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 ...

We consider the effect on the distribution of pairwise differences between mitochondrial DNA sequences of the incorporation into the underlying population genetics model of two particular effects that seem realistic for human populations. The first is that the population size was roughly constant before growing to its current level. The second is that the population is geographically subdivided rather than panmictic. In each case these features tend to encourage multimodal distributions of pairwise differences, in contrast to existing, unimodal datasets. We argue that population genetics models currently used to analyze such data may thus fail to reflect important features of human mitochondrial DNA evolution. These may include selection on the mitochondrial genome, more realistic mutation mechanisms, or special population or migration dynamics. Particularly in view of the variability inherent in the single available human mitochondrial genealogy, it is argued that until these effects are better ...

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 theory presented here relates a subdivided population with frequency-dependent selection (including the case of dominance) to an equivalent panmictic population characterized by different parameters. Subdivision alters both the size of the equivalent panmictic population (the effective population size Ne) and the effective values of all of the parameters describing selection. In the case of dominance, the dominance parameter h is in effect moved toward ½ by subdivision; i.e., fitness is made effectively closer to additive. For frequency dependence described by any polynomial in allele frequency, the effective values of all of the polynomial coefficients are altered by subdivision.. The theoretical treatment assumed that selection was weak in one sense, but allowed that it was strong in another sense. The requirement is that selection is weak compared to drift in a subpopulation, i.e., that the product of deme size (N) and (marginal) selection coefficient is always small in magnitude ...

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 ...

We describe a novel method for assessing the strength of disease association with single nucleotide polymorphisms (SNPs) in a candidate gene or small candidate region, and for estimating the corresponding haplotype relative risks of disease, using unphased genotype data directly. We begin by estimating the relative frequencies of haplotypes consistent with observed SNP genotypes. Under the Bayesian partition model, we specify cluster centres from this set of consistent SNP haplotypes. The remaining haplotypes are then assigned to the cluster with the nearest centre, where distance is defined in terms of SNP allele matches. Within a logistic regression modelling framework, each haplotype within a cluster is assigned the same disease risk, reducing the number of parameters required. Uncertainty in phase assignment is addressed by considering all possible haplotype configurations consistent with each unphased genotype, weighted in the logistic regression likelihood by their probabilities, calculated

With novel developments in sequencing technologies, time-sampled data are becoming more available and accessible. Naturally, there have been efforts in parallel to infer population genetic parameters from these data sets. Here, we compare and analyse four recent approaches based on the Wright-Fisher model for inferring selection coefficients (s) given effective population size (N-e), with simulated temporal data sets. Furthermore, we demonstrate the advantage of a recently proposed approximate Bayesian computation (ABC)-based method that is able to correctly infer genomewide average N-e from time-serial data, which is then set as a prior for inferring per-site selection coefficients accurately and precisely. We implement this ABC method in a new software and apply it to a classical time-serial data set of the medionigra genotype in the moth Panaxia dominula. We show that a recessive lethal model is the best explanation for the observed variation in allele frequency by implementing an estimator ...

Microsatellite loci mutate at an extremely high rate and are generally thought to evolve through a stepwise mutation model. Several differentiation statistics taking into account the particular mutation scheme of the microsatellite have been proposed. The most commonly used is R(ST) which is independent of the mutation rate under a generalized stepwise mutation model. F(ST) and R(ST) are commonly reported in the literature, but often differ widely. Here we compare their statistical performances using individual-based simulations of a finite island model. The simulations were run under different levels of gene flow, mutation rates, population number and sizes. In addition to the per locus statistical properties, we compare two ways of combining R(ST) over loci. Our simulations show that even under a strict stepwise mutation model, no statistic is best overall. All estimators suffer to different extents from large bias and variance. While R(ST) better reflects population differentiation

Buy Phylogeny, Molecular Population Genetics, Evolutionary Biology & Conservation of the Neotropical Primates (9781634851657): NHBS - Manuel Ruiz-Garcia, Joseph Mark Shostell, Nova Science Publishers

Published on 04. May 2019 Genetic population structure and demography of an apex predator, the tiger shark Galeocerdo cuvier Agathe Pirog, Sébastien Jaquemet,

Read Narrow hybrid zone between Moscow and Western Dvina chromosomal races and specific features of population isolation in common shrew Sorex araneus (Mammalia), Russian Journal of Genetics on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.

An important goal of population genetics is to determine the forces that have shaped the pattern of genetic variation in natural populations. We developed a maximum likelihood method that allows us to infer demographic changes and detect recent positive selection (selective sweeps) in populations of varying size from DNA polymorphism data. Applying this approach to single nucleotide polymorphism data at more than 250 noncoding loci on the X chromosome of Drosophila melanogaster from an (ancestral) African population and a (derived) European, we found that the African population expanded about 60,000 y ago and that the European population split off from the African lineage about 15,800 y ago, thereby suffering a severe population size bottleneck. We estimated that about 160 beneficial mutations (with selection coefficients s between 0.05% and 0.5%) were fixed in the euchromatic portion of the X in the African population since population size expansion, and about 60 mutations (with s around 0.5%) in the

The present paper investigates the origins of the Aegean pre-palatial civilizations (5th-3rd millennium BC) by applying cutting-edge methods of molecular biology and population genetics. The term Aegean Civilizations refers to the novel human lifeway (agriculture and craft specialization, redistribution systems, intensive trade) that appeared during the end of the Neolithic and the beginning of the Bronze Age in the Aegean. Although many studies exist on archaeological constructions of ethnic and cultural identity on mainland Greece, the Cyclades and Crete, not enough efforts have been made to explore this direction on a population history basis. We have investigated Late, Final Neolithic and Early Bronze Age human skeletons (n=127) from the Aegean using ancient DNA methods, next generation sequencing (NGS) technology and statistical population genetic inferences to i) gather information on diversity, population size, and origin of the pre-palatial Aegean Cultures, ii) to compare them on a ...

A key question in molecular evolutionary biology concerns the relative roles of mutation and selection in shaping genomic data. Moreover, features of mutation and selection are heterogeneous along the genome and over time. Mechanistic codon substitution models based on the mutation-selection framework are promising approaches to separating these effects. In practice, however, several complications arise, since accounting for such heterogeneities often implies handling models of high dimensionality (e.g., amino acid preferences), or leads to across-site dependence (e.g., CpG hypermutability), making the likelihood function intractable. Approximate Bayesian Computation (ABC) could address this latter issue. Here, we propose a new approach, named Conditional ABC (CABC), which combines the sampling efficiency of MCMC and the flexibility of ABC. To illustrate the potential of the CABC approach, we apply it to the study of mammalian CpG hypermutability based on a new mutation-level parameter implying

The aim of this study was to explore the hierarchical nature of the two major bone types in rats. By using a variety of analytical techniques, we were able to characterize the structural and compositional properties of cortical and trabecular bone, as well as to determine the best mathematical model to predict the tissues mechanical properties.. Our hierarchical analysis demonstrated that the differences between cortical and trabecular bone reside mainly at the micro- and macrostructural levels. Our findings are consistent with those of previous studies: modulus of elasticity and yield strength values were significantly lower in trabecular bone specimens [7,24,26,27,29,30]. Although not evidenced in our study, Choi & Goldstein [7] made the same asseveration, emphasizing the higher mineral density values seen in trabecular bone. These findings can be explained by the configuration of lamellar/collagen fibres within the tissue, along with other microstructural characteristics that altogether ...

TY - JOUR. T1 - Population Genetics of Latvians in the Context of Admixture between North-Eastern European Ethnic Groups. AU - Krumiņa, Astrida. AU - Pliss, Liana. AU - Zariņa, Gunita. AU - Puzuka, Agrita. AU - Zariņa, Agnese. AU - Lace, Baiba. AU - Elferts, Didzis. AU - Khrunin, Andrey. AU - Limborska, Svetlana. AU - Kloviņš, Janis. AU - Gailite Piekuse, Linda. N1 - Publisher Copyright: © 2018 Astrida Krumiņa et al., published by Sciendo.. PY - 2018/6/1. Y1 - 2018/6/1. N2 - This article presents a review on population genetics of Latvians, which alongside Lithuanians are the two extant Baltic speaking populations. The article provides a description of genome-wide single nucleotide polymorphism (SNP) data and contains a comparative analysis of the results of studies performed on classical autosomal genetic markers, mitochondrial DNA (mtDNA) and the non-recombining part of the Y chromosome (NRY), with data on neighbouring populations. The study also covers data of recently performed ...

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.

The Distribution of Human Genetic Diversity: A Comparison of Mitochondrial, Autosomal, and Y-Chromosome Data L. B. Jorde,1 W. S. Watkins,1 M. J. Bamshad,2 M. E. Dixon,1 C. E. Ricker,1 M. T. Seielstad,3 and M. A. Batzer4 Departments of 1Human Genetics and 2Pediatrics, University of Utah Health Sciences Center, Salt Lake City; 3Program for Population Genetics, Harvard School of Public Health, Boston; and 4Departments of Pathology, Biometry and Genetics, Biochemistry and Molecular Biology,

Read From population genetics to population genomics of forest trees: Integrated population genomics approach, Russian Journal of Genetics on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.

Influence of host plant and host population structure on physiological and behavioural characteristics of Chilocorus nigritus and the efficacy of control of the scale insect, Aspidiotus nerii (Bouche ...

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...

Anderson, G. J.; G. Bernardello, T. F. Stuessy & D. J. Crawford. 2001. Breeding system and pollination of selected plants endemic to Juan Fernández Islands. American Journal of Botany 88: 220-233. Arrigo, N.; J. W. Tuszynski, D. Ehrich, T. Gerdes & N. Álvarez. 2009. Evaluating the impact of scoring parameters on the structure of intra-specific genetic variation using RawGeno, an R package for automating AFLP scoring. BMC Bioinformatics 10: 33. de Queiroz, K. 2007. Species concepts and species delimitation. Systematic Biology 56: 879-886. Doyle, J. J. & J. L. Doyle. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15. Ehrich, D. 2006. AFLPDAT: a collection of R functions for convenient handling of AFLP data. Molecular Ecology Notes 6: 603-604. Excoffier, L. & H. E. L. Lischer. 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10: ...

Across-nation differences in the mean values for complex traits are common(1-8), but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European countries. Using discovery data on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95% CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively, reflect population genetic differences. Population genetic divergence differed significantly from that in a null model (height, P , 3.94 x 10(-8); BMI, P , 5.95 x 10(-4)), and we find an among-population genetic correlation for tall and slender individuals (r = -0.80, 95% CI = -0.95, -0.60), consistent with correlated selection for both phenotypes. Observed differences in height among populations reflected the predicted genetic ...

Southeast Asia houses various culturally and linguistically diverse ethnic groups. In Malaysia, where the Malay, Chinese, and Indian ethnic groups form the majority, there exist minority groups such as the negritos who are believed to be descendants of the earliest settlers of Southeast Asia. Here we report patterns of genetic substructure and admixture in two Malaysian negrito populations (Jehai and Kensiu), using ~50,000 genome-wide single-nucleotide polymorphism (SNP) data. We found traces of recent admixture in both the negrito populations, particularly in the Jehai, with the Malay through principal component analysis and STRUCTURE analysis software, which suggested that the admixture was as recent as one generation ago. We also identified significantly differentiated nonsynonymous SNPs and haplotype blocks related to intracellular transport, metabolic processes, and detection of stimulus. These results highlight the different levels of admixture experienced by the two Malaysian negritos.

It is not yet clear under what conditions empirical studies can reliably detect progress toward ecological speciation through the analysis of allelic variation at neutral loci. We use a simulation approach to investigate the range of parameter space under which such detection is, and is not, likely. We specifically test for the conditions under which divergent natural selection can cause a generalized barrier to gene flow that is present across the genome. Our individual-based numerical simulations focus on how population divergence at neutral loci varies in relation to recombination rate with a selected locus, divergent selection on that locus, migration rate and population size. We specifically test whether genetic differences at neutral markers are greater between populations in different environments than between populations in similar environments. We find that this expected signature of ecological speciation can be detected under part of the parameter space, most consistently when ...

This latest research article, A Reassessment of Genetic Diversity in Icelanders: Strong Evidence from Multiple Loci for Relative Homogeneity Caused by Genetic Drift by A. Helgason, G. Nicholson, K. Stefánsson and P. Donnelly, both greatly expands sample sizes from individual populations and the number of genetic loci analysed, and uses population genetics simulations to demonstrate that genetic drift, not admixture (as claimed by E. Árnason), has been the overriding factor influencing patterns of genetic variation in Iceland. Moreover, these simulations also reveal that the summary statistics (gene diversity and mean pairwise mutational differences) used by E. Árnason, to argue for the relative genetic heterogeneity of Icelanders in his analysis of mitochondrial DNA (mtDNA) sequences, are poor comparative measures of genetic diversity in closely related populations such as those of Iceland and other European countries ...

In this months issue of the leading scientific journal Genome Research, scientists from Kyushu University report how environmentally damaged DNA may contribute to human genetic diversity.

The objective of this project is to study population genetics and genetic structure of phytoplankton based on single-cell genomics. Specifically, the focus will be on genomic variation in Gonyostomum semen (raphidophyceae), a harmful invasive microalga.. Populations of Gonyostomum have expanded invasively across N. Europe, but populations in N. America are less invasive and display less disruptive phenotypes despite similar environments. A population genomic approach can be used to explore the detailed dispersal patterns, and to understand the genetic basis of the differentiation among populations. By using single-cell genome amplification, the effort and bias of algal culturing is circumvented.. This research project is part of SINGEK, a Marie Skłodowska-Curie Innovative Training Network devised to provide a unique and structured training programme to a new generation of scientists with the highest expertise in Single Cell Genomics, from the initial stages of cell sorting to genome sequencing ...

This paper introduces and applies a genome wide predictive study to learn a model that predicts whether a new subject will develop breast cancer or not, based on her SNP profile. We first genotyped 696 female subjects (348 breast cancer cases and 348 apparently healthy controls), predominantly of Caucasian origin from Alberta, Canada using Affymetrix Human SNP 6.0 arrays. Then, we applied EIGENSTRAT population stratification correction method to remove 73 subjects not belonging to the Caucasian population. Then, we filtered any SNP that had any missing calls, whose genotype frequency was deviated from Hardy-Weinberg equilibrium, or whose minor allele frequency was less than 5%. Finally, we applied a combination of MeanDiff feature selection method and KNN learning method to this filtered dataset to produce a breast cancer prediction model. LOOCV accuracy of this classifier is 59.55%. Random permutation tests show that this result is significantly better than the baseline accuracy of 51.52%. Sensitivity

Random genetic drift is the process whereby some allele frequencies change in a population by chance alone. The alleles are not being fixed or eliminated by natural selection. Most of the alleles affected by drift are neutral or nearly neutral with respect to selection. Some are deleterious, in which case they may be accidentally fixed in spite of being selected against. Modern evolutionary theory incorporates random genetic drift as part of population genetics and modern textbooks contain extensive discussions of drift and the influence of population size. The scientific literature has focused recently on the Drift-Barrier Hypothesis, which emphasizes random genetic drift [Learning about modern evolutionary theory: the drift-barrier hypothesis].. Most of the alleles that become fixed in a population are fixed by random genetic drift and not by natural selection. Thus, in a very real sense, drift is the dominant mechanism of evolution. This is especially true in species with large genomes full ...

The knowledge of a species population structure is essential for the development of adequate conservation actions as well as for the understanding of its evolution. The population structure is unknown in all species of the Genus Psammodromus, including the Western Sand Racer (Psammodromus occidentalis; a recently described species), the Edwards Sand Racer (P. edwardsianus) and the Spanish Sand Racer (P. hispanicus). In this article, the genetic variability and population structure of Psammodromus edwardsianus, P. hispanicus, and P. occidentalis were studied in the Iberian Peninsula covering their natural geographic distribution. Mitochondrial DNA showed genetically different units in all species with higher genetic variability in their southern populations (latitudinal variation). Genetic differentiation was different among species and contrasted to those of species with similar characteristics. Our results therefore highlight the importance of species-specific studies analysing population structure.

How do you interpret the admixture proportion percentage on each chromosome? For example is there any significance as to which chromosome has the largest percentage? (i.e. chromosome 22 has 40% West Asian but chromosome 16 has only 6%). Does this mean one would share 40% of DNA from this particular marker? Any feedback would be appreciated Thank you

This tasks estimates the pairwise distances per genomic window between at least two genomes in glf format. This format can be created with the atlas task glf.. In a first step, the frequencies of nine genotype configurations aa/aa, aa/ab, ab/aa, aa/bb, ab/ab, ab/ac, aa/bc, ab/cc and ab/cd are estimated. The genotype configuration aa/aa e.g. corresponds to a locus where both individuals are homozygous for the same allele and the configuration ab/cc corresponds to a locus where one individual is heterozygous and the other is homozygous for a different allele.. In a second step, these genotype configuration frequencies are multiplied by the user-specified distance weights and summed up to produce the genetic distance. Depending on the genetic distance you want to use you will give different weights to the genotype configurations.. Predefined distance weights:. ...

TY - JOUR. T1 - A map of human genome variation from population-scale sequencing. AU - Altshuler, David L.. AU - Durbin, Richard M.. AU - Abecasis, Gonçalo R.. AU - Bentley, David R.. AU - Chakravarti, Aravinda. AU - Clark, Andrew G.. AU - Collins, Francis S.. AU - De La Vega, Francisco M.. AU - Donnelly, Peter. AU - Egholm, Michael. AU - Flicek, Paul. AU - Gabriel, Stacey B.. AU - Gibbs, Richard A.. AU - Knoppers, Bartha M.. AU - Lander, Eric S.. AU - Lehrach, Hans. AU - Mardis, Elaine R.. AU - McVean, Gil A.. AU - Nickerson, Debbie A.. AU - Peltonen, Leena. AU - Schafer, Alan J.. AU - Sherry, Stephen T.. AU - Wang, Jun. AU - Wilson, Richard K.. AU - Deiros, David. AU - Metzker, Mike. AU - Muzny, Donna. AU - Reid, Jeff. AU - Wheeler, David. AU - Wang, Shenzhen Jun. AU - Li, Jingxiang. AU - Jian, Min. AU - Li, Guoqing. AU - Li, Ruiqiang. AU - Liang, Huiqing. AU - Tian, Geng. AU - Wang, Bo. AU - Wang, Jian. AU - Wang, Wei. AU - Yang, Huanming. AU - Zhang, Xiuqing. AU - Zheng, Huisong. AU - ...

Joseph F. Pachut; Population genetics of four species of Ordovician bryozoans; stereology and jackknifed analysis of variance. Journal of Paleontology ; 61 (5): 927-941. doi: Download citation file:. ...

This paper summarizes the main results obtained on Trypanosoma cruzi genetic diversity and population structure since this parasite became the theme of many genetic and molecular studies in the early seventies. T. cruzi exibits a paradigmatic pattern of long-term, clonal evolution, which has structured its natural populations into several discrete genetic subdivisions or

Judaism is a religion and not an attribute definable by a DNA mutation, but we can give you hints about having Jewish ancestry by comparing your results against our database. Look on the Y-DNA - Ancestral Origins page to see whether or not the people you match have listed Jewish ancestry. Those in our Jewish database have a listing in the Comments column denoting Jewish ancestry. There are four situations when testing for Jewish ancestry. These situations are as follows:. ...

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 ...

The following m files are included: discrimination_MLE.m Calculates the discrimination ability of a given population of neurons. This program may take an hour to run categorization_llikhd.m Calculates the identification ability of a given population of neurons. This program may take 4 minutes to run. Both scripts above use the following helper functions: MNRRS.m Gets the response of the population of neurons to a specific frequency. likhood.m The likelihood function (equation 2 in manuscript) get_params.m The parameters used for the simulation (population parameters and testing parameters) Editing this file will suffice to change population or testing parameters smth_gass_distr.m Helper function for get_params to redefine over-representation. categorization_llikhd also includes: binornd_sim.m The Bernoulli random process simulation (Eq 5 in paper) In addition, the following mat files are included: discr_temp.mat output expected at line 93 of discrimination_MLE to plot, use lines 98-103 ...

I have put up a few posts warning readers to be careful of confusing PCA plots with real genetic variation. PCA plots are just ways to capture variation in large data sets and extract out the independent dimensions. Its great at detecting population substructure because the largest components of variation often track between population differences, which consist of sets of correlated allele frequencies. Remeber that PCA plots usually are constructed from the two largest dimensions of variation, so they will be drawn from just these correlated allele frequency differences between populations which emerge from historical separation and evolutionary events. Observe that African Americans are distributed along an axis between Europeans and West Africans. Since we know that these are the two parental populations this makes total sense; the between population differences (e.g., SLC24A5 and Duffy) are the raw material from which independent dimensions can pop out. But on a finer scale one has to be ...

Incidence. The number or rate (per head of population) of new cases of a disease diagnosed in a given population during a specified time period (usually a calendar year). The crude rate is the total number of cases divided by the mid-year population, usually expressed per 100,000 population.. Malignant. Malignant tumours which grow by invasion into surrounding tissues and have the ability to metastasise to distant sites. Mortality. The number or rate (per head of population) of deaths in a given population during a specified time period (usually a calendar year). The crude rate is the total number of deaths divided by the mid-year population, usually expressed per 100,000 population.. Non-malignant. Not cancerous. Non-malignant tumours may grow larger but do not spread to other parts of the body.. Survival The length of time from the date of diagnosis for a disease, such as cancer, that patients diagnosed with the disease are still alive. In a clinical trial, measuring the survival is one way to ...

Soon after the PAH cDNA was cloned, it was used as a probe to detect restriction fragment length polymorphisms (RFLPs) by Southern blotting (Lidsky et al, 45; Woo et al, 63). The linkage between PKU and PAH was, of course, very strong. In the effort to discover the mutation(s) leading to the hyperphenylalanemias, searching for a nonrandom association of disease with alleles of normal polymorphisms [linkage disequilibrium (LD)] in the PAH gene was a strategy to consider. The use of this strategy has now reached epidemic proportions in human genetics, especially for complex diseases (Capon et al, 6; Horikawa et al, 32; Kim et al, 41; Myers et al, 47; Sawcer et al, 52; Scapoli et al, 53; Vaessen et al, 60), but often has low power unless there is strong prior support for a specific gene. In the case of PAH and PKU there was no question that the disorder is biochemically a deficiency of the enzyme and genetically inherited at (or very close to) the PAH gene. This is the very circumstance in which LD ...