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Search Results: 1 - 10 of 133105 matches for " David W Coltman "
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Genetic linkage map of a wild genome: genomic structure, recombination and sexual dimorphism in bighorn sheep
Jocelyn Poissant, John T Hogg, Corey S Davis, Joshua M Miller, Jillian F Maddox, David W Coltman
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-524
Abstract: Bighorn sheep population-specific maps differed slightly in contiguity but were otherwise very similar in terms of genomic structure and recombination rates. The joint analysis of the two pedigrees resulted in a highly contiguous map composed of 247 microsatellite markers distributed along all 26 autosomes and the X chromosome. The map is estimated to cover about 84% of the bighorn sheep genome and contains 240 unique positions spanning a sex-averaged distance of 3051 cM with an average inter-marker distance of 14.3 cM. Marker synteny, order, sex-averaged interval lengths and sex-averaged total map lengths were all very similar between sheep species. However, in contrast to domestic sheep, but consistent with the usual pattern for a placental mammal, recombination rates in bighorn sheep were significantly greater in females than in males (~12% difference), resulting in an autosomal female map of 3166 cM and an autosomal male map of 2831 cM. Despite differing genome-wide patterns of heterochiasmy between the sheep species, sexual dimorphism in recombination rates was correlated between orthologous intervals.We have developed a first-generation bighorn sheep linkage map that will facilitate future studies of the genetic architecture of trait variation in this species. While domestication has been hypothesized to be responsible for the elevated mean recombination rate observed in domestic sheep, our results suggest that it is a characteristic of Ovis species. However, domestication may have played a role in altering patterns of heterochiasmy. Finally, we found that interval-specific patterns of sexual dimorphism were preserved among closely related Ovis species, possibly due to the conserved position of these intervals relative to the centromeres and telomeres. This study exemplifies how transferring genomic resources from domesticated species to close wild relative can benefit evolutionary ecologists while providing insights into the evolution of genomic structure and
Depauperate genetic variability detected in the American and European bison using genomic techniques
Cino Pertoldi, Ma?gorzata Tokarska, Jan M Wójcik, Ditte Demontis, Volker Loeschcke, Vivi R Gregersen, David Coltman, Gregory A Wilson, Ettore Randi, Michael M Hansen, Christian Bendixen
Biology Direct , 2009, DOI: 10.1186/1745-6150-4-48
Abstract: This article was reviewed by: Fyodor Kondrashov and Shamil SunyaevFifty-four EB (Bison bonasus bonasus), 30 WB (Bison bison athabascae) and 26 PB (Bison bison bison) were used for genome screening. The PB samples derive from Elk Island National Park while WB samples come from Wood Buffalo National Park (Canada). The relationships (mother, father and offspring) of three EB families were used in the SNP screening to verify Mendelian segregation. Genome-wide screening encompassed 54, 000 single nucleotide polymorphisms (SNPs) across the entire bovine genome. More than half of the SNPs were discovered using the sequencing system Genome Analyzer (Illumina?) [1]. The additional SNP content was derived from publicly available sources such as Btau (ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Btaurus/fasta webcite), the bovine reference genome, and the Bovine HapMap Consortium data set (). The BeadChip has an MAF of 0.25 across all loci and has been validated in both dairy and beef cattle. SNPs were genotyped on the BovineSNP50 BeadChip according to the Infinium II Multi-Sample assay protocol provided by Illumina? (Manual Experienced User Card, 11208000 Rev. A., Illumina Inc.).Despite the fact that the Bos and Bison lineages split about 1 million years ago [2], a total of 2, 209 polymorphic SNPs were found when EB, PB and WB were pooled. The average call rate for the bison samples was relatively high (96.60%) compared to the call rate found for the cattle samples (99.5%) (Illumina, Inc. Pub No. 370-2007-029) [1]. The small difference in call rate (2.9%) confirms the reliability of our comparisons and also reflects differences in the genomic DNA between the two groups such as the possibility of different alleles or deletions in SNPs.The P% for each bison species was calculated relative to the total number of loci that were polymorphic when EB, WB and PB samples were pooled. The pairwise FST used as a measure of differentiation between EB, PB and WB was estimated using FSTAT version 2
Spatial Genetic Structure of a Symbiotic Beetle-Fungal System: Toward Multi-Taxa Integrated Landscape Genetics
Patrick M. A. James, Dave W. Coltman, Brent W. Murray, Richard C. Hamelin, Felix A. H. Sperling
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0025359
Abstract: Spatial patterns of genetic variation in interacting species can identify shared features that are important to gene flow and can elucidate co-evolutionary relationships. We assessed concordance in spatial genetic variation between the mountain pine beetle (Dendroctonus ponderosae) and one of its fungal symbionts, Grosmanniaclavigera, in western Canada using neutral genetic markers. We examined how spatial heterogeneity affects genetic variation within beetles and fungi and developed a novel integrated landscape genetics approach to assess reciprocal genetic influences between species using constrained ordination. We also compared landscape genetic models built using Euclidean distances based on allele frequencies to traditional pair-wise Fst. Both beetles and fungi exhibited moderate levels of genetic structure over the total study area, low levels of structure in the south, and more pronounced fungal structure in the north. Beetle genetic variation was associated with geographic location while that of the fungus was not. Pinevolume and climate explained beetle genetic variation in the northern region of recent outbreak expansion. Reciprocal genetic relationships were only detectedin the south where there has been alonger history of beetle infestations. The Euclidean distance and Fst-based analyses resulted in similar models in the north and over the entire study area, but differences between methods in the south suggest that genetic distances measures should be selected based on ecological and evolutionary contexts. The integrated landscape genetics framework we present is powerful, general, and can be applied to other systems to quantify the biotic and abiotic determinants of spatial genetic variation within and among taxa.
Environmental Coupling of Selection and Heritability Limits Evolution
A. J. Wilson,J. M. Pemberton,J. G. Pilkington,D. W. Coltman,D. V. Mifsud,T. H. Clutton-Brock,L. E. B. Kruuk
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0040216
Abstract: There has recently been great interest in applying theoretical quantitative genetic models to empirical studies of evolution in wild populations. However, while classical models assume environmental constancy, most natural populations exist in variable environments. Here, we applied a novel analytical technique to a long-term study of birthweight in wild sheep and examined, for the first time, how variation in environmental quality simultaneously influences the strength of natural selection and the genetic basis of trait variability. In addition to demonstrating that selection and genetic variance vary dramatically across environments, our results show that environmental heterogeneity induces a negative correlation between these two parameters. Harsh environmental conditions were associated with strong selection for increased birthweight but low genetic variance, and vice versa. Consequently, the potential for microevolution in this population is constrained by either a lack of heritable variation (in poor environments) or by a reduced strength of selection (in good environments). More generally, environmental dependence of this nature may act to limit rates of evolution, maintain genetic variance, and favour phenotypic stasis in many natural systems. Assumptions of environmental constancy are likely to be violated in natural systems, and failure to acknowledge this may generate highly misleading expectations for phenotypic microevolution.
Environmental Coupling of Selection and Heritability Limits Evolution
A. J Wilson ,J. M Pemberton,J. G Pilkington,D. W Coltman,D. V Mifsud,T. H Clutton-Brock,L. E. B Kruuk
PLOS Biology , 2006, DOI: 10.1371/journal.pbio.0040216
Abstract: There has recently been great interest in applying theoretical quantitative genetic models to empirical studies of evolution in wild populations. However, while classical models assume environmental constancy, most natural populations exist in variable environments. Here, we applied a novel analytical technique to a long-term study of birthweight in wild sheep and examined, for the first time, how variation in environmental quality simultaneously influences the strength of natural selection and the genetic basis of trait variability. In addition to demonstrating that selection and genetic variance vary dramatically across environments, our results show that environmental heterogeneity induces a negative correlation between these two parameters. Harsh environmental conditions were associated with strong selection for increased birthweight but low genetic variance, and vice versa. Consequently, the potential for microevolution in this population is constrained by either a lack of heritable variation (in poor environments) or by a reduced strength of selection (in good environments). More generally, environmental dependence of this nature may act to limit rates of evolution, maintain genetic variance, and favour phenotypic stasis in many natural systems. Assumptions of environmental constancy are likely to be violated in natural systems, and failure to acknowledge this may generate highly misleading expectations for phenotypic microevolution.
Mutated elements of a complex promoter (Amh) can help to demonstrate the role of certain elements in controlling differential gene expression  [PDF]
David W. Dresser
American Journal of Molecular Biology (AJMB) , 2012, DOI: 10.4236/ajmb.2012.24036
Abstract: Amh is a single copy gene which is expressed in different ways during mammalian development. Several potential promoter elements have been identified using physiological experimentation and on the basis of interspecific sequence comparison. The role of putative promoter elements in controlling gene expression has been investigated by many workers over the last two decades and here by individually mutating each element. Expression was measured in vitro in cells of Sertoli descent by flowcytometry using EGFP as a reporter gene. Three lines of murine cells were used; pre- and post-pubertal Sertoli and granulosa cells. Differences between the three lines of cells, support the view that differentiation in this in vitro model system is likely to be at the level of available transcription factors at given points in development.
Interaction between the Wilms tumour factor-1 element in the promoter of Amh and a downstream enhancer is required for a strong expression of the gene in pre-pubertal sertoli cells  [PDF]
David W. Dresser
American Journal of Molecular Biology (AJMB) , 2013, DOI: 10.4236/ajmb.2013.33022
Abstract:

Amh (anti-Müllerian hormone) is a single copy gene which is expressed strongly in Sertoli cells in the foetal testis and participates in the onset of sexual differentiation. Its promoter driving the expression of a reporter gene (d2EGFP) has been used to analyse the role of certain defined putative elements and a downstream enhancer element in gene expression. These experiments were carried out in vitro using a line of pre-pubertal mouse Sertoli cells, transienly transfected with circular DNA constructs with variously mutated promoter elements. A downstream enhancer element, situated immediately 3’ of the polyadenylation (PA) signal for Amh, has been inserted in an equivalent position in the d2EGFP construct. When the Amh promoter is unmodified, the downstream enhancer (DE) is positively associated with a large increase in EGFP expression. This is at least partly the consequence of an increased rate of expression by individual cells. Experiments using variously truncated Amh promoters indicate that an upstream region (-214 to -336) may play a minor role in facilitating enhancement. However mutation of the Wilms tumour factor-1 element, situated between the tata box and the start of translation, results in an almost complete suppression of enhancement.

Marketing Accountability: Defining Expectations and Measuring Outcomes  [PDF]
David W. Stewart
Open Journal of Business and Management (OJBM) , 2014, DOI: 10.4236/ojbm.2014.23019
Abstract: This paper calls for work that focuses on the relationships of marketing activities and outcomes and measures of the financial performance of the firm. More specifically, the paper suggests the need to link marketing outcomes to the cash flow of the firm and the business model that generates the cash flow. The paper also calls for greater alignment of measures of marketing accountability with expectations and responsibilities of the marketing organization.
The Transcription Factors GATA-1 and GATA-4 Have Opposite Effects on DNA Expression Driven by an Amh Promoter  [PDF]
David W. Dresser
American Journal of Molecular Biology (AJMB) , 2014, DOI: 10.4236/ajmb.2014.43016
Abstract:

An Amh promoter driving expression of a reporter gene (d2EGFP) has been used to analyze the role of two specific promoter transcription factor binding elements. In addition a downstream (3’) enhancer (DE) was also investigated. The transcription factors GATA-1 and GATA-4 had opposite effects, the former being incremental and the latter decremental. The quantitative balance between these two factors may provide a degree of control over the level of gene expression.

Optimal Consumption under Uncertainties: Random Horizon Stochastic Dynamic Roy’s Identity and Slutsky Equation  [PDF]
David W. K. Yeung
Applied Mathematics (AM) , 2014, DOI: 10.4236/am.2014.52028
Abstract:

This paper extends Slutsky’s classic work on consumer theory to a random horizon stochastic dynamic framework in which the consumer has an inter-temporal planning horizon with uncertainties in future incomes and life span. Utility maximization leading to a set of ordinary wealth-dependent demand functions is performed. A dual problem is set up to derive the wealth compensated demand functions. This represents the first time that wealth-dependent ordinary demand functions and wealth compensated demand functions are obtained under these uncertainties. The corresponding Roy’s identity relationships and a set of random horizon stochastic dynamic Slutsky equations are then derived. The extension incorporates realistic characteristics in consumer theory and advances the conventional microeconomic study on consumption to a more realistic optimal control framework.

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