Publications

Letelier J, Naranjo S, Sospedra I, Lopez-Rios J, Martinez-Morales JR, Shubin N, Gomez-Skarmeta JL. The Shh/Gli3 gene regulatory network precedes the origin of paired fins and reveals the deep homology between distal fins and digits. PNAS. 2021 Nov 16; 118 (46) e2100575118.

Mika K, Okamoto AS, Shubin NH, Mark Welch DB. Bacterial community dynamics during embryonic development of the little skate (Leucoraja erinacea). Animal microbiome. 2021 Dec;3(1):1-4.

Nakamura T, Schneider I, Shubin NH. Evolution: The deep genetic roots of tetrapod-specific traits. Current Biology. 2021 May 24;31(10):R467-9.

Ali S, Arif I, Iqbal A, Hussain I, Abrar M, Khan MR, Shubin N, Abbasi AA. Comparative genomic analysis of human GLI2 locus using slowly evolving fish revealed the ancestral gnathostome set of early developmental enhancers. Developmental Dynamics. 2021 May;250(5):669-83.

Lemberg JB, Daeschler EB, Shubin NH. The feeding system of Tiktaalik roseae: an intermediate between suction feeding and biting. Proc Natl Acad Sci U S A. 2021 Feb 16;118(7):e2016421118. doi: 10.1073/pnas.2016421118. PMID: 33526593; PMCID: PMC7896305.

Verissimo KM, Perez LN, Dragalzew AC, Senevirathne G, Darnet S, Barroso Mendes WR, Ariel dos Santos Neves C, Monteiro dos Santos E, Nazare de Sousa Moraes C, Elewa A, Shubin N, Fröbisch NB, de Freitas Sousa J, Schneider I. Salamander-like tail regeneration in the West African lungfish. Proceedings of the Royal Society B. 2020 Sep 30;287(1935):20192939.

Senevirathne G, Baumgart S, Shubin N, Hanken J, Shubin NH. Ontogeny of the anuran urostyle and the developmental context of evolutionary novelty. Proc Natl Acad Sci U S A. 2020 Feb 11;117(6):3034-3044. doi: 10.1073/pnas.1917506117. Epub 2020 Jan 27. PMID: 31988131; PMCID: PMC7022158.

Stewart TA, Lemberg JB, Taft NK, Yoo I, Daeschler EB, Shubin NH. Fin ray patterns at the fin-to-limb transition. Proc Natl Acad Sci U S A. 2020 Jan 21;117(3):1612-1620. doi: 10.1073/pnas.1915983117. Epub 2019 Dec 30. PMID: 31888998; PMCID: PMC6983361. 

Turner N, Mikalauskaite D, Barone K, Flaherty K, Senevirathne G, Adachi N, Shubin NH, Nakamura T. The evolutionary origins and diversity of the neuromuscular system of paired appendages in batoids. Proc Biol Sci. 2019 Nov 6;286(1914):20191571. doi: 10.1098/rspb.2019.1571. Epub 2019 Oct 30. PMID: 31662089; PMCID: PMC6842844.

Lemberg JB, Shubin NH, Westneat MW. Feeding kinematics and morphology of the alligator gar (Atractosteus spatula, Lacépède, 1803). J Morphol. 2019 Oct;280(10):1548-1570. doi: 10.1002/jmor.21048. Epub 2019 Aug 6. PMID: 31385619.

Zhou T, Li N, Jin Y, Zeng Q, Prabowo W, Liu Y, Tian C, Bao L, Liu S, Yuan Z, Fu Q, Gao S, Gao D, Dunham R, Shubin NH, Liu Z. Chemokine C-C motif ligand 33 is a key regulator of teleost fish barbel development. Proc Natl Acad Sci U S A. 2018 May 29;115(22):E5018-E5027. doi: 10.1073/pnas.1718603115. Epub 2018 May 14. PMID: 29760055; PMCID: PMC5984497.

Letelier J, de la Calle-Mustienes E, Pieretti J, Naranjo S, Maeso I, Nakamura T, Pascual-Anaya J, Shubin NH, Schneider I, Martinez-Morales JR, Gómez-Skarmeta JL. A conserved Shh cis-regulatory module highlights a common developmental origin of unpaired and paired fins. Nat Genet. 2018 Apr;50(4):504-509. doi: 10.1038/s41588-018-0080-5. Epub 2018 Mar 19. PMID: 29556077; PMCID: PMC5896732.

Shubin N. Gene regulatory networks and network models in development and evolution. Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):5782-5783. doi: 10.1073/pnas.1610618114. PMID: 28584088; PMCID: PMC5468640.

Davies TG, Rahman IA, Lautenschlager S, Cunningham JA, Asher RJ, Barrett PM, Bates KT, Bengtson S, Benson RB, Boyer DM, Braga J, Bright JA, Claessens LP, Cox PG, Dong XP, Evans AR, Falkingham PL, Friedman M, Garwood RJ, Goswami A, Hutchinson JR, Jeffery NS, Johanson Z, Lebrun R, Martínez-Pérez C, Marugán-Lobón J, O’Higgins PM, Metscher B, Orliac M, Rowe TB, Rücklin M, Sánchez-Villagra MR, Shubin NH, Smith SY, Starck JM, Stringer C, Summers AP, Sutton MD, Walsh SA, Weisbecker V, Witmer LM, Wroe S, Yin Z, Rayfield EJ, Donoghue PC. Open data and digital morphology. Proc Biol Sci. 2017 Apr 12;284(1852):20170194. doi: 10.1098/rspb.2017.0194. Epub 2017 Apr 12. PMID: 28404779; PMCID: PMC5394671.

Nakamura T, Gehrke AR, Lemberg J, Szymaszek J, Shubin NH. Digits and fin rays share common developmental histories. Nature. 2016 Sep 8;537(7619):225-228. doi: 10.1038/nature19322. Epub 2016 Aug 17. PMID: 27533041; PMCID: PMC5161576.

Adachi N, Robinson M, Goolsbee A, Shubin NH. Regulatory evolution of Tbx5 and the origin of paired appendages. Proc Natl Acad Sci U S A. 2016 Sep 6;113(36):10115-20. doi: 10.1073/pnas.1609997113. Epub 2016 Aug 8. PMID: 27503876; PMCID: PMC5018757.

Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alfo Ldi J, Lindblad-Toh K, Postlethwait JH. Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet. 2016 May 27;48(6):700. doi: 10.1038/ng0616-700c. PMID: 27230688.

Gehrke AR, Shubin NH. Cis-regulatory programs in the development and evolution of vertebrate paired appendages. Semin Cell Dev Biol. 2016 Sep;57:31-39. doi: 10.1016/j.semcdb.2016.01.015. Epub 2016 Jan 16. PMID: 26783722; PMCID: PMC5360378.

Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, Postlethwait JH. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet. 2016 Apr;48(4):427-37. doi: 10.1038/ng.3526. Epub 2016 Mar 7. PMID: 26950095; PMCID: PMC4817229.

Nakamura T, Klomp J, Pieretti J, Schneider I, Gehrke AR, Shubin NH. Molecular mechanisms underlying the exceptional adaptations of batoid fins. Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):15940-5. doi: 10.1073/pnas.1521818112. Epub 2015 Dec 7. PMID: 26644578; PMCID: PMC4702995.

Luo ZX, Gatesy SM, Jenkins FA Jr, Amaral WW, Shubin NH. Mandibular and dental characteristics of Late Triassic mammaliaform Haramiyavia and their ramifications for basal mammal evolution. Proc Natl Acad Sci U S A. 2015 Dec 22;112(51):E7101-9. doi: 10.1073/pnas.1519387112. Epub 2015 Nov 16. PMID: 26630008; PMCID: PMC4697399.

Pieretti J, Gehrke AR, Schneider I, Adachi N, Nakamura T, Shubin NH. Organogenesis in deep time: A problem in genomics, development, and paleontology. Proc Natl Acad Sci U S A. 2015 Apr 21;112(16):4871-6. doi: 10.1073/pnas.1403665112. PMID: 25901307; PMCID: PMC4413340.

Jablonski D, Shubin NH. The future of the fossil record: Paleontology in the 21st century. Proc Natl Acad Sci U S A. 2015 Apr 21;112(16):4852-8. doi: 10.1073/pnas.1505146112. PMID: 25901304; PMCID: PMC4413349.

Gehrke AR, Schneider I, de la Calle-Mustienes E, Tena JJ, Gomez-Marin C, Chandran M, Nakamura T, Braasch I, Postlethwait JH, Gómez-Skarmeta JL, Shubin NH. Deep conservation of wrist and digit enhancers in fish. Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):803-8. doi: 10.1073/pnas.1420208112. Epub 2014 Dec 22. PMID: 25535365; PMCID: PMC4311833.

Shubin N. QnAs with Neil Shubin. Proc Natl Acad Sci U S A. 2014 Jan 21;111(3):881-2. doi: 10.1073/pnas.1321499110. Epub 2014 Jan 15. PMID: 24429347; PMCID: PMC3903218.

Shubin NH, Daeschler EB, Jenkins FA Jr. Pelvic girdle and fin of Tiktaalik roseae. Proc Natl Acad Sci U S A. 2014 Jan 21;111(3):893-9. doi: 10.1073/pnas.1322559111. Epub 2014 Jan 13. PMID: 24449831; PMCID: PMC3903263.

Schneider I, Shubin NH. The origin of the tetrapod limb: from expeditions to enhancers. Trends Genet. 2013 Jul;29(7):419-26. doi: 10.1016/j.tig.2013.01.012. Epub 2013 Feb 21. PMID: 23434323.

Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K. The African coelacanth genome provides insights into tetrapod evolution. Nature. 2013 Apr 18;496(7445):311-6. doi: 10.1038/nature12027. PMID: 23598338; PMCID: PMC3633110.

Mayer GC, Coyne JA, Losos JB, Foufopoulos J, Shubin N, Futuyma DJ, Campbell BC, Edwards SV. Museums’ role: increasing knowledge. Science. 2013 Mar 8;339(6124):1148-9. doi: 10.1126/science.339.6124.1148-b. PMID: 23471386.

Schneider I, Shubin NH. Making limbs from fins. Dev Cell. 2012 Dec 11;23(6):1121-2. doi: 10.1016/j.devcel.2012.11.011. PMID: 23237946.

Shubin N. Farish A. Jenkins Jr (1940-2012). Nature. 2012 Dec 6;492(7427):42. doi: 10.1038/492042a. PMID: 23222601. 

Gao KQ, Shubin NH. Late Jurassic salamandroid from western Liaoning, China. Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5767-72. doi: 10.1073/pnas.1009828109. Epub 2012 Mar 12. Erratum in: Proc Natl Acad Sci U S A. 2012 Jul 24;109(30):12260. PMID: 22411790; PMCID: PMC3326464.

King HM, Shubin NH, Coates MI, Hale ME. Behavioral evidence for the evolution of walking and bounding before terrestriality in sarcopterygian fishes. Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21146-51. doi: 10.1073/pnas.1118669109. Epub 2011 Dec 12. PMID: 22160688; PMCID: PMC3248479.

Schneider I, Aneas I, Gehrke AR, Dahn RD, Nobrega MA, Shubin NH. Appendage expression driven by the Hoxd Global Control Region is an ancient gnathostome feature. Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12782-6. doi: 10.1073/pnas.1109993108. Epub 2011 Jul 15. PMID: 21765002; PMCID: PMC3150877.

Fröbisch NB, Shubin NH. Salamander limb development: integrating genes, morphology, and fossils. Dev Dyn. 2011 May;240(5):1087-99. doi: 10.1002/dvdy.22629. Epub 2011 Apr 4. PMID: 21465623.

Gillis JA, Rawlinson KA, Bell J, Lyon WS, Baker CV, Shubin NH. Holocephalan embryos provide evidence for gill arch appendage reduction and opercular evolution in cartilaginous fishes. Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1507-12. doi: 10.1073/pnas.1012968108. Epub 2011 Jan 10. PMID: 21220324; PMCID: PMC3029744.

Gillis JA, Shubin NH. The evolution of gnathostome development: Insight from chondrichthyan embryology. Genesis. 2009 Dec;47(12):825-41. doi: 10.1002/dvg.20567. PMID: 19882670.

Gillis JA, Dahn RD, Shubin NH. Shared developmental mechanisms pattern the vertebrate gill arch and paired fin skeletons. Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5720-4. doi: 10.1073/pnas.0810959106. Epub 2009 Mar 24. PMID: 19321424; PMCID: PMC2667079.

Gillis JA, Dahn RD, Shubin NH. Chondrogenesis and homology of the visceral skeleton in the little skate, Leucoraja erinacea (Chondrichthyes: Batoidea). J Morphol. 2009 May;270(5):628-43. doi: 10.1002/jmor.10710. PMID: 19117064.

Shubin N, Tabin C, Carroll S. Deep homology and the origins of evolutionary novelty. Nature. 2009 Feb 12;457(7231):818-23. doi: 10.1038/nature07891. PMID: 19212399.

Shubin NH. This old body. Sci Am. 2009 Jan;300(1):64-7. doi: 10.1038/scientificamerican0109-64. PMID: 19186751.

Downs JP, Daeschler EB, Jenkins FA Jr, Shubin NH. The cranial endoskeleton of Tiktaalik roseae. Nature. 2008 Oct 16;455(7215):925-9. doi: 10.1038/nature07189. PMID: 18923515.

Davis MC, Dahn RD, Shubin NH. An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish. Nature. 2007 May 24;447(7143):473-6. doi: 10.1038/nature05838. PMID: 17522683 

Dahn RD, Davis MC, Pappano WN, Shubin NH. Sonic hedgehog function in chondrichthyan fins and the evolution of appendage patterning. Nature. 2007 Jan 18;445(7125):311-4. doi: 10.1038/nature05436. Epub 2006 Dec 24. PMID: 17187056.

Daeschler EB, Shubin NH, Jenkins FA Jr. A Devonian tetrapod-like fish and the evolution of the tetrapod body plan. Nature. 2006 Apr 6;440(7085):757-63. doi: 10.1038/nature04639. PMID: 16598249.

Shubin NH, Daeschler EB, Jenkins FA Jr. The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb. Nature. 2006 Apr 6;440(7085):764-71. doi: 10.1038/nature04637. PMID: 16598250.

Franssen RA, Marks S, Wake D, Shubin N. Limb chondrogenesis of the seepage salamander, Desmognathus aeneus (amphibia: plethodontidae). J Morphol. 2005 Jul;265(1):87-101. doi: 10.1002/jmor.10339. PMID: 15880507.

Davis MC, Shubin NH, Force A. Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. J Morphol. 2004 Nov;262(2):608-28. doi: 10.1002/jmor.10264. PMID: 15376275 

Shubin NH, Dahn RD. Evolutionary biology: lost and found. Nature. 2004 Apr 15;428(6984):703-4. doi: 10.1038/428703a. PMID: 15085113.

Shubin NH, Daeschler EB, Coates MI. The early evolution of the tetrapod humerus. Science. 2004 Apr 2;304(5667):90-3. doi: 10.1126/science.1094295. PMID: 15064415.

Gao KQ, Shubin NH. Earliest known crown-group salamanders. Nature. 2003 Mar 27;422(6930):424-8. doi: 10.1038/nature01491. PMID: 12660782.

Shubin NH. Origin of evolutionary novelty: examples from limbs. J Morphol. 2002 Apr;252(1):15-28. doi: 10.1002/jmor.10017. PMID: 11921033.

Gao KQ, Shubin NH. Late Jurassic salamanders from northern China. Nature. 2001 Mar 29;410(6828):574-7. doi: 10.1038/35069051. PMID: 11279493.

Torok MA, Gardiner DM, Shubin NH, Bryant SV. Expression of HoxD genes in developing and regenerating axolotl limbs. Dev Biol. 1998 Aug 15;200(2):225-33. doi: 10.1006/dbio.1998.8956. PMID: 9705229.

Shubin N, Tabin C, Carroll S. Fossils, genes and the evolution of animal limbs. Nature. 1997 Aug 14;388(6643):639-48. doi: 10.1038/41710. PMID: 9262397.

Jenkins FA Jr, Gatesy SM, Shubin NH, Amaral WW. Haramiyids and Triassic mammalian evolution. Nature. 1997 Feb 20;385(6618):715-8. doi: 10.1038/385715a0. PMID: 9034187.

Shubin N, Wake DB, Crawford AJ. MORPHOLOGICAL VARIATION IN THE LIMBS OF TARICHA GRANULOSA (CAUDATA: SALAMANDRIDAE): EVOLUTIONARY AND PHYLOGENETIC IMPLICATIONS. Evolution. 1995 Oct;49(5):874-884. doi: 10.1111/j.1558-5646.1995.tb02323.x. PMID: 28564880.

Daeschler EB, Shubin NH, Thomson KS, Amaral WW. A devonian tetrapod from north america. Science. 1994 Jul 29;265(5172):639-42. doi: 10.1126/science.265.5172.639. PMID: 17752761.

Shubin NH, Crompton AW, Sues HD, Olsen PE. New fossil evidence on the sister-group of mammals and early mesozoic faunal distributions. Science. 1991 Mar 1;251(4997):1063-5. doi: 10.1126/science.251.4997.1063. PMID: 17802092.

Oster GF, Shubin N, Murray JD, Alberch P. EVOLUTION AND MORPHOGENETIC RULES: THE SHAPE OF THE VERTEBRATE LIMB IN ONTOGENY AND PHYLOGENY. Evolution. 1988 Sep;42(5):862-884. doi: 10.1111/j.1558-5646.1988.tb02508.x. PMID: 28581162.

Olsen PE, Shubin NH, Anders MH. Response: triassic-jurassic extinctions. Science. 1988 Sep 9;241(4871):1359-60. doi: 10.1126/science.241.4871.1359. PMID: 17828938.

Olsen PE, Shubin NH, Anders MH. New early Jurassic tetrapod assemblages constrain Triassic-Jurassic tetrapod extinction event. Science. 1987 Aug 28;237(4818):1025-9. doi: 10.1126/science.3616622. PMID: 3616622

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