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Neil H. Shubin

Professor
nshubin@uchicago.edu
Websites
Research Summary
I seek to understand the mechanisms behind the evolutionary origin of new anatomical features and faunas. The philosophy that underlies all of my empirical work is derived from the conviction that progress in the study of evolutionary biology results from linking research across diverse temporal, phylogenetic, and structural scales. The Origin of Novel Faunas and Anatomical Systems: Much of today's vertebrate diversity was defined by ecological and evolutionary shifts that happened during two critical intervals in the history of the Earth: the Devonian and the Triassic. These periods serve as the focal point for my research because they witness the origin of both new ecosystems and new anatomical designs. My expeditionary research supplies new fossils and a paleoenvironmental context to understand the origin of faunas, whereas our morphological, functional, and developmental studies yield hypotheses on anatomical transformations. Over the past fifteen years, I have developed expeditionary research programs in Canada, Africa, the continental United States, Asia, and Greenland. These expeditions have led to new insights on the origin of major groups of vertebrates (mammals, frogs, crocodiles, tetrapods, and sarcopterygian fish). Future studies on the origins of pterosaurs, rhizodontid fish, dinosaurs, and salamanders will rely heavily on fossils discovered over the past five years. Examples include the newly discovered adult fin and juvenile skeleton of the fish, Sauripterus. These fossils are providing evidence on the ways that appendage function and skeletal development shifted during the evolutionary radiation of lobe-finned fish. Indeed, this evolutionary radiation is temporally linked to the origin of new freshwater environments. Consequently, the analysis of Sauripterus will place comparative studies of fin structure, development and function in a phylogenetic and paleoenvironmental context. The goals of the paleontological research dovetail with those of my neontological studies. New fossils, such as Sauripterus, offer tests of hypotheses that derive from our comparative analysis of genetic and morphogenetic processes. For example, the comparison of developmental pathways common to the appendages of all animals suggests genetic mechanisms for parallel evolution and homology. Regularities of variation may reflect the fact that similar regulatory genes are used in the developmental patterning of diverse types of animals. The Origin of Morphological Variation: The ~400 million year history of terrestrial animals reveals surprising patterns of anatomical stasis and parallel evolution: similar designs crop up in different species living in different environments. Salamanders, for example, arose over 150 million years ago, but have retained a very stable body plan in the face of environmental change and genetic variation. The study of these regularities transcends ecological and paleontological timescales because explanations of larger-scale patterns can be sought in the mechanisms that structure anatomical variation in populations today. Accordingly, my research has involved collecting data on intraspecific variation from diverse populations, developing predictive models of variation based on ontogeny, and comparing developmental processes in diverse salamanders that live in different environmental settings. Salamander limbs are a model system to approach these issues because of the diversity of their developmental systems and life histories. In addition, the widespread occurrence of parallelism provides us with a window to develop predictive rules about the origin of variation in populations. Over the past seven years, colleagues and I have composed a database of limb variation and ontogeny in populations of diverse salamanders. Virtually all of the species analyzed to date possess variant conditions that both restore ancient features and anticipate more derived conditions seen in distantly-related species. Much of the observed intraspecific variation is predictable from a knowledge of phylogenetic history or development. Ultimately, if these historical and developmental effects resulted in long-term evolutionary patterns, they must have acted over geological timescales. Tests of this hypothesis will come from the study of the Chinese Cretaceous where, in collaboration with colleagues, I am studying variation of salamanders in a Cretaceous pond that were killed in a single mass-mortality event. Phylogenetic analysis of ontogenetic trajectories in salamanders affords critical assessments of the role of historical, ecological, and structural factors in evolution. Analysis of development in salamanders with different life histories suggests certain aspects of early limb development are highly sensitive to variation in larval biology. I intend to explore this link between ontogenetic diversity and anatomical variation in the future by using experimental and comparative studies of ontogeny.
Education
  • University of Pennsylvania, Philadelphia, PA, A.M. Biology 06/1996
  • Harvard University, Cambridge, MA, Ph.D. Organismal and Evolutionary Biology 05/1987
  • Harvard University , Cambridge, MA, A.M. Organismal and Evolutionary Biology 05/1985
  • Columbia University, New York City, NY, A.B. Biology 05/1982
Biosciences Graduate Program Association
Publications

  1. 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. Dev Dyn. 2020 Dec 30. View in: PubMed

  2. 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. Proc Biol Sci. 2020 09 30; 287(1935):20192939. View in: PubMed

  3. 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 02 11; 117(6):3034-3044. View in: PubMed

  4. 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 01 21; 117(3):1612-1620. View in: PubMed

  5. 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 11 06; 286(1914):20191571. View in: PubMed

  6. Lemberg JB, Shubin NH, Westneat MW. Feeding kinematics and morphology of the alligator gar (Atractosteus spatula, Lacépède, 1803). J Morphol. 2019 10; 280(10):1548-1570. View in: PubMed

  7. 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 05 29; 115(22):E5018-E5027. View in: PubMed

  8. 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 04; 50(4):504-509. View in: PubMed

  9. Shubin N. Gene regulatory networks and network models in development and evolution. Proc Natl Acad Sci U S A. 2017 06 06; 114(23):5782-5783. View in: PubMed

  10. 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. View in: PubMed

  11. 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. View in: PubMed

  12. 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). View in: PubMed

  13. Nakamura T, Gehrke AR, Lemberg J, Szymaszek J, Shubin NH. Digits and fin rays share common developmental histories. Nature. 2016 09 08; 537(7619):225-228. View in: PubMed

  14. 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 09 06; 113(36):10115-20. View in: PubMed

  15. 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 05 27; 48(6):700. View in: PubMed

  16. 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. View in: PubMed

  17. Gehrke AR, Shubin NH. Cis-regulatory programs in the development and evolution of vertebrate paired appendages. Semin Cell Dev Biol. 2016 09; 57:31-39. View in: PubMed

  18. 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. View in: PubMed

  19. Luo ZX, Gatesy SM, Jenkins FA, 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. View in: PubMed

  20. 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. View in: PubMed

  21. 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. View in: PubMed

  22. 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. View in: PubMed

  23. Shubin NH, Daeschler EB, Jenkins FA. Pelvic girdle and fin of Tiktaalik roseae. Proc Natl Acad Sci U S A. 2014 Jan 21; 111(3):893-9. View in: PubMed

  24. Shubin N. QnAs with Neil Shubin. Proc Natl Acad Sci U S A. 2014 Jan 21; 111(3):881-2. View in: PubMed

  25. 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. View in: PubMed

  26. Mayer GC, Coyne JA, Losos JB, Foufopoulos J, Shubin N, Futuyma DJ, Campbell BC, Edwards SV. Museums' role: increasing knowledge. Science. 2013 Mar 08; 339(6124):1148-9. View in: PubMed

  27. Schneider I, Shubin NH. The origin of the tetrapod limb: from expeditions to enhancers. Trends Genet. 2013 Jul; 29(7):419-26. View in: PubMed

  28. Schneider I, Shubin NH. Making limbs from fins. Dev Cell. 2012 Dec 11; 23(6):1121-2. View in: PubMed

  29. Shubin N. Farish A. Jenkins Jr (1940-2012). Nature. 2012 Dec 06; 492(7427):42. View in: PubMed

  30. 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. View in: PubMed

  31. 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. View in: PubMed

  32. 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 02; 108(31):12782-6. View in: PubMed

  33. Fröbisch NB, Shubin NH. Salamander limb development: integrating genes, morphology, and fossils. Dev Dyn. 2011 May; 240(5):1087-99. View in: PubMed

  34. 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. View in: PubMed

  35. Gillis JA, Shubin NH. The evolution of gnathostome development: Insight from chondrichthyan embryology. Genesis. 2009 Dec; 47(12):825-41. View in: PubMed

  36. 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 07; 106(14):5720-4. View in: PubMed

  37. Shubin N, Tabin C, Carroll S. Deep homology and the origins of evolutionary novelty. Nature. 2009 Feb 12; 457(7231):818-23. View in: PubMed

  38. Shubin NH. This old body. Sci Am. 2009 Jan; 300(1):64-7. View in: PubMed

  39. 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. View in: PubMed

  40. Downs JP, Daeschler EB, Jenkins FA, Shubin NH. The cranial endoskeleton of Tiktaalik roseae. Nature. 2008 Oct 16; 455(7215):925-9. View in: PubMed

  41. Olsen PE, Shubin NH, Anders MH. Response: triassic-jurassic extinctions. Science. 1988 Sep 09; 241(4871):1359-60. View in: PubMed

  42. 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 01; 251(4997):1063-5. View in: PubMed

  43. Daeschler EB, Shubin NH, Thomson KS, Amaral WW. A devonian tetrapod from north america. Science. 1994 Jul 29; 265(5172):639-42. View in: PubMed

  44. 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. View in: PubMed

  45. 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. View in: PubMed

  46. Shubin NH, Daeschler EB, Jenkins FA. The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb. Nature. 2006 Apr 06; 440(7085):764-71. View in: PubMed

  47. Daeschler EB, Shubin NH, Jenkins FA. A Devonian tetrapod-like fish and the evolution of the tetrapod body plan. Nature. 2006 Apr 06; 440(7085):757-63. View in: PubMed

  48. 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. View in: PubMed

  49. 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. View in: PubMed

  50. Shubin NH, Dahn RD. Evolutionary biology: lost and found. Nature. 2004 Apr 15; 428(6984):703-4. View in: PubMed

  51. Shubin NH, Daeschler EB, Coates MI. The early evolution of the tetrapod humerus. Science. 2004 Apr 02; 304(5667):90-3. View in: PubMed

  52. Gao KQ, Shubin NH. Earliest known crown-group salamanders. Nature. 2003 Mar 27; 422(6930):424-8. View in: PubMed

  53. Shubin NH. Origin of evolutionary novelty: examples from limbs. J Morphol. 2002 Apr; 252(1):15-28. View in: PubMed

  54. Gao KQ, Shubin NH. Late Jurassic salamanders from northern China. Nature. 2001 Mar 29; 410(6828):574-7. View in: PubMed

  55. 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. View in: PubMed

  56. Shubin N, Tabin C, Carroll S. Fossils, genes and the evolution of animal limbs. Nature. 1997 Aug 14; 388(6643):639-48. View in: PubMed

  57. Jenkins FA, Gatesy SM, Shubin NH, Amaral WW. Haramiyids and Triassic mammalian evolution. Nature. 1997 Feb 20; 385(6618):715-8. View in: PubMed

  58. 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. View in: PubMed
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