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Andrew M. Shedlock

Ph.D. University of Washington

Dept. of Organismic and Evolutionary Biology
Museum of Comparative Zoology
Harvard University
26 Oxford Street
Cambridge, MA 02138

Tel: 617-496-2397
Fax: 617-495-5667

email: shedlock(at)

Andy and his paradise birds


B.S., Cornell University
M.S., Ph.D., University of Washington

Postdoctoral Positions:

Postdoctoral Fellow, University of California at Berkeley
NSF-JSPS Research Fellow, The Institute of Statistical Mathematics, Tokyo
Research Associate, University of Washington Center for Conservation Biology



I'm interested in the genetic architecture of biological diversity. I have used molecular systematics to examine the speciation of Pacific salmon, the life history evolution of deep sea anglerfishes, and the demographic structure and complex social behavior of African elephants. Recently I have been investigating mobile repetitive elements as both agents of eukaryotic genome evolution and as powerful diagnostic markers for inferring common ancestry among lineages. This work has informed the debate about cetacean macroevolution and has highlighted the major impact of historical retropositional dynamics on generating genotypic diversity. Further characterizing the repetitive DNA landscape of phylogenetically diverse species promises to advance a general theory of genome evolution presently lacking in modern comparative biology and to provide a wealth of valuable molecular markers for systematic and population biology.


SB Cover


My research at Harvard is aimed at advancing the emerging field of phylogenomics via multi-megabase-scale sequence analysis and macro-array hybridization studies of Bacterial Artificial Chromosome (BAC) libraries. Characterizing genome structure in reptiles, in particular, using BAC resources is helping close the present large information gap in the study of comparative vertebrate genomics. For example, we still do not understand the pathways by which amniote (terrestrial egg laying vertebrates) genomes diversified, and phylogenetic methods using available genomic data from only model experimental organisms are insufficient to accomplish this. Understanding the details of reptile genome structure is allowing us to better reconstruct ancestral states, describe how the human and other mammalian genomes have changed since divergence from the common amniote ancestor some 310 million years ago, and determine what molecular processes may have led to the substantial genomic diversity apparent today among major vertebrate taxa.



In addition to my work in genomics and evolutionary genetics, I maintain broad interests in conservation biology and the curation of systematic collections of zoological specimens. This includes optimizing DNA diagnostics based on non-invasive sampling of endangered species in the wild, molecular analysis of archived tissues, and participation in field surveys aimed at advancing the strength and diversity of museum-based research.


My teaching experience spans a diversity of undergraduate and graduate courses in zoology, genetics and evolution, emphasizing vertebrate biology, systematics and genomics. In addition to my research position, I hold a Teaching Fellowship in Harvard's Department of Molecular and Cell Biology and also serve as Core Teaching Faculty for Cornell University's Shoals Marine Laboratory (SML), located on Appledore Island in the Gulf of Maine. At Harvard, I help teach the Life Science Division's introductory series in integrative biology, including LS1B: Genetics, Genomics and Evolution and MCB52: Molecular Biology. At SML, I am in charge of an intensive four-credit laboratory- and field-oriented summer course, BIOSM 472, Marine Phylogenomics. The Harvard courses integrate evolutionary principles and genetic concepts across a wide set of issues in basic biology, molecular medicine and science in society. The Cornell course is aimed at helping motivated students and working professionals integrate advances in molecular biology and genomics with field-based research in ecology and evolution. In addition to student teaching I also provide lectures as Study Leader for adult educational field trips offered through the Harvard Museum of Natural History's International Travel Program.




Thomson, R.C., A.M. Shedlock, S.V. Edwards, and H.B. Shaffer. 2008. Developing markers for multi-locus phylogenetics in non-model organisms: A test case with turtles. Molecular Phylogenetics and Evolution (In press).

Shedlock, A. M. and S. V. Edwards. 2007. Amniota. In: The Timetree of Life (S. B. Hedges and S. Kumar, Eds.), Oxford University Press, New York (in press).

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.

Ishengoma, D. R. S., A. M. Shedlock, C. A. H. Foley, L. J. Foley, S. K. Wasser, S. T. Balthazary, and B. M. Mutayoba. 2007. Effects of poaching on bull mating success in a free-ranging African elephant (Loxodonta africana) population in Tarangire National Park, Tanzania. Conservation Genetics (in press, avail. online).

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.

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

Shedlock, A. M. 2006. Exploring frontiers in the DNA landscape: An introduction to the symposium "Genome analysis and the molecular systematics of retroelements".  Systematic Biology 55(6): 871-874.

Shedlock, A. M. 2006. Phylogenomic investigation of CR1 LINE diversity in reptiles.  Systematic Biology 55(6): 902-911. [cover article]

Sasaki, T., Y. Yasukawa, K. Takahashi, S. Miura, A. M. Shedlock, and N. Okada. 2006. Extensive morphological convergence and rapid radiation in the evolutionary history of the family Geoemydidae (Old World Pond Turtles) revealed by SINE insertion analysis.  Systematic Biology 55(6): 912-927.

Edwards, S.V., W. B. Jennings, and A. M. Shedlock. 2005. Phylogenetics of modern birds in the era of genomics. Proceedings of the Royal Society of London B 272: 979-992.

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.

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]

Shedlock, A. M., T. W. Pietsch, M. G. Haygood, P. Bentzen and M. Hasegawa. 2004. Molecular systematics and life history evolution of anglerfishes (Teleostei: Lophiiformes): evidence from mitochondrial DNA. Steenstrupia, J. Zool. Mus. Univ. Copenhagen 28(2): 129-144.

Okada, N., A. M. Shedlock, and M. Nikaido. 2004. Retroposon Mapping in Molecular Systematics. In: MobileGenetic Elements: Protocols and Genomic Applications (W. J. Miller and P. Capy, Eds.), Methods in Molecular Biology Series, Humana Press, Totowa, NJ, USA.

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.

Saruwatari, T., T. W. Pietsch, A. M. Shedlock et al. 2001. Sibling analysis between female and parasitic males of a ceratioid anglerfish, Cryptopsaras couesii (Teleostei: Lophiiformes). DNA Polymorphism 9:82-85.

Shedlock, A. M. and N. Okada. 2000. SINE insertions: Powerful tools for molecular systematics. Bioessays 22:148-160.

Shedlock, A. M., M. C. Milinkovitch, and N. Okada. 2000. SINE evolution, missing data, and the origin of whales. Systematic Biology 49(4):808-817. [cover article]

Lum, J.K., M. Nikaido, M. Shimamura, A. M. Shedlock, H. Shimodaira, N. Okada, and M. Hasegawa. 2000. SINE insertions and flanking sequences: Quantifying relationships among cetartiodactyls. Molecular Biology and Evolution 17(10):1417-1424.

Shedlock, A. M., M. G. Haygood, T. W. Pietsch and P. Bentzen.  1997.  Enhanced DNA extraction and PCR amplification of mitochondrial genes from formalin-fixed museum specimens.  Biotechniques  22:394-400.

Shedlock, A. M., J. D. Parker, D. A. Crispin, T. W. Pietsch and G. C. Burmer.  1992.  Evolution of the salmonid mitochondrial control region. Molecular Phylogenetics and Evolution.  1(3):179-192.


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