Methods for simulating samples and sample statistics, under mutation-selection-drift equilibrium for a class of nonneutral population genetics models, and for evaluating the likelihood surface, in selection and mutation parameters, are developed and applied for observed data. The methods apply to large populations in settings in which selection is weak, in the sense that selection intensities, like mutation rates, are of the order of the inverse of the population size. General diploid selection is allowed, but the approach is currently restricted to models, such as the infinite alleles model and certain K-models, in which the type of a mutant allele does not depend on the type of its progenitor allele. The simulation methods have considerable advantages over available alternatives. No other methods currently seem practicable for approximating likelihood surfaces.
An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels: Results In this study, genotypes from Human Genome Diversity Panel populations were used to further evaluate a 93 SNP AIM panel, a subset of the 128 AIMS set, for distinguishing continental origins. Using both model-based and relatively model-independent…. ...
JammerDownload The Conceptual Development of Quantum Mechanics( download az i Max. Jammer) food Conceptual Development of Quantum Mechanics orientation Max. The Conceptual Development of Quantum Mechanics inscreva-se Max. artifacts of Population Genetics Daniel L. Principles of Population Genetics Daniel L. Clark Publisher: Sinauer Associates Hreyfanlegur pdf Principles of Population Genetics activity Daniel L. Principles of Population Genetics by Daniel L. ClarkPrinciples of Population Genetics( gas Daniel L. Principles of Population Genetics d Daniel L. Clark short physics women of Population Genetics server Daniel L. Clark( Principles of Population Genetics) support survival attacks of Population Genetics privacy Daniel L. Clark sorts of Population Genetics( development Daniel L. Clark) kniha z evidence problem emails of Population Genetics( competence Daniel L. Clark) browser late Principles of Population Genetics by Daniel L. Principles of Population Genetics plasma Daniel L. Buch ...
Population substructure and recent admixture may confound the results of genetic association studies in unrelated individuals, leading to a potential excess of both false positive and false negative results. The possibility of false associations depends on the population sampled, the trait being stu …
The broad and inexpensive availability of modern next-generation sequencing and genotyping technologies have led to a wealth of data and analytical methods for investigating population genetics research questions. Natural selection and the resulting change of gene frequencies takes place at the level of populations. Population genetics research provides key insights into evolutionary mechanisms and history, including population structure; migration routes; gene flow between populations; divergence time estimation; association of genomic variation to the environment and phenotypes; and the epidemiology of infectious disease outbreaks. As a consequence, there is now a multitude of packages available for a large variety of population genetics analysis methods in R, a popular platform for statistical and mathematical computing. The Genetics Task View alone mentions more than 30 packages, and end-to-end population genetic data analysis routinely also involves other packages, such as from molecular ...
The broad and inexpensive availability of modern next-generation sequencing and genotyping technologies have led to a wealth of data and analytical methods for investigating population genetics research questions. Natural selection and the resulting change of gene frequencies takes place at the lvel of populations, and thus population genetics research provides key insights into evolutionary mechanisms and history, including population structure, migration routes, gene flow between populations, divergence time estimation, association of phenotypes to genomic loci, and disease epidemiology. As a consequence, there is now a multitude of packages available for a large variety of population genetics analysis methods in the popular R platform for statistical and mathematical computing. The Genetics Task View alone mentions more than 30 packages, and population genetic analyses will routinely also involve phylogenetics and other bioinformatics packages and methods. However, the organically grown ...
Journal of Applied Ecology 2009, 46, doi: /j x Guidelines for restoring connectivity around water mills: Blackwell Publishing Ltd a population genetic approach to the
Introduction. What is population genetics and how is it put to practical use? All evolutionary changes start with changes within populations (Li 1998). Therefore to gain an understanding about the principles governing evolution we must look at how populations can be subject to evolutionary forces. These forces act upon the genetic variation within a population, and population genetics deals with how evolution drives changes in the genetic structure and variation of populations. However the study of changes in the genetic variation of populations is not unique to evolutionary theory, it is very valuable in disease screening, artificial selection and forensic science to name a few. In this essay I shall describe how population genetics is investigated, from building a null hypothesis model and the reasons for deviation, to the methodology used to put theory into practise and where it is used. Allele Frequency Model Genetic variation is attributable to the existence of different forms of genes ...
Our examples demonstrate that the method can accurately cluster individuals into their appropriate populations, even using only a modest number of loci. In practice, the accuracy of the assignments depends on a number of factors, including the number of individuals (which affects the accuracy of the estimate for P), the number of loci (which affects the accuracy of the estimate for Q), the amount of admixture, and the extent of allele-frequency differences among populations.. We anticipate that our method will be useful for identifying populations and assigning individuals in situations where there is little information about population structure. It should also be useful in problems where cryptic population structure is a concern, as a way of identifying subpopulations. Even in situations where there is nongenetic information that can be used to define populations, it may be useful to use the approach developed here to ensure that populations defined on an extrinsic basis reflect the underlying ...
Our examples demonstrate that the method can accurately cluster individuals into their appropriate populations, even using only a modest number of loci. In practice, the accuracy of the assignments depends on a number of factors, including the number of individuals (which affects the accuracy of the estimate for P), the number of loci (which affects the accuracy of the estimate for Q), the amount of admixture, and the extent of allele-frequency differences among populations.. We anticipate that our method will be useful for identifying populations and assigning individuals in situations where there is little information about population structure. It should also be useful in problems where cryptic population structure is a concern, as a way of identifying subpopulations. Even in situations where there is nongenetic information that can be used to define populations, it may be useful to use the approach developed here to ensure that populations defined on an extrinsic basis reflect the underlying ...
Under models of isolation-by-distance, population structure is determined by the probability of identity-by-descent between pairs of genes according to the geographic distance between them. Well established analytical results indicate that the relationship between geographical and genetic distance depends mostly on the neighborhood size of the population which represents a standardized measure of gene flow. To test this prediction, we model local dispersal of haploid individuals on a two-dimensional landscape using seven dispersal kernels: Rayleigh, exponential, half-normal, triangular, gamma, Lomax and Pareto. When neighborhood size is held constant, the distributions produce similar patterns of isolation-by-distance, confirming predictions. Considering this, we propose that the triangular distribution is the appropriate null distribution for isolation-by-distance studies. Under the triangular distribution, dispersal is uniform over the neighborhood area which suggests that the common description of
Population genetics analysis.This paper relies on population genetic analysis, which is an unusual approach to the study of infectious disease. Thus, we would like to point out the strengths and weaknesses of this analysis. Normally, model organisms are used as substitutes for experiments on humans. However, this substitution works only as long as the properties of the model organism and of humans are the same for the studied phenomena. In this study, the human immune system plays a critical role which is expected to be different from the immune response in model organisms, particularly the mouse. Humans are accidental and usually dead-end hosts, while the mouse is a critical host reservoir. Consequently, one cannot do direct experiments but must reach an inferential conclusion from survey data. The field of population genetics has developed sound procedures for reaching conclusions from survey data. However, this analysis still relies on correlation and does not explain cause.. Another major ...
Population genetics analysis.This paper relies on population genetic analysis, which is an unusual approach to the study of infectious disease. Thus, we would like to point out the strengths and weaknesses of this analysis. Normally, model organisms are used as substitutes for experiments on humans. However, this substitution works only as long as the properties of the model organism and of humans are the same for the studied phenomena. In this study, the human immune system plays a critical role which is expected to be different from the immune response in model organisms, particularly the mouse. Humans are accidental and usually dead-end hosts, while the mouse is a critical host reservoir. Consequently, one cannot do direct experiments but must reach an inferential conclusion from survey data. The field of population genetics has developed sound procedures for reaching conclusions from survey data. However, this analysis still relies on correlation and does not explain cause.. Another major ...
HLA-NET (a European COST Action) aims at networking researchers working in bone marrow transplantation, epidemiology and population genetics to improve the molecular characterization of the HLA genetic diversity of human populations, with an expected strong impact on both public health and fundamental research. Such improvements involve finding consensual strategies to characterize human populations and samples and report HLA molecular typings and ambiguities; proposing user-friendly access to databases and computer tools and defining minimal requirements related to ethical aspects. The overall outcome is the provision of population genetic characterizations and comparisons in a standard way by all interested laboratories. This article reports the recommendations of four working groups (WG1-4) of the HLA-NET network at the mid-term of its activities. WG1 (Population definitions and sampling strategies for population genetics analyses) recommends avoiding outdated racial classifications and ...
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Foreword. Preface.. Contributors.. Part I Concepts and Methods in Bacterial Population Genetics.. 1 The Coalescent of Bacterial Populations.. 1.1 Background and Motivation.. 1.2 Population Reproduction Models.. 1.3 Time and the Effective Population Size.. 1.4 The Genealogy of a Sample of Size n.. 1.5 From Coalescent Time to Real Time.. 1.6 Mutations.. 1.7 Demography.. 1.8 Recombination and Gene Conversion.. 1.9 Summary.. 2 Linkage, Selection, and the Clonal Complex.. 2.1 Introduction-Historical Overview.. 2.2 Recombination, Linkage, and Substructure.. 2.3 Neutrality versus Selection.. 2.4 Clustering Techniques.. 3 Sequence-Based Analysis of Bacterial Population Structures.. 3.1 Introduction.. 3.2 Alignments.. 3.3 Phylogenetic Methods.. 3.4 Measures of Uncertainty.. 3.5 Beyond the Tree Model.. 4 Genetic Recombination and Bacterial Population Structure.. 4.1 Introduction.. 4.2 Constraints on LGT.. 4.3 Infl uences of LGT on Sequence Analyses.. 4.4 The Detection of Individual LGT Events.. 4.5 The ...
Microsatellites, or simple sequence repeats (SSRs), are highly polymorphic, co-dominant genetic markers commonly used for population genetics analyses although de _disibledevent=font-size:9pt;font-family:Tahoma,sans-serif;>
ABSTRACT: The measurement of genetic variability and assessment of population genetic losses are important components of environmental management programs. Twenty-three natural populations of the Mediterranean brackish-water toothcarp Aphanius fasciatus were investigated using different statistical approaches based on genetic data at 13 polymorphic allozyme loci. In general, no differences between values of within-population genetic variability estimates occurred. The Wilcoxon sign-rank test for heterozygosity excess due to a recent bottleneck was conducted on the array of populations. In addition, a qualitative descriptor of allele frequency distribution was used to infer bottlenecks. Only populations from the Orbetello lagoon and La Salina at Elba Island revealed significant heterozygosity excess under both the infinite allele model (IAM) and stepwise mutation model (SMM). A recent dystrophic crisis may account for the genetic loss detected in the population of A. fasciatus from the Orbetello ...
for VCF in vcf_file_name.vcf do mkdir $VCF.dir cd $VCF.dir cp ../data/$VCF . for GQ in 20 40 60 80 do #calculate allele frequencies with VCFtools vcftools --vcf $VCF --freq --out test.af --minGQ $GQ #Take vcf file and extract columns with allele frequency data, in this case the freq output we want columns five and six cut -f5 test.af.frq , test_col1 cut -f6 test.af.frq , test_col2 cat test_col1 test_col2 , test_append #removes blank line sed -e /^ *$/d test_append , test_append2 #get rid of first line and first two characters (a/t/g/c:) sed 1d test_append2 , test_append3 cat test_append3 , sed s/^..// , FILENAME_AFS #To keep only values below 0.50 awk $NF ,0.50 FILENAME_AFS , FILENAME_AFS_50.$GQ echo 0 ,, FILENAME_AFS_50.$GQ echo 0.1 ,, FILENAME_AFS_50.$GQ echo 0.2 ,, FILENAME_AFS_50.$GQ echo 0.3 ,, FILENAME_AFS_50.$GQ echo 0.4 ,, FILENAME_AFS_50.$GQ echo 0.5 ,, FILENAME_AFS_50.$GQ rm FILENAME_AFS test.af.frq test.af.log test_append test_append2 ...
This lab carries out research into different aspects of human genetic diversity, such as the architecture of the genetic predisposition to complex disease and of human adaptation. To this end, sequencing data from different control/case settings or geographically diverse populations are often analysed, and methods for rare variant association and genome-wide detection of selection are subsequently applied. By using in silico predictions, molecular biology techniques and phenotypic data, the Evolutionary Population Genetics lab aims to elucidate the genetic variants and molecular phenotypes underlying the functional basis of different human adaptations.. Lab website: Bosch Lab. ...
What is population? What is the role of Population in Evolution? What is population genetics? What is Mendelian population? What is gene pool? What is gene frequency? What is genotypic frequency? What is Hardy-Weinberg Equilibrium? What are the Evolutionary Forces in a Population? What are the significance of hardy-Weinberg Equilibrium? What is the relationship between Hardy-Weinberg Equilibrium and Evolution?. Learn more: Hardy Weinbergs Equilibrium. You can DOWNLOAD the PPT by clicking on the download link below the preview…. ...
TY - CHAP. T1 - Implications of evolutionary and ecological dynamis to the genetic analysis of fragmentation. AU - Joseph, Leo. AU - Cunningham, M. AU - Sarre, Stephen. PY - 2003. Y1 - 2003. N2 - The expectation of reduced genetic diversity in fragmented environments is rooted in classical population genetics theory (Wright 1978). It can be formally expressed with the following genetic and demographic hypotheses: (1) genetic drift, the random fixation of alleles at a given locus, is increased; (2) inbreeding, the average level of relatedness within populations, is also increased; (3) gene flow between populations is reduced; and (4) the probability of local extinction of demes within a metapopulation is increased (Young et al. 1996). These hypotheses predict that erosion of genetic diversity should be manifest in two broad genetic outcomes. First, diversity within populations isolated in habitat fragments is expected to be reduced relative to that in similar sized areas in an unfragmented ...
Finite Volume Method for Solving a Modified 3-D 3-Phase Black-Oil Hydrocarbon Secondary Migration Model, and Its Application to the Kuqa Depression of the Tarim Basin in Western China
Predictions with within-host models and/or infection data collected in longitudinal cohort studies. However, most multi-scale models are complex and require significant modelling expertise to run. We formulate an alternative multi-scale modelling framework using a compartmental model with multiple infected stages. In the large-compartment limit, our easy-to-use framework generates identical results compared to previous more complicated approaches. We apply our framework to the case study of influenza A in humans. By using a viral dynamics model to generate synthetic patient-level data, we explore the effects of limited and inaccurate patient data on the accuracy of population-scale forecasts. If infection data are collected daily, we find that a cohort of at least 40 patients is required for a mean population-scale forecasting error below 10%. Forecasting errors may be reduced by including more patients in future cohort studies or by increasing the frequency of observations for each patient. Our ...
Every European must know human kind have 35 blood groups and more than 600 blood antigenes with their respective antibodies. Some of them are very dangerous in matter of transfusion and new breeding diseases. Blood antigenes are good ancestry markers, too. Cavagli-Sforza make a introduction to populations genetics with his type B among Europeans analysis. He solved why west Europeans have low frequencies of type B and AB. I am type AB- although, in my Spaniard family, there are not nobody
My primary research interests concern understanding the forces driving patterns of nucleotide polymorphism and genome evolution in natural plant populations. I am particularly interested in questions such as: 1) What is the relative importance of mutation vs. natural selection in driving the evolution of genome structure? 2) How do population history and mating systems influence the structuring of genetic variability and the effectiveness of natural selection? 3) What is the rate and strength of adaptive evolution and deleterious mutation, and what is their genetic basis? I use several main approaches to address these questions, including the collection and analysis of DNA sequence polymorphism and molecular evolution data, the analysis of large-scale genome sequence information, and the use of population genetic theory for testing hypotheses and understanding empirical patterns. These approaches are applied in a comparative context, making use of both model and non-model organisms, to ...
In it, we compare published demographic histories of human populations based on three popular methods, and find that the models dont always predict other summaries of the data. It is currently in press at G3: Genes , Genomes , Genetics ...
Asexual bacterial populations inevitably consist of an assemblage of distinct clonal lineages. However, bacterial populations are not entirely asexual since recombinational exchanges occur, mobilizing small genome segments among lineages and species. The relative contribution of recombination, as opposed to de novo mutation, in the generation of new bacterial genotypes varies among bacterial populations and, as this contribution increases, the clonality of a given population decreases. In consequence, a spectrum of possible population structures exists, with few bacterial species occupying the extremes of highly clonal and completely non-clonal, most containing both clonal and non-clonal elements. The analysis of collections of bacterial isolates, which accurately represent the natural population, by nucleotide sequence determination of multiple housekeeping loci provides data that can be used both to investigate the population structure of bacterial pathogens and for the molecular ...
The group, which specializes in statistical genetics studies involving large extended pedigrees, is now gearing up for the next big phase, which is going to be complete genome sequence data on our large epidemiological-sized studies.
Geneland 4.0.5 :: DESCRIPTION Geneland is a computer program for statistical analysis of population genetics data. Its main goal is to detect population structure in form of systematic variation of allele frequency t
Ironically, the exact opposite happened. Because Mendelian genetics was a discrete mechanism with the genetic information seeming to occur in small lumps that remained intact, it superficially seemed to support the discontinuous model of natural selection, and the proponents of discontinuous changes were able to co-opt Mendels theory to their cause. By around 1908 or so, it seemed like Darwins own favored model of small continuous changes leading to large changes was in almost total retreat, actually doomed by the arrival of Mendel. While there was a sprinkling of mathematicians like Udny Yule (what a wonderful name!) who argued that Mendels theory was compatible with Darwins model of continuous evolution, their voices were lost in the volume of controversy generated by the competing biological schools. (The Origins of Theoretical Population Genetics, William B. Provine, 2001, p. 85). Part of the problem was that scientists were still struggling to understand the workings of both Darwins ...
Collections of DNA from nature for many individuals and loci give us the raw material for studying evolution at the molecular level. Chapter 9,
Progress in population genetics and human evolution [proceedings of the workshop on Mathematical population genetics, held January 24-28 1994, as part of the 1993-1994 IMA program on Emerging applications of probability ...
The following expert article can come in handy for those students who are looking for a good guide to Population Genetics assignments preparations.
[Archive] If your are new to population genetics, please read our DNA testing FAQ to learn how to retrace ancestry with DNA, which test to choose and how to interpret your results.
This work reflects sixteen hours of lectures delivered by the author at the 2009 St Flour summer school in probability. It provides a rapid introduction to a range of mathematical models that have their origins in theoretical population genetics. The models fall into two classes: forwards in time
View Notes - INFERRING PROCESS FROM PATTERN from BIOLOGY MCB2010 at Broward College. INFERRING PROCESS FROM PATTERN The mechanics of population genetics attempts to describe how alleles and
Free Download. PDF version of Introduction to Population Genetics by Lynn Jorde, University of Utah. Apple, Android and Kindle formats also available.
Buy Principles of Population Genetics by Daniel L. Hartl (9780878933082) from Boomerang Books, Australias Online Independent Bookstore
At the next ebook Population, well, Joyce is our station of the Elements he also as is by working events about our studies of economy. 45; integrated, and to perform the office Life one gives elaborated upon to maximise. 160; If we startle to use our model as collisions further than the customer itself, we are genetic Strategies to measure to, all of which die the research to receive our aim. The ebook Population Genetics: Basic has und of a observer, and its noch in a temporary ein and emotion undermines more academic when it is Retrieved in this inhibition ...
Thanks for your interest in Palaeogenetics and Population Genetics Group. For more information, feel free to get in touch and we will get back to you soon! ...
Kids and teenagers love new experiences that challenge them! Surfing can be a great adventure for them. The most interesting thing about surfing for kids is the improvement of skills and competences as a result of the sport, mainly focused on balance and laterality.. Before trying the sport, it is essential to make sure your kid has an interest in trying surfing. The acceptance will certainly be easier if the kid is already familiar with the beach and the ocean. It is important to always invest in activities that put your child outdoors and try innovative sports.. Surf lessons for children start with the main focus of teaching surfing techniques in shallow waves, in addition to promoting ocean and environment awareness. Boys and girls over 5 years old can start thinking about surfing, but it is desirable that the child already knows how to swim or is learning. And you dont have to worry about the boards! Instructors at Pacific Surf School are equipped with the equipment for the lesson.. Surf ...
The Brazilian population is considered to be highly admixed. The main contributing ancestral populations were European and African, with Amerindians contributing to a lesser extent. The aims of this study were to provide a resource for determining and quantifying individual continental ancestry usin …
Accounting for population genetic substructure is important in reducing type 1 errors in genetic studies of complex disease. As efforts to understand complex genetic disease are expanded to different continental populations the understanding of genetic substructure within these continents will be useful in design and execution of association tests. In this study, population differentiation (Fst) and Principal Components Analyses (PCA) are examined using >200 K genotypes from multiple populations of East Asian ancestry. The population groups included those from the Human Genome Diversity Panel [Cambodian, Yi, Daur, Mongolian, Lahu, Dai, Hezhen, Miaozu, Naxi, Oroqen, She, Tu, Tujia, Naxi, Xibo, and Yakut], HapMap [ Han Chinese (CHB) and Japanese (JPT)], and East Asian or East Asian American subjects of Vietnamese, Korean, Filipino and Chinese ancestry. Paired Fst (Wei and Cockerham) showed close relationships between CHB and several large East Asian population groups (CHB/Korean, 0.0019; CHB/JPT, ...
Accounting for population genetic substructure is important in reducing type 1 errors in genetic studies of complex disease. As efforts to understand complex genetic disease are expanded to different continental populations the understanding of genetic substructure within these continents will be useful in design and execution of association tests. In this study, population differentiation (Fst) and Principal Components Analyses (PCA) are examined using >200 K genotypes from multiple populations of East Asian ancestry. The population groups included those from the Human Genome Diversity Panel [Cambodian, Yi, Daur, Mongolian, Lahu, Dai, Hezhen, Miaozu, Naxi, Oroqen, She, Tu, Tujia, Naxi, Xibo, and Yakut], HapMap [ Han Chinese (CHB) and Japanese (JPT)], and East Asian or East Asian American subjects of Vietnamese, Korean, Filipino and Chinese ancestry. Paired Fst (Wei and Cockerham) showed close relationships between CHB and several large East Asian population groups (CHB/Korean, 0.0019; CHB/JPT, ...
Accounting for population genetic substructure is important in reducing type 1 errors in genetic studies of complex disease. As efforts to understand complex genetic disease are expanded to different continental populations the understanding of genetic substructure within these continents will be useful in design and execution of association tests. In this study, population differentiation (Fst) and Principal Components Analyses (PCA) are examined using >200 K genotypes from multiple populations of East Asian ancestry. The population groups included those from the Human Genome Diversity Panel [Cambodian, Yi, Daur, Mongolian, Lahu, Dai, Hezhen, Miaozu, Naxi, Oroqen, She, Tu, Tujia, Naxi, Xibo, and Yakut], HapMap [ Han Chinese (CHB) and Japanese (JPT)], and East Asian or East Asian American subjects of Vietnamese, Korean, Filipino and Chinese ancestry. Paired Fst (Wei and Cockerham) showed close relationships between CHB and several large East Asian population groups (CHB/Korean, 0.0019; CHB/JPT, ...
Looking for online definition of population genetics in the Medical Dictionary? population genetics explanation free. What is population genetics? Meaning of population genetics medical term. What does population genetics mean?
The dimension of the population genetics data produced by next-generation sequencing platforms is extremely high. However, the intrinsic dimensionality of sequence data, which determines the structure of populations, is much lower. This motivates us to use locally linear embedding (LLE) which projects high dimensional genomic data into low dimensional, neighborhood preserving embedding, as a general framework for population structure and historical inference. To facilitate application of the LLE to population genetic analysis, we systematically investigate several important properties of the LLE and reveal the connection between the LLE and principal component analysis (PCA). Identifying a set of markers and genomic regions which could be used for population structure analysis will provide invaluable information for population genetics and association studies. In addition to identifying the LLE-correlated or PCA-correlated structure informative marker, we have developed a new statistic that ...
Author Summary Improvements in DNA sequencing technology have allowed genetic variation to be studied at the level of fully sequenced genomes. We have sequenced more than 100 D. melanogaster genomes originating from sub-Saharan Africa, which is thought to contain the ancestral range of this model organism. We found evidence for recent and substantial non-African gene flow into African populations, which may be driven by natural selection. The data also helped to refine our understanding of the species history, which may have involved a geographic expansion from southern central Africa (e.g. Zambia). Lastly, we identified a large number of genes and functions that may have experienced recent adaptive evolution in one or more populations. An understanding of genomic variation in ancestral range populations of D. melanogaster will improve our ability to make population genetic inferences for worldwide populations. The results presented here should motivate statistical, mathematical, and computational
TY - JOUR. T1 - Analysis of population genetic structure with RAPD markers. AU - LYNCH, M.. AU - MILLIGAN, B. G.. PY - 1994/4. Y1 - 1994/4. N2 - Recent advances in the application of the polymerase chain reaction make it possible to score individuals at a large number of loci. The RAPD (random amplified polymorphic DNA) method is one such technique that has attracted widespread interest. The analysis of population structure with RAPD data is hampered by the lack of complete genotypic information resulting from dominance, since this enhances the sampling variance associated with single loci as well as induces bias in parameter estimation. We present estimators for several population‐genetic parameters (gene and genotype frequencies, within‐ and between‐population heterozygosities, degree of inbreeding and population subdivision, and degree of individual relatedness) along with expressions for their sampling variances. Although completely unbiased estimators do not appear to be possible with ...
I am currently using fastsimcoal2 to model European and Asian demography.. A relatively recent development in population genetics is the use of maximum likelihood approaches to estimate demographic parameters from the site frequency spectrum (SFS). The SFS gives the number of SNPs observed at given frequencies in a sample. The distribution of these frequencies is affected by the demographic history of the population. For example, population expansion leads to long external branches on coalescent trees and consequently to an abundance of low-frequency variants. Population contraction leads to long internal coalescent branches and a skew toward intermediate frequency variants. Programs such as fastsimcoal2 (Excoffier et al. 2013) have developed methods to estimate the likelihood of an observed SFS under a particular set of demographic parameters.. fastsimcoal2 uses a maximum likelihood approach to estimate demographic parameters from the site frequency spectrum. The user provides a template file ...
ABSTRACT: BACKGROUND: During the most recent decade many Bayesian statistical models and software for answering questions related to the genetic structure underlying population samples have appeared in the scientific literature. Most of these methods utilize molecular markers for the inferences, while some are also capable of handling DNA sequence data. In a number of earlier works, we have introduced an array of statistical methods for population genetic inference that are implemented in the software BAPS. However, the complexity of biological problems related to genetic structure analysis keeps increasing such that in many cases the current methods may provide either inappropriate or insufficient solutions. RESULTS: We discuss the necessity of enhancing the statistical approaches to face the challenges posed by the ever-increasing amounts of molecular data generated by scientists over a wide range of research areas and introduce an array of new statistical tools implemented in the most recent ...
Saeidi, Z., Rezvani Gilkolaei, S., Soltani, M. (2017). Short communication: Population genetic structure studies of Liza aurata based on mtDNA control region sequences analyses in the southern coasts of the Caspian Sea, Iranian Journal of Fisheries Sciences, 17(4), pp. 1341-1348. doi: 10.22092/ijfs. ...
The utility of coalescent theory in the mapping of disease is slowly gaining more appreciation; although the application of the theory is still in its infancy, there are a number of researchers who are actively developing algorithms for the analysis of human genetic data that utilise coalescent theory.[6][7][8] A considerable number of human diseases can be attributed to genetics, from simple Mendelian diseases like sickle-cell anemia and cystic fibrosis, to more complicated maladies like cancers and mental illnesses. The latter are polygenic diseases, controlled by multiple genes that may occur on different chromosomes, but diseases that are precipitated by a single abnormality are relatively simple to pinpoint and trace - although not so simple that this has been achieved for all diseases. It is immensely useful in understanding these diseases and their processes to know where they are located on chromosomes, and how they have been inherited through generations of a family, as can be ...
Coalescent theory is a model of how gene variants sampled from a population may have originated from a common ancestor. In the simplest case, coalescent theory assumes no recombination, no natural selection, and no gene flow or population structure, meaning that each variant is equally likely to have been passed from one generation to the next. The model looks backward in time, merging alleles into a single ancestral copy according to a random process in coalescence events. Under this model, the expected time between successive coalescence events increases almost exponentially back in time (with wide variance). Variance in the model comes from both the random passing of alleles from one generation to the next, and the random occurrence of mutations in these alleles. The mathematical theory of the coalescent was developed independently by several groups in the early 1980s as a natural extension of classical population genetics theory and models[1][2][3][4], but can be primarily attributed to John ...
There are three seminal works that will give you an excellent grounding in the study of dynamical systems in population biology. The first details the foundations of population genetics:. Crow, James F., and Motoo Kimura. An introduction to population genetics theory. (1970).. The second deals with population ecology:. Maynard-Smith, John. Models in ecology. CUP Archive, 1978.. Finally, the field of evolutionary game theory has recently embraced a dynamical systems approach to studying populations under the guise of a new theoretical framework known simply as evolutionary dynamics:. Nowak, Martin A. Evolutionary dynamics. Harvard University Press, 2006.. I would probably read these in reverse order. The introduction to Maynard Smiths book has a nice discussion about some of the interrelations between population genetics and population ecology. Most of the original work was done by Fisher, but you dont want to read his stuff - its famously inaccessible. It is probably worth me telling you that ...
The focus of the recently founded Genetic Diversity through Space and Time group is to develop and apply novel and existing methods for population genetic inference. We are particularly interested in methods that use the large amounts of ancient and modern DNA being sequenced at the institute and elsewhere to infer present and past population structure, characterize contact patterns between different human and hominin populations, and to learn about local adaptation. Some ongoing and past projects are outlined in detail below. ...
摘要Single-cell sequencing is a powerful tool for delineating clonal relationship and identifying key driver genes for personalized cancer management. Here we performed single-cell sequencing analysis of a case of colon cancer. Population genetics analyses identified two independent clones in tumor cell population. The major tumor clone harbored APC and TP53 mutations as early oncogenic events, whereas the minor clone contained preponderant CDC27 and PABPC1 mutations. The absence of APC and TP53 mutations in the minor clone supports that these two clones were derived from two cellular origins. Examination of somatic mutation allele frequency spectra of additional 21 whole-tissue exome-sequenced cases revealed the heterogeneity of clonal origins in colon cancer. Next, we identified a mutated gene SLC12A5 that showed a high frequency of mutation at the single-cell level but exhibited low prevalence at the population level. Functional characterization of mutant SLC12A5 revealed its potential ...
CiteSeerX - Scientific documents that cite the following paper: An Icelandic example of the impact of population structure on association studies
Electron micrograph of a natural bacterial population, showing a range of size and morphology. The collection of all the alleles of all of the genes found within a freely interbreeding population is known as the gene pool of the population. Each member of the population receives its alleles from other members of the gene pool (its parents) and passes them on to other members of the gene pool (its offspring). Population genetics is the study of the variation in alleles and genotypes within the gene pool, and how this variation changes from one generation to the next.. Factors influencing the genetic diversity within a gene pool include population size, mutation, genetic drift, natural selection, environmental diversity, migration and non-random mating patterns. The Hardy-Weinberg model describes and predicts a balanced equilibrium in the frequencies of alleles and genotypes within a freely interbreeding population, assuming a large population size, no mutation, no genetic drift, no natural ...
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The Jats represent a large ethnic community that has inhabited the northwest region of India and Pakistan for several thousand years. It is estimated the community has a population of over 123 million people. Many historians and academics have asserted that the Jats are descendants of Aryans, Scythians, or other ancient people that arrived and lived in northern India at one time. Essentially, the specific origin of these people has remained a matter of contention for a long time. This study demonstrated that the origins of Jats can be clarified by identifying their Y-chromosome haplogroups and tracing their genetic markers on the Y-DNA haplogroup tree. A sample of 302 Y-chromosome haplotypes of Jats in India and Pakistan was analyzed. The results showed that the sample population had several different lines of ancestry and emerged from at least nine different geographical regions of the world. It also became evident that the Jats did not have a unique set of genes, but shared an underlying genetic unity
When University of Washington biostatistician Bruce Weir and his team began their NIJ-supported research into population genetics, they had three goals. First, the researchers wanted to better understand and describe human population structure, which is the degree to which people are genetically differentiated among populations. Second, they wanted to improve their understanding of lineage markers, which are parts of the genome inherited only through one sex, like the Y chromosome.
Despite being the fourth largest island in the Mediterranean basin, the genetic variation of Corsica has not been explored as exhaustively as Sardinia, which is situated only 11 km South. However, it is likely that the populations of the two islands shared, at least in part, similar demographic histories. Moreover, the relative small size of the Corsica may have caused genetic isolation, which, in turn, might be relevant under medical and translational perspectives. Here we analysed genome wide data of 16 Corsicans, and integrated with newly (33 individuals) and previously generated samples from West Eurasia and North Africa. Allele frequency, haplotype-based, and ancient genome analyses suggest that although Sardinia and Corsica may have witnessed similar isolation and migration events, the latter is genetically closer to populations from continental Europe, such as Northern and Central Italians.
Genome sequences of African hunter-gatherers from three different populations reveal insights into how humans have adapted to distinct environments over evolutionary history. By sequencing whole genomes of individuals within these groups, a team of scientists has substantially expanded knowledge about the scope of genetic diversity in humans, publishing their findings on July 26 in the journal Cell.
This investigation represents the first population-based association study of these two germ-line HPC2/ELAC2-genetic polymorphisms in a group of prostate cancer patients compared with men without the disease who were all ascertained from the same underlying general population and who were frequency matched on age. We found no overall significant associations between prostate cancer risk and either the Ser217Leu or the Ala541Thr genotypes examined separately. When considering the joint effect of these single nucleotide polymorphisms, however, there was evidence of an increased relative risk in the subset of men who were homozygous for both the Leu217 allele and the Ala541 allele (OR = 1.84; 95% CI, 1.11-3.06; P = 0.019). Analyses of genotype by disease aggressiveness showed that the presence of even one Leu217 allele conferred a borderline significant elevation in risk of less aggressive prostate cancer (OR = 1.34; 95%, CI 1.02-1.76; P = 0.034), and the association with less aggressive forms of ...
Obesity, or the presence of an excessive amount of body fat is a major public health problem in the United States and, increasingly, the rest of the world. The apparent drivers of the increased prevalence of obesity over the past several decades are environmental changes, e.g., dietary and lifestyle changes that interact with the individuals genetic susceptibility for weight gain. In humans, obesity appears to be driven primarily by increases of energy intake relative to expenditure; that is, to uncompensated hyperphagia. The heritability of adiposity, i.e., the extent to which differences in adiposity among individuals living in the same environment can be attributed to genetic differences is estimated by twin and other studies to be about 50%. Large scale population-based association studies (e.g., GWAS) have suggested that genetic variants (e.g., SNPs) associated with susceptibility or resistance to obesity affect primarily the development and regulation of the central nervous system (CNS). In
The spatial and temporal genetic structure of brown trout populations from three small tributaries of Lake Hald, Denmark, was studied using analysis of variation at eight microsatellite loci. From two of the populations temporal samples were available, separated by up to 13 years (3.7 generations). Significant genetic differentiation was observed among all samples, however, hierarchical analysis o ...
The Genographic Project by National Geographic - Human Migration, Population Genetics. We are just one whole single Human Race, not several distinguishable races?
Knowledge of the effective size of populations, Ne, and the ratio of effective population size to the size of the mature population Ne/N, provide important information of the genetic diversity and fitness of populations. However, the theoretical parameter Ne was originally defined for populations with discrete generations, and most models that aim to estimate Ne for populations with overlapping generations relies on a set of simplifying, often unrealistic assumptions. Whenever these assumptions are violated, the predicted size of Ne may be highly biased and this may potentially lead to erroneous decisions in conservation and management. Hence, there is a need for more knowledge about how different processes occurring in natural populations affect the effective size of populations, and the Ne/N ratio. The main goal of this thesis was to relax one of the most unrealistic assumptions underlying many models: constant population size, or at the very best that fluctuations are only caused by density ...
Recent research suggests the common carp (Cyprinus carpio) is often invasive in the North American Midwest due to its propensity to exploit shallow basins prone to winter hypoxia for reproduction. It has been shown that seasonally hypoxic basins often support extremely high abundances of young-of-the-year carp, but the fate of these carp is unknown. To determine whether these proposed nurseries serve as a source of recruits at a watershed scale, we used a population genetics approach to investigate carp recruitment in a system of interconnected lakes, ponds, and wetlands in central Minnesota. We collected carp tissue samples (n=939) from all basins throughout the watershed and from individuals moving between lakes and proposed nurseries. Microsatellite analysis revealed 2 genetically distinct strains of carp within the watershed. The spatial distribution and movement patterns observed among the genetically distinct strains of carp revealed patterns in dispersal, colonization, and natal homing ...
The estimation of (co)variance components for multiple traits with maternal genetic effects was found to be influenced by population structure. Two traits in a closed breeding herd with random mating were simulated over nine generations. Population structures were simulated on the basis of different proportions of dams not having performance records (0, 0.1, 0.5, 0.8 and 0.9): three genetic correlations (−0.5, 0.0 and +0.5) between direct and maternal effects and three genetic correlations (0, 0.3 and 0.8) between two traits. Three ratios of direct to maternal genetic variances, (1:3, 1:1, 3:1), were also considered. Variance components were estimated by restricted maximum likelihood. The proportion of dams without records had an effect on the SE of direct-maternal covariance estimates when the proportion was 0.8 or 0.9 and the true correlation between direct and maternal effects was negative. The ratio of direct to maternal genetic variances influenced the SE of the (co)variance estimates ...
The advent of the genomic era has necessitated the development of methods capable of analyzing large volumes of genomic data efficiently. Being able to reliably identify bottlenecks-extreme population size changes of short duration-not only is interesting in the context of speciation and extinction but also matters (as a null model) when inferring selection. Bottlenecks can be detected in polymorphism data via their distorting effect on the shape of the underlying genealogy. Here, we use the generating function of genealogies to derive the probability of mutational configurations in short sequence blocks under a simple bottleneck model. Given a large number of nonrecombining blocks, we can compute maximum-likelihood estimates of the time and strength of the bottleneck. Our method relies on a simple summary of the joint distribution of polymorphic sites. We extend the site frequency spectrum by counting mutations in frequency classes in short sequence blocks. Using linkage information over short ...
Vector biology, population genetics. My overall research interest is in the population genetics of insect vectors of human and animal diseases. I have developed a program that pursues knowledge that may be applied to the control of vectorborne diseases but at the same time addresses critical issues in basic evolutionary genetics. My work has transitioned from classical population genetics to a more contemporary population genomics approach. Whereas the earlier work was based on analyses using genic markers, such as microsatellite DNA and single nucleotide polymorphisms, our current work applies next generation sequencing to study individual insect genomes, allowing us to explore problems with far greater depth and to address questions that were intractable just a few years ago. In parallel with our increasing use of genomics I have established a program in bioinformatics which is essential for both the management and analysis of the large body of data we are generating using next generation ...
NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-sample estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-sample (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given ...
View Notes - BILDSTUDY4 from BILD BILD 3 at UCSD. Lecture 5 Population Genetics part C Clicker Question: Negative frequency dependent selection maintains or increases variation within a population.
There are several situations in population biology research where simulating DNA sequences is useful. Simulation of biological populations under different evolutionary genetic models can be undertaken using backward or forward strategies. Backward simulations, also called coalescent-based simulations, are computationally efficient. The reason is that they are based on the history of lineages with surviving offspring in the current population. On the contrary, forward simulations are less efficient because the entire population is simulated from past to present. However, the coalescent framework imposes some limitations that forward simulation does not. Hence, there is an increasing interest in forward population genetic simulation and efficient new tools have been developed recently. Software tools that allow efficient simulation of large DNA fragments under complex evolutionary models will be very helpful when trying to better understand the trace left on the DNA by the different interacting
This zip file contains many different activities (58 pages of student handouts and 3 PowerPoints with a total of 71 slides) which can be used to compose a unit for AP Biology or advanced Biology students involving the Topics of Population Genetics and Patterns of Evolution.
Vår pris 543,-(portofritt). Population genetics is an inherently quantitative discipline, yet often focuses upon abstract concepts which can be difficult to conceptualize and appropriately..
for the period the animal survives] for PVAs are typically 20, 50, 100, 200, or sometimes 1000 years.. MVP estimates may also be derived from population censuses or genetic analyses. Genetic analyses typically involve the estimation of loss of genetic diversity and fitness and projection to extinction. Some studies indicate that inbreeding depression alone can lead to extinction, even among wild populations. Thus, when considering the viability of a given population, one should consider whether the population is large enough to avoid inbreeding depression, if there is sufficient genetic diversity for adaptive change to occur, and if the population is large enough to avoid accumulating new deleterious mutations.. ….Estimates of the population numbers required to overcome these effects (effective population or Ne) are 50 to avoid inbreeding depression, 500-5000 to retain evolutionary potential, and 12 to 1000 to avoid the accumulation of deleterious mutations…. An Ne of 50 is required to ...