TY - JOUR. T1 - The nature of quantitative genetic variation in drosophila. II* average dominance of abdominal bristle polygenes. AU - Frankham, R.. PY - 1974. Y1 - 1974. N2 - A comparison of 13 abdominal bristle selection lines with their base population and with reciprocal Fls between the selection lines and the base population was carried out. There was no significant directional contribution of maternally inherited factors to selection response.Different estimates of average dominance ranged from 0·28 to 0·43 with a mean of 0·39. This indicates that the alleles increasing abdominal bristle number are, on average, partly recessive. Some of the possible consequences of this are discussed.. AB - A comparison of 13 abdominal bristle selection lines with their base population and with reciprocal Fls between the selection lines and the base population was carried out. There was no significant directional contribution of maternally inherited factors to selection response.Different estimates of ...
Phylogenetic studies, particularly those based on rDNA sequences from plant roots and basidiomata, have revealed a strikingly high genetic diversity in the Sebacinales. However, the factors determining this genetic diversity at higher and lower taxonomic levels within this order are still unknown. In this study, we analysed patterns of genetic variation within two morphological species, Sebacina epigaea and S. incrustans, based on 340 DNA haplotype sequences of independent genetic markers from the nuclear (ITS + 5.8S + D1/D2, RPB2) and mitochondrial (ATP6) genomes for 98 population samples. By characterising the genetic population structure within these species, we provide insights into species boundaries and the possible factors responsible for genetic diversity at a regional geographic scale. We found that recombination events are relatively common between natural populations within Sebacina epigaea and S. incrustans, and play a significant role in generating intraspecific genetic diversity.
View Notes - Ch 3 - Nature Nurture & Human Diversity from PSYC 101 at UBC. Nature, Nurture & Nature, Human Diversity 100 Oct 6 08 True or False 1) Even complex human traits are determined by a
Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expression regulation underlying CGV is scarce. Here we investigated the transcriptional architecture of CGV in response to rapid temperature changes in the nematode Caenorhabditis elegans. We analyzed regulatory variation in gene expression (and mapped eQTL) across the course of a heat stress and recovery response in a recombinant inbred population. We measured gene expression over three temperature treatments: i) control, ii) heat stress, and iii) recovery from heat stress. Compared to control, exposure to heat stress affected the transcription of 3305 genes, whereas 942 were affected in recovering animals. These affected genes were mainly involved in metabolism and
Different variations in the same gene influence how well different ethnic groups, and people within the same ethnic group, respond to various antipsychotic medications, report NIMH-funded researchers. If confirmed, their findings could one day help clinicians predict which medication is most likely to help a patient, based on his or her genetic makeup.. A medication that works well for one person with schizophrenia often doesnt work well for another. Genetic variations are thought to play a key role in this difference in response. While patients search for the right medications, their illnesses may worsen. Studies such as this one are aimed at discovering how specific gene variations affect patients responses to specific medications, to better match patients to treatments.. The gene containing the variations, RGS4, had been implicated in schizophrenia in previous studies. It makes a protein that is thought to regulate the effects of receptors found on brain cells. The receptors, called ...
Human genetic variation may directly or indirectly influence response to modern antiretroviral therapies for HIV. It is already known that some immunogenetic and other human genetic variations affect the natural history of HIV disease progression where individuals are untreated, but less information is available as to whether these differences are still relevant in the context of HAART. Antiretroviral therapy adds additional opportunities for human genetic contributions to affect variable prognosis--in particular for those genes which influence pharmacokinetics and/or adverse events.
Nucleotide diversity provides a measure of genetic variation that is normalized by the number of chromosomes sampled. We calculated two conventional measures of nucleotide diversity for each gene: π, the average heterozygosity per site (28, 29), and θ, the population mutation parameter (13, 30). The average nucleotide diversity for the 292 autosomal genes (π = 0.058% and θ = 0.096%) and the 21 X-linked genes (π = 0.028% and θ = 0.045%) were within the range of values previously described (2-4). The fact that the average nucleotide diversity for the X-linked genes was reduced compared with the average autosomal nucleotide diversity is consistent with an equal number of males and females in the human population, in which males have only a single copy of the X chromosome.. We also calculated the autosomal nucleotide diversity values separately for each functional gene region and for each population. Exon-intron boundaries showed significantly higher average π values (P , 0.01 by ...
Human genetic variation is expected to play a central role in personalized medicine. Yet only a fraction of the natural genetic variation that is harbored by humans has been discovered to date. Here we report almost 2 million small insertions and deletions (INDELs) that range from 1 bp to 10,000 bp …
Author Summary Like many primate species, the mating system of humans is considered to be moderately polygynous (i.e., males exhibit a higher variance in reproductive success than females). As a consequence, males are expected to have a lower effective population size (Ne) than females, and the proportion of neutral genetic variation on the X chromosome (relative to the autosomes) should be higher than expected under the assumption of strict neutrality and an equal breeding sex ratio. We test for the effects of polygyny by measuring levels of neutral polymorphism at 40 independent loci on the X chromosome and autosomes in six human populations. To correct for mutation rate heterogeneity among loci, we divide our diversity estimates within human populations by divergence with orangutan at each locus. Consistent with expectations under a model of polygyny, we find elevated levels of X-linked versus autosomal diversity. While it is possible that multiple demographic processes may contribute to the observed
The origin and evolution of ORFans (suspected genes without known relatives) remain unclear. Here, we take advantage of a unique opportunity to examine the population diversity of thousands of ORFans, based on a collection of 35 complete genomes of isolates of Escherichia coli and Shigella (which is included phylogenetically within E. coli). As expected from previous studies, ORFans are shorter and AT-richer in sequence than non-ORFans. We find that ORFans often are very narrowly distributed: the most common pattern is for an ORFan to be found in only one genome. We compared within-species population diversity of ORFan genes with those of two control groups of non-ORFan genes. Patterns of population variation suggest that most ORFans are not artifacts, but encode real genes whose protein-coding capacity is conserved, reflecting selection against nonsynonymous mutations. Nevertheless, nonsynonymous nucleotide diversity is higher than for non-ORFans, whereas synonymous diversity is roughly the ...
Background: A molecular process based genotype-to-phenotype map will ultimately enable us to predict how genetic variation among individuals results in phenotypic alterations. Building such a map is, however, far from straightforward. It requires understanding how molecular variation reshapes developmental and metabolic networks, and how the functional state of these networks modifies phenotypes in genotype specific way. We focus on the latter problem by describing genetic variation in transcript levels of genes in the InR/TOR pathway among 72 Drosophila melanogaster genotypes. Results: We observe tight co-variance in transcript levels of genes not known to influence each other through direct transcriptional control. We summarize transcriptome variation with factor analyses, and observe strong co-variance of gene expression within the dFOXO-branch and within the TOR-branch of the pathway. Finally, we investigate whether major axes of transcriptome variation shape phenotypes expected to be influenced
Wright himself believed that values ,0.25 represent very great genetic variation and that an FST of 0.15-0.25 represented great variation. However, about 5% of human variation occurs between populations within continents, therefore FST values between continental groups of humans (or races) of as low as 0.1 (or possibly lower) have been found in some studies, suggesting more moderate levels of genetic variation.[56] Graves (1996) has countered that FST should not be used as a marker of subspecies status, as the statistic is used to measure the degree of differentiation between populations,[56] although see also Wright (1978).[59]. Jeffrey Long and Rick Kittles give a long critique of the application of FST to human populations in their 2003 paper Human Genetic Diversity and the Nonexistence of Biological Races. They find that the figure of 85% is misleading because it implies that all human populations contain on average 85% of all genetic diversity. They argue the underlying statistical model ...
Genetic diversity provides the capacity for plants to meet changing environments. It is fundamentally important in crop improvement. Fifty-nine local maize lines developed at INERA and 41 exotic (temperate and tropical) inbred lines were characterized using 1057 SNP markers to (1) analyse the genetic diversity in a diverse set of maize inbred lines; (2) determine the level of genetic diversity in INERA inbred lines and patterns of relationships of these inbred lines developed from two sources; and (3) examine the genetic differences between local and exotic germplasms. Rogers genetic distance for about 64% of the pairs of lines fell between 0.300 and 0.400. Sixty one per cent of the pairs of lines also showed relative kinship values of zero. Model-based population structure analysis and principal component analysis revealed the presence of 5 groups that agree, to some extent, with the origin of the germplasm. There was genetic diversity among INERA inbred lines, which were genetically less closely
Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites. Using outlier analyses, we identified the MHC II exon 2 (corresponding to the β-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the
View Notes - 640Lecture0705 from EEOB 640 at Ohio State. TYPES OF GENETIC VARIATION protein variation how do we measure variability structural similarity? how immunology Variation in enzyme
Selection against deleterious alleles maintained by mutation may cause a reduction in the amount of genetic variability at linked neutral sites. This is because a new neutral variant can only remain in a large population for a long period of time if it is maintained in gametes that are free of deleterious alleles, and hence are not destined for rapid elimination from the population by selection. Approximate formulas are derived for the reduction below classical neutral values resulting from such background selection against deleterious mutations, for the mean times to fixation and loss of new mutations, nucleotide site diversity, and number of segregating sites. These formulas apply to random-mating populations with no genetic recombination, and to populations reproducing exclusively asexually or by self-fertilization. For a given selection regime and mating system, the reduction is an exponential function of the total mutation rate to deleterious mutations for the section of the genome ...
TY - JOUR. T1 - PCSK9 Loss-of-Function Variants, Low-Density Lipoprotein Cholesterol, and Risk of Coronary Heart Disease and Stroke. T2 - Data from 9 Studies of Blacks and Whites. AU - Kent, Shia T.. AU - Rosenson, Robert S.. AU - Avery, Christy L.. AU - Chen, Yii Der I.. AU - Correa, Adolfo. AU - Cummings, Steven R.. AU - Cupples, L. Adrienne. AU - Cushman, Mary. AU - Evans, Daniel S.. AU - Gudnason, Vilmundur. AU - Harris, Tamara B.. AU - Howard, George. AU - Irvin, Marguerite R.. AU - Judd, Suzanne E.. AU - Jukema, J. Wouter. AU - Lange, Leslie. AU - Levitan, Emily B.. AU - Li, Xiaohui. AU - Liu, Yongmei. AU - Post, Wendy S.. AU - Postmus, Iris. AU - Psaty, Bruce M.. AU - Rotter, Jerome I.. AU - Safford, Monika M.. AU - Sitlani, Colleen M.. AU - Smith, Albert V.. AU - Stewart, James D.. AU - Trompet, Stella. AU - Sun, Fangui. AU - Vasan, Ramachandran S.. AU - Woolley, J. Michael. AU - Whitsel, Eric A.. AU - Wiggins, Kerri L.. AU - Wilson, James G.. AU - Muntner, Paul. PY - 2017/8/1. Y1 - ...
TY - JOUR. T1 - A systematic survey of loss-of-function variants in human protein-coding genes. AU - MacArthur, Daniel G.. AU - Balasubramanian, Suganthi. AU - Frankish, Adam. AU - Huang, Ni. AU - Morris, James. AU - Walter, Klaudia. AU - Jostins, Luke. AU - Habegger, Lukas. AU - Pickrell, Joseph K.. AU - Montgomery, Stephen B.. AU - Albers, Cornelis A.. AU - Zhang, Zhengdong. AU - Conrad, Donald F.. AU - Lunter, Gerton. AU - Zheng, Hancheng. AU - Ayub, Qasim. AU - DePristo, Mark A.. AU - Banks, Eric. AU - Hu, Min. AU - Handsaker, Robert E.. AU - Rosenfeld, Jeffrey A.. AU - Fromer, Menachem. AU - Jin, Mike. AU - Mu, Xinmeng Jasmine. AU - Khurana, Ekta. AU - Ye, Kai. AU - Kay, Mike. AU - Saunders, Gary Ian. AU - Suner, Marie Marthe. AU - Hunt, Toby. AU - Barnes, If H A. AU - Amid, Clara. AU - Carvalho-Silva, Denise R.. AU - Bignell, Alexandra H.. AU - Snow, Catherine. AU - Yngvadottir, Bryndis. AU - Bumpstead, Suzannah. AU - Cooper, David N.. AU - Xue, Yali. AU - Romero, Irene Gallego. AU - Wang, ...
The rare orchid, Isotria medeoloides (Pursh) Raf., is a threatened species native to the Eastern United States. The species range extends from Maine to Georgia, with many populations including fewer than 25 individuals. The degree of genetic variation among populations could have important implications for conservation strategies. This study evaluated the level of genetic variation within and among I. medeoloides populations through analysis of microsatellite regions, which contain dinucleotide repeats. The lengths of these regions are highly variable and have high mutation rates, making microsatellites a powerful genetic marker. Genetic variation was assessed at two microsatellite loci among 15 populations and three regions (New England, Virginia and Georgia). In this largely self-pollinating species, the inbreeding coefficient was high (Fis =0.964) indicating a high rate of self-fertilization. Populations in New England harbor the most genetic diversity. Southern populations are monomorphic, or
A graphical representation of the typical human karyotype. The human mitochondrial DNA.Human genetic variation is the genetic differences in and among populations. There may be multiple variants of a
AFTER the establishment of the field of ecological genetics more than 30 years ago (Clarke 1975) rapid progress in molecular marker development and analysis technology has generated a surge of renewed interest in identification of selective footprints of natural selection in a wide range of species (e.g., Schlötterer 2002). Among numerous research strategies developed to infer the evidence of selection in natural populations at the molecular level (reviewed by Nielsen 2005; Vasemägi and Primmer 2005), associations between environmental variables and molecular marker polymorphisms are commonly taken as strong support for the hypothesis that natural selection maintains single-locus clinal variation (e.g., Eanes 1999; Baines et al. 2004). However, it has often been overlooked that single-locus clines can also be the result of various neutral evolutionary processes, such as hybridization of previously isolated populations, founder events, and migrational patterns, such as spatially restricted gene ...
Estimating KIR Haplotype Frequencies on a Cohort of 10,000 Individuals: A Comprehensive Study on Population Variations, Typing Resolutions, and Reference Haplotypes. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
It is well known that the effective size of a population (Ne) is one of the major determinants of the amount of genetic variation within the population. However, it is unclear whether the types of genetic variations are also dictated by the effective population size. To examine this, we obtained whole genome data from over 100 populations of the world and investigated the patterns of mutational changes. Our results revealed that for low frequency variants, the ratio of AT→GC to GC→AT variants (β) was similar across populations, suggesting the similarity of the pattern of mutation in various populations. However, for high frequency variants, β showed a positive correlation with the effective population size of the populations. This suggests a much higher proportion of high frequency AT→GC variants in large populations (e.g. Africans) compared to those with small population sizes (e.g. Asians). These results imply that the substitution patterns vary significantly between populations. These
9780131838765 Our cheapest price for Race and Human Diversity: A Biocultural Approach is $44.89. Free shipping on all orders over $35.00.
Most biological traits of human importance are complex in nature; their manifestation controlled by the cumulative effect of many genetic factors interacting with one another and with the individuals life history. Because of this, mouse genetic reference populations (GRPs) consisting of collections of inbred lines or recombinant inbred lines (RIL) derived from crosses between inbred lines are of particular value in analysis of complex traits, since massive amounts of data can be accumulated on the individual lines. However, existing mouse GRPs are derived from inbred lines that share a common history, resulting in limited genetic diversity, and reduced mapping precision due to long-range gametic disequilibrium. To overcome these limitations, the Collaborative Cross (CC) a genetically highly diverse collection of mouse RIL was established. The CC, now in advanced stages of development, will eventually consist of about 500 RIL derived from reciprocal crosses of eight divergent founder strains of mice,
Some people experience more bitterness and less sweetness when drinking alcoholic beverages, and this relates to inherited genes.
KVAR1 : Diagnostic or predictive testing for specific conditions when a DNA sequence variant of interest has been previously identified in a family member, and follow-up testing for this specific variant in other family members is desired   Carrier screening for individuals at risk for having a DNA sequence variant that was previously identified in a family member   Segregation analysis for a single familial DNA sequence variant
NKX3.1 and β-catenin expression variations might be related to macrophage infiltration in tissues consequent to inflammation.Tissues adjacent to the sections w
Scientists use cancer biomarkers to predict a patients risk of developing cancer, their prognosis and response to therapy and their chance of disease recurrence. A biomarker could be a genetic mutation, the presence of a particular protein or an inherited genetic variation. Moffitt researchers focused their attention on inherited genetic variations in genes called interleukins. They genotyped the DNA of 33 interleukin genes from 651 NSCLC patients. Interleukins have important roles in regulating cell growth, cell death and in the activation of the immune system, explained Matthew Schabath, Ph.D., assistant member of the Cancer Epidemiology Program at Moffitt. Inherited genetic variations in interleukins and other genes can change their function and promote cancer development or control a patients response to therapy. The researchers discovered that patients who had certain genetic variations in interleukin genes had a better response to either surgery or chemotherapy, resulting in ...
Alternative splicing of genes is an efficient means of generating variation in protein function. Several disease states have been associated with rare genetic variants that affect splicing patterns. Conversely, splicing efficiency of some genes is known to vary between individuals without apparent ill effects. What is not clear is whether commonly observed phenotypic variation in splicing patterns, and hence potential variation in protein function, is to a significant extent determined by naturally occurring DNA sequence variation and in particular by single nucleotide polymorphisms (SNPs). In this study, we surveyed the splicing patterns of 250 exons in 22 individuals who had been previously genotyped by the International HapMap Project. We identified 70 simple cassette exon alternative splicing events in our experimental system; for six of these, we detected consistent differences in splicing pattern between individuals, with a highly significant association between splice phenotype and neighbouring
Since the extent and distribution of disease predisposing genetic variation in the human species today is the result of a long and complicated evolutionary, migratory, and demographic history, we are interested in investigating population and evolutionary processes affecting genetic variations in modern human populations. We have been working on assessing the extent of inter- and intra-population genomic variation and detecting signatures of positive natural selection as well as investigating genomic variation across multiple global and regional populations. In addition, we are also interested in understanding the history of introgression from archaic sister species and their distribution into extant human populations as well as the convergent evolution between domesticated species (e.g. dogs) and human beings. Such population and evolutionary genomic studies provide a unique opportunity to look at disease genetics at a much broader scale. Furthermore, we are also interested in developing novel ...
TY - JOUR. T1 - Distribution and effects of nonsense polymorphisms in human genes. AU - Yamaguchi-Kabata, Yumi. AU - Shimada, Makoto K.. AU - Hayakawa, Yosuke. AU - Minoshima, Shinsei. AU - Chakraborty, Ranajit. AU - Gojobori, Takashi. AU - Imanishi, Tadashi. PY - 2008/10/14. Y1 - 2008/10/14. N2 - Background: A great amount of data has been accumulated on genetic variations in the human genome, but we still do not know much about how the genetic variations affect gene function. In particular, little is known about the distribution of nonsense polymorphisms in human genes despite their drastic effects on gene products. Methodology/Principal Findings: To detect polymorphisms affecting gene function, we analyzed all publicly available polymorphisms in a database for single nucleotide polymorphisms (dbSNP build 125) located in the exons of 36,712 known and predicted protein-coding genes that were defined in an annotation project of all human genes and transcripts (H-InvDB ver3.8). We found a total ...
The nature of standing genetic variation and its relation to phenotypic variation in plants affects our understanding of evolution (1), sustainable agriculture, and preservation of inter- and intraspecific variation in times of environmental change. Maize inbred lines have an average nucleotide diversity in genic regions around 1% (π = 1 to 1.4%) (2, 3), similar to the divergence between humans and chimpanzees (4). It is not uncommon to find maize haplotypes that are 5% divergent from one another (5), which indicates that the maize gene pool reaches back 2 to 4 million years (with one generation per year).. Maize is adapted to a range of environments from the lowland tropics to the Andean highlands and has been widely introduced worldwide into both temperate and tropical regions. Maizes genetic architecture for flowering time has evolved as its wild relatives adapted to distinct ecological zones in elevations differing by more than 3000 m in Mexico and then under both natural and artificial ...
Photo: Dr. Andrew Olshan]. This is the finding of a new large-scale genetic study of head and neck cancers co-authored by Dr. Andrew Olshan, Barbara Sorenson Hulka Distinguished Professor in cancer epidemiology and chair of the department of epidemiology at the University of North Carolinas Gillings School of Global Public Health. A write-up of the study appears in the October 17 issue of Nature Genetics.. The study, which involved nearly 12,000 people - half with cancer of the oral cavity or pharynx, and half without any such cancer - showed why some individuals infected with HPV may go on to develop oropharyngeal cancer while others do not. The researchers conducted extensive DNA analysis of more than seven million variants for each individual. The UNC site contributed samples from the Carolina Head and Neck Cancer (CHANCE) study, led by Dr. Olshan.. These new findings on the association of immune system-related genetic variation may provide new insight into the mechanisms of protection ...
Habitat fragmentation threatens the maintenance of genetic diversity of affected populations. Assessment of the risks associated with habitat fragmentation is a big challenge as the change in population genetic diversity is a dynamic process, often acting over long time periods and depending on various characteristics pertaining to both species (life history traits) and their populations (extrinsic characteristics). With this survey, we provide an introductory overview for persons who have to make or are interested in making predictions about the fate of forest-dwelling plant populations which have recently become fragmented and isolated from their main occurrences. We provide a concise introduction to the field of population genetics focusing on terms, processes and phenomena relevant to the maintenance of genetic diversity and vitality of plant populations. In particular the antagonistic effects of gene flow and random genetic drift are covered. A special chapter is devoted to Central European tree
Some genetic variations may affect our health by altering how DNA coils and interacts in its 3-D shape - Highlight https://debuglies.com
Genetic variations may hold clues to rheumatoid arthritis -- suggesting not only who will develop the condition, but also predicting its severity and a patients mortality risk.
These results illustrate the highly dynamic pattern of CGV across three different environmental conditions that can be evoked by a stress response over a relatively short time-span (2 h) and that CGV is mainly determined by response related trans regulatory eQTL.
The identification and characterization of functional genetic variation is essential for future advances in molecular diagnostics, pharmacogenomics, and personalized medicine. Recent attempts at identifying nucleotide level variation (somatic mutations and single nucleotide polymorphisms [SNPs]) on a genomic scale have linked variation to gene expression, however fail to provide mechanisms for how variation can affect protein function. Herein I have identified nucleotide variation that affects the activity of two proto-oncogenes, MYC (c-Myc) and MYB (c-Myb), and characterized the role this variation plays in oncogenesis and cell differentiation. Burkitts Lymphomas (BLs) acquire consistent point mutations in a conserved Myc Box I domain. In Chapter 2, I report that the enhanced transforming activity of BL-associated MYC mutants can be uncoupled from loss of phosphorylation and increased protein stability. Furthermore, two different BL-associated MYC mutations induced similar gene expression ...
Variation is the driving force behind evolution and the reason why any species persists on this planet. Yet the science of human diversity is curtailed by controversial politics and outcries against racism. Some resistance comes from indigenous groups who feel they would be lab rats, but most comes from cautious government groups like the European Union, who at one point banned all research into human diversity. As a result gene studies were forced to obliterate the ethnic source of their samples.. Of course it is important to be sensitive to the threat of racism; historically human diversity science has led to eugenic groups, the sterilisation of undesirables and most infamously, the hideous acts committed by the Nazis. However science is the only real route to defeating ignorance (listening Daily Mail?) and as gene trials have progressed it has become obvious that the main differences are ones we see - hair, skin colour and facial features. We might have just our mothers eyes, but we all ...
Professor Louis Bernatchez - Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec; Canada Research Chair in Genetic Management of Freshwater Species. Species across the globe are experiencing drastic changes in environmental conditions as a result of human activities. Understanding and predicting how organisms respond to human-driven environmental change is therefore a major concern.
According to current research, the African continent is the ancestral home of modern humans. Scientists studying patterns in human genetic variation have observed the greatest amount of human genetic diversity in African populations. Genetic variation outside of Africa-in Europe and Asia-includes some, but not all, of the genetic variation found in Africa, which suggests that between 140,000 and 290,000 years ago, Homo sapiens migrated out of Africa to colonize Europe, Asia and the Americas. This Out of Africa theory is supported by studies of mtDNA, the Y chromosome, portions of the X chromosome, and some but not all autosomal (non-sex determining) regions, as well as the archaeological record. The role of genetics in human variation had to evolve before the Out of Africa theory of ancestry could be fully understood. Perhaps the most significant scientific development in helping to further understand human biological variation was the discovery of genes and the growth of genetic research. In ...
A study carried out by dozens of scientists, and published in Nature Genetics, identified 15 new genetic markers that can increase the risk of breast cancer. Each of these genetic variations, identified through this study and other research, is known to raise a womans risk of breast cancer by a small amount. Its another step towards a better understanding of how genetic variations work to increase the risk of this type of cancer. ...
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Genetic improvement programmes: Selection using molecular information - Lecture Sessions, , 0944, ...
The blobs are constructed and arranged so that the average distance between two points (individuals) within the same cluster is almost as big as the average distance between two points (individuals) in different clusters. This is easy to achieve if the ellipsoids are big and flat (like pancakes) and placed close to each other along the flat directions. The figure is meant to show how one can have small Fst, as in humans, yet easily resolved clusters. The direction in which the gap between the clusters appears is one of the principal components in the space of human genetic variation, as recently found by bioinformaticists. The figure at the top of this post plots individuals as points in the space generated by the two largest principal components extracted from the combination of data from HapMap and from large statistics sampling of Europeans. Exhibited this way, isolated clusters (races) are readily apparent ...
TY - JOUR. T1 - Genetic variation and neurological disease. AU - Rosenberg, Roger N.. PY - 1980. Y1 - 1980. N2 - Genetic mutants inevitably affect enzyme structure or modify protein metabolism. In some cases a single genetic defect can give rise to a neurological syndrome, but in most cases the genetic basis of neurological disease is far more complex. In this review Roger Rosenberg examines the rapid progress which is being made in identifying the patterns of genetic variation which underlie these problems, and their effective treatment.. AB - Genetic mutants inevitably affect enzyme structure or modify protein metabolism. In some cases a single genetic defect can give rise to a neurological syndrome, but in most cases the genetic basis of neurological disease is far more complex. In this review Roger Rosenberg examines the rapid progress which is being made in identifying the patterns of genetic variation which underlie these problems, and their effective treatment.. UR - ...
Leprosy continues to remain a major health problem in many parts of the world, regardless of long history of research, advances in the medical field and the introduction of Multidrug therapy (MDT) in 1980s. The inability to grow the bacterium in vitro has been one of the inadequacies to unravel the intricacies of the biology of the disease. Yet efforts have been made to identify the role of host genetic factors to understand susceptibility mechanisms, especially in the background of limited genetic diversity between different isolates of M. leprae. Research has progressed over the years in identifying many candidates as risk providers, using genome wide linkage, association and candidate gene studies. However, search for common genetic variants across the afflicted population groups in the world has emerged equivocal. Looking for genes and its variants which are proposed either by genome wide linkage or association studies with an assumed importance in the pathway biology of the disease does ...
TY - JOUR. T1 - RNA-seq analysis reveals considerable genetic diversity and provides genetic markers saturating all chromosomes in the diploid wild wheat relative Aegilops umbellulata. AU - Okada, Moeko. AU - Yoshida, Kentaro. AU - Nishijima, Ryo. AU - Michikawa, Asami. AU - Motoi, Yuka. AU - Sato, Kazuhiro. AU - Takumi, Shigeo. PY - 2018/11/8. Y1 - 2018/11/8. N2 - Background: Aegilops umbellulata Zhuk. (2n=14), a wild diploid wheat relative, has been the source of trait improvement in wheat breeding. Intraspecific genetic variation of Ae. umbellulata, however, has not been well studied and the genomic information in this species is limited. Results: To develop novel genetic markers distributed over all chromosomes of Ae. umbellulata and to evaluate its genetic diversity, we performed RNA sequencing of 12 representative accessions and reconstructed transcripts by de novo assembly of reads for each accession. A large number of single nucleotide polymorphisms (SNPs) and insertions/deletions ...
Aberrations in chromosomal copy number are one of the most common molecular features observed in cancer. Quantifying the degree of numerical chromosomal variation in single cells across a population of cells is of interest to researchers studying whole chromosomal instability (W-CIN). W-CIN, a state of high numerical chromosomal variation, contributes to treatment resistance in cancer. Here, we introduce aneuvis, a web application that allows users to determine whether numerical chromosomal variation exists between experimental treatment groups. The web interface allows users to upload molecular cytogenetic or processed whole-genome sequencing data in a cell-by-chromosome matrix format and automatically generates visualizations and summary statistics that reflect the degree of numeric chromosomal variability. Aneuvis is the first user-friendly web application to help researchers identify the genetic and environmental perturbations that promote numerical chromosomal variation.
Genetic diversity and population structure analysis between Indian red jungle fowl and domestic chicken using microsatellite markers. ...
Ex situ conservation, while helpful in humankinds efforts to sustain and protect our environment, is rarely enough to save a species from extinction. It is to be used as a last resort, or as a supplement to in situ conservation because it cannot recreate the habitat as a whole: the entire genetic variation of a species, its symbiotic counterparts, or those elements which, over time, might help a species adapt to its changing surroundings. Instead, ex situ conservation removes the species from its natural ecological contexts, preserving it under semi-isolated conditions whereby natural evolution and adaptation processes are either temporarily halted or altered by introducing the specimen to an unnatural habitat. In the case of cryogenic storage methods, the preserved specimens adaptation processes are (quite literally) frozen altogether. The downside to this is that, when re-released, the species may lack the genetic adaptations and mutations which would allow it to thrive in its ever-changing ...
Analysis of the amount and distribution of genetic variation can yield information about the number of introductions and history of an invasive species, which may be relevant for understanding the evolutionary potential and spread of invaders, as well as for creating best management practices for curbing them. We explored the genetic patterns and invasion history of the perennial, ornamental herb Lupinus polyphyllus Lindl. in Finland, where the species has spread rapidly during the past hundred years. Using 13 microsatellite loci, we determined the genetic variation of L. polyphyllus in 51 sites across a latitudinal gradient that reflected the invasion history of the species in this country. We found that the sampled populations were significantly genetically differentiated among sites, as indicated by the global F(ST) value (0.19) and AMOVA results (16.7 % of total genetic variation occurred among sites), and this differentiation slightly increased with increasing geographic distance (r = ...
Rapid development of sequencing technologies and bioinformatic tools makes the complete genome sequencing of many species possible, which provides a starting point to unravel the tremendous genetic variation and diversity at the genome scale. Amongst several model organisms examined to date, such as human, mouse, Arabidopsis, rice, and maize, genome-wide patterns of genetic variation are able to be captured by sampling a relatively small number of genomes [14, 20, 50-52]. By resequencing two sweet and one grain sorghum inbred lines, we uncovered nearly two million SNPs and indels, along with large numbers of PAVs and CNVs. This is a first report on the genome-wide patterns of genetic variation in sorghum, which will be valuable for further genotype-phenotype studies and for molecular breeding of this important C4 model crop.. Our study shows that the proportions of genic SNPs identified as in coding regions, intronic regions, or UTRs are 42.3%, 50.2%, and 7.5%, respectively. Compared to ...
The genetic diversity of Setipinna taty, which is commercially fished in the China Sea, was studied based on mitochondrial DNA control region sequences. PCR was used to amplify the control region fragment in 100 individuals of S. taty collected from Weihai (WH), Yantai (YT), Zhoushan (ZS), Xiangshan (XS), and Ninghai (NH) in China. A control region fragment of 656 bp was successfully sequenced in these 100 individuals. The A+T content of this S. taty control region was 71.7%; 172 variable sites and 62 haplotypes were found.
Population genetic structure and intrapopulation levels of genetic variation have important implications for population dynamics and evolutionary processes. Habitat fragmentation is one of the major threats to biodiversity. It leads to smaller population sizes and reduced gene flow between populations and will thus also affect genetic structure. We use a natural system of island and mainland populations of house sparrows along the coast of Norway to characterize the different population genetic properties of fragmented populations. We genotyped 636 individuals distributed across 14 populations at 15 microsatellite loci. The level of genetic differentiation was estimated using F-statistics and specially designed Mantel tests were conducted to study the influence of population type (i.e. mainland or island) and geographic distance on the genetic population structure. Furthermore, the effects of population type, population size and latitude on the level of genetic variation within populations were ...
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes ,99% of SNP variants with a frequency of ,1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies ...
Background: Population differentiation has proved to be effective for identifying loci under geographically-localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes. Results: We demonstrate that while sites of low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established ...
In most existing genetic variant association studies, common trait, common variants, which asserts that common genetic variants contribute to most of traits (disease susceptibilities), serves as the central assumption. Researchers have successfully identified some significant associations between common single nucleotide polymorphisms (SNPs) and disease traits [1]. However, despite the enormous efforts expended on association studies of complex traits, common genetic variants only show a moderate influence on different phenotypes in many reported disease associations and consequently have limited diagnostic value [2, 3]. While the identification of common variants creates a dilemma, known as common trait, rare variants, an alternative hypothesis, which asserts that multiple rare variants with moderate to high penetrances may collectively influence disease susceptibilities, has been suggested in some literatures [3-5]. Rare variants are defined as those whose minor allele frequencies (MAF) ...
TY - JOUR. T1 - Neandertal origin of genetic variation at the cluster of OAS immunity genes. AU - Mendez, Fernando L.. AU - Watkins, Joseph C.. AU - Hammer, Michael F.. PY - 2013/4/1. Y1 - 2013/4/1. N2 - Analyses of ancient DNA from extinct humans reveal signals of at least two independent hybridization events in the history of non-African populations. To date, there are very few examples of specific genetic variants that have been rigorously identified as introgressive. Here, we survey DNA sequence variation in the OAS gene cluster on chromosome 12 and provide strong evidence that a haplotype extending for ∼185 kb introgressed from Neandertals. This haplotype is nearly restricted to Eurasians and is estimated to have diverged from the Neandertal sequence ∼125 kya. Despite the potential for novel functional variation, the observed frequency of this haplotype is consistent with neutral introgression. This is the second locus in the human genome, after STAT2, carrying distinct haplotypes that ...
An international team of more than 1,000 scientists participated in a new study showing an integrated map of genetic variation from 1,092 human genomes.. A newly published compendium of the genetic alphabets of more than 1000 individuals from around the world illustrates how similar humans are - but also how crucial genetic variations can be.. The publication on November 1 in the journal Nature of the 1000 Genomes Project provides the most comprehensive catalog of human variations to date and will be indispensable to the practice of personalized medicine.. Sequencing an individuals DNA is useless in medicine unless there is a frame of reference to compare it to, said Yale Universitys Mark Gerstein, the Albert L. Williams Professor of Biomedical Informatics and one of more than 1,000 scientists who participated in international effort.. An individual human genome contains on an average 3 million variations. Without a reference library of variations, trying to hone in on the most informative ...
...Two genes in which variation affects intake of caffeine the most wide...The genes identified were CYP1A2 which has previously been implicated...Caffeine is implicated in numerous physiological and medical condition...Apart from smoking genetic determinants of lifestyle behaviors have g...,Genetic,variants,associated,with,caffeine,intake,identified,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
Genetic diversity within species may promote resilience to environmental change, yet little is known about how such variation is distributed at broad geographic scales. Here we develop a novel Bayesian methodology to analyse multi-species genetic diversity data in order to identify regions of high or low genetic diversity. We apply this method to co-distributed taxa from Australian marine waters. We extracted published summary statistics of population genetic diversity from 118 studies of 101 species and | 1000 populations from the Australian marine economic zone. We analysed these data using two approaches: a linear mixed model for standardised data, and a mixed beta-regression for unstandardised data, within a Bayesian framework. Our beta-regression approach performed better than models using standardised data, based on posterior predictive tests. The best model included region (Integrated Marine and Coastal Regionalisation of Australia (IMCRA) bioregions), latitude and latitude squared. Removing
TY - JOUR. T1 - POT1 loss-of-function variants predispose to familial melanoma. AU - Robles-Espinoza, Carla Daniela. AU - Harland, Mark. AU - Ramsay, Andrew J.. AU - Aoude, Lauren G.. AU - Quesada, Victor. AU - Ding, Zhihao. AU - Pooley, Karen A.. AU - Pritchard, Antonia L.. AU - Tiffen, Jessamy C.. AU - Petljak, Mia. AU - Palmer, Jane M.. AU - Symmons, Judith. AU - Johansson, Peter A.. AU - Stark, Mitchell S.. AU - Gartside, Michael G.. AU - Snowden, Helen. AU - Montgomery, Grant W.. AU - Martin, Nicholas G.. AU - Lite, Jimmy Z.. AU - Choi, Jiyeon. AU - Makowski, Matthew. AU - Brown, Kevin M.. AU - Dunning, Alison M.. AU - Keane, Thomas M.. AU - Lopez-Otin, Carlos. AU - Gruis, Nelleke A.. AU - Hayward, Nicholas K.. AU - Bishop, D. Timothy. AU - Newton-Bishop, Julia A.. AU - Adams, David J.. N1 - © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.. PY - 2014/5. Y1 - 2014/5. N2 - Deleterious germline variants in CDKN2A account for around 40% of familial melanoma ...
The historical demography of the populations of domestic pigs in Europe and China was examined using mismatch distributions, which represent the frequency distribution of pairwise differences among all sampled haplotypes. Theoretical studies have shown that population bottlenecks and population expansions have a strong effect on the pattern of genetic polymorphism among haplotypes in the population (Rogers & Harpending 1992). For instance, populations in long and stable demographic equilibrium have multimodal mismatch distribution (ragged and chaotic) whereas the distribution appears unimodal after recent demographic expansions (Rogers & Harpending 1992; Harpending 1994). The mismatch distributions as well as the network analysis were consistent with population expansions in the ancestors for both contemporary Chinese and European domestic pigs (figures 3 and 4). The crucial question is whether the population expansion occurred before or after domestication. Similar signatures of population ...
Brewer, N., DeFrank, J., Chiu, W., Ibrahim, J., Walko, C., Rubin, P., ... Irvin, W. (2014). Patient understanding of how genotype variation affects benefits of tamoxifen therapy for breast cancer. Public Health Genomics, 17(1), 43 - 47 ...
BackgroundSesame is an important oil crop widely cultivated in Africa and Asia continent. Characterization of genetic diversity and population structure of sesame genotypes in these continents can be used to designing breeding methods. In the present study, 300 sesame g...
The Society runs two themed meetings each year as satellites to either the American or European Societies of Human Genetics annual meeting as a forum for scientists to exchange ideas and form collaborations. Prominent speakers in the field are invited. The meetings are designed to update and increase knowledge of human genome variation and generally attract a stimulating and interesting collection of abstracts in all fields of human genome variation making it an ideal forum to share information and results. We invite members and non-members alike to attend these meetings.. FORTHCOMING HGVS MEETINGS ...
Comparing different methods of estimating the genetic diversity could define their usefulness in plant breeding programs. In this study, a total of 18 morphological traits and 20 simple sequence repeat (SSR) loci were used to study the morphological and genetic diversity among 20 maize hybrids selected from different countries, and to classify the hybrids into groups based on molecular profiles and morphological traits. To collect morphological data, a field experiment was carried out using an RBCD design with three replications in Moghan, Ardabil, Iran. The highest estimates for genetic coefficients of variation were observed in anthesis-silking interval, followed by grain yields, leaf chlorophyll rates, kernel row numbers, and ear heights. The total number of PCR-amplified products was 84 bands, all of which were polymorphic. Among the studied primers,NC009,BNLG1108,BNLG1194,PHI026 and PHI057 showed the maximum polymorphism information content(PIC) and the greatest diversity. To determine the genetic
TY - JOUR. T1 - Lipid and sterol gene sequence variation in autism and correlates with neurodevelopmental status. T2 - A pilot study. AU - Hall, Trevor A.. AU - Steiner, Robert D.. AU - Wright, Hollis. AU - Wilmot, Beth. AU - Roullet, Jean Baptiste. AU - Peters, Meaghan. AU - Harris, Michael. N1 - Funding Information: Research reported in this publication was also supported by National Center for Advancing Translational Sciences of the National Institutes of Health under award number UL1TR000128 . The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Funding Information: Research reported in this publication was supported by the Northwest Health Foundation under the Mark O. Hatfield Research Fellowship on Autism. The content is solely the responsibility of the authors and does not necessarily represent the official views of the Northwest Health Foundation. PY - 2015/9/1. Y1 - 2015/9/1. N2 - Objective: ...
There were more than one thousand soybean(Glycine max(L.) Merr)germplasms in Hubei province.In order to evaluate the genetic diversity of summer sowing soybean landraces from different agricultural divisions of Hubei,we analyzed allelic profiles at 28 simple-sequence repeat(SSR) loci of 92 accessions.The SSR loci produced 134 alleles,and each SSR loci could detect 2 to 9 alleles with an average of 4.78 alleles per loci.The highest averages of both genetic diversity index and alleles were all occurred in southwest division,and second one was Jianghan Plain division.More than 83.6% of total variation was produced by geographical differentiation.By using the cluster analysis with Within-groups Linkage method,92 landraces were classified into three major groups at DNA level.Many landraces from southwest division and Jianghan Plain were clustered in Ⅰand Ⅲ group respectively.It was suggested that the diversity level of soybean landrace from both southwest and Jianghan Plain division were higher than
Understanding genome to phenotype linkages has been greatly enabled by genomic sequencing. However, most genome analysis is typically confined to the nuclear genome. We conducted a metabolomic QTL analysis on a reciprocal RIL population structured to examine how variation in the organelle genomes affects phenotypic variation. This showed that the cytoplasmic variation had effects similar to, if not larger than, the largest individual nuclear locus. Inclusion of cytoplasmic variation into the genetic model greatly increased the explained phenotypic variation. Cytoplasmic genetic variation was a central hub in the epistatic network controlling the plant metabolome. This epistatic influence manifested such that the cytoplasmic background could alter or hide pairwise epistasis between nuclear loci. Thus, cytoplasmic genetic variation plays a central role in controlling natural variation in metabolomic networks. This suggests that cytoplasmic genomes must be included in any future analysis of natural ...
Soybean (Glycine max) cultivars adapted to high latitudes have a weakened or absent sensitivity to photoperiod. The purposes of this study were to determine the molecular basis for photoperiod insensitivity in various soybean accessions, focusing on the sequence diversity of the E4 (GmphyA2) gene, which encodes a phytochrome A (phyA) protein, and its homoeolog (GmphyA1), and to disclose the evolutionary consequences of two phyA homoeologs after gene duplication. We detected four new single-base deletions in the exons of E4, all of which result in prematurely truncated proteins. A survey of 191 cultivated accessions sourced from various regions of East Asia with allele-specific molecular markers reliably determined that the accessions with dysfunctional alleles were limited to small geographical regions, suggesting the alleles recent and independent origins from functional E4 alleles. Comparison of nucleotide diversity values revealed lower nucleotide diversity at non-synonymous sites in GmphyA1 than in
In this thesis, I combine molecular analyses, common-garden and field experiments to examine how evolutionary and ecological processes influence patterns of genetic variation among and within populations of the declining, insect-pollinated, self-incompatible, perennial herb Primula farinosa. More specifically I examined 1) whether genetic diversity at neutral marker loci was related to habitat fragmentation and habitat stability, 2) whether floral display and flowering time were more strongly differentiated among populations than were putatively neutral marker loci, 3) whether adaptive population differentiation could be detected on a local spatial scale, and 4) whether floral display differentially affected male and female reproductive success.. Genetic diversity at neutral marker loci was lower within fragmented populations on the Swedish mainland than within the more densely occurring populations on the island Öland, SE Sweden. On Öland, fluctuations in population size were more pronounced ...
This week, the MalariaGEN P. falciparum genetic crosses project released a new data resource, comprising whole-genome sequence and genetic variation data from the parents and offspring of three parasite crosses.. This open access resource provides a foundation for further research into how genetic variation and sexual recombination affects parasite biology, at a much higher resolution than previously possible. These data are being made available at a time of intense interest in studying the genetic basis for evolutionary changes in the malaria-causing P. falciparum parasite, such as the emergence and spread of antimalarial drug resistance.. A lot of progress has been made in recent years in mapping out variation in the P. falciparum genome, however there are still big gaps in our knowledge, including many genes that are relevant to vaccine development or drug resistance, explains Alistair Miles, Head of Informatics with the MRC Centre for Genomics and Global Health. These new data on the ...
HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran ,3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. We observed significant human SNP associations to a total of 48 HIV-1 amino acid variants (p,2.4 × 10(-12)). All associated SNPs mapped to the HLA class I region. Clinical relevance of host and pathogen variation was assessed using VL results. We identified two critical advantages to the use of viral variation for identifying host factors: (1) association signals are much stronger for HIV-1 sequence variants than VL, reflecting the intermediate phenotype nature of viral variation; (2) association testing can be run without any clinical data. The proposed genome-to-genome approach highlights sites of genomic conflict and is a strategy generally ...
Theories of Population Variation in Genes and Genomes by Christiansen, Freddy Bugge available in Hardcover on Powells.com, also read synopsis and reviews. This textbook provides an authoritative introduction to both classical and coalescent approaches to...
Leiopotherapon unicolor is the most widespread freshwater fish species in Australia. A comprehensive allozyme and mitochondrial DNA 16S rRNA data set was assembled from 141 specimens of L. unicolor collected Australia-wide in order to test for cryptic speciation in this far-ranging species. Surprisingly, little genetic diversity was observed within L. unicolor and provided no evidence for the existence of cryptic species within this lineage. In contrast, a small sample set of L. aheneus used as the outgroup showed two highly divergent haplotypes strongly suggestive of cryptic speciation. L. unicolor has a number of ecological and life history attributes that may explain the lack of significant genetic divergence over substantial geographical distances. The occurrence of other widespread fish and crustacean species that also display only limited genetic diversity indicate that climate conditions more favourable to dispersal across central and northern Australia than is suggested by the extent of ...
Studies on genetic variation can reveal effects on traits and disease, both in humans and in model organisms. Good technology for the analysis of DNA sequence variations is critical. Currently the development towards assays for large-scale and parallel DNA sequencing and genotyping is progressing rapidly. Single base primer extension (SBE) is a robust reaction principle based on four-colour fluorescent terminating nucleotides to interrogate all four DNA nucleotides in a single reaction. In this thesis, SBE methods were applied to the analysis and discovery of single nucleotide polymorphism (SNP) in the model organism Drosophila melanogaster and in humans.. The tag-array minisequencing system in a microarray format is convenient for intermediate sized genotyping projects. The system is scalable and flexible to adapt to specialized and novel applications. In Study I of the thesis a tool was established to automate quality control of clustered genotype data. By calculating Silhouette scores, the ...
Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft selective sweeps at a single genetic locus. However, in linked regions of rapidly adapting genomes, multiple beneficial mutations at different loci can segregate simultaneously within the population, an effect known as clonal interference. This leads to a subtle interplay between hitchhiking and interference effects, which leads to a unique signature of rapid adaptation on genetic variation both at the selected sites and at linked neutral loci. Here, we introduce an effective coalescent theory (a fitness-class coalescent) that describes how positive selection at many perfectly linked sites alters the structure of genealogies. We use this theory to calculate several simple statistics describing genetic variation within a rapidly adapting population and to implement efficient ...
Over the past several years, Genome Wide Association Studies (GWAS) have discovered hundreds of genetic variants involved in complex diseases(10.1056/NEJMra0905980). The vast majority of these variants do not lie in the protein coding regions of genes and thus do not affect what the gene produces, but instead likely affect how the genes are regulated. For this reason, the study of how genetic variation affect gene activity levels (referred to as expression levels) has been a major focus of research for many years. Genetic variation that affects gene expression are referred to as expression quantitative trait loci (eQTL)(10.1038/nrg2969).. Several studies collect expression from multiple tissues which leads to the question of whether or not the same genetic variants affect expression in multiple tissues(10.1038/ng.2653). Another way to ask this question is: Are eQTLs tissue specific or not tissue specific?. A challenge in this type of analysis is that an eQTL may affect expression in multiple ...
Genetic diversity of the human immunodeficiency virus type 1 (HIV-1) population within an individual is lost during transmission to a new host. The demography of transmission is an important determinant of evolutionary dynamics, particularly the relative impact of natural selection and genetic drift immediately following HIV-1 infection. Despite this, the magnitude of this population bottleneck is unclear. We use coalescent methods to quantify the bottleneck in a single case of homosexual transmission and find that over 99% of the env and gag diversity present in the donor is lost. This was consistent with the diversity present at seroconversion in nine other horizontally infected individuals. Furthermore, we estimated viral diversity at birth in 27 infants infected through vertical transmission and found there to be no difference between the two modes of transmission. Assuming the bottleneck at transmission is selectively neutral, such a severe reduction in genetic diversity has important implications
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So traits that have large additive genetic components are more easily changed by selection. The authors set out to investigate the genetic basis of gene expression level in Drosophila (for many genes measured on array) and how this differs between males and females. By a series of crosses, the authors find that many more genes show additive genetic variation in their expression level in males than in females, and that a number of these genes are found on the X chromosome (as well as on the autosomes). Now the X chromosome seems to be be the key to this difference in the form of genetic variation (and the authors conduct further experiments to show this). As males have only a single X chromosome there simply is not any dominance due to genetic variation on the X chromosome (at least not simple non-epistatic dominance). The genetic variation on the X chromosome in males mainly contributes to the additive genetic component of variation (as there is no second allele to cause dominance). So genes on ...
October 3, 2004. October 3, 2004 - In a paper published today in the online edition of Nature Genetics, a deCODE-led team of scientists present the results of a large-scale population study linking recombination rate with maternal age and fertility. In the paper, entitled Recombination rate and reproductive success in humans, the deCODE team establish a novel and significant correlation between recombination - the shuffling of chromosomal material that takes place in the formation of eggs and sperm - and maternal age and fertility. Specifically, the average number of recombinations in eggs that go on to become successful live births tends to increase with the mothers age, and mothers with a higher recombination rate in general also tend to have more children than do those with a lower recombination rate. The authors conclude that the most likely explanation for this phenomenon is that recombination, which is one of the most important mechanisms for generating genetic diversity in ...
Cancer cells are intrinsically heterogeneous. Multiple clones with their unique variants co-exist in tumor tissues. The variants include point mutations and structural variations. Point mutations, or single nucleotide variants are those variants on one base; structural variations are variations involving sequence with length not smaller than 50 bases. Approaches to estimate the number of clones and their respective percentages from point mutations have been recently proposed. However, structural variations, although involving more reads than point mutations, have not been quantitatively studied in characterizing cancer heterogeneity. I describe in this thesis a maximum likelihood approach to estimate variant allele fraction of a putative structural variation, as a step towards the characterization of tumor heterogeneity. A software tool, BreakDown, implemented in Perl realizing this statistical model is publicly available. I studied the performance of BreakDown through both simulated and real ...
The WHI GWAS examines the genome, which is the individuals complete set of DNA, of women who have participated in WHI to see if there are genetic variations associated with a particular disease. To do this, the genomes of women with a particular disease are compared to similar women without the disease. If certain genetic variations are seen in participants with the disease compared to those without, the variations are said to be associated with the disease. The genetic variations themselves do not necessarily cause the disease, but may put individuals with the variant at increased risk. Other influences (diet, smoking, environment) may also be important factors that work along with genetic variations to influence risk. Once new genetic associations are identified, it may be possible to use the information to detect, treat, and prevent the disease. We hope to learn much more about this using the WHI blood samples. ...
Genetic variation in three Iranian pelt sheep breeds namely: Gray Shiraz, Zandi and Karakul were investigated using fifteen microsatellite loci. Genomic DNA was extracted from 360 blood samples by extraction kits and salting-out procedure with some modifications. The total number of alleles ranged from 6 to12 in loci. The fifteen tested loci were all polymorphic in the three breeds. The average direct count of heterozygosity overall loci in each tested breed was more than the expected heterozygosity. Tests of genotype frequencies for deviation from the Hardy-Weinberg equilibrium (HWE) were performed at each locus of overall breeds and revealed significant departure from HWE (P , 0.001) due to heterozygote excess. Polymorphism information content value in Gray Shiraz, Zandi and Karakul were 0.815, 0.808 and 0.808, respectively. Rate of inbreeding within the three breeds was not noticeable (global Fis = - 0.19). Low genetic differentiation was detected by estimation of Fst index between all pairs ...
In 1974, Richard Lewontin published The Genetic Basis of Evolutionary Change, focusing enormous attention on protein variation as both a model of underlying genetic variation and a level of selection itself. In the twenty years since, scientific research has been shifted by the power of molecular biological techniques to explore the nature of variation directly at the DNA and gene levels. The protein chapter is coming to a close. In this book, Jeff Mitton explains the questions that geneticists hoped to answer by studying protein variation. He reviews the extensive literature on protein variation, describes the successes and failures of the research program, and evaluates the results of a rich and controversial body of research. The laboratory and field studies using protein polymorphisms revealed dynamic interactions among genotypes, fitness differentials, and fluctuating environmental conditions, and inadvertently wedded the fields of physiological ecology and population biology. Mittons book is a
The most important biological role of meiosis compared with asexual reproduction is providing genetic diversity of individuals as a result of mixing of paternal and maternal genes in the gamete. This is achieved in two ways.. Firstly, in the first division of meiosis the distribution of paternal and maternal chromosomes into the daughter cells is random, which results in gametes bearing different combinations of parental chromosomes (Smith and Nicolas 204). The second fundamental mechanism for the maintenance of genetic diversity is that in the initial phase of the first meiotic division homologous chromosomes are arranged opposite to each other and couple, forming one or more areas of contact (chiasm) between individual unsisterly chromatids. Next, the pair of chromatids that formed chiasm exchanges the sections of DNA (crossing-over process). As a result of crossing-over recombinant chromosomes are formed consisting of sections originating from different parent lines. Upon the completion of ...
After the recent discovery that common genetic variation in 15q24-25.1 influences inherited risk of lung cancer (3-7), we identified a second sequence variant at 15q24-25.1 associated with familial lung cancer (8) and further validated this new association in large sporadic lung cancer populations. We showed that these two genetic variants on 15q24-25.1 have independent genetic effects on lung cancer risk. The second variant on 15q24-25.1, marked by rs481134, explains an additional 13.2% of the population attributable risk for lung cancer. These results further confirm the complexity of the chromosomal region 15q24-25.1 underlying lung cancer susceptibility.. Interestingly, the second variant did not show association with lung cancer in single-marker analysis. However, haplotype analysis of SNPs rs1051730 and rs481134 provided stronger evidence for association with lung cancer. SNPs rs1051730 and rs481134 are in moderate LD (r2 = 0.30), which can mask or change the genetic effects of those loci ...
The distribution of variation in a quantitative trait and its underlying distribution of genotypic diversity can both be shaped by stabilizing and directional selection. Understanding either distribution is important, because it determines a populations response to natural selection. Unfortunately, existing theory makes conflicting predictions about how selection shapes these distributions, and very little pertinent experimental evidence exists. Here we study a simple genetic system, an evolving RNA enzyme (ribozyme) in which a combination of high throughput genotyping and measurement of a biochemical phenotype allow us to address this question. We show that directional selection, compared to stabilizing selection, increases the genotypic diversity of an evolving ribozyme population. In contrast, it leaves the variance in the phenotypic trait unchanged. ...