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The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus.

Herman A, Brandvain Y, Weagley J, Jeffery WR, Keene AC, Kono TJY, Bilandžija H, Borowsky R, Espinasa L, O'Quin K, Ornelas-García CP, Yoshizawa M, Carlson B, Maldonado E, Gross JB, Cartwright RA, Rohner N, Warren WC, McGaugh SE.

Mol Ecol. 2018 Nov;27(22):4397-4416. doi: 10.1111/mec.14877. Epub 2018 Oct 16.


Progenitor targeting by adult stem cells in Ciona homeostasis, injury, and regeneration.

Jeffery WR.

Dev Biol. 2019 Apr 15;448(2):279-290. doi: 10.1016/j.ydbio.2018.09.005. Epub 2018 Sep 8.


Seeing a bright future for a blind fish.

Gore AV, Rohner N, Rétaux S, Jeffery WR.

Dev Biol. 2018 Sep 15;441(2):207-208. doi: 10.1016/j.ydbio.2018.08.004. No abstract available.


Maternal genetic effects in Astyanax cavefish development.

Ma L, Strickler AG, Parkhurst A, Yoshizawa M, Shi J, Jeffery WR.

Dev Biol. 2018 Sep 15;441(2):209-220. doi: 10.1016/j.ydbio.2018.07.014. Epub 2018 Jul 19.


An epigenetic mechanism for cavefish eye degeneration.

Gore AV, Tomins KA, Iben J, Ma L, Castranova D, Davis AE, Parkhurst A, Jeffery WR, Weinstein BM.

Nat Ecol Evol. 2018 Jul;2(7):1155-1160. doi: 10.1038/s41559-018-0569-4. Epub 2018 May 28.


Behavioural changes controlled by catecholaminergic systems explain recurrent loss of pigmentation in cavefish.

Bilandžija H, Abraham L, Ma L, Renner KJ, Jeffery WR.

Proc Biol Sci. 2018 May 16;285(1878). pii: 20180243. doi: 10.1098/rspb.2018.0243.


Neural Crest Transplantation Reveals Key Roles in the Evolution of Cavefish Development.

Yoshizawa M, Hixon E, Jeffery WR.

Integr Comp Biol. 2018 Sep 1;58(3):411-420. doi: 10.1093/icb/icy006.


Environmental DNA in subterranean biology: range extension and taxonomic implications for Proteus.

Gorički Š, Stanković D, Snoj A, Kuntner M, Jeffery WR, Trontelj P, Pavićević M, Grizelj Z, Năpăruş-Aljančič M, Aljančič G.

Sci Rep. 2017 Mar 27;7:45054. doi: 10.1038/srep45054.


Genome Editing in Astyanax mexicanus Using Transcription Activator-like Effector Nucleases (TALENs).

Kowalko JE, Ma L, Jeffery WR.

J Vis Exp. 2016 Jun 20;(112). doi: 10.3791/54113.


The Comparative Organismal Approach in Evolutionary Developmental Biology: Insights from Ascidians and Cavefish.

Jeffery WR.

Curr Top Dev Biol. 2016;116:489-500. doi: 10.1016/bs.ctdb.2015.10.006. Epub 2016 Jan 7. Review.


Complex Evolutionary and Genetic Patterns Characterize the Loss of Scleral Ossification in the Blind Cavefish Astyanax mexicanus.

O'Quin KE, Doshi P, Lyon A, Hoenemeyer E, Yoshizawa M, Jeffery WR.

PLoS One. 2015 Dec 9;10(12):e0142208. doi: 10.1371/journal.pone.0142208. eCollection 2015.


Regeneration, Stem Cells, and Aging in the Tunicate Ciona: Insights from the Oral Siphon.

Jeffery WR.

Int Rev Cell Mol Biol. 2015;319:255-82. doi: 10.1016/bs.ircmb.2015.06.005. Epub 2015 Jul 17. Review.


Evolution of the chordate regeneration blastema: Differential gene expression and conserved role of notch signaling during siphon regeneration in the ascidian Ciona.

Hamada M, Goricki S, Byerly MS, Satoh N, Jeffery WR.

Dev Biol. 2015 Sep 15;405(2):304-15. doi: 10.1016/j.ydbio.2015.07.017. Epub 2015 Jul 20.


Genome editing using TALENs in blind Mexican Cavefish, Astyanax mexicanus.

Ma L, Jeffery WR, Essner JJ, Kowalko JE.

PLoS One. 2015 Mar 16;10(3):e0119370. doi: 10.1371/journal.pone.0119370. eCollection 2015.


Distinct genetic architecture underlies the emergence of sleep loss and prey-seeking behavior in the Mexican cavefish.

Yoshizawa M, Robinson BG, Duboué ER, Masek P, Jaggard JB, O'Quin KE, Borowsky RL, Jeffery WR, Keene AC.

BMC Biol. 2015 Feb 20;13:15. doi: 10.1186/s12915-015-0119-3.


The cavefish genome reveals candidate genes for eye loss.

McGaugh SE, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, Hinaux H, Jeffery WR, Keene A, Ma L, Minx P, Murphy D, O'Quin KE, Rétaux S, Rohner N, Searle SM, Stahl BA, Tabin C, Volff JN, Yoshizawa M, Warren WC.

Nat Commun. 2014 Oct 20;5:5307. doi: 10.1038/ncomms6307.


The role of a lens survival pathway including sox2 and αA-crystallin in the evolution of cavefish eye degeneration.

Ma L, Parkhurst A, Jeffery WR.

Evodevo. 2014 Aug 28;5:28. doi: 10.1186/2041-9139-5-28. eCollection 2014.


Closing the wounds: one hundred and twenty five years of regenerative biology in the ascidian Ciona intestinalis.

Jeffery WR.

Genesis. 2015 Jan;53(1):48-65. doi: 10.1002/dvg.22799. Epub 2014 Jul 7. Review.


Enhanced prey capture skills in Astyanax cavefish larvae are independent from eye loss.

Espinasa L, Bibliowicz J, Jeffery WR, Rétaux S.

Evodevo. 2014 Oct 3;5:35. doi: 10.1186/2041-9139-5-35. eCollection 2014.


Cryptic variation in morphological evolution: HSP90 as a capacitor for loss of eyes in cavefish.

Rohner N, Jarosz DF, Kowalko JE, Yoshizawa M, Jeffery WR, Borowsky RL, Lindquist S, Tabin CJ.

Science. 2013 Dec 13;342(6164):1372-5. doi: 10.1126/science.1240276.


A potential benefit of albinism in Astyanax cavefish: downregulation of the oca2 gene increases tyrosine and catecholamine levels as an alternative to melanin synthesis.

Bilandžija H, Ma L, Parkhurst A, Jeffery WR.

PLoS One. 2013 Nov 25;8(11):e80823. doi: 10.1371/journal.pone.0080823. eCollection 2013.


The sensitivity of lateral line receptors and their role in the behavior of Mexican blind cavefish (Astyanax mexicanus).

Yoshizawa M, Jeffery WR, van Netten SM, McHenry MJ.

J Exp Biol. 2014 Mar 15;217(Pt 6):886-95. doi: 10.1242/jeb.094599. Epub 2013 Nov 21.


Convergence in feeding posture occurs through different genetic loci in independently evolved cave populations of Astyanax mexicanus.

Kowalko JE, Rohner N, Linden TA, Rompani SB, Warren WC, Borowsky R, Tabin CJ, Jeffery WR, Yoshizawa M.

Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16933-8. doi: 10.1073/pnas.1317192110. Epub 2013 Oct 1.


Loss of schooling behavior in cavefish through sight-dependent and sight-independent mechanisms.

Kowalko JE, Rohner N, Rompani SB, Peterson BK, Linden TA, Yoshizawa M, Kay EH, Weber J, Hoekstra HE, Jeffery WR, Borowsky R, Tabin CJ.

Curr Biol. 2013 Oct 7;23(19):1874-83. doi: 10.1016/j.cub.2013.07.056. Epub 2013 Sep 12.


QTL clustering as a mechanism for rapid multi-trait evolution.

Yoshizawa M, O'Quin KE, Jeffery WR.

Commun Integr Biol. 2013 Jul 1;6(4):e24548. doi: 10.4161/cib.24548. Epub 2013 Apr 12.


Evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish: response to Borowsky (2013).

Yoshizawa M, O'Quin KE, Jeffery WR.

BMC Biol. 2013 Jul 11;11:82. doi: 10.1186/1741-7007-11-82.


Evolution and development in cave animals: from fish to crustaceans.

Protas M, Jeffery WR.

Wiley Interdiscip Rev Dev Biol. 2012 Nov-Dec;1(6):823-45. doi: 10.1002/wdev.61. Review.


Quantitative genetic analysis of retinal degeneration in the blind cavefish Astyanax mexicanus.

O'Quin KE, Yoshizawa M, Doshi P, Jeffery WR.

PLoS One. 2013;8(2):e57281. doi: 10.1371/journal.pone.0057281. Epub 2013 Feb 20.


De novo sequencing of Astyanax mexicanus surface fish and Pachón cavefish transcriptomes reveals enrichment of mutations in cavefish putative eye genes.

Hinaux H, Poulain J, Da Silva C, Noirot C, Jeffery WR, Casane D, Rétaux S.

PLoS One. 2013;8(1):e53553. doi: 10.1371/journal.pone.0053553. Epub 2013 Jan 9.


Evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish.

Yoshizawa M, Yamamoto Y, O'Quin KE, Jeffery WR.

BMC Biol. 2012 Dec 27;10:108. doi: 10.1186/1741-7007-10-108.


Evolution of albinism in cave planthoppers by a convergent defect in the first step of melanin biosynthesis.

Bilandžija H, Cetković H, Jeffery WR.

Evol Dev. 2012 Mar-Apr;14(2):196-203. doi: 10.1111/j.1525-142X.2012.00535.x.


Parental genetic effects in a cavefish adaptive behavior explain disparity between nuclear and mitochondrial DNA.

Yoshizawa M, Ashida G, Jeffery WR.

Evolution. 2012 Sep;66(9):2975-82. doi: 10.1111/j.1558-5646.2012.01651.x. Epub 2012 May 7.


Siphon regeneration capacity is compromised during aging in the ascidian Ciona intestinalis.

Jeffery WR.

Mech Ageing Dev. 2012 Sep-Oct;133(9-10):629-36. doi: 10.1016/j.mad.2012.08.003. Epub 2012 Aug 19.


Evolution of space dependent growth in the teleost Astyanax mexicanus.

Gallo ND, Jeffery WR.

PLoS One. 2012;7(8):e41443. doi: 10.1371/journal.pone.0041443. Epub 2012 Aug 1.


Evolutionary tuning of an adaptive behavior requires enhancement of the neuromast sensory system.

Yoshizawa M, Jeffery WR.

Commun Integr Biol. 2011 Jan;4(1):89-91. doi: 10.4161/cib.4.1.14118.


Evolution of a behavioral shift mediated by superficial neuromasts helps cavefish find food in darkness.

Yoshizawa M, Goricki S, Soares D, Jeffery WR.

Curr Biol. 2010 Sep 28;20(18):1631-6. doi: 10.1016/j.cub.2010.07.017. Epub 2010 Aug 12.


Pleiotropy and eye degeneration in cavefish.

Jeffery WR.

Heredity (Edinb). 2010 Nov;105(5):495-6. doi: 10.1038/hdy.2010.7. Epub 2010 Feb 24. No abstract available.


Regeneration of oral siphon pigment organs in the ascidian Ciona intestinalis.

Auger H, Sasakura Y, Joly JS, Jeffery WR.

Dev Biol. 2010 Mar 15;339(2):374-89. doi: 10.1016/j.ydbio.2009.12.040. Epub 2010 Jan 6.


Regressive evolution in Astyanax cavefish.

Jeffery WR.

Annu Rev Genet. 2009;43:25-47. doi: 10.1146/annurev-genet-102108-134216. Review.


Chapter 8. Evolution and development in the cavefish Astyanax.

Jeffery WR.

Curr Top Dev Biol. 2009;86:191-221. doi: 10.1016/S0070-2153(09)01008-4. Review.


Current topics in developmental biology. Evolution and development. Preface.

Jeffery WR.

Curr Top Dev Biol. 2009;86:xi-xii. doi: 10.1016/S0070-2153(09)01012-6. No abstract available.


Pleiotropic functions of embryonic sonic hedgehog expression link jaw and taste bud amplification with eye loss during cavefish evolution.

Yamamoto Y, Byerly MS, Jackman WR, Jeffery WR.

Dev Biol. 2009 Jun 1;330(1):200-11. doi: 10.1016/j.ydbio.2009.03.003. Epub 2009 Mar 11.


Differentially expressed genes identified by cross-species microarray in the blind cavefish Astyanax.

Strickler AG, Jeffery WR.

Integr Zool. 2009 Mar;4(1):99-109. doi: 10.1111/j.1749-4877.2008.00139.x.


Synteny and candidate gene prediction using an anchored linkage map of Astyanax mexicanus.

Gross JB, Protas M, Conrad M, Scheid PE, Vidal O, Jeffery WR, Borowsky R, Tabin CJ.

Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20106-11. doi: 10.1073/pnas.0806238105. Epub 2008 Dec 22.


Trunk lateral cells are neural crest-like cells in the ascidian Ciona intestinalis: insights into the ancestry and evolution of the neural crest.

Jeffery WR, Chiba T, Krajka FR, Deyts C, Satoh N, Joly JS.

Dev Biol. 2008 Dec 1;324(1):152-60. doi: 10.1016/j.ydbio.2008.08.022. Epub 2008 Sep 3.


Emerging model systems in evo-devo: cavefish and microevolution of development.

Jeffery WR.

Evol Dev. 2008 May-Jun;10(3):265-72. doi: 10.1111/j.1525-142X.2008.00235.x.


Special feature--roundtable discussion. Fish models for studying adaptive evolution and speciation.

Kocher TD, Jeffery WR, Parichy DM, Peichel CL, Streelman JT, Thorgaard GH.

Zebrafish. 2005;2(3):147-56. doi: 10.1089/zeb.2005.2.147.


Shadow response in the blind cavefish Astyanax reveals conservation of a functional pineal eye.

Yoshizawa M, Jeffery WR.

J Exp Biol. 2008 Feb;211(Pt 3):292-9. doi: 10.1242/jeb.012864.

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