Source: PURDUE UNIVERSITY submitted to
THE MOLECULAR EVOLUTIONARY GENETICS OF VERTEBRATE POPULATIONS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
REVISED
Funding Source
Reporting Frequency
Annual
Accession No.
0190980
Grant No.
(N/A)
Project No.
IND011556
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Oct 1, 2010
Project End Date
Sep 30, 2015
Grant Year
(N/A)
Project Director
DeWoody, J. A.
Recipient Organization
PURDUE UNIVERSITY
(N/A)
WEST LAFAYETTE,IN 47907
Performing Department
Forestry & Natural Resources
Non Technical Summary
Many genes involved in routine physiological processes are well-characterized in model organisms such as Drosophila, Arabidopsis, and Mus. For example, three genes that are related to mouse kidney function include Aqp2, Avpr2, and Agtr1a. Aqp2 (aquaporin 2) is involved in water transport, Avpr2 (arginine vasopressin receptor 2) actives a cascade for water retention, and Agtr1a (antiotensin II receptor type 1a) increases vasopressin and aldosterone. Unfortunately, we know little about the evolution of these Mus genes in the other ~1000 rodent species. Are Aqp2, Avpr2, and Agtr1a highly conserved (i.e., evolving slowly) or are they dramatically different in closely related taxa How does their function differ in species that occupy arid habitats compared to species which inhabit rain forest Comparative studies have the potential to reveal otherwise-unappreciated aspects of gene and genome evolution, and this is one of my primary objectives over the next five years. Beyond gene and genome evolution, future research in my lab will use molecular data to better understand contemporary population structure in light of historical demography and phylogeography. We have already conducted some of this research in salamanders, but our future efforts will be focused on Carribean birds in collaboration with Bob Ricklefs at the University of Missouri St. Louis (UMSL). This project will relate genetic indices of population size and change in size for about 100 island populations of West Indian birds to island area, geographic and habitat distribution of species, body size, diet, and other attributes of individuals. Its statistical approach has the potential to transform prediction of population response to climate change from anecdote to statistically supported relationships and to establish a model system for the study of comparative demography.
Animal Health Component
15%
Research Effort Categories
Basic
85%
Applied
15%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3040830108020%
3050830108020%
1320899106020%
1353999107020%
1360899107020%
Goals / Objectives
My research lies at the juncture of population genetics, genomics, and molecular evolution. My primary objectives are to understand the pattern and process of natural selection on genes that code for phenotypes of evolutionary interest. This includes discovery-based science (characterizing the candidate genes) and hypothesis testing (evaluating evidence of natural selection on candidate genes). In addition, my secondary objectives are to use molecular data to better understand contemporary population structure in light of historical demography and phylogeography.
Project Methods
The primary objectives, to characterize genes responsible for key evolutionary innovations, will be addressed using next-generation sequencing technologies such as pyrosequencing. In order to do this, the transcriptome (the expressed mRNA) of relevant tissues will be pyrosequenced using the Roche 454 system. This pyrosequencing system provides long sequencing reads and deep coverage, which are invaluable in studies of non-model species. Rodent osmoregulation is but one example of our future efforts to identify genes responsible for key evolutionary innovations or transitions. We will also use pyrosequencing to compare the pattern of gene expression in larval amphibian gills compared to adult amphibian lungs, to better understand the process of oxygen retention in aquatic and terrestrial environments. Our secondary objectives (to address vertebrate population structure, phylogeography, and historical demography) will be addressed using microsatellites, mitochondrial DNA (mtDNA), and nuclear DNA (nuDNA) sequences. This collaborative research project focuses on birds on islands in the West Indies to address the ways in which population size can be influenced by climate change (which affects all species) and by particular ecological relationships that influence few species independently. This will be the first study in which change in population size in response to climate change during Ice Age glacial cycles will be characterized by contemporary patterns of genetic diversity in a broad sample of populations based on ca. 7000 DNA samples from West Indian birds. By taking a statistical approach, we shall seek generalizable relationships between demographic responses to climate change and characteristics of islands, the biogeographic history of species, habitat distributions of populations, and ecological and behavioral characteristics of individuals. Several measures of genetic polymorphism and genetic diversity can indicate variation in population size over long periods. Variation in mitochondrial DNA sequences is appropriately sensitive to the environmental changes that accompany glacial cycles, which caused climates on Caribbean islands to alternate between cooler, drier conditions (glacial) and warmer, wetter conditions (interglacial, as at present). In addition, variation in MHC sequences, which are the basis of pathogen recognition by the adaptive immune system, will be linked to our survey of haemosporidian parasites in West Indian birds to investigate potential connections between population change and emerging disease.

Progress 10/01/11 to 09/30/12

Outputs
OUTPUTS: ZipTrips, http://www.agriculture.purdue.edu/zipTrips/ . Program on genetic parentage, oriented towards middle school students. Live public television on 17 Feb 2011; simultaneous internet streaming to 222 schools (7,754 students) in 32 states, Puerto Rico, Shetland UK, and Calgary Canada; a second live performance was broadcast on 16 February 2012: "It's a Gene Thing!" reached more than 5,000 students at 127 schools in 30 states. In conjunction with Purdue Ag Communications (J. Loizzo and S. Doyle) and R. Williams (Purdue FNR Extension). The ZipTrip team was awarded the 2012 Purdue College of Agriculture TEAM award for interdisciplinary teamwork. PARTICIPANTS: PhD students: Anna Fahey Janna Willoughby Nick Marra Yanzhu Ji Kendra Abts Bhagya Wijawayardewa TARGET AUDIENCES: K-12 students and the evolutionary biology community of scientists PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
1) We identified several important genes responsible for mammalian osmoregulation via urine concentration in the kidney. 2) We used contemporary DNA sequences to study historical climatic effects on genetic diversity, in an effort to understand how climate change impacts gene pools. 3) Finally, we developed a new genetic diversity metric that adds sequencing coverage (depth) to the industry-standard sequence length.

Publications

  • 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 492:329-338.
  • 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.
  • 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, in press.


Progress 10/01/10 to 09/30/11

Outputs
OUTPUTS: The outputs of our project have been published in the primary scientific literature. We have also contributed molecular data to public repositories (e.g., GenBank, DataDryad, etc). PARTICIPANTS: Grad students trained in association with this project include: Kendra Abts (Native American heritage) Anna Fahey Nick Marra Janna Willoughby TARGET AUDIENCES: The scientific community PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Dr. DeWoody's research is in molecular ecology and evolution, where he studies genes and their host organisms. His research at two hierarchical levels (genes in genomes, and organisms in populations) has led to fundamental insights into genome dynamics, the distribution of genetic variation in wild populations, and the partitioning of genetic variation into biological lineages. Collectively, his body of research has had a significant impact on the scientific community as evidenced by growing references to his published work, by his service as a reviewer for top journals and funding organizations, and by his various speaking invitations.

Publications

  • 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.


Progress 10/01/09 to 09/30/10

Outputs
OUTPUTS: DeWoody's lab group conducted several major experiments over the last year, and these include efforts to characterize genes underlying amphibian metamorphosis, fish sex determination, and rodent osmoregulation. In doing so, DeWoody advised many graduate students and postdocs; one M.S. student (Jamie Griggs) graduated in 2010. DeWoody also presented several invited seminars in the last year, including: Black Hills State University, Spearfish SD. 2009. Murray State University, Murray KY. 2010. Indiana State University, Terre Haute IN. 2010. "From Molecules to Ecosystems" series Smithsonian National Zoo, Washington DC. 2010. He also published a book and numerous journal articles (see below). PARTICIPANTS: Anna Fahey, Nick Marra, Kendra Abts, Yangzhu Ji (PhD students), Soo Hyung Eo (postdoc) TARGET AUDIENCES: Scientists interested in evolutionary genetics PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
DeWoody's research led to a change in knowledge through scientific publications in the fields of evolutionary genetics and molecular ecology. These scientific advances have been used by the scientific community, as his collective body of research was cited in the literature over 380 times in 2009-2010 (ISI Web of Knowledge). These publications have led to a better understanding of organismal biology, biodiversity, evolution, and conservation.

Publications

  • 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, 374 pp. See http://www.cambridge.org/us/catalogue/catalogue.aspisbn=978052151564 1&ss=toc for topics and contributors. ISBN 978-0-521-51564-1 Hardback
  • 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.
  • 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.
  • DeWoody J.A., Hale M.C. & Avise J.C. (2010) Vertebrate sex determining genes and their potential utility in conservation, with particular emphasis on fishes. pp. 74-100 in: Molecular approaches in natural resource conservation (DeWoody JA, Bickham JW, Michler C, Nichols K, Rhodes OE, Woeste K, eds). Cambridge University Press (374 pp.).
  • 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


Progress 10/01/08 to 09/30/09

Outputs
OUTPUTS: The outputs of our research projects are reported in peer-reviewed books and primary journal articles. Furthermore, the data we have generated have been presented in public forums (scientific meetings, invited seminars, etc.). PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Our research is providing a better understanding of how major histocompatibility complex genes and genome-wide relatedness impacts offspring survivorship of Atlantic salmon, and hence, may lead to improved breeding strategies that increase yield in farmed fishes. We have also conducted similar research in a terrestrial vertebrate, the tiger salamander. Our research may have implications for other livestock species as well.

Publications

  • 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 (>1700x) 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.
  • Rudnick J.A., DeWoody J.A., & Katzner T.E. (2009) Genetic analyses of noninvasively collected feathers can provide new insights into avian demography and behavior. Pp. 181-197, in: Handbook of Nature Conservation, Nova Science Publishers. Invited book chapter.
  • 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.


Progress 10/01/07 to 09/30/08

Outputs
OUTPUTS: DeWoody gave a number of invited seminars over the last year, including: Wabash College, IN. 2007. State University of New York, Binghamton NY. 2008. Cornell University, Ithaca NY. 2008. Cornell Herpetological Society Cornell University, Ithaca NY. 2008. Dept. of Ecology and Evolutionary Biology University of Missouri, St. Louis MO. 2008. In October 2008, he and other FNR faculty members hosted a 3 day symposium on Ecological Genetics that was attended by contributors to a book edited by FNR geneticists. The book should be published by Cambridge University Press in 2009. PARTICIPANTS: Dr. Joseph Busch graduated from Purdue (FNR) in 2008. Two new students, Jamie Nogle (MS) and Anna Fahey (PhD) began their graduate studies. Jennifer McCreight (BS) continues her work in DeWoody's lab. TARGET AUDIENCES: Wildlife biologists PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
Our research over the past year has largely been on three fronts: 1) using molecules to make broad inferences about avian population demography; 2) studying the evolutionary biology of salamanders; and 3) studying the molecular evolution of MHC genes, those of the major histocompatibility complex. The major impact of our bird work is that more ornithologists are realizing that feathers can be a source of DNA for population genetics studies. On the salamander front, we have learned that sexual selection may operate in females as well as in males, overturning the conventional wisdom. We have also discovered that MHC genes are often alternatively spliced, and that there is significant within-population variation for alternative splicing.

Publications

  • 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.
  • 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.
  • 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.
  • Bragin E.A., Rudnick J.A., Katzner T., & DeWoody J.A. (2008) New methods for raptors research: results of research on the imperial eagle in north Kazakhstan. Research and conservation of birds of prey of northern Eurasia. Materials of the 5th international conference on birds of prey of northern Eurasia. Ivanovo State University Press. Edited by V.M. Galushin, V.N. Melnikov, A.I. Shretaikov, & D.I. Chudnenko. 360 pp. In Russian.


Progress 10/01/06 to 09/30/07

Outputs
OUTPUTS: Over the last year, we have made significant advances in molecular genetics and ecology. One example involves our work on salamanders. We are attempting to unite two different disciplines, molecular and population biology, through our studies of genetic parentage and sexual selection. For example, genes of the major histocompatibility complex (MHC) have been implicated in vertebrate (human, mice, salmon) mate choice. Presumably, when MHC-dissimilar adults mate, their progeny are more diverse at MHC genes and can better fight infections of foreign pathogens. In some salamanders (axolotl), there is no diversity at key MHC genes and they are immunodeficient (cannot clear infections). Our data on wild salamanders indicate they harbor substantial genetic variation at MHC genes and further, this variation is actively maintained via balancing selection. It remains to be determined whether or not salamanders choose mates on the basis of the variation at MHC genes, but we have now collected the data required to test this hypothesis. Our work with endangered Asian eagles has direct conservation relevance. We used naturally shed eagle feathers to construct genetic "tags" based upon multi-locus DNA microsatellite genotypes. These tags were used to evaluate philopatry (breeders return to the same nest year after year), mating system (these eagles are strictly monogamous), and population dynamics (our study population is marginally self-sustaining). Furthermore, we used genetic tags to estimate the size of the nonbreeding (juveniles and itinerant adults) eagle population and discovered that hundreds of nonbreeders use our study site each summer, presumably because of the vast food resources (large rodent colonies). PARTICIPANTS: Sara Turner was a PhD student who defended her dissertation in summer 2007. She is now a postdoc at the Univ. of Alaska (Fairbanks). Jamie Rudnick was a PhD student who defended in summer 2006, and is now a postdoc at the Brookfield Zoo. Deb Triant defended (PhD) in summer 2006 and is now a postdoc at LSU. David Gopureko was a postdoc who now has returned to a permanent job in his native Australia. David Bos was a postdoc who now has a position in the Biology Dept. at Purdue. Rod Williams is a PhD student who is planning to defend his work in Nov. 2007. TARGET AUDIENCES: Conservation biologists and population geneticists

Impacts
Our research is having a theoretical impact (population genetics theory) as well as a practical impact (conservation biology). By using DNA to study animals in their native environment, we paint a more accurate picture of their natural history and diversity.

Publications

  • 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.
  • 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.


Progress 10/01/05 to 09/30/06

Outputs
Over the last year, we have made significant advances in molecular genetics and ecology. One example involves our work on salamanders. We are attempting to unite two different disciplines, behavioral ecology and immunology, through our studies of genetic parentage and sexual selection. For example, genes of the major histocompatibility complex (MHC) have been implicated in vertebrate (human, mice, salmon) mate choice. Presumably, when MHC-dissimilar adults mate, their progeny are more diverse at MHC genes and can better fight infections of foreign pathogens. In some salamanders (axolotl), there is no diversity at key MHC genes and they are immunodeficient (cannot clear infections). Our data on wild salamanders indicate they harbor substantial genetic variation at MHC genes and further, this variation is actively maintained via balancing selection. It remains to be determined whether or not salamanders choose mates on the basis of the variation at MHC genes. Our work with endangered Asian eagles has direct conservation relevance. We used naturally shed eagle feathers to construct genetic tags based upon multi-locus DNA microsatellite genotypes. These tags were used to evaluate philopatry (breeders return to the same nest year after year), mating system (these eagles are strictly monogamous), and population dynamics (our study population is marginally self-sustaining). Furthermore, we used genetic tags to estimate the size of the nonbreeding (juveniles and itinerant adults) eagle population and discovered that hundreds of nonbreeders use our study site each summer, presumably because of the vast food resources (large rodent colonies).

Impacts
Our research is having a theoretical impact (population genetics theory) as well as a practical impact (conservation biology). By using DNA to study animals in their native environment, we paint a more accurate picture of their natural history and diversity.

Publications

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


Progress 10/01/04 to 09/30/05

Outputs
Over the last year, we have made significant advances in theoretical population genetics as well as in conservation biology. In one example of the former, we used an experimental model organism, the Japanese medakafish, to test the possibility of transgene introgression into natural populations. Our work shows that in medaka, growth-hormone transgenic males grow significantly larger than wild-type males. Females prefer to mate with larger males, and molecular assessments of parentage indicate that larger males obtain more fertilizations than smaller males. Despite this mating advantage, transgenic males have a viability disadvantage. Our model shows that under certain circumstances, transgene introgression into a natural gene pool can have devastating consequences, including extinction of the natural population. A second example of our theoretical work involves the use of analytical theory to illustrate that small suites of codominant molecular markers (e.g., <20 microsatellite loci) are insufficient to accurately gauge genome-wide heterozygosity. In other words, the expected correlation between marker-estimated zygosity and true genome-wide zygosity is very poor (<0.01) in most vertebrate genomes. This work has implications for conservation biology, where heterozygosity as judged by molecular markers is often used as an indicator of genetic health. Our work with endangered Asian eagles has direct conservation relevance, as profiled in the New York Times on 26 July 2005. We used naturally shed eagle feathers to construct genetic tags based upon multi-locus DNA microsatellite genotypes. These tags were used to evaluate philopatry (breeders return to the same nest year after year), mating system (these eagles are strictly monogamous), and population dynamics (our study population is marginally self-sustaining). In addition to the direct implications of this research to our study population, the broader scientific community has already embraced our approach as a novel and practical method for monitoring bird populations around the world.

Impacts
Our research is having a theoretical impact (population genetics theory) as well as a practical impact (conservation biology). By using DNA to study animals in their native environment, we paint a more accurate picture of their natural history and diversity.

Publications

  • 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.


Progress 10/01/03 to 09/29/04

Outputs
We have developed a suite of novel genetic markers for the study of salamander biology. These markers include microsatellites, major histocompatibility genes, and mitochondrial genes (D-loop). Collectively, these markers will help us evaluate the influence of an organism's genotype on its chances of survival in nature. In addition, we developed a novel molecular marker for the Japanese medaka and used this marker to evaluate breeding success of wildtype and transgenic males. Our experiments show that large, transgenic males have a clear mating advantage over wildtype males and this mating advantage could--in theory--lead to devasting consequences if the transgenic fish escape to mate with wild brethren.

Impacts
Our work on medaka has illustrated some of the potential problems associated with genetically-modified organisms (GMOs) that breed with their wild kin. Clearly, agricultural operations that rely on transgenic animals must vigilantly guard against the unintentional escape of GMOs into the wild.

Publications

  • 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.


Progress 10/01/02 to 09/30/03

Outputs
Over the past year, we have been working in two primary arenas. The first is in the assessment of novel DNA markers for population genetic research. Single-nucleotide polymorphisms, called SNPs, are at the forefront of human population genetics. We have evaluated their feasibility in non-model organisms and found them to be inferior to existing markers (e.g., microsatellites). SNPs are more difficult to identify and genotype and provide less information per genotype. Secondly, we have investigated the influence of genotype on survivorship in Atlantic salmon. We have mated individual salmon pairs and monitored the hatching success of their offspring. We are now in the process of genotyping the parents, the dead embryos, and the survivors in an attempt to determine whether or not overall relatedness of the parents influences survival.

Impacts
We have developed new methods for the evaluation of genetic diversity in natural fish populations. Using both empirical and theoretical techniques, our research has highlighted many of the problems related to genotyping wild individuals and estimating relatedness among individuals.

Publications

  • 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.


Progress 10/01/01 to 09/30/02

Outputs
Our proposed work on microsatellite mutation rates (MMRs) was not funded, so we turned to less expensive endeavors that could be supported by modest start-up funds. Ultimately, we hope to find funding for the MMR studies and will pursue this further in the future. In the meantime, we have made substantial progress on other fronts. The first is with regard to ascertaining the influence of parental genotype on embryo hatching success in an economically important fish. It is well known that genetically diverse individuals are usually very fit, and this phenomenon is referred to as heterosis or heterozygote advantage. Conversely, genetically depauperate individuals are usually less fit (e.g., those that are inbred). We are testing the hypothesis that individual genetic diversity bears upon hatching success (and ultimately, survivorship) in a species with huge family sizes, the Atlantic salmon. Hatching success is typically about 75% in salmon, and this may be due in part to the random mating of adult fish during aquaculture operations. If we could genotype all of the broodstock prior to spawning and hand-pick spawnings on the basis of parental genotypes, we might be able to substantially boost hatching success, thus increasing the yield of aquaculturists everywhere. Over the last 12 months, we have identified a study population, characterized a suite of molecular genetic markers in this population, and have designed experiments to test our hypotheses. Our first fish are scheduled to arrive later this month, and we will then proceed according to plan. In the genomics arena, we are studying the horizontal transfer of genes from one genome to another. To date, most horizontal gene transfer studies have considered the transfer of genes from the nuclear genome of one species to the nuclear genome of another species (e.g., mite genes to Drosophila). However, we are studying the intraspecific transfer of genes to the mammalian nuclear genome (23 pairs of linear chromosomes comprising roughly 3 billion nucleotides) from the mammalian mitochondrial genome (a circular, 17kb molecule--0.0006% the size of the nuclear genome). Our discovery of a cytochrome b pseudogene has served as a wonderful model of molecular evolution and the dynamic nature of genomes. As of this time last year, the pseudogene was characterized in only a single species (the vole Microtus arvalis). Over the last 12 months, we have discovered orthologs of the pseudogene in at least 10 more species of Microtus. Furthermore, we have used a molecular clock to date the translocation to approximately 6.0 million years ago. Paleontological evidence suggests that the genus Microtus is only 2-3 million years old, so we will soon expand our studies of the pseudogene to closely related genera (e.g., Cleithrionomys). Ultimately, we hope to more accurately characterize the relatively common transfer of DNA from one genome to another.

Impacts
Our basic research in molecular evolutionary genetics will have a substantial impact on the fields of immunology and genomics. In the first instance, we are suggesting that the immune response (or lack thereof) may have an impact on mortality and furthermore, the survivorship curves for each genotype may be predictable. In the second instance, our genomic research will help answer questions about the molecular transfer of genes from cytoplasmic to nuclear genomes (e.g., are such events RNA-mediated or DNA-mediated?).

Publications

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