J Andrew DeWoody

Summary

Affiliation: Purdue University
Country: USA

Publications

  1. doi request reprint Of contigs and quagmires: next-generation sequencing pitfalls associated with transcriptomic studies
    J Andrew DeWoody
    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
    Mol Ecol Resour 13:551-8. 2013
  2. ncbi request reprint Universal method for producing ROX-labeled size standards suitable for automated genotyping
    J Andrew DeWoody
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47905 1159, USA
    Biotechniques 37:348, 350, 352. 2004
  3. ncbi request reprint On the estimation of genome-wide heterozygosity using molecular markers
    Y D Dewoody
    The Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907 1159, USA
    J Hered 96:85-8. 2005
  4. doi request reprint Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis)
    Jacqueline M Doyle
    a Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
    Genome 56:407-14. 2013
  5. doi request reprint Inferring population history and demography using microsatellites, mitochondrial DNA, and major histocompatibility complex (MHC) genes
    David H Bos
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana 47906, USA
    Evolution 62:1458-68. 2008
  6. doi request reprint Condition-dependent mate choice and a reproductive disadvantage for MHC-divergent male tiger salamanders
    David H Bos
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA
    Mol Ecol 18:3307-15. 2009
  7. doi request reprint Microsatellite mutation rates in the eastern tiger salamander (Ambystoma tigrinum tigrinum) differ 10-fold across loci
    Zafer Bulut
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907 1159, USA
    Genetica 136:501-4. 2009
  8. ncbi request reprint Extensive mitochondrial DNA transfer in a rapidly evolving rodent has been mediated by independent insertion events and by duplications
    Deborah A Triant
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
    Gene 401:61-70. 2007
  9. doi request reprint Characterization of expressed class II MHC sequences in the banner-tailed kangaroo rat (Dipodomys spectabilis) reveals multiple DRB loci
    Joseph D Busch
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
    Immunogenetics 60:677-88. 2008
  10. doi request reprint Comparative transcriptomics and gene expression in larval tiger salamander (Ambystoma tigrinum) gill and lung tissues as revealed by pyrosequencing
    Soo Hyung Eo
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
    Gene 492:329-38. 2012

Detail Information

Publications35

  1. doi request reprint Of contigs and quagmires: next-generation sequencing pitfalls associated with transcriptomic studies
    J Andrew DeWoody
    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
    Mol Ecol Resour 13:551-8. 2013
    ..We are very optimistic about the future of molecular ecology, but we hope this cautionary overview will help neophytes better recognize some key challenges associated with new technologies...
  2. ncbi request reprint Universal method for producing ROX-labeled size standards suitable for automated genotyping
    J Andrew DeWoody
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47905 1159, USA
    Biotechniques 37:348, 350, 352. 2004
  3. ncbi request reprint On the estimation of genome-wide heterozygosity using molecular markers
    Y D Dewoody
    The Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907 1159, USA
    J Hered 96:85-8. 2005
    ..Thus, associations between fitness (or other phenotypes) and heterozygosity should be established firmly on causative factors and not on simple correlations...
  4. doi request reprint Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis)
    Jacqueline M Doyle
    a Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
    Genome 56:407-14. 2013
    ..Our results reinforce the idea that microsatellites do not always occur in noncoding DNA, but commonly occur in expressed genes. ..
  5. doi request reprint Inferring population history and demography using microsatellites, mitochondrial DNA, and major histocompatibility complex (MHC) genes
    David H Bos
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana 47906, USA
    Evolution 62:1458-68. 2008
    ..We find strong evidence of natural selection acting on MHC genes and estimate long-term effective population sizes (N(e)) that are very large, making small selection intensities significant evolutionary forces in this population...
  6. doi request reprint Condition-dependent mate choice and a reproductive disadvantage for MHC-divergent male tiger salamanders
    David H Bos
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA
    Mol Ecol 18:3307-15. 2009
    ....
  7. doi request reprint Microsatellite mutation rates in the eastern tiger salamander (Ambystoma tigrinum tigrinum) differ 10-fold across loci
    Zafer Bulut
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907 1159, USA
    Genetica 136:501-4. 2009
    ....
  8. ncbi request reprint Extensive mitochondrial DNA transfer in a rapidly evolving rodent has been mediated by independent insertion events and by duplications
    Deborah A Triant
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
    Gene 401:61-70. 2007
    ..Our data suggest that numt translocation in Microtus is more extensive than in either Mus or in Rattus, consistent with the elevated rate of speciation, karyotypic rearrangement, and mitochondrial DNA evolution in Microtus...
  9. doi request reprint Characterization of expressed class II MHC sequences in the banner-tailed kangaroo rat (Dipodomys spectabilis) reveals multiple DRB loci
    Joseph D Busch
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
    Immunogenetics 60:677-88. 2008
    ..Collectively, these data suggest that class II diversity in heteromyid rodents is based on polylocism and departs from the muroid architecture...
  10. doi request reprint Comparative transcriptomics and gene expression in larval tiger salamander (Ambystoma tigrinum) gill and lung tissues as revealed by pyrosequencing
    Soo Hyung Eo
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
    Gene 492:329-38. 2012
    ..Given the tissue-specific differences we observed in transcriptomes, these data reinforce the idea that changes in gene expression serve as a primary mechanism underlying phenotypic plasticity...
  11. doi request reprint The influence of density and sex on patterns of fine-scale genetic structure
    Joseph D Busch
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana 47907, USA
    Evolution 63:2302-14. 2009
    ..Because few organisms maintain discreet kin clusters, we predict that density will be negatively associated with SGS in other species...
  12. ncbi request reprint Parental relatedness and major histocompatibility effects on early embryo survivorship in Atlantic salmon
    Sara M Turner
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
    Genetica 137:99-109. 2009
    ..Overall, our data are consistent with the contention that excess MHC heterozygosity in Atlantic salmon juveniles is due to sexual selection as well as differential survival of offspring due to MHC genotype...
  13. doi request reprint 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)
    Nicholas J Marra
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
    Comp Biochem Physiol Part D Genomics Proteomics 7:328-39. 2012
    ..Mutations in two of these genes, Slc12a1 and Slc12a3, cause human renal diseases that result in the inability to concentrate urine. These genes are likely key determinants of physiological water conservation in desert rodents...
  14. doi request reprint Polymorphism of alternative splicing of major histocompatibility complex transcripts in wild tiger salamanders
    Zafer Bulut
    The Bindley Bioscience Center and Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907 1159, USA
    J Mol Evol 67:68-75. 2008
    ..However, indirect evidence (comparative expression patterns across 3 million years of evolution) suggests that the truncated Amti-DAB transcript may be functional and maintained by natural selection...
  15. ncbi request reprint Discovery and evaluation of candidate sex-determining genes and xenobiotics in the gonads of lake sturgeon (Acipenser fulvescens)
    Matthew C Hale
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47906, USA
    Genetica 138:745-56. 2010
    ..Our results suggest that exogenous parasites (trematodes) and pathogens (protozoans) apparently have infected lake sturgeon gonads, and the trematodes have horizontally transferred some genes to the lake sturgeon genome...
  16. pmc The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos)
    Jacqueline M Doyle
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
    PLoS ONE 9:e95599. 2014
    ..Because the genome sequence includes ∼800,000 novel polymorphisms, markers can now be chosen based on their proximity to functional genes involved in migration, carnivory, and other biological processes. ..
  17. pmc 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 of tiger salamanders (Ambystoma tigrinum)
    Soo Hyung Eo
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
    BMC Genomics 13:259. 2012
    ..g., mean SNPs/kb). However, both read length and contig depth are highly variable and thus raise doubt about simple methods of SNP frequency estimation...
  18. pmc Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery
    Matthew C Hale
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
    BMC Genomics 10:203. 2009
    ..We used Roche 454 pyrosequencing to characterize gene expression in polyploid lake sturgeon (Acipenser fulvescens) gonads...
  19. pmc Amphibian malformations and inbreeding
    Rod N Williams
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
    Biol Lett 4:549-52. 2008
    ..Environmental contaminants or other extrinsic factors may lead to genome alternations that ultimately cause malformations, but our data indicate that inbreeding is not a causal mechanism...
  20. ncbi request reprint Recent demographic bottlenecks are not accompanied by a genetic signature in banner-tailed kangaroo rats (Dipodomys spectabilis)
    Joseph D Busch
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
    Mol Ecol 16:2450-62. 2007
    ..We interpret our kangaroo rat data in light of the broader literature and conclude that in natural populations connected by dispersal, demographic bottlenecks may prove difficult to detect using molecular genetic data...
  21. ncbi request reprint Molecular analyses of mitochondrial pseudogenes within the nuclear genome of arvicoline rodents
    Deborah A Triant
    Department of Forestry and Natural Resources, Purdue University, 195 Marsteller Street, West Lafayette, IN 47907, USA
    Genetica 132:21-33. 2008
    ..3 x 10(-8) substitutions/per site/per year. Furthermore, we performed comparative analyses among all species to estimate the age of this mitochondrial transfer at nearly 4 MYA, predating the origin of most arvicolines...
  22. ncbi request reprint Prospects for inferring pairwise relationships with single nucleotide polymorphisms
    Jeffrey C Glaubitz
    Purdue University, Department of Forestry and Natural Resources, 195 Marsteller St, West Lafayette, Indiana 47907 2033, USA
    Mol Ecol 12:1039-47. 2003
    ....
  23. ncbi request reprint Molecular characterization of major histocompatibility complex class II alleles in wild tiger salamanders (Ambystoma tigrinum)
    David H Bos
    Department of Forestry and Natural Resources, Purdue University, 715 W State St, West Lafayette, IN 47907, USA
    Immunogenetics 57:775-81. 2005
    ..Our tiger salamander data suggest that the monomorphism and immunodeficiencies associated with axolotl class II genes is a relic of their unique historical demography, not their phylogenetic legacy...
  24. doi request reprint Hosts, parasites, and horizontal gene transfer
    Bhagya K Wijayawardena
    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
    Trends Parasitol 29:329-38. 2013
    ..We also highlight future research directions that could prove illuminating with regard to the occurrence, prevalence, and overall importance of HGT in host-parasite coevolution. ..
  25. ncbi request reprint Insights into the mating habits of the tiger salamander (Ambystoma tigrinum tigrinum) as revealed by genetic parentage analyses
    David Gopurenko
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
    Mol Ecol 15:1917-28. 2006
    ..Collectively, these data provide the first direct evidence for polygynandry in a wild population of tiger salamanders...
  26. doi request reprint The quantification of spermatozoa by real-time quantitative PCR, spectrophotometry, and spermatophore cap size
    Jacqueline M Doyle
    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
    Mol Ecol Resour 11:101-6. 2011
    ..These methods may help explain variation in fertilization success where sperm competition is mediated by sperm quantity...
  27. pmc Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles
    Soo Hyung Eo
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907 1159, USA
    Proc Biol Sci 277:3587-92. 2010
    ..Thus, the nuclear data buttress our mtDNA findings...
  28. ncbi request reprint Parentage analysis detects cryptic precapture dispersal in a philopatric rodent
    Peter M Waser
    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
    Mol Ecol 15:1929-37. 2006
    ..For species in which mothers can be more reliably trapped than juveniles, using offspring genotypes to locate parents is a novel way that genetic techniques can contribute to the analysis of animal dispersal...
  29. doi request reprint Haplotype inference from diploid sequence data: evaluating performance using non-neutral MHC sequences
    David H Bos
    Bindley Bioscience Center and Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA
    Hereditas 144:228-34. 2007
    ....
  30. ncbi request reprint Accelerated molecular evolution in Microtus (Rodentia) as assessed via complete mitochondrial genome sequences
    Deborah A Triant
    Department of Forestry and Natural Resources, Purdue University, 195 Marsteller Street, West Lafayette, IN 47907, USA
    Genetica 128:95-108. 2006
    ..The root cause of accelerated evolution in Microtus remains uncertain, but merits further investigation...
  31. ncbi request reprint Using naturally shed feathers for individual identification, genetic parentage analyses, and population monitoring in an endangered Eastern imperial eagle (Aquila heliaca) population from Kazakhstan
    Jamie A Rudnick
    Department of Forestry and Natural Resources, Purdue University, West Lafayette IN 47907 1159, USA
    Mol Ecol 14:2959-67. 2005
    ..The pristine habitat at our study site supports an EIE population that is probably the most demographically robust in the world; thus, our results caution that populations in marginal habitats may not be self-sustaining...
  32. pmc Transgenic male mating advantage provides opportunity for Trojan gene effect in a fish
    Richard D Howard
    Departments of Biological Sciences, Forestry and Natural Resources, and Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
    Proc Natl Acad Sci U S A 101:2934-8. 2004
    ..Finally, we model the impact of alternative mating tactics by WT males on transgene spread. Such tactics may reduce the rate of transgene spread, but not the outcome...
  33. ncbi request reprint Natural selection and the genetic basis of osmoregulation in heteromyid rodents as revealed by RNA-seq
    Nicholas J Marra
    Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA
    Mol Ecol 23:2699-711. 2014
    ..Thus, our data suggest that both the coding sequence and expression of genes have been shaped by natural selection to provide the genetic architecture for efficient osmoregulation in desert-adapted heteromyid rodents...
  34. ncbi request reprint The spatial distribution of avian relatives: do obligate army-ant-following birds roost and feed near family members?
    Johel Chaves-Campos
    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
    Mol Ecol 17:2963-74. 2008
    ..Hence, we found limited potential for kin selection to favour group living and suggest that other factors, particularly direct benefits (e.g. food intake), are probably more important than indirect effects (nepotism)...
  35. ncbi request reprint Genetic mating systems and reproductive natural histories of fishes: lessons for ecology and evolution
    John C Avise
    Department of Genetics, University of Georgia, Athens, Georgia, 30602, USA
    Annu Rev Genet 36:19-45. 2002
    ..Additional phenomena addressed by genetic parentage analyses in fishes include clustered mutations, filial cannibalism, and local population size. All results are discussed in the context of relevant behavioral and evolutionary theory...