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Genomic transitions during host race and species formation.

Doellman MM, Feder JL.

Curr Opin Insect Sci. 2019 Feb;31:84-92. doi: 10.1016/j.cois.2018.11.006. Epub 2018 Nov 26. Review.


Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies.

Doellman MM, Egan SP, Ragland GJ, Meyers PJ, Hood GR, Powell THQ, Lazorchak P, Hahn DA, Berlocher SH, Nosil P, Feder JL.

Ecol Evol. 2018 Dec 14;9(1):393-409. doi: 10.1002/ece3.4758. eCollection 2019 Jan.


Target-Enriched Endosymbiont Sequencing (TEEseq): A New High-Throughput Sequencing Approach Applied to the Comprehensive Characterization of Endosymbionts.

Schuler H, Lopez JA, Doellman MM, Hood GR, Egan SP, Feder JL.

Methods Mol Biol. 2019;1858:195-212. doi: 10.1007/978-1-4939-8775-7_14.


Pleistocene climate cycling and host plant association shaped the demographic history of the bark beetle Pityogenes chalcographus.

Schebeck M, Dowle EJ, Schuler H, Avtzis DN, Bertheau C, Feder JL, Ragland GJ, Stauffer C.

Sci Rep. 2018 Sep 21;8(1):14207. doi: 10.1038/s41598-018-32617-6.


Identification of a New Blend of Host Fruit Volatiles from Red Downy Hawthorn, Crataegus mollis, Attractive to Rhagoletis pomonella Flies from the Northeastern United States.

Cha DH, Powell THQ, Feder JL, Linn CE Jr.

J Chem Ecol. 2018 Aug;44(7-8):671-680. doi: 10.1007/s10886-018-0977-6. Epub 2018 Jun 20.


Transitions from Single- to Multi-Locus Processes during Speciation with Gene Flow.

Schilling MP, Mullen SP, Kronforst M, Safran RJ, Nosil P, Feder JL, Gompert Z, Flaxman SM.

Genes (Basel). 2018 May 24;9(6). pii: E274. doi: 10.3390/genes9060274.


Genomic Differentiation during Speciation-with-Gene-Flow: Comparing Geographic and Host-Related Variation in Divergent Life History Adaptation in Rhagoletis pomonella.

Doellman MM, Ragland GJ, Hood GR, Meyers PJ, Egan SP, Powell THQ, Lazorchak P, Glover MM, Tait C, Schuler H, Hahn DA, Berlocher SH, Smith JJ, Nosil P, Feder JL.

Genes (Basel). 2018 May 18;9(5). pii: E262. doi: 10.3390/genes9050262.


Cryptic Species - More Than Terminological Chaos: A Reply to Heethoff.

Struck TH, Feder JL, Bendiksby M, Birkeland S, Cerca J, Gusarov VI, Kistenich S, Larsson KH, Liow LH, Nowak MD, Stedje B, Bachmann L, Dimitrov D.

Trends Ecol Evol. 2018 May;33(5):310-312. doi: 10.1016/j.tree.2018.02.008. Epub 2018 Mar 24. No abstract available.


Natural selection and the predictability of evolution in Timema stick insects.

Nosil P, Villoutreix R, de Carvalho CF, Farkas TE, Soria-Carrasco V, Feder JL, Crespi BJ, Gompert Z.

Science. 2018 Feb 16;359(6377):765-770. doi: 10.1126/science.aap9125.


Finding Evolutionary Processes Hidden in Cryptic Species.

Struck TH, Feder JL, Bendiksby M, Birkeland S, Cerca J, Gusarov VI, Kistenich S, Larsson KH, Liow LH, Nowak MD, Stedje B, Bachmann L, Dimitrov D.

Trends Ecol Evol. 2018 Mar;33(3):153-163. doi: 10.1016/j.tree.2017.11.007. Epub 2017 Dec 11.


Genetic Evidence for the Introduction of Rhagoletis pomonella (Diptera: Tephritidae) into the Northwestern United States.

Sim SB, Doellman MM, Hood GR, Yee WL, Powell THQ, Schwarz D, Goughnour RB, Egan SP, Jean GS, Smith JJ, Arcella TE, Dzurisin JDK, Feder JL.

J Econ Entomol. 2017 Dec 5;110(6):2599-2608. doi: 10.1093/jee/tox248.


Comparative Responses of Rhagoletis zephyria and Rhagoletis pomonella (Diptera: Tephritidae) to Commercial and Experimental Sticky Traps and Odors in Washington State.

Yee WL, Goughnour RB, Feder JL, Linn CE Jr, Cha DH.

Environ Entomol. 2017 Dec 8;46(6):1351-1358. doi: 10.1093/ee/nvx130.


Tipping points in the dynamics of speciation.

Nosil P, Feder JL, Flaxman SM, Gompert Z.

Nat Ecol Evol. 2017 Jan 24;1(2):1. doi: 10.1038/s41559-016-0001.


Barnacles, barrier loci and the systematic building of species.

Feder JL, Nosil P, Gompert Z, Flaxman SM, Schilling MP.

J Evol Biol. 2017 Aug;30(8):1494-1497. doi: 10.1111/jeb.13105. No abstract available.


A test of genomic modularity among life-history adaptations promoting speciation with gene flow.

Ragland GJ, Doellman MM, Meyers PJ, Hood GR, Egan SP, Powell THQ, Hahn DA, Nosil P, Feder JL.

Mol Ecol. 2017 Aug;26(15):3926-3942. doi: 10.1111/mec.14178. Epub 2017 Jun 24.


Identification of Host Fruit Volatiles from Snowberry (Symphoricarpos albus), Attractive to Rhagoletis zephyria Flies from the Western United States.

Cha DH, Olsson SB, Yee WL, Goughnour RB, Hood GR, Mattsson M, Schwarz D, Feder JL, Linn CE Jr.

J Chem Ecol. 2017 Feb;43(2):188-197. doi: 10.1007/s10886-016-0814-8. Epub 2017 Jan 11.


Sensory specificity and speciation: a potential neuronal pathway for host fruit odour discrimination in Rhagoletis pomonella.

Tait C, Batra S, Ramaswamy SS, Feder JL, Olsson SB.

Proc Biol Sci. 2016 Dec 28;283(1845). pii: 20162101. doi: 10.1098/rspb.2016.2101.


Multilocus approaches for the measurement of selection on correlated genetic loci.

Gompert Z, Egan SP, Barrett RD, Feder JL, Nosil P.

Mol Ecol. 2017 Jan;26(1):365-382. doi: 10.1111/mec.13867. Epub 2016 Oct 27.


Divergence of the diapause transcriptome in apple maggot flies: winter regulation and post-winter transcriptional repression.

Meyers PJ, Powell TH, Walden KK, Schieferecke AJ, Feder JL, Hahn DA, Robertson HM, Berlocher SH, Ragland GJ.

J Exp Biol. 2016 Sep 1;219(Pt 17):2613-22. doi: 10.1242/jeb.140566. Epub 2016 Jun 16.


Sequential divergence and the multiplicative origin of community diversity.

Hood GR, Forbes AA, Powell TH, Egan SP, Hamerlinck G, Smith JJ, Feder JL.

Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):E5980-9. doi: 10.1073/pnas.1424717112. Epub 2015 Oct 23.


Hybridization and the spread of the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae), in the northwestern United States.

Arcella T, Hood GR, Powell TH, Sim SB, Yee WL, Schwarz D, Egan SP, Goughnour RB, Smith JJ, Feder JL.

Evol Appl. 2015 Sep;8(8):834-46. doi: 10.1111/eva.12298. Epub 2015 Aug 13.


Chilling and Host Plant/Site-Associated Eclosion Times of Western Cherry Fruit Fly (Diptera: Tephritidae) and a Host-Specific Parasitoid.

Yee WL, Goughnour RB, Hood GR, Forbes AA, Feder JL.

Environ Entomol. 2015 Aug;44(4):1029-42. doi: 10.1093/ee/nvv097. Epub 2015 Jul 1.


Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow.

Egan SP, Ragland GJ, Assour L, Powell TH, Hood GR, Emrich S, Nosil P, Feder JL.

Ecol Lett. 2015 Aug;18(8):817-25. doi: 10.1111/ele.12460. Epub 2015 Jun 15.


Differences in performance and transcriptome-wide gene expression associated with Rhagoletis (Diptera: Tephritidae) larvae feeding in alternate host fruit environments.

Ragland GJ, Almskaar K, Vertacnik KL, Gough HM, Feder JL, Hahn DA, Schwarz D.

Mol Ecol. 2015 Jun;24(11):2759-76. doi: 10.1111/mec.13191. Epub 2015 May 14.


Rapid molecular detection of invasive species in ballast and harbor water by integrating environmental DNA and light transmission spectroscopy.

Egan SP, Grey E, Olds B, Feder JL, Ruggiero ST, Tanner CE, Lodge DM.

Environ Sci Technol. 2015 Apr 7;49(7):4113-21. doi: 10.1021/es5058659. Epub 2015 Mar 13.


Assessing when chromosomal rearrangements affect the dynamics of speciation: implications from computer simulations.

Feder JL, Nosil P, Flaxman SM.

Front Genet. 2014 Aug 26;5:295. doi: 10.3389/fgene.2014.00295. eCollection 2014.


Genome-wide congealing and rapid transitions across the speciation continuum during speciation with gene flow.

Feder JL, Nosil P, Wacholder AC, Egan SP, Berlocher SH, Flaxman SM.

J Hered. 2014;105 Suppl 1:810-20. doi: 10.1093/jhered/esu038.


Ammonium carbonate is more attractive than apple and hawthorn fruit volatile lures to Rhagoletis pomonella (Diptera: Tephritidae) in Washington State.

Yee WL, Nash MJ, Goughnour RB, Cha DH, Linn CE, Feder JL.

Environ Entomol. 2014 Aug;43(4):957-68. doi: 10.1603/EN14038. Epub 2014 Jun 9.


Stick insect genomes reveal natural selection's role in parallel speciation.

Soria-Carrasco V, Gompert Z, Comeault AA, Farkas TE, Parchman TL, Johnston JS, Buerkle CA, Feder JL, Bast J, Schwander T, Egan SP, Crespi BJ, Nosil P.

Science. 2014 May 16;344(6185):738-42. doi: 10.1126/science.1252136. Epub 2014 May 15.


Theoretical models of the influence of genomic architecture on the dynamics of speciation.

Flaxman SM, Wacholder AC, Feder JL, Nosil P.

Mol Ecol. 2014 Aug;23(16):4074-88. doi: 10.1111/mec.12750. Epub 2014 May 9.


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.


Experimental evidence for ecological selection on genome variation in the wild.

Gompert Z, Comeault AA, Farkas TE, Feder JL, Parchman TL, Buerkle CA, Nosil P.

Ecol Lett. 2014 Mar;17(3):369-79. doi: 10.1111/ele.12238. Epub 2013 Dec 19.


Ecological adaptation and reproductive isolation in sympatry: genetic and phenotypic evidence for native host races of Rhagoletis pomonella.

Powell TH, Forbes AA, Hood GR, Feder JL.

Mol Ecol. 2014 Feb;23(3):688-704. doi: 10.1111/mec.12635.


Molecular species identification of cryptic apple and snowberry maggots (Diptera: Tephritidae) in western and central Washington.

Green E, Almskaar K, Sim SB, Arcella T, Yee WL, Feder JL, Schwarz D.

Environ Entomol. 2013 Oct;42(5):1100-9. doi: 10.1603/EN13038.


Genetic hitchhiking and the dynamic buildup of genomic divergence during speciation with gene flow.

Flaxman SM, Feder JL, Nosil P.

Evolution. 2013 Sep;67(9):2577-91. doi: 10.1111/evo.12055. Epub 2013 Feb 12.


Genetic divergence along the speciation continuum: the transition from host race to species in rhagoletis (Diptera: tephritidae).

Powell TH, Hood GR, Murphy MO, Heilveil JS, Berlocher SH, Nosil P, Feder JL.

Evolution. 2013 Sep;67(9):2561-76. doi: 10.1111/evo.12209. Epub 2013 Jul 29.


Genome evolution and speciation: toward quantitative descriptions of pattern and process.

Nosil P, Feder JL.

Evolution. 2013 Sep;67(9):2461-7. doi: 10.1111/evo.12191. Epub 2013 Jul 4. Review.


Evidence for a recent horizontal transmission and spatial spread of Wolbachia from endemic Rhagoletis cerasi (Diptera: Tephritidae) to invasive Rhagoletis cingulata in Europe.

Schuler H, Bertheau C, Egan SP, Feder JL, Riegler M, Schlick-Steiner BC, Steiner FM, Johannesen J, Kern P, Tuba K, Lakatos F, Köppler K, Arthofer W, Stauffer C.

Mol Ecol. 2013 Aug;22(15):4101-11. doi: 10.1111/mec.12362. Epub 2013 Jul 12.


Abundance of apple maggot, Rhagoletis pomonella, across different areas in central Washington, with special reference to black-fruited hawthorns.

Yee WL, Klaus MW, Cha DH, Linn CE Jr, Goughnour RB, Feder JL.

J Insect Sci. 2012;12:124. doi: 10.1673/031.012.12401.


Hybridization and the build-up of genomic divergence during speciation.

Feder JL, Flaxman SM, Egan SP, Nosil P.

J Evol Biol. 2013 Feb;26(2):261-6. doi: 10.1111/jeb.12009. No abstract available.


Patterns of genomic differentiation between ecologically differentiated M and S forms of Anopheles gambiae in West and Central Africa.

Reidenbach KR, Neafsey DE, Costantini C, Sagnon N, Simard F, Ragland GJ, Egan SP, Feder JL, Muskavitch MA, Besansky NJ.

Genome Biol Evol. 2012;4(12):1202-12. doi: 10.1093/gbe/evs095.


Spatially explicit models of divergence and genome hitchhiking.

Flaxman SM, Feder JL, Nosil P.

J Evol Biol. 2012 Dec;25(12):2633-50. doi: 10.1111/jeb.12013. Epub 2012 Oct 30.


Behavioral evidence for fruit odor discrimination and sympatric host races of Rhagoletis pomonella flies in the Western United States.

Linn CE Jr, Yee WL, Sim SB, Cha DH, Powell TH, Goughnour RB, Feder JL.

Evolution. 2012 Nov;66(11):3632-41. doi: 10.1111/j.1558-5646.2012.01719.x. Epub 2012 Aug 10.


DNA-based species detection capabilities using laser transmission spectroscopy.

Mahon AR, Barnes MA, Li F, Egan SP, Tanner CE, Ruggiero ST, Feder JL, Lodge DM.

J R Soc Interface. 2013 Jan 6;10(78):20120637. doi: 10.1098/rsif.2012.0637. Epub 2012 Nov 8.


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.

Powell TH, Cha DH, Linn CE Jr, Feder JL.

Evolution. 2012 Sep;66(9):2739-56. doi: 10.1111/j.1558-5646.2012.01625.x. Epub 2012 Apr 16.


Do highly divergent loci reside in genomic regions affecting reproductive isolation? A test using next-generation sequence data in Timema stick insects.

Nosil P, Parchman TL, Feder JL, Gompert Z.

BMC Evol Biol. 2012 Aug 31;12:164. doi: 10.1186/1471-2148-12-164.


Genomic consequences of multiple speciation processes in a stick insect.

Nosil P, Gompert Z, Farkas TE, Comeault AA, Feder JL, Buerkle CA, Parchman TL.

Proc Biol Sci. 2012 Dec 22;279(1749):5058-65. doi: 10.1098/rspb.2012.0813. Epub 2012 Jun 13.


Widespread yet heterogeneous genomic divergence.

Nosil P, Feder JL.

Mol Ecol. 2012 Jun;21(12):2829-32. doi: 10.1111/j.1365-294X.2012.05580.x.


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