If you’d like to see these papers in reverse chronological order, please see my Google Scholar Profile. 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
Molecular Approaches in Natural Resource Conservation
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 for book details .
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 Ecology11:1877-1883.
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 Ecology16:549-565.
Glaubitz J.C., Rhodes O.E. & DeWoody J.A. (2003) Prospects for inferring pairwise relationships with single nucleotide polymorphisms (SNPs). Molecular Ecology12:1039-1048.
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 NationalAcademy 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 Ecology15:1929-1937.
Triant D.A. & DeWoody J.A. (2006) Accelerated molecular evolution in Microtus(Rodentia) as assessed via complete mitochondrial genome sequences. Genetica128:95-108.
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 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
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 Sociobiology65:775-785
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 492:329-38.
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 relative to its age.
Marra N.J., Eo S.H., Hale M.C., Waser P.M., & DeWoody J.A. (2012) A priori and aposteriori approaches for finding genes of evolutionary interest in non-model species: osmoregulatory genes in the kidney transcriptome of the desert rodentDipodomys 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 Resources13:551-558.
Wijayawardena B., Minchella D.J. & DeWoody J.A. (2013) Hosts, parasites, and horizontal gene transfer. Trends in Parasitology 29:329-338. In March 2014, this paper was voted a Top 10 article of 2013 by the journal Editorial Board.
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 156: 395-403.
Doyle J.M., Katzner T.E., Bloom P.H., Ji Y., Wijayawardena B.K. & DeWoody J.A. (2014) The genome sequence of a widespread apex predator, the Golden Eagle (Aquila chrysaetos). PLoS ONE 9(4): e95599. DOI: 10.1371/journal.pone.0095599.
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 112:367–386.
Marra N.J., Romero A. & DeWoody J.A. (2014) Natural selection and the genetic basis of osmoregulation in Heteromyid rodents as revealed by RNA-seq. Molecular Ecology 23:2699–2711.
Nowakowski A.J., Willoughby J.R., DeWoody J.A. & Donnelly M.A. (2014) Polymorphic microsatellite loci for a neotropical leaf-litter frog (Craugastor bransfordii) characterized through Illumina sequencing. Conservation Genetics Resources 10.1007/s12686-014-0185-9.
DeWoody J.A. (2014) Heirloom genomes and bison conservation. Science 345:1009.
Marra N.J. & DeWoody J.A. (2014) Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents. BMC Genomics 15:929 | DOI:10.1186/1471-2164-15-929.
Willoughby J.R., Fernandez N.B., Lamb M.C., Ivy J., Lacy R. & DeWoody J.A. (2015) The impacts of inbreeding, drift, and selection on genetic diversity in captive breeding populations. Molecular Ecology 24:98-110.
Nowakowski A.J., DeWoody J.A., Fagan M.E., Willoughby J.R. & Donnelly M.A. (2015) Mechanistic insights into landscape genetic structure of two tropical amphibians using field-derived resistance surfaces. Molecular Ecology 24:580-595.
Abts K.C., Ivy J. & DeWoody J.A. (2015) Immunomics of the koala (Phascolarctos cinereus). Immunogenetics 67:305-321.
Wijayawardena B., DeWoody J.A. & Minchella D.J. (2015) The genomic proliferation of transposable elements is facilitated by the invasion of new habitats: Schistosoma mansoni in the new world. Genetica 143:287-298.
Tracy K.E., Kiemnec-Tyburczy K.M., DeWoody J.A., Parra-Olea G. & Zamudio K.R. (2015) Positive selection drives the evolution of a major histocompatibility complex gene in an endangered Mexican salamander species complex. Immunogenetics 67:323-335.
Ji Y., Marra N.M. & DeWoody J.A. (2015) Comparative analysis of active retrotransposons in the transcriptomes of three species of Heteromyid rodents. Gene 562:95-106.
Doyle J.M., Hacking C.C, Willoughby J.R., Sundaram M. & DeWoody J.A. (2015) Mammalian genetic diversity as a function of habitat, body size, trophic class, and conservation status. Journal of Mammalogy 96:564-572.
Wijayawardena B., Minchella D.J. & DeWoody J.A. (2015) Horizontal gene transfer in schistosomes: a critical assessment. Molecular & Biochemical Parasitology 201:57-65.
Fahey A.L., Ricklefs R.E. & DeWoody J.A. (2015) Historical demography of bird populations from Hispaniola assessed by nuclear and mitochondrial gene sequences. Folia Zoologica 64:259-272. Invited paper.
Willoughby J.R., Sundaram M., Wijayawardena B.K., Lamb M.C., Kimble S.J.A., Ji Y., Fernandez N.B., Antonides J.D., Marra N.J. & DeWoody J.A. (2015) The reduction of genetic diversity in threatened vertebrates and new recommendations regarding effective population size and IUCN conservation rankings. Biological Conservation 191:495-503.
Swihart R.K., Sundaram M., Hook T.O. & DeWoody J.A. (2016) Factors affecting scholarly performance by wildlife and fisheries faculty. Journal of Wildlife Management 80: 563–572.
Swihart R.K., Sundaram M., Hook T.O., Kellner K.F. & DeWoody J.A. (2016) Performance benchmarks for scholarly metrics associated with fisheries and wildlife faculty. PLoS ONE 11(5): e0155097.
Willoughby J.R., Wijayawardena B.K., Sundaram M., Swihart R.K & DeWoody J.A. (2016) The importance of including imperfect detection models in eDNA experimental design. Molecular Ecology Resources 16:837-844.
Ji Y. & DeWoody J.A. (2016) Genomic landscape of long terminal repeat retrotransposons (LTR-RTs) and solo LTRs as shaped by ectopic recombination in chicken and zebra finch. Journal of Molecular Evolution 82:251-263.
Abdel Moniem H.M., Schemerhorn B.J., DeWoody J.A. & Holland J.D. (2016) Landscape genetics of a pollinator longhorn beetle [Typocerus v. velutinus(Olivier)] on a continuous habitat surface. Molecular Ecology 25:5015-5028.
Wijayawardena B.K, Minchella D.J. & DeWoody J.A. (2016) The influence of trematode parasite burden on gene expression in a mammalian host. BMC Genomics 17:600 DOI: 10.1186/s12864-016-2950-5.
Doyle J.M., Katzner T.E., Roemer G.W., Cain III J.W., Milsap B., McIntire C., Sonsthagen S., Fernandez N., Wheeler M., Bulut Z., Bloom P. & DeWoody J.A. (2016) Novel single nucleotide polymorphisms reveal genetic structure and viability selection in the Golden Eagle (Aquila chrysaetos), a vagile raptor with a holarctic distribution. Conservation Genetics 17:1307-1322. DOI: 10.1007/s10592-016-0863-0.
DeWoody J.A. (2016) The tangled bank, ecology, and Gordian knots. BioScience 66:1079-1080.
Bulut Z., Bragin E., DeWoody J.A., Braham M., Katzner T.E., & Doyle J.M. (2016) Raptor space use and philopatry as assessed using non-invasive genetic methods: eagles on the Asian steppe. Journal of Raptor Research 50:351-362.
Katzner T.E., Nelson D., Braham M., Doyle J.M., Fernandez N., Duerr A.E., Bloom P., Miller T. & DeWoody J.A. (2017). Golden eagle fatalities and the continental-scale consequences of local wind-energy generation. Conservation Biology 31: 406-415. DOI: 10.1111/cobi.12836.
Antonides J., Ricklefs R.E. & DeWoody J.A. (2017) The genome sequence and insights into the immunogenetics of the bananaquit (Passeriformes: Coereba flaveola). Immunogenetics 69:175-186. DOI:10.1007/s00251-016-0960-8
Ji Y. & DeWoody J.A. (2017) Relationships among powered flight, metabolic rate, body mass, genome size, and the retrotransposon complement of volant birds. Evolutionary Biology 44:261-272. DOI:10.1007/s11692-016-9405-4.
Willoughby J.R., Sundaram M., Wijayawardena B.K., Lamb M.C., Kimble S.J.A., Ji Y., Fernandez N.B., Antonides J.D., Marra N.J. & DeWoody J.A. (2017) Biome and migratory behavior significantly influence vertebrate genetic diversity. Biological Journal of the Linnean Society 121:446–457.
Feiner Z.S., DeWoody J.A., Breck J.E. & Hook T.O. (2017) Multilocus heterozygosity interacts with environment to influence early life size. Ecology and Evolution 2017:1-13. DOI: 10.1002/ece3.2781
Willoughby J.R., Ivy J.A., Lacy R.C., Doyle J.M. & DeWoody J.A. (2017) Inbreeding and selection shape genomic diversity in captive populations: implications for the conservation of endangered species. PLoS ONE DOI: 10.1371/journal.pone.0175996
DeWoody J.A., Fernandez N.B., Brüniche-Olsen A., Antonides J.D., Doyle J.M., San Miguel P., Westerman R., Vertankin V., Codard-Codding C. & Bickham J.W. (2017) Characterization of the gray whale (Eschrichtius robustus) genome and a genotyping array based on single nucleotide polymorphisms in candidate genes. Biological Bulletin 232:186-197.
Katzner T., Driscoll D., Jackman R., Bloom P., Thomas S., Cooper J., Living S., Grubb T., Doyle J., Bell D., J. Didonato & DeWoody J.A. (2018) Non-anthropogenic diet-based oiling of predatory birds. Journal of Raptor Research 52:82-88.
Leroy G., Carroll E.L., Bruford M., DeWoody J.A., Strand A., Waits L., & Wang J. (2018) Next-generation metrics for monitoring genetic erosion within populations of conservation concern. Evolutionary Applications 11:1066-1083. https://doi.org/10.1111/eva.12564.
Carroll E.L., Bruford M., DeWoody J.A., Leroy G., Strand A., Waits L., & Wang J. (2018) Genetic and genomic monitoring with minimally invasive sampling methods. Evolutionary Applications 11:1094-1119. https://doi.org/10.1111/eva.12600.
Doyle J.M., Bell D.A., Bloom P.H., Emmons G., Fesnock A., Katzner T.E., LaPre L., Leonard K., San Miguel P., Westerman R. & DeWoody J.A. (2018) New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus). BMC Genomics 19(1):233. doi: 10.1186/s12864-018-4615-z.
Brüniche-Olsen A., Westerman R., Kazmierczyk Z., Vertyankin V.V., Godard-Codding C., Bickham J.W. & DeWoody J.A. (2018) The inference of gray whale (Eschrichtius robustus) population attributes from whole-genome sequences. BMC Evolutionary Biology18(87) https://doi.org/10.1186/s12862-018-1204-3
Brüniche-Olsen A., R. Urban, J., Vertyankin V.V., Godard-Codding C.A.J., Bickham J.W. & DeWoody J.A. (2018) Genetic data reveal mixed-stock aggregations of gray whales in the North Pacific Ocean. Biology Letters 14: doi.org/10.1098/rsbl.2018.0399.
Brüniche-Olsen A., Kellner K.F., Anderson C.J. & DeWoody J.A. (2018) Runs of homozygosity have utility in mammalian conservation and evolutionary studies. Conservation Genetics 19:1295–1307.
Abts K.C., Ivy J.A. & DeWoody J.A. (2018) Behavioral, environmental, and genetic determinants of mating success in captive koalas (Phascolarctos cinereus). Zoo Biology 37:416-433.
Antonides J.D., Mathur S., Sundaram M., Ricklefs R.E. & DeWoody J.A. (2019) Immunogenetic response of the bananaquit (Coereba flaveola) in the face of hemosporidian parasites. BMC Evolutionary Biology 19:107.
Romero A., Mort M.E., DeWoody J.A. & Timm R.M. (2019) Genetic relationships of Caribbean lowland spiny pocket mice (Heteromys desmarestianus: Rodentia; Heteromyidae): evidence of a distinct mitochondrial lineage. Therya 10:309-318.
Doyle J.M., Willoughby J., Bell D.A., Bloom P.H., Bragin E.A., Fernandez N.B., Katzner T.E., Leonard K. & DeWoody J.A. (2019) Elevated heterozygosity in adults relative to juveniles provides evidence of viability selection in eagles and falcons. Journal of Heredity 110:696-706.
Brykov V.A., Efimova K.V., Brüniche-Olsen A., DeWoody J.A. & Bickham J.W. (2019) Population structure of Sakhalin gray whales revealed by DNA sequences of four mtDNA genes. Population structure of Sakhalin gray whales (Eschrichtius robustus) revealed by DNA sequences of four mtDNA genes. Pp. 441–454 in From field to laboratory: a memorial volume in honor of Robert J. Baker (R. D. Bradley, H. H. Genoways, D. J. Schmidly, and L. C. Bradley, eds.). Special Publications, Museum of Texas Tech University 71:xi+1–911.
DeWoody J.A. (2019) Robert J. Baker—Encomium. Pp. 886–887 in From field to laboratory: a memorial volume in honor of Robert J. Baker (R. D. Bradley, H. H. Genoways, D. J. Schmidly, and L. C. Bradley, eds.). Special Publications, Museum of Texas Tech University 71:xi+1–911.
DeWoody J.A. & DeWoody Y.D. (2019) Our unexpected ride. Science 366:542.
Mathur S., Tomecek J.M., Heniff A., Luna R. & DeWoody J.A. (2019) Evidence of genetic erosion in a peripheral population of a North American game bird: the Montezuma quail (Cyrtonyx montezumae). Conservation Genetics 20:1369–1381.
Brüniche-Olsen A., Kellner K.F. & DeWoody J.A. (2019) Body size, geographic range, and demographic history are key drivers of genomic diversity and inbreeding levels in Darwin’s finches and related tanagers. Molecular Ecology 28: 4914-4925.
Antonides J.D., Mathur S. & DeWoody J.A. (2019) Episodic positive diversifying selection on key immune system genes in major avian lineages. Genetica 147:337-350.
Marsden E., Abbot R.J., Austerlitz F., Ortiz-Barrientos D., Baucom R.S., Bongaerts P., Bonin A., Bonneaud C., Browne L., Buerkle C.A., Caicedo A.L., Cruzan M.B., Davison A., DeWoody J.A. and 42 others. Sharing and reporting benefits from biodiversity research. (2020) Molecular Ecology 30:1103-1107. DOI: 10.1111/mec.15702
Mathur S. & DeWoody J.A. (2021) Genetic load has potential in large populations but is realized in small inbred populations. Evolutionary Applications 14:1540-1557. https://doi.org/10.1111/eva.13216
Brüniche-Olsen A., Bickham J.W., Godard-Codding C.A., Brykov V.A., Kellner K., Urban R.J. & DeWoody J.A. (2021) Influence of Holocene habitat availability and commercial whaling on Pacific gray whale (Eschrichtius robustus) population dynamics as inferred from whole mitochondrial genome sequences and environmental niche modelling. Journal of Mammalogy 102: 986-999. https://doi.org/10.1093/jmammal/gyab032
Black A.N., Willoughby J.R., Brüniche-Olsen A., Pierce B.L. & DeWoody J.A. (2021) The endangered White Sands pupfish (Cyprinodon tularosa) genome reveals low diversity and heterogenous patterns of differentiation. Molecular Ecology Resources 21:2520–2532. https://doi.org/10.1111/1755-0998.13447
DeWoody J.A., Harder H., Mathur S. & Willoughby J. (2021) The long-standing significance of genetic diversity in conservation. Molecular Ecology30:4147–4154. https://doi.org/10.1111/mec.16051
Brüniche-Olsen A., Kellner K.F., Belant J.L. & DeWoody J.A. (2021) Life-history traits and habitat availability shape genomic diversity in birds: implications for conservation. Proceedings of the Royal Society https://doi.org/10.1098/rspb.2021.1441
Bylsma R., Walkup D.K., Hibbits T.J., Ryberg W.A., Black A.N. & DeWoody J.A. (2022) Population genetic and genomic analyses of Western Massasauga (Sistrurus tergeminus ssp.): implications for subspecies delimitation and conservation. Conservation Genetics 23:271-283. https://doi.org/10.1007/s10592-021-01420-8
Lamka G.F., Harder A.M., Sundaram M., Schwartz T., Christie M.R., DeWoody J.A. & Willoughby J.R. (2022) Epigenetics in ecology, evolution, and conservation. Frontiers in Ecology and Evolution 10:871791 https://doi.org/10.3389/fevo.2022.871791
Mularo A.J., Bernal X.E. & DeWoody J.A. (2022) Dominance can increase genetic variance after a population bottleneck: a synthesis of the theoretical and empirical evidence. Journal of Heredity 113:257-271. https://doi.org/10.1093/jhered/esac007
Commission on Novel Technologies for Neurodevelopmental Copy Number Variants [Buttermore E.D., Chamberlain S.J., Codeey J.D., Costain G., Dang L.T., DeWoody J.A., DeWoody Y.D., Dies K.A., Eichler E.E., Girirajan S., Halladay A., Lal D., Lalli M.A., Levy T., Logsdon G.A., Lowenstein D.H., Mefford H.G., Mulle J.G., Muotri A.R., Murphy M.M., Pinter S.F., Pollak R.M., Purcell R.H., Samaco R.C., Shah B.M., Singh K.K., So, J., Sundberg M., Veeraragavan S., Vogel-Farley V., Wynshaw-Boris A.] (2022) Neurodevelopmental copy number variants: a roadmap to improving outcomes by uniting patient advocates, researchers, and clinicians for collective impact. American Journal of Human Genetics 109:1353-1365. https://authors.elsevier.com/c/1fXEK_4GsWG5p
DeWoody J.A., Jeon J.Y., Bickham J.W., Heenkenda E., Janjua S., Lamka G.F., Mularo A., Black, A., Brüniche-Olsen A. & Willoughby J.R. (2022) The Threatened Species Imperative: Conservation assessments would benefit from population genomic insights. Proceedings of the National Academy of Sciences USA 119 (35) e2210685119 https://www.pnas.org/doi/10.1073/pnas.2210685119
Ji Y., Feng S., Wu L., Fang Q., Brüniche-Olsen A., DeWoody J.A., Cheng Y., Zhang D., Hao Y., Song G., Qu Y., Suh A., Zhang G., Hackett S.J. & Lei F. (2022) Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds. Science Advances 8(35) https://www.science.org/doi/10.1126/sciadv.abo0099.
Mathur S., Tomeček J.M., Tarango- Arámbula L.A., Perez R.M. & DeWoody J.A. (2023) An evolutionary perspective on genetic load in small, isolated populations as informed by whole genome resequencing and forward-time simulations. Evolution 77:690-704. https://doi.org/10.1093/evolut/qpac061 [Dr. Samarth Mathur won the Society for the Study of Evolution’s 2023 President’s Award for Oustanding Dissertation Paper published in Evolution for this paper.]
Black A.N., Bondo K.J., Mularo A., Hernandez A., Yu Y., Stein C.M., Gregory A., Fricke K.A., Prendergast J., Sullins D., Haukos D., Whitson M., Grisham B., Lowe Z.E. & DeWoody J.A. (2023) A highly contiguous and annotated genome assembly of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus). Genome Biology and Evolution evad043, DOI: 10.1093/gbe/evad043.
Mularo A.J., DeWoody J.A. & Bernal X.E. (2023) The establishment and occurrence history of three invasive anuran species across the Florida peninsula. Journal of Herpetology 57:381-389.
Heenkenda E., Fisher B., Albers G., & DeWoody J.A. (2024) A DNA-based evaluation of North American river otter diet with respect to fishes: implications for the conservation of aquatic predators and their prey. Aquatic Conservation, 34:e4078. https://doi.org/10.1002/aqc.4078.
Jeon J.Y., Shin Y., Mularo A.J., Feng X. & DeWoody J.A. (2024) Whole-genome resequencing meets ecological niche modeling to identify and conserve adaptive potential. Diversity and Distributions, in press.
Black A.N., Heenkenda E.J., Mathur S., Willoughby J.R., Pierce B.L., Turner S., Rizzuto D., DeWoody J.A. (2024) Cryptic and rapid speciation due to isolation and drift in an endangered pupfish. Proceedings of the National Academy of Sciences USA (PNAS), in press.
DeLisle Z.J., Cain R.L., Andritsch A.M., Janjua S., DeWoody J.A. & Swihart R.K. (2024) Coyote (Canis latrans) density estimation using camera traps and genetic spatial capture recapture. Submitted.
Black A.N., Mularo A.J., Jeon J.Y., Haukos D., Bondo K.J., Fricke K.A., Gregory A., Grisham B., Lowe Z.E., & DeWoody J.A. (2024) Discordance between taxonomy and population genomic data can complicate conservation policies. Submitted.
Black A.N., Jeon J.Y., McCreedy C., Janjua S., Heenkenda E.J., Mathur S., Ferree E., Fesnock-Parker A.L., Hernandez A., & J.A. DeWoody. (2024) Conservation genomics of California towhee (Melozone crissalis) in relation to the official list of endangered and threatened wildlife. Submitted.
Jeon J.Y., Black A., Heenkenda E., Mularo A., Lamka G., Janjua S., Bruniche-Olsen A., Bickham J.W., Willoughby J. & DeWoody J.A. (2024) Genomic diversity as a key conservation criterion: proof-of-concept from mammalian whole-genome resequencing data. Submitted.
Hoban S., Paz-Vina I., Shaw R.E., Castillo-Reina L., Da Silva J.M., DeWoody J.A., Ekblom R., Fedorca A., Forester B.R. Funk C.W., Geue J.C., Heuertz M., Hughes A.C., Hunter M.E., Hvilsom C., Ishihama F., Jordan R., Kalamujic Stroil B., Kershaw F., Khoury C.K., Koppa V., Laikre L., MacDonald A.J., Mastretta-Yanes A., Meek M.H., Mergeay J., Millette K.L., O’Brien D., Rincon-Parra D., Rodriguez-Moralies M.A., Schuman M.C., Segelbacher G., Sunnucks P., Taylor R.S., Thurfjell H., Vernesi C. & Grueber C.E. (2024) DNA-based studies and genetic indicator assessments are complementary approaches to conserving evolutionary potential. Submitted.
Personal use e-prints are available upon request from dewoody@purdue.edu.