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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.

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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.

Alcaide, M., S. V. Edwards, and J. J. Negro. 2007. Characterization, polymorphism and evolution of MHC class II genes in birds of prey. Journal of Molecular Evolution 65: 541-554.

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;

Janes, D. E., T. Ezaz, J. A. M. Graves and S. V. Edwards.  2008 Characterization, chromosomal location and genomic neighborhood of a ratite ortholog of a gene with gonadal expression in mammals. Integrative and Comparative Biology 48: 505 - 511.

Organ, C. L., R. G. Moreno, and S. V.  Edwards. 2008. Three tiers of genome evolution in reptiles. Integrative and Comparative Biology 48: 494 - 504.

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.

Bonneaud, C., Burnside, J., and S. V. Edwards. 2008. High-speed developments in avian genomics. Bioscience. 58: 587-595.

Liu, L., D. K. Pearl, R. T. Brumfield, S. V. Edwards. 2008. Estimating species trees using multiple-allele DNA sequence data. Evolution. 62: 2080-2091.

Alcaide, M., S. V. Edwards, J. J. Negro, D. Serrano, and J. L. Tella. 2008. Extensive polymorphism and geographical variation at a positively selected MHC class II B gene of the lesser kestrel (Falco naumanni). Molecular Ecology 17: 2652-2665.

Thomson, R. C., 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: 514–525

Brito, P. and Edwards, S. V. 2008. Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica. DOI 10.1007/s10709-008-9293-3

Janes, D. E., T. Ezaz, J. A. M. Graves and S. V. Edwards. 2008. Recombination and nucleotide diversity in the pseudoautosomal region of minimally differentiated sex chromosomes in the Emu, Dromaius novaehollandiae. doi:10.1093/jhered/esn065

Brumfield, R., L. Liu, D. E. Lum, and S. V. Edwards. 2008. Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae, Manacus) from multilocus sequence data. Systematic Biology 57: 719-731.

Lee, J. Y. and S. V. Edwards. 2008. Divergence across the Carpentarian barrier: Statistical phylogeography of the Red-backed Fairy Wren (Malurus melanocephalus). Evolution. doi:10.1111/j.1558-5646.2008.00543.x

Silva, M. C. and Edwards, S. V. 2009. Structure and evolution of a new avian MHC class II B gene in a sub-Antarctic seabird, the Thin-Billed Prion (Procellariiformes: Pachyptila belcheri).Structure and evolution of a new avian MHC class II B gene in a sub-Antarctic seabird, the Thin-Billed Prion (Procellariiformes: Pachyptila belcheri). Journal of Molecular Evolution 68: 279-291.

Edwards, S. V. 2009. Is a new and general theory of molecular systematics emerging? Evolution 63: 1-19.

Edwards, S. V. 2009. Natural selection and phylogenetic analysis. Proceedings of the National Academy of Sciences USA 106: 8799-8800.

Balakrishnan, C. B. and S. V. Edwards. 2009. Nucleotide variation, linkage disequilibrium and founder-faciliated speciation in wild populations of the zebra finch Taeniopygia guttata. Genetics 181: 645-660.

Alcaide M, Edwards SV, Cadahia SV and Negro J.J. 2009. MHC class I genes of birds of prey: isolation, polymorphism and diversifying selection. Conservation Genetics 10: 1349-1355.

Liu, L., L. Yu, L. Kubatko, D. K. Pearl, and S. V. Edwards. 2009. Coalescent methods for estimating phylogenetic trees. Molecular Phylogenetics and Evolution 53:320-328.

Liu, L. and Edwards, S. V. 2009. Phylogenetic analysis in the anomaly zone. Systematic Biology 58: 452-460.

Liu, L., L. Yu, D. K. Pearl, and S. V. Edwards. 2009. Estimating species phylogenies using coalescence times among sequences. Systematic Biology 58: 468-477.

Anna M. Kearns, Leo Joseph, Scott V. Edwards and Michael C. Double. 2009. Inferring the phylogeography and evolutionary history of the splendid fairy-wren Malurus splendens from mitochondrial DNA and spectrophotometry. Journal of Avian Biology. 40.1: 7-17.

Chapus, C. and S. V. Edwards. 2009. Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird. BMC Genomics. 10(Suppl 2):S8. doi:10.1186/1471-2164-10-S2-S8.

Christopher N. Balakrishnan, R. Ekblom, M. Völker, H. Westerdahl, H. Kotkiewicz, R. Godinez, D. W. Burt, T. Graves, D. K. Griffin, W. Warren, and Scott V. Edwards. 2010. Gene duplication and fragmentation in the zebra finch major histocompatibility complex. BMC Biology 8:29

Organ, C. L., M. Rasmussen, M. W. Baldwin, M. Kellis, and S. V. Edwards. 2010. Phylogenomic approach to the evolutionary dynamics of gene duplication in birds. Pp. 253-267 In Evolution After Gene Duplication. Eds. K. Dittmar and D. Liberles. Wiley & Sons.

Liu, L., L. Yu , S. V. Edwards. 2010. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evolutionary Biology 10:302. doi:10.1186/1471-2148-10-302.

Castillo-Ramírez, S., L. Liu, D. Pearl, and S. V. Edwards. 2010. Bayesian estimation of species trees: a practical guide to optimal sampling and analysis. Pages 15-33 in Estimating Species Trees: Practical and Theoretical Aspects (L. L. Knowles, and L. S. Kubatko, eds.). Wiley-Blackwell, New Jersey.

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. 11: 239-264  

Warren, W. C…..C. N. Balakrishnan, ….N. Backström, S. V. Edwards, et al. 2010. The genome of a songbird. Nature 464: 757- 762. doi:10.1038/nature08819

Janes, D.E., N. Valenzuela, T. Ezaz, C. Amemiya, and S.V. Edwards. 2011. Sex chromosome evolution in Amniotes: Applications for Bacterial Artificial Chromosome libraries. Journal of Biomedicine and Biotechnology 2011:132975.

O'Keefe, K., Silander, O., McCreery, H., Weinreich, D., Wright, K.M., Chao, L., Edwards, S.V., Remold, S.K., Turner, P.E. 2010. Geographic Differences in Sexual Reassortment in RNA Phage. Evolution. 2011:132975.

Miguel Alcaide and S. V. Edwards. 2011. Molecular evolution of the Toll-like receptor multigene family in birds. Molecular Biology and Evolution. 28: 1703-1715.

Janes, D.E., C. Chapus, Y. Gondo, D.F. Clayton, S. Sinha, C.A. Blatti, C.L. Organ, M.K. Fujita, C.N. Balakrishnan, and S.V. Edwards. 2011. Reptiles and mammals have differentially retained long conserved non-coding sequences from the amniote ancestor. Genome Biology and Evolution 3:102–113.

Vo, A.-T. E., M. S. Bank, J. P. Shine, and S. V. Edwards. 2011. Temporal increase in organic mercury in an endangered pelagic seabird assessed via century-old museum specimens. Proc. Natl. Acad. Sci. (USA) 108: 7466-7471.

Bonneaud, C. S. L. Balenger, A. F. Russell, J. Zhang, G. E. Hill, and S. V. Edwards. 2011. Rapid evolution of disease resistance is accompanied by functional changes in gene expression in a wild bird Proc. Natl. Acad. Sci. (USA) 108: 7866-7871.

Organ, C. L., and S. V. Edwards. 2011. Major events in avian genome evolution. Pp. 325-337 in Living Dinosaurs: The Evolutionary History of Modern Birds (G. Dyke and G. Kaiser, eds). Wiley-Blackwell.

Alfoldi, J….Edwards, S.V…..Lindblad-Toh, K. 2011. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 477: 587-591.

Fujita, M., Edwards, S.V., Ponting, C. 2011. The Anolis lizard genome: an amniote genome without isochores. Genome Biol. Evol. 3:974–984.

Rheindt, F. & S. V. Edwards. 2011. Genetic introgression: an integral but neglected component of speciation in birds. Auk 128: 620-632.

Rheindt, F. E., T. Székely, S. V. Edwards, P. L. M. Lee, T. Burke, P. R. Kennerley, D. N. Bakewell et al. 2011.Conflict between Genetic and Phenotypic Differentiation: The Evolutionary History of a ‘Lost and Rediscovered’ Shorebird. PLoS One 6:e26995.

Delaney, N. F., S. Balenger, C. Bonneaud, C. J. Marx, G. E. Hill, N. Ferguson-Noel, P. Tsai et al. 2012. Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum. PLoS Genetics 8:e1002511.

Lee, J. Y., L. Joseph, and S. V. Edwards. 2012. A Species Tree for the Australo-Papuan Fairy-wrens and Allies (Aves: Maluridae). Systematic Biology 61:253-271.

Edwards, S. V., Cameron Devitt, S. & M. Fujita. 2012.  “Phylogeography”. Pp. 557-565 in Encyclopedia of Theoretical Ecology. A. Hastings and L. Gross (eds.). University of California Press, Berkeley.

Bonneaud, C. S. L. Balenger, G. E. Hill, and S. V. Edwards. 2012. Innate immunity and the evolution of resistance to an emerging infectious disease in a wild bird. Molecular Ecology 21: 2628-2639.

Küpper, C. et al. 2012. Triploid plover female provides support for a role of the W chromosome in avian sex determination. Published online doi:10.1098/rsbl.2012.0329.

Anderson, C., L. Liu, D. Pearl, S. V. Edwards. 2012. Tangled trees: The challenge of inferring species trees from coalescent and non-coalescent genes. Pp. 3-28 in Evolutionary Genomics: Statistical and Computational Methods, vol. 2 (M. Anisimova, Ed.) Springer (Humana), New York.

Edwards, S. V. 2012. Afterward [on genetics and the evolutionary history of avian brood parasitism, a response to chapter by Langmore and Spottiswoode]. Pp. 116-118 in Host Manipulation By Parasites. (David P. Hughes, Jacques Brodeur & Frédéric Thomas (eds.) Oxford University Press, New York.

Sen Song, Liang Liu, Scott V. Edwards, and Shaoyuan Wu. 2012. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc. Natl. Acad. Sci. (USA); published ahead of print August 28, 2012, doi:10.1073/pnas.1211733109

Q. Zhang, S.V. Edwards. 2012. The evolution of intron size in amniotes: a role for powered flight? Genome Biology and Evolution. doi: 10.1093/gbe/evs070.

Shaoyuan Wu, Wenyu Wu, Fuchun Zhang, Jie Ye, Xijun Ni, Jimin Sun, Scott V. Edwards, Jin Meng, Chris L. Organ. 2012. Molecular and Paleontological Evidence for a Post-Cretaceous Origin of Rodents. PLoS ONE 7(10): e46445. doi:10.1371/journal.pone.0046445

Shane C. Campbell-Staton,R. M. Goodman, N. Backström, S. V. Edwards, J. B. Losos, J. J. Kolbe. 2012. Out of Florida: mtDNA reveals patterns of migration and Pleistocene range expansion of the Green Anole lizard (Anolis carolinensis). Ecology and Evolution 2: 2274-2284.

Raposo do Amaral, F., Scott V Edwards, Cristina Y Miyaki. 2012. Eight anonymous nuclear loci for the squamate antbird (Myrmeciza squamosa), cross-amplifiable in other species of typical antbirds (Aves, Thamnophilidae). Conservation Genetics Resources 4: 645-647.

Küpper, C. et al. 2012. High gene flow over large geographic distances in a polyandrous shorebird. Molecular Ecology 21: 5864–5879.

Backström, N., Zhang, Q., and Scott V. Edwards. 2012. Evidence for adaptive evolution and increased biased gene conversion in passerines from a house finch (Carpodacus mexicanus) Molecular Biology and Evolution 30:1046–1050.

Backström, N. Daria Shipilina, Mozes P. K. Blom, and Scott V. Edwards. 2012. Cis-regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch (Carpodacus mexicanus). Ecology and Evolution 3: 655–666.

Janes, D., R. Elsey, E. Langan, N. Valenzuela, and S. Edwards. 2013. Sex-Biased Expression of Sex-Differentiating Genes FOXL2 and FGF9 in American Alligators, Alligator mississippiensis. Sexual Development 7:253-260.

Kültz, D., D. F. Clayton, G. E. Robinson, C. Albertson, H. V. Carey, M. E. Cummings, K. Dewar, S. V. Edwards, H. A. Hofmann, L. J. Gross, J. G. Kingsolver, M. J. Meaney, B. A. Schlinger, A. W. Shingleton, M. B. Sokolowski, G. N. Somero, D. C. Stanzione, and A. E. Todgham. . 2013. New Frontiers for Organismal Biology. Bioscience 63:464-471.

Edwards, S. V. 2013. Next-generation QTL mapping: crowdsourcing SNPs, without pedigrees. Molecular Ecology 22:3885-3887.

Dennehy, J. J., S. Duffy, K. J. O’Keefe, S. V. Edwards, and P. E. Turner. 2013. Frequent coinfection reduces RNA virus population genetic diversity. Journal of Heredity 104:704-712.

Alcaide, M., Liu, M., Edwards, S. V.  (2013) Major histocompatibility complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3. PeerJ 1:e86

Joseph, L. S. Edwards, A. McLean. 2013. The Maluridae: inferring avian biology and evolutionary history from DNA sequences. Emu 113: 195–207.

Raposo do Amaral, Fábio, Patrick K. Albers, Scott V. Edwards and Cristina Y. Miyaki. 2013. Multilocus tests of Pleistocene refugia and ancient divergence in a pair of Atlantic Forest antbirds (Myrmeciza). Molecular Ecology 22, 3996–4013.

Shaffer, H. B., P. Minx, D. Warren, A. Shedlock, R. Thomson, N. Valenzuela, J. Abramyan, C. Amemiya, D. Badenhorst, K. Biggar, G. Borchert, C. Botka, R. Bowden, E. Braun, A. Bronikowski, B. Bruneau, L. Buck, B. Capel, T. Castoe, M. Czerwinski, K. Delehaunty, S. Edwards, C. Fronick, M. Fujita, L. Fulton, T. Graves, R. Green, W. Haerty, R. Hariharan, O. Hernandez 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.

Rheindt, F. E., Fujita, M. K., Wilton, P. R., Edwards, S. V. 2013. Introgression and Phenotypic Assimilation in Zimmerius Flycatchers (Tyrannidae): Population Genetic and Phylogenetic Inferences from Genome-Wide SNPs. Systematic Biology 63: 134–152.

Ezaz, T., B. Azad, D. O'Meally, M. J. Young, K. Matsubara, M. J. Edwards, X. Zhang, C. E. Holleley, J. E. Deakin, J. A. Marshall Graves, A. Georges, S. V. Edwards, and S. D. Sarre. 2013. Sequence and gene content of a large fragment of a lizard sex chromosome and evaluation of candidate sex differentiating gene R-spondin 1. BMC Genomics 14:899.

Zhang et al. : A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines. 2014. BMC Genomics 15: 305.

Baldwin, M. W., Y. Toda, T. Nakagita, M. J. O'Connell, K. C. Klasing, T. Misaka, S. V. Edwards, and S. D. Liberles. 2014. Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor. Science 345:929-933.

Wu, S. Y., F. C. Zhang, S. V. Edwards, W. Y. Wu, J. Ye, S. D. Bi, X. J. Ni, C. Quan, J. Meng, and C. L. Organ. 2014. The Evolution of Bipedalism in Jerboas (Rodentia: Dipodoidea): Origin in Humid and Forested Environments. Evolution 68:2108-2118.

Cook, J. A., S. V. Edwards, E. A. Lacey, R. P. Guralnick, P. S. Soltis, D. E. Soltis, C. K. Welch, K. C. Bell, K. E. Galbreath, C. Himes, J. M. Allen, T. A. Heath, A. C. Carnaval, K. L. Cooper, M. Liu, J. Hanken, and S. Ickert-Bond. 2014. Natural History Collections as Emerging Resources for Innovative Education. Bioscience 64:725-734.

McGlothlin, J. W., J. P. Chuckalovcak, D. E. Janes, S. V. Edwards, C. R. Feldman, E. D. Brodie, M. E. Pfrender, and E. D. Brodie. 2014. Parallel Evolution of Tetrodotoxin Resistance in Three Voltage-Gated Sodium Channel Genes in the Garter Snake Thamnophis sirtalis. Molecular Biology and Evolution. doi:10.1093/molbev/msu237

Riehl, C., Strong, M. J., & Edwards, S. V. 2014. Inferential reasoning and egg rejection in a cooperatively breeding cuckoo. Animal Cognition. doi:10.1007/s10071-014-0778-4

Lowe, C., Clarke, J. Baker, A. J., Haussler, D., Edwards, S. V. 2014. Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Molecular Biology and Evolution.

Jarvis, E. D., et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 346: 1320-1331.

Green, R. E., et al. 2014. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science. 346: 1254449.

Zhang, G. J., et al. 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 346: 1311-1320.

Janes, Daniel E., Christopher L. Organ, Rami Stiglec, Denis O’Meally, Stephen D. Sarre, Arthur Georges, Jennifer A.M. Graves, Nicole Valenzuela, Robert A. Literman, Kim Rutherford, Neil Gemmell, John B. Iverson, Jeffrey W. Tamplin, Scott V. Edwards, and Tariq Ezaz. 2014. Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in Reptilia.  Biology Letters 10: 10.1098/rsbl.2014.0809


Liu, L. and Edwards, S. V. 2015. Technical Comment on “Statistical binning enables an accurate coalescent-based estimation of the avian tree”. Science.

Balenger, S. L.  C. Bonneaud, S. Sefick, J. Zhang, S. V. Edwards, G. E. Hill. 2015.  Plumage color predicts pathogen-induced gene expression in a wild bird. Behavioral Ecology

Liu, L., Z. Xi, S. Wu, C. C. Davis, and S. V. Edwards. 2015. Estimating phylogenetic trees from genome-scale data. Annals of the NY Academy of Sciences.

Dierickx, Elisa G., Allison J. Shultz, Fumio Sato, Takashi Hiraoka, Scott V. Edwards. 2015. Morphological and genomic comparisons of Hawaiian and Japanese black-footed albatrosses Phoebastria nigripes using double digest RADseq: implications for conservation. Evolutionary Applications




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