H, Hohenlohe PA, Burridge CP, Margres MJ, Jones ME, Storfer A. 2024. Disease-driven top predator decline affects mesopredator population genomic structure. Nature Ecology & Evolution 8: 293-303. [pdf]

Bertola LD, Brüniche-Olsen A, Kershaw F, Russo I-RM, MacDonald AJ, Sunnucks P, Bruford MW, Cadena CD, Ewart KM, de Bruyn M, Eldridge MDB, Frankham R, Guayasamin JM, Grueber CE, Hoareau TB, Hoban S, Hohenlohe PA, Hunter ME, Kotze A, Kuja J, Lacy RC, Laikre L, Lo N, Meek MH, Mergeay J, Mittan-Moreau C, Neaves LE, O'Brien D, Ochieng JW, Ogden R, Orozco-terWengel P, Páez-Vacas M, Pierson J, Ralls K, Shaw RE, Sogbohossou EA, Stow A, Steeves T, Vernesi C, Watsa M, Segelbacher G. 2023. A pragmatic approach for integrating molecular tools into biodiversity conservation. Conservation Science and Practice 2024: e13053. [pdf]

2023

Dean LL, Magalhaes IS, D'Agostino D, Hohenlohe PA, MacColl ADC. 2023. On the origins of phenotypic parallelism in benthic and limnetic stickleback. Molecular Biology and Evolution 40: msad191. [pdf]

Tumendemberel O, Hendricks SA, Hohenlohe PA, Sullivan J, Zedrosser A, Sæbø M, Proctor MF, Koprowski JL, Waits LP. 2023. Range-wide evolutionary relationships and historical demography of brown bears (Ursus arctos) revealed by whole-genome sequencing of isolated central Asian populations. Molecular Ecology 32: 5156-5169. [pdf]

van Elst T, Schüßler D, Rakotondravony R, Rovanirina VST, Veillet A, Hohenlohe PA, Ratsimbazafy JH, Rasoloarison RM, Rasoloharijaona S, Randrianambinina B, Ramilison M, Yoder AD, Louis EE Jr, Radespiel U. 2023. Diversification processes in Gerp's mouse lemur demonstrate the importance of rivers and altitude as biogeographic barriers in Madagascar's humid rainforests. Ecology and Evolution 13: e10254. [pdf]

Grossfurthner LP, Milano ER, Hohenlohe PA, Waits LP, Richardson BA. 2023. Population structure and hybridization under contemporary and future climates in a heteroploid foundational shrub species (Artemisia tridentata). Frontiers in Plant Science 14: 1155868. [pdf]

Hamede R, Fountain-Jones NM, Arce F, Jones M, Storfer A, Hohenlohe PA, McCallum H, Roche B, Ujvari B, Thomas F. 2023. The tumour is in the detail: local phylogenetic, population and epidemiological dynamics of a transmissible cancer in Tasmanian devils. Evolutionary Applications 16: 1316-1327. [pdf]

Andrews KR, Seaborn T, Egan JP, Fagnan MW, New DD, Chen Z, Hohenlohe PA, Waits LP, Caudill CC, Narum SR. 2023. Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout. Molecular Ecology 32: 800-818. [pdf]

Clark EI, Stahlke AR, Gaskin JF, Bean DW, Hohenlohe PA, Hufbauer RA, Bitume EV. 2023. Fitness and host use remain stable in a biological control agent after many years of hybridization. Biological Control 177: 105102. [pdf]

2022

Grossfurthner LP. 2022. Hybridisierung im Kontext gefährdeter Arten. Pp. 41-45 in Rote Liste der Farn- und Blütenpflanzen Österreichs. Stapfia 114.

Clark EI, Bitume EV, Bean DW, Stahlke AR, Hohenlohe PA, Hufbauer RA. 2022. Evolution of reproductive life-history and dispersal traits during the range expansion of a biological control agent. Evolutionary Applications 15: 2089-2099. [pdf]

Hendricks SA, King JL, Duncan CL, Vickers W, Hohenlohe PA, Davis BW. 2022. Genomic assessment of cancer susceptibility in the threatened Catalina island fox (Urocyon littoralis catalinae). Genes 13: 1496. [pdf]

Poelstra JW, Montero BK, Lüdeman J, Yang Z, Rakotondranary SJ, Hohenlohe PA, Stetter N, Ganzhorn JU, Yoder AD. 2022. RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results. Proceedings B 289: 20220596. [pdf]

*Tiley GP, *van Elst T, Teixeira H, Schüßler D, Salmona J, Blanco MB, Ralison JM, Randrianambinina B, Rasoloarison RM, Stahlke AR, Hohenlohe PA, Chikhi L, Louis EE, Radespiel U, Yoder AD. 2022. Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests. Molecular Ecology 31: 4901-4918. [pdf]

Peterson K, Hendricks SA, Hohenlohe PA, Parent CE. 2022. Panmixia in spiders (Mecaphesa celer, Thomisidae) despite fragmented habitat at Craters of the Moon in Idaho. Ecological Entomology 47: 645-656. [pdf]

*Stahlke AR, *Bitume EV, Oszoy AZ, Bean DW, Veillet A, Clark MI, Clark EI, Moran P, Hufbauer RA, Hohenlohe PA. 2022. Hybridization and range expansion in tamarisk beetles (Diorhabda spp.) introduced to North America for classical biological control. Evolutionary Applications 15: 60-77. [pdf]

Chen Z, Grossfurthner L, Loxterman J, Masingale J, Richardson BA, Seaborn T, Smith B, Waits LP, Narum SR. 2022. Applying genomics in assisted migration under climate change: framework, empirical applications, and case studies. Evolutionary Applications 15: 3-21. [pdf]

Clancey E, Johnson TR, Harmon LJ, Hohenlohe PA. 2022. Estimation of the strength of mate preference from mated pairs observed in the wild. Evolution 76: 29-41. [pdf]

2021

Seaborn T, Andrews KR, Applestein CV, Breech TM, Garrett MJ, Zaiats A, Coughlin TT. 2021. Integrating genomics in population models to forecast translocation success. Restoration Ecology 29: e13395. [pdf]

Kozakiewicz CP, Fraik AK, Patton AH, Ruiz-Aravena M, Hamilton DG, Hamede R, McCallum H, Hohenlohe PA, Margres MJ, Jones ME, Storfer A. 2021. Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection. BMC Genomics 22: 698. [pdf]

Barbosa S, Andrews K, Goldberg A, Gour D, Hohenlohe P, Conway C, Waits L. 2021. The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern. Molecular Ecology 30: 4673-4694. [pdf]

Stahlke AR, Epstein B, Barbosa S, Margres MJ, Patton A, Hendricks SA, Veillet A, Fraik AK, Schönfeld B, McCallum HI, Hamede R, Jones ME, Storfer A, Hohenlohe PA. 2021. Contemporary and historical selection in Tasmanian devils (Sarcophilus harrisii) support novel, polygenic response to transmissible cancer. Proceedings B 288: 20210577. [pdf] [article in The Scientist]

Fu Z, Crossley MS, Epstein B, Bates C, Crowder DW, Elling AA, Hohenlohe PA, Jabbour R, Ramirez RA, Snyder WE. 2021. Using fine-scale relatedness to infer natural enemy movement. Biological Control 160: 104662. [pdf]

Laikre L, Hohenlohe PA, Allendorf FW, Bertola LD, Breed MF, Bruford MW, Funk WC, Gajardo G, González-Rodríguez A, Grueber CE, Hedrick PW, Heuertz M, Hunter ME, Johannesson J, Liggins L, MacDonald AJ, Mergeay J, Moharrek F, O'Brien D, Ogden R, Orozco-terWengel P, Palma-Silva C, Pierson J, Paz-Vinas I, Russo I-RM, Ryman N, Segelbacher G, Sjögren-Gulve P, Waits LP, Vernesi C, Hoban S. 2021. Authors' reply to letter to the editor: continued improvement to genetic diversity indicator for CBD. Conservation Genetics 22: 533-536. [pdf] [original letter]

Marden E et al [57 authors, editors of Molecular Ecology and Molecular Ecology Resources]. 2021. Sharing and reporting benefits from biodiversity research. Molecular Ecology 30: 1103-1107. [pdf]

*Magalhaes IS, *Whiting JR, D'Agostino D, Hohenlohe PA, Mahmoud M, Bell MA, Skúlason S, MacColl ADC. 2021. Intercontinental genomic parallelism in multiple three-spined stickleback adaptive radiations. Nature Ecology & Evolution 5: 251-261. [pdf]

*Poelstra J, *Salmona J, *Tiley GP, Schüßler D, Blanco MB, Andriambeloson JB, Bouchez O, Campbell CR, Etter PD, Hohenlohe PA, Hunnicutt KE, Iribar A, Johnson EA, Kappeler PM, Larsen PA, Manzi S, Ralison JM, Randrianambinina B, Rasoloarison RM, Rasolofoson DW, Stahlke AR, Weisrock D, Williams RC, Chikhi L, Louis EE Jr, *Radespiel U, *Yoder AD. 2021. Cryptic patterns of speciation in cryptic primates: microendemic mouse lemurs and the multispecies coalescent. Systematic Biology 70: 203-218. [pdf]

Hoban S, Paz-Vinas I, Aitken S, Bertola LD, Breed MF, Bruford MW, Funk WC, Grueber CE, Heuertz M, Hohenlohe PA, Hunter ME, Jaffé R, Lopes Fernandes M, Mergeay J, Moharrek F, O'Brien D, Segelbacher G, Vernesi C, Waits L, Laikre L. 2021. Effective population size remains a suitable, pragmatic indicator of genetic diversity for all species, including forest trees. Biological Conservation 253: 108906. [pdf]

Hohenlohe PA, Funk WC, Rajora OP. 2021. Population genomics for wildlife conservation and management. Molecular Ecology 30: 62-82. [pdf]

Hamede R, Madsen TR, McCallum H, Storfer A, Hohenlohe PA, Siddle H, Kaufman J, Giraudeau M, Jones M, Thomas F, Ujvari B. 2021. Darwin, the devil, and the management of transmissible cancers. Conservation Biology 35: 748-751. [pdf]

2020

Hohenlohe PA, Rajora OP, eds. Population Genomics: Wildlife. Springer. [link] [chapter pdfs available on request]

Patton AH, Lawrance MF, Margres MJ, Kozakiewicz CP, Hamede R, Ruiz-Aravena M, Hamilton DG, Comte S, Ricci LE, Taylor RL, Stadler T, Leaché A, McCallum H, Jones ME, Hohenlohe PA, Storfer A. 2020. A transmissible cancer shifts from emergence to endemism in Tasmanian devils. Science 370: eabb9772. [pdf]

Hamilton DG, Jones ME, Cameron EZ, Kerlin DH, McCallum H, Storfer A, Hohenlohe PA, Hamede RK. 2020. Infectious disease and sickness behavior: tumour progression affects interaction patterns and social network structure in wild Tasmanian devils. Proceedings B 287: 20202454. [pdf]

*Barbosa S, *Hendricks SA, Funk WC, Rajora OP, Hohenlohe PA. 2020. Wildlife population genomics: applications and approaches. In Hohenlohe PA, Rajora OP, eds. Population Genomics: Wildlife. Springer. [pdf]

Kozakiewicz CP, Ricci L, Patton AH, Stahlke AR, Hendricks SA, Margres MJ, Ruiz-Aravena, Hamilton DG, Hamede R, McCallum H, Jones ME, Hohenlohe PA, Storfer A. 2020. Comparative landscape genetics reveals differential effects of environment on host and pathogen genetic structure in Tasmanian devils (Sarcophilus harrisii) and their transmissible tumor. Molecular Ecology 29: 3217-3233. [pdf]

Andrews KR, Gerritsen A, Rashed A, Crowder DW, Rondon SI, van Herk WG, Vernon R, Wanner KW, Wilson CM, New DD, Fagnan MW, Hohenlohe PA, Hunter SS. 2020. Wireworm (Coleoptera: Elateridae) genomic analysis reveals putative cryptic species, population structure, and adaptation to pest control. Communications Biology 3: 489. [pdf]

Hoban S, Bruford M, D'Urban Jackson J, Lopes-Fernandes M, Heuertz M, Hohenlohe PA, Paz-Vinas I, Sjögren-Gulve P, Segelbacher G, Vernesi C, Aitken S, Bertola LD, Bloomer P, Breed M, Rodríguez-Correa H, Funk WC, Grueber CE, Hunter ME, Jaffe R, Liggins L, Mergeay J, Moharrek F, O'Brien D, Ogden R, Palma-Silva C, Pierson J, Ramakrishnan U, Simo-Droissart M, Tani N, Waits L, Laikre L. 2020. Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved. Biological Conservation 248: 108654. [pdf]

Margres MJ, Ruiz-Aravena M, Hamede R, Chawla K, Patton AH, Lawrance MF, Fraik AK, Stahlke AR, Davis BW, Ostrander EA, Jones ME, McCallum H, Paddison PJ, Hohenlohe PA, Hockenberry D, Storfer A. 2020. Spontaneous tumor regression in Tasmanian devils associated with RASL11A activation. Genetics 215: 1143-1152. [pdf]

Maselko J, Andrews KR, Hohenlohe PA. 2020. Long-lived marine species may be resilient to environmental variability through a temporal portfolio effect. Ecology and Evolution 10: 6435-6448. [pdf]

Fraik AK, Margres MJ, Epstein B, Barbosa S, Jones M, Hendricks SA, Schönfeld B, Stahlke AR, Veillet A, Hamede R, McCallum H, Lopez-Contreras E, Kallinen SJ, Hohenlohe PA, Kelley JL, Storfer A. 2020. Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations. Evolution 74: 1392-1408. [pdf]

Hendricks SA, Storfer A, Hohenlohe PA. 2020. Population genomics of wildlife cancer. In Hohenlohe PA, Rajora OP, eds. Population Genomics: Wildlife. Springer. [pdf]

Laikre L, Hoban S, Bruford MW, Segelbacher G, Allendorf FW, Gajardo G, González Rodríguez A, Hedrick PW, Heuertz M, Hohenlohe PA, Jaffé R, Johannesson K, Liggins L, MacDonald AJ, Orozco ter Wengel P, Reusch TBH, Rodríguez-Correa H, Russo I-RM, Ryman N, Vernesi C. 2020. Post-2020 goals overlook genetic diversity. Science 367: 1083-1085. letter [pdf]

Stahlke AR, Bell D, Dhendup T, Kern B, Pannoni S, Robinson Z, Strait J, Smith S, Hand BK, Hohenlohe PA, Luikart G. 2020. Population genomics training for the next generation of conservation geneticists: ConGen 2018 workshop. Journal of Heredity 111: 227-236. [pdf]

Clendenin HR, Adams JR, Ausband DE, Hayden JA, Hohenlohe PA, Waits LP. 2020. Combining harvest and genetics to estimate reproduction in wolves. Journal of Wildlife Management 84: 492-504. [pdf]

Hohenlohe PA, Magalhaes IS. 2020. The population genomics of parallel adaptation: lessons from threespine stickleback. Pp. 249-276 in Oleksiak M, Rajora OP, eds. Population Genomics: Marine Organisms. Springer. [pdf]

2019

Fraik AK, Quackenbush C, Margres MJ, Comte S, Hamilton DG, Kozakiewicz CP, Jones M, Hamede R, Hohenlohe PA, Storfer A, Kelley JL. 2019. Transcriptomics of Tasmanian devil (Sarcophilus harrisii) ear tissue reveal homogeneous gene expression patterns across a heterogeneous landscape. Genes 10:801. [pdf]

Stahlke AR, Ozsoy AZ, Bean DW, Hohenlohe PA. 2019. Mitochondrial genome sequences of Diorhabda carinata and Diorhabda carinulata, two beetle species introduced to North America for biological control. Microbiology Resource Announcements 8:e00690-19. [pdf]

Patton AH, Margres MJ, Stahlke AR, Hendricks S, Lewallen K, Hamede RK, Ruiz-Aravena M, Ryder O, McCallum HI, Jones ME, Hohenlohe PA, Storfer A. 2019. Contemporary demographic reconstruction methods are robust to genome assembly quality: A case study in Tasmanian devils. Molecular Biology and Evolution 36: 2906-2921. [pdf]

James S, Jennings G, Kwon YM, Stamnitz M, Fraik A, Storfer A, Comte S, Pemberton D, Fox S, Brown B, Pye R, Woods G, Lyons B, Hohenlohe PA, McCallum H, Siddle H, Thomas F, Ujvari B, Murchison EP, Jones ME, Hamede R. 2019. Tracing the rise of malignant cell lines: Distribution, epidemiology and evolutionary interactions of two transmissible cancers in Tasmanian devils. Evolutionary Applications 12: 1772-1780. [pdf]

Hamilton DG, Jones ME, Cameron EZ, McCallum HI, Storfer A, Hohenlohe PA, Hamede RK. 2019. Rate of inter-sex interactions affects injury likelihood in Tasmanian devil contact networks. Behavioral Ecology 30: 1087-1095. [pdf]

Hohenlohe PA, McCallum HI, Jones ME, Lawrance MF, Hamede RK, Storfer A. 2019. Conserving adaptive potential: lessons from Tasmanian devils and their transmissible cancer. Conservation Genetics 20: 81-87. [pdf]

Jones ME, Hamede RK, Storfer A, Hohenlohe PA, Murchison E, McCallum HI. 2019. Emergence, transmission and evolution of an uncommon enemy: Tasmanian devil facial tumour disease. In Wilson K, Fenton A, Tompkins D, eds. Wildlife Disease Ecology: Linking Theory to Data and Application. Cambridge University Press.

Wells K, Hamede RK, Jones ME, Hohenlohe PA, Storfer A, McCallum HI. 2019. Individual and temporal variation in pathogen load predicts long-term impacts of an emerging infectious disease. Ecology e02613. [pdf]

Hendricks SA, Schweizer R, Harrigan R, Pollinger R, Brown R, Paquet P, Darimont C, Adams J, Waits L, vonHoldt B, Hohenlohe PA, Wayne R. 2019. Natural re-colonization and admixture of wolves (Canis lupus) in the US Pacific Northwest: challenges for the protection and management of rare and endangered taxa. Heredity 122: 133-149. [pdf] [Northwest Public Radio coverage]

2018

Heppenheimer E, Harrigan RJ, Rutledge LY, Koepfli K-P, DeCandia AL, Brzeski KE, Benson JF, Wheeldon T, Patterson BR, Kays R, Hohenlohe PA, vonHoldt BM. 2018. Population genomic analysis of North American eastern wolves (Canis lycaon) supports their conservation priority status. Genes 9: 606. [pdf]

Heppenheimer E, Brzeski KE, Hinton JW, Patterson BR, Rutledge LY, DeCandia AL, Wheeldon T, Fain SR, Hohenlohe PA, Kays R, White BN, Chamberlain MJ, vonHoldt BM. 2018. High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote (Canis latrans) populations. Ecology and Evolution 8: 12641-12655. [pdf]

Luikart G, Kardos M, Hand BK, Rajora OP, Aitken SN, Hohenlohe PA. 2018. Population genomics: advancing understanding of nature. In Rajora O, ed. Population Genomics Concepts, Strategies, and Approaches. Springer. [pdf]

Hendricks SA,Schweizer RM, Wayne RK. 2018. Conservation genomics illuminates the adaptive uniqueness of North American gray wolves. Conservation Genetics in press. [pdf]

Margres MJ, Ruiz-Aravena M, Hamede R, Jones ME, Lawrance MF, Hendricks SA, Patton A, Davis BW, Ostrander EA, McCallum H, Hohenlohe PA, Storfer A. 2018. The genomic basis of tumor regression in Tasmanian devils (Sarcophilus harrisii). Genome Biology and Evolution 10: 3012-3025. [pdf]

Margres MJ, Jones M, Epstein B, Kerlin DH, Comte S, Fox S, Fraik AK, Hendricks SA, Huxtable S, Lachish S, Lazenby B, O'Rourke SM, Stahlke AR, Wiench CG, Hamede R, Schönfeld B, McCallum H, Miller MR, Hohenlohe PA, Storfer A. 2018. Large-effect loci affect survival in Tasmanian devils (Sarcophilus harrisii) infected with a transmissible cancer. Molecular Ecology 27: 4189-4199. [pdf]

Hohenlohe PA, Hand BK, Andrews KR, Luikart G. 2018. Population genomics provides key insights in ecology and evolution. In Rajora O, ed. Population Genomics Concepts, Strategies, and Approaches. Springer. [pdf]

Andrews KR, Adams J, Cassirer F, Plowright R, Gardner C, Dwire M, Hohenlohe PA, Waits L. 2018. A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data. Molecular Ecology Resources 18: 1263-1281. [pdf]

Hendricks SA, Anderson E, Antao T, Bernatchez L, Forester B, Garner B, Hand B, Hohenlohe PA, Kardos M, Koop B, Sethuraman A, Waples R, Luikart G. 2018. Recent advances in conservation and popoulation genomics data analysis. Evolutionary Applications 11: 1197-1211. [pdf]

Storfer A, Hohenlohe PA, Margres MJ, Patton A, Fraik AK, Lawrance M, Ricci LE, Stahlke AR, McCallum HI, Jones ME. 2018. The devil is in the details: genomics of transmissible cancers in Tasmanian devils. PLoS Pathogens 14(8): e1007098. [pdf]

2017

Hendricks SA, Koblmüller S, Harrigan RJ, Leonard JA, Schweizer RM, vonHoldt BM, Kays R, Wayne RK. 2017. Defense of an expanded historical range for the Mexican wolf: a comment on Heffelfinger et al. Journal of Wildlife Management 81: 1331-1333. [pdf]

Bitume EV, Bean D, Stahlke AR, Hufbauer RA. 2017. Hybridization affects life-history traits and host specificity in Diorhabda spp. Biological Control 111: 45-52. [pdf]

Wells K, Hamede RK, Kerlin DH, Storfer A, Hohenlohe PA, Jones ME, McCallum HI. 2017. Infection of the fittest: devil facial tumor disease has greatest effect on individuals with highest reproductive output. Ecology Letters 20: 770-778. [pdf]

Catchen J, Hohenlohe PA, Bernatchez L, Funk WC, Andrews KR, Allendorf F. 2017. Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations. Molecular Ecology Resources 17: 362-365. [pdf] [supplemental file] [in response to this article] [see also this response]

*Hohenlohe PA, *Rutledge LY, Waits LP, Andrews KR, Adams JR, Hinton JW, Nowak RM, Patterson BR, Wydeven AP, Wilson PA, White BN. 2017. Comment on "Whole genome sequence analysis shows two endemic species of North American wolf are admixtures of the coyote and gray wolf". Science Advances 3: e1602250. [pdf] [in response to this article]

Hendricks SA, Epstein B, Schönfeld B, Wiench C, Hamede R, Jones M, Storfer A, Hohenlohe PA. 2017. Conservation implications of limited genetic diversity and population structure in Tasmanian devils (Sarcophilus harrisii). Conservation Genetics 18: 977-982. [pdf] [supplemental file]

2016

Kovach RP, Hand BK, Hohenlohe PA, Cosart TF, Boyer MC, Neville HH, Muhlfeld CC, Amish SJ, Carim K, Narum SR, Lowe WH, Allendorf FW, Luikart G. 2016. Vive la resistance: genome-wide selection against introduced alleles in invasive hybrid zones. Proceedings B 283: 20161380. [pdf]

Cleary KA, Waits LP, Hohenlohe PA. 2016. Development and characterization of fourteen novel microsatellite markers for the chestnut short-tailed fruit bat (Carollia castanea), and cross-amplifcation to related species . PeerJ 4: e2465. [pdf]

Epstein B, Jones M, Hamede R, Hendricks S, McCallum H, Murchison EP, Schönfeld B, Wiench C, *Hohenlohe P, *Storfer A. 2016. Rapid evolutionary response to a transmissible cancer in Tasmanian devils. Nature Communications 7: 12684. [pdf] [supplemental file] [supplemental table] [Nature story] [Science story]

Trumbo DR, Epstein B, Hohenlohe PA, Alford RA, Schwarzkopf L, Storfer A. 2016. Mixed population genomics support for the central marginal hypothesis across the invasive range of the cane toad (Rhinella marina) in Australia. Molecular Ecology 25: 4161-4176. [pdf]

Magalhaes IS, D'Agostino D, Hohenlohe PA, MacColl ADC. 2016. The ecology of an adaptive radiation of three-spined stickleback from North Uist, Scotland. Molecular Ecology 25: 4319-4336. [pdf]

*Benestan LM, *Ferchaud A, Hohenlohe PA, Garner BA, Naylor GJP, Baums IB, Schwartz MK, Kelley JL, Luikart G. 2016. Conservation genomics of natural and managed populations: building a conceptual and practical framework. Molecular Ecology 25: 2967–2977. [pdf]

Funk WC, Lovich RE, Hohenlohe PA, Hofman CA, Morrison SA, Sillett TS, Ghalambor CK, Maldonado JE, Rick TC, Day MD, Polato NR, Fitzpatrick SW, Coonan TJ, Crooks KR, Dillon A, Garcelon DK, King JL, Boser CL, Lyren LM, Boydston EE, Gould N, Andelt WF. 2016. Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis). Molecular Ecology 25: 2176–2194. [pdf]

Rutledge LY, Devillard S, Hohenlohe PA, White BN. 2016. Considering all the evidence: a reply to Sefc and Koblmüller. Biology Letters 12: 20151009. [pdf]

Kim M-S, Hohenlohe PA, Kim K-H, Seo S-T, Klopfenstein NB. 2016. Genetic diversity and population structure of Raffaelea quercus-mongolicae, a fungus associated with oak mortality in South Korea. Forest Pathology 46: 164-167. [pdf]

Gerritsen AT, New DD, Robison BD, Rashed A, Hohenlohe PA, Forney L, Rashidi M, Wilson CM, Settles ML. 2016. Full mitochondrial genome sequence of the sugar beet wireworm Limonius californicus (Coleoptera: Elateridae), a common agricultural pest. Genome Announcements 4: e01628-15. [pdf]

Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA. 2016. Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics 17: 81-92. [pdf] [supplementary information]

Hendricks SA, Sesink Clee PR, Harrigan RJ, Pollinger JP, Freedman AH, Callas R, Figura PJ, Wayne RK. 2016. Re-defining historical geographic range in species with sparse records: Implications for the Mexican wolf reintroduction program. Biological Conservation 194: 48-57. [pdf]

2015

Hendricks SA, Charruau PC, Pollinger JP, Callas R, Figura PJ, Wayne RK. 2015. Polyphyletic ancestry of historic gray wolves inhabiting U.S. Pacific states. Conservation Genetics 16: 759-764. [pdf]

Rutledge LY, Devillard S, Boone JQ, Hohenlohe PA, White BN. 2015. RAD sequencing and genomic simulations resolve hybrid origins within North American Canis. Biology Letters 11: 20150303. [pdf] [supplemental text] [supplemental table] [cover photo]

Hand BK, Hether TD, Kovach RP, Muhlfeld CC, Amish SJ, Boyer MC, O'Rourke SM, Miller MR, Lowe WH, Hohenlohe PA, Luikart G. 2015. Genomics and introgression: discovery and mapping of thousands of species-diagnostic SNPs using RAD sequencing. Current Zoology 61: 146-154. [pdf]

MacPherson A, Hohenlohe PA, Nuismer SL. 2015. Trait dimensionality explains widespread variation in local adaptation. Proceedings B 282: 20141570. [pdf] [supplemental text] [supplemental figures]

2014

*Stuart YE, *Campbell TS, Hohenlohe PA, Reynolds RG, Revell LJ, Losos JB. 2014. Rapid evolution of a native species following invasion by a congener. Science 346: 463-466. [pdf] [supplemental materials]

Andrews KR, Hohenlohe PA, Miller MR, Hand B, Seeb JE, Luikart G. 2014. Trade-offs and utility of alternative RADseq methods. Molecular Ecology 23: 5943-5946. [pdf]

Hohenlohe PA. 2014. Ecological genomics in full colour. Molecular Ecology 23: 5129-5131. [pdf]

Seehausen O, Butlin RK, Keller I, Wagner CE, Boughman JW, Hohenlohe PA, Peichel CL, Saetre G-P, and 26 others. 2014. Genomics and the origin of species. Nature Reviews Genetics 15: 176-192. [link]

Hether TD, Hohenlohe PA. 2014. Genetic regulatory network motifs constrain adaptation through curvature in the landscape of mutational (co)variance. Evolution 68: 950-964. [pdf]

2013

Catchen JM, Hohenlohe PA, Bassham S, Amores A, Cresko WA. 2013. Stacks: an analysis tool set for population genomics. Molecular Ecology 22: 3124-3140. [pdf]

Narum SR, Buerkle CA, Davey JW, Miller MR, Hohenlohe PA. 2013. Genotyping-by-sequencing in ecological and conservation genomics. Molecular Ecology 22: 2841-2847. [pdf]

Hohenlohe PA, Day MD, Amish SJ, Miller MR, Kamps-Hughes N, Boyer MC, Muhlfeld CC, Allendorf FW, Johnson EA, Luikart G. 2013. Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing. Molecular Ecology 22: 3002-3013. [pdf]

2012

Jones AG, Bürger R, Arnold SJ, Hohenlohe PA, Uyeda JC. 2012. The effects of stochastic and episodic movement of the optimum on the evolution of the G-matrix and the response of the trait mean to selection. Journal of Evolutionary Biology 25: 2210-2231. [pdf]

Nosil P, Hohenlohe PA. 2012. Dimensionality of sexual isolation during reinforcement and ecological speciation in Timema cristinae stick insects. Evolutionary Ecology Research 14: 467-485. [pdf] [software and dataset]

Anderson JL, Rodríguez-Marí A, Braasch I, Amores A, Hohenlohe PA, Batzel P, Postlethwait JH. 2012. Multiple sex-associated regions and a putative sex chromosome in zebrafish revealed by RAD mapping and population genomics. PLoS ONE 7: e40701. [pdf]

Funk WC, McKay JK, Hohenlohe PA, Allendorf FW. 2012. Harnessing genomics for delineating conservation units. Trends in Ecology & Evolution 27: 489-496. [pdf]

Kimmel CB, Hohenlohe PA, Ullmann B, Currey M, Cresko WA. 2012. Developmental dissociation in morphological evolution of the stickleback opercle. Evolution & Development 14: 326-337. [pdf]

Amish SJ, Hohenlohe PA, Painter S, Leary RF, Muhlfeld C, Allendorf FW, Luikart G. 2012. RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays. Molecular Ecology Resources 12: 653-660. [pdf]

Hohenlohe PA, Catchen JM, Cresko WA. 2012. Population genomic analysis of model and nonmodel organisms using sequenced RAD tags. In Bonin A, Pompanon F, eds. Data Production and Analysis in Population Genomics. Humana Press, New York.

Hohenlohe PA, Bassham S, Currey M, Cresko WA. 2012. Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes. Philosophical Transactions B 367: 395-408. [pdf] [supplemental figures] [special issue]

2011

Catchen JM, Amores A, Hohenlohe PA, Cresko WA, Postlethwait JH. 2011. Stacks: building and genotyping loci de novo from short-read sequences. G3 Genes Genomes Genetics 1: 171-182. [pdf] [software]

Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics 12: 499-510. [pdf]

Hohenlohe PA, Amish S, Catchen JM, Allendorf FW, Luikart G. 2011. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources 11(Supp. 1): 117-122. [pdf] [special issue]

Etter P, Bassham S, Hohenlohe PA, Johnson E, Cresko WA. 2011. SNP discovery and genotyping for evolutionary genetics using RAD sequencing. In Orgogozo V, Rockman MV, eds. Molecular Methods for Evolutionary Genetics. Humana Press, New York.

2010

Hohenlohe PA, Phillips PC, Cresko WA. 2010. Using population genomics to detect selection in natural populations: key concepts and methodological considerations. International Journal of Plant Sciences 171(9): 1059-1071. [pdf] [cover image]

Allendorf FW, Hohenlohe PA, Luikart G. 2010. Genomics and the future of conservation genetics. Nature Reviews Genetics 11(10): 697-709. [pdf] [supporting information] [faculty of 1000 review]

Hohenlohe PA, Arnold SJ. 2010. Dimensionality of mate choice, sexual isolation, and speciation. Proceedings of the National Academy of Sciences 107(38): 16583-16588. [pdf] [supporting information] [software]

Emerson KJ, Merz CR, Catchen JM, Hohenlohe PA, Cresko WA, Bradshaw WE, Holzapfel CM. 2010. Resolving post-glacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of Sciences 107(37): 16196-16200. [pdf] [supporting information] [write up in Science]

*Hohenlohe PA, *Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA. 2010. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genetics 6(2): e1000862 (23 pp). [pdf] [online supporting information] [cover image] [faculty of 100 review]

2009 and prior

Uyeda JC, Arnold SJ, Hohenlohe PA, Mead LS. 2009. Drift promotes speciation by sexual selection. Evolution 63(3): 583-594. [pdf]

Calcott B, Balcan D, Hohenlohe PA. 2008. A publish-subscribe model of genetic networks. PLoS ONE 3(9):e3245. [pdf] [link]

Arnold SJ, Bürger R, Hohenlohe PA, Ajie BC, Jones AG. 2008. Understanding the evolution and stability of the G-matrix. Evolution 62(10): 2451-2461. [pdf] [supplemental information]

Stinchcombe JR, Agrawal AF, Hohenlohe PA, Arnold SJ, Blows MW. 2008. Estimating non-linear selection gradients using quadratic regression coefficients: double or nothing? Evolution 62(9): 2435-2440. [pdf]

Hohenlohe PA, Arnold SJ. 2008. MIPoD: A hypothesis-testing framework for microevolutionary inference from patterns of divergence. American Naturalist 171(3): 366-385. [pdf] [appendix] [faculty of 1000 review] [software]

Marcot BG, Hohenlohe PA, Morey S, Holmes R, Molina R, Turley M, Huff M, Laurence J. 2006. Characterizing species at risk II: using Bayesian belief networks as decision support tools to determine species conservation categories under the Northwest Forest Plan. Ecology and Society 11:12 (22pp.). [pdf]

Hohenlohe PA. 2004. Limits to gene flow in marine animals with planktonic larvae: models of Littorina species around Point Conception, California. Biological Journal of the Linnean Society 82(2): 169-187. [pdf]

Hohenlohe PA. 2003. Distribution of sister Littorina species, II: geographic and tidal-height patterns do not support sympatric speciation. The Veliger 46(3): 211-219. [pdf]

Hohenlohe PA. 2003. Distribution of sister Littorina species, I: tenacity and the wave-exposure gradient. The Veliger 46(2): 162-168. [pdf]

Hohenlohe PA. 2002. Life history of Littorina scutulata and L. plena, sibling gastropod species with planktotrophic larvae. Invertebrate Biology 121(1): 25-37. [pdf]

Hohenlohe PA, Boulding EG. 2001. A molecular assay identifies morphological characters useful for distinguishing the sibling species Littorina scutulata and L. plena. Journal of Shellfish Research 19(2): 452-457. [pdf]

Hohenlohe PA. 2000. Larval dispersal, gene flow and speciation in the marine gastropod genus Littorina. PhD dissertation, University of Washington. [pdf]

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