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

Was the Cerebellum the Center of Evolutionary Change That Makes Us Human?

When we search for the seat of humanity, are we looking at the wrong part of the brain? Most neuroscientists assume that the neocortex, the brain’s distinctive folded outer layer, is the thing that makes us uniquely human. But a new study suggests that another part of the brain, the cerebellum, grew much faster in our ape ancestors.

Read more on this new research in Current Biology.

 

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: Max Cooper, M.D.

Friday Lecture Series

How Did Our Adaptive Immune System Evolve?

Max Cooper, M.D., professor, Emory Vaccine Center and Emory Center for AIDS Research, Emory University School of Medicine

January 31, 2014

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

Caspary Auditorium

Recommended Readings

Alder, M. N., Rogozin, I. B., Iyer, L. M., Glazko, G. V., Cooper, M. D., & Pancer, Z. (2005). Immunology: Diversity and function of adaptive immune receptors in a jawless vertebrate. Science, 310(5756), 1970-1973

Cooper, M. D. (2010). A life of adventure in immunobiology. Annual Review of Immunology 28, 11-19

Cooper, M. D., & Herrin, B. R. (2010). How did our complex immune system evolve? Nature Reviews Immunology, 10(1), 2-3

Guo, P., Hirano, M., Herrin, B. R., Li, J., Yu, C., Sadlonova, A., & Cooper, M. D. (2009). Dual nature of the adaptive immune system in lampreys. Nature, 459(7248), 796-801

Hirano, M., Das, S., Guo, P., & Cooper, M. D. (2011). The evolution of adaptive immunity in vertebrates. Advances in Immunology 109, pp. 125-157

Pancer, Z., & Cooper, M. D. (2006). The evolution of adaptive immunity. Annual Review of Immunology 24 , pp. 497-518

 

Recommended Readings: Kristin Tessmar-Raible Ph.D. February 3

SPECIAL SEMINAR
Monday, February 3, 2014
4:00 p.m., Carson Family Auditorium

Kristin Tessmar-Raible, Ph.D.
Junior Group Leader
Max F. Perutz Laboratories
University of Vienna

The Impact of Light on Nervous System Function

Recommended Readings:

Empirical Papers

Backfisch, B., Veedin Rajan, V. B., Fischer, R. M., Lohs, C., Arboleda, E., Tessmar-Raible, K., & Raible, F. (2013). Stable transgenesis in the marine annelid Platynereis dumerilii sheds new light on photoreceptor evolution. Proceedings of the National Academy of Sciences of the United States of America, 110(1), 193–198. doi:10.1073/pnas.1209657109

Fischer, R. M., Fontinha, B. M., Kirchmaier, S., Steger, J., Bloch, S., Inoue, D., … Tessmar-Raible, K. (2013). Co-expression of VAL- and TMT-opsins uncovers ancient photosensory interneurons and motorneurons in the vertebrate brain. PLoS Biology, 11(6), e1001585. doi:10.1371/journal.pbio.1001585

Zantke, J., Ishikawa-Fujiwara, T., Arboleda, E., Lohs, C., Schipany, K., Hallay, N., … Tessmar-Raible, K. (2013). Circadian and circalunar clock interactions in a marine annelid. Cell Reports, 5(1), 99–113. doi:10.1016/j.celrep.2013.08.031

Review Articles

Roenneberg, T., & Merrow, M. (2005). Circadian clocks – the fall and rise of physiology. Nature Reviews Molecular Cell Biology, 6(12), 965–971. doi:10.1038/nrm1766

Tessmar-Raible, K., Raible, F., & Arboleda, E. (2011). Another place, another timer: Marine species and the rhythms of life. BioEssays, 33(3), 165–172. doi:10.1002/bies.201000096

Recommended Readings: Harmit S. Malik, Ph.D.

Friday Lecture Series

Genetic Conflicts: Beyond the Usual Suspects

Harmit S. Malik, Ph.D., principal investigator, basic sciences division,

Fred Hutchinson Cancer Research Center;

early career scientist, Howard Hughes Medical Institute

December 13, 2013

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

Caspary Auditorium

Recommended Readings

Malik, H. S. (2009). Evolution of TRIM antiviral genes in primate genomes. Retrovirology, 6(SUPPL. 2)

Malik, H. S., & Bayes, J. J. (2006). Genetic conflicts during meiosis and the evolutionary origins of centromere complexity. Biochemical Society Transactions, 34(4), 569-573

Malik, H. S., & Henikoff, S. (2002). Conflict begets complexity: The evolution of centromeres. Current Opinion in Genetics and Development, 12(6), 711-718

Moran, J. V., & Malik, H. S. (2009). Diamonds and rust: How transposable elements influence mammalian genomes. conference on mobile elements in mammalian genomes. EMBO Reports, 10(12), 1306-1310

Oliver, P. L., Goodstadt, L., Bayes, J. J., Birtle, Z., Roach, K. C., Phadnis, N., . . . Ponting, C. P. (2009). Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genetics, 5(12)

Vermaak, D., & Malik, H. S. (2009). Multiple roles for heterochromatin protein 1 genes in drosophila. Annual Review of Genetic 43 , pp. 467-492

 

Alfred Russel Wallace (8 January 1823 – 7 November 1913)

Alfred Russel Wallace (8 January 1823 – 7 November 1913) was a British naturalist, explorer, geographer, anthropologist, and biologist. He is best known for independently conceiving the theory of evolution through natural selection; his paper on the subject was jointly published with some of Charles Darwin’s writings in 1858. This prompted Darwin to publish his own ideas in On the Origin of Species. Wallace did extensive fieldwork, first in the Amazon River basin and then in the Malay Archipelago, where he identified the Wallace Line that divides the Indonesian archipelago into two distinct parts: a western portion in which the animals are largely of Asian origin, and an eastern portion where the fauna reflect Australasia.

He was considered the 19th century’s leading expert on the geographical distribution of animal species and is sometimes called the “father of biogeography”. Wallace was one of the leading evolutionary thinkers of the 19th century and made many other contributions to the development of evolutionary theory besides being codiscoverer of natural selection. These included the concept of warning coloration in animals, and the Wallace effect, a hypothesis on how natural selection could contribute to speciation by encouraging the development of barriers against hybridization.

Wallace was strongly attracted to unconventional ideas (such as evolution). His advocacy of spiritualism and his belief in a non-material origin for the higher mental faculties of humans strained his relationship with some members of the scientific establishment. In addition to his scientific work, he was a social activist who was critical of what he considered to be an unjust social and economic system in 19th-century Britain. His interest in natural history resulted in his being one of the first prominent scientists to raise concerns over the environmental impact of human activity.

In honor of the centennial of his death, this short film celebrates the extraordinary life and lasting scientific contributions of the other, arguably more colorful discoverer of natural selection.

‘The Animated Life of A.R. Wallace’

Recommended Readings: Leslie M Turner PhD Oct 22, 2012

Genomic Networks of Hybrid Sterility

Leslie M Turner  PhD

Postdoctoral Fellow

Laboratory of Genetics, University of Wisconsin – Madison

Monday, October 22,  2012

4 p.m. , Caspary Auditorium.   Refreshments 3:45 p.m.

Recommended Readings:

Janousek, V; Wang, LY; Luzynski, K; et al.  2012.  Genome-wide architecture of reproductive isolation in naturally occurring hybrid zone between Mus musculus musculus and M. m. domesticus.   Molecular Ecology.  21(12):3032-3047.  DOI:10.111/j.1365-294X.2012.05583.x

White, MA; Steffy, B; Wiltshire, T; et al.  2011.  Genetic dissection of a key reproductive barrier between nascent species of house mice.  Genetics. 189(1):289-U988.  DOI:10.1534/genetics.111.129171

Turner, LM; Schwahn, DJ; Harr, B.  2012.  Reduced male fertility is common but highly variable in form and severity in a natural house mouse hybrid zone.   Evolution.  66(2):443-458 DOI:10.1111/j.1558-5646.2011.01445.x

Turner, LM; Young, AR; Roempler, H; et al.  2010.  Monogamy evolves through multiple mechanisms: evidence from V1aR in deer mice.  Molecular Biology and Evolution.  27(6)1269-1278.  DOI:10.1093/molbev/msq013

Harr, B; Turner, LM.  2010.  Genome-wide analysis of alternative splicing evolution among Mus subspecies.  Molecular Ecology.  19(suppl 1):228-239.  DOI:10.1111/j.1365-294X.04490.x

Gompert, Z; Buerkle, CA.  2009.  A powerful regression-based method for admixture mapping of isolation across the genome of hybrids.  Molecular Ecology.  18(6):1207-1224.  DOI:10.1111/j.1365-0294X.04098.x

Elliott, RW; Miller, DR; Pearsall, RS; et al.  2001.  Genetic analysis of testis weight and fertility in an interspecies hybrid congenic strain for chromosome X.   Mammalian Genome.  12(1):45-51.  DOI:10.1007/s003350010234

New Research on Antagonistic Coevolution

Biologists have found new evidence for why mice, people and other vertebrate animals carry thousands of varieties of genes to make immune-system proteins named MHCs — even though some of those genes make us susceptible to infections and to autoimmune diseases.  Findings are published in the Feb 6, 2012 issue of PNAS.