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        J. Andrew DeWoody

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Research, Dr. J. Andrew DeWoody

Publications

If you would like a reprint of a paper, please email me at dewoody@purdue.edu and I'll send you an electronic version.

 

BOOKS

 

J.A DeWoody, J.W. Bickham, C. Michler, K. Nichols, O.E. Rhodes, and K. Woeste (eds.) Molecular approaches in natural resource conservation.� (2010) Cambridge University Press, 392 pp.� ISBN 978-0-521-51564-1 Hardback. �To see the Table of Contents, click here .

Description: DeWoody cover image.jpg

 

 

OTHER PEER-REVIEWED PUBLICATIONS

(journal articles & book chapters)

DeWoody J.A., Honeycutt R.L. & Skow L.C. (1995) Microsatellite markers in white-tailed deer. Journal of Heredity 86:317-319.

Cathey J.C., Smith L.M., Baker R.J. & DeWoody J.A. (1996) Trinucleotide repeat polymorphism at the alpha-enolase/taucrystallin locus in ducks. Animal Genetics 27:130-131.

Cathey J.C., Schmidt C.A. & DeWoody J.A. (1997) Incorporation of bromophenol blue enhances visibility of polyacrylamide gels. Biotechniques 22:222.

Cathey J.C., DeWoody J.A. & Smith L.M. (1998) Microsatellite markers in Canada geese (Branta canadenensis). Journal of Heredity 89:173-175.

DeWoody J.A., Fletcher D., Wilkins, S.D., Nelson W. & Avise J.C. (1998) Molecular genetic dissection of spawning, parentage, and reproductive tactics in a population of redbreast sunfish, Lepomis auritus. Evolution 52:1802-1810.

DeWoody J.A. (1999) Nucleotide variation in the p53 tumor-suppressor gene of voles from Chernobyl, Ukraine. Mutation Research 439:25-36.

DeWoody J.A., Chesser R.K. & Baker R.J. (1999) A translocated cytochrome b pseudogene in voles (Rodentia: Microtus) from Chernobyl, Ukraine. Journal of Molecular Evolution 48:380-382.

Baker R.J., DeWoody J.A., Wright A.J. & Chesser R.K. (1999) On the utility of heteroplasmy in genotoxic studies:  an example from Chernobyl. Ecotoxicology 8:301-309.

Chesser R.K., Sugg D.W., Lomakin M.D., Van Den Bussche R.A., DeWoody J.A., Jagoe C.H., Dallas C.E., Whicker W., Smith M.H., Gaschak S.P., Chizhevsky I.V., Lyabik V.V., Buntova E.G., Holloman K. & Baker R.J. (2000)  Concentrations and dose rate estimates of 134,137Cesium and 90strontium  in small mammals at Chornobyl, Ukraine. Environmental Toxicology and Chemistry 19:305-312.

DeWoody J.A. & Avise J.C. (2000) Microsatellite variation in animal populations, with special emphasis on marine, freshwater, and anadromous fishes. Journal of Fish Biology 56:461-473.

DeWoody J.A., DeWoody Y.D., Fiumera A. & Avise J.C. (2000) On the number of reproductives contributing to a half-sib progeny array. Genetical Research (Cambridge) 75:95-105.

DeWoody J.A., Walker D., & Avise J.C. (2000) Genetic parentage in large half-sib clutches: theoretical estimates and empirical appraisals. Genetics 154:1907-1912.

DeWoody J.A., Fletcher D.E., Wilkins S.D. & Avise J.C. (2000) Microsatellite analyses of parentage and nest guarding in the tessellated darter (Pisces: Percidae). Copeia 2000:740-747.

DeWoody J.A., Fletcher D., Wilkins S.D., Mackiewicz M. & Avise J.C. (2000) The genetic mating system of the spotted sunfish (Lepomis punctatus): mate numbers and the influence of male reproductive parasites. Molecular Ecology 9:2119-2128.

DeWoody J.A., Fletcher D., Wilkins S.D., Nelson, W. & Avise J.C. (2000) Biparental care and genetic monogamy in an externally-fertilizing fish, the largemouth bass (Micropterus salmoides). Proceedings of the Royal Society B267:2431-2437.

Fiumera A.C, DeWoody Y.D., DeWoody J.A., Asmussen M.A. & Avise J.C. (2001) Accuracy and precision of methods to estimate the numbers of parents contributing to a half-sib progeny array. Journal of Heredity 92:120-126.  Invited contribution.

DeWoody J.A. & Avise J.C. (2001) Genetic perspectives on the natural history of fish mating systems. Journal of Heredity 92:167-172.  Invited review paper.

DeWoody J.A., Fletcher D.E., Wilkins S.D. & Avise J.C. (2001) Genetic documentation of filial cannibalism. Proceedings of the National Academy of Sciences USA 98:5090-5092.

Mackiewicz, M., Fletcher D.E., Wilkins S.D., DeWoody J.A. & Avise J.C. (2002) A genetic assessment of parentage in a natural population of dollar sunfish (Lepomis marginatus) based on microsatellite markers. Molecular Ecology 11:1877-1883.

Avise J.C., Jones A.G., Walker D. & DeWoody J.A. (2002) Microsatellite profiles of the genetic mating systems and reproductive natural histories of fishes. Annual Review of Genetics 36:19-45.

Fiumera A.C., DeWoody J.A., Asmussen M.A. & Avise J.C. (2002) Estimating the proportion of offspring attributable to candidate adults. Evolutionary Ecology 16:549-565.

Glaubitz J.C., Rhodes O.E. & DeWoody J.A. (2003) Prospects for inferring pairwise relationships with single nucleotide polymorphisms (SNPs). Molecular Ecology 12:1039-1048.

Belfiore T., Hoffman F.G., Baker R.J. & DeWoody J.A. (2003) The use of nuclear and mitochondrial single nucleotide polymorphisms (SNPs) to identify cryptic species.  Molecular Ecology 12:2011-2017.

Williams R.N. & DeWoody J.A. (2004) Fluorescent dUTP helps characterize ten novel tetranucleotide microsatellites from an enriched salamander (Ambystoma texanum) genomic library. Molecular Ecology Notes 4:17-19.

Howard R.D., DeWoody J.A. & Muir W. (2004) Alternative mating tactics may halt a Trojan gene despite transgenic mating advantage. Proceedings of the National Academy of Sciences USA 101:2934-2938.

DeWoody J.A., Schupp J., Kenefic L., Busch J., Murfitt L. & Keim P. (2004) A universal method for producing ROX-labeled size standards suitable for automated genotyping.  Biotechniques 37:348-352.

DeWoody Y.D. & DeWoody J.A. (2005) On the estimation of genome-wide heterozygosity using molecular markers. Journal of Heredity 96:85-88.

Rudnick J.A., Katzner T.E., Bragin E.A., Rhodes O.E. & DeWoody J.A. (2005) Using naturally shed feathers for individual identification, genetic parentage analyses, and population monitoring in an endangered Eastern imperial eagle (Aquila heliaca) population from Kazakhstan. Molecular Ecology 14:2959-2967.

Bos D.H. & DeWoody J.A. (2005) Molecular characterization of major histocompatibility complex class II alleles in wild tiger salamanders (Ambystoma tigrinum). Immunogenetics 57:775-781.

DeWoody J.A. (2005) Molecular approaches to the study of parentage, relatedness and fitness: practical applications for wild animals. Journal of Wildlife Management 69:1400-1418.  Invited review paper.

Gopurenko, D., Williams R.N., McCormick C. & DeWoody J.A. (2006) Insights into the aggregate breeding biology of the tiger salamander (Ambystoma tigrinum) as revealed by genetic parentage analyses. Molecular Ecology 15:1917-1928.

Waser, P.M., Busch J., McCormick C.R. & DeWoody J.A. (2006) Parentage analysis detects cryptic pre-capture dispersal in a philopatric rodent. Molecular Ecology 15:1929-1937.

Triant D.A. & DeWoody J.A. (2006) Accelerated molecular evolution in Microtus (Rodentia) as assessed via complete mitochondrial genome sequences. Genetica 128:95-108.

Waser, P.M. & DeWoody J.A. (2006) Multiple paternity in a philopatric rodent:  the interaction of competition and choice.  Behavioral Ecology 17:971-978.

Busch J.D., Waser P.M. & DeWoody J.A. (2007) Recent demographic bottlenecks are not accompanied by a genetic signature in two populations of banner-tailed kangaroo rats (Dipodomys spectabilis).  Molecular Ecology 16:2450-2462.

Triant D.A. & DeWoody J.A. (2007) The occurrence, detection, and avoidance of mitochondrial DNA translocations in mammalian systematics and phylogeography.  Journal of Mammalogy 88:908-920.

Rudnick J.A., Katzner T.E., Bragin E.A. & DeWoody J.A. (2007) Species identification of birds through genetic analysis of naturally shed feathers.  Molecular Ecology Notes 7:757-762.

Triant D.A. & DeWoody J.A. (2007) Extensive numt transfer in a rapidly evolving rodent has been mediated by independent insertion events and by duplications.  Gene 401:61-70.

Bos D.H., Turner S.M. & DeWoody J.A. (2007) Haplotype inference from diploid sequence data: evaluating the performance of Bayesian methods using non-neutral MHC sequences.  Hereditas 144:228-234.

Turner S.M., Faisal M. & DeWoody J.A. (2007) Major histocompatibility complex (MHC) genotype predicts susceptibility to Renibacterium salmoninarum in Atlantic salmon (Salmo salar L.).  Animal Genetics 38:517-519.

Gopurenko D., Williams R.N. & DeWoody J.A. (2007) Reproductive and mating success in the small-mouthed salamander (Ambystoma texanum) estimated via microsatellite parentage analysis.  Evolutionary Biology 34:130-139.

Triant D.A. & DeWoody J.A. (2008) Molecular analyses of mitochondrial pseudogenes within the nuclear genome of arvicoline rodents.  Genetica 132:21-33.

Rudnick J.A., Katzner T.E., Bragin E.A. & DeWoody J.A. (2008) A noninvasive genetic evaluation of population size, philopatry, and communal roosting behavior of non-breeding imperial eagles (Aquila heliaca).  Conservation Genetics 9:667-676.

Glista D.J., DeVault T.L & DeWoody J.A. (2008) Vertebrate road mortality and its impact on amphibians.  Herpetological Conservation and Biology 3:77-87.

Bos D.H., Gopurenko D., Williams R.N. & DeWoody J.A. (2008) Inferring population history and demography using microsatellites, mitochondrial DNA, and major histocompatibility complex (MHC) genes.  Evolution 62:1458-1468.

Chaves-Campos, J. & DeWoody J.A. (2008) The spatial distribution of avian relatives:  do obligate army-ant-following birds roost and feed near family members?  Molecular Ecology 17:2963-2974.

Bulut, Z., McCormick C.R., Bos D.H. & DeWoody J.A. (2008) Polymorphism for alternative splicing of major histocompatibility complex (MHC) transcripts in wild tiger salamanders.  Journal of Molecular Evolution 67:68-75.

Williams R.N., Bos D.H., Gopurenko D. & DeWoody J.A. (2008) Amphibian malformations and inbreeding.  Biology Letters 4:549-552.

Busch J.D., Waser P.M. & DeWoody J.A. (2008) Characterization of expressed class II MHC loci in the banner-tailed kangaroo rat (Dipodomys spectabilis) reveals multiple DRB loci.  Immunogenetics 60:677-688.

McCormick, C.R., Bos D.H. & DeWoody J.A. (2008)  Multiple molecular approaches yield no evidence for sex-determining genes in lake sturgeon (Acipenser fulvescens).  Journal of Applied Ichthyology 24:643-645.

DeVault T., Glista D. & DeWoody J.A. (2009) A review of mitigation measures for reducing wildlife mortality on roadways.  Landscape and Urban Planning 91:1-7.

Triant D.A. & DeWoody J.A. (2009) Integrating numt pseudogenes into mitochondrial phylogenies: comment on Mitochondrial phylogeny of Arvicolinae using comprehensive taxonomic sampling yields new insights.  Biological Journal of the Linnean Society 97:223-224.

Hale M.C., McCormick C.R., Jackson J.R. & DeWoody J.A. (2009) Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens):  the relative merits of normalization and rarefaction in gene discovery.  BMC Genomics 10:203.  Designated a Highly Accessed paper by the journal, indicating this paper has been especially highly accessed (>7400x) relative to its age

Williams R.N. & DeWoody J.A. (2009) Reproductive success and sexual selection in wild tiger salamanders (Ambystoma tigrinum tigrinum).  Evolutionary Biology 36:201-213.

Bulut Z., McCormick C.R., Gopurenko D., Williams R.N., Bos D.H. & DeWoody J.A. (2009) Microsatellite mutation rates in the eastern tiger salamander (Ambystoma tigrinum tigrinum) differ 10-fold across loci.  Genetica 136:501-504.

Triant D.A. & DeWoody J.A. (2009) Demography and phylogenetic utility of numt pseudogenes in the southern red-backed vole (Myodes gapperi).  Journal of Mammalogy 90:561-570.

Rudnick J.A., Miller A., Lacy R.C. & DeWoody J.A. (2009) Methods and prospects for using molecular data in the genetic management of populations:  an empirical example using parma wallabies (Macropus parma).  Journal of Heredity 100:441-454.

Turner S.M., Chaves-Campos J. & DeWoody J.A. (2009) Parental relatedness and major histocompatibility effects on early embryo survivorship in Atlantic salmon (Salmo salar).  Genetica 137:99-109.

Bos D.H., Gopurenko D., Williams R.N., Bulut Z. & DeWoody J.A. (2009) Condition-dependant mate choice and a reproductive disadvantage for MHC-divergent tiger salamanders. Molecular Ecology 18:3307-3315.  Highlighted by an accompanying News and Views Perspective article in Molecular Ecology; recommended reading by the Faculty of 1000.

Busch J.D., Waser P.M. & DeWoody J.A. (2009) The influence of density and sex on patterns of fine-scale genetic structure.  Evolution 63:2302-2314.

Williams R.N., Kemp K., Williams B. & DeWoody J.A. (2009) Breeding chronology, sexual dimorphism, and genetic diversity of congeneric Ambystomatid salamanders.  Journal of Herpetology 43: 438-449.

Araya-Ajoy Y., Chaves-Campos J., Kalko E.K.V. & DeWoody J.A. (2009) High-pitched notes during vocal contests signal genetic diversity in ocellated antbirds.  PLoS ONE 4(12): e8137. doi:10.1371/journal.pone.0008137  Viewed >2900x online.

Cooper J.D., Waser P.M., Vitalis R., Gopurenko D., Hellgren E.C., Gabor T.M. & DeWoody J.A. (2010) Quantifying male-biased dispersal among social groups in the collared peccary (Pecari tajacu) using analyses based on mtDNA variation.  Heredity 104:79-87.

Hale M.C., Jackson J.R. & DeWoody J.A. (2010) Discovery and evaluation of candidate sex-determining genes and xenobiotics in the gonads of lake sturgeon (Acipenser fulvescens).  Genetica 138:745-756. DOI: 10.1007/s10709-010-9455-y

Eo S.H. & DeWoody J.A. (2010) Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles.  Proceedings of the Royal Society 277:3587-3592.

Cooper J.D., Waser P., Gopurenko D., Hellgren E., Gabor T. & DeWoody J.A. (2010) Measuring sex-biased dispersal in social mammals: comparisons of nuclear and mitochondrial genes in collared peccaries.  Journal of Mammalogy 91:1413-1424.

Doyle J.M., McCormick C.R. & DeWoody J.A. (2011) The quantification of spermatozoa by real-time quantitative PCR, spectrophotometry, and spermatophore cap size. Molecular Ecology Resources 11:101-106.

DeWoody J.A. (2011) Transformational discoveries and paradigm shifts in evolutionary biology.  Review of Remarkable Creatures: Epic Adventures in the Search for the Origin of Species by Sean B. Carroll.  BioScience 61:154-155.  Invited review.

Eo S.H., Doyle J.M. & DeWoody J.A. (2011) Genetic diversity in birds is associated with body mass and habitat type.  Journal of Zoology 283:220-226.

Cooper J.D, Waser P.M., Hellgren E.C., Gabor T.M. & DeWoody J.A. (2011) Is sexual monomorphism a predictor of polygynandry?  Evidence from a social mammal, the collared peccary (Pecari tajacu).  Behavioral Ecology and Sociobiology 65:775-785

Katzner T.E., Ivy J.A., Bragin E.A., Milner-Gulland E.J. & DeWoody J.A. (2011) Conservation implications of inaccurate estimation of cryptic population size.Animal Conservation 14:328-332 Feature Article, highlighted on journal cover with three accompanying Commentary articles.

Katzner T.E., Ivy J.A., Bragin E.A., Milner-Gulland E.J. & DeWoody J.A. (2011) Cryptic population size and conservation: consequences of making the unknown known. Animal Conservation 14:340-341. Response to three Commentaries on our Feature Article.

McCreight J., DeWoody J.A & Waser P.M. (2011) DNA from copulatory plugs provides insights into sexual selection. Journal of Zoology 284:300-304

Eo S.H., Doyle J.M., Hale M.C., Marra N.J., Ruhl J.D. & DeWoody J.A. (2012) Comparative transcriptomics and gene expression in larval tiger salamander (Ambystoma tigrinum) gill and lung tissues as revealed by pyrosequencing. Gene

Katzner T.E., Wheeler M., Negro J.J., Kapetanakos Y., DeWoody J.A., Horvath M. & Lovette I. (2012) To pluck or not to pluck: scientific methodologies should be carefully chosen, not one size fits all. Journal of Avian Biology 43:1-3.

Campomizzi, A. J., M. L. Morrison, J. A. DeWoody, S. L. Farrell & R.N. Wilkins. (2012) Win-stay, lose-switch and public information strategies for patch fidelity of songbirds with rare extra-pair paternity. Scientific Reports 2:294 | DOI: 10.1038/srep00294.

Fahey A.L., Ricklefs R.E., Latta S. & DeWoody J.A. (2012) Comparative historical demography of migratory and nonmigratory birds from the Carribean island of Hispaniola. Evolutionary Biology 39:400-414

Eo, S.H. & DeWoody J.A. (2012) The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts. BMC Genomics 13:259 DOI:10.1186/1471-2164-13-259. Designated a Highly Accessed paper by the journal, indicating this paper has been especially highly accessed (~1900x) relative to its age.

Marra N.J., Eo S.H., Hale M.C., Waser P.M., & DeWoody J.A. (2012) A priori and a posteriori approaches for finding genes of evolutionary interest in non-model species: osmoregulatory genes in the kidney transcriptome of the desert rodent Dipodomys spectabilis (banner-tailed kangaroo rat). Comparative Biochemistry and Physiology Part D 2012:328-339.

DeWoody J.A., Abts K.C., Fahey A.L., Ji Y., Kimble S.J., Marra N.J., Wijayawardena B.K. & Willoughby J.R. (2013) Of contigs and quagmires: next-gen sequencing pitfalls associated with transcriptomic studies. Molecular Ecology Resources 13:551-558.

Wijayawardena B., Minchella D.J. & DeWoody J.A. (2013) Hosts, parasites, and horizontal gene transfer. Trends in Parasitologyin press). DOI: 10.1016/j.pt.2013.05.001

Doyle J.M., Siegmund G., Ruhl J.D., Eo S.H., Hale M.C., Marra N.J., Waser P.M. & DeWoody J.A. (2013) Microsatellite analyses across transcriptomes of lake sturgeon, tiger salamanders, and kangaroo rats. Genome (in revision)

Wijayawardena B., Minchella D.J. & DeWoody J.A. (2013) Hosts, parasites, and horizontal gene transfer.  Trends in Parasitology 29:329-338.

Doyle J.M., Siegmund G., Ruhl J.D., Eo S.H., Hale M.C., Marra N.J., Waser P.M. & DeWoody J.A. (2013) Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis). Genome 56:407-414.

Katzner T.E., Jackson D.S., Ivy J., Bragin E.A. & DeWoody J.A. (2014) Variation in offspring sex ratio of a sexually dimorphic, long-lived raptor, the Eastern Imperial Eagle. Ibis, in press.

Fahey A.L., Ricklefs R.E. & DeWoody J.A. (2014) DNA-based approaches for evaluating historical demography in terrestrial vertebrates.  Biological Journal of the Linnean Society, in press.

Doyle J.M., Katzner T.E., Bloom P.H., Ji Y. & DeWoody J.A. (2014) The genome sequence of a widespread apex predator, the Golden Eagle (Aquila chrysaetos).  PLoS ONE, in revision.

 

If you would like a reprint of a paper, please email me at dewoody@purdue.edu and I'll send you an electronic version.

 

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