Scott's publications, 1981 - 1995
Undergraduate publications:
Second Sightings: A History of Ornitholgy in Riverdale, N. Y. 1981. [Catalogue for an exhibit of bird/wildlife paintings at Wave Hill Enfvironmental Center, Riverdale, N.Y.]. Private publication, 16 pp. [and "widely unread" in the words of R. T. Paine!]
Honeycutt, S. V. Edwards, K. Nelson, and E. Nevo. 1987. Mitochondrial DNA variation and the phylogeny of African mole-rats (Rodentia: Bathyergidae). Systematic Zoology 36: 280-292.
Papers from graduate work:
Kocher, T.D, W. K. Thomas, A. Meyer, S. V. Edwards, S. Pääbo, F. X. Villablanca and A. C. Wilson. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences (USA) 86: 6196-6200.
Edwards, S.V., and A.C. Wilson. 1990. Phylogenetically informative length polymorphism and sequence variability in mitochondrial DNA of Australian songbirds (Pomatostomus). Genetics 126: 695-711.
Edwards, S.V., P. Arctander, and A.C. Wilson. 1991. Mitochondrial resolution of a deep branch in the genealogical tree for perching birds. Proceedings of the Royal Society of London series B 243:99-107.
Honeycutt, R.L., M.W. Allard, S.V. Edwards and D.A. Schlitter. 1991. Systematics and evolution of the family Bathyergidae. Pages 45-65 in P.W. Sherman, J.U.M. Jarvis and R.D. Alexander, eds. The Biology of the Naked Mole-Rat. Princeton University Press, Princeton, New Jersey.
Edwards, S. V. & Naeem, S. 1993. The phylogenetic component of cooperative breeding in perching birds. The American Naturalist 141: 754-789.
Edwards, S. V. 1993. Long-distance gene flow in a cooperative breeder detected in genealogies of mitochondrial DNA sequences. Proceedings of the Royal Society of London series B 252: 177-185.
Edwards, S. V. 1993. Mitochondrial gene genealogy and gene flow among island and mainland populations of a sedentary songbird, the grey-crowned babbler (Pomatostomus temporalis). Evolution 47: 1118-1137.
Edwards, S. V. & Naeem, S. 1994. Homology and comparative methods in the study of avian cooperative breeding. The American Naturalist 143: 723-733.
Edwards, S. V. & M. Kot. 1995. Comparative methods at the species level: geographic variation in morphology and group size in grey-crowned babblers (Pomatostomus temporalis). Evolution 49: 1134-1146.
Papers from Postdoctoral Work:
Edwards, S. V., M. Grahn and W. K. Potts. 1995. Dynamics of Mhc evolution in birds and crocodilians: amplification with degenerate primers. Molecular Ecology 4: 719-729.
Edwards, S.V., E. K. Wakeland and W. K. Potts. 1995. Contrasting histories of avian and mammalian MHC genes revealed by class II B genes of songbirds. Proceedings of the National Academy of Sciences. 92: 12200-12204.
Edwards, S. V., and W. K. Potts. 1996. Polymorphism of Mhc genes: implications for conservation genetics of vertebrates. Pp. 214-237 in Molecular Genetic Approaches to Conservation (T. B. Smith and R. K. Wayne, eds). Oxford University Press, Oxford.
Edwards, S. V., K. Chesnut, K., Y. Satta, and E. K.Wakeland, 1997. Ancestral polymorphism of Mhc class II genes in mice: implications for balancing selection and the mammalian molecular clock. Genetics 148: 655-668.
Publications from the Edwards Lab, 1996 - present
Edwards, S. V. 1996. Short- and long-term evolution of Mhc class II B genes in birds: first glimpses. Pp. 169-178 in Current Topics in Molecular Evolution (M. Nei and N. Takahata, eds.). Penn State University Press, Institute of Molecular Evolutionary Genetics, Penn State University.
Lum, P. Y., Edwards, S. V., and Wright, R. 1996. Molecular, functional and evolutionary characterization of the gene encoding HMG-CoA reductase in the fission yeast, Schizosaccharomyces pombe. Yeast 12: 1107-1124.
Edwards, S. V., and P. Arctander. 1997. Congruence and phylogenetic re-analysis of perching bird cytochrome b sequences. Molecular Phylogenetics and Evolution 7: 266-271.
Edwards, S. V. 1997. Relevance of microevolutionary processes to higher level molecular systematics. Pp. 251-278 in Avian Molecular Systematics and Evolution (D. P. Mindell, ed.) Academic Press, New York.
Edwards, S. V., Gasper, J., March, M. 1998. Genomics and polymorphism of Agph-DAB1, and Mhc class II B gene in Red-winged Blackbirds (Agelaius phoeniceus). Molecular Biology and Evolution 15: 236-250.
Edwards, S. V., and P. Hedrick. 1998. Evolution and ecology of MHC molecules: from genomics to sexual selection. Trends in Ecology and Evolution 13: 305-311.
Edwards, S. V. 1998. Diversity of Birds. Pp. 358-369, in Encyclopedia of Reproduction (E. Knobil, J. D. Neill, Editors-in-Chief), Academic Press, San Diego, CA.
Voelker, G. and S. V. Edwards. 1998. Can weighting improve bushy trees?: models of cytochrome b evolution and the molecular systematics of pipits and wagtails (Motacillidae). Systematic Biology 47: 589-603.
Edwards, S. V. [Book Review] “Molecular Evolution and Adaptive Radiation” (eds. T. Givnish and K. Sytsma) . 1998. Cambridge University Press, Cambridge. American Zoologist 38: 986-988.
Edwards, S. V., C. Hess, J. Gasper, and D. Garrigan. 1999. Toward an evolutionary genomics of the avian Mhc. Immunological Reviews, 167: 119-132.
Garrigan D. & Edwards S.V. (1999). Polymorphism across an exon-intron boundary in an avian Mhc class II B gene. Molecular Biology andl Evolution 16:1599-1606.
Hess, C. M., Gasper, J., Hoekstra, H., Hill, C. & Edwards, S. V. 2000 MHC class II pseudogene and genomic signature of a 32-kb cosmid in the House Finch (Carpodacus mexicanus). Genome Research 10 (May): 13-23.
Edwards, S. V., Nusser, J. & Gasper, J. Characterization and evolution of Mhc genes from non-model organisms, with examples from birds.PP. 168-207 in Molecular Methods in Ecology (ed. Baker, A. J.) (Blackwell Scientific, Cambridge, 2000).
Edwards, S. V., Gasper, J., Garrigan, D., Martindale, D. A. & Koop, B. F. 2000. A 39-kb sequence around a blackbird Mhc class II B gene: ghost of selection past and songbird genome architecture. Molecular Biology and Evolution 17: 1384-1395
Edwards, S. V., M. C. Silva, T. Burg, V. Friesen and K. I. Warheit. (2000). Molecular genetic markers in the analysis of seabird bycatch populations. In Seabird Bycatch: Trends, Roadblocks and Solutions. (ed. E. Melvin and J. Parrish), pp. 115-140: Alaska Seagrant Program.
Edwards, S. V., Nusser, J. and Gasper, J. (2000). Characterization and evolution of Mhc genes from non-model organisms, with examples from birds. In Molecular Methods in Ecology (ed. A. J. Baker), pp. 168-207. Cambridge: Blackwell Scientific.
Hoekstra, H. E. and Edwards, S. V. (2000). Multiple origins of XY female mice (genus Akodon): phylogenetic and chromosomal evidence. Proceedings of the Royal Society of London Series B Biological Sciences 267, 1825-1831.
Saunders, M. and Edwards, S. V. (2000). Dynamics and phylogenetic implications of mtDNA control region in New World Jays (Aves: Corvidae). Journal of Molecular Evolution 51, 97-109.
Gasper, J., Shiina, T., Inoko, H. and Edwards, S. V. (2001). Songbird genomics: analysis of 45-kb upstream of a polymorphic Mhc class II gene in Red-winged Blackbird (Agelaius phoeniceus). Genomics 75, 26-34.
Miura, G. and Edwards, S. V. (2001). Cryptic differentiation and geographic variation in genetic diversity of Hall's Babbler (Pomatostomus halli). Journal of Avian Biology 32, 102-110.
Edwards, S. V., Fertil, B., Giron, A. and Deschavanne, P. J. (2002). A genomic schism in birds revealed by phylogenetic analysis of DNA strings. Systematic Biology 51:599-613
Hess, C. M. and Edwards, S. V. (2002). The evolution of major histocompatibility genes in birds. Bioscience 52:423-431.
Edwards, S. V. and W. E. Boles. (2002). Out of Gondwana: the origin of passerine birds. Trends in Ecology and Evolution 17: 347-349.
Birks, S. and Edwards, S. V. (2002). A phylogeny of megapodes (Aves: Megapodidae) based on nuclear and mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 23:408-421.
Waltari, E. and Edwards, S. V. (2002). The evolutionary dynamics of intron size, genome size, and physiological correlates in archosaurs. American Naturalist 160: 539-552.
Brian S. Arbogast, Scott V. Edwards, John Wakeley, Peter Beerli, and Joseph B. Slowinski. (2002). Estimating divergence times from molecular data on population genetic and phylogenetic time scales Annual Review of Ecology and Systematics 33: 707-740
Zelano, B. and Edwards, S. V. (2002). An Mhc component to kin recognition and mate choice in birds: predictions, progress, and prospects. American Naturalist 160: S225 -S237.
Brumfield, R., D. Nickerson, P. Beerli and S. V. Edwards. (2003). The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology and Evolution 18: 249-256.
Edwards, S. V. (2003). Australo-Papuan Babblers. In Encyclopedia of Birds (Andromeda Oxford Ltd., Abingdon, U. K.)
Wang, Z., Hill, G. E., Baker, A. J. and Edwards, S. V. (2003). Reconciling actual and inferred population histories in the House FInch (Carpodacus mexicanus) by AFLP analysis. Evolution 57, 2852-2864.
Edwards, S. V. and Smith, M. (2004). Hitchhiking and recombination in birds: evidence from Mhc-linked and unlinked loci in red-winged blackbirds (Agelaius phoeniceus). Genetical Research 84: 175-192
Edwards, S. V. 2005. Gene and Genome Evolution. Chapter 19, in Evolution , by Douglas Futuyma. Sinauer Associates, Sunderland , MA .
Edwards, S. V., Kingan, S. B., Calkins, J. D., Balakrishnan, C. N., W. Bryan Jennings, Swanson, W. J. and Sorenson, M. D. (2005). Speciation in birds: genes, geography and sexual selection. Proc. Natl. Acad. Sci. ( USA ) 102: 6550-6557.
Edwards, S. V., Jennings , W. B. and Shedlock, A. M. (2005). Phylogenetics of modern birds in the era of genomics. Proceeding of the Royal Society of London series B 272: 979-992.
Jennings , W. B. and Edwards, S. V. 2005. Speciational history of Australian grass finches ( Poephila ) inferred from 30 gene trees. Evolution 59:2033-2047
Edwards, S. V., S. Birks, R. T. Brumfield, and R. Hanner. (2005). Avian Genetic Resources Collections: Archives of Evolutionary and Environmental History. Auk 122:979-984.
Walsh, H. E. and Edwards, S. V. (2005). Conservation genetics and Pacific fisheries bycatch: mitochondrial differentiation and population assignment in black-footed albatrosses ( Phoebastria nigripes ). Conservation Genetics 6:289-295.
Chapus, C., C. Dufraigne, S. Edwards, A. Giron, B. Fertil, and P. Deschavanne. 2005. Exploration of phylogenetic data using a global sequence analysis method. BMC Evolutionary Biology 5:63.
Robert C. Fleischer, Jeremy J. Kirchman, John P. Dumbacher, Louis Bevier, Carla Dove, Nancy C. Rotzel, Scott V. Edwards, Martjan Lammertink, Kathleen J. Miglia, William S. Moore. Mid-Pleistocene divergence of Cuban and North American ivory-billed woodpeckers. Biology Letters 16 May 2006.
Wang, Z., K. Farmer, G. E. Hill, and S. V. Edwards. 2006. A cDNA macroarray approach to parasite-induced gene expression changes in a songbird host: genetic response of house finches to experimental infection by Mycoplasma gallisepticum. Mol Ecol 15:1263-1273.
Aguilar, A., S. V. Edwards, T. B. Smith, and R. K. Wayne. 2006. Patterns of variation in MHC class II beta loci of the little greenbul (Andropadus virens) with comments on MHC evolution in birds. Journal of Heredity 97:133-142.
Fleischer, R. C., J. J. Kirchman, J. P. Dumbacher, L. Bevier, C. Dove, N. C. Rotzel, S. V. Edwards, M. Lammertink, K. J. Miglia, W. S. Moore. 2006. Mid-Pleistocene divergence of Cuban and North American ivory-billed woodpeckers. Biology Letters 2: 466-469.
Wang, Z., T. Miyake, S. V. Edwards and C. T. Amemiya. 2006. Tuatara (Sphenodon) genomics: BAC library construction, sequence survey and application to the DMRT gene family.J. Heredity 97: 541-548.
Hess, C. M., Z. Wang, and S. V. Edwards. 2007. Evolutionary genetics of Carpodacus mexicanus, a recently colonized host of a bacterial pathogen, Mycoplasma gallisepticum. Genetica 129:217-225.
Organ, C., A. Shedlock, A. Meade, M. Pagel, and S. V. Edwards. 2007. Origin of avian genome size and structure in therapod dinosaurs. Nature 446: 180-184
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.
Edwards, S. V., L. Liu, D. K. Pearl. 2007. High resolution species trees without concatenation. Proc. Natl. Acad. Sci. USA 104: 5936-5941.
Brumfield, R. T., and S. V. Edwards. 2007. Evolution into and out of the Andes: a Bayesian analysis of historical diversification in Thamnophilus antshrikes. Evolution 61:346-367.
Edwards, S. V. 2007. Genomics and ornithology. Journal of Ornithology (Suppl 1): S27-S33.
Edwards, S. V. 2008. A smörgåsbord of markers for avian ecology and evolution. Mol. Ecol. 17: 945-946.
Limaye, N., K. A. Belobrajdic, A. E. Wandstrat, F. Bonhomme, S. V. Edwards and E. K. Wakeland. 2008. Prevalence and evolutionary origins of autoimmune susceptibility alleles in natural mouse populations. Genes and Immunity 9: 61-68;
MANUSCRIPTS IN PRESS
Shedlock, A. M., Janes, D., Edwards, S. V. 2008. Amniote phylogenomics: Testing hypotheses with large-scale sequence data from reptiles. In Phylogenomics (W. Murphy, Ed.) Humana Press, Inc., Totowa, NJ.