Research Topics
| Scott V EdwardsSummaryAffiliation: Harvard University Country: USA Publications
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Publications
Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotesJohn A St John
Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
Genome Biol 13:415. 2012..The status of these projects and our planned analyses are described...- Exploration of phylogenetic data using a global sequence analysis methodCharles Chapus
Equipe de Bioinformatique Genomique et Moleculaire, INSERM U 726, case 7113, Tour 53 54, 2 place Jussieu, 75005 Paris, France
BMC Evol Biol 5:63. 2005..The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets... - A maximum pseudo-likelihood approach for estimating species trees under the coalescent modelLiang Liu
Department of Agriculture and Natural Resources, Delaware State University, Dover, DE 19901, USA
BMC Evol Biol 10:302. 2010..In this paper, we develop a pseudo-likelihood function of the species tree to obtain maximum pseudo-likelihood estimates (MPE) of species trees, with branch lengths of the species tree in coalescent units... - High-resolution species trees without concatenationScott V Edwards
Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 104:5936-41. 2007..These results make accessible an alternative paradigm for combining data in phylogenomics that focuses attention on the singularity of species histories and away from the idiosyncrasies and multiplicities of individual gene histories... - Phylogenetics of modern birds in the era of genomicsScott V Edwards
Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
Proc Biol Sci 272:979-92. 2005.... - Speciation in birds: genes, geography, and sexual selectionScott V Edwards
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 102:6550-7. 2005.... - Is a new and general theory of molecular systematics emerging?Scott V Edwards
Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Evolution 63:1-19. 2009.... - Estimating species trees using multiple-allele DNA sequence dataLiang Liu
Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
Evolution 62:2080-91. 2008..The Bayesian approach described here provides a powerful framework for statistical testing and integration of population genetics and phylogenetics... - Estimating species phylogenies using coalescence times among sequencesLiang Liu
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Syst Biol 58:468-77. 2009..Two real genomic data sets were analyzed by the 2 methods and produced species trees that are consistent with previous results... - Innate immunity and the evolution of resistance to an emerging infectious disease in a wild birdCamille Bonneaud
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Mol Ecol 21:2628-39. 2012..These observations suggest population differences in the temporal course of the response to infection with MG and imply that innate immune processes were targets of selection in response to MG in the eastern U.S. population... - Divergence across Australia's Carpentarian barrier: statistical phylogeography of the red-backed fairy wren (Malurus melanocephalus)June Y Lee
Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
Evolution 62:3117-34. 2008..By contrast, gene flow between the CY and the TE populations has been dampened by divergence across the Carpentarian barrier... - Coalescent methods for estimating phylogenetic treesLiang Liu
Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
Mol Phylogenet Evol 53:320-8. 2009..In addition, further elaboration of the simplest of coalescent models will be required to incorporate commonly known issues such as deviation from the molecular clock, gene flow and other genetic forces... - Amniote phylogenomics: testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large-scale DNA sequences from reptilesAndrew M Shedlock
Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA
Methods Mol Biol 422:91-117. 2008..Taken together, the genome scanning and shotgun sequencing techniques offer complementary diagnostic potential and can substantially increase the scale and power of analyses aimed at testing evolutionary hypotheses for nonmodel species... - Speciational history of Australian grass finches (Poephila) inferred from thirty gene treesW Bryan Jennings
Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Evolution 59:2033-47. 2005..Although the errors around the population size parameter estimates are considerable, they are the first for birds taking into account multiple sources of variance... - Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal birdCharles Chapus
Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
BMC Genomics 10:S8. 2009.... - The Anolis lizard genome: an amniote genome without isochoresMatthew K Fujita
Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
Genome Biol Evol 3:974-84. 2011..Our results demonstrate that GC composition in Anolis is not associated with important features of genome structure, including gene density and intron size, in contrast to patterns seen in mammal and bird genomes... - Genome evolution in Reptilia, the sister group of mammalsDANIEL E JANES
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Annu Rev Genomics Hum Genet 11:239-64. 2010..Reptilia exhibit a wide range of evolutionary rates of different subgenomes and, from isochores to mitochondrial DNA, provide a critical contrast to the genomic paradigms established in mammals... - Multilocus phylogeography and phylogenetics using sequence-based markersPatrícia H Brito
Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
Genetica 135:439-55. 2009..Whole genomes provide a powerful common yardstick on which both phylogeography and phylogenetics can assume their proper place as ends of a continuum... - Gene duplication and fragmentation in the zebra finch major histocompatibility complexChristopher N Balakrishnan
Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
BMC Biol 8:29. 2010.... - The genome of the green anole lizard and a comparative analysis with birds and mammalsJessica Alföldi
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Nature 477:587-91. 2011..Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations... - Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genomeAndrew M Shedlock
Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 104:2767-72. 2007..The sequences reported in this paper have been deposited in the GenBank database (accession nos. CZ 250707-CZ 257443 and DX 390731-DX 389174)... - A species tree for the Australo-Papuan Fairy-wrens and allies (Aves: Maluridae)June Y Lee
Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
Syst Biol 61:253-71. 2012..Our study shows that ILS is common at the family level in birds yet, despite this, species tree methods converge on broadly similar results for this family... - Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticumNigel F Delaney
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
PLoS Genet 8:e1002511. 2012..Our results suggest that genome evolution in bacterial pathogens of wild birds can be extremely rapid and in this case is accompanied by apparent functional loss of CRISPRs... - Nucleotide variation, linkage disequilibrium and founder-facilitated speciation in wild populations of the zebra finch (Taeniopygia guttata)Christopher N Balakrishnan
Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachussetts 02138, USA
Genetics 181:645-60. 2009..Our analysis provides a quantitative framework for studying the role of selection and drift in shaping patterns of molecular evolution in the zebra finch genome... - Origin of avian genome size and structure in non-avian dinosaursChris L Organ
Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138, USA
Nature 446:180-4. 2007..These genomic characteristics should be added to the list of attributes previously considered avian but now thought to have arisen in non-avian dinosaurs, such as feathers, pulmonary innovations, and parental care and nesting... - Tangled trees: the challenge of inferring species trees from coalescent and noncoalescent genesChristian N K Anderson
Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
Methods Mol Biol 856:3-28. 2012.... - Sex chromosome evolution in amniotes: applications for bacterial artificial chromosome librariesDANIEL E JANES
Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
J Biomed Biotechnol 2011:132975. 2011..Here, we review studies of sex chromosome evolution in amniotes and the ways in which the field of research has been affected by the advent of BAC libraries... - Molecular evolution of the toll-like receptor multigene family in birdsMiguel Alcaide
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Muscat
Mol Biol Evol 28:1703-15. 2011.... - High gene flow on a continental scale in the polyandrous Kentish plover Charadrius alexandrinusClemens Küpper
Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield, Sheffield, S10 2TN, UK
Mol Ecol 21:5864-79. 2012..Adult males were more related than females within genetic clusters. Taken together, our results suggest a prominent role for polyandrous females in maintaining genetic homogeneity across large geographic distances... - Recombination and nucleotide diversity in the sex chromosomal pseudoautosomal region of the emu, Dromaius novaehollandiaeDANIEL E JANES
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
J Hered 100:125-36. 2009..This study provides a snapshot of the population genetics of avian sex chromosomes at an early stage of differentiation... - Characterization, chromosomal location, and genomic neighborhood of a ratite ortholog of a gene with gonadal expression in mammalsDANIEL E JANES
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA Comparative Genomics Group, Research School of Biological Sciences, Australian National University, PO Box 475, Canberra ACT 2601, Australia
Integr Comp Biol 48:505-11. 2008..Future experimentation will report the expression of SubA in ratites, other birds, and nonavian reptiles... - Molecular and paleontological evidence for a post-cretaceous origin of rodentsShaoyuan Wu
Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
PLoS ONE 7:e46445. 2012..The example of the present study suggests that more reliable fossil calibration points may represent the key to resolving these controversies... - Conflict between Genetic and Phenotypic Differentiation: The Evolutionary History of a 'Lost and Rediscovered' ShorebirdFrank E Rheindt
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
PLoS ONE 6:e26995. 2011..Alternatively, gene expression differences may be crucial in producing different phenotypes whereas neutral differentiation may be lagging behind... - Rapid evolution of disease resistance is accompanied by functional changes in gene expression in a wild birdCamille Bonneaud
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 108:7866-71. 2011..We hypothesize that host resistance arose and spread from standing genetic variation in the eastern US and highlight that natural selection can lead to rapid phenotypic evolution in populations when acting on such variation... - Temporal increase in organic mercury in an endangered pelagic seabird assessed by century-old museum specimensAnh Thu E Vo
Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 108:7466-71. 2011..These data show that remote seabird colonies in the Pacific basin exhibit temporal changes in methylmercury levels consistent with historical global and recent regional increases in anthropogenic emissions... - Three tiers of genome evolution in reptilesChris L Organ
Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
Integr Comp Biol 48:494-504. 2008..These findings suggest that the mode of reptilian genome evolution varies across three hierarchical levels of the genome, a pattern consistent with a mosaic model of genomic evolution... - A genomic schism in birds revealed by phylogenetic analysis of DNA stringsScott V Edwards
Department of Zoology and Burke Museum, University of Washington, Box 351800, Seattle, Washington 98195, USA
Syst Biol 51:599-613. 2002..Despite clear problems with phylogenetic analysis of genomic signatures, our study raises intriguing issues about the biological and genomic differences that fundamentally differentiate paleognaths and neognaths... - Reconciling actual and inferred population histories in the house finch (Carpodacus mexicanus) by AFLP analysisZhenshan Wang
Department of Biology, University of Washington, Seattle, Washington 98195, USA
Evolution 57:2852-64. 2003..Our results indicate that AFLPs are a useful tool for population genetic and evolutionary studies of birds, particularly as a prelude to finding molecular markers linked to traits subjected to recent adaptive evolution... - Hitchhiking and recombination in birds: evidence from Mhc-linked and unlinked loci in Red-winged Blackbirds (Agelaius phoeniceus)Scott V Edwards
Department of Biology, University of Washington, Seattle, WA 98195, USA
Genet Res 84:175-92. 2004.... - A phylogeny of the megapodes (Aves: Megapodiidae) based on nuclear and mitochondrial DNA sequencesSharon M Birks
University of Washington, Burke Museum, Seattle 98195 3010, USA
Mol Phylogenet Evol 23:408-21. 2002..It differs significantly from previous hypotheses based on morphology but is consistent with affiliations suggested by a recent study of parasitic chewing lice... - Evolutionary genetics of Carpodacus mexicanus, a recently colonized host of a bacterial pathogen, Mycoplasma gallisepticumChristopher M Hess
Department of Biology, University of Washington, Seattle, USA
Genetica 129:217-25. 2007..These results will be further expanded using experimental studies as well as examination of evolution of the pathogen genome itself... - Tuatara (Sphenodon) genomics: BAC library construction, sequence survey, and application to the DMRT gene familyZhenshan Wang
Department of Biology, University of Washington, Seattle, WA 98195, USA
J Hered 97:541-8. 2006..A deep coverage contig spanning nearly 300 kb was generated, supporting the deep coverage and utility of the library for exploring tuatara genomics... - Mid-Pleistocene divergence of Cuban and North American ivory-billed woodpeckersRobert C Fleischer
Genetics Program, National Museum of Natural History and National Zoological Park, Smithsonian Institution, Washington, DC 20008, USA
Biol Lett 2:466-9. 2006..Our sequences of all three woodpeckers also provide an important DNA barcoding resource for identification of non-invasive samples or remains of these critically endangered and charismatic woodpeckers... - Evolution into and out of the Andes: a Bayesian analysis of historical diversification in Thamnophilus antshrikesRobb T Brumfield
Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, Louisiana 70803, USA
Evolution 61:346-67. 2007..These results highlight the need for additional comparative studies in elucidating processes associated with the colonization of high-elevation habitats and the differentiation of populations within them... - A smörgåsbord of markers for avian ecology and evolutionScott V Edwards
Mol Ecol 17:945-6. 2008..These resources pave the way for easy multilocus study of evolving populations and lineages of birds, and bring the goal of quickly turning nonmodel species in to ecological genomic models tantalizingly close... - Extensive polymorphism and geographical variation at a positively selected MHC class II B gene of the lesser kestrel (Falco naumanni)Miguel Alcaide
Estación Biológica de Doñana CSIC Pabellón de Perú, Avenida Maria Luisa s n 41013, Sevilla, Spain
Mol Ecol 17:2652-65. 2008..Our results therefore underscore the role of balancing selection as well as spatial variations in parasite-mediated selection regimes in shaping MHC diversity when gene flow is limited... - A cDNA macroarray approach to parasite-induced gene expression changes in a songbird host: genetic response of house finches to experimental infection by Mycoplasma gallisepticumZhenshan Wang
Department of Biology, University of Washington, Seattle, WA 98195, USA
Mol Ecol 15:1263-73. 2006..Our results and macroarray resources provide a foundation for molecular co-evolutionary studies of the Mycoplasma parasite and its recently colonized avian host... - Patterns of variation in MHC class II beta loci of the little greenbul (Andropadus virens) with comments on MHC evolution in birdsAndres Aguilar
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
J Hered 97:133-42. 2006..virens genomic or transcribed MHC sequences. The use of conserved MHC primers followed by analysis of cloned sequences allows rapid isolation of MHC loci from exotic species and avoids laborious large-scale cloning and sequencing... - Characterization, polymorphism, and evolution of MHC class II B genes in birds of preyMiguel Alcaide
Estacion Biologica de Donana, CSIC Pabellón de Perú, Avda Ma Luisa s n, 41013, Sevilla, Spain
J Mol Evol 65:541-54. 2007..Finally, through interlocus comparisons and phylogenetic analysis, we also discuss genetic evidence for concerted and transspecies evolution in the raptor MHC... - Ecology of avian influenza virus in birdsDouglas Causey
Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA
J Infect Dis 197:S29-33. 2008....