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Search Results: 1 - 10 of 17604 matches for " Chris Tyler-Smith "
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An Exceptional Gene: Evolution of the TSPY Gene Family in Humans and Other Great Apes
Yali Xue,Chris Tyler-Smith
Genes , 2011, DOI: 10.3390/genes2010036
Abstract: The TSPY gene stands out from all other human protein-coding genes because of its high copy number and tandemly-repeated organization. Here, we review its evolutionary history in great apes in order to assess whether these unusual properties are more likely to result from a relaxation of constraint or an unusual functional role. Detailed comparisons with chimpanzee are possible because a finished sequence of the chimpanzee Y chromosome is available, together with more limited data from other apes. These comparisons suggest that the human-chimpanzee ancestral Y chromosome carried a tandem array of TSPY genes which expanded on the human lineage while undergoing multiple duplication events followed by pseudogene formation on the chimpanzee lineage. The protein coding region is the most highly conserved of the multi-copy Y genes in human-chimpanzee comparisons, and the analysis of the d N/d S ratio indicates that TSPY is evolutionarily highly constrained, but may have experienced positive selection after the human-chimpanzee split. We therefore conclude that the exceptionally high copy number in humans is most likely due to a human-specific but unknown functional role, possibly involving rapid production of a large amount of TSPY protein at some stage during?spermatogenesis.
The Peopling of Korea Revealed by Analyses of Mitochondrial DNA and Y-Chromosomal Markers
Han-Jun Jin,Chris Tyler-Smith,Wook Kim
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0004210
Abstract: The Koreans are generally considered a northeast Asian group because of their geographical location. However, recent findings from Y chromosome studies showed that the Korean population contains lineages from both southern and northern parts of East Asia. To understand the genetic history and relationships of Korea more fully, additional data and analyses are necessary.
A world in a grain of sand: human history from genetic data
Vincenza Colonna, Luca Pagani, Yali Xue, Chris Tyler-Smith
Genome Biology , 2011, DOI: 10.1186/gb-2011-12-11-234
Abstract: To see a world in a grain of sand ...William Blake, Auguries of InnocenceThe genome of each individual is a temporary assemblage of DNA segments brought together for a single generation by a combination of chance, ancestry, recombination and natural selection. These segments have different histories because of recombination and can thus provide independent information about ancestry, the focus of this review. However, the ancestry of different segments is not entirely independent. Humans are not a single randomly mating population: we are subdivided, and these subdivisions into bands, tribes, clans, ethnic groups, nations and so on are of great interest to both scientists and non-scientists. Thus the thousands of different genomic segments in any individual do not trace back to ancestors randomly spread around the globe; segment ancestry is constrained by population history. Two non-recombining segments of the genome, mitochondrial DNA (mtDNA) and the Y chromosome, have been used for decades to study genetic histories [1,2]. Sometimes mtDNA and the Y chromosome share the same history, but often they do not, and such differences alert us to some of the complexities of the human past [3]. But mtDNA and the Y chromosome provide only two perspectives. Recent advances in technology provide access to most of the genome, and increasingly to the genomes of companion species. Here, we consider how this wider perspective is beginning to inform our view of human history. We will see that it is possible to probe much further back into the past, into a period in which the uniparental markers are uninformative yet key evolutionary events took place, and even to speculate about when humans might have begun to wear clothes or to start reconstructing the genomics of former populations before their contact with modern expansions.Genome-wide data can be obtained by either genotyping samples or re-sequencing them. Genotyping provides information about the allelic state of positions in
Reading the human Y chromosome: the emerging DNA markers and human genetic history
Santos, Fabrício R.;Tyler-Smith, Chris;
Brazilian Journal of Genetics , 1996, DOI: 10.1590/S0100-84551996000400025
Abstract: reading the human y chromosome: the emerging dna markers and human genetic history.
Geographical Affinities of the HapMap Samples
Miao He, Jane Gitschier, Tatiana Zerjal, Peter de Knijff, Chris Tyler-Smith, Yali Xue
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0004684
Abstract: Background The HapMap samples were collected for medical-genetic studies, but are also widely used in population-genetic and evolutionary investigations. Yet the ascertainment of the samples differs from most population-genetic studies which collect individuals who live in the same local region as their ancestors. What effects could this non-standard ascertainment have on the interpretation of HapMap results? Methodology/Principal Findings We compared the HapMap samples with more conventionally-ascertained samples used in population- and forensic-genetic studies, including the HGDP-CEPH panel, making use of published genome-wide autosomal SNP data and Y-STR haplotypes, as well as producing new Y-STR data. We found that the HapMap samples were representative of their broad geographical regions of ancestry according to all tests applied. The YRI and JPT were indistinguishable from independent samples of Yoruba and Japanese in all ways investigated. However, both the CHB and the CEU were distinguishable from all other HGDP-CEPH populations with autosomal markers, and both showed Y-STR similarities to unusually large numbers of populations, perhaps reflecting their admixed origins. Conclusions/Significance The CHB and JPT are readily distinguished from one another with both autosomal and Y-chromosomal markers, and results obtained after combining them into a single sample should be interpreted with caution. The CEU are better described as being of Western European ancestry than of Northern European ancestry as often reported. Both the CHB and CEU show subtle but detectable signs of admixture. Thus the YRI and JPT samples are well-suited to standard population-genetic studies, but the CHB and CEU less so.
The promise and reality of personal genomics
Bryndis Yngvadottir, Daniel G MacArthur, Hanjun Jin, Chris Tyler-Smith
Genome Biology , 2009, DOI: 10.1186/gb-2009-10-9-237
Abstract: Which country has published the largest per-capita number of personal genomes? The United States, the United Kingdom? Actually, it is Korea. A recent article in Nature by Kim et al. [1] presents the genome sequence of a Korean male, AK1 - the seventh published sequence of an individual human genome and the second from Korea. The rapid progress in personal genome sequencing is possible because so-called 'next-generation' sequencing technology has decreased costs by orders of magnitude and increased throughput. But those advantages come at a price: short, error-prone reads derived from single molecules that have to be stitched back together to make a best-guess at the starting sequence. We are still at the stage of working out how to apply the available technologies to coax out biological information: the goal of a US$1,000 genome providing life-changing personal medical insights is still some way off.The first aim of a genome-sequencing project is to assemble around 6 billion As, Cs, Gs and Ts, comprising the diploid genome of the individual, in the right order. This is a challenge both of scale and because of sequence complexities such as repeated elements. By a series of frankly heroic measures, Kim et al. [1] have succeeded in generating a sequence that is likely to be substantially more complete and accurate than any other individual human genome derived so far using the new sequencing technology. Nonetheless, the effort invested in producing such a high-quality sequence, including the cloning and high-coverage sequencing of large segments of the genome from bacterial artificial chromosomes (BACs), is not routinely feasible and the final product is still far from complete. The clear message is that sequencing technology still has a long way to go before we enter the era of cheap, complete and reliable individual genome sequencing.The high depth of coverage for the AK1 sequence (most parts of the genome were sequenced around 28 times (28×)) meant that most variant
‘Sifting the significance from the data’ - the impact of high-throughput genomic technologies on human genetics and health care
Clarke Angus J,Cooper David N,Krawczak Michael,Tyler-Smith Chris
Human Genomics , 2012, DOI: 10.1186/1479-7364-6-11
Abstract: This report is of a round-table discussion held in Cardiff in September 2009 for Cesagen, a research centre within the Genomics Network of the UK’s Economic and Social Research Council. The meeting was arranged to explore ideas as to the likely future course of human genomics. The achievements of genomics research were reviewed, and the likely constraints on the pace of future progress were explored. New knowledge is transforming biology and our understanding of evolution and human disease. The difficulties we face now concern the interpretation rather than the generation of new sequence data. Our understanding of gene-environment interaction is held back by our current primitive tools for measuring environmental factors, and in addition, there may be fundamental constraints on what can be known about these complex interactions.
A Genome-Wide Survey of Genetic Variation in Gorillas Using Reduced Representation Sequencing
Aylwyn Scally, Bryndis Yngvadottir, Yali Xue, Qasim Ayub, Richard Durbin, Chris Tyler-Smith
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0065066
Abstract: All non-human great apes are endangered in the wild, and it is therefore important to gain an understanding of their demography and genetic diversity. Whole genome assembly projects have provided an invaluable foundation for understanding genetics in all four genera, but to date genetic studies of multiple individuals within great ape species have largely been confined to mitochondrial DNA and a small number of other loci. Here, we present a genome-wide survey of genetic variation in gorillas using a reduced representation sequencing approach, focusing on the two lowland subspecies. We identify 3,006,670 polymorphic sites in 14 individuals: 12 western lowland gorillas (Gorilla gorilla gorilla) and 2 eastern lowland gorillas (Gorilla beringei graueri). We find that the two species are genetically distinct, based on levels of heterozygosity and patterns of allele sharing. Focusing on the western lowland population, we observe evidence for population substructure, and a deficit of rare genetic variants suggesting a recent episode of population contraction. In western lowland gorillas, there is an elevation of variation towards telomeres and centromeres on the chromosomal scale. On a finer scale, we find substantial variation in genetic diversity, including a marked reduction close to the major histocompatibility locus, perhaps indicative of recent strong selection there. These findings suggest that despite their maintaining an overall level of genetic diversity equal to or greater than that of humans, population decline, perhaps associated with disease, has been a significant factor in recent and long-term pressures on wild gorilla populations.
YFitter: Maximum likelihood assignment of Y chromosome haplogroups from low-coverage sequence data
Luke Jostins,Yali Xu,Shane McCarthy,Qasim Ayub,Richard Durbin,Jeff Barrett,Chris Tyler-Smith
Quantitative Biology , 2014,
Abstract: Low-coverage short-read resequencing experiments have the potential to expand our understanding of Y chromosome haplogroups. However, the uncertainty associated with these experiments mean that haplogroups must be assigned probabilistically to avoid false inferences. We propose an efficient dynamic programming algorithm that can assign haplogroups by maximum likelihood, and represent the uncertainty in assignment. We apply this to both genotype and low-coverage sequencing data, and show that it can assign haplogroups accurately and with high resolution. The method is implemented as the program YFitter, which can be downloaded from http://sourceforge.net/projects/yfitter/
PoolHap: Inferring Haplotype Frequencies from Pooled Samples by Next Generation Sequencing
Quan Long,Daniel C. Jeffares,Qingrun Zhang,Kai Ye,Viktoria Nizhynska,Zemin Ning,Chris Tyler-Smith,Magnus Nordborg
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015292
Abstract: With the advance of next-generation sequencing (NGS) technologies, increasingly ambitious applications are becoming feasible. A particularly powerful one is the sequencing of polymorphic, pooled samples. The pool can be naturally occurring, as in the case of multiple pathogen strains in a blood sample, multiple types of cells in a cancerous tissue sample, or multiple isoforms of mRNA in a cell. In these cases, it's difficult or impossible to partition the subtypes experimentally before sequencing, and those subtype frequencies must hence be inferred. In addition, investigators may occasionally want to artificially pool the sample of a large number of individuals for reasons of cost-efficiency, e.g., when carrying out genetic mapping using bulked segregant analysis. Here we describe PoolHap, a computational tool for inferring haplotype frequencies from pooled samples when haplotypes are known. The key insight into why PoolHap works is that the large number of SNPs that come with genome-wide coverage can compensate for the uneven coverage across the genome. The performance of PoolHap is illustrated and discussed using simulated and real data. We show that PoolHap is able to accurately estimate the proportions of haplotypes with less than 2% error for 34-strain mixtures with 2X total coverage Arabidopsis thaliana whole genome polymorphism data. This method should facilitate greater biological insight into heterogeneous samples that are difficult or impossible to isolate experimentally. Software and users manual are freely available at http://arabidopsis.gmi.oeaw.ac.at/quan/p?oolhap/.
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