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D J Schoen

Publications and source records attributed to D J Schoen.

13 recordsLinked to original sources
PubMed2003

Somatic stability of microsatellite loci in Eastern white pine, Pinus strobus L.

Variation at nuclear- and chloroplast-encoded microsatellite loci was studied among and within clonally propagated individuals of Eastern white pine. Total DNA was extracted and assayed from gamete-bearing tissue (megagametophytes) located on six different branch positions on each of 12 individual genets. No within-individual variation was observed among 12 loci studied. Estimates of numbers of mitotic cell divisions required to produce the tissue used as the source of genomic DNA were obtained by combining tree growth and anatomical data. This allowed for the calculation of upper bound estimates of numbers of mutations per locus per somatic cell division. The estimated somatic mutation rate was found to be substantially lower than those published for genomic microsatellite mutation rates in other plant species.

Genetic Variation↗
PubMed2001

Population dynamics of an Ac-like transposable element in self- and cross-pollinating arabidopsis.

Theoretical models predict that the mating system should be an important factor driving the dynamics of transposable elements in natural populations due to differences in selective pressure on both element and host. We used a PCR-based approach to examine the abundance and levels of insertion polymorphism of Ac-III, a recently identified Ac-like transposon family, in natural populations of the selfing plant Arabidopsis thaliana and its close outcrossing relative, Arabidopsis lyrata. Although several insertions appeared to be ancient and shared between species, there is strong evidence for recent activity of this element family in both species. Sequences of the regions flanking insertions indicate that all Ac-III transposons segregating in natural populations are in noncoding regions and provide no evidence for local transposition events. Transposon display analysis suggests the presence of slightly higher numbers of insertion sites per individual but fewer total polymorphic insertions in the self-pollinating A. thaliana than A. lyrata. Element insertions appear to be segregating at significantly lower frequencies in A. lyrata than A. thaliana, which is consistent with a reduction in transposition rate, reduction in effective population size, or reduced efficacy of natural selection against element insertions in selfing populations.

Arabidopsis↗
PubMed2000

Comparative genomics, marker density and statistical analysis of chromosome rearrangements.

Estimates of the number of chromosomal breakpoints that have arisen (e.g., by translocation and inversion) in the evolutionary past between two species and their common ancestor can be made by comparing map positions of marker loci. Statistical methods for doing so are based on a random-breakage model of chromosomal rearrangement. The model treats all modes of chromosome rearrangement alike, and it assumes that chromosome boundaries and breakpoints are distributed randomly along a single genomic interval. Here we use simulation and numerical analysis to test the validity of these model assumptions. Mean estimates of numbers of breakpoints are close to those expected under the random-breakage model when marker density is high relative to the amount of chromosomal rearrangement and when rearrangements occur by translocation alone. But when marker density is low relative to the number of chromosomes, and when rearrangements occur by both translocation and inversion, the number of breakpoints is underestimated. The underestimate arises because rearranged segments may contain markers, yet the rearranged segments may, nevertheless, be undetected. Variances of the estimate of numbers of breakpoints decrease rapidly as markers are added to the comparative maps, but are less influenced by the number or type of chromosomal rearrangement separating the species. Variances obtained with simulated genomes comprised of chromosomes of equal length are substantially lower than those obtained when chromosome size is unconstrained. Statistical power for detecting heterogeneity in the rate of chromosomal rearrangement is also investigated. Results are interpreted with respect to the amount of marker information required to make accurate inferences about chromosomal evolution.

Biological Evolution↗
PubMed1999

Transposon dynamics and the breeding system.

The selfish DNA hypothesis predicts that natural selection is responsible for preventing the unregulated build up of transposable elements in organismal genomes. Accordingly, between-species differences in the strength and effectiveness of selection against transposons should be important in driving the evolution of transposon activity and abundance. We used a modeling approach to investigate how the rate of self-fertilization influences the population dynamics of transposable elements. Contrasting effects of the breeding system were observed under selection based on transposon disruption of gene function versus selection based on element-mediated ectopic exchange. This suggests that the comparison of TE copy number in organisms with different breeding systems may provide a test of the relative importance of these forces in regulating transposon multiplication. The effects of breeding system also interacted with population size, particularly when there was no element excision. The strength and effectiveness of selection against transposons was reflected not only in their equilibrium abundance, but also in the per-site element frequency of individual insertions and the coefficient of variation in copy number. These results are discussed in relation to evidence on transposon abundance available from the literature, and suggestions for future data collection.

Breeding↗
PubMed1998

Deleterious mutation accumulation and the regeneration of genetic resources.

The accumulation of mildly deleterious mutations accompanying recurrent regeneration of plant germ plasm was modeled under regeneration conditions characterized by different amounts of selection and genetic drift. Under some regeneration conditions (sample sizes >/=75 individuals and bulk harvesting of seed) mutation accumulation was negligible, but under others (sample sizes <75 individuals or equalization of seed production by individual plants) mutation numbers per genome increased significantly during 25-50 cycles of regeneration. When mutations also are assumed to occur (at elevated rates) during seed storage, significant mutation accumulation and fitness decline occurred in 10 or fewer cycles of regeneration regardless of the regeneration conditions. Calculations also were performed to determine the numbers of deleterious mutations introduced and remaining in the genome of an existing variety after hybridization with a genetic resource and subsequent backcrossing. The results suggest that mutation accumulation has the potential to reduce the viability of materials held in germ plasm collections and to offset gains expected by the introduction of particular genes of interest from genetic resources.

Alleles↗
PubMed1996

Neutral genetic markers and conservation genetics: simulated germplasm collections.

This study examines the use of neutral genetic markers to guide sampling from a large germplasm collection with the objective of establishing from it a smaller, but genetically representative sample. We simulated evolutionary change and germplasm sampling in a subdivided population of a diploid hermaphrodite annual plant to create an initially large collection. Several strategies of sampling from this collection were then compared. Our results show that a strategy based on information obtained from marker genes led to retention of the maximum number of neutral and nonneutral alleles in the smaller sample. This occurred when demes were composed of self-fertilizing individuals or when no migration occurred among demes, but not when demes of an outcrossing population were connected by high levels of migration.

Algorithms↗
PubMed1993

Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers.

Wild crop relatives are an important source of genetic variation for improving domesticated species. Given limited resources, methods for maximizing the genetic diversity of collections of wild relatives are needed to help spread protection over a larger number of populations and species. Simulations were conducted to investigate the optimal strategy of sampling materials from populations of wild relatives, with the objective of maximizing the number of alleles (allelic richness) in collections of fixed size. Two methods, based on assessing populations for variation at marker loci (e.g., allozymes, restriction fragment length polymorphisms), were developed and compared with several methods that are not dependent on markers. Marker-assisted methods yielded higher overall allelic richness in the simulated collections, and they were particularly effective in conserving geographically localized alleles, the class of alleles that is most subject to loss.

Agriculture↗
PubMed1993

Cytotoxic T lymphocyte lines specific for human immunodeficiency virus type 1 Gag and reverse transcriptase derived from a vertically infected child.

Cytotoxic T lymphocytes (CTL) specific for human immunodeficiency virus type 1 (HIV-1) are thought to play an important role in controlling HIV-1 infection. HIV-1-specific CTL are readily demonstrated in unstimulated peripheral blood mononuclear cells (PBMC) of HIV-infected adults but less frequently in PBMC from vertically infected children. HIV-1-specific CTL lines were derived from a long-term survivor of vertical HIV-1 infection using PBMC stimulated with a CD3-specific monoclonal antibody and interleukin-2; these lines had Gag- or reverse transcriptase (RT)-specific cytotoxicity. Cytotoxicity was restricted by major histocompatibility complex class I antigen and blocked by antibody to the T cell receptor complex. Fluorescence-activated cell sorting analysis demonstrated their phenotype to be CD3+CD4-CD8+. Unstimulated PBMC from this patient had no detectable HIV-1-specific cytotoxicity when tested against autologous HIV-1 envelope-, Gag-, or RT-expressing target cells. Thus, this child with vertically acquired HIV-1 infection likely has HIV-1-specific CTL precursors despite the absence of circulating, activated HIV-1-specific CTL.

CD3 Complex↗
PubMed1991

Intraspecific variation in population gene diversity and effective population size correlates with the mating system in plants.

Published data on allele frequencies at isozyme loci in inbreeding and outbreeding plant species were analyzed to examine intraspecific variation in gene diversity and effective population size (Ne). Compared with outbreeders, inbreeding species showed markedly greater variation among populations in average values of Nei's gene diversity statistic. Effective population size was estimated by assuming that the variation observed at isozyme loci is selectively neutral. Inbreeding species showed greater levels of variation in Ne than did outbreeders, although the upper range of Ne was similar in the two classes of species. The results suggest that there may be considerable genetic variation and potential for evolutionary change in some but not all populations of inbreeders. Moreover, these findings are important with respect to the conservation of genetic resources. In particular, that the amount of intraspecific variation in population genetic diversity and Ne differs between inbreeding and outbreeding species should be taken into account in sampling efforts designed to optimize the diversity of germplasm collections.

Journal Article↗
PubMed1984

Estimation of mating system parameters when outcrossing events are correlated.

Many plant species have mating systems characterized by a mixture of self-fertilization and outcrossing. Statistical estimation of the outcrossing rate has relied on a model of the mating process that assumes that successive outcross events within a family arise from independent draws of pollen from the total population of male plants. Although this assumption is likely to be most appropriate for wind-pollinated plants, it is not appropriate in certain insect-pollinated plants. An alternative model is developed that assumes that successive outcross events within a family involve pollen drawn from a single male parent. The estimation of the parameters that index this model is outlined and a procedure for calculating the variances of the parameter estimates is presented. Monte Carlo simulations of the sampling processes assumed by each model are also presented. The simulations show that application of the incorrect estimation model to data can lead to a large bias in parameter estimates.

Journal Article↗