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Post-2020 goals overlook genetic diversity.

Laikre L, Hoban S, Bruford MW, Segelbacher G, Allendorf FW, Gajardo G, Rodríguez AG, Hedrick PW, Heuertz M, Hohenlohe PA, Jaffé R, Johannesson K, Liggins L, MacDonald AJ, OrozcoterWengel P, Reusch TBH, Rodríguez-Correa H, Russo IM, Ryman N, Vernesi C.

Science. 2020 Mar 6;367(6482):1083-1085. doi: 10.1126/science.abb2748. No abstract available.


Population genomics training for the next generation of conservation geneticists: ConGen 2018 Workshop.

Stahlke A, Bell D, Dhendup T, Kern B, Pannoni S, Robinson Z, Strait J, Smith S, Hand BK, Hohenlohe PA, Luikart G.

J Hered. 2020 Feb 10. pii: esaa001. doi: 10.1093/jhered/esaa001. [Epub ahead of print]


Transcriptomics of Tasmanian Devil (Sarcophilus Harrisii) Ear Tissue Reveals Homogeneous Gene Expression Patterns across a Heterogeneous Landscape.

Fraik AK, Quackenbush C, Margres MJ, Comte S, Hamilton DG, Kozakiewicz CP, Jones M, Hamede R, Hohenlohe PA, Storfer A, Kelley JL.

Genes (Basel). 2019 Oct 12;10(10). pii: E801. doi: 10.3390/genes10100801.


Conserving adaptive potential: lessons from Tasmanian devils and their transmissible cancer.

Hohenlohe PA, McCallum HI, Jones ME, Lawrance MF, Hamede RK, Storfer A.

Conserv Genet. 2019 Feb;20(1):81-87. doi: 10.1007/s10592-019-01157-5. Epub 2019 Feb 14.


Tracing the rise of malignant cell lines: Distribution, epidemiology and evolutionary interactions of two transmissible cancers in Tasmanian devils.

James S, Jennings G, Kwon YM, Stammnitz 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 M, Hamede R.

Evol Appl. 2019 Jun 28;12(9):1772-1780. doi: 10.1111/eva.12831. eCollection 2019 Oct.


Mitochondrial Genome Sequences of Diorhabda carinata and Diorhabda carinulata, Two Beetle Species Introduced to North America for Biological Control.

Stahlke AR, Ozsoy AZ, Bean DW, Hohenlohe PA.

Microbiol Resour Announc. 2019 Aug 29;8(35). pii: e00690-19. doi: 10.1128/MRA.00690-19.


Contemporary Demographic Reconstruction Methods Are Robust to Genome Assembly Quality: A Case Study in Tasmanian Devils.

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.

Mol Biol Evol. 2019 Dec 1;36(12):2906-2921. doi: 10.1093/molbev/msz191.


Individual and temporal variation in pathogen load predicts long-term impacts of an emerging infectious disease.

Wells K, Hamede RK, Jones ME, Hohenlohe PA, Storfer A, McCallum HI.

Ecology. 2019 Mar;100(3):e02613. doi: 10.1002/ecy.2613. Epub 2019 Feb 15.


High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote (Canis latrans) populations.

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.

Ecol Evol. 2018 Dec 4;8(24):12641-12655. doi: 10.1002/ece3.4688. eCollection 2018 Dec.


Population Genomic Analysis of North American Eastern Wolves (Canis lycaon) Supports Their Conservation Priority Status.

Heppenheimer E, Harrigan RJ, Rutledge LY, Koepfli KP, DeCandia AL, Brzeski KE, Benson JF, Wheeldon T, Patterson BR, Kays R, Hohenlohe PA, von Holdt BM.

Genes (Basel). 2018 Dec 4;9(12). pii: E606. doi: 10.3390/genes9120606.


The Genomic Basis of Tumor Regression in Tasmanian Devils (Sarcophilus harrisii).

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.

Genome Biol Evol. 2018 Nov 1;10(11):3012-3025. doi: 10.1093/gbe/evy229.


Large-effect loci affect survival in Tasmanian devils (Sarcophilus harrisii) infected with a transmissible cancer.

Margres MJ, Jones ME, 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.

Mol Ecol. 2018 Nov;27(21):4189-4199. doi: 10.1111/mec.14853. Epub 2018 Oct 5.


The devil is in the details: Genomics of transmissible cancers in Tasmanian devils.

Storfer A, Hohenlohe PA, Margres MJ, Patton A, Fraik AK, Lawrance M, Ricci LE, Stahlke AR, McCallum HI, Jones ME.

PLoS Pathog. 2018 Aug 2;14(8):e1007098. doi: 10.1371/journal.ppat.1007098. eCollection 2018 Aug. No abstract available.


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.

Hendricks SA, Schweizer RM, Harrigan RJ, Pollinger JP, Paquet PC, Darimont CT, Adams JR, Waits LP, vonHoldt BM, Hohenlohe PA, Wayne RK.

Heredity (Edinb). 2019 Feb;122(2):133-149. doi: 10.1038/s41437-018-0094-x. Epub 2018 Jun 7.


A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data.

Andrews KR, Adams JR, Cassirer EF, Plowright RK, Gardner C, Dwire M, Hohenlohe PA, Waits LP.

Mol Ecol Resour. 2018 Nov;18(6):1263-1281. doi: 10.1111/1755-0998.12910. Epub 2018 Jul 9.


Correction to 'RAD sequencing and genomic simulations resolve hybrid origins within North American Canis'.

Rutledge LY, Devillard S, Boone JQ, Hohenlohe PA, White BN.

Biol Lett. 2017 Nov;13(11). pii: 20170594. doi: 10.1098/rsbl.2017.0594. No abstract available.


Conservation implications of limited genetic diversity and population structure in Tasmanian devils (Sarcophilus harrisii).

Hendricks S, Epstein B, Schönfeld B, Wiench C, Hamede R, Jones M, Storfer A, Hohenlohe P.

Conserv Genet. 2017 Aug;18(4):977-982. doi: 10.1007/s10592-017-0939-5. Epub 2017 Feb 7.


Comment on "Whole-genome sequence analysis shows two endemic species of North American wolf are admixtures of the coyote and gray wolf".

Hohenlohe PA, Rutledge LY, Waits LP, Andrews KR, Adams JR, Hinton JW, Nowak RM, Patterson BR, Wydeven AP, Wilson PA, White BN.

Sci Adv. 2017 Jun 7;3(6):e1602250. doi: 10.1126/sciadv.1602250. eCollection 2017 Jun.


Infection of the fittest: devil facial tumour disease has greatest effect on individuals with highest reproductive output.

Wells K, Hamede RK, Kerlin DH, Storfer A, Hohenlohe PA, Jones ME, McCallum HI.

Ecol Lett. 2017 Jun;20(6):770-778. doi: 10.1111/ele.12776. Epub 2017 May 10.


Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations.

Catchen JM, Hohenlohe PA, Bernatchez L, Funk WC, Andrews KR, Allendorf FW.

Mol Ecol Resour. 2017 May;17(3):362-365. doi: 10.1111/1755-0998.12669. Epub 2017 Apr 11.


Vive la résistance: genome-wide selection against introduced alleles in invasive hybrid zones.

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.

Proc Biol Sci. 2016 Nov 30;283(1843). pii: 20161380.


Rapid evolutionary response to a transmissible cancer in Tasmanian devils.

Epstein B, Jones M, Hamede R, Hendricks S, McCallum H, Murchison EP, Schönfeld B, Wiench C, Hohenlohe P, Storfer A.

Nat Commun. 2016 Aug 30;7:12684. doi: 10.1038/ncomms12684.


Mixed population genomics support for the central marginal hypothesis across the invasive range of the cane toad (Rhinella marina) in Australia.

Trumbo DR, Epstein B, Hohenlohe PA, Alford RA, Schwarzkopf L, Storfer A.

Mol Ecol. 2016 Sep;25(17):4161-76. doi: 10.1111/mec.13754. Epub 2016 Aug 8.


The ecology of an adaptive radiation of three-spined stickleback from North Uist, Scotland.

Magalhaes IS, D'Agostino D, Hohenlohe PA, MacColl AD.

Mol Ecol. 2016 Sep;25(17):4319-36. doi: 10.1111/mec.13746. Epub 2016 Aug 8.


Genetic diversity and population structure of Raffaelea quercus-mongolicae, a fungus associated with oak mortality in South Korea.

Kim MS, Hohenlohe PA, Kim KH, Seo ST, Klopfenstein NB.

For Pathol. 2016 Apr;46(2):164-167. Epub 2016 Feb 13.


Conservation genomics of natural and managed populations: building a conceptual and practical framework.

Benestan LM, Ferchaud AL, Hohenlohe PA, Garner BA, Naylor GJ, Baums IB, Schwartz MK, Kelley JL, Luikart G.

Mol Ecol. 2016 Jul;25(13):2967-77. doi: 10.1111/mec.13647. Epub 2016 May 18.


Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis).

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, Gould N, Andelt WF.

Mol Ecol. 2016 May;25(10):2176-94. doi: 10.1111/mec.13605. Epub 2016 Apr 5.


Considering all the evidence: a reply to Sefc and Koblmüller (2016).

Rutledge LY, Devillard S, Hohenlohe PA, White BN.

Biol Lett. 2016 Feb;12(2):20151009. doi: 10.1098/rsbl.2015.1009. No abstract available.


Full Mitochondrial Genome Sequence of the Sugar Beet Wireworm Limonius californicus (Coleoptera: Elateridae), a Common Agricultural Pest.

Gerritsen AT, New DD, Robison BD, Rashed A, Hohenlohe P, Forney L, Rashidi M, Wilson CM, Settles ML.

Genome Announc. 2016 Jan 21;4(1). pii: e01628-15. doi: 10.1128/genomeA.01628-15.


Harnessing the power of RADseq for ecological and evolutionary genomics.

Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA.

Nat Rev Genet. 2016 Feb;17(2):81-92. doi: 10.1038/nrg.2015.28. Epub 2016 Jan 5. Review.


RAD sequencing and genomic simulations resolve hybrid origins within North American Canis.

Rutledge LY, Devillard S, Boone JQ, Hohenlohe PA, White BN.

Biol Lett. 2015 Jul;11(7). pii: 20150303. doi: 10.1098/rsbl.2015.0303. Erratum in: Biol Lett. 2017 Nov;13(11):.


Trait dimensionality explains widespread variation in local adaptation.

MacPherson A, Hohenlohe PA, Nuismer SL.

Proc Biol Sci. 2015 Mar 7;282(1802). pii: 20141570. doi: 10.1098/rspb.2014.1570.


Rapid evolution of a native species following invasion by a congener.

Stuart YE, Campbell TS, Hohenlohe PA, Reynolds RG, Revell LJ, Losos JB.

Science. 2014 Oct 24;346(6208):463-6. doi: 10.1126/science.1257008.


Ecological genomics in full colour.

Hohenlohe PA.

Mol Ecol. 2014 Nov;23(21):5129-31. doi: 10.1111/mec.12945.


Trade-offs and utility of alternative RADseq methods: reply to Puritz et al.

Andrews KR, Hohenlohe PA, Miller MR, Hand BK, Seeb JE, Luikart G.

Mol Ecol. 2014 Dec;23(24):5943-6. doi: 10.1111/mec.12964.


Genomics and the origin of species.

Seehausen O, Butlin RK, Keller I, Wagner CE, Boughman JW, Hohenlohe PA, Peichel CL, Saetre GP, Bank C, Brännström A, Brelsford A, Clarkson CS, Eroukhmanoff F, Feder JL, Fischer MC, Foote AD, Franchini P, Jiggins CD, Jones FC, Lindholm AK, Lucek K, Maan ME, Marques DA, Martin SH, Matthews B, Meier JI, Möst M, Nachman MW, Nonaka E, Rennison DJ, Schwarzer J, Watson ET, Westram AM, Widmer A.

Nat Rev Genet. 2014 Mar;15(3):176-92. doi: 10.1038/nrg3644. Review.


Genetic regulatory network motifs constrain adaptation through curvature in the landscape of mutational (co)variance.

Hether TD, Hohenlohe PA.

Evolution. 2014 Apr;68(4):950-64. doi: 10.1111/evo.12313. Epub 2013 Dec 4.


Genotyping-by-sequencing in ecological and conservation genomics.

Narum SR, Buerkle CA, Davey JW, Miller MR, Hohenlohe PA.

Mol Ecol. 2013 Jun;22(11):2841-7. doi: 10.1111/mec.12350. Epub 2013 May 25. No abstract available.


Stacks: an analysis tool set for population genomics.

Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA.

Mol Ecol. 2013 Jun;22(11):3124-40. doi: 10.1111/mec.12354. Epub 2013 May 24.


Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing.

Hohenlohe PA, Day MD, Amish SJ, Miller MR, Kamps-Hughes N, Boyer MC, Muhlfeld CC, Allendorf FW, Johnson EA, Luikart G.

Mol Ecol. 2013 Jun;22(11):3002-13. doi: 10.1111/mec.12239. Epub 2013 Feb 21.


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.

Jones AG, Bürger R, Arnold SJ, Hohenlohe PA, Uyeda JC.

J Evol Biol. 2012 Nov;25(11):2210-31. doi: 10.1111/j.1420-9101.2012.02598.x. Epub 2012 Sep 7.


Multiple sex-associated regions and a putative sex chromosome in zebrafish revealed by RAD mapping and population genomics.

Anderson JL, Rodríguez Marí A, Braasch I, Amores A, Hohenlohe P, Batzel P, Postlethwait JH.

PLoS One. 2012;7(7):e40701. doi: 10.1371/journal.pone.0040701. Epub 2012 Jul 9.


Developmental dissociation in morphological evolution of the stickleback opercle.

Kimmel CB, Hohenlohe PA, Ullmann B, Currey M, Cresko WA.

Evol Dev. 2012 Jul;14(4):326-37. doi: 10.1111/j.1525-142X.2012.00551.x.


Harnessing genomics for delineating conservation units.

Funk WC, McKay JK, Hohenlohe PA, Allendorf FW.

Trends Ecol Evol. 2012 Sep;27(9):489-96. doi: 10.1016/j.tree.2012.05.012. Epub 2012 Jun 21.


RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays.

Amish SJ, Hohenlohe PA, Painter S, Leary RF, Muhlfeld C, Allendorf FW, Luikart G.

Mol Ecol Resour. 2012 Jul;12(4):653-60. doi: 10.1111/j.1755-0998.2012.03157.x. Epub 2012 Jun 6.


Population genomic analysis of model and nonmodel organisms using sequenced RAD tags.

Hohenlohe PA, Catchen J, Cresko WA.

Methods Mol Biol. 2012;888:235-60. doi: 10.1007/978-1-61779-870-2_14.


Stacks: building and genotyping Loci de novo from short-read sequences.

Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH.

G3 (Bethesda). 2011 Aug;1(3):171-82. doi: 10.1534/g3.111.000240. Epub 2011 Aug 1.


Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes.

Hohenlohe PA, Bassham S, Currey M, Cresko WA.

Philos Trans R Soc Lond B Biol Sci. 2012 Feb 5;367(1587):395-408. doi: 10.1098/rstb.2011.0245.


SNP discovery and genotyping for evolutionary genetics using RAD sequencing.

Etter PD, Bassham S, Hohenlohe PA, Johnson EA, Cresko WA.

Methods Mol Biol. 2011;772:157-78. doi: 10.1007/978-1-61779-228-1_9.

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