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Publications

Publications in Press

156) Nosil, P., Feder, J.L., Flaxman, S.M., Gompert, Z. 2017. Dynamics of Speciation: from gradualism to regime shifts. Nature Ecology and Evolution (In press).

155) Feder, J.L., Hood, G.R., Doellman, M.M., Schuler, H., Miller, A., Tait, C., Glover, M.M., and Meyers, P. Speciation, Process of. 2017. Reference Module in Life Sciences (LIFE). Elsevier Press.

154) Feder, J.L., and Egan, S.P. 2017. Sympatry and Patterns of Genetic Differentiation in Sympatry. Reference Module in Life Sciences (LIFE). Elsevier Press.

153) Feder, J.L. Allopatric. 2017. Reference Module in Life Sciences (LIFE). Elsevier Press.

152) Feder, J.L. 2016. Foreward. Encyclopedia of Evolutionary Biology Elsevier Press (In press).

151) Hood, G.R. and Feder, J.L. 2016. Sequential Speciation and Biodiversity. Encyclopedia of Evolutionary Biology Elsevier Press (In press).

150) Egan, S.P., G.R. Hood, & J.L. Feder. 2016. Chapter 69: Speciation-with-gene-flow. In: Encyclopedia of Evolutionary Biology. Elsevier Press (In press).

Reviewed Publications

149) Schuler, H., Hood, G.R., Egan, S.P., and Feder, J.L. 2016. Modes and Mechanisms of Speciation. Reviews in Cell Biology and Molecular Medicine. Published Online: 26 JUL 2016 DOI: 10.1002/3527600906.mcb.201600015

148) Gompert, Z., Egan, S.P., Barrett, R., Feder, J.L, and Nosil, P. 2016. The measurement of selection on correlated genetic loci. Molecular Ecology Online Oct. 3 DOI 10.1111/mec.13867.

147) Meyers, P., Powell, T.H.Q., Walden, K.K.O., Shieferecke, A., Feder, J.L., Hahn, D.A., Robertson, H.M., Berlocher, S.H. and Ragland, G.J. 2016. Evolutionary divergence of the diapause transcriptome in apple maggot flies: winter regulation and post-winter transcriptional repression. Journal Experimental Biology 0, 1-11 doi:10.1242/jeb.140566.

146) Mattsson, M., Hood, G.R., Feder, J.L., and Ruedas, L.A. 2015. Rapid and repeatable shifts in life‐history timing of Rhagoletis pomonella (Diptera: Tephritidae) following colonization of novel host plants in the Pacific Northwestern United States . Ecology and Evolution 5: 5823-5837. DOI: 10.1002/ece3.1826.

145) Hood, G.R., Forbes, A.A., Powell, T.H.Q., Egan, S.P., Smith, J.J., and Feder, J.L. 2015. Sequential divergence and the multiplicative origin of community diversity. Proceedings of the National Academy of Sciences U.S.A. doi:10.1073/pnas. 1424717112.

144) Arcella, T., Sim, S.B., Yee, W.L., Hood, G.R., Powell, T.H.Q., Schwarz, D., Egan, S.P., Goughnour, R.B., and Feder, J.L. 2015. Hybridization and the spread of the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae), in the Northwestern United States. Evolutionary Applications 8: 834–846. doi: 10.1111/eva.12298.

143) Yee, W.L., Goughnour, R.B., Hood, G.R., Forbes, A.A., and Feder, J.L. 2015. Chilling and Host Plant/Site-Associated Eclosion Times of Western Cherry Fruit Fly (Diptera: Tephritidae) and a Host-Specific Parasitoid. Environmental Entomology 44:4 1029-1042.

142) Ragland, G.J., Almskaar, K., Duong, K.L., Gough, H.M., Huddleston, J., Feder, J.L., Hahn, D.A., and Schwarz, D. 2015. Differences in fitness and transcriptome-wide gene expression associated with Rhagoletis (Diptera: Tephritidae) larvae feeding in alternate host fruit environments. Molecular Ecology DOI: 10.1111/mec.13191.

141) Egan, S.P., Greg Ragland, G.J., Assour, L., Powell, T.H. Q.Hood, G.R., Emrich, S., Nosil, P. and Feder, J.L. 2015. Experimental evidence natural selection drives genome-wide divergence during sympatric speciation. Ecology Letters 18: 817-825. (F1000 recommended; Featured on NSF website).

140) Tadeo, E., Feder, J.L., Egan, S.P., Schuler, H., Aluja , M., and and Rull, J. 2015. Divergence and evolution of reproductive barriers among three allopatric populations of Rhagoletis cingulata across eastern North America and México. Entomologia Exp. et. App. 156: 301-311.

139) Egan, S.P., Grey, Olds, E.B., Feder, J.L., Ruggiero, S.T., Tanner, C.E., and Lodge, D.M. 2015. Molecular detection of invasive species in ballast and harbor water using environmental DNA and Light Transmission Spectroscopy. Environmental Science and Technology 49(7):4113-21. doi: 10.1021/es5058659. Epub 2015 Mar 13.

138) Yee, W.L., Lawrence, T.W., Hood, G.R. and Feder, J.L. 2015. New records of Rhagoletis species (Diptera: Tephritidae) and their host plants in western Montana, U.S.A. Pan Pacific Entomologist 91: 39-57.

137) Yee W.L., Nash, M.J., Goughnour, R.B., Cha, D.H., Linn C.E., and Feder, J.L. 2014. Ammonium carbonate is more attractive than apple and hawthorn fruit volatile Lures to Rhagoletis pomonella (Diptera: Tephritidae) in Washington State. Environ Entomol. 43: 957-68. doi: 10.1603/EN14038. Epub 2014 Jun 9.

136) Feder, J.L., Flaxman, S.M., and Nosil, P. 2014. Assessing when chromosomal rearrangements affect the dynamics of speciation: implications from computer simulations. Frontiers in Genetics doi: 10.3389/fgene.2014.00295.

135) Soria-Carrasco, V., Gompert, Z., Comeault, A.A., Farkas, T.E., Parchman, T.L., Johnson, J.S., Buerkle, C.A., Feder, J.L., Bast, J., Schwander, T., Egan, S.P., Crespi, B.J., and Nosil, P. 2014. Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation. Science 344: 738-742 (Research featured on cover of journal Science and in feature in Science on Aug. 8th, 2014 issue).

134) Feder, J.L., Nosil, P., Wacholder, A.C., Egan, S.P., Berlocher, S.H.,and Flaxman, S.M. 2014. Genome Wide Congealing and Rapid Transitions across the Speciation Continuum. Journal of Heredity 105: Suppl 1:810-20. doi: 10.1093/jhered/esu038.

133) Flaxman, S.M., Wacholder, A.C., Feder, J.L. and Nosil, P. 2014. Genomic architecture drives the rapid origin of new species. Molecular Ecology 23: 4074–4088. DOI: 10.1111/mec.12750.

132) Hood, G.R., Glover, M.M., Tait, C., Yee, W.L. and Feder, J.L. 2014. Detection of an apple-infesting population of Rhagoletis pomonella 1867 (Walsh) (Diptera: Tephritidae) in the state of Colorado, USA. The Pan Pacific-Entomologist 90: 4-10.

131) Deines, A.M., Ian Bbole, I., Katongo, C., Powell, T.H.Q., Feder, J.L., and Lodge, D.M. 2014. Hybridization of native Oreochromis species (Cichlidae) and the introduced Nile tilapia (O. niloticus) in the Kafue River, Zambia. African Journal of Aquatic Science: DOI:10.2989/16085914.2013.864965

130) Seehausen, O., Feder, J.L., and co-authors. 2014. Integrating Genomic Data and Theory in the Study of Speciation. Nature Genetics Reviews 15: 176–192.

129) Feder, J.L., S.P. Egan, and P. Nosil. 2014. Speciation and Genome Evolution. Pg. 549-559. In: Princeton Guide to Evolution (J. Losos, D. Schluter, eds.) Princeton University Press, New Jersey.

128) Smith, J.J., Powell T.Q.H., Teixeira, L., Armstrong, W.O., McClowry, R.J., Isaacs, R., R. Hood, G.R., Feder, J.L., and Gut, L. 2014. Genetic Structure of Cherry Fruit Fly (Rhagoletis Cingulata) Populations across Managed, Unmanaged, and Natural Habitats. Entomologia exp. et. Applicata 150(2): 157–165.

127) 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.

126) Powell, T., Hood, G.R., Egan, S.P., and Feder, J.L. 2014. Genetic differentiation among hawthorn-infesting populations of Rhagoletis pomonella (Diptera: Tephritidae) in the southern United States and its implication for endemic host race formation. Molecular Ecology 23: 688-704.

125) Arcella, T.E, Perry, W.L., Lodge, D.M., and Feder, J.L. 2013. The role of hybridization in a species invasion and extirpation of resident fauna: Hybrid vigor and breakdown in the rusty crayfish (Orconectes rusticus). Crustacean Biology DOI: 10.1163/1937240X-00002204.

124) Rull, J., Aluja, M., Tadeo, E. , Guillen, L., Egan, S.P., Glover, M., and Feder, J.L. Distribution, host plant affiliation, phenology, and phylogeny of walnut-infesting Rhagoletis flies (Diptera: Tephritidae) in Mexico. 2013. Biological Journal of the Linnean Society DOI: 10.1111/bij.12157.

123) Green, E., Almskaar, K., Sim, S.B., Arcella, T., Yee, W.L., Feder, J.L., and Schwarz, D. 2013. Molecular Species Identification of Cryptic Apple and Snowberry Maggots (Diptera: Tephritidae) in Western and Central Washington. 2013. Environmental Entomology 42(5):1100-1109.

122) Powell, T., Murphy, M., Egan, S.P., Hood, G., Sheina, S., Arcella, T., Berlocher, S., Nosil, P. and J.L., Feder. 2013. Widespread genomic divergence between sister taxa of Rhagoletis flies undergoing speciation-with-gene-flow. Special Issue “Genomic Evolution and Speciation” edited by J.L. Feder and P. Nosil. Evolution 67: 2561-2576.

121) Feder, J.L, Flaxman, S.M., Egan, S.P., Comeault, A.A., and P. Nosil. 2013. Geographic Mode of Speciation and Genomic Divergence. Annual Review of Ecology, Evolution, and Systematics 44:73-97.

120) Feder, J.L. and S.P. Egan. 2013. Sympatry and patterns of genetic differentiation in sympatry. Pgs. 606-608. In: Brenner’s Encyclopedia of Genetics, 2nd edition (S. Malloy & K. Hughes, eds.). Elsevier Press.

119) Egan, S.P., Barnes, M.A., Hwang, C.T., Mahon, A.R., Feder, J.L., Ruggiero, S.T., Tanner, C.E, and D.M. Lodge. 2013. Rapid invasive species detection by combining environmental DNA with Light Transmission Spectroscopy. Conservation Letters DOI: 10.1111/conl. 12017.

118) St. Jean, G., Egan, S.P., Yee, W.L. and J.L. Feder. 2013. Genetic Identification of an Unknown Rhagoletis Fruit Fly (Diptera: Tephritidae) Infesting Chinese Crabapple: Implications for Apple Pest Management. Journal of Economic Entomology 106: 1511-1515.

117) Nosil, P. and Feder, J.L. 2013. Genome evolution and speciation: towards quantitative descriptions of pattern and process. Special Issue “Genomic Evolution and Speciation” edited by J.L. Feder and P. Nosil. Evolution 67: 2461-2467.

116) Schuler, H., Bertheau, C., Egan, S.P., Feder, J.L., Johannesen, J., Riegler, M., Köppler, K., Schlick-Steiner, B.C., Steiner, F.M., Arthofer, W., and C. Stauffer. 2013. Recent horizontal transfer of Wolbachia between native and introduced cherry-infesting Rhagoletis fruit flies in Europe. Molecular Ecology 22: 4101–4111.

115) Flaxman, S.M.¬¬, Feder, J.L., and P. Nosil. 2013. Genetic Hitchhiking and the Dynamic Buildup of Genomic Divergence During Speciation-with-Gene-Flow. Special Issue “Genomic Evolution and Speciation” edited by J.L. Feder and P. Nosil. Evolution 67: 2577-2591. DOI: 10.1111/evo.12055.

114) Hood, G.R., Yee, W., Goughnour, R., Sim, S.B., Egan, S.P., Arcella, T., St. Jean, G., Xu, C.C., and Feder, J.L. 2013. The geographic distribution of Rhagoletis pomonella (Diptera: Tephritidae) in the western United States. Annals Ent. Soc. Amer. 106: 59-65.

113) Feder, J.L., Flaxman, S.M., Egan, S.P., and P. Nosil. 2013. Hybridization and the buildup of genomic divergence during speciation. Journal of Evol. Biol. 26: 261–266. doi: 10.1111/jeb.12009.

112) Reidenbach, K.R., Neafsey, D.E., Costantini, C., Sagnon, N’Fale, Ragland, G.J., Egan, S.P., Feder, J.L., Muskavitch, M.A.T., and N. J. Besansky. 2012. Patterns of genomic differentiation between ecologically differentiated M and S forms of Anopheles gambiae in West and Central Africa. Genome Biology and Evolution 4: 1202-1212.

111) Hood G.R, S.P. Egan, and J.L. Feder. 2012. Evidence for sexual isolation as a prezygotic barrier to gene flow between morphologically divergent species of Rhagoletis fruit flies. Ecological Entomology 37(6): 521-528.

110) Flaxman, S.M.¬¬, J.L. Feder, and P. Nosil. 2012. Spatially explicit models of divergence and genome hitchhiking. Journal Evolutionary Biology 25: 2633-2650.

109) Mahon, A.R., Barnes, M.A., Li, F., Egan, S.P., Tanner, C.E., Ruggiero, S.T., Feder, J.L., and Lodge D.M. 2012. Invasive species detection capabilities using Laser Transmission Spectroscopy. Journal of the Royal Society Interface DOI: 10.1098/rsif.2012.0637.

108) Rull, J., E. Tadeo, M. Aluja, L Guuillen, S.P. Egan, and J.L. Feder. 2012. Hybridization and sequential components of reproductive isolation between parapatric walnut-infesting sister species Rhagoletis completa and R. zoqui. Biological Journal of the Linnean Society DOI: 10.1111/j.1095-8312.2012.01977.x

107) Lodge, D.M., Arcella, T., Baldridge, A.K., Barnes, M.A., Chadderton, L., Deines, A., Feder, J.L., Gantz, C., Gherardi, F., Howard, G.W., Jerde, C.L., Peters, B., Peters, J.A., Sargent, L., Wittmann, M.E.,Yeo, D.C.J., Zeng , Y. 2012. Global Introductions of Crayfishes: Evaluating the Impact of Species Invasions on Ecosystem Services. Annual Review of Ecology, Evolution, and Systematics 43: 449–472.

106) Nosil, P., Parchman, T.L., Feder, J.L. and Gompert, Z. 2012. Do highly divergent loci reside in genomic regions affecting speciation? A test in Timema stick insects. BMC Evolutionary Biology 12:164 DOI:10.1186/1471-2148-12-164

105) Hood, G.R., S.P. Egan, and J.L. Feder. 2012. Interspecific Competition and Speciation in Endoparasitoids. Evolutionary Biology 39: 219-230.

104) Feder, J.L. Egan, S.P., and Nosil, P. 2012. The Genomics of Speciation-With-Gene-Flow. Trends in Genetics 28: 342-50. Epub 2012 Apr 18.

103) Ragland, G.J., S.B. Sim, S. Goudarzi, J.L. Feder, and D.A. Hahn. 2012. Environmental interactions during host race formation: host fruit environment moderates a seasonal shift in phenology in host races of Rhagoletis pomonella. Functional Ecology DOI: 10.1111/j.1365-2435.2012.01992.x

102) Nosil¬¬, P., Z. Gompert, T.A. Farkas, A. Comeault, J.L. Feder, C.A. Buerkle, and T.L. Parchman. Genomic consequences of multiple speciation processes. 2012. Proceedings Royal Society B DOI: 10.1098/rspb.2012.0813

101) Linn, C.E. Jr. W.L. Yee, S.B. Sim, D.H. Cha, T.H.Q. Powell, R.B. Goughnour, and J.L. Feder. 2012. Behavioral evidence for fruit odor discrimination and sympatric host races of Rhagoletis pomonella flies in the western United States. Evolution DOI: 10.1111/j.1558-5646.2012.01719.×.

100) Nosil, P. and Feder, J.L. 2012. Widespread yet heterogeneous genomic divergence. Molecular Ecology 21: 2829–2832.

99) Lodge, D.M., Turner, C.R., Jerde, C.L., Barnes, M.A., Chadderton, L., Egan, S.P., Feder, J.L., Mahon, A.R., Pfrender, M.E. 2012. Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA. Molecular Ecology 21: 2555–2558.

98) Sim, S.B., M. Mattsson, Jasmine L. Feder, C.E. Linn Jr., D.H. Cha, W.L. Yee, R.B. Goughnour, and J.L. Feder. 2012. A field test for host fruit odour discrimination and avoidance behaviour for Rhagoletis pomonella flies in the western United States. Journal of Evolutionary Biology 25: 961-971.

97) Powell, T.H.Q., D. Cha, C.E. Linn Jr., and J.L. Feder. 2012. On the scent of standing variation for speciation: Behavioral evidence for native sympatric host races of Rhagoletis pomonella (Diptera: Tephritidae) in the southern United States. Evolution 66: 2739-2756.

96) Cha, D., T.H.Q. Powell, J.L. Feder, and C.E. Linn Jr. 2012. Geographic variation in fruit volatiles emitted by the hawthorn Crataegus mollis and its consequences for host race formation in the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae). Entomologia Exp. et. Appl. 143: 254-268.

95) Egan, S.P., G.R. Hood, J.L. Feder, and J.R. Ott. 2012. Divergent host plant use promotes reproductive isolation among cynipid gall wasp populations. Biology Letters 8: 605-608 doi: 10.1098/rsbl.2011.1205.

94) Cha, D., Y. Wee, R. Groughour, S.B. Sim, J.L. Feder, and C.E. Linn Jr. 2012. Identification of Host Fruit Volatiles from Domesticated Apple (Malus domestica), Native Black Hawthorn (Crataegus douglasii) and Introduced Ornamental Hawthorn (C. monogyna) Attractive to Rhagoletis pomonella flies from the Western United States. J. Chemical Ecology 38: 319-29. Epub 2012 Mar 8.

93) Feder, J.L., S.P. Egan, and A.A. Forbes. 2012. Ecological adaptation and speciation: The evolutionary significance of habitat avoidance as a postzygotic reproductive barrier to gene flow. International Journal of Ecology Vol. 2012: Article ID 456374, 15 pages
doi:10.1155/2012/456374

92) Yee W.L., D.H. Cha, C.E. Linn, Jr., M.W. Klaus, R.B. Goughnour, and J.L. Feder. 2012. Abundances of apple maggot, Rhagoletis pomonella, across different areas in central Washington, with special reference to black-fruited hawthorns. Journal of Insect Science 12:124. Available online: http://www.insectscience.org/12.124.

91) Nosil P., and J.L. Feder. 2012. Genomic divergence during speciation: causes and consequences. Phil. Trans. Royal Society 367: 332-342.

90) Feder J.L., R. Gejji, S. Yeaman, and P. Nosil. 2012. Divergence and ‘Genomic’ Hitchhiking across the Speciation Continuum. Phil. Trans. Royal Society 367: 461-474 doi: 10.1098/rstb.2011.0256

89) Yee W.L., R.B. Goughnour, and J.L. Feder. 2012. Differences in Body Size and Egg Loads of Rhagoletis indifferens (Diptera: Tephritidae) from Introduced and Native Cherries. Environmental Entomology 40:1353-1362. doi: http://dx.doi.org/10.1603/EN11128.

88) Li, F., Mahon, A.R., Barnes, M.A., Feder, J., Lodge, D.M., Hwang, C-T, Schafer, R., Ruggiero, S.T., Carol E. Tanner, C.E. 2011.Quantitative and Rapid DNA Detection By Laser Transmission Spectroscopy. PLoS ONE 6: e29224. doi:10.1371/journal.pone.

87) Ragland, G.J., S.P. Egan, J.L. Feder, S.H. Berlocher, and D.A. Hahn. 2011. Developmental trajectories of gene expression reveal regulatory candidates for diapause termination, a key life history transition in the apple maggot fly, Rhagoletis pomonella. Journal of Experimental Biology 214: 3948-3960.

86) Cha, D.H., Powell T.H.Q., J.L. Feder, and C.E. Linn, Jr. 2011. Identification of Host Fruit Volatiles from Green Hawthorn (Crataegus series Aestivales) and Blueberry Hawthorn attractive to Southern Rhagoletis pomonella Flies. J. Chemical Ecology 37: 974-83. Epub 2011 Sep 2.

85) Cha, D.H., Powell T.H.Q., J.L. Feder, and C.E. Linn, Jr. 2011. Identification of Host Fruit Volatiles from Mayhaw (Crataegus series Aestivales) Attractive to Mayhaw Origin Rhagoletis pomonella flies. J. Chemical Ecology 37: 961-73. Epub 2011 Sep 3.

84) Agarwal A.F., J L. Feder, and P. Nosil. 2011. Ecological divergence and the evolution of intrinsic postmating isolation despite gene flow. International Journal of Ecology Article ID 435357, 15 pages doi:10.1155/2011/435357

83) Feder J.L., R. Gejji, T.H.Q. Powell, and Patrik Nosil. 2011. Adaptive Chromosomal Divergence Driven by Mixed Geographic Mode of Speciation. Evolution 65:2157-2170. doi: 10.1111/j.1558-5646.2011.01321.×. Epub 2011 May 12.

82) Feder, J.L. 2011. The Mystery of Speciation. pp. 117-152. In: Biological Evolution: Facts and Theories. (G. Auletta, M. LeClerc, R. A. Matinez, eds.). Gregorian & Biblical Press, Rome.

81) Mahon, A.R., M.A. Barnes, S. Senapati, J.L. Feder, J.A. Darling, H-C. Chang, D.M. Lodge. D.M. 2011. Molecular detection of invasive species in heterogeneous mixtures using a microfluidic carbon nanotube platform. PLoS One Feb 18; 6(2):e17280

80) Rull, J., M Aluja, and J.L. Feder. 2011. Distribution and basic biology of black cherry-infesting Rhagoletis (Diptera: Tephritidae) in Mexico. Annals Ent. Soc. Amer. 104: 202-211.

79) Forbes, A.A., G.R. Hood, T.H.Q. Powell, and J.L. Feder. 2010. Geographic and ecological overlap of parasitoid wasps associated with the Rhagoletis pomonella (Diptera: Tephritidae) species complex. Annals Ent. Soc. Amer. 103: 908-915.

78) Rull, J., M. Aluja, and J.L. Feder. 2010. Evolution of intrinsic reproductive isolation among four North American populations of R. Pomonella. Biol Journal of the Linnean Society 100: 213-233.

77) Michel, A.P., S. Sim, T.H.Q. Powell, M. S. Taylor, P. Nosil and J. L. Feder. 2010. Widespread genomic divergence during sympatric speciation. Proceedings of the National Academy of Sciences U.S.A. 107: 9724-9729.
(Research featured in Nature news and views and Science editor’s choice sections)

76) Feder, J.L., T.H.Q. Powell, K. Filchak and Brian Leung. 2010. The Diapause Response of Rhagoletis pomonella to Varying Environmental Conditions and its Significance for Geographic and Host-Plant Related Adaptation. Entomologia Exp. et Appl. 136: 31-44.

75) Feder, J.L., and P. Nosil. 2010. The efficacy of divergence hitchhiking in generating genomic islands during ecological speciation. Evolution 64:1729-1747.

74) Feder, J.L., and A.A. Forbes. 2010. Sequential Speciation and the Diversity of Parasitic Insects. Ecological Entomology 35: (Suppl 1) 67-76.

73) Ramsdell, K.M.M., S.A. Lyons-Sobaski, H. M. Robertson, K. K. O. Walden, J. L. Feder, K. Wanner and S. H. Berlocher. 2010. Expressed sequence tags from cephalic chemosensory organs of the northern walnut husk fly, Rhagoletis suavis, including a putative canonical odorant receptor. Journal of Insect Science 51: 1-11.

72) Schwarz, D., H. M. Robertson, J. L. Feder, K. Varala, M. E. Hudson, G. J. Ragland, D. A. Hahn and S. H. Berlocher. 2009. Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella. BMC Genomics 10:633doi:10.1186/1471-2164-10-633.

71) Mallet, J., A. Meyer, P. Nosil, and J.L. Feder. 2009. Space, sympatry and speciation. J. Evol. Biol. Sept. 1. [Epub ahead of print] PubMed PMID: 19732264.

70) Senapati, S., A.R. Mahon, J. Gordon, C. Nowak, S. Sengupta, T.H.Q. Powell, J. Feder,
D.M. Lodge,and H-C Chang. 2009. Rapid on-chip genetic detection microfluidic platform for real world applications. Biofludics 3: 022407.

69) Feder, J.L. and P. Nosil. 2009. Chromosomal inversions and species differences: are genes affecting adaptive divergence and reproductive isolation expected to reside within inversions? Evolution 63: 3061-75.

68) Berlocher, S.H. and J.L. Feder. 2009. The road less traveled: Ron Prokopy and sympatric speciation. In: Biorational Fruit Tree Pest Management. (M. Aluja, C. Vincent, T. Laskey, eds.) CABI Publishing.

67) Forbes, A.A., T.H.Q. Powell, L.L. Stelinski, J.J. Smith, Feder J.L.. 2009. Sequential Sympatric Speciation across Trophic Levels. Science 323: 776-779.

66) Rull, J., R. Wharton, J.L. Feder, L. Guillén, J. Sivinski A.A. Forbes and M. Aluja. 2009. Latitudinal variation in parasitoid guild composition and parasitism rates of the North American hawthorn infesting Rhagoletis pomonella. Environ. Entomol. 38: 588-599.

65) Ragland , G.J., J. Fuller, J.L. Feder, and D.A. Hahn. 2009. Respriormetric monitoring reveals a biphasic metabolic rate trajectory of pupal diapause break and post diapause development in a tephritid fly. Journal of Insect Physiology 55:344-350.

64) Feder, J.L. and S. Velez. 2009. Intergenic Exchange, Geographic Isolation, and the Evolution of Bioluminescent Color for Pyrophorus Click Beetles. Evolution 63: 1203-1216.

63) Olsson SB; Linn CE; Feder JL; Michel A; Dambroski HR; Berlocher SH; Roelofs WL 2009: Comparing Peripheral Olfactory Coding with Host Preference in the Rhagoletis Species Complex. Chemical Senses 33: 34(1):37-48

62) Feder, J.L. and Forbes, A.A. 2008. Host Fruit-Odor Discrimination and Sympatric Host-Race Formation. Pp. 101-116. In: Specialization, Speciation, and Radiation: The Evolutionary Biology of Herbivorous Insects. (edited by Kelly J. Tilmon) University of California Press.

61) Xie, X., A.P. Michel, D. Schwarz, J. Rull, S. Velez, A.A. Forbes, M. Aluja, and J.L. Feder. 2008. Radiation and divergence in the Rhagoletis pomonella species complex: Inferences from DNA sequence data. Journal Evolutionary Biol. 21: 900-913.

60) Forbes, A.A., T.H.Q. Powell, N. F. Lobo, M.A.F. Noor and J.L. Feder. 2007. Polymorphic microsatellite loci for Diachasma alloeum (Hymenoptera: Braconidae) Molecular Ecology Notes.

59) Feder, J.L. and V. Anderson. 2007. Trials and Tribulations of Integrative Graduate Training in the Era of the IGERT. Midwestern Association of Graduate Studies.

58) Dambroski, H.R. and JL. Feder. 2007. Host plant and latitude-related diapause variation in Rhagoletis pomonella: A test for multifaceted life history adaptation on different stages of diapause development. Journal Evol. Biol. 20: 2101-2112.

57) Forbes, A.A., T.H.Q. Powell, N. F. Lobo, and J.L. Feder. 2007. Resolving a DNA sequencing artifact associated with topoisomerase I generated clones in the plasmid pCR®2.1. BioTechniques 42: 458-462.

56) Xie, X., J. Rull, A.P. Michel, S. Velez, A.A. Forbes, N.F. Lobo, M. Aluja, and J.L. Feder. 2007. Hawthorn-Infesting Populations of Rhagoletis pomonella in Mexico and Speciation Mode Plurality. Evolution 61: 1091-1105.

55) Michel, A.P., J. Rull, M. Aluja and J.L. Feder. 2007. The Genetic Structure of Hawthorn-infesting Rhagoletis pomonella Populations in Mexico: Implications for Sympatric Host Race Formation. Molecular Ecology 16: 2867-2878.

54) Feder, J.L. and Forbes, A.A. 2007. Habitat avoidance and sympatric speciation. Functional
Ecology 21: 589-597.

53) Noor, M.A.F. and Feder, J.L. 2006. Genetics of Speciation. Nature Genetics 7: 851-861.

52) Olsson, SB., C.E. Linn, Jr., A. Michel, H.R. Dambroski, S.H. Berlocher, J.L. Feder, and W.L. Roelofs. 2006. Receptor Expression and Sympatric Speciation: Unique Olfactory Receptor Neuron Responses in F1 Hybrid Rhagoletis Populations. Journal Experimental Biol. 209: 3729-3741.

51) Forbes, A.A., and Feder, J.L. 2006. Divergent Preferences of Rhagoletis pomonella Host Races for Olfactory and Visual Fruit Cues. Entomologia Experimentalis et Applicata 119: 121-127.

50) Rull, J., Aluja, M., Feder, J.L., and Berlocher, S.H. 2006. The distribution and host range of hawthorn-infesting Rhagoletis pomonella (Diptera: Tephritidae) in Mexico. Annals Entomological Society of America 99: 662-672.

49) Velez, S. and Feder, J.L. 2006. Integrating Biogeographic and Genetic Approaches to Investigate the History of Bioluminescent Color Alleles in the Jamaican click beetle Pyrophorus plagiophthalamus Molecular Ecology 15: 1339-1404.

48) Velez, S., Taylor, M.S., Noor M.A.F., Lobo N.F., and Feder, J.L. 2006. Isolation and characterization of microsatellite loci from the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae). Molecular Ecology Notes 6: 90-92.

47) Velez, S. and Feder, J.L. 2006. Isolation and characterization of novel dinucleotide repeat microsatellites in the Jamaican click beetle Pyrophorus plagiophthalamus (Coleoptera: Elateridae). Molecular Ecology Notes 5: 899-901.

46) Dambroski, H.R., Linn, C. Jr, Berlocher, S.H., Forbes, A., Roelofs, W., and Feder, J.L. 2005. The Genetic Basis for fruit odor discrimination in Rhagoletis flies and its significance for sympatric host shifts. Evolution 59: 1953-1964.

45) Forbes, A., Fisher, J. and Feder, J.L. 2005. Habitat Avoidance: Overlooking an Important Aspect of Host Specific Mating and Sympatric Speciation? Evolution 59: 1552-1559

44) Feder, J.L., Xie, X. Rull, J., Velez, S., Forbes, A., Dambroski, H., Filchak, K. and Aluja, M. 2005. Mayr, Dobzhansky, Bush and the complexities of sympatric speciation in Rhagoletis. Proceedings of the National Academy of Sciences U.S.A. 102: 6573-6580.

43) Linn, C. Jr, Nojima, S., Dambroski, H., Feder, J.L., Berlocher, S.H, Roelofs, W.L. 2005. Variability in Response Specificity of Apple, Hawthorn, and Flowering Dogwood-Infesting Rhagoletis Flies to Host Fruit Volatile Blends: Implications for Sympatric Host Shifts. Entomologia Experimentalis et Applicata 116: 55-64.

42) Filchak, K.E., W. J. Etges, N. J. Besansky, and J. L. Feder. 2005. The ecological genetics of host use in the Diptera. In: The Evolutionary Biology of Flies. B. M. Wiegman and D. K. Yeates (eds.), Columbia University Press.

41) Linn, C. Jr, Dambroski, H.R., Feder, J.L, Berlocher, S.H., Nojima, S. and Roelofs, W.L. 2004 Postzygotic isolating factor in sympatric speciation in Rhagoletis Flies: Reduced response of hybrids to parental host-fruit odors. Proceedings of the National Academy of Sciences U.S.A. 101: 17753-17758

40) Stolz, U., Velez, S., Wood, K., Wood, M. and Feder, J.L. 2003. Positive Darwinian Natural Selection for Orange Bioluminescent Color in a Jamaican Click Beetles. Proceedings of the National Academy of Sciences U.S.A. 100: 14955-14959.

(Click beetle research from the paper above was featured in Editor’s choice section of journal Science on Jan. 9, 2004 and Samplings page of Mar. 2004 volume of Natural History)

39) Feder, J.L., Berlocher, S.H., Roethele, J.B., Smith, J.J., Perry, W.L., Gavrilovic, V., Filchak, K.E., Rull, J. and Aluja, M. 2003. Allopatric Genetic Origins for Sympatric Host Race Formation in Rhagoletis. Proceedings of the National Academy of Sciences U.S.A. 100: 10314-10319.
38) Linn, C., Feder, J.L., Nojima, S., Dambroski, H.R., Berlocher, S.H., and Roelofs, W. 2003. Fruit Odor Discrimination and Sympatric Host Race Formation in Rhagoletis. Proceedings of the National Academy of Sciences U.S.A. 100: 11490-11493.

37) Feder, J.L., Roethele, J.B., Filchak, K.E., Niedbalski, J. and Romero-Severson, J. 2003. Evidence for inversions related to sympatric host race formation in the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae). Genetics 163: 939-953.

(The research in the three papers above were featured in a research focus article written by C. Jiggins and J. Bridle appearing in the Trends in Ecology & Evolution Mar. 3, 2004).

36) Funk, D., K.E. Filchak, and J.L Feder. 2002. Herbivorous insects as model systems for the comparative study of speciation ecology. Genetica 116: 251–267.

35) Perry, W.L., Lodge, D.M. and Feder, J.L. 2002. Nonindigenous Species Threaten North American biodiversity: Systematics, hybridization and introgression. Systematic Biology 51:255-275.

34) Berlocher, S.H. and Feder, J.L. 2002. Sympatric speciation in phytophagous insects: moving beyond controversy? Annual Review of Entomology 47:773-815.

33) Funk, D., K.E. Filchak, and J.L Feder. 2002. Herbivorous insects: model systems for the comparative study of speciation ecology. In: Genetics of Mate Choice: From Sexual Selection to Sexual Isolation (W.J. Etges & M.A.F. Noor, eds.), Kluwer Academic Press.

32) Roethele, J.B., Romero-Severson, J. and Feder, J.L. 2001. Evidence for Broad-Scale Conservation of Linkage Map Relationships between Rhagoletis pomonella and Drosophila melanogaster. Annals Entomological Society of America 94:936-947.

31) Filchak, K.E., Roethele, J.B., and Feder, J.L. 2001. The effects of photoperiod and light intensity on the genetics of diapause in the apple maggot fly, Rhagoletis pomonella (Walsh) (Diptera: Tephritidae). Annals Entomological Society of America 94:902-908

30) Perry, W. L., Feder, J.L. and Lodge, D.M. 2001. Hybridization and introgression between introduced and resident Orconectes crayfishes. Conservation Biology 15: 1656-1666.

29) Perry, W.L., Feder, J.L., Dwyer, G. and Lodge, D.M. 2001. Hybrid zone dynamics and species replacement between Orconectes crayfishes in a northern Wisconsin lake. Evolution 55: 1153-1166.

(The work from the two Crayfish papers above was featured in Research News section of the journal Science, Jul. 18, 1997).

28) K.E. Filchak, Roethele, J.B. and Feder, J.L. 2000. Natural Selection and sympatric divergence in the apple maggot, Rhagoletis pomonella. Nature 407: 739-742.

27) Lewis, K.M., Feder, J.L., and Lamberti, G.A. 2000. Heterozygosity and fitness: No association in North American populations of zebra mussel. Malacologia 42:113-122.

26) Lewis, K.M., Feder, J.L., and Lamberti, G.A. 2000. Population genetics of the zebra mussel, Dreissena polymorpha: Local allozyme differentiation within Midwestern lakes and streams. Canadian Journal of Fisheries and Aquatic Sciences 57: 637-643.

25) Feder, J.L. and Filchak, K.E. 1999. It’s About Time: The Evidence for Host Plant-Mediated Selection in the Apple Maggot Fly, Rhagoletis pomonella, and its Implications for Fitness Trade-offs in Phytophagous Insects. Entomologia Experimentalis et Applicata 91:211-225.

24) Filchak, K.E., Feder, J.L., Roethele, J.B. and Stolz, U. 1999. A Field Test for Host-Plant Dependent Selection on larvae of the Apple Maggot Fly, Rhagoletis pomonella. Evolution 53: 187-200.

23) Feder, J.L., Williams, S.M., Berlocher, S.H., McPheron, B.A., and Bush, G.L. 1999. The population genetics of the apple maggot fly and the snowberry maggot: implications for models of sympatric speciation. Entomologia Experimentalis et Applicata 90: 9-24.

22) Frey, J.E., Feder, J.L., Palma, J., and Bush, G.L. 1998. Differences in the Electroantennal Responses of Apple- and Hawthorn-Infesting Races of Rhagoletis pomonella to Host Fruit Volatile Compounds. Chemoecology 8: 175-186.

21) Feder, J.L., S.H. Berlocher and S.B. Opp. 1998. Sympatric Host Race Formation and Speciation in Rhagoletis (Diptera: Tephritidae): A Tale of Two Species for Charles D. Pp. 408-441 In: Genetic Structure in Natural Insect Populations: Effects of Host Plants and Life History (S. Mopper and S. Strauss, eds.). Chapman and Hall. New York.

20) Feder, J.L. 1998. The apple maggot fly, Rhagoletis pomonella: Flies in the face of conventional wisdom about speciation? Pp. 130-144. In: Endless forms: Species and Speciation. (D. Howard and S.H. Berlocher, eds.) Oxford Univ. Press, Oxford, U.K.

(Research from the book chapter above was featured in Special News Report section of the journal Science, Sept. 13, 1996)

19) Feder, J.L., Stolz, U., Lewis, K.M., Perry, W., Roethele, J.B. and Rogers, A. 1997. The Effects of Winter Length on the Genetics of Apple and Hawthorn Races of Rhagoletis pomonella (Diptera: Tephritidae). Evolution 51:1862-1876.

18) Feder, J.L., Roethele, J.B., Wlazlo, B. and Berlocher, S.H. 1997. Selective maintenance of allozyme differences between sympatric host races of the apple maggot fly. Proceedings National Academy of Sciences U.S.A. 94:11417-11421.

17) Roethele, J.B., Feder, J.L., Berlocher, S.H. , Kreitman, M.E. and Lashkari, D. 1997. Towards a Molecular Genetic Linkage Map for the Apple Maggot Fly, Rhagoletis pomonella (Diptera:Tephritidae): A Comparison of Alternative Strategies. Annals Entomological Society of America 90: 470-479.

16) Feder, J.L. 1995. The Effects of Parasitoids on Sympatric Host Races of the Apple Maggot Fly, Rhagoletis pomonella (Diptera: Tephritidae). Ecology 76:801-813.

15) Feder, J.L., Reynolds, K., Go, W., and Wang, E.C. 1995. Intra- and Interspecific Competition and Host Race Formation in the Apple Maggot Fly, Rhagoletis pomonella (Diptera: Tephritidae). Oecologia 101:416-425.

14) Feder, J.L., Opp, S., Wlazlo, B., Reynolds, K., Go, W. and Spisak, S. 1994. Host fidelity is an effective pre-mating barrier between sympatric races of the Apple Maggot Fly. Proceedings National Academy of Sciences U.S.A. 91(17):7990-7994.

13) Feder, J.L., Hunt, T.A. and Bush, G.L. 1993. The Effects of Climate, Host Plant Phenology and Host Fidelity on the Genetics of Apple and Hawthorn Infesting Races of Rhagoletis pomonella. Entomologia Experimentalis et Applicata 69:117-135.

12) Berlocher, S.H., McPheron, B.A., Feder, J.L. and Bush, G.L. 1993. A revised phylogeny of the Rhagoletis pomonella (Diptera: Tephritidae) sibling species group. Annals of the Entomology Society of America 86(6):716-727.

11) Feder, J.L. and Bush, G.L. 1991. Genetic variation among apple and hawthorn host races of Rhagoletis pomonella (Diptera: Tephritidae) across an ecological transition zone in the mid-western United States. Entomologia Experimentalis et Applicata 59: 249-265.

10) Feder, J.L., Chilcote, C.A., and Bush, G.L. 1990. The Geographic Pattern of Genetic Differentiation between Host Associated Populations of Rhagoletis pomonella (Diptera: Tephritidae) in the eastern United States and Canada. Evolution 44:570-594.

9) Feder, J.L. and Bush, G.L. 1990. Regional, Local and Micro-geographic Allele Frequency Variation between Apple and Hawthorn Populations of Rhagoletis pomonella in western Michigan. Evolution 44:595-608.

8) Feder, J.L. and Bush, G.L. 1989. A Field Test of Differential Host Plant Usage between Two Sibling Species Rhagoletis pomonella Fruit Flies (Diptera: Tephritidae) and Its Consequences for Sympatric Models of Speciation. Evolution 43:1813-1819.

(Research from the seven papers above was featured in the Pulitzer Prize winning book “The Beak of the Finch” by Jonathan Weiner 1995 pg. 230-235)

7) Feder, J.L., Chilcote, C.A., and Bush, G.L. 1989. Inheritance and Linkage Relationships of Allozymes in the Apple Maggot Fly. Journal of Heredity 80: 277-283.

6) Bush, G.L., Feder, J.L., Berlocher, S.H., McPheron, B.A., Smith, D.C. and Chilcote, C.A. 1989. Sympatric Origins of R. pomonella. Nature 339: 346.

5) Feder, J.L. and Bush, G.L. 1989. Gene Frequency Clines for Host Races of Rhagoletis pomonella (Diptera: Tephritidae) in the Midwestern Unites States. Heredity 63:245-266.

4) Feder, J.L., Chilcote, C.A. and Bush, G.L. 1989. Are the Apple Maggot, Rhagoletis pomonella, and the Blueberry Maggot, R. mendax, Distinct Species? Implications for Sympatric Speciation. Entomologia Experimentalis et Applicata 51: 113-123.

3) Feder, J.L., Chilcote, C.A. and Bush, G.L. 1988. Genetic Differentiation between Sympatric Host Races of Rhagoletis pomonella. Nature 336: 61-64.

(Research from the above paper was featured in the News and Views section of Nature in Nov. 1988 and Scientific American)

2) Williams, S.M., Debry, R.W. and Feder, J.L. 1988. A Commentary on the Use of Ribosomal DNA in Systematic Studies. Systematic Zoology 37(1): 60-62.

1) Feder, J.L., Smith, M.H., Chesser, R.K., Godt, M.J.W. and Asbury, K. 1984. Biochemical Genetics of Mosquitofish. II. Demographic Differentiation of Populations in Thermally Altered Reservoir. Copeia 1984(1): 108-119.