TY - JOUR. T1 - RNA-seq analysis reveals considerable genetic diversity and provides genetic markers saturating all chromosomes in the diploid wild wheat relative Aegilops umbellulata. AU - Okada, Moeko. AU - Yoshida, Kentaro. AU - Nishijima, Ryo. AU - Michikawa, Asami. AU - Motoi, Yuka. AU - Sato, Kazuhiro. AU - Takumi, Shigeo. PY - 2018/11/8. Y1 - 2018/11/8. N2 - Background: Aegilops umbellulata Zhuk. (2n=14), a wild diploid wheat relative, has been the source of trait improvement in wheat breeding. Intraspecific genetic variation of Ae. umbellulata, however, has not been well studied and the genomic information in this species is limited. Results: To develop novel genetic markers distributed over all chromosomes of Ae. umbellulata and to evaluate its genetic diversity, we performed RNA sequencing of 12 representative accessions and reconstructed transcripts by de novo assembly of reads for each accession. A large number of single nucleotide polymorphisms (SNPs) and insertions/deletions ...

Aberrations in chromosomal copy number are one of the most common molecular features observed in cancer. Quantifying the degree of numerical chromosomal variation in single cells across a population of cells is of interest to researchers studying whole chromosomal instability (W-CIN). W-CIN, a state of high numerical chromosomal variation, contributes to treatment resistance in cancer. Here, we introduce aneuvis, a web application that allows users to determine whether numerical chromosomal variation exists between experimental treatment groups. The web interface allows users to upload molecular cytogenetic or processed whole-genome sequencing data in a cell-by-chromosome matrix format and automatically generates visualizations and summary statistics that reflect the degree of numeric chromosomal variability. Aneuvis is the first user-friendly web application to help researchers identify the genetic and environmental perturbations that promote numerical chromosomal variation.

Genetic diversity and population structure analysis between Indian red jungle fowl and domestic chicken using microsatellite markers. ...

Ex situ conservation, while helpful in humankinds efforts to sustain and protect our environment, is rarely enough to save a species from extinction. It is to be used as a last resort, or as a supplement to in situ conservation because it cannot recreate the habitat as a whole: the entire genetic variation of a species, its symbiotic counterparts, or those elements which, over time, might help a species adapt to its changing surroundings. Instead, ex situ conservation removes the species from its natural ecological contexts, preserving it under semi-isolated conditions whereby natural evolution and adaptation processes are either temporarily halted or altered by introducing the specimen to an unnatural habitat. In the case of cryogenic storage methods, the preserved specimens adaptation processes are (quite literally) frozen altogether. The downside to this is that, when re-released, the species may lack the genetic adaptations and mutations which would allow it to thrive in its ever-changing ...

Analysis of the amount and distribution of genetic variation can yield information about the number of introductions and history of an invasive species, which may be relevant for understanding the evolutionary potential and spread of invaders, as well as for creating best management practices for curbing them. We explored the genetic patterns and invasion history of the perennial, ornamental herb Lupinus polyphyllus Lindl. in Finland, where the species has spread rapidly during the past hundred years. Using 13 microsatellite loci, we determined the genetic variation of L. polyphyllus in 51 sites across a latitudinal gradient that reflected the invasion history of the species in this country. We found that the sampled populations were significantly genetically differentiated among sites, as indicated by the global F(ST) value (0.19) and AMOVA results (16.7 % of total genetic variation occurred among sites), and this differentiation slightly increased with increasing geographic distance (r = ...

Rapid development of sequencing technologies and bioinformatic tools makes the complete genome sequencing of many species possible, which provides a starting point to unravel the tremendous genetic variation and diversity at the genome scale. Amongst several model organisms examined to date, such as human, mouse, Arabidopsis, rice, and maize, genome-wide patterns of genetic variation are able to be captured by sampling a relatively small number of genomes [14, 20, 50-52]. By resequencing two sweet and one grain sorghum inbred lines, we uncovered nearly two million SNPs and indels, along with large numbers of PAVs and CNVs. This is a first report on the genome-wide patterns of genetic variation in sorghum, which will be valuable for further genotype-phenotype studies and for molecular breeding of this important C4 model crop.. Our study shows that the proportions of genic SNPs identified as in coding regions, intronic regions, or UTRs are 42.3%, 50.2%, and 7.5%, respectively. Compared to ...

The genetic diversity of Setipinna taty, which is commercially fished in the China Sea, was studied based on mitochondrial DNA control region sequences. PCR was used to amplify the control region fragment in 100 individuals of S. taty collected from Weihai (WH), Yantai (YT), Zhoushan (ZS), Xiangshan (XS), and Ninghai (NH) in China. A control region fragment of 656 bp was successfully sequenced in these 100 individuals. The A+T content of this S. taty control region was 71.7%; 172 variable sites and 62 haplotypes were found.

Population genetic structure and intrapopulation levels of genetic variation have important implications for population dynamics and evolutionary processes. Habitat fragmentation is one of the major threats to biodiversity. It leads to smaller population sizes and reduced gene flow between populations and will thus also affect genetic structure. We use a natural system of island and mainland populations of house sparrows along the coast of Norway to characterize the different population genetic properties of fragmented populations. We genotyped 636 individuals distributed across 14 populations at 15 microsatellite loci. The level of genetic differentiation was estimated using F-statistics and specially designed Mantel tests were conducted to study the influence of population type (i.e. mainland or island) and geographic distance on the genetic population structure. Furthermore, the effects of population type, population size and latitude on the level of genetic variation within populations were ...

We previously concluded that selective sweeps could not account for the reduced diversity in L. uniflora populations (Liuet al. 1998), on the basis of the finding of different alleles in different populations. It is now clear, however, that the populations studied represent two different species, L. uniflora and L. torulosa. Low diversity, without between-population differences, as in the two L. uniflora populations studied, could be explained by either hitchhiking or bottlenecks. In either interpretation, many loci in the genome should be similarly affected and have low diversity. This is, in fact, the case for several loci (Liu 1998).. Selective sweeps should certainly be considered a possibility, because the evolutionary loss of self-incompatibility in the selfing taxa must have involved hitchhiking events while the gene causing selfing was spreading through the populations. In an outcrosser, or in partially selfing populations such as L. crassa, a hitchhiking event at one locus would almost ...

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes ,99% of SNP variants with a frequency of ,1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies ...

Background: Population differentiation has proved to be effective for identifying loci under geographically-localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes. Results: We demonstrate that while sites of low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established ...

We have analyzed nucleotide sequence variation in an approximately 900-base pair region of the human mitochondrial DNA molecule encompassing the heavy strand origin of replication and the D-loop. Our analysis has focused on nucleotide sequences available from seven humans. Average nucleotide diversity among the sequences is 1.7%, several-fold higher than estimates from restriction endonuclease site variation in mtDNA from these individuals and previously reported for other humans. This disparity is consistent with the rapidly evolving nature of this noncoding region. However, several instances of convergent or parallel gain and loss of restriction sites due to multiple substitutions were observed. In addition, other results suggest that restriction site (as well as pairwise sequence) comparisons may underestimate the total number of substitutions that have occurred since the divergence of two mtDNA sequences from a common ancestral sequence, even at low levels of divergence. This emphasizes the ...

In most existing genetic variant association studies, common trait, common variants, which asserts that common genetic variants contribute to most of traits (disease susceptibilities), serves as the central assumption. Researchers have successfully identified some significant associations between common single nucleotide polymorphisms (SNPs) and disease traits [1]. However, despite the enormous efforts expended on association studies of complex traits, common genetic variants only show a moderate influence on different phenotypes in many reported disease associations and consequently have limited diagnostic value [2, 3]. While the identification of common variants creates a dilemma, known as common trait, rare variants, an alternative hypothesis, which asserts that multiple rare variants with moderate to high penetrances may collectively influence disease susceptibilities, has been suggested in some literatures [3-5]. Rare variants are defined as those whose minor allele frequencies (MAF) ...

TY - JOUR. T1 - Neandertal origin of genetic variation at the cluster of OAS immunity genes. AU - Mendez, Fernando L.. AU - Watkins, Joseph C.. AU - Hammer, Michael F.. PY - 2013/4/1. Y1 - 2013/4/1. N2 - Analyses of ancient DNA from extinct humans reveal signals of at least two independent hybridization events in the history of non-African populations. To date, there are very few examples of specific genetic variants that have been rigorously identified as introgressive. Here, we survey DNA sequence variation in the OAS gene cluster on chromosome 12 and provide strong evidence that a haplotype extending for ∼185 kb introgressed from Neandertals. This haplotype is nearly restricted to Eurasians and is estimated to have diverged from the Neandertal sequence ∼125 kya. Despite the potential for novel functional variation, the observed frequency of this haplotype is consistent with neutral introgression. This is the second locus in the human genome, after STAT2, carrying distinct haplotypes that ...

An international team of more than 1,000 scientists participated in a new study showing an integrated map of genetic variation from 1,092 human genomes.. A newly published compendium of the genetic alphabets of more than 1000 individuals from around the world illustrates how similar humans are - but also how crucial genetic variations can be.. The publication on November 1 in the journal Nature of the 1000 Genomes Project provides the most comprehensive catalog of human variations to date and will be indispensable to the practice of personalized medicine.. Sequencing an individuals DNA is useless in medicine unless there is a frame of reference to compare it to, said Yale Universitys Mark Gerstein, the Albert L. Williams Professor of Biomedical Informatics and one of more than 1,000 scientists who participated in international effort.. An individual human genome contains on an average 3 million variations. Without a reference library of variations, trying to hone in on the most informative ...

...Two genes in which variation affects intake of caffeine the most wide...The genes identified were CYP1A2 which has previously been implicated...Caffeine is implicated in numerous physiological and medical condition...Apart from smoking genetic determinants of lifestyle behaviors have g...,Genetic,variants,associated,with,caffeine,intake,identified,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters

Genetic diversity within species may promote resilience to environmental change, yet little is known about how such variation is distributed at broad geographic scales. Here we develop a novel Bayesian methodology to analyse multi-species genetic diversity data in order to identify regions of high or low genetic diversity. We apply this method to co-distributed taxa from Australian marine waters. We extracted published summary statistics of population genetic diversity from 118 studies of 101 species and | 1000 populations from the Australian marine economic zone. We analysed these data using two approaches: a linear mixed model for standardised data, and a mixed beta-regression for unstandardised data, within a Bayesian framework. Our beta-regression approach performed better than models using standardised data, based on posterior predictive tests. The best model included region (Integrated Marine and Coastal Regionalisation of Australia (IMCRA) bioregions), latitude and latitude squared. Removing

TY - JOUR. T1 - POT1 loss-of-function variants predispose to familial melanoma. AU - Robles-Espinoza, Carla Daniela. AU - Harland, Mark. AU - Ramsay, Andrew J.. AU - Aoude, Lauren G.. AU - Quesada, Victor. AU - Ding, Zhihao. AU - Pooley, Karen A.. AU - Pritchard, Antonia L.. AU - Tiffen, Jessamy C.. AU - Petljak, Mia. AU - Palmer, Jane M.. AU - Symmons, Judith. AU - Johansson, Peter A.. AU - Stark, Mitchell S.. AU - Gartside, Michael G.. AU - Snowden, Helen. AU - Montgomery, Grant W.. AU - Martin, Nicholas G.. AU - Lite, Jimmy Z.. AU - Choi, Jiyeon. AU - Makowski, Matthew. AU - Brown, Kevin M.. AU - Dunning, Alison M.. AU - Keane, Thomas M.. AU - Lopez-Otin, Carlos. AU - Gruis, Nelleke A.. AU - Hayward, Nicholas K.. AU - Bishop, D. Timothy. AU - Newton-Bishop, Julia A.. AU - Adams, David J.. N1 - © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.. PY - 2014/5. Y1 - 2014/5. N2 - Deleterious germline variants in CDKN2A account for around 40% of familial melanoma ...

The historical demography of the populations of domestic pigs in Europe and China was examined using mismatch distributions, which represent the frequency distribution of pairwise differences among all sampled haplotypes. Theoretical studies have shown that population bottlenecks and population expansions have a strong effect on the pattern of genetic polymorphism among haplotypes in the population (Rogers & Harpending 1992). For instance, populations in long and stable demographic equilibrium have multimodal mismatch distribution (ragged and chaotic) whereas the distribution appears unimodal after recent demographic expansions (Rogers & Harpending 1992; Harpending 1994). The mismatch distributions as well as the network analysis were consistent with population expansions in the ancestors for both contemporary Chinese and European domestic pigs (figures 3 and 4). The crucial question is whether the population expansion occurred before or after domestication. Similar signatures of population ...

Brewer, N., DeFrank, J., Chiu, W., Ibrahim, J., Walko, C., Rubin, P., ... Irvin, W. (2014). Patient understanding of how genotype variation affects benefits of tamoxifen therapy for breast cancer. Public Health Genomics, 17(1), 43 - 47 ...

BackgroundSesame is an important oil crop widely cultivated in Africa and Asia continent. Characterization of genetic diversity and population structure of sesame genotypes in these continents can be used to designing breeding methods. In the present study, 300 sesame g...

The Society runs two themed meetings each year as satellites to either the American or European Societies of Human Genetics annual meeting as a forum for scientists to exchange ideas and form collaborations. Prominent speakers in the field are invited. The meetings are designed to update and increase knowledge of human genome variation and generally attract a stimulating and interesting collection of abstracts in all fields of human genome variation making it an ideal forum to share information and results. We invite members and non-members alike to attend these meetings.. FORTHCOMING HGVS MEETINGS ...

Comparing different methods of estimating the genetic diversity could define their usefulness in plant breeding programs. In this study, a total of 18 morphological traits and 20 simple sequence repeat (SSR) loci were used to study the morphological and genetic diversity among 20 maize hybrids selected from different countries, and to classify the hybrids into groups based on molecular profiles and morphological traits. To collect morphological data, a field experiment was carried out using an RBCD design with three replications in Moghan, Ardabil, Iran. The highest estimates for genetic coefficients of variation were observed in anthesis-silking interval, followed by grain yields, leaf chlorophyll rates, kernel row numbers, and ear heights. The total number of PCR-amplified products was 84 bands, all of which were polymorphic. Among the studied primers,NC009,BNLG1108,BNLG1194,PHI026 and PHI057 showed the maximum polymorphism information content(PIC) and the greatest diversity. To determine the genetic

TY - JOUR. T1 - Lipid and sterol gene sequence variation in autism and correlates with neurodevelopmental status. T2 - A pilot study. AU - Hall, Trevor A.. AU - Steiner, Robert D.. AU - Wright, Hollis. AU - Wilmot, Beth. AU - Roullet, Jean Baptiste. AU - Peters, Meaghan. AU - Harris, Michael. N1 - Funding Information: Research reported in this publication was also supported by National Center for Advancing Translational Sciences of the National Institutes of Health under award number UL1TR000128 . The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Funding Information: Research reported in this publication was supported by the Northwest Health Foundation under the Mark O. Hatfield Research Fellowship on Autism. The content is solely the responsibility of the authors and does not necessarily represent the official views of the Northwest Health Foundation. PY - 2015/9/1. Y1 - 2015/9/1. N2 - Objective: ...

There were more than one thousand soybean(Glycine max(L.) Merr)germplasms in Hubei province.In order to evaluate the genetic diversity of summer sowing soybean landraces from different agricultural divisions of Hubei,we analyzed allelic profiles at 28 simple-sequence repeat(SSR) loci of 92 accessions.The SSR loci produced 134 alleles,and each SSR loci could detect 2 to 9 alleles with an average of 4.78 alleles per loci.The highest averages of both genetic diversity index and alleles were all occurred in southwest division,and second one was Jianghan Plain division.More than 83.6% of total variation was produced by geographical differentiation.By using the cluster analysis with Within-groups Linkage method,92 landraces were classified into three major groups at DNA level.Many landraces from southwest division and Jianghan Plain were clustered in Ⅰand Ⅲ group respectively.It was suggested that the diversity level of soybean landrace from both southwest and Jianghan Plain division were higher than

Understanding genome to phenotype linkages has been greatly enabled by genomic sequencing. However, most genome analysis is typically confined to the nuclear genome. We conducted a metabolomic QTL analysis on a reciprocal RIL population structured to examine how variation in the organelle genomes affects phenotypic variation. This showed that the cytoplasmic variation had effects similar to, if not larger than, the largest individual nuclear locus. Inclusion of cytoplasmic variation into the genetic model greatly increased the explained phenotypic variation. Cytoplasmic genetic variation was a central hub in the epistatic network controlling the plant metabolome. This epistatic influence manifested such that the cytoplasmic background could alter or hide pairwise epistasis between nuclear loci. Thus, cytoplasmic genetic variation plays a central role in controlling natural variation in metabolomic networks. This suggests that cytoplasmic genomes must be included in any future analysis of natural ...

Soybean (Glycine max) cultivars adapted to high latitudes have a weakened or absent sensitivity to photoperiod. The purposes of this study were to determine the molecular basis for photoperiod insensitivity in various soybean accessions, focusing on the sequence diversity of the E4 (GmphyA2) gene, which encodes a phytochrome A (phyA) protein, and its homoeolog (GmphyA1), and to disclose the evolutionary consequences of two phyA homoeologs after gene duplication. We detected four new single-base deletions in the exons of E4, all of which result in prematurely truncated proteins. A survey of 191 cultivated accessions sourced from various regions of East Asia with allele-specific molecular markers reliably determined that the accessions with dysfunctional alleles were limited to small geographical regions, suggesting the alleles recent and independent origins from functional E4 alleles. Comparison of nucleotide diversity values revealed lower nucleotide diversity at non-synonymous sites in GmphyA1 than in

In this thesis, I combine molecular analyses, common-garden and field experiments to examine how evolutionary and ecological processes influence patterns of genetic variation among and within populations of the declining, insect-pollinated, self-incompatible, perennial herb Primula farinosa. More specifically I examined 1) whether genetic diversity at neutral marker loci was related to habitat fragmentation and habitat stability, 2) whether floral display and flowering time were more strongly differentiated among populations than were putatively neutral marker loci, 3) whether adaptive population differentiation could be detected on a local spatial scale, and 4) whether floral display differentially affected male and female reproductive success.. Genetic diversity at neutral marker loci was lower within fragmented populations on the Swedish mainland than within the more densely occurring populations on the island Öland, SE Sweden. On Öland, fluctuations in population size were more pronounced ...

This week, the MalariaGEN P. falciparum genetic crosses project released a new data resource, comprising whole-genome sequence and genetic variation data from the parents and offspring of three parasite crosses.. This open access resource provides a foundation for further research into how genetic variation and sexual recombination affects parasite biology, at a much higher resolution than previously possible. These data are being made available at a time of intense interest in studying the genetic basis for evolutionary changes in the malaria-causing P. falciparum parasite, such as the emergence and spread of antimalarial drug resistance.. A lot of progress has been made in recent years in mapping out variation in the P. falciparum genome, however there are still big gaps in our knowledge, including many genes that are relevant to vaccine development or drug resistance, explains Alistair Miles, Head of Informatics with the MRC Centre for Genomics and Global Health. These new data on the ...

Natural genetic variation can cause significant differences in gene expression, but little is known about the polymorphisms that affect gene regulation. We analyzed regulatory variation in a cross between laboratory and wild strains of Saccharomyces cerevisiae. Clustering and linkage analysis define …

HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran ,3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. We observed significant human SNP associations to a total of 48 HIV-1 amino acid variants (p,2.4 × 10(-12)). All associated SNPs mapped to the HLA class I region. Clinical relevance of host and pathogen variation was assessed using VL results. We identified two critical advantages to the use of viral variation for identifying host factors: (1) association signals are much stronger for HIV-1 sequence variants than VL, reflecting the intermediate phenotype nature of viral variation; (2) association testing can be run without any clinical data. The proposed genome-to-genome approach highlights sites of genomic conflict and is a strategy generally ...

Author Summary Infectious diseases have undoubtedly played an important role in ancient and modern human history. Yet, there are relatively few regions of the genome involved in resistance to pathogens that show a strong selection signal in current genome-wide searches for this kind of signal. We revisit the evolutionary history of a gene associated with resistance to the most common malaria-causing parasite, Plasmodium vivax, and show that it is one of regions of the human genome that has been under strongest selective pressure in our evolutionary history (selection coefficient: 4.3%). Our results are consistent with a complex evolutionary history of the locus involving selection on a mutation that was at a very low frequency in the ancestral African population (standing variation) and subsequent differentiation between European, Asian and African populations.

Theories of Population Variation in Genes and Genomes by Christiansen, Freddy Bugge available in Hardcover on Powells.com, also read synopsis and reviews. This textbook provides an authoritative introduction to both classical and coalescent approaches to...

Leiopotherapon unicolor is the most widespread freshwater fish species in Australia. A comprehensive allozyme and mitochondrial DNA 16S rRNA data set was assembled from 141 specimens of L. unicolor collected Australia-wide in order to test for cryptic speciation in this far-ranging species. Surprisingly, little genetic diversity was observed within L. unicolor and provided no evidence for the existence of cryptic species within this lineage. In contrast, a small sample set of L. aheneus used as the outgroup showed two highly divergent haplotypes strongly suggestive of cryptic speciation. L. unicolor has a number of ecological and life history attributes that may explain the lack of significant genetic divergence over substantial geographical distances. The occurrence of other widespread fish and crustacean species that also display only limited genetic diversity indicate that climate conditions more favourable to dispersal across central and northern Australia than is suggested by the extent of ...

Although nucleotide diversity at this gene (5.19 per kb) was comparable to that observed between red JF and domestic fowl (5.36 per kb on average) [2], the substantial excess of haplotypes was suggestive of non-neutral evolution. Despite this, the significantly positive Fu and Lis D and F values show that there was a relative deficit of singletons [39]. A deficit of rare alleles in commercial chicken lines has been observed in other studies comparing wild and standard breeds [65]. In this study, the Hd and Fus F S values highlighted this rare allele deficiency in the commercial broilers, in contrast with the excess of haplotypes in the Asian and African samples. In addition, the significantly high R M values indicated that some recombinant alleles were present in the populations, implying either relaxed selective constraint or adaptive processes favouring allelic diversity.. Tajimas D compares the proportions of low- to medium-frequency alleles and is an indicator of directional selection ...

Studies on genetic variation can reveal effects on traits and disease, both in humans and in model organisms. Good technology for the analysis of DNA sequence variations is critical. Currently the development towards assays for large-scale and parallel DNA sequencing and genotyping is progressing rapidly. Single base primer extension (SBE) is a robust reaction principle based on four-colour fluorescent terminating nucleotides to interrogate all four DNA nucleotides in a single reaction. In this thesis, SBE methods were applied to the analysis and discovery of single nucleotide polymorphism (SNP) in the model organism Drosophila melanogaster and in humans.. The tag-array minisequencing system in a microarray format is convenient for intermediate sized genotyping projects. The system is scalable and flexible to adapt to specialized and novel applications. In Study I of the thesis a tool was established to automate quality control of clustered genotype data. By calculating Silhouette scores, the ...

Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft selective sweeps at a single genetic locus. However, in linked regions of rapidly adapting genomes, multiple beneficial mutations at different loci can segregate simultaneously within the population, an effect known as clonal interference. This leads to a subtle interplay between hitchhiking and interference effects, which leads to a unique signature of rapid adaptation on genetic variation both at the selected sites and at linked neutral loci. Here, we introduce an effective coalescent theory (a fitness-class coalescent) that describes how positive selection at many perfectly linked sites alters the structure of genealogies. We use this theory to calculate several simple statistics describing genetic variation within a rapidly adapting population and to implement efficient ...

Over the past several years, Genome Wide Association Studies (GWAS) have discovered hundreds of genetic variants involved in complex diseases(10.1056/NEJMra0905980). The vast majority of these variants do not lie in the protein coding regions of genes and thus do not affect what the gene produces, but instead likely affect how the genes are regulated. For this reason, the study of how genetic variation affect gene activity levels (referred to as expression levels) has been a major focus of research for many years. Genetic variation that affects gene expression are referred to as expression quantitative trait loci (eQTL)(10.1038/nrg2969).. Several studies collect expression from multiple tissues which leads to the question of whether or not the same genetic variants affect expression in multiple tissues(10.1038/ng.2653). Another way to ask this question is: Are eQTLs tissue specific or not tissue specific?. A challenge in this type of analysis is that an eQTL may affect expression in multiple ...

Genetic diversity of the human immunodeficiency virus type 1 (HIV-1) population within an individual is lost during transmission to a new host. The demography of transmission is an important determinant of evolutionary dynamics, particularly the relative impact of natural selection and genetic drift immediately following HIV-1 infection. Despite this, the magnitude of this population bottleneck is unclear. We use coalescent methods to quantify the bottleneck in a single case of homosexual transmission and find that over 99% of the env and gag diversity present in the donor is lost. This was consistent with the diversity present at seroconversion in nine other horizontally infected individuals. Furthermore, we estimated viral diversity at birth in 27 infants infected through vertical transmission and found there to be no difference between the two modes of transmission. Assuming the bottleneck at transmission is selectively neutral, such a severe reduction in genetic diversity has important implications

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So traits that have large additive genetic components are more easily changed by selection. The authors set out to investigate the genetic basis of gene expression level in Drosophila (for many genes measured on array) and how this differs between males and females. By a series of crosses, the authors find that many more genes show additive genetic variation in their expression level in males than in females, and that a number of these genes are found on the X chromosome (as well as on the autosomes). Now the X chromosome seems to be be the key to this difference in the form of genetic variation (and the authors conduct further experiments to show this). As males have only a single X chromosome there simply is not any dominance due to genetic variation on the X chromosome (at least not simple non-epistatic dominance). The genetic variation on the X chromosome in males mainly contributes to the additive genetic component of variation (as there is no second allele to cause dominance). So genes on ...

October 3, 2004. October 3, 2004 - In a paper published today in the online edition of Nature Genetics, a deCODE-led team of scientists present the results of a large-scale population study linking recombination rate with maternal age and fertility. In the paper, entitled Recombination rate and reproductive success in humans, the deCODE team establish a novel and significant correlation between recombination - the shuffling of chromosomal material that takes place in the formation of eggs and sperm - and maternal age and fertility. Specifically, the average number of recombinations in eggs that go on to become successful live births tends to increase with the mothers age, and mothers with a higher recombination rate in general also tend to have more children than do those with a lower recombination rate. The authors conclude that the most likely explanation for this phenomenon is that recombination, which is one of the most important mechanisms for generating genetic diversity in ...

Cancer cells are intrinsically heterogeneous. Multiple clones with their unique variants co-exist in tumor tissues. The variants include point mutations and structural variations. Point mutations, or single nucleotide variants are those variants on one base; structural variations are variations involving sequence with length not smaller than 50 bases. Approaches to estimate the number of clones and their respective percentages from point mutations have been recently proposed. However, structural variations, although involving more reads than point mutations, have not been quantitatively studied in characterizing cancer heterogeneity. I describe in this thesis a maximum likelihood approach to estimate variant allele fraction of a putative structural variation, as a step towards the characterization of tumor heterogeneity. A software tool, BreakDown, implemented in Perl realizing this statistical model is publicly available. I studied the performance of BreakDown through both simulated and real ...

The WHI GWAS examines the genome, which is the individuals complete set of DNA, of women who have participated in WHI to see if there are genetic variations associated with a particular disease. To do this, the genomes of women with a particular disease are compared to similar women without the disease. If certain genetic variations are seen in participants with the disease compared to those without, the variations are said to be associated with the disease. The genetic variations themselves do not necessarily cause the disease, but may put individuals with the variant at increased risk. Other influences (diet, smoking, environment) may also be important factors that work along with genetic variations to influence risk. Once new genetic associations are identified, it may be possible to use the information to detect, treat, and prevent the disease. We hope to learn much more about this using the WHI blood samples. ...

Genetic variation in three Iranian pelt sheep breeds namely: Gray Shiraz, Zandi and Karakul were investigated using fifteen microsatellite loci. Genomic DNA was extracted from 360 blood samples by extraction kits and salting-out procedure with some modifications. The total number of alleles ranged from 6 to12 in loci. The fifteen tested loci were all polymorphic in the three breeds. The average direct count of heterozygosity overall loci in each tested breed was more than the expected heterozygosity. Tests of genotype frequencies for deviation from the Hardy-Weinberg equilibrium (HWE) were performed at each locus of overall breeds and revealed significant departure from HWE (P , 0.001) due to heterozygote excess. Polymorphism information content value in Gray Shiraz, Zandi and Karakul were 0.815, 0.808 and 0.808, respectively. Rate of inbreeding within the three breeds was not noticeable (global Fis = - 0.19). Low genetic differentiation was detected by estimation of Fst index between all pairs ...

In 1974, Richard Lewontin published The Genetic Basis of Evolutionary Change, focusing enormous attention on protein variation as both a model of underlying genetic variation and a level of selection itself. In the twenty years since, scientific research has been shifted by the power of molecular biological techniques to explore the nature of variation directly at the DNA and gene levels. The protein chapter is coming to a close. In this book, Jeff Mitton explains the questions that geneticists hoped to answer by studying protein variation. He reviews the extensive literature on protein variation, describes the successes and failures of the research program, and evaluates the results of a rich and controversial body of research. The laboratory and field studies using protein polymorphisms revealed dynamic interactions among genotypes, fitness differentials, and fluctuating environmental conditions, and inadvertently wedded the fields of physiological ecology and population biology. Mittons book is a

The most important biological role of meiosis compared with asexual reproduction is providing genetic diversity of individuals as a result of mixing of paternal and maternal genes in the gamete. This is achieved in two ways.. Firstly, in the first division of meiosis the distribution of paternal and maternal chromosomes into the daughter cells is random, which results in gametes bearing different combinations of parental chromosomes (Smith and Nicolas 204). The second fundamental mechanism for the maintenance of genetic diversity is that in the initial phase of the first meiotic division homologous chromosomes are arranged opposite to each other and couple, forming one or more areas of contact (chiasm) between individual unsisterly chromatids. Next, the pair of chromatids that formed chiasm exchanges the sections of DNA (crossing-over process). As a result of crossing-over recombinant chromosomes are formed consisting of sections originating from different parent lines. Upon the completion of ...

After the recent discovery that common genetic variation in 15q24-25.1 influences inherited risk of lung cancer (3-7), we identified a second sequence variant at 15q24-25.1 associated with familial lung cancer (8) and further validated this new association in large sporadic lung cancer populations. We showed that these two genetic variants on 15q24-25.1 have independent genetic effects on lung cancer risk. The second variant on 15q24-25.1, marked by rs481134, explains an additional 13.2% of the population attributable risk for lung cancer. These results further confirm the complexity of the chromosomal region 15q24-25.1 underlying lung cancer susceptibility.. Interestingly, the second variant did not show association with lung cancer in single-marker analysis. However, haplotype analysis of SNPs rs1051730 and rs481134 provided stronger evidence for association with lung cancer. SNPs rs1051730 and rs481134 are in moderate LD (r2 = 0.30), which can mask or change the genetic effects of those loci ...

The distribution of variation in a quantitative trait and its underlying distribution of genotypic diversity can both be shaped by stabilizing and directional selection. Understanding either distribution is important, because it determines a populations response to natural selection. Unfortunately, existing theory makes conflicting predictions about how selection shapes these distributions, and very little pertinent experimental evidence exists. Here we study a simple genetic system, an evolving RNA enzyme (ribozyme) in which a combination of high throughput genotyping and measurement of a biochemical phenotype allow us to address this question. We show that directional selection, compared to stabilizing selection, increases the genotypic diversity of an evolving ribozyme population. In contrast, it leaves the variance in the phenotypic trait unchanged. ...

TY - JOUR. T1 - Intracolonial genetic variation affects reproductive skew and colony productivity during colony foundation in a parthenogenetic termite. AU - Miyazaki, Satoshi. AU - Yoshimura, Miho. AU - Saiki, Ryota. AU - Hayashi, Yoshinobu. AU - Kitade, Osamu. AU - Tsuji, Kazuki. AU - Maekawa, Kiyoto. PY - 2014/1/1. Y1 - 2014/1/1. N2 - Background: In insect societies, intracolonial genetic variation is predicted to affect both colony efficiency and reproductive skew. However, because the effects of genetic variation on these two colony characteristics have been tested independently, it remains unclear whether they are affected by genetic variation independently or in a related manner. Here we test the effect of genetic variation on colony efficiency and reproductive skew in a rhinotermitid termite, Reticulitermes speratus, a species in which female-female pairs can facultatively found colonies. We established colonies using two types of female-female pairs: colonies founded by sisters (i.e., ...

Human Genetic Diversity: Lewontins Fallacy is a 2003 paper by A. W. F. Edwards. He criticises an argument first made by Richard Lewontin in his 1972 article The Apportionment of Human Diversity, which argued that division of humanity into races is taxonomically invalid. Edwards critique is discussed in a number of academic and popular science books, with varying degrees of support. In the 1972 study The Apportionment of Human Diversity, Richard Lewontin performed a fixation index (FST) statistical analysis using 17 markers, including blood group proteins, from individuals across classically defined races (Caucasian, African, Mongoloid, South Asian Aborigines, Amerinds, Oceanians, and Australian Aborigines). He found that the majority of the total genetic variation between humans (i.e., of the 0.1% of DNA that varies between individuals), 85.4%, is found within populations, 8.3% of the variation is found between populations within a race, and only 6.3% was found to account for the ...

Genetic diversity at loci concerned with fitness is an important part of the ability of a wild population to adapt to changes in its environment, including climatic events, disease and pollution. Research into the effects of genetic diversity on the impacts of disease on wildlife populations has focussed on genes of the major histocompatibility complex (MHC). This study investigated the genetic diversity at the MHC class II DZB gene, as well as the distribution of alleles of the same gene, for platypuses Ornithorhynchus anatinus in the Seabrook Creek Catchment in northwest Tasmania. This study detected 10 previously identified alleles and two previously unreported alleles at the MHC Class II DZB locus in 18 platypuses from the Seabrook Creek Catchment. An additional sequence isolated from two individuals was consistent with a pseudogene. Alleles were reasonably well distributed geographically through the catchment, but there was evidence of a degree of isolation at one site. Consistent with ...

Since the human genome draft sequence was in public for the first time in 2000, genomic analyses have been intensively extended to the population level. The following three international projects are good examples for large-scale studies of human genome variations: 1) HapMap Data (1,417 individuals) (http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/2010-08_phaseII+III/forward/), 2) HGDP (Human Genome Diversity Project) Data (940 individuals) (http://www.hagsc.org/hgdp/files.html), 3) 1000 genomes Data (2,504 individuals) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ If we can integrate all three data into a single volume of data, we should be able to conduct a more detailed analysis of human genome variations for a total number of 4,861 individuals (= 1,417+940+2,504 individuals). In fact, we successfully integrated these three data sets by use of information on the reference human genome sequence, and we conducted the big data analysis. In particular, we constructed a ...

Because selection is often sex-dependent, alleles can have positive effects on fitness in one sex and negative effects in the other, resulting in intralocus sexual conflict. Evolutionary theory predicts that intralocus sexual conflict can drive the evolution of sex limitation, sex-linkage, and sex chromosome differentiation. However, evidence that sex-dependent selection results in sex-linkage is limited. Here, we formally partition the contribution of Y-linked and non-Y-linked quantitative genetic variation in coloration, tail, and body size of male guppies (Poecilia reticulata)-traits previously implicated as sexually antagonistic. We show that these traits are strongly genetically correlated, both on and off the Y chromosome, but that these correlations differ in sign and magnitude between both parts of the genome. As predicted, variation in attractiveness was found to be associated with the Y-linked, rather than with the non-Y-linked component of genetic variation in male ornamentation. ...

1. This study investigated whether sand-dune willow Salix cordata, exhibits genetic variation in resistance and tolerance to herbivory. 2. A field experiment using cuttings from nine willow clones demonstrated genetic variation in resistance to the specialist herbivore Altica subplicata, as measured by beetle densities. Willow clones differed significantly in both total biomass and leaf trichome densities, and herbivore densities were marginally correlated with both of these parameters. 3. Tolerance to herbivory was measured in a greenhouse experiment by comparing growth response of plants experiencing 50% artificial defoliation and plants experiencing no defoliation. Clones showed significant differences in tolerance to herbivory for some growth measures (changes in height and number of leaves), but not for other growth measures (stem diameter growth and final biomass). 4. Despite the significant genetic variation in both resistance and tolerance, no trade-off was found between resistance and ...

Xiao Bingbing, Han Lingxia, Niu Chengming, Si Changde and Han Jianlin. 2010. Population genetic variation in BWEL-SPF chickens inferred from microsatellite DNA markers. China Animal Husbandry and Veterinary Medicine 37(9):106-111 ...

TY - JOUR. T1 - Dopamine D4 receptor gene variation moderates the efficacy of bupropion for smoking cessation. AU - Leventhal, A. M.. AU - David, S. P.. AU - Brightman, M.. AU - Strong, D.. AU - McGeary, J. E.. AU - Brown, R. A.. AU - Lloyd-Richardson, E. E.. AU - Munafò, M.. AU - Uhl, G. R.. AU - Niaura, R.. N1 - Funding Information: This research was supported by NIH grants DA025041 (AML), HL32318 and CA84719 (RN), DA08511 (RAB), DA14276 and DA27331 (SPD) and NIDA-IRP.. PY - 2012/2. Y1 - 2012/2. N2 - Smokers (10 cigarettes per day, N331) of European ancestry taking part in a double-blind placebo-controlled randomized trial of 12 weeks of treatment with bupropion along with counseling for smoking cessation were genotyped for a variable number of tandem repeats polymorphism in exon III of the dopamine D4 receptor gene. Generalized estimating equations predicting point-prevalence abstinence at end of treatment and 2, 6 and 12 months after the end of treatment indicated that bupropion (vs ...

Variability of the human mitochondrial DNA control region sequences in the Lithuanian population. Kasperaviciute D, Kucinskas V. Human Genetics Centre, Vilnius University, Lithuania. The Lithuanians and Latvians are the only two Baltic cultures that survived until today. Since the Neolithic period the native inhabitants of the present-day Lithuanian territory have not been replaced by any other ethnic group. Therefore the genetic characterization of the present-day Lithuanians may shed

Overall diversity values for the ITS region were usually an order of magnitude higher in S. fimbriatum than in S. squarrosum, however all values were very low. Moreover, in S. fimbriatum, a considerable portion of the diversity was due to the genetic differentiation between Atlantic and Non-Atlantic clades. In contrast, GapC sequences of the species showed nearly the same nucleotide diversity values. This is an unexpected result because the pioneer characteristic of S. fimbriatum (Sundberg et al. 2006), even when combined with a parallel reduction of the historical population size of S. squarrosum, implies lower level of molecular polymorphism in the first species. Peat moss populations are likely to function as a metapopulation [49, 50]. Theory shows that species-wide genetic diversity is rapidly lost in metapopulations of pioneer species if among population migration rates are lower than extinction/recolonization rates [51, 52]. Although pioneer characteristic reduces the level of molecular ...

Understanding the patterns of genetic variation of traits subject to sexual selection is fundamental for explaining its evolutionary dynamics and potential for sexual coevolution. The signa of female Lepidoptera are sclerotized structures located on the inner surface of the genital receptacle that receives the spermatophore during copulation (the corpus bursae), whose main function is tearing the spermatophore envelope. Comparative data indicate that the evolution of signa has been influenced by sexually antagonistic coevolution with spermatophore envelopes. We looked for additive genetic variation in the size and shape of signa in females of the butterfly Callophrys xami (Lycaenidae) from two localities (BG and FC) in Mexico City. We also looked for genetic variation in female body size and in the size of corpus bursae. There were significant between-population differences in female body size, signa width and three signa shape traits. We found significant extranuclear maternal effects in one component

New Brunswick, N.J.- Researchers from The Cancer Institute of New Jersey (CINJ) are converging on Washington, D.C., this week for the 101st Annual Meeting of the American Association for Cancer Research (AACR) to share their findings on how a common genetic variation can impact diagnosis of breast cancer in postmenopausal women. They are joining other top investigators from around the globe for the event, which is highlighting interdisciplinary approaches to cancer research. CINJ is a Center of Excellence of UMDNJ-Robert Wood Johnson Medical School. At focus is the tumor-suppressor gene known as TSC1 and the role it plays in tumor growth in breast cancer. Mutation in either TSC1 or a companion gene known as TSC2, a relatively rare occurrence, is known to cause non-cancerous growths in multiple vital organs - a genetic condition known as tuberous sclerosis. Less clear is a possible association between more common variations in these genes known as polymorphisms, and the formation of breast ...

TY - JOUR. T1 - Exploring hepsin functional genetic variation association with disease specific protein expression in bipolar disorder. T2 - Applications of a proteomic informed genomic approach. AU - Nassan, Malik. AU - Jia, Yun Fang. AU - Jenkins, Greg. AU - Colby, Colin. AU - Feeder, Scott. AU - Choi, Doo Sup. AU - Veldic, Marin D. AU - McElroy, Susan L.. AU - Bond, David J.. AU - Weinshilboum, Richard M. AU - Biernacka, Joanna M. AU - Frye, Mark A. PY - 2017/12/1. Y1 - 2017/12/1. N2 - In a prior discovery study, increased levels of serum Growth Differentiation Factor 15 (GDF15), Hepsin (HPN), and Matrix Metalloproteinase-7 (MMP7) were observed in bipolar depressed patients vs controls. This exploratory post-hoc analysis applied a proteomic-informed genomic research strategy to study the potential functional role of these proteins in bipolar disorder (BP). Utilizing the Genotype-Tissue Expression (GTEx) database to identify cis-acting blood expression quantitative trait loci (cis-eQTLs), five ...

In this study microsatellite markers were applied to investigate the genetic diversity and population structure of the six local chicken lines kept in the Fowls for Africa program, for better clarification of parameters for breed differentiation and genetic conservation of this valuable resource. The lines included the Black Australorp, Potchefstroom Koekoek, New Hampshire, Ovambo, Lebova- Venda and a Naked Neck line. Unbiased estimates for heterozygosity ranged from 50% in the Potchefstroom Koekoek to as high as 65% in the Naked Neck chickens. FIS values varied from as low as 0.16 for the Black Australorp line to as high as 0.35 for the Ovambo chickens. The FST values indicated moderate to high genetic differentiation between the Naked Neck and New Hampshire (0.11); Ovambo and Naked Neck lines (0.12), and Naked Neck and Lebowa- Venda (0.14). A total of 13% of the total genetic variation observed was between the chicken lines and 87% within the lines, supporting moderate genetic ...

Robust information of genetic diversity among Bt cotton genotypes is still lacking and availability of several marker systems has prompted us to compare their utility for the detection of genetic diversity. Here, we report the comparative efficiency of morphological and molecular markers (EST-SSRs and ISSRs) in determining the genetic diversity among 30 Pakistani Bt cotton genotypes. Three different dendrograms based on 20 EST-SSRs, 13 ISSRs and 20 morphological markers divided the 30 Bt cotton genotypes into five, six, and three clusters, respectively. EST-SSRs and ISSRs revealed 0.73-1.00 and 0.77-0.97 genetics similarity among Bt cotton genotypes which indicated low level of genetic diversity. Further population structure analysis showed extensive allelic admixture among Bt cotton cultivars and identified three (EST-SSRs) and six (ISSRs) subgroups. The MGHES-31 (EST-SSRs) and UBC-807 and UBC-815 (ISSRs) showed maximum values of Polymorphic Information Contents(PIC) and Dj and had low value of Cj. The

Attalea vitrivir Zona (synonym Orbignya oleifera) is one of the six species of Arecaceae known as ?babassu?. This species is used to make cosmetics, food, and detergents due to the high concentration of oil in the seeds. It is found only in fragmented areas of southern Bahia State and northern Minas Gerais State, southeast Brazil, and this fragmentation has affected both its ecological and genetic characteristics. We evaluated the genetic diversity and population genetic structure of A. vitrivir in six areas of two different regions at the extremes of its geographical range, in order to gain a better understanding of the factors that affect the distribution and partitioning of its diversity. Nine inter simple sequence repeat (ISSR) markers amplified 74 polymorphic bands, resulting in large diversity values (Shannon diversity index, 0.37-0.47; intrapopulation genetic diversity, 0.25-0.34). Analysis of molecular variance (AMOVA) revealed considerable differentiation between sampling sites (30.03%) ...

Cymbidium is a genus of 68 species in the orchid family, with extremely high ornamental value. Marker-assisted selection has proven to be an effective strategy in accelerating plant breeding for many plant species. Analysis of cymbidiums genetic background by molecular markers can be of great value in assisting parental selection and breeding strategy design, however, in plants such as cymbidiums limited genomic resources exist. In order to obtain efficient markers, we deep sequenced the C. ensifolium transcriptome to identify simple sequence repeats derived from gene regions (genic-SSR). The 7,936 genic-SSR markers were identified. A total of 80 genic-SSRs were selected, and primers were designed according to their flanking sequences. Of the 80 genic-SSR primer sets, 62 were amplified in C. ensifolium successfully, and 55 showed polymorphism when cross-tested among 9 Cymbidium species comprising 59 accessions. Unigenes containing the 62 genic-SSRs were searched against Non-redundant (Nr), Gene Ontology

The genetic diversity and population structure of the small yellow croaker (Larimichthys polyactis) were investigated based on seven microsatellite markers. Two hundred and twenty-six individuals were collected from ten locations from the Bohai Sea, the Yellow Sea and the East China Sea. Relatively high genetic variation (He = 0.826-0.873) and very low genetic differentiation (Fst = 0.001-0.029) between populations were checked, which were attributed by high mutation rate, large population size, wide distribution and diverse habitats. L. polyactis had not undergone recent genetic bottleneck events, which was supported by Wilcoxon signed-rank test and mode-shift indicator of allele frequency distribution. UPGMA tree revealed that the cluster results had no connection with isolation by distance. The knowledge on genetic diversity and population structure will be crucial to establish appropriate fishery management for the species.

Downloadable! We examine the effect of genetic diversity on economic development in the United States. Our estimation strategy exploits that immigrants from different countries of origin differed in their genetic diversity and that these immigrants settled in different regions. Based on a sample of over 2250 counties, we find that increases in genetic diversity of US counties that arose due to immigration during the 19th century had a significant positive effect on US counties economic development. We also detect a significant positive long-run effect of 19th century immigrants genetic diversity on contemporaneous measures of income.

Aggressive behavior is an important component of fitness in most animals. Aggressive behavior is genetically complex, with natural variation attributable to multiple segregating loci with allelic effects that are sensitive to the physical and social environment. However, we know little about the genes and genetic networks affecting natural variation in aggressive behavior. Populations of Drosophila melanogaster harbor quantitative genetic variation in aggressive behavior, providing an excellent model system for dissecting the genetic basis of naturally occurring variation in aggression. Correlating variation in transcript abundance with variation in complex trait phenotypes is a rapid method for identifying candidate genes. We quantified aggressive behavior in 40 wild-derived inbred lines of D. melanogaster and performed a genome-wide association screen for quantitative trait transcripts and single feature polymorphisms affecting aggression. We identified 266 novel candidate genes associated with

A background study is important for the conservation and stock management of a species. Terapon jarbua is a coastal Indo-Pacific species, sourced for human consumption. This study examined 134 samples from the central west and east coasts of Peninsular (West) Malaysia and East Malaysia. A 1446-bp concatenated dataset of mtDNA COI and Cyt b sequences was used in this study and 83 haplotypes were identified, of which 79 are unique haplotypes and four are shared haplotypes. Populations of T. jarbua in Malaysia are genetically heterogenous as shown by the high level of haplotype diversity ranging from 0.9167-0.9952, low nucleotide diversity ranging from 0.0288-0.3434, and high FST values (within population genetic variation). Population genetic structuring is not distinct as shown by the shared haplotypes between geographic populations and mixtures of haplotypes from different populations within the same genetic cluster. The gene flow patterns and population structuring observed among these regions are

The social environment is expected to have substantial effects on behavior, and as a consequence its heritability and evolvability. We investigated these effects by exposing Australian field crickets (Teleogryllus oceanicus) to either silence or recordings of male acoustic sexual signals. We used a combined pedigree and full-sib/half-sib breeding design to estimate the repeatability, heritability, and evolvability of behaviors related to boldness, exploration, and activity. All behaviors measured were significantly repeatable in both social environments. Additionally, most behaviors showed significant heritabilities in the two environments. We found no difference in repeatabilities between the silent and the acoustic environment but did find significant differences in the heritabilities and evolvabilities between these environments. There was a high degree of similarity between the phenotypic covariance matrices across the two environments, while the genotypic covariance matrices were highly ...

TY - JOUR. T1 - Genetic variation and population differentiation of Michelia formosana (Magnoliaceae) based on cpDNA variation and RAPD fingerprints. T2 - Relevance to post-Pleistocene recolonization. AU - Lu, Sheng You. AU - Hong, Kuo Hsiang. AU - Liu, Show Ling. AU - Cheng, Yu Pin. AU - Wu, Wen Luan. AU - Chiang, Tzen Yuh. PY - 2002/12/1. Y1 - 2002/12/1. N2 - We used sequence variation of the atpB-rbcL intergenic spacer of cpDNA and nested clade analysis to assess the phylogeographic pattern of Michelia formosana, a species restricted to Taiwan and the Ryukyus. In total, 31 haplotypes were identified and clustered into four major chlorotypes. Genetic composition of nearly all populations was heterogeneous and paraphyletic phylogenetically. Although the apportionment of cpDNA variation hardly revealed a geographic pattern due to the coancestry of dominant sequences, some chlorotypes were restrictedly distributed. According to the patterns of clade dispersion and displacement, a reconstructed ...

ABSTRACT = { Genome-wide association studies are powerful tools to elucidate the genome-to-phenome relationship. In order to explain most of the observed heritability of a phenotypic trait, a sufficient number of individuals and a large set of genetic variants must be examined. The development of high-throughput technologies and cost-efficient resequencing of complete genomes have enabled the genome-wide identification of genetic variation at large scale. As such, almost all existing genetic variation becomes available, and it is now possible to identify rare genetic variants in a population sample. Rare genetic variants that were usually filtered out in most genetic association studies are the most numerous genetic variations across genomes and hold great potential to explain a significant part of the missing heritability observed in association studies. Rare genetic variants must be identified with high confidence, as they can easily be confounded with sequencing errors. In this study, we used ...

The genetic diversity of 89 flue-cured tobacco varieties was examined using 12 ISSR primers. These cultivarswere evaluated at the Guilan Tobacco Research Center, Rasht, Iran, using a 7×7 simple lattice design with two replications, and 12 morphological traits. The total number of PCR amplified products was 143 bands ranging from 450 to 3000 bp, of which 108 bands (74.28%) were polymorphic. Primers UBC 811 and UBC 814 with 16 bands and UBC 825 with 6 bands generated the highest and lowest number of bands, respectively. Of all the primers, UBC817, UBC824 and UBC873 showed the maximum amount (0.47) of polymorphism information content (PIC) and the greatest diversity. To determine the genetic relationship among tobacco cultivars, cluster analysis was performed based on either morphological traits or ISSR markers using the un-weighted pair-group method with arithmetic average (UPGMA). Tobacco genotypes were divided into five main groups. Principal coordinate analysis (PCoA) on a similarity matrix of

Approximately 2.4% of the human mitochondrial DNA (mtDNA) genome exhibits common homoplasmic genetic variation. We analyzed 12,975 whole-genome sequences to show that 45.1% of individuals from 1526 mother-offspring pairs harbor a mixed population of mtDNA (heteroplasmy), but the propensity for maternal transmission differs across the mitochondrial genome. Over one generation, we observed selection both for and against variants in specific genomic regions; known variants were more likely to be transmitted than previously unknown variants. However, new heteroplasmies were more likely to match the nuclear genetic ancestry as opposed to the ancestry of the mitochondrial genome on which the mutations occurred, validating our findings in 40,325 individuals. Thus, human mtDNA at the population level is shaped by selective forces within the female germ line under nuclear genetic control, which ensures consistency between the two independent genetic lineages.

VAN MARLE-KOSTER, E.; HEFER, C.A.; NEL, L.H. y GROENEN, M.A.M.. Genetic diversity and population structure of locally adapted South African chicken lines: implications for conservation. S. Afr. j. anim. sci. [online]. 2008, vol.38, n.4, pp.271-281. ISSN 2221-4062.. In this study microsatellite markers were applied to investigate the genetic diversity and population structure of the six local chicken lines kept in the Fowls for Africa program, for better clarification of parameters for breed differentiation and genetic conservation of this valuable resource. The lines included the Black Australorp, Potchefstroom Koekoek, New Hampshire, Ovambo, Lebova- Venda and a Naked Neck line. Unbiased estimates for heterozygosity ranged from 50% in the Potchefstroom Koekoek to as high as 65% in the Naked Neck chickens. FIS values varied from as low as 0.16 for the Black Australorp line to as high as 0.35 for the Ovambo chickens. The FST values indicated moderate to high genetic differentiation between the ...

Université Lille 1 (GEPV-Lille), Lille - France. The project summary follows:. Plants that have expanded their geographic ranges tend to show lower genetic diversity at their new range margins, and thus may have lost their adaptive potential as a result of the repeated genetic bottlenecks that occur during colonisation. In outcrossing species, however, range-edge populations might maintain sufficient genetic variation for continued responses to selection, either because colonisation bottlenecks are less severe for outcrossers, or because outcrossing facilitates continued gene flow into range-edge populations from elsewhere. We propose to test this hypothesis by studying the impact of range expansions and natural selection on the genome and patterns of gene expression of the European plant Mercurialis annua, a wind-pollinated dioecious (and thus outcrossing) annual plant that currently occupies a wide environmental range in Europe following range expansion from an eastern Mediterranean refugium. ...

CD8(+) cytotoxic T-lymphocytes (CTLs) perform a critical role in the immune control of viral infections, including those caused by human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV). As a result, genetic variation at CTL epitopes is strongly influenced by host-specific selection for either escape from the immune response, or reversion due to the replicative costs of escape mutations in the absence of CTL recognition. Under strong CTL-mediated selection, codon positions within epitopes may immediately toggle in response to each host, such that genetic variation in the circulating virus population is shaped by rapid adaptation to immune variation in the host population. However, this hypothesis neglects the substantial genetic variation that accumulates in virus populations within hosts. Here, we evaluate this quantity for a large number of HIV-1-(n ,= 3,000) and HCV-infected patients (n ,= 2,600) by screening bulk RT-PCR sequences for sequencing mixtures (i. e., ...

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. ...

TY - JOUR. T1 - Common genetic variation in GLP1R and insulin secretion in response to exogenous GLP-1 in nondiabetic subjects. T2 - A pilot study. AU - Sathananthan, Airani. AU - Dalla Man, Chiara. AU - Micheletto, Francesco. AU - Zinsmeister, Alan R.. AU - Camilleri, Michael. AU - Giesler, Paula D.. AU - Laugen, Jeanette M.. AU - Toffolo, Gianna. AU - Rizza, Robert A.. AU - Cobelli, Claudio. AU - Vella, Adrian. PY - 2010/9. Y1 - 2010/9. N2 - OBJECTIVE - Glucagon-like peptide (GLP)-1 receptor is encoded by GLP1R. The effect of genetic variation at this locus on the response to GLP-1 is unknown. This study assessed the effect of GLP1R polymorphisms on insulin secretion in response to hyperglycemia and to infused GLP-1 in nondiabetic subjects. RESEARCH DESIGN AND METHODS - Eighty-eight healthy individuals (aged 26.3 ± 0.6 years, fasting glucose 4.83 ± 0.04 mmol/l) were studied using a hyperglycemic clamp. GLP-1 was infused for the last 2 h of the study (0.75 pmol/kg/min over 121-180 min, 1.5 ...

Understanding the influences of population structure, selection, and recombination on polymorphism and linkage disequilibrium (LD) is integral to mapping genes contributing to drug resistance or virulence in Plasmodium falciparum. The parasites short generation time, coupled with a high cross-over rate, can cause rapid LD break-down. However, observations of low genetic variation have led to suggestions of effective clonality: selfing, population admixture, and selection may preserve LD in populations. Indeed, extensive LD surrounding drug-resistant genes has been observed, indicating that recombination and selection play important roles in shaping recent parasite genome evolution. These studies, however, provide only limited information about haplotype variation at local scales. Here we describe the first (to our knowledge) chromosome-wide SNP haplotype and population recombination maps for a global collection of malaria parasites, including the 3D7 isolate, whose genome has been sequenced previously.

Some examples of a bottleneck effect are the American bison in the late 1800s, the Northern elephant seal in the 1890s and the greater prairie chicken during the 19th and 20th centuries. A bottleneck...

The secrets of our genetic heritage are finally being unlocked. The massive scientific effort to sequence the human genome is in fact just the beginning of a long journey as the extraordinary genetic diversity that exists between individuals becomes clear. Work in this field is yielding profound insights into the wider implications for understanding biology, human health and history. It promises much: to understand our evolutionary origins, to define us as individuals, to predict our risk of disease and to more effectively understand, treat and prevent illness. Genetics can help us understand both rare inherited disorders and common multifactorial diseases like asthma, heart diseases and diabetes. Huge investments are being made and great advances have been achieved, but the challenges remain daunting. This book provides an authoritative overview of this topical and very rapidly advancing field of biomedical research. Human Genetic Diversity provides a concise, authoritative overview of human ...

The Cuatro Ciénegas killifish Lucania interioris is an endemic fundulid in the Chihuahuan Desert valley of Cuatro Ciénegas, Coahuila, México. It occurs in 3 major drainage regions of the basin and is limited primarily to naturally fragmented and physicochemically severe habitats of the valley floor. We assessed mitochondrial DNA variation and population genetic structure in L. interioris from 8 populations representative of the entire geographic range of this species, including its distribution within and among major drainage regions (western, central, and southeastern) of the valley. Five populations were invariant, including both populations in the western region (Haplotype A only), whereas 2 haplotypes were observed in each of the remaining populations. Haplotype diversity was low in the central basin (HD = 0.10 and HD = 0.19) and moderate in the southeastern basin (HD = 0.52). Low levels of divergence among haplotypes (0.3%-0.9%), together with high levels of genetic differentiation among regions

That would be over-optimistic. I think Y-chromosomes are not even a quarter of the story, maybe even much less. Worse still, there isnt a more or less fixed ratio of overall genetic diversity that we can confidently deduce from the Y-chromosome. These factors make Y-chromosome practically useless as a tool for measuring overall genetic diversity. We must make genome-wide studies, and whole-genome studies if feasible, to be able to learn something real about the overall genetic diversity and distances of populations. ...

The simultaneous analysis of multiple genomic loci is a powerful approach to studying the effects of population history and natural selection on patterns of genetic variation of a species. By surveying nucleotide sequence polymorphism at 334 randomly distributed genomic regions in 12 accessions of Arabidopsis thaliana, we examined whether a standard neutral model of nucleotide sequence polymorphism is consistent with observed data. The average nucleotide diversity was 0.0071 for total sites and 0.0083 for silent sites. Although levels of diversity are variable among loci, no correlation with local recombination rate was observed, but polymorphism levels were correlated for physically linked loci ...

Numerous rye accessions are stored in ex situ genebanks worldwide. Little is known about the extent of genetic diversity contained in any of them and its relation to contemporary varieties, since to date rye genetic diversity studies had a very limited scope, analyzing few loci and/ or few accessions. Development of high throughput genotyping methods for rye opened the possibility for genome wide characterizations of large accessions sets. In this study we used 1054 Diversity Array Technology (DArT) markers with defined chromosomal location to characterize genetic diversity and population structure in a collection of 379 rye accessions including wild species, landraces, cultivated materials, historical and contemporary rye varieties. Average genetic similarity (GS) coefficients and average polymorphic information content (PIC) values varied among chromosomes. Comparison of chromosome specific average GS within and between germplasm sub-groups indicated regions of chromosomes 1R and 4R as being targeted

This analysis reveals global patterns of genetic variation providing resolution that hasnt been possible with smaller datasets of genetic variation. Exome sequencing is a method for sequencing a subset of the human DNA genome that encodes proteins, known as exons. Humans have about 180,000 exons, constituting about one per cent of the human genome, or approximately 30 million base pairs. A base pair is a unit comprising two nucleotide bases bound to each other that form the building blocks of the DNA double helix. The human genome contains about 3.2 billion nucleotides and about 23,500 genes.. Three-quarters of the known genetic disease-causing variants are located in the protein-coding exome. Given the cost and technical challenges in analysing the all genomic sequence data, researchers are focusing much of their research primarily on exome sequencing.. Interpreting findings is a significant challenge at the heart of genetic sequencing. Each exome contains about 13,500 single nucleotide ...

Water conservation and thermotolerance are crucial to the ecological success of different insect taxa from diverse types of habitats (Hadley, 1994; Willmer et al., 2000; Angilletta, 2009). Several studies have compared desiccation as well as cold and heat resistance levels of Drosophila species of temperate and tropical origin but few studies have investigated genetic variation for stress-related traits (Parsons, 1983; Hoffmann, 2010; Kellermann et al., 2012a; Kellermann et al., 2012b). Kellermann and co-workers have shown low genetic variation for desiccation and cold resistance (estimated as additive genetic variance and narrow sense heritability) in D. bipectinata and four other tropical species, whereas five widespread Drosophila species have been shown to have higher genetic variation (Kellermann et al., 2009). For the two tropical species (D. malerkotliana and D. bipectinata), there are no studies that have investigated the overall levels of genetic variation. However, D. malerkotliana has ...