Andrew M. Shedlock, Ph.D.

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Marine Biomedicine and Environmental Sciences | Faculty | Andrew M. Shedlock, Ph.D.

Andrew M. Shedlock, Ph.D.

Research Interest:
The Shedlock Lab promotes integration of field biology with experimental advances in molecular medicine and genomics to test hypotheses about organismal genotype-phenotype relationships and to address complex applied problems in the environmental sciences. Recent areas of research include: 1) the evolutionary dynamics of mobile DNA and its role in shaping eukaryotic genome architecture; 2) the use of interspersed genomic repeats as powerful biomarkers; and 3) the conservation genetics and geographic structure of legally protected and commercially important wild populations. Our taxonomic focus is comparative vertebrate biology, especially globally distributed marine species and incorporation of fossil data. New projects employ de novo genome mapping and molecular evolutionary analysis of global repeat content in all major clades of amniotes. Reference genome assemblies are used to guide parallel cDNA and bisulfite methylation sequencing efforts to investigate tissue- and condition-specific differential gene expression and vertebrate transcriptome evolution. These projects target locus-specific importance of mobile elements as agents of new gene function and novel regulatory pathways in the genomic neighborhoods of marine tetrapods. They also provide insight into the systems biology of ecological communities being impacted by human activities and promote a more predictive vs. reactive approach to environmental management upon which we ultimately depend for our sustained public health.

Selected Publications:
1. Alfoldi, J., F. DiPalma, M. Grabherr, C. Williams, L. Kong, E. Mauceli, P. Russell., C. Lowe, R. Glor, J. D. Jaffe, D. Ray, A. M. Shedlock, et al. 2011. The green anole lizard genome: the first reptilian genome and a comparative analysis with birds and mammals. Nature 477:587-591.

2. Janes. D. E., C. L. Organ, M. K. Fujita, A. M. Shedlock, and S. V. Edwards. 2010. Genome evolution in Reptilia, the sister group of mammals. Annual Review of Genomics and Human Genetics. Volume 11: 239-264.

3. Shedlock, A. M., and S. V. Edwards. 2009. Amniotes (Amniota). Pp. 373-380 In: The Timetree of Life (S. B. Hedges and S. Kumar, Eds.), Oxford University Press, New York.

4. Shedlock, A. M., C. W. Botka, S. Zhao, J. Shetty,T. Zhang, J. S. Liu, P. J. Deschavanne, and S. V. Edwards. 2007. Phylogenomics of non-avian reptiles and the structure of the ancestral amniote genome. Proc. Natl. Acad. Sci. USA. 104:2767-2772.

5. Organ, C. L., A. M. Shedlock, A. Meade, M. Pagel, and S. V. Edwards. 2007. Origin of avian genome size and structure in nonavian dinosaurs. Nature 446:180-184.

6. Shedlock, A. M., D Janes, and S. V. Edwards. 2007. Amniote phylogenomics: Testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large-scale DNA sequences from reptiles. In: Phylogenomics (W. Murphy, Ed.), Methods in Molecular Biology Series, Humana Press, Totowa, NJ, USA.

7. Shedlock, A. M., K. Takahashi, and N. Okada. 2004. SINEs of speciation: tracking lineages with retroposons. Trends in Ecology and Evolution. 19(10): 545-553.

8. Wasser, S. K., A. M. Shedlock, , K. E. Comstock, E. O. Ostrander, B. Mutayoba and M. Stephens. 2004. Assigning African elephant ivory to a geographic region of origin: Applications to the ivory trade. Proc. Natl. Acad. Sci. USA 101(41): 14847-14852 [cover article ].

9. Nikaido, M., F. Matsuno, H. Hamilton, R. L. Brownell Jr., W. Ding, Z. Zuoyan, Y. Cao, A. M. Shedlock, E. Fordyce, M. Hasegawa, and N. Okada. 2001. Retroposon analysis of major cetacean lineages: The monophyly of toothed whales and the paraphyly of river dolphins. Proc. Natl. Acad. Sci. USA. 98:7384-7389.