David J. Witherspoon

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Tibetans have lived at very high altitudes for thousands of years, and they have a distinctive suite of physiological traits that enable them to tolerate environmental hypoxia. These phenotypes are clearly the result of adaptation to this environment, but their genetic basis remains unknown. We report genome-wide scans that reveal positive selection in(More)
Ti?El s are " cut-and-paste " transposable elements found in high copy number in the germline genomes of the ciliates Oxytricha fallax and 0. trifullux. TBEl " family " sequence (sequence of mixed polymerase chain reaction products generated using primers that match roughly half the TBEZs in host whole-cell DNA) was obtained from both host species. Although(More)
We present a maximum likelihood model to estimate the age of retrotransposon subfamilies. This method is designed around a master gene model which assumes a constant retrotransposition rate. The statistical properties of this model and an ad hoc estimation procedure are compared using two simulated data sets. We also test whether each estimation procedure(More)
The determination of the relationship between a pair of individuals is a fundamental application of genetics. Previously, we and others have demonstrated that identity-by-descent (IBD) information generated from high-density single-nucleotide polymorphism (SNP) data can greatly improve the power and accuracy of genetic relationship detection. Whole-genome(More)
of Chimerism Analysis Data. a. Simulated distributions of the proportion of allele A reads out of the total number of reads at a locus for a marmoset with chimeric fraction Φ BLOCKIN BLOCKIN = 0.33 (green) and BLOCKIN BLOCKIN Φ BLOCKIN BLOCKIN = 0 (i.e., not chimeric; yellow). b. Standard deviation in the proportion of allele A reads across loci vs.(More)
BACKGROUND Mobile elements (MEs) are diverse, common and dynamic inhabitants of nearly all genomes. ME transposition generates a steady stream of polymorphic genetic markers, deleterious and adaptive mutations, and substrates for further genomic rearrangements. Research on the impacts, population dynamics, and evolution of MEs is constrained by the(More)
BACKGROUND Recombination rates vary widely across the human genome, but little of that variation is correlated with known DNA sequence features. The genome contains more than one million Alu mobile element insertions, and these insertions have been implicated in non-homologous recombination, modulation of DNA methylation, and transcriptional regulation. If(More)
BACKGROUND Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations. RESULTS We report new data on 155 individuals from four Tamil caste(More)
P elements, like mariners, inhabit eukaryotic genomes and transpose via a DNA intermediate. Mutant and wild-type elements in the same genome should be transposed with equal probability by trans-acting transposase, and so no selection should counteract the accumulation of inactivating mutations in transposase genes. Thus, copies of mariner elements diverge(More)
Deedu (DU) Mongolians, who migrated from the Mongolian steppes to the Qinghai-Tibetan Plateau approximately 500 years ago, are challenged by environmental conditions similar to native Tibetan highlanders. Identification of adaptive genetic factors in this population could provide insight into coordinated physiological responses to this environment. Here we(More)