Battey, C.J., Linck, E.B., Epperly, K.L., French, C., Slager, D.L., Sykes, P.W., Klicka, J., 2017. A Migratory Divide In The Painted Bunting (Passerina ciris). bioRxiv.

Battey, C.J., Klicka, J., 2017. Cryptic speciation and gene flow in a migratory songbird Species Complex: Insights from the Red-Eyed Vireo ( Vireo olivaceus ). Molecular Phylogenetics and Evolution 113, 67–75.

Bryson, R.W., Linkem, C.W., Pavón-Vázquez, C.J., Nieto-Montes de Oca, A., Klicka, J., McCormack, J.E., 2017. A phylogenomic perspective on the biogeography of skinks in the Plestiodon brevirostris group inferred from target enrichment of ultraconserved elements. Journal of Biogeography 44, 2033–2044.

Halley, M.R., Klicka, J.C., Clee, P.R.S., Weckstein, J.D., 2017. Restoring the species status of Catharus maculatus (Aves: Turdidae), a secretive Andean thrush, with a critique of the yardstick approach to species delimitation. Zootaxa 4276, 387.

Linck, E.B., Hanna, Z.R., Sellas, A., Dumbacher, J.P., 2017. Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens. Ecology and Evolution 7, 4755–4767.

Sandoval, L., Epperly, K.L., Klicka, J., Mennill, D.J., 2017. The biogeographic and evolutionary history of an endemic clade of Middle American sparrows: Melozone and Aimophila (Aves: Passerellidae). Molecular Phylogenetics and Evolution 110, 50–59.

Barrowclough, G.F., Cracraft, J., Klicka, J., Zink, R.M., 2016. How Many Kinds of Birds Are There and Why Does It Matter? PLOS ONE 11, e0166307.

Linck, E., Bridge, E.S., Duckles, J.M., Navarro-Sigüenza, A.G., Rohwer, S., 2016. Assessing migration patterns in Passerina ciris using the world’s bird collections as an aggregated resource. PeerJ 4, e1871.

Zarza, E., Faircloth, B.C., Tsai, W.L.E., Bryson, R.W., Klicka, J., McCormack, J.E., 2016. Hidden histories of gene flow in highland birds revealed with genomic markers. Molecular Ecology 25, 5144–5157.

Bryson, R.W., Faircloth, B.C., Tsai, W., McCormack, J.E., Klicka, J. Target enrichment of thousands of ultraconserved elements shed new light on early relationships within New World sparrows (Aves: Passerellidae) (2016) The Auk: Ornithological Advances, 133, pp. 451-458.

Linck, E., Schaack, S., Dumbacher, J.P. Genetic differentiation within a widespread “supertramp” taxon: Molecular phylogenetics of the Louisiade White-eye (Zosterops griseotinctus) (2016) Molecular Phylogenetics and Evolution, 94, art. no. 5280, pp. 113-121.

Slager, D.L., Rodewald, P.G., Heglund, P.J. Experimental effects of habitat type on the movement ecology and stopover duration of spring migrant Northern Waterthrushes (Parkesia noveboracensis) (2015) Behavioral Ecology and Sociobiology, 69 (11), pp. 1809-1819.

Slager, D.L., Rodewald, P.G. Disjunct nocturnal roosting by a yellow-rumped warbler (setophaga coronata) during migratory stopover (2015) Wilson Journal of Ornithology, 127 (1), pp. 109-114.

Barker, K., Burns, K.J., Klicka, J., Lanyon, S.M., Lovette, I.J. New insights into New World biogeography: An integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies (2015) Auk, 132 (2), pp. 333-348.

Manthey, J.D., Klicka, J., Spellman, G.M. Effects of climate change on the evolution of Brown Creeper (Certhia americana) lineages (2014) Auk, 131 (4), pp. 559-570.

Bryson Jr, R.W., Chaves, J., Smith, B.T., Miller, M.J., Winker, K., Pérez-Emán, J.L., Klicka, J. Diversification across the New World within the ‘blue’ cardinalids (Aves: Cardinalidae) (2014) Journal of Biogeography, 41 (3), pp. 587-599.

Powell, A.F.L.A., Barker, F.K., Lanyon, S.M., Burns, K.J., Klicka, J., Lovette, I.J. A comprehensive species-level molecular phylogeny of the New World blackbirds (Icteridae) (2014) Molecular Phylogenetics and Evolution, 71 (1), pp. 94-112.

Klicka, J., Keith Barker, F., Burns, K.J., Lanyon, S.M., Lovette, I.J., Chaves, J.A., Bryson Jr., R.W. A comprehensive multilocus assessment of sparrow (Aves: Passerellidae) relationships (2014) Molecular Phylogenetics and Evolution, 77 (1), pp. 177-182.

Slager, D.L., Klicka, J. Polyphyly of Hylophilus and a new genus for the Tawny-crowned Greenlet (Aves: Passeriformes: Vireonidae) (2014) Zootaxa, 3884 (2), pp. 194-196.

Slager, D.L., Battey, C.J., Bryson, R.W., Voelker, G., Klicka, J. A multilocus phylogeny of a major New World avian radiation: The Vireonidae (2014) Molecular Phylogenetics and Evolution, 80 (1), pp. 95-104.

Battey, C.J., Ross, T., 2014. Impacts of Habitat  Restoration and the Status of Avian Communities  in Seattle City Parks. A Technical Report by the  Seattle Audubon Society.

Slager, D. L., and J. Klicka. 2014. A new genus for the American Tree Sparrow (Aves: Passeriformes: Passerellidae). Zootaxa 3821: 398–400.

van Els, P., G. M. Spellman, B. T. Smith, and J. Klicka. 2014. Extensive gene flow characterizes the phylogeography of a North American migrant bird: Black-headed Grosbeak (Pheucticus melanocephalus). Molecular Phylogenetics and Evolution 78: 148-159.

Klicka, J., F. K. Barker, K. J. Burns, S. M. Lanyon, I. J. Lovette, J. A. Chaves, and R. W. Bryson. 2014. A comprehensive multilocus assessment of sparrow (Aves: Passerellidae) relationships. Molecular Phylogenetics and Evolution 77: 177-182.

Burns, K. J., A. J. Shultz, P. O. Title, N. A. Mason, F. K. Barker, J. Klicka, S. M. Lanyon, and I. J. Lovette. 2014. Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds. Molecular Phylogenetics and Evolution 75: 41–77.

Powell, A. F. L. A., F. K. Barker, S. M. Lanyon, K. J. Burns, J. Klicka, and I. J. Lovette. 2014. A comprehensive species-level molecular phylogeny of the New World blackbirds (Icteridae). Molecular Phylogenetics and Evolution 71:  94–112.

Bryson, R. W., J. Chaves, B. T. Smith, M. Miller, K. Winker,  J. L. Pérez-Emán, and J. Klicka. 2013. Diversification across the New World within the ‘blue’ cardinalids (Aves: Cardinalidae). Journal of Biogeography. doi:10.1111/jbi.12218

Chaves, J. A., J. R. Hidalgo, and J. Klicka. 2013. Biogeography and evolutionary history of the Neotropical genus Saltator (Aves: Thraupini). Journal of Biogeography 40: 2180–2190.

Pulgarín-Ra, P. C., B. T. Smith, R. W. Bryson, and J. Klicka. 2013. Multilocus phylogeny and biogeography of the New World Pheucticus grosbeaks (Aves: Cardinalidae). Molecular Phylogenetics and Evolution 69: 1222–1227.

Voelker, G., R. C. K. Bowie and J. Klicka. 2013. Gene trees, species trees and Earth history combine to shed light on the evolution of migration in a model avian system. Molecular Ecology 22: 3333-3344.

Barker, F. K., K. J. Burns, J. Klicka, S. M. Lanyon, and I. J. Lovette. 2013. Going to extremes: contrasting rates of diversification in a recent radiation of New World passerine birds. Systematic Biology 62: 298-320.

Smith, B. T., and J. Klicka. 2013. Examining the role of effective population size on mitochondrial and multilocus divergence time discordance in a songbird. PLoS ONE 8: ee55161.

Manthey, J. D., J. Klicka, and G. M. Spellman. 2012. Is gene flow promoting the reversal of Pleistocene divergence in the Mountain Chickadee (Poecile gambeli)? PLoS ONE 7: e49218.

Smith, B. T., R. W. Bryson, V. Chua, L. Africa,  and J. Klicka. 2012. Speciational history of North American Haemorhous finches (Aves: Fringillidae) inferred from multilocus data. Molecular Phylogenetics and Evolution 66: 1055-1059.

Smith, B. T., C. Ribas, B. Whitney, B. Hernández-Baños, and J. Klicka. 2012. Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genus Forpus. Molecular Ecology 22: 483-494.

Smith B.T., A. Amei, and J. Klicka. 2012. Evaluating the role of contracting and expanding rainforest in initiating cycles of speciation across the Isthmus of Panama. Proceedings of the Royal Society B: Biological Sciences 79: 3520-3526.

Smith, B. T., R. W, Bryson, D. D. Houston, and J. Klicka. 2012. An asymmetry in niche conservatism contributes to the latitudinal species diversity gradient in New World vertebrates. Ecology Letters 15: 1318-1325.

Van Els, P., C. Cicero, J. Klicka. 2012. High latitudes and high genetic diversity: Phylogeography of a widespread boreal bird, the Gray Jay (Perisoreus canadensis). Molecular Phylogenetics and Evolution 63: 456-465.

Walstrom, W., J. Klicka, and G. Spellman. 2012. Speciation in the White-breasted Nuthatch (Sitta carolinensis): a multilocus perspective. Molecular Ecology 21: 907-920.

Miller, M. J., M. J. Lelevier, E. Bermingham, J. T. Klicka, P. Escalante, and K. Winker. 2011. Phylogeography Phylogeography of the Rufous-tailed Hummingbird (Amazilia tzacatl). The Condor 113: 806-816.

Manthey, J. D., Klicka, F., and G. M. Spellman. 2011. Isolation driven divergence: speciation in a widespread North American songbird (Aves: Certhiidae). Molecular Ecology 20: 4371-4384.

Smith, B. T., P. Escalante, B. E. Hernández-Baños, A. G. Navarro-Sigüenza, S. Rohwer, and J. Klicka. 2011. The role of historical and contemporary processes on the phylogeography of the Northern Cardinal, Cardinalis cardinalis. BMC Evolutionary Biology 11: 136.

Herr, C. A., P. W. Sykes, JR., and J. Klicka. 2011. Phylogeography of a vanishing North American songbird: The Painted Bunting (Passerina ciris). Conservation Genetics 12: 1395-1410.

Van Els, P., R. Canales, and J. Klicka. 2011. A northern range extension for the Botteri’s Sparrow in Mexico. Wilson Bulletin 123: 414-416.

Klicka, J., G. M. Spellman, K. Winker, V. Chua, and B. T. Smith. 2011. A phylogeographic and population genetic analysis of a widespread, sedentary North American bird: The Hairy Woodpecker (Picoides villosus). The Auk 128: 346-362.

Klicka, J., and Richard C. Banks. 2011. A new generic name for some sparrows (AVES: Emberizidae). Zootaxa 2793: 67-68.

Manthey, J. D., J. Klicka, and G. M. Spellman. 2011. Cryptic diversity in a widespread North American songbird: Phylogography of the Brown Creeper (Certhia americana). Molecular Phylogenetics and Evolution 58: 502-512.

Canales, R., J. Klicka, S, Favela, and J. Gonzalez-Rojas. 2010. Molecular phylogenetic analysis of an endangered Mexican sparrow: Spizella wortheni. Molecular Phylogenetics and Evolution 57: 1319–1322.

Lovette, I. J, J. L. Perez, J. Sullivan, R. C. Banks, I. Fiorentino, S. Cordoba, M. Echeveray-Galvis, F. K. Barker, K. J. Burns, J. Klicka, S. Lanyon, and E. Bermingham. 2010. A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Aves). Molecular Phylogenetics and Evolution 57: 753-770.

Barber, B., and J. Klicka. 2010. Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna. Proceedings of the Royal Society B. 277: 2675-2681.

Miller, M. J., E. Bermingham, J. Klicka. P. Escalante, and K. S, Winker. 2010. Neotropical birds show a humped distribution of within-population genetic diversity along a latitudinal transect. Ecology Letters 13: 576-586.

Smith, B. T. and J. Klicka. 2010. The profound influence of the Late-Pliocene Panamanian uplift on the exchange, diversification, and distribution of New World Birds. Ecography 33: 333-342.

Escalante, P., L. Marquez-Valdelamar, P. de la Torre, J. P. Laclette, and J. Klicka. 2009. Evolutionary history of a prominent North American warbler clade: The OporornisGeothlypis complex. Molecular Phylogenetics and Evolution 53: 668-678.

DaCosta, J. M., G. M. Spellman, P. Escalante-Pliego, and J. Klicka. 2009. A molecular systematic revision of two historically problematic songbird clades: Aimophila and Pipilo. The Journal of Avian Biology 40: 1-11.

Weir, J. T., E. Bermingham, M. J. Miller, M. A, Gonzalez, and J. Klicka. 2008. Phylogeography of a morphologically diverse Neotropical montane species, the Common Bush-tanager (Chlorospingus ophthalmicus). Molecular Phylogenetics and Evolution 47: 650-654.

Voelker, G., and J. Klicka. 2008. Systematics of Zoothera thrushes, and a synthesis of true thrush molecular systematic relationships. Molecular Phylogenetics and Evolution 49: 377-381.

DaCosta, J. M., and J. Klicka. 2008. Historic genetic structuring and paraphyly within the Great-tailed Grackle. The Condor 110: 170-176.

Miller, M. J., E. Bermingham, J. Klicka. P. Escalante, F. S. Raposo, J. Weir, and K. Winker. 2008. Out of Amazonia again and again: Episodic crossing of the Andes promotes diversification in a lowland forest flycatcher. Proceedings of the Royal Society B. 275: 1133-1142.

Pagenkopp, K. M., J. Klicka, K. L. Durant., J. C. Garvin, and R. C. Fleischer. 2008. Geographic variation in malarial parasite lineages in the Common Yellowthroat (Geothlypis trichas). Conservation Genetics 9: 1577-1588.

DaCosta, J. M., and J. Klicka. 2008. The great American interchange in birds: a phylogenetic perspective with the genus Trogon. Molecular Ecology 17: 1328-1343.

Klicka, J., G. Spellman, and K. Burns. 2007. Defining a monophyletic Cardinalini: A molecular perspective. Molecular Phylogenetics and Evolution 45: 1014-1032.

DaCosta, J. M., G. M. Spellman, and J. Klicka. 2007. Bilateral gynandromorphy in a White-ruffed Manakin (Corapipo altera). The Wilson Journal of Ornithology 119: 290-292.

Spellman, G., and J. Klicka. 2007. Phylogeography of the White-Breasted Nuthatch (Sitta carolinensis), Diversification in North American pine and oak woodlands. Molecular Ecology 16: 1729-1740.

Spellman, G., B. Riddle, and J. Klicka. 2007. Phylogeography of the Mountain Chickadee (Poecile gambeli): diversification, introgression, and expansion in response to Quaternary climate change. Molecular Ecology 16: 1055-1068.

Klicka, J., and G. Spellman. 2007. A molecular evaluation of the North American “Grassland” sparrow clade. The Auk 124: 537-551.

Cadena, C. D., J. Klicka, and R. E. Ricklefs. 2007. Evolutionary differentiation in the neotropical montane region: Molecular phylogenetics and phylogeography of Buarremon brush-finches (Aves, Emberizinae). Molecular Phylogenetics and Evolution 44: 993-1016.

Spellman, G., and J. Klicka. 2006. Testing hypotheses of Pleistocene population history using coalescent simulations: phylogeography of the Pygmy Nuthatch (Sitta pygmaea). Proceedings of the Royal Society Series B 273: 3057-3063.

Zink, R. M., and J. Klicka. 2006. The tempo of avian diversification: A response to Johnson and Cicero. Evolution 60: 411-412.

Klicka. J., G.Voelker, and G. Spellman. 2005. A molecular phylogenetic analysis of the “true thrushes” (Aves: Turdinae). Molecular Phylogenetics and Evolution 34: 486-500.

Zink, R. M., J. Klicka, B. R. Barber. 2004. The tempo of avian diversification during the Quaternary. Philosophical Transactions of the Royal Society of London, Series B. 359: 215-220.

Klicka, J., R. M. Zink, and K. S. Winker. 2003. Longspurs and Snow Buntings: Phylogeny and biogeography of a high-latitude clade (Calcarius). Molecular Phylogenetics and Evolution 26: 165-175.

Klicka, J., C. W. Thompson, A. Fry, and R. M. Zink. 2001. A molecular phylogeny for the avian genus Passerina and some allies. The Auk 118: 611-623.

Klicka, J., R. M. Zink, J. C. Barlow, W. B. McGillivray, and T. J. Doyle. 2001. The taxonomic rank of Spizella taverneri: A response to Mayr and Johnson. The Condor 103: 420-422.

Sweet, P. R., G. F. Barrowclough, J. Klicka, L. Montanez-Godoy, and P. Escalante-Pliego. 2001. Notes on the birds of Isla Guadalupe, Mexico. Western Birds 32: 71-80.

Klicka, J., K. P. Johnson, and S. M. Lanyon. 2000. New World nine-primaried oscine relationships: constructing a molecular framework. The Auk 117: 321-336.

Zink, R. M., and J. Klicka. 2000. Avian Evolution during the Pleistocene in North America. In The Biology of Biodiversity, (M. Kato Ed.). Springer Verlag Press, Tokyo, pp. 275-288.

Klicka, J., J. C. Barlow, W. B. McGillivray, T. J. Doyle, and R. M. Zink. 1999. Evidence supporting the recent origin and species status of the Timberline Sparrow. The Condor 101: 577-588.

Zink, R. M., D. L. Dittmann, J. Klicka, and R. C. Blackwell. 1999. Evolutionary patterns of morphometrics, allozymes and mitochondrial DNA in thrashers (Genus Toxostoma). The Auk 116: 1021-1038.

Klicka, J., and R. M. Zink. 1999. Pleistocene phylogeographic effects on avian evolution. Proceedings of the Royal Society of London, Series B. 266: 695-700.

Klicka, J., and R. M. Zink. 1998. Pleistocene speciation and the mitochondrial DNA clock: A response to Arbogast and Slowinski. Science 282: 1955a.

Klicka, J., and R. M. Zink. 1997. The importance of recent ice ages in speciation: A failed paradigm. Science 277: 1666-1669.