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Search Results: 1 - 10 of 92042 matches for " W Scott Watkins "
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Culture creates genetic structure in the Caucasus: Autosomal, mitochondrial, and Y-chromosomal variation in Daghestan
Elizabeth E Marchani, W Scott Watkins, Kazima Bulayeva, Henry C Harpending, Lynn B Jorde
BMC Genetics , 2008, DOI: 10.1186/1471-2156-9-47
Abstract: We found that the highland Daghestani populations had contrasting histories for the mitochondrial DNA and Y-chromosome data sets. Y-chromosomal haplogroup diversity was reduced among highland Daghestani populations when compared to other populations and to highland Daghestani mitochondrial DNA haplogroup diversity. Lowland Daghestani populations showed Turkish and Central Asian affinities for both mitochondrial and Y-chromosomal data sets. Autosomal population histories are strongly correlated to the pattern observed for the mitochondrial DNA data set, while the correlation between the mitochondrial DNA and Y-chromosome distance matrices was weak and not significant.The reduced Y-chromosomal diversity exhibited by highland Daghestani populations is consistent with genetic drift caused by patrilocal endogamy. Mitochondrial and Y-chromosomal phylogeographic comparisons indicate a common Near Eastern origin of highland populations. Lowland Daghestani populations show varying influence from Near Eastern and Central Asian populations.The populations of the Caucasus region have complex histories of isolation and gene flow. The region as a whole has served as a gateway between continents, with waves of human migration leaving rich cultural and linguistic diversity in their wake [1,2]. The Caucasus Mountains have shaped the routes of migrating populations and military invasions, diverting these travellers away from the remote highlands and into the more easily accessible lowlands. Differences between highland and lowland populations are exaggerated by the marriage practices of highland populations: wives move to the home of their husbands, while husbands remain in the land of their forefathers for generations [3,4].We have identified five populations from Daghestan that have been influenced by both physical and cultural barriers to gene flow. Three are highland isolates, while two lowland populations represent admixed groups influenced by Turkic and Mongolian migrants. We i
Mobile element scanning (ME-Scan) by targeted high-throughput sequencing
David J Witherspoon, Jinchuan Xing, Yuhua Zhang, W Scott Watkins, Mark A Batzer, Lynn B Jorde
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-410
Abstract: Here we present a novel method for identifying nearly all insertions of a ME subfamily in the whole genomes of multiple individuals and simultaneously genotyping (for presence or absence) those insertions that are variable in the population. We use ME-specific primers to construct DNA libraries that contain the junctions of all ME insertions of the subfamily, with their flanking genomic sequences, from many individuals. Individual-specific "index" sequences are designed into the oligonucleotide adapters used to construct the individual libraries. These libraries are then pooled and sequenced using a ME-specific sequencing primer. Mobile element insertion loci of the target subfamily are uniquely identified by their junction sequence, and all insertion junctions are linked to their individual libraries by the corresponding index sequence. To test this method's feasibility, we apply it to the human AluYb8 and AluYb9 subfamilies. In four individuals, we identified a total of 2,758 AluYb8 and AluYb9 insertions, including nearly all those that are present in the reference genome, as well as 487 that are not. Index counts show the sequenced products from each sample reflect the intended proportions to within 1%. At a sequencing depth of 355,000 paired reads per sample, the sensitivity and specificity of ME-Scan are both approximately 95%.Mobile Element Scanning (ME-Scan) is an efficient method for quickly genotyping mobile element insertions with very high sensitivity and specificity. In light of recent improvements to high-throughput sequencing technology, it should be possible to employ ME-Scan to genotype insertions of almost any mobile element family in many individuals from any species.Mobile elements (MEs) are DNA sequences that can replicate and insert themselves into new loci within larger host genomes. This strategy has proved very successful: MEs are evolutionarily ancient, highly diversified in form, ubiquitous in distribution, and often extremely numerous with
Optimal Moments for the Analysis of Peculiar Velocity Surveys II: Testing
Hume A. Feldman,Richard Watkins,Adrian L. Melott,Scott W. Chambers
Physics , 2003, DOI: 10.1086/379363
Abstract: Analyses of peculiar velocity surveys face several challenges, including low signal--to--noise in individual velocity measurements and the presence of small--scale, nonlinear flows. This is the second in a series of papers in which we describe a new method of overcoming these problems by using data compression as a filter with which to separate large--scale, linear flows from small--scale noise that can bias results. We demonstrate the effectiveness of our method using realistic catalogs of galaxy velocities drawn from N--body simulations. Our tests show that a likelihood analysis of simulated catalogs that uses all of the information contained in the peculiar velocities results in a bias in the estimation of the power spectrum shape parameter $\Gamma$ and amplitude $\beta$, and that our method of analysis effectively removes this bias. We expect that this new method will cause peculiar velocity surveys to re--emerge as a useful tool to determine cosmological parameters.
Optimal Moments for the Analysis of Peculiar Velocity Surveys
Richard Watkins,Hume A. Feldman,Scott W. Chambers,Patrick Gorman,Adrian L. Melott
Physics , 2001, DOI: 10.1086/324280
Abstract: We present a new method for the analysis of peculiar velocity surveys which removes contributions to velocities from small scale, nonlinear velocity modes while retaining information about large scale motions. Our method utilizes Karhunen--Lo\`eve methods of data compression to construct a set of moments out of the velocities which are minimally sensitive to small scale power. The set of moments are then used in a likelihood analysis. We develop criteria for the selection of moments, as well as a statistic to quantify the overall sensitivity of a set of moments to small scale power. Although we discuss our method in the context of peculiar velocity surveys, it may also prove useful in other situations where data filtering is required.
Genetic analysis of ancestry, admixture and selection in Bolivian and Totonac populations of the New World
W Scott Watkins, Jinchuan Xing, Chad Huff, David J Witherspoon, Yuhua Zhang, Ugo A Perego, Scott R Woodward, Lynn B Jorde
BMC Genetics , 2012, DOI: 10.1186/1471-2156-13-39
Abstract: We analyzed common genomic regions from native Bolivian and Totonac populations to identify 324 highly predictive Native American ancestry informative markers (AIMs). As few as 40–50 of these AIMs perform nearly as well as large panels of random genome-wide SNPs for predicting and estimating Native American ancestry and admixture levels. These AIMs have greater New World vs. Old World specificity than previous AIMs sets. We identify highly-divergent New World SNPs that coincide with high-frequency haplotypes found at similar frequencies in all populations examined, including the HGDP Pima, Maya, Colombian, Karitiana, and Surui American populations. Some of these regions are potential candidates for positive selection. European admixture in the Bolivian sample is approximately 12%, though individual estimates range from 0–48%. We estimate that the admixture occurred ~360–384?years ago. Little evidence of European or African admixture was found in Totonac individuals. Bolivians with pre-Columbian mtDNA and Y-chromosome haplogroups had 5–30% autosomal European ancestry, demonstrating the limitations of Y-chromosome and mtDNA haplogroups and the need for autosomal ancestry informative markers for assessing ancestry in admixed populations.
Genetic diversity in India and the inference of Eurasian population expansion
Jinchuan Xing, W Scott Watkins, Ya Hu, Chad D Huff, Aniko Sabo, Donna M Muzny, Michael J Bamshad, Richard A Gibbs, Lynn B Jorde, Fuli Yu
Genome Biology , 2010, DOI: 10.1186/gb-2010-11-11-r113
Abstract: To analyze an unbiased sample of genetic diversity in India and to investigate human migration history in Eurasia, we resequenced one 100-kb ENCODE region in 92 samples collected from three castes and one tribal group from the state of Andhra Pradesh in south India. Analyses of the four Indian populations, along with eight HapMap populations (692 samples), showed that 30% of all SNPs in the south Indian populations are not seen in HapMap populations. Several Indian populations, such as the Yadava, Mala/Madiga, and Irula, have nucleotide diversity levels as high as those of HapMap African populations. Using unbiased allele-frequency spectra, we investigated the expansion of human populations into Eurasia. The divergence time estimates among the major population groups suggest that Eurasian populations in this study diverged from Africans during the same time frame (approximately 90 to 110 thousand years ago). The divergence among different Eurasian populations occurred more than 40,000 years after their divergence with Africans.Our results show that Indian populations harbor large amounts of genetic variation that have not been surveyed adequately by public SNP discovery efforts. Our data also support a delayed expansion hypothesis in which an ancestral Eurasian founding population remained isolated long after the out-of-Africa diaspora, before expanding throughout Eurasia.The Indian subcontinent is currently populated by more than one billion people who belong to thousands of linguistic and ethnic groups [1,2]. Genetic and anthropological studies have shown that the peopling of the subcontinent is characterized by a complex history, with contributions from different ancestral populations [2-5]. Studies of maternal lineages by mitochondrial resequencing have shown that the two major mitochondrial lineages that emerged from Africa (haplogroups M and N, dating to approximately 60 thousand years ago (kya)) are both very diverse among Indian populations [6,7]. Additional
Alu repeats increase local recombination rates
David J Witherspoon, W Scott Watkins, Yuhua Zhang, Jinchuan Xing, Whitney L Tolpinrud, Dale J Hedges, Mark A Batzer, Lynn B Jorde
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-530
Abstract: We carried out sequencing, SNP identification, and SNP genotyping around 19 AluY insertion loci in 347 individuals sampled from diverse populations, then used the SNP genotypes to estimate local recombination rates around the AluY loci. The loci and SNPs were chosen so as to minimize other factors (such as SNP ascertainment bias and SNP density) that could influence recombination rate estimates. We detected a significant increase in recombination rate within ~2 kb of the AluY insertions in our African population sample. To test this observation against a larger set of AluY insertions, we applied our locus- and SNP-selection design and analyses to the HapMap Phase II data. In that data set, we observed a significantly increased recombination rate near AluY insertions in both the CEU and YRI populations.We show that the presence of a fixed AluY insertion is significantly predictive of an elevated local recombination rate within 2 kb of the insertion, independent of other known predictors. The magnitude of this effect, approximately a 6% increase, is comparable to the effects of some recombinogenic DNA sequence motifs identified via their association with recombination hot spots.Approximately one-half of the human genome consists of the remnants of past transpositional bursts [1]. LINE-1 non-LTR retrotransposons and the Alu elements they mobilize continue to replicate in the human gene pool to this day [2]. As a result of Alu retroposition, our genomes are littered with more than one million small (~300 bp), non-allelic regions whose DNA sequences are nearly identical to each other. Their recombinogenic impact is evident: these scattered homologies trigger non-allelic homologous recombination (NAHR) events that lead to translocations, deletions, duplications, and other chromosomal abnormalities and copy number variations [2-6]. These events have affected the long-term evolution of the human genome and of the Alu insertions themselves [7-11]. Alu repeats have been impli
Scaling in the space climatology of the auroral indices: is SOC the only possible description?
N. W. Watkins
Nonlinear Processes in Geophysics (NPG) , 2002,
Abstract: The study of the robust features of the magnetosphere is motivated both by new "whole system" approaches, and by the idea of "space climate" as opposed to "space weather". We enumerate these features for the AE index, and discuss whether self-organised criticality (SOC) is the most natural explanation of the "stylised facts" so far known for AE. We identify and discuss some open questions, answers to which will clarify the extent to which AE's properties provide evidence for SOC. We then suggest an SOC-like reconnection-based scenario drawing on the result of Craig (2001) as an explanation of the very recent demonstration by Uritsky et al. (2001b) of power laws in several properties of spatiotemporal features seen in auroral images.
Ancestry of the Iban Is Predominantly Southeast Asian: Genetic Evidence from Autosomal, Mitochondrial, and Y Chromosomes
Tatum S. Simonson,Jinchuan Xing,Robert Barrett,Edward Jerah,Peter Loa,Yuhua Zhang,W. Scott Watkins,David J. Witherspoon,Chad D. Huff,Scott Woodward,Bryan Mowry,Lynn B. Jorde
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0016338
Abstract: Humans reached present-day Island Southeast Asia (ISEA) in one of the first major human migrations out of Africa. Population movements in the millennia following this initial settlement are thought to have greatly influenced the genetic makeup of current inhabitants, yet the extent attributed to different events is not clear. Recent studies suggest that south-to-north gene flow largely influenced present-day patterns of genetic variation in Southeast Asian populations and that late Pleistocene and early Holocene migrations from Southeast Asia are responsible for a substantial proportion of ISEA ancestry. Archaeological and linguistic evidence suggests that the ancestors of present-day inhabitants came mainly from north-to-south migrations from Taiwan and throughout ISEA approximately 4,000 years ago. We report a large-scale genetic analysis of human variation in the Iban population from the Malaysian state of Sarawak in northwestern Borneo, located in the center of ISEA. Genome-wide single-nucleotide polymorphism (SNP) markers analyzed here suggest that the Iban exhibit greatest genetic similarity to Indonesian and mainland Southeast Asian populations. The most common non-recombining Y (NRY) and mitochondrial (mt) DNA haplogroups present in the Iban are associated with populations of Southeast Asia. We conclude that migrations from Southeast Asia made a large contribution to Iban ancestry, although evidence of potential gene flow from Taiwan is also seen in uniparentally inherited marker data.
Genomic Analysis of Natural Selection and Phenotypic Variation in High-Altitude Mongolians
Jinchuan Xing equal contributor,Tana Wuren equal contributor,Tatum S. Simonson equal contributor,W. Scott Watkins,David J. Witherspoon,Wilfred Wu,Ga Qin,Chad D. Huff,Lynn B. Jorde ,Ri-Li Ge
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003634
Abstract: 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 examine genomic and phenotypic variation in this unique population and present the first complete analysis of a Mongolian whole-genome sequence. High-density SNP array data demonstrate that DU Mongolians share genetic ancestry with other Mongolian as well as Tibetan populations, specifically in genomic regions related with adaptation to high altitude. Several selection candidate genes identified in DU Mongolians are shared with other Asian groups (e.g., EDAR), neighboring Tibetan populations (including high-altitude candidates EPAS1, PKLR, and CYP2E1), as well as genes previously hypothesized to be associated with metabolic adaptation (e.g., PPARG). Hemoglobin concentration, a trait associated with high-altitude adaptation in Tibetans, is at an intermediate level in DU Mongolians compared to Tibetans and Han Chinese at comparable altitude. Whole-genome sequence from a DU Mongolian (Tianjiao1) shows that about 2% of the genomic variants, including more than 300 protein-coding changes, are specific to this individual. Our analyses of DU Mongolians and the first Mongolian genome provide valuable insight into genetic adaptation to extreme environments.
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