Recommended Readings: Neil H. Shubin, Ph.D. December 17

Special Seminar Series
Wednesday, December 17, 2014,
4:00 p.m., Carson Family Auditorium (CRC)

Neil H. Shubin, Ph.D.
Robert R. Bensley Distinguished Service Professor,
Senior Advisor to the President,
Department of Organismal Biology and Anatomy,
The University of Chicago

Organogenesis in Deep Time

Recommended Readings

Empirical Papers

Amemiya, C. T., Alföldi, J., Lee, A. P., Fan, S., Philippe, H., Maccallum, I., … Lindblad-Toh, K. (2013). The African coelacanth genome provides insights into tetrapod evolution. Nature, 496(7445), 311–316. doi:10.1038/nature12027

Dahn, R. D., Davis, M. C., Pappano, W. N., & Shubin, N. H. (2007). Sonic hedgehog function in chondrichthyan fins and the evolution of appendage patterning. Nature, 445(7125), 311–314. doi:10.1038/nature05436

Davis, M. C., Dahn, R. D., & Shubin, N. H. (2007). An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish. Nature, 447(7143), 473–476. doi:10.1038/nature05838

Shubin, N. H., Daeschler, E. B., & Jenkins, F. a. (2006). The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb. Nature, 440(7085), 764–771. doi:10.1038/nature04637

Review Articles

Schneider, I., & Shubin, N. H. (2013). The origin of the tetrapod limb: from expeditions to enhancers. Trends in Genetics, 29(7), 419–426. doi:10.1016/j.tig.2013.01.012

Shubin, N., Tabin, C., & Carroll, S. (2009). Deep homology and the origins of evolutionary novelty. Nature, 457(7231), 818–823. doi:10.1038/nature07891

Recommended Readings: David Kingsley, Ph.D.

Friday Lecture Series

The Fairfield Osborn Memorial Lecture

Fishing for the Secrets of Vertebrate Evolution

David Kingsley, Ph.D., professor, developmental biology, Stanford University;

investigator, Howard Hughes Medical Institute

April 18, 2014

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

han, Y. F., Marks, M. E., Jones, F. C., Villarreal Jr., G., Shapiro, M. D., Brady, S. D., . . . Kingsley, D. M. (2010). Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a pitxl enhancer. Science, 327(5963), 302-305

Haussler, D., O’Brien, S. J., Ryder, O. A., Keith Barker, F., Clamp, M., Crawford, A. J., . . . Turner, S. (2009). Genome 10K: A proposal to obtain whole-genome sequence for 10000 vertebrate species. Journal of Heredity, 100(6), 659-674

Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., . . . Kingsley, D. M. (2012). The genomic basis of adaptive evolution in threespine sticklebacks. Nature, 484(7392), 55-61

Kingsley, D. M., Zhu, B., Osoegawa, K., De Jong, P. J., Schein, J., Marra, M., . . . Myers, R. (2004). New genomic tools for molecular studies of evolutionary change in threespine sticklebacks. Behaviour, 141(11-12), 1331-1344

Lowe, C. B., Kellis, M., Siepel, A., Raney, B. J., Clamp, M., Salama, S. R., . . . Haussler, D. (2011). Three periods of regulatory innovation during vertebrate evolution. Science, 333(6045), 1019-1024

Shapiro, M. D., Bell, M. A., & Kingsley, D. M. (2006). Parallel genetic origins of pelvic reduction in vertebrates. Proceedings of the National Academy of Sciences of the United States of America, 103(37), 13753-13758


Recommended Readings: David Kingsley, Ph.D. April 18

Friday Lecture Series
Friday, April 18, 2014
3:45 p.m., Caspary Auditorium

David Kingsley, Ph.D.
HHMI and Department of Developmental Biology
Stanford University School of Medicine

Fishing for the secrets of vertebrate evolution

Recommended Readings:

Empirical Papers

Chan, Y. F., Marks, M. E., Jones, F. C., Villarreal, G., Shapiro, M. D., Brady, S. D., … Kingsley, D. M. (2010). Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science, 327(5963), 302–305. doi:10.1126/science.1182213

Colosimo, P. F., Hosemann, K. E., Balabhadra, S., Villarreal, G., Dickson, M., Grimwood, J., … Kingsley, D. M. (2005). Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles. Science, 307(5717), 1928–1933. doi:10.1126/science.1107239

Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., … Kingsley, D. M. (2012). The genomic basis of adaptive evolution in threespine sticklebacks. Nature, 484(7392), 55–61. doi:10.1038/nature10944

Miller, C. T., Beleza, S., Pollen, A. a, Schluter, D., Kittles, R. a, Shriver, M. D., & Kingsley, D. M. (2007). cis-Regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans. Cell, 131(6), 1179–1189. doi:10.1016/j.cell.2007.10.055

Shapiro, M. D., Marks, M. E., Peichel, C. L., Blackman, B. K., Nereng, K. S., Jónsson, B., … Kingsley, D. M. (2004). Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature, 428(6984), 717–723. doi:10.1038/nature02415

Review Articles

McKinnon, J. S., & Rundle, H. D. (2002). Speciation in nature: the threespine stickleback model systems. Trends in Ecology & Evolution, 17(10), 480–488. doi:10.1016/S0169-5347(02)02579-X

Recommended Readings:Detlev Arendt, Ph.D.

Friday Lecture Series

The Evolutionary Origin of the Vertebrate Brain

Detlev Arendt, Ph.D., honorary professor, University of Heidelberg, Germany;

group leader and senior scientist, European Molecular Biology Laboratory

May 3, 2013

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Arendt, D., Tessmar-Raible, K., Snyman, H., Dorresteijn, A. W., & Wittbrodf, J. (2004). Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain. Science, 306(5697), 869-871

Christodoulou, F., Raible, F., Tomer, R., Simakov, O., Trachana, K., Klaus, S., . . . Arendt, D. (2010). Ancient animal microRNAs and the evolution of tissue identity. Nature, 463(7284), 1084-1088

Raible, F., Tessmar-Raible, K., Osoegawa, K., Wincker, P., Jubin, C., Balavoine, G., . . . Arendt, D. (2005). Evolution: Vertebrate-type intron-rich genes in the marine annelid platynereis dumerilii. Science, 310(5752), 1325-1326

Tessmar-Raible, K., & Arendt, D. (2003). Emerging systems: Between vertebrates and arthropods, the lophotrochozoa. Current Opinion in Genetics and Development, 13(4), 331-340

Tomer, R., Denes, A. S., Tessmar-Raible, K., & Arendt, D. (2010). Profiling by image registration reveals common origin of annelid mushroom bodies and vertebrate pallium. Cell, 142(5), 800-809


The Consequences of Having Evolved: Our Uniquely Human Flaws

The latest issue of Smithsonian Magazine names and explains those daily consequences of having evolved into Homo sapiens via Mother Nature’s crafty use of the gene pool at her disposal. 

evolution of man From hiccups to wisdom teeth, our own bodies are worse off than most because of the differences between the wilderness in which we evolved and the modern world in which we live.

Read more:

Recommended Readings: Otger Campas, PH.D. Oct 25, 2010

Monday Lecture Series

Quantifying Morphogenesis and Morphological Variation

Otger Campas, Ph.D.,

SysCODE Fellow 

School of Engineering and Applied Sciences and Department of Organismic

 and Evolutionary Biology

Harvard University and Harvard Medical School

October 25, 2010

4:00 p.m.  Welch Hall Level Two


Recommended Readings:

Campas, O; Mallarino, R; Herrel, A  et al.  2010.  Scaling and shear transformations capture beak shape variation in Darwin’s finches.  PNAS  107(8): 3356-3360

Van Bocxlaer, B; Schultheiss, R.  2010.  Comparison of morphometric techniques for shapes with few homologous landmarks based on machine-learning approaches to biological discrimination. Paleobiology.  36(3):497-515  Please request from Markus Library.

Abzhanov, A; Kuo, WP; Hartmann, C; Grant, BR; Grant, PR; Tabin, CJ.  2006.  The Calmodulin pathway and evolution of elongated beak morphology of Darwin’s finches.  NATURE.  442(7102):563-567

Burns, KJ; Hackett, SJ; Klein, NK.  2002.  Phylogenetic relationships and morphological diversity in Darwin’s finches and their relatives.  Evolution  56(6):1240-1252

Arthur, W.  2006.   D’Arcy Thompson and the theory of transformationsNATURE  Reviews Genetics.  7(5):401-U3

Kirschn er, M; Gerhart, J.  1998.  Evolvability.  PNAS.  95(15): 8420-8427

Sato, A; Tichy, H; O’huigin, C; Grant, PR; Grant, BR; Klein, J.   2001.  On the origin of Darwin’s finchesMolecular Biology and Evolution.  18(3):299-311

Petren, K; Grant, PR; Grant, BR; Keller, LF.  2005.  Comparative landscape genetics and the adaptive radiation of Darwin’s finches: the role of peripheral isolation.   Molecular Ecology.  14(10):2943-2957

Stone, JR.  1997.  The spirit of D’Arcy Thompson dwells in empirical morphospace.  Mathematical Biosciences.  142(1):13-30    Please request from Markus Library


Recommended Readings: Marcus Kronforst Ph.D. March 15, 2010

Monday Lecture Series

Exploring the Evolution and Genetics of Adaptation and

Speciation in Tropical Butterflies

Marcus Kronforst, Ph.D.,

Bauer Fellow, FAS Center for Systems Biology

Harvard University

March 15, 2010

Welch Hall,  Level Two

4:00 p.m.-5:00 p.m

Recommended Readings:

Chamberlain NL, Hill RI, Kapan DD, et al.  2009.  Polymorphic Butterfly Reveals the Missing Link in Ecological Speciation. SCIENCE   326(5954):847-850

Wheat CW, Watt WB.  2008.  A mitochondrial-DNA-based phylogeny for some evolutionary-genetic model species of Colias butterflies (Lepidoptera, Pieridae) . MOLECULAR PHYLOGENETICS AND EVOLUTION    47(3):893-902

Salazar C, Jiggins CD, Taylor JE, et al.  2008.  Gene flow and the genealogical history of Heliconius heurippa . BMC EVOLUTIONARY BIOLOGY    8:Article Number  132

Allen CE, Beldade P, Zwaan BJ, et al.  2008.  Differences in the selection response of serially repeated color pattern characters: Standing variation, development, and evolution. BMC EVOLUTIONARY BIOLOGY    8:Article Number  94

Kronforst MR .   2008.  Gene flow persists millions of years after speciation in Heliconius butterflies. BMC EVOLUTIONARY BIOLOGY   8 :Article Number 98

Kronforst MR, Gilbert LE.  2008.  The population genetics of mimetic diversity in Heliconius butterflies. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES    275(1634):493-500

Frentiu FD, Bernard GD, Sison-Mangus MP, et al.  2007.   Gene duplication is an evolutionary mechanism for expanding spectral diversity in the long-wavelength photopigments of butterflies. MOLECULAR BIOLOGY AND EVOLUTION    24(9):2016-2028

Kronforst MR, Young LG, Gilbert LE.   2007.  Reinforcement of mate preference among hybridizing Heliconius butterflies.    JOURNAL OF EVOLUTIONARY BIOLOGY   20(1):278-285

Kronforst MR, Kapan DD, Gilbert LE.   2006.  Parallel genetic architecture of parallel adaptive radiations in mimetic heliconius butterflies. GENETICS   174(1):535-539

Parchem RJ, Perry MW, Patel NH.   2007.  Patterns on the insect wing. CURRENT OPINION IN GENETICS & DEVELOPMENT    17(4):300-308

Recommended Readings: Daniel Kronauer Ph.D. March 8 2010

Monday Lecture Series

The Birth, Life and Death of an Army Ant Superorganism

Daniel Kronauer, Ph.D.,

Junior Fellow, Harvard Society of Fellows

Museum of Comparative Zoology, Harvard University

March 8, 2010

Welch Hall,  Level Two

4:00 p.m.-5:00 p.m

Recommended Readings:

Kronauer DJC, Schoning C, d’Ettorre P, et al.   2010.  Colony fusion and worker reproduction after queen loss in army ants. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 277(1682):755-763

Tarapore D, Floreano D, Keller L.   2010.   Task-dependent influence of genetic architecture and mating frequency on division of labour in social insect societies. BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY 64(4):675-684

Kronauer DJC.   2009.   Recent advances in army ant biology (Hymenoptera: Formicidae) . MYRMECOLOGICAL NEWS 12:51-65

Powell S.    2009.   How ecology shapes caste evolution: linking resource use, morphology, performance and fitness in a superorganism. JOURNAL OF EVOLUTIONARY BIOLOGY   22(5):1004-1013

Berghoff SM, Kronauer DJC, Edwards KJ, et al.  2008. Dispersal and population structure of a New World predator, the army ant Eciton burchellii. JOURNAL OF EVOLUTIONARY BIOLOGY 21(4):1125-1132

Kronauer DJC, Berghoff SM, Powell S, et al.  2006.   A reassessment of the mating system characteristics of the army ant Eciton burchellii. NATURWISSENSCHAFTEN 93(8):402-406

Kronauer DJC, Johnson RA, Boomsma JJ.   2007.  The evolution of multiple mating in army ants. EVOLUTION 61(2):413-422

Kronauer DJC, Schoning C, Pedersen JS, et al.  2004.  Extreme queen-mating frequency and colony fission in African army ants.  MOLECULAR ECOLOGY 13(8):2381-2388      Request full article from Markus Library.

Recommended Readings: Richard Leakey, Ph. D.; September 25, 2009

Friday Lecture Series

Fairfield Osborn Memorial Lecture

Richard E. Leakey, Professor

Stony Brook University; chairman, Wildlife Direct

September 25, 2009

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Articles:

Brown, B., A. Walker, C. V. Ward, and R. E. Leakey. 1993. New australopithecus boisei calvaria from east Lake Turkana, Kenya. American Journal of Physical Anthropology 91, (2): 137-159.

Brown, F., J. Harris, R. Leakey, and A. Walker. 1985. Early homo erectus skeleton from west Lake Turkana, Kenya. Nature 316, (6031): 788-792.

Harris, J. M., F. H. Brown, M. G. Leakey, A. C. Walker, and R. E. Leakey. 1988. Pliocene and pleistocene hominid-bearing sites from west of Lake Turkana, Kenya. Science 239, (4835): 27-33.

Leakey, R. E., and M. G. Leakey. 1986. A new miocene hominoid from Kenya. Nature 324, (6093): 143-146.

Walker, A., M. R. Zimmerman, and R. E. F. Leakey. 1982. A possible case of hypervitaminosis A in homo erectus. Nature 296, (5854): 248-250.

Recommended Books:

Leakey, Richard.   Wildlife wars: my battle to save Kenya’s elephants.   Pan Books.  2002

Leakey, Richard and Roger Lewin.  Origins: the emergence and evolution of our species and its possible future.  Penguin Books.  1991

Walker, Alan and Richard Leakey (eds).  The Nariokotome Homo erectus skeleton.  Springer. 1993

Leakey, Richard and Roger Lewin. The sixth extinction: patters of life and the future of humankind.  Anchor. 1996.

Leakey, Richard.  The origin of humankind.  Orion Publishing Group. 1994.

Leakey, Richard.  Origins reconsidered: in search of what makes us human.  Anchor.  1993.

Darwin’s Mystery Of Appearance Of Flowering Plants Explained

The rapid increase in the fantastic diversity of flowering plants – linked to their rapid conquest of the Earth during the Cretaceous period – was one of the greatest puzzles faced by Charles Darwin.  In an article in Ecology Letters,  ecologists Frank Berendse and Marten Scheffer have postulated an entirely new explanation for what Charles Darwin considered to be one of the greatest mysteries with which he was confronted.  

Frank Berendse and Marten Scheffer. The angiosperm radiation revisited, an ecological explanation for Darwin’s ‘abominable mystery’. Ecology Letters, Published Online: 2 Jul 2009 DOI: 10.1111/j.1461-0248.2009.01342.x