*denotes UNR graduate student

Harrison, J. G., L. P. Beltran, C. A. Buerkle, D. Cook, D. R. Gardner, T. L. Parchman, M. L. Forister. 2021. A suite of rare microbes interacts with a dominant, heritable, fungal endophyte to influence plant trait expression. The IMSE Journal, In press.

V. Shastry, P. Adams, D. Lindtke, E. G. Mandeville, T. L. Parchman, Z. Gompert, C. A. Buerkle. 2021. Model-based genotype and ancestry estimation for potential hybrids with mixed-ploidy. Molecular Ecology Resources, In press.

*Klingler, K. B., J. P. Jahner, T. L. Parchman, C. Ray, M. M. Peacock. 2021. Genomic variation in the American pika: signatures of geographic isolation and implications for conservation. BMC Ecology and Evolution, 21:1-19.

Johnson, P., D M. Calhoun, W. E. Moss, T. McDevitt-Galles, T. B. Riepe, *J. M. Hallas, T. L. Parchman, C. R. Feldman, T. J. Achatz, V. Tkach, J. Cropanzano, J. Bowerman, J. Koprivnikar. 2021. The cost of travel: how dispersal ability limits local adaptation in host-parasite interactions. Journal of Evolutionary Biology, 34:512-524.

*Uckele, K. A., R. P. Adams, A. E. Schwarzbach, T. L. Parchman. 2021. Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf juniperus and highlights discordance with chloroplast phylogenies. Molecular Phylogenetics and Evolution,156:107022.

*McClinton, J. D., T. L. Parchman, K. L. Torrence, P. S. Verburg, E. A. Leger. 2020. How specialized is a soil specialist? Early life history responses of a rare Eriogonum to site-level variation in volcanic soils. American Journal of Botany, 107:1663-1676.

Nosil P., R. Villoutreix, C. F. de Carvalho, J. L. Feder, T. L. Parchman, Z. Gompert. 2020. Ecology shapes epistasis in a genotype-phenotype-fitness map. Nature Ecology and Evolution, Sep 14:1-12.

Feng, S., J. Stiller, Y. Deng, J. Armstrong, Q. Fang, A. H. Reeve, D. Xie, G. Chen, C. Guo, B. C. Faircloth, B, Petersen, Z. Wang , Q. Zhou, M. Diekhans, W. Chen, S. Andreu-Sánchez, A. Margaryan, J. T. Howard, G. Pacheco, M. H. S. Sinding, L. Puetz, E. Cavill, Â. M. Ribeiro, J. Fjeldså, P. A. Hosner, R. T. Brumfield, L. Christidis, M. F. Bertelsen, D. T. Tietze, B. C. Robertson, G. Song, G. Borgia, S. Claramunt, I. J. Lovette, S. J. Cowen, P. Njoroge, J. P. Dumbacher, O. A. Ryder, J. Fuchs, M. Bunce, D. W. Burt, J. Cracraft, G. Meng, S. J. Hackett, P. G. Ryan, K. A. Jønsson, I. G. Jamieson, R. R. da Fonseca, E. L. Braun, P. Houde, S. Mirarab, A. Suh, M. Stervander, B. Hansson, H. Sigeman, S. Ponnikas, P. Frandsen, H. Van der Zwan, C. N. Balakrishnan, A. G. Clark, J. W. Fitzpatrick, R. Bowman, N. Chen, A. Cloutier, T. B. Sackton, D. J. Foote, S. B. Shakya, F. H. Sheldon, A. Vignal, A. E. R. Soares, B. Shapiro, J. González-Solís, J. Ferrer-Obiol, J. Rozas, M. Riutort, A. Tigano, V. Friesen, L. Dalén, A. O. Urrutia, T. Székely, Y. Liu, M. G. Campana, A. Corvelo, R. C. Fleischer, K. M. Rutherford, N. J. Gemmell, N. Dussex, H. Mouritsen, N. Thiele, K. Delmore, M. Liedvogel, A. Franke, M. P. Hoeppner, O. Krone, A. M. Fudickar, B. Milá, E. D. Ketterson, A. E. Fidler, G. Friis, Á. M. Parody-Merino, P. F. Battley, M. P. Cox, N. C. B. Lima, F. Prosdocimi, T. L. Parchman, B. A. Schlinger, B. A. Loiselle, J. G. Blake, H. C. Lim, L. B. Day, M. J. Fuxjager, M. W. Baldwin, M. J. Braun, M. Wirthlin, R. B. Dikow, T. B. Ryder, G. Camenisch, L. F. Keller, J. M. DaCosta, M. E. Hauber, M. I. M. Louder, C. C. Witt, J. A. McGuire, J. Mudge, L. C. Megna, M. D. Carling, B. Wang, S. A. Taylor, G. Del-Rio, A. Aleixo, A. T. R. Vasconcelos, C. V. Mello, J. T. Weir, D. Haussler, Q. Li, H. Yang, J. Wang, F. Lei, C. Rahbek, M. T. P. Gilbert, G. R. Graves, E. D. Jarvis, B. Paten, G. Zhang. 2020. Densely sampling genomes across the diversity of birds increases power of comparative genomics analyses. Nature 587: 252-257.

Villoutreix, R, C. F. de Carvalho, V. Soria-Carrasco, D. Lindtke, M. De-la-Mora, M. Muschick, J. L. Feder, T. L. Parchman, Z. Gompert, P. Nosil. 2020. Large-scale mutation in the evolution of a gene complex for cryptic coloration. Science 369: 460-466.

Epps, C. W., L. Bowen, M. R. Buchalski, R. Cassirer, D. Coltman, W. C. Conway, M. Cox, R. Harris, J. P. Jahner, M. Matocq, T. L. Parchman, C. D. Phillips, H. Schwantje, Z. Sim, L. Waits, J. D. Wehausen, Wild Sheep Genomics Working Group. 2019. Frequently-asked questions about wild sheep genetics and genomics. Proceedings of the Northern Wild Sheep and Goat Council 21:48-75.

Haselhorst, M., T. L. Parchman, C. A. Buerkle. 2019. Genetic evidence for species cohesion and substructure in spruce and the potential pitfalls of limited geographic sampling. Molecular Ecology, 28:2029-2045.

*Harrison, J. G., M. L. Forister, S. R. Mcknight, E. Nordin, T. L. Parchman. 2019. Rarity does not lead to loss of genetic variation in the geographically restricted desert forb Astragalus lentiginosus var. piscinensis. American Journal of Botany, 106:260-269.

Jahner, J. P., M. D. Matocq, J. L. Malaney, M. Cox, P. Wolff, M. Gritts, T. L. Parchman. 2019. The genetic legacy of 50 years of desert bighorn sheep translocations. Evolutionary Applications, 12:198-213.

• Jahner,J. P., Matocq, MD, Malaney, J. L., Cox, M., Wolff, P., Gritts, M., Parchman, T. L.  2018. The genetic legacy of 50 years of desert bighorn sheep translocations. Evolutionary Applications, In press.
• Parchman, T. L., P. Edelaar, *K. A. Uckele, E. T. Mezquida, D. Alonso, J. P. Jahner, R. Summers, C. W. Benkman. 2018. Resource stability and geographic isolation are associated with genome divergence in western Palearctic crossbills. Journal of Evolutionary Biology, In press.
• Parchman, T. L., J. P. Jahner, *K. A. Uckele, *L. M. Galland, A. J. Eckert. 2018. RADseq approaches and applications for forest tree genetics. Tree Genetics and Genomes 14:39.
• Dyer, L., *C. S. Philbin, K. M. Ochsenrider, L. R. Richards, T. J. Massad, A. M. Smilanich, M. L. Forister, T. L.Parchman, *L. M. Galland, P. Hurtado, *A. Espeset, *A. E. Glassmire, *J. G. Harrison, *C. Mo, *S. Yoon, *N. Pardikes, *N. Muchoney, J. P. Jahner, H. Slinn, *O. Shelef, C. S. Jeffrey. 2018. Modern chemical ecology theory for plant insect interactions. Nature Reviews Chemistry. 2:50-64.
• *Harrison, J.G., T. L.Parchman, D. Cook, D. R. Gardner, M. L. Forister. 2018.A heritable symbiont and host-associated factors shape fungal endophyte communities across spatial scales. Journal of Ecology 00:1–13.
• Jahner, J. P., M. L. Forister, T. L. Parchman, A. M. Smilanich, J. S. Miller, J. S. Wilson, T. R. Walla, E. J. Tepe, L. A. Richards, M. A. Quijano-Abril, C. S. Jeffrey, *A. E. Glassmire, L. A. Dyer. 2017. Host conservatism, geography, and elevation in the evolution of a Neotropical moth radiation. Evolution 71:2885-2900.
• Mandeville, E.G.,T. L. Parchman,K. G.Thompson, R. I. Compton, K. R. Gelwicks, S. J. Song, C. A. Buerkle. 2017. Interactions between Catostomusfish species reveal inconsistent reproductive isolation. Evolution Letters 1:255-268. 
• *Branch, C. L., J. P. Jahner, *D. Y. Kozlovsky, *R. Croston, *A. M. Pitera, T. L. Parchman, V. V.Pravosudov.2017. Absence of population genetic structure across elevational gradients despite limited movement in mountain chickadees (Poecile gambeli). Royal Society Open Science 4:170057.
• Kingston, S. E, Parchman, T. L., Gompert, Z., Buerkle, C. A., and Braun, M. J. (2017). Heterogeneity and concordance in locus-specific differentiation and introgression between species of towhees. Journal of Evolutionary Biology. 30:474-485.
• Croston, R., Branch, C. L., Pitera, A. Kozlovsky, D. Y., Parchman, T. L., Bridge, E. S., Pravosudov, V. V. (2017). Predictably harsh environment is associated with reduced cognitive flexibility in wild mountain chickadees. Animal Behaviour: 123:139-149.
• Harrison, J. G., Koch, G. W., Parchman, T. L., Forister, M. L. (2017). A room with a view: vertical stratification of the foliar fungal community in the world’s tallest trees. American Journal of Botany 103: 1-9. **Featured on the cover, and in issue highlight article.
• Parchman, T. L., Buerkle, C. A., Soria-Carrasco, V., Benkman, C. W.  Genome divergence and diversification within a geographic mosaic of coevolution. Molecular Ecology 25: 5705-5718. ** Featured in News and Views article (Thompson 2016, Molecular Ecology 25: 5608-5610).
• Wilkins, M. R. Karaardıç H., Vortman, Y., Parchman, T. L., Albrecht, T., Tomáš, Petrzelkova, A., Özkan, L, Pap, P., Hubbard, J, Hund, A. K., Safran, R. J. Divergent sexual selection explains phenotypic differentiation among closely related barn swallow populations. Journal of Evolutionary Biology 29:2410- 2421.
• Glassmire, A. E., Jeffrey, C. S. Christopher S. Jeffrey, Forister, M. L. Matthew,   Parchman, T. L., Nice, C. C., Jahner, J. P., Wilson, J. S., Walla, T. R., Richards,  L. A., Smilanich, A. M. Leonard, M. D., Morrison, C. R., Simbana, W., Salagaje,   L. A, Dodson, C. C, Miller, J. S., Tepe, E. J. Eric J. Tepe, Villamarin-Cortez, S., and Dyer, L. A. 2016. Intraspecific phytochemical variation drives community and population structure for specialist caterpillars. New Phytologist,. New Phytologist 212:208-219. ** Featured in Commentary article (Kessler 2016, New Phytologist, 212:8-10).
• Safran, R. J., Scordato, E. S. C., Wilkins M. R., Hubbard, J. K., Jenkins, B. R^.,  Albrecht, T., Flaxman, S. M., Karaardıç, H^., Vortman, Y^., Lotem, A., Nosil, P.,  Pap, P., Shen, S., Chan, S-F. Parchman, T. L., Kane, N.C. (2016). Genome-wide differentiation in closely related populations: the roles of selection and geographic isolation. Molecular Ecology, 25, 3865-3883
• Jahner, J. P., Gibson, D., Weitzman, C., Blomberg, E. J., Sedinger, J. S., Parchman, T. L. 2016. Fine-scale genetic structure of greater sage- grouse leks in central Nevada. BMC Evolutionary Biology 16, 127.
• Croston, R., Kovlovsky, D. Y., Branch, C. L., Parchman, T. L., Bridge, E. S., Pravosudov, V. V. (2016). Individual variation in spatial memory performance in wild mountain chickadees from different elevations. Animal Behavior 111, 225- 234.
• Comeault, A. A., Flaxman, S. M., Riesch, R., Curran, E., Soria-Carrasco, V.,  Gompert, Z., Farkas, T., Muschick, M., Parchman, T. L., Schwander, T., Slate, J.,  Nosil, P. 2015. Selection on a Genetic Polymorphism Counteracts Ecological Speciation in a Stick Insect. Current Biology, 25(15), 1975-1981. ** Featured in highlight article (Rogers 2015, Current Biology 25 R726-R728)
• Mandeville, E. G., Parchman, T. L., McDonald, D. B., Buerkle, C. A. 2015.  Highly variable reproductive isolation among pairs of Catostomus species.  Molecular Ecology, 24(8), 1856-1872.** Featured in News and Views article (Cutter 2015, Molecular Ecology 24, 1643-1644).
• Dyer, L. A, T. L. Parchman, C. S. Jeffrey, L. A. Richards. 2014. New dimensions of tropical diversity: an inordinate fondness for insect molecules, taxa, and trophic interactions. 2014. Current Opinion in Insect Science: 2:14-19. PDF
• Soria-Carrasco, V., Z. Gompert, A. A. Comeault, T. E. Farkas, T. L. Parchman, J. S. Johnston, C. A. Buerkle, J. L. Feder, J. Bast, T. Schwander, Scott P. Egan, B. J. Crespi, P. Nosil. 2014. Stick insect genomes reveal natural selections role in parallel speciation. Science 344:738-742. PDF
• Gompert, Z., A. A. Comeault, T. E. Farkas, J. L. Feder, T. L. Parchman, C. A. Buerkle, and P. Nosil. 2014. Experimental evidence for ecological selection on genome variation in the wild. Ecology Letters 17:369-379. PDF
• Comeault, A., V. Soria-Carrasco, Z. Gompert, T. E. Farkas, C. A. Buerkle, T. L. Parchman, and P. Nosil. 2014. Genome-wide association mapping of phenotypic traits subject to a range of intensities of natural selection in Timema cristinae. American Naturalist 183:711-727. PDF
• Benkman, C. W., and T. L. Parchman. 2013. When divergent selection reduces geographic variation in
  traits mediating species interactions. Ecology and Evolution 3: 961-970. PDF
• Parchman, T. L., Z. Gompert, M. J. Braun, R. T. Brumfield, D. B. McDonald, J. A. C. Uy, G. Zhang, E. D. Jarvis, B. A. Schlinger, and C. A. Buerkle. 2013. The genomic consequences of adaptive divergence and reproductive isolation between species of manakins. Molecular Ecology 22: 3304-3317. Featured in News and Views Article. Molecular Ecology 22: 3304-3317. PDF
• Lesser, M. R., T. L. Parchman, and S. T. Jackson. 2013. Development of genetic diversity,
  differentiation and structure over 500 years in four Ponderosa pine populations. Molecular Ecology 22: 2640-2652. PDF
• Nosil, P., T. L. Parchman, J. L. Feder, and Z. Gompert. 2012. Do highly divergent loci reside in genomic regions affecting speciation? A test using next-generation sequence data in Timema stick insects
  BMC Evolutionary Biology 12: 164. PDF.
• Nosil, P., Z. Gompert, T. A. Farkas, A. Comeault, J. L. Feder, C. A. Buerkle, and T. L. Parchman 2012.
  Genomic consequences of multiple speciation processes in a stick insect. Proceedings of the Royal
  Society B doi:10.1098/rspb.2012.0813. PDF Featured in Editor’s Choice article in July 2012 issue of
  Science.
• Parchman, T. L., Z. Gompert, C. W. Benkman, F. D. Schilkey, J. Mudge, and C. A. Buerkle 2012.
  Genome wide association mapping of an adaptive trait in lodgepole pine. Molecular Ecology 21:2991-
  3005. PDF. Featured in News and Views article: Eckert and Dyer, Molecular Ecology 21:2836-2838.
  **Faculty of 1000 paper.
• Comeault, A. A., M. Sommers, T. Schwander, C. A. Buerkle, T. A. Farkas, P. Nosil, and T. L. Parchman. 2012. Inference of multi-locus genetic divergence in Timema stick insects facilitated by transcriptome sequencing. Molecular Ecology Resources 12:549-561. PDF
• Lesser, M. R., T. L. Parchman, and C. A. Buerkle. 2012. Cross-species transferability of SSR loci
  developed from 454 transcriptome sequencing in lodgepole pine. Molecular Ecology Resources 12:448-455. PDF
• Edwards, C. E., T. L. Parchman, and C. W. Weekly. 2012. Assembly, gene annotation and marker development using 454 floral transcriptome sequences in Ziziphus celata (Rhamnaceae), a highly endangered, Florida endemic plant. DNA Research 19:1-9. PDF
• Gompert, Z., T. L. Parchman, and C. A. Buerkle. 2012. Genomics of isolation in hybrids. Philosophical Transactions of the Royal Society 367:439-450. PDF
• Buerkle, C. A., Z. Gompert, and Parchman, T. L. 2011. The n=1 constraint in population genomics. Molecular Ecology 20:1575-1581. PDF
• Parchman, T. L., C. W. Benkman, B. Jenkins, and C. A. Buerkle. 2011. Low levels of population genetic structure in Pinus contorta (Pinaceae) across a geographic mosaic of co-evolution. American Journal of Botany 98:669-679. PDF
• Benkman, C. W., T. L. Parchman, and E. T. Mezquida. 2010. Patterns of coevolution in the adaptive radiation of crossbills. Annals of the New York Academy of Sciences 1206:1-16. PDF
• T. L. Parchman, K. S. Geist, J. A. Grahnen, C. W. Benkman and C. A. Buerkle. 2010. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 11:180. PDF.
• Benkman, C. W., J. W. Smith, P. C. Keenan, T. L. Parchman, and L. Santisteban. 2009. A new species of red crossbill (Fringillidae: Loxia) from Idaho. Condor 111:169-176. PDF.
• Benkman, C. W., and T. L. Parchman. 2009. Coevolution between crossbills and black pine: the importance of competitors, forest area, and resource stability. Journal of Evolutionary Biology 22:942-953. PDF
• Quist, M. C., M. R. Bower, W. A. Hubert, D. B. McDonald, and T. L. Parchman. 2008. Morphometric and meristic differences of bluehead sucker, flannelmouth sucker, white sucker, and their hybrids: tools for the management of native species in the upper Colorado River basin. North American Journal of Fisheries Management 29: 460-467. PDF .
• McDonald, D.B., T.L. Parchman, M.R. Bower, W.A. Hubert, and F.J. Rahel. 2008. An introduced and a native vertebrate hybridize to form a genetic bridge to a second native species. Proceedings of the National Academy of the Sciences USA 105:10842-10847. PDF.
• Parchman, T. L., and C. W. Benkman. 2008. The geographic selection mosaic for crossbills and ponderosa pine: a tale of two squirrels. Evolution 62: 348-360. PDF. Featured in Science Magazine Editors Choice PDF.
• Benkman, C. W., Parchman, T. L., and A. M. Siepielski. 2008. The geographic mosaic theory of coevolution and its’ conservation significance. In Evolution in Action: Evolutionary Conservation Biology, eds. Charles Fox and Scott Carroll.
• Benkman, C. W., A. M. Siepielski, and T. L. Parchman. 2008. The local introduction of strongly interacting species and the loss of geographic variation in species and species interactions. Molecular Ecology 17:394-405. PDF
• Parchman, T. L., C. W. Benkman, and E. T. Mezquida. 2007. Coevolution between the Hispaniolan crossbill and pine: does more time allow for greater phenotypic escalation at lower latitudes? Evolution 61:2142-2153. PDF
• Parchman, T. L., C. W. Benkman, and S. C. Britch. 2006. Patterns of genetic variation in the adaptive radiation of North American crossbills (Aves: Loxia). Molecular Ecology 15: 1873-1887. PDF
• Benkman, C. W., T. L. Parchman, A. Favis, and A. M. Siepielski. 2003. Reciprocal Selection causes a coevolutionary arms race between crossbills and lodgepole pine. American Naturalist 162: 182-194. PDF
• Parchman, T. L., and C. W. Benkman. 2002. Diversifying coevolution between crossbills and black spruce on Newfoundland. Evolution 56: 1663-1672. * featured in February 2003 issue of Natural History magazine. PDF.
• Siepielski, A. M., T. L. Parchman, and C. W. Benkman. 2002. A book review of Evolutionary Ecology: concepts and case studies. Animal Behaviour 64: 323-324.