Publications and Resources

The Western Painted Turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage
Shaffer, H. B, P. Minx, D. E. Warren, A. M. Shedlock, R. C. Thomson, N. Valenzuela, J. Abrahamian, C. T. Amemiya, et al. 2013. The Western Painted Turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology 14:R28 doi:10.1186/gb-2013-14-3-r28.
Shaffer et al. 2013 GB.pdf
Adobe Acrobat Document 3.0 MB
High altitude adaptation of the schizothoracine fishes (Cyprinidae) revealed by the mitochondrial genome analyses
Li, Y., Ren, Z., Shedlock, A.M., Wu, J., Sang, L., Tersing, T., Hasegawa, M., Yonezawa, T., Zhong, Y. 2013. High altitude adaptation of the schizothoracine fishes (Cyprinidae) revealed by the mitochondrial genome analyses. Gene. 517: 169-178.
Li et al. Gene_2013.pdf
Adobe Acrobat Document 1.1 MB
The green anole lizard genome: the first reptilian genome and a comparative analysis with birds and mammals.
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.
Alfoldi et al. Nature_2011.pdf
Adobe Acrobat Document 779.6 KB
Genome evolution in Reptilia, the sister group of mammals.
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.
Janes et al. AnnuRevGenomicsHumGenet_201
Adobe Acrobat Document 463.3 KB
Mitochondrial phylogenomics and evolutionary history of anglerfishes (Teleostei: Lophiiformes): A new perspective.
Miya, M., T. W. Pietsch, J. W. Orr, R. J. Arnold, T. P. Satoh, A. M. Shedlock , H-C. Ho, M. Shimazaki, M. Yabe, and M.Nishida. 2010. Mitochondrial phylogenomics and evolutionary history of anglerfishes (Teleostei: Lophiiformes): A new perspective. BMC Evolutionary Biology, http://www.biomedcentral.com/1471-2148/10/58.
Miya et al. BMC Evolutionary Bio_2010.pd
Adobe Acrobat Document 4.3 MB
Amniotes (Amniota)
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.
Shedlock et al. Timetree of Life_2009.pd
Adobe Acrobat Document 430.9 KB
Paleogenomics of pterosaurs and the evolution of small genome size in flying vertebrates
Organ, C. L. and A. M. Shedlock 2009. Paleogenomics of pterosaurs and the evolution of small genome size in flying vertebrates. Biology Letters 5:47-50.
Organ et al. BiolLett_2009.pdf
Adobe Acrobat Document 264.6 KB
Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles.
R. C. Thompson, A. M. Shedlock, S. V. Edwards, and H. B. Shaffer 2008. Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles. Molecular Phylogenetics and Evolution 49:524-525.
Thompson et al. MolPhylogenetEvol_2008.p
Adobe Acrobat Document 533.9 KB
Phylogenomics of non-avian reptiles and the structure of the ancestral amniote genome
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.
Shedlock et al. PNAS_2007.pdf
Adobe Acrobat Document 1.1 MB
Origin of avian genome size and structure in nonavian dinosaurs
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.
Organ et al. Nature_2007.pdf
Adobe Acrobat Document 379.7 KB
Amniote phylogenomics: Testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large-scale DNA sequences from reptiles
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.
Shedlock et al. MethMolecBioPhylogenet_2
Adobe Acrobat Document 396.0 KB
Effects of poaching on bull mating success in a free-ranging African elephant (Loxodonta africana)population in Tarangire National Park, Tanzania
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 9:247-255.
Ishengoma et al. Conserv Genet_2007.pdf
Adobe Acrobat Document 183.6 KB
Exploring frontiers in the DNA landscape: An introduction to the symposium "Genome analysis and the molecular systematics of retroelements"
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 AM. Systematic Bio_2006.pdf
Adobe Acrobat Document 94.9 KB
Phylogenomic investigation of CR1 LINE diversity in reptiles
Shedlock, A. M. 2006. Phylogenomic investigation of CR1 LINE diversity in reptiles. Systematic Biology 55(6):902-911. [cover article]
Shedlock AM. Systematic Bio_2006_cover a
Adobe Acrobat Document 557.4 KB
Extensive morphological convergence and rapid radiation in the evolutionary history of the family Geoemydidae (Old World Pond Turtles) revealed by SINE insertion analysis
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.
Sasaki et al. Systematic Bio_2006.pdf
Adobe Acrobat Document 4.0 MB
Phylogenetics of modern birds in the era of genomics
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.
Edwards et al. The Royal Society_2005.pd
Adobe Acrobat Document 274.2 KB
Retroposon Mapping in Molecular Systematics
Okada, N., A. M. Shedlock, and M. Nikaido. 2004. Retroposon Mapping in Molecular Systematics. In: Mobile Genetic Elements: Protocols and Genomic Applications (W. J. Miller and P. Capy, Eds.), Methods in Molecular Biology Series, Humana Press, Totowa, NJ, USA.
SINE_Mapping_Chapter_13.open.pdf
Adobe Acrobat Document 6.5 MB
Molecular systematics and life history evolution of anglerfishes (Teleostei: Lophiiformes): evidence from mitochondrial DNA
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. J. Zool. Mus. Univ. Copenhagen 28(2): 129-144.
Shedlock et al. J. Zool. Mus. Univ. Cope
Adobe Acrobat Document 920.6 KB
SINEs of speciation: tracking lineages with retroposons
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.
Shedlock et al. Trends in Eco and Ev_200
Adobe Acrobat Document 161.9 KB
Assigning African elephant ivory to a geographic region of origin: Applications to the ivory trade.
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 ].
Wasser et al. PNAS_2004.pdf
Adobe Acrobat Document 622.7 KB
Retroposon analysis of major cetacean lineages: The monophyly of toothed whales and the paraphyly of river dolphins
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.
Nikaido et al. PNAS_2001.pdf
Adobe Acrobat Document 765.2 KB
Sibling analysis between female and parasitic males of a ceratioid anglerfish, Cryptopsaras couesii (Teleostei: Lophiiformes)
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. PDF NOT AVAILABE
Ref_20.pdf not avail.rtf
Text Document 357 Bytes
SINE insertions: Powerful tools for molecular systematics
Shedlock, A. M. and N. Okada. 2000. SINE insertions: Powerful tools for molecular systematics. Bioessays 22:148-160.
Shedlock et al. Bioessays_2000.pdf
Adobe Acrobat Document 227.4 KB
SINE evolution, missing data, and the origin of whales
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].
Shedlock et al. Systematic Bio_2000.pdf
Adobe Acrobat Document 218.4 KB
SINE insertions and flanking sequences: Quantifying relationships among cetartiodactyls.
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 Evolution17(10)1417-1424.
Lum et al. Molec Bio and Ev_2000.pdf
Adobe Acrobat Document 94.6 KB
Enhanced DNA extraction and PCR amplification of mitochondrial genes from formalin-fixed museum specimens
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 et al. Biotechniques_1997.pdf
Adobe Acrobat Document 126.2 KB
Evolution of the salmonid mitochondrial control region
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.
Shedlock et al. Molec Phylogenet and Evo
Adobe Acrobat Document 2.9 MB