WorldWideScience

Sample records for classification population genetics

  1. Genetic classification of populations using supervised learning.

    LENUS (Irish Health Repository)

    Bridges, Michael

    2011-01-01

    There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case-control studies and quality control (when participants in a study have been genotyped at different laboratories). This latter application is of particular importance in the era of large scale genome wide association studies, when collections of individuals genotyped at different locations are being merged to provide increased power. The traditional method for detecting structure within a population is some form of exploratory technique such as principal components analysis. Such methods, which do not utilise our prior knowledge of the membership of the candidate populations. are termed unsupervised. Supervised methods, on the other hand are able to utilise this prior knowledge when it is available.In this paper we demonstrate that in such cases modern supervised approaches are a more appropriate tool for detecting genetic differences between populations. We apply two such methods, (neural networks and support vector machines) to the classification of three populations (two from Scotland and one from Bulgaria). The sensitivity exhibited by both these methods is considerably higher than that attained by principal components analysis and in fact comfortably exceeds a recently conjectured theoretical limit on the sensitivity of unsupervised methods. In particular, our methods can distinguish between the two Scottish populations, where principal components analysis cannot. We suggest, on the basis of our results that a supervised learning approach should be the method of choice when classifying individuals into pre-defined populations, particularly in quality control for large scale genome wide association studies.

  2. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4 for classification, population genetics and epidemiology

    Directory of Open Access Journals (Sweden)

    Sajduda Anna

    2006-03-01

    Full Text Available Abstract Background The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1 Unique Events Polymorphism (UEP (2 Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. Results The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown

  3. Population Genetics with Fluctuating Population Sizes

    CERN Document Server

    Chotibut, Thiparat

    2016-01-01

    Standard neutral population genetics theory with a strictly fixed population size has important limitations. An alternative model that allows independently fluctuating population sizes and reproduces the standard neutral evolution is reviewed. We then study a situation such that the competing species are neutral at the equilibrium population size but population size fluctuations nevertheless favor fixation of one species over the other. In this case, a separation of timescales emerges naturally and allows adiabatic elimination of a fast population size variable to deduce the fluctuations-induced selection dynamics near the equilibrium population size. The results highlight the incompleteness of the standard population genetics with a strictly fixed population size.

  4. Population genetics without intraspecific data

    DEFF Research Database (Denmark)

    Thorne, Jeffrey L; Choi, Sang Chul; Yu, Jiaye;

    2007-01-01

    populations, and parameters of interspecific models should have population genetic interpretations. We show, with two examples, how population genetic interpretations can be assigned to evolutionary models. The first example considers the impact of RNA secondary structure on sequence change, and the second...... genetic interpretation. Udgivelsesdato: 2007-Aug...

  5. Towards a genetic classification of uranium deposits

    International Nuclear Information System (INIS)

    As the IAEA's uranium deposit classification is based on the deposit nature and morphology, some deposits which have been formed by very different genetic processes and located in very different geological environments, are grouped according to this classification. In order to build up a reliable genetic classification based on the mechanism at the origin of the formation of the deposit, the author presents the five main categories according to which uranium deposits can be classified: magmatic, hydrothermal, evapotranspiration, syn-sedimentary, and infiltration of meteoric water

  6. Population Genomics and the Statistical Values of Race:An Interdisciplinary Perspective on the Biological Classification of Human Populations and Implications for Clinical Genetic Epidemiological Research

    Directory of Open Access Journals (Sweden)

    Koffi N. Maglo

    2016-02-01

    Full Text Available The biological status and biomedical significance of the concept of race as applied to humans continue to be contentious issues despite the use of advanced statistical and clustering methods to determine continental ancestry. It is thus imperative for researchers to understand the limitations as well as potential uses of the concept of race in biology and biomedicine. This paper deals with the theoretical assumptions behind cluster analysis in human population genomics. Adopting an interdisciplinary approach, it demonstrates that the hypothesis that attributes the clustering of human populations to frictional effects of landform barriers at continental boundaries is empirically incoherent. It then contrasts the scientific status of the cluster and cline constructs in human population genomics, and shows how cluster may be instrumentally produced. It also shows how statistical values of race vindicate Darwin’s argument that race is evolutionarily meaningless. Finally, the paper explains why, due to spatiotemporal parameters, evolutionary forces and socio-cultural factors influencing population structure, continental ancestry may be pragmatically relevant to global and public health genomics. Overall, this work demonstrates that, from a biological systematic and evolutionary taxonomical perspective, human races/continental groups or clusters have no natural meaning or objective biological reality. In fact, the utility of racial categorizations in research and in clinics can be explained by spatiotemporal parameters, socio-cultural factors and evolutionary forces affecting disease causation and treatment response.

  7. Population Genomics and the Statistical Values of Race: An Interdisciplinary Perspective on the Biological Classification of Human Populations and Implications for Clinical Genetic Epidemiological Research.

    Science.gov (United States)

    Maglo, Koffi N; Mersha, Tesfaye B; Martin, Lisa J

    2016-01-01

    The biological status and biomedical significance of the concept of race as applied to humans continue to be contentious issues despite the use of advanced statistical and clustering methods to determine continental ancestry. It is thus imperative for researchers to understand the limitations as well as potential uses of the concept of race in biology and biomedicine. This paper deals with the theoretical assumptions behind cluster analysis in human population genomics. Adopting an interdisciplinary approach, it demonstrates that the hypothesis that attributes the clustering of human populations to "frictional" effects of landform barriers at continental boundaries is empirically incoherent. It then contrasts the scientific status of the "cluster" and "cline" constructs in human population genomics, and shows how cluster may be instrumentally produced. It also shows how statistical values of race vindicate Darwin's argument that race is evolutionarily meaningless. Finally, the paper explains why, due to spatiotemporal parameters, evolutionary forces, and socio-cultural factors influencing population structure, continental ancestry may be pragmatically relevant to global and public health genomics. Overall, this work demonstrates that, from a biological systematic and evolutionary taxonomical perspective, human races/continental groups or clusters have no natural meaning or objective biological reality. In fact, the utility of racial categorizations in research and in clinics can be explained by spatiotemporal parameters, socio-cultural factors, and evolutionary forces affecting disease causation and treatment response. PMID:26925096

  8. Kingman and mathematical population genetics

    OpenAIRE

    Ewens, Warren J.; Watterson, Geoffrey A.

    2010-01-01

    Mathematical population genetics is only one of Kingman's many research interests. Nevertheless, his contribution to this field has been crucial, and moved it in several important new directions. Here we outline some aspects of his work which have had a major influence on population genetics theory.

  9. Population Characteristics in Forensic Genetics

    OpenAIRE

    Faltus, Václav

    2007-01-01

    The aim of this paper is to present some methods used in forensic genetics. Forensic genetics is only one part of a wide spectrum of sciences called forensics. It includes identification of victims of natural disasters, mass transportation accidents and industry accidents. It also includes identification of offenders of a crime and determination of paternity. Our current work involves analysis of the genetic data from the Czech population. Therefore and in concordance with other international...

  10. Genetic diversity in populations

    Czech Academy of Sciences Publication Activity Database

    Martínková, Natália; Zemanová, Barbora

    Brno: Akademické nakladatelství CERM, 2011 - (Jarkovský, J.), s. 21-27 ISBN 978-80-7204-756-7. [International Summer School on Computational Biology /7./. Lednice (CZ), 15.09.2011-17.09.2011] Institutional research plan: CEZ:AV0Z60930519 Keywords : nucleotide diversity * haplotype diversity * heterozygosity * Hardy-Weinberg equilibrium Subject RIV: EB - Genetics ; Molecular Biology

  11. [Population genetics of plant pathogens].

    Science.gov (United States)

    Zhu, Wen; Zhan, Jia-Sui

    2012-02-01

    Comparing to natural ecosystems, the evolution of plant pathogens in agricultural ecosystems is generally faster due to high-density monocultures, large-scale application of agrochemicals, and international trade in agricultural products. Knowledge of the population genetics and evolutionary biology of plant pathogens is necessary to understand disease epidemiology, effectively breed and use resistant cultivars, and control plant diseases. In this article, we outlined the aims of population genetic studies in plant pathogens, discuss contributions of five evolutionary forces (i.e., mutation, gene flow, recombination, random genetic drift, and natural selection) to origin, maintenance, and distribution of genetic variation in time and space, and gave an overview of current research status in this field. PMID:22382057

  12. Genetic Structure of Chimpanzee Populations

    OpenAIRE

    Celine Becquet; Nick Patterson; Anne C Stone; Molly Przeworski; David Reich

    2007-01-01

    Author Summary Common chimpanzees have been traditionally classified into three populations: western, central, and eastern. While the morphological or behavioral differences are very small, genetic studies of mitochondrial DNA and the Y chromosome have supported the geography-based designations. To obtain a crisp picture of chimpanzee population structure, we gather far more data than previously available: 310 microsatellite markers genotyped in 78 common chimpanzees and six bonobos, allowing...

  13. Mining Online Store Client Assessment Classification Rules with Genetic Algorithms

    OpenAIRE

    Galinina, A; Paršutins, S

    2011-01-01

    The paper presents the results of the research into algorithms that are not meant to mine classification rules, yet they contain all the necessary functions which allow us to use them for mining classification rules such as Genetic algorithm (GA). The main task of the research is associated with the application of GA to classification rule mining. A classic GA was modified to match the chosen classification task and was compared with other popular classification algorithms – JRip, J48 and Nai...

  14. Stochastic problems in population genetics

    CERN Document Server

    Maruyama, Takeo

    1977-01-01

    These are" notes based on courses in Theoretical Population Genetics given at the University of Texas at Houston during the winter quarter, 1974, and at the University of Wisconsin during the fall semester, 1976. These notes explore problems of population genetics and evolution involving stochastic processes. Biological models and various mathematical techniques are discussed. Special emphasis is given to the diffusion method and an attempt is made to emphasize the underlying unity of various problems based on the Kolmogorov backward equation. A particular effort was made to make the subject accessible to biology students who are not familiar with stochastic processes. The references are not exhaustive but were chosen to provide a starting point for the reader interested in pursuing the subject further. Acknowledgement I would like to use this opportunity to express my thanks to Drs. J. F. Crow, M. Nei and W. J. Schull for their hospitality during my stays at their universities. I am indebted to Dr. M. Kimura...

  15. Feature Selection and Molecular Classification of Cancer Using Genetic Programming

    Directory of Open Access Journals (Sweden)

    Jianjun Yu

    2007-04-01

    Full Text Available Despite important advances in microarray-based molecular classification of tumors, its application in clinical settings remains formidable. This is in part due to the limitation of current analysis programs in discovering robust biomarkers and developing classifiers with a practical set of genes. Genetic programming (GP is a type of machine learning technique that uses evolutionary algorithm to simulate natural selection as well as population dynamics, hence leading to simple and comprehensible classifiers. Here we applied GP to cancer expression profiling data to select feature genes and build molecular classifiers by mathematical integration of these genes. Analysis of thousands of GP classifiers generated for a prostate cancer data set revealed repetitive use of a set of highly discriminative feature genes, many of which are known to be disease associated. GP classifiers often comprise five or less genes and successfully predict cancer types and subtypes. More importantly, GP classifiers generated in one study are able to predict samples from an independent study, which may have used different microarray platforms. In addition, GP yielded classification accuracy better than or similar to conventional classification methods. Furthermore, the mathematical expression of GP classifiers provides insights into relationships between classifier genes. Taken together, our results demonstrate that GP may be valuable for generating effective classifiers containing a practical set of genes for diagnostic/ prognostic cancer classification.

  16. Population genetics and cryptic species

    International Nuclear Information System (INIS)

    Does the definition of a species matter for pest management purposes? Taxonomists provide us with tools - usually morphological characters - to identify a group of organisms that we call a species. The implication of this identification is that all of the individuals that fit the provided description are members of the species in question. The taxonomists have considered the range of variation among individuals in defining the species, but this variation is often forgotten when we take the concept of species to the level of management. Just as there is morphological variation among individuals, there is also variation in practically any character we might imagine, which has implications for the short and long term success of our management tactics. The rich literature on insecticide resistance should be a constant reminder of the fact that the pressure on pest survival and reproduction applied by our management approaches frequently leads to evolutionary changes within the pest species. The degree of variation within a particular species is a defining characteristic of that species. This level of variability may have very important implications for successful management, so it is very important to measure variation and, whenever possible, the genetic basis of that variation, in a target species. Population genetic approaches can provide evidence of genetic structure (or lack thereof) among populations of a species. These types of data can be used to discuss the movement of pest populations on a local or global scale. In other cases, we may have a complex of species that share some, but not all, characteristics. Species complexes that share morphological characters (i.e., cannot be easily distinguished) but not biological characters are referred to as sibling or cryptic species

  17. Genetic variation and population structure in native Americans.

    Directory of Open Access Journals (Sweden)

    Sijia Wang

    2007-11-01

    Full Text Available We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians--signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1 a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2 a relative lack of differentiation between Mesoamerican and Andean populations, (3 a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4 a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.

  18. [Genetic structure of natural populations

    International Nuclear Information System (INIS)

    Our efforts in the first eight months were concentrated in obtaining a genomic clone of the copper-zinc superoxide dismutase (SOD) in Drosophila melanogaster and other Drosophila species. This we have now successfully accomplished. We seek to understand the role of SOD in radioresistance; how genetic variation in this enzyme is maintained in populations; and relevant aspects of its evolution that may contribute to these goals as well as to an understanding of molecular evolution in general. To accomplish these goals we are undertaking the following experiments: cloning and sequencing of (at least) one F allele, one S allele, and the null allele for SOD; cloning and sequencing SOD from species related to D. melanogaster; and cloning and sequencing the SOD gene from several independently sampled S and F alleles in D. melanogaster. We are also preparing to test the radioprotective effects of SOD. 67 refs

  19. Genetic variability and population genetic structure

    Czech Academy of Sciences Publication Activity Database

    Hájková, Petra

    Banská Bystrica : Faculty of Natural Sciences, Matthias Belius University, 2010 - (Urban, P.; Kadlečík, J.; Topercer, J.; Kadlečíková, Z.), s. 54-55 ISBN 978-80-557-0030-4 R&D Projects: GA AV ČR KJB600930804 Institutional research plan: CEZ:AV0Z60930519 Keywords : Eurasian otter * genetics Subject RIV: EG - Zoology

  20. Genetic Variation Among White Croaker Populations

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    To investigate the genetic structures and differentiation of different wild populations of white croaker (Pennahia argentata), horizontal starch gel electrophoresis was performed on 133 individuals collected from five different locations in China and Japan. The eleven enzyme systems revealed 15 loci, of which eleven were polymorphic. The percentage ofpolymorphic loci of white croaker populations varied from 6.67% to 53.33%; the mean observed and expected heterozygosity ranged from 0.0033 to 0.0133and 0.0032 to 0.0191, respectively. The expected heterozygosity revealed a low genetic variability for white croaker in comparison with other marine fishes. The genetic distances between populations ranged from 0.00005 to 0.00026. A weak differentiation was observed within each clade and between clades; and no significant differences in gene frequencies among populations were observed in white croaker. Among the five populations, three Chinese populations showed more genetic diversity than that in Japanese populations.

  1. Discovering Fuzzy Censored Classification Rules (Fccrs: A Genetic Algorithm Approach

    Directory of Open Access Journals (Sweden)

    Renu Bala

    2012-07-01

    Full Text Available Classification Rules (CRs are often discovered in the form of ‘If-Then’ Production Rules (PRs. PRs, being high level symbolic rules, are comprehensible and easy to implement. However, they are not capable of dealing with cognitive uncertainties like vagueness and ambiguity imperative to real word decision making situations. Fuzzy Classification Rules (FCRs based on fuzzy logic provide a framework for a flexible human like reasoning involving linguistic variables. Moreover, a classification system consisting of simple ‘If-Then’ rules is not competent in handling exceptional circumstances. In this paper, we propose a Genetic Algorithm approach to discover Fuzzy Censored Classification Rules (FCCRs. A FCCR is a Fuzzy Classification Rule (FCRs augmented with censors. Here, censors are exceptional conditions in which the behaviour of a rule gets modified. The proposed algorithm works in two phases. In the first phase, the Genetic Algorithm discovers Fuzzy Classification Rules. Subsequently, these Fuzzy Classification Rules are mutated to produce FCCRs in the second phase. The appropriate encoding scheme, fitness function and genetic operators are designed for the discovery of FCCRs. The proposed approach for discovering FCCRs is then illustrated on a synthetic dataset.

  2. Discovering Fuzzy Censored Classification Rules (Fccrs: A Genetic Algorithm Approach

    Directory of Open Access Journals (Sweden)

    Renu Bala

    2012-08-01

    Full Text Available Classification Rules (CRs are often discovered in the form of ‘If-Then’ Production Rules (PRs. PRs, beinghigh level symbolic rules, are comprehensible and easy to implement. However, they are not capable ofdealing with cognitive uncertainties like vagueness and ambiguity imperative to real word decision makingsituations. Fuzzy Classification Rules (FCRs based on fuzzy logic provide a framework for a flexiblehuman like reasoning involving linguistic variables. Moreover, a classification system consisting of simple‘If-Then’ rules is not competent in handling exceptional circumstances. In this paper, we propose aGenetic Algorithm approach to discover Fuzzy Censored Classification Rules (FCCRs. A FCCR is aFuzzy Classification Rule (FCRs augmented with censors. Here, censors are exceptional conditions inwhich the behaviour of a rule gets modified. The proposed algorithm works in two phases. In the firstphase, the Genetic Algorithm discovers Fuzzy Classification Rules. Subsequently, these FuzzyClassification Rules are mutated to produce FCCRs in the second phase. The appropriate encodingscheme, fitness function and genetic operators are designed for the discovery of FCCRs. The proposedapproach for discovering FCCRs is then illustrated on a synthetic dataset.

  3. Using Genetic Algorithms for Texts Classification Problems

    Directory of Open Access Journals (Sweden)

    A. A. Shumeyko

    2009-01-01

    Full Text Available The avalanche quantity of the information developed by mankind has led to concept of automation of knowledge extraction – Data Mining ([1]. This direction is connected with a wide spectrum of problems - from recognition of the fuzzy set to creation of search machines. Important component of Data Mining is processing of the text information. Such problems lean on concept of classification and clustering ([2]. Classification consists in definition of an accessory of some element (text to one of in advance created classes. Clustering means splitting a set of elements (texts on clusters which quantity are defined by localization of elements of the given set in vicinities of these some natural centers of these clusters. Realization of a problem of classification initially should lean on the given postulates, basic of which – the aprioristic information on primary set of texts and a measure of affinity of elements and classes.

  4. Discovering comprehensible classification rules with a genetic algorithm

    OpenAIRE

    Fidelis, M.V.; Lopes, Heitor S.; Freitas, Alex. A.

    2000-01-01

    Presents a classification algorithm based on genetic algorithms (GAs) that discovers comprehensible IF-THEN rules, in the spirit of data mining. The proposed GA has a flexible chromosome encoding, where each chromosome corresponds to a classification rule. Although the number of genes (the genotype) is fixed, the number of rule conditions (the phenotype) is variable. The GA also has specific mutation operators for this chromosome encoding. The algorithm was evaluated on two public-domain real...

  5. The Etruscans: a population-genetic study

    DEFF Research Database (Denmark)

    Vernesi, Cristiano; Caramelli, David; Dupanloup, Isabelle;

    2004-01-01

    by modern DNA might have occurred. On the basis of data from the remaining 30 individuals, the Etruscans appeared as genetically variable as modern populations. No significant heterogeneity emerged among archaeological sites or time periods, suggesting that different Etruscan communities shared not...... only a culture but also a mitochondrial gene pool. Genetic distances and sequence comparisons show closer evolutionary relationships with the eastern Mediterranean shores for the Etruscans than for modern Italian populations. All mitochondrial lineages observed among the Etruscans appear typically...

  6. Population genetics of African ungulates

    DEFF Research Database (Denmark)

    Lorenzen, Eline

    Molecular genetic techniques were used to gain insights into the evolutionary forces that have shaped the present day diversity of African savannah ungu-lates, which constitute the most species-rich mega faunal assemblage on earth. The studies included in this thesis represent individual species......-specific data sets, which are used to elucidate evolutionary processes of importance to the savannah ungulate community. Patterns of DNA variation were analyzed to assess the genetic signatures of Pleistocene refugia and investigate aspects of speciation, intraspecific structuring, hybridization, and historic...

  7. Population Characteristics in Forensic Genetics

    Czech Academy of Sciences Publication Activity Database

    Faltus, Václav

    Praha: Ústav informatiky AV ČR, v. v. i. & MATFYZPRESS, 2007 - (Hakl, F.), s. 8-12 ISBN 978-80-7378-019-7. [Doktorandské dny '07 Ústavu informatiky AV ČR, v. v. i.. Malá Úpa (CZ), 17.09.2007-19.09.2007] R&D Projects: GA MŠk(CZ) 1M06014 Institutional research plan: CEZ:AV0Z10300504 Keywords : forensic genetics * identification * STR * statistical methods Subject RIV: IN - Informatics, Computer Science

  8. Genetic structure of forensic populations.

    OpenAIRE

    Morton, N. E.

    1992-01-01

    DNA-based identification depends on the probability that two different individuals have the same phenotype, which is given by kinship theory. Together with the large and consistent body of evidence on human population structure, kinship theory provides a sound basis for forensic use of DNA markers.

  9. The geometry of population genetics

    CERN Document Server

    Akin, Ethan

    1979-01-01

    The differential equations which model the action of selection and recombination are nonlinear equations which are impossible to It is even difficult to describe in general the solve explicitly. Recently, Shahshahani began using qualitative behavior of solutions. differential geometry to study these equations [28]. with this mono­ graph I hope to show that his ideas illuminate many aspects of pop­ ulation genetics. Among these are his proof and clarification of Fisher's Fundamental Theorem of Natural Selection and Kimura's Maximum Principle and also the effect of recombination on entropy. We also discover the relationship between two classic measures of 2 genetic distance: the x measure and the arc-cosine measure. There are two large applications. The first is a precise definition of the biological concept of degree of epistasis which applies to general (i.e. frequency dependent) forms of selection. The second is the unexpected appearance of cycling. We show that cycles can occur in the two-locus-two-allele...

  10. The Genetic Deafness in Chinese Population

    Institute of Scientific and Technical Information of China (English)

    LIU Xuezhong; Ouyang Xiaomei; Denise Yan

    2006-01-01

    Deafness is an etiologically heterogeneous trait with many known genetic, environmental causes or a combination thereof. The identification of more than 120 independent genes for deafness has provided profound new insights into the pathophysiology of hearing. However, recent findings indicate that a large proportion of both syndromic and nonsyndromic forms of deafness in Chinese population are caused by a small number of mutations.This review is focused on syndromic and nonsyndromic deafness as well as on the latest information linking inherited mitochondrial pathologies to a variety of etiologies of sensorineural deafness in Chinese population. Better understanding of the genetic causes of deafness in Chinese population is important for accurate genetics counseling and early diagnosis for timely intervention and treatment options.

  11. Genetic variation in cultivated Rheum tanguticum populations

    Directory of Open Access Journals (Sweden)

    Yanping Hu

    2014-09-01

    Full Text Available To examine whether cultivation reduced genetic variation in the important Chinese medicinal plant Rheum tanguticum, the levels and distribution of genetic variation were investigated using ISSR markers. Fifty-eight R. tanguticum individuals from five cultivated populations were studied. Thirteen primers were used and a total of 320 DNA bands were scored. High levels of genetic diversity were detected in cultivated R. tanguticum (PPB = 82.19, H = 0.2498, H B = 0.3231, I = 0.3812 and could be explained by the outcrossing system, as well as long-lived and human-mediated seed exchanges. Analysis of molecular variance (AMOVA showed that more genetic variation was found within populations (76.1% than among them (23.9%. This was supported by the coefficient of gene differentiation (Gst = 0.2742 and Bayesian analysis (θB = 0.1963. The Mantel test revealed no significant correlation between genetic and geographic distances among populations (r = 0.1176, p = 0.3686. UPGMA showed that the five cultivated populations were separated into three clusters, which was in good accordance with the results provided by the Bayesian software STRUCTURE (K = 3. A short domestication history and no artificial selection may be an effective way of maintaining and conserving the gene pools of wild R. tanguticum.

  12. Population extinction and the genetics of adaptation.

    Science.gov (United States)

    Orr, H Allen; Unckless, Robert L

    2008-08-01

    Theories of adaptation typically ignore the effect of environmental change on population size. But some environmental challenges--challenges to which populations must adapt--may depress absolute fitness below 1, causing populations to decline. Under this scenario, adaptation is a race; beneficial alleles that adapt a population to the new environment must sweep to high frequency before the population becomes extinct. We derive simple, though approximate, solutions to the probability of successful adaptation (population survival) when adaptation involves new mutations, the standing genetic variation, or a mixture of the two. Our results show that adaptation to such environmental challenges can be difficult when relying on new mutations at one or a few loci, and populations will often decline to extinction. PMID:18662122

  13. Population genetic structure of Aldabra giant tortoises

    OpenAIRE

    Balmer, Oliver; Ciofi, Claudio; Galbraith, David A.; Swingland, Ian R.; Zug, George R.; Caccone, Adalgisa

    2011-01-01

    Evolution of population structure on islands is the result of physical processes linked to volcanism, orogenic events, changes in sea level, as well as habitat variation. We assessed patterns of genetic structure in the giant tortoise of the Aldabra atoll, where previous ecological studies suggested population subdivisions as a result of landscape discontinuity due to unsuitable habitat and island separation. Analysis of mitochondrial DNA (mtDNA) control region sequences and allelic variation...

  14. Population genetic analysis of ascertained SNP data

    OpenAIRE

    Nielsen Rasmus

    2004-01-01

    Abstract The large single nucleotide polymorphism (SNP) typing projects have provided an invaluable data resource for human population geneticists. Almost all of the available SNP loci, however, have been identified through a SNP discovery protocol that will influence the allelic distributions in the sampled loci. Standard methods for population genetic analysis based on the available SNP data will, therefore, be biased. This paper discusses the effect of this ascertainment bias on allelic di...

  15. Genetic Heterogeneity in Algerian Human Populations

    Science.gov (United States)

    Deba, Tahria; Calafell, Francesc; Benhamamouch, Soraya; Comas, David

    2015-01-01

    The demographic history of human populations in North Africa has been characterized by complex processes of admixture and isolation that have modeled its current gene pool. Diverse genetic ancestral components with different origins (autochthonous, European, Middle Eastern, and sub-Saharan) and genetic heterogeneity in the region have been described. In this complex genetic landscape, Algeria, the largest country in Africa, has been poorly covered, with most of the studies using a single Algerian sample. In order to evaluate the genetic heterogeneity of Algeria, Y-chromosome, mtDNA and autosomal genome-wide makers have been analyzed in several Berber- and Arab-speaking groups. Our results show that the genetic heterogeneity found in Algeria is not correlated with geography or linguistics, challenging the idea of Berber groups being genetically isolated and Arab groups open to gene flow. In addition, we have found that external sources of gene flow into North Africa have been carried more often by females than males, while the North African autochthonous component is more frequent in paternally transmitted genome regions. Our results highlight the different demographic history revealed by different markers and urge to be cautious when deriving general conclusions from partial genomic information or from single samples as representatives of the total population of a region. PMID:26402429

  16. Genetic classification and molecular mechanisms of primary dystonia

    Institute of Scientific and Technical Information of China (English)

    Xueping Chen; Huifang Shang; Zuming Luo

    2008-01-01

    BACKGROUND: Primary dystonia is a heterogeneous disease, with a complex genetic basis. In previous studies, primary dystonia was classified according to age of onset, involved regions, and other clinical characteristics. With the development of molecular genetics, new virulence genes and sites have been discovered. Therefore, there is a gradual understanding of the various forms of dystonia, based on new viewpoints. There are 15 subtypes of dystonia, based on the molecular level, i.e., DYT1 to DYT15. OBJECTIVE: To analyze the genetic development of dystonia in detail, and to further investigate molecular mechanisms of dystonia. RETRIEVAL STRATEGY: A computer-based online search was conducted in PubMed for English language publications containing the keywords "dystonia and genetic" from January 1980 to March 2007. There were 105 articles in total. Inclusion criteria: ① the contents of the articles should closely address genetic classification and molecular mechanisms of primary dystonia; ② the articles published in recent years or in high-impact journals took preference. Exclusion criteria: duplicated articles. LITERATURE EVALUATION: The selected articles were on genetic classification and molecular genetics mechanism of primary dystonia. Of those, 27 were basic or clinical studies. DATA SYNTHESIS: ① Dystonia is a heterogeneous disease, with a complex genetic basis. According to the classification of the Human Genome Organization, there are 15 dystonia subtypes, based on genetics, i.e., DYT1-DYT15,including primary dystonia, dystonia plus syndrome, degeneration plus dystonia, and paroxysmal dyskinesia plus dystonia. ② To date, the chromosomes of 13 subtypes have been localized; however, DYT2 and DYT4 remain unclear. Six subtypes have been located within virulence genes. Specifically, torsinA gene expression results in the DYT1 genotype; autosomal dominant GTP cyclohydrolase I gene expression and recessive tyrosine hydroxylase expression result in the DYT5

  17. The population genetics of the Jewish people.

    Science.gov (United States)

    Ostrer, Harry; Skorecki, Karl

    2013-02-01

    Adherents to the Jewish faith have resided in numerous geographic locations over the course of three millennia. Progressively more detailed population genetic analysis carried out independently by multiple research groups over the past two decades has revealed a pattern for the population genetic architecture of contemporary Jews descendant from globally dispersed Diaspora communities. This pattern is consistent with a major, but variable component of shared Near East ancestry, together with variable degrees of admixture and introgression from the corresponding host Diaspora populations. By combining analysis of monoallelic markers with recent genome-wide variation analysis of simple tandem repeats, copy number variations, and single-nucleotide polymorphisms at high density, it has been possible to determine the relative contribution of sex-specific migration and introgression to map founder events and to suggest demographic histories corresponding to western and eastern Diaspora migrations, as well as subsequent microevolutionary events. These patterns have been congruous with the inferences of many, but not of all historians using more traditional tools such as archeology, archival records, linguistics, comparative analysis of religious narrative, liturgy and practices. Importantly, the population genetic architecture of Jews helps to explain the observed patterns of health and disease-relevant mutations and phenotypes which continue to be carefully studied and catalogued, and represent an important resource for human medical genetics research. The current review attempts to provide a succinct update of the more recent developments in a historical and human health context. PMID:23052947

  18. Great ape genetic diversity and population history

    DEFF Research Database (Denmark)

    Prado-Martinez, Javier; Sudmant, Peter H.; Kidd, Jeffrey M.;

    2013-01-01

    species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central...

  19. A population genetics model of linkage disequilibrium in admixed populations

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Understanding linkage disequilibrium (LD) created in admixed population and the rate of decay in the disequilibrium over evolution is an important subject in population genetics theory and in disease gene mapping in human populations. The present study represents the theoretical investigation of effects of gene frequencies, levels of LD and admixture proportions of donor populations on the evolutionary dynamics of the LD of the admixed population. We examined the conditions under which the admixed population reached linkage equilibrium or the peak level of the LD. The study reveals the inappropriateness in approximating the dynamics of the LD generated by population admixture by the commonly used formula in literature. An appropriate equation for the dynamics is proposed. The distinct feature of the newly suggested formula is that the value of the nonlinear component of the LD remains constant in the first generation of the population evolution. Comparison between the predicted disequilibrium dynamics shows that the error will be caused by using the old formula, and thus resulting in a misguidance in using the evolutionary information of the admixed population in gene mapping.

  20. Population genetics of malaria resistance in humans.

    Science.gov (United States)

    Hedrick, P W

    2011-10-01

    The high mortality and widespread impact of malaria have resulted in this disease being the strongest evolutionary selective force in recent human history, and genes that confer resistance to malaria provide some of the best-known case studies of strong positive selection in modern humans. I begin by reviewing JBS Haldane's initial contribution to the potential of malaria genetic resistance in humans. Further, I discuss the population genetics aspects of many of the variants, including globin, G6PD deficiency, Duffy, ovalocytosis, ABO and human leukocyte antigen variants. Many of the variants conferring resistance to malaria are 'loss-of-function' mutants and appear to be recent polymorphisms from the last 5000-10 000 years or less. I discuss estimation of selection coefficients from case-control data and make predictions about the change for S, C and G6PD-deficiency variants. In addition, I consider the predicted joint changes when the two β-globin alleles S and C are both variable in the same population and when there is a variation for α-thalassemia and S, two unlinked, but epistatic variants. As more becomes known about genes conferring genetic resistance to malaria in humans, population genetics approaches can contribute both to investigating past selection and predicting the consequences in future generations for these variants. PMID:21427751

  1. Deep Learning for Population Genetic Inference.

    Directory of Open Access Journals (Sweden)

    Sara Sheehan

    2016-03-01

    Full Text Available Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data to the output (e.g., population genetic parameters of interest. We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history. Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme.

  2. Extensive population genetic structure in the giraffe

    Directory of Open Access Journals (Sweden)

    Grether Gregory F

    2007-12-01

    Full Text Available Abstract Background A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation. Results By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations. Conclusion Such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate in situ and ex situ management, not only of pelage morphs, but also of local populations.

  3. Deep Learning for Population Genetic Inference.

    Science.gov (United States)

    Sheehan, Sara; Song, Yun S

    2016-03-01

    Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme. PMID:27018908

  4. Restoration of coral populations in light of genetic diversity estimates

    OpenAIRE

    Shearer, T. L.; Porto, I; Zubillaga, A. L.

    2009-01-01

    Due to the importance of preserving the genetic integrity of populations, strategies to restore damaged coral reefs should attempt to retain the allelic diversity of the disturbed population; however, genetic diversity estimates are not available for most coral populations. To provide a generalized estimate of genetic diversity (in terms of allelic richness) of scleractinian coral populations, the literature was surveyed for studies describing the genetic structure of coral populations using ...

  5. Approximate Bayesian computation in population genetics.

    OpenAIRE

    Beaumont, Mark A; Zhang, Wenyang; Balding, David J.

    2002-01-01

    We propose a new method for approximate Bayesian statistical inference on the basis of summary statistics. The method is suited to complex problems that arise in population genetics, extending ideas developed in this setting by earlier authors. Properties of the posterior distribution of a parameter, such as its mean or density curve, are approximated without explicit likelihood calculations. This is achieved by fitting a local-linear regression of simulated parameter values on simulated summ...

  6. Human genetics: lessons from Quebec populations.

    Science.gov (United States)

    Scriver, C R

    2001-01-01

    The population of Quebec, Canada (7.3 million) contains approximately 6 million French Canadians; they are the descendants of approximately 8500 permanent French settlers who colonized Nouvelle France between 1608 and 1759. Their well-documented settlements, internal migrations, and natural increase over four centuries in relative isolation (geographic, linguistic, etc.) contain important evidence of social transmission of demographic behavior that contributed to effective family size and population structure. This history is reflected in at least 22 Mendelian diseases, occurring at unusually high prevalence in its subpopulations. Immigration of non-French persons during the past 250 years has given the Quebec population further inhomogeneity, which is apparent in allelic diversity at various loci. The histories of Quebec's subpopulations are, to a great extent, the histories of their alleles. Rare pathogenic alleles with high penetrance and associated haplotypes at 10 loci (CFTR, FAH, HBB, HEXA, LDLR, LPL, PAH, PABP2, PDDR, and SACS) are expressed in probands with cystic fibrosis, tyrosinemia, beta-thalassemia, Tay-Sachs, familial hypercholesterolemia, hyperchylomicronemia, PKU, oculopharyngeal muscular dystrophy, pseudo vitamin D deficiency rickets, and spastic ataxia of Charlevoix-Saguenay, respectively) reveal the interpopulation and intrapopulation genetic diversity of Quebec. Inbreeding does not explain the clustering and prevalence of these genetic diseases; genealogical reconstructions buttressed by molecular evidence point to founder effects and genetic drift in multiple instances. Genealogical estimates of historical meioses and analysis of linkage disequilibrium show that sectors of this young population are suitable for linkage disequilibrium mapping of rare alleles. How the population benefits from what is being learned about its structure and how its uniqueness could facilitate construction of a genomic map of linkage disequilibrium are discussed

  7. Bacterial Population Genetics in a Forensic Context

    Energy Technology Data Exchange (ETDEWEB)

    Velsko, S P

    2009-11-02

    This report addresses the recent Department of Homeland Security (DHS) call for a Phase I study to (1) assess gaps in the forensically relevant knowledge about the population genetics of eight bacterial agents of concern, (2) formulate a technical roadmap to address those gaps, and (3) identify new bioinformatics tools that would be necessary to analyze and interpret population genetic data in a forensic context. The eight organisms that were studied are B. anthracis, Y. pestis, F. tularensis, Brucella spp., E. coli O157/H7, Burkholderia mallei, Burkholderia pseudomallei, and C. botulinum. Our study focused on the use of bacterial population genetics by forensic investigators to test hypotheses about the possible provenance of an agent that was used in a crime or act of terrorism. Just as human population genetics underpins the calculations of match probabilities for human DNA evidence, bacterial population genetics determines the level of support that microbial DNA evidence provides for or against certain well-defined hypotheses about the origins of an infecting strain. Our key findings are: (1) Bacterial population genetics is critical for answering certain types of questions in a probabilistic manner, akin (but not identical) to 'match probabilities' in DNA forensics. (2) A basic theoretical framework for calculating likelihood ratios or posterior probabilities for forensic hypotheses based on microbial genetic comparisons has been formulated. This 'inference-on-networks' framework has deep but simple connections to the population genetics of mtDNA and Y-STRs in human DNA forensics. (3) The 'phylogeographic' approach to identifying microbial sources is not an adequate basis for understanding bacterial population genetics in a forensic context, and has limited utility, even for generating 'leads' with respect to strain origin. (4) A collection of genotyped isolates obtained opportunistically from international locations

  8. The paradoxical population genetics of Plasmodium falciparum.

    Science.gov (United States)

    Hartl, Daniel L; Volkman, Sarah K; Nielsen, Kaare M; Barry, Alyssa E; Day, Karen P; Wirth, Dyann F; Winzeler, Elizabeth A

    2002-06-01

    Among the leading causes of death in African children is cerebral malaria caused by the parasitic protozoan Plasmodium falciparum. Endemic forms of this disease are thought to have originated in central Africa 5000-10000 years ago, coincident with the innovation of slash-and-burn agriculture and the diversification of the Anopheles gambiae complex of mosquito vectors. Population genetic studies of P. falciparum have yielded conflicting results. Some evidence suggests that today's population includes multiple ancient lineages pre-dating human speciation. Other evidence suggests that today's population derives from only one, or a small number, of these ancient lineages. Resolution of this issue is important for the evaluation of the long-term efficacy of drug and immunological control strategies. PMID:12036741

  9. A novel hybrid classification model of genetic algorithms, modified k-Nearest Neighbor and developed backpropagation neural network.

    Directory of Open Access Journals (Sweden)

    Nader Salari

    Full Text Available Among numerous artificial intelligence approaches, k-Nearest Neighbor algorithms, genetic algorithms, and artificial neural networks are considered as the most common and effective methods in classification problems in numerous studies. In the present study, the results of the implementation of a novel hybrid feature selection-classification model using the above mentioned methods are presented. The purpose is benefitting from the synergies obtained from combining these technologies for the development of classification models. Such a combination creates an opportunity to invest in the strength of each algorithm, and is an approach to make up for their deficiencies. To develop proposed model, with the aim of obtaining the best array of features, first, feature ranking techniques such as the Fisher's discriminant ratio and class separability criteria were used to prioritize features. Second, the obtained results that included arrays of the top-ranked features were used as the initial population of a genetic algorithm to produce optimum arrays of features. Third, using a modified k-Nearest Neighbor method as well as an improved method of backpropagation neural networks, the classification process was advanced based on optimum arrays of the features selected by genetic algorithms. The performance of the proposed model was compared with thirteen well-known classification models based on seven datasets. Furthermore, the statistical analysis was performed using the Friedman test followed by post-hoc tests. The experimental findings indicated that the novel proposed hybrid model resulted in significantly better classification performance compared with all 13 classification methods. Finally, the performance results of the proposed model was benchmarked against the best ones reported as the state-of-the-art classifiers in terms of classification accuracy for the same data sets. The substantial findings of the comprehensive comparative study revealed that

  10. Population genetic inference from genomic sequence variation

    OpenAIRE

    Pool, John E.; Hellmann, Ines; Jeffrey D. Jensen; Nielsen, Rasmus

    2010-01-01

    Population genetics has evolved from a theory-driven field with little empirical data into a data-driven discipline in which genome-scale data sets test the limits of available models and computational analysis methods. In humans and a few model organisms, analyses of whole-genome sequence polymorphism data are currently under way. And in light of the falling costs of next-generation sequencing technologies, such studies will soon become common in many other organisms as well. Here, we assess...

  11. Genetic Programming for Document Segmentation and Region Classification Using Discipulus

    Directory of Open Access Journals (Sweden)

    Priyadharshini N

    2013-02-01

    Full Text Available Document segmentation is a method of rending the document into distinct regions. A document is an assortment of information and a standard mode of conveying information to others. Pursuance of data from documents involves ton of human effort, time intense and might severely prohibit the usage of data systems. So, automatic information pursuance from the document has become a big issue. It is been shown that document segmentation will facilitate to beat such problems. This paper proposes a new approach to segment and classify the document regions as text, image, drawings and table. Document image is divided into blocks using Run length smearing rule and features are extracted from every blocks. Discipulus tool has been used to construct the Genetic programming based classifier model and located 97.5% classification accuracy.

  12. What is new in genetics and osteogenesis imperfecta classification?

    Directory of Open Access Journals (Sweden)

    Eugênia R. Valadares

    2014-12-01

    Full Text Available OBJECTIVE: Literature review of new genes related to osteogenesis imperfecta (OI and update of its classification. SOURCES: Literature review in the PubMed and OMIM databases, followed by selection of relevant references. SUMMARY OF THE FINDINGS: In 1979, Sillence et al. developed a classification of OI subtypes based on clinical features and disease severity: OI type I, mild, common, with blue sclera; OI type II, perinatal lethal form; OI type III, severe and progressively deforming, with normal sclera; and OI type IV, moderate severity with normal sclera. Approximately 90% of individuals with OI are heterozygous for mutations in the COL1A1 and COL1A2 genes, with dominant pattern of inheritance or sporadic mutations. After 2006, mutations were identified in the CRTAP, FKBP10, LEPRE1, PLOD2, PPIB, SERPINF1, SERPINH1, SP7, WNT1, BMP1, and TMEM38B genes, associated with recessive OI and mutation in the IFITM5 gene associated with dominant OI. Mutations in PLS3 were recently identified in families with osteoporosis and fractures, with X-linked inheritance pattern. In addition to the genetic complexity of the molecular basis of OI, extensive phenotypic variability resulting from individual loci has also been documented. CONCLUSIONS: Considering the discovery of new genes and limited genotype-phenotype correlation, the use of next-generation sequencing tools has become useful in molecular studies of OI cases. The recommendation of the Nosology Group of the International Society of Skeletal Dysplasias is to maintain the classification of Sillence as the prototypical form, universally accepted to classify the degree of severity in OI, while maintaining it free from direct molecular reference.

  13. Classification of Big Data with Application to Imaging Genetics

    CERN Document Server

    Ulfarsson, Magnus O; Sigurdsson, Jakob; Sveinsson, Johannes R

    2016-01-01

    Big data applications, such as medical imaging and genetics, typically generate datasets that consist of few observations n on many more variables p, a scenario that we denote as p>>n. Traditional data processing methods are often insufficient for extracting information out of big data. This calls for the development of new algorithms that can deal with the size, complexity, and the special structure of such datasets. In this paper, we consider the problem of classifying p>>n data and propose a classification method based on linear discriminant analysis (LDA). Traditional LDA depends on the covariance estimate of the data, but when p>>n the sample covariance estimate is singular. The proposed method estimates the covariance by using a sparse version of noisy principal component analysis (nPCA). The use of sparsity in this setting aims at automatically selecting variables that are relevant for classification. In experiments, the new method is compared to state-of-the art methods for big data problems using bot...

  14. Genetic Diversity of RAPD Mark for Natural Davidia involucrata Populations

    Institute of Scientific and Technical Information of China (English)

    Congwen Song; Manzhu Bao

    2006-01-01

    The genetic diversity and genetic variation within and among populations of five natural Davidia involucrata populations were studied from 13 primers based on random amplified polymorphic DNA (RAPD) analysis.The results show that natural D.involucrata population has a rich genetic diversity,and the differences among populations are significant.Twenty-six percent of genetic variation exists among D.involucrata populations,which is similar to that of the endangered tree species Liriodendron chinense and Cathaya argyrophylla in China,but different from more widely distributed tree species.The analysis of the impacts of sampling method on genetic diversity parameters shows that the number of sampled individuals has little effect on the effective number of alleles and genetic diversity,but has a marked effect on the genetic differentiation among populations and gene flows.This study divides the provenances of D.involucrata into two parts,namely,a southeast and a northwest provenance.

  15. Perfect Simulation From Nonneutral Population Genetic Models: Variable Population Size and Population Subdivision.

    OpenAIRE

    Fearnhead, Paul

    2006-01-01

    We show how the idea of monotone coupling from the past can produce simple algorithms for simulating samples at a nonneutral locus under a range of demographic models. We specifically consider a biallelic locus and either a general variable population size mode or a general migration model for population subdivision. We investigate the effect of demography on the efficacy of selection and the effect of selection on genetic divergence between populations.

  16. Genetic diversity and differentiation of Mongolian indigenous cattle populations

    International Nuclear Information System (INIS)

    and relationship of Mongolian cattle populations with breeds from neighboring countries and exotic breeds, data from the ILRI cattle genotyping database were included. More particularly, we used previously obtained data from Asian taurine (Hanwoo, Yanbian and Japanese Black), two European taurine (Friesian and Charolais), two African taurine (Baoule and N'Dama) and two zebu breeds (Sahiwal and Ongole). For each breed, observed (Ho) and expected (He) heterozygosities as well as the mean number of alleles (MNA) across the nine loci were calculated between pairs of populations were also estimated and a UPGMA tree was constructed. The heterozygosities (Ho and He) in Mongolian cattle populations are similar to those obtained in Northeast Asian taurine breeds but the values are higher compared to the ones obtained for the European and African taurine breeds. The Mongol cattle in North Hangay has the highest corrected MNA value (all animals or 28 animals only). The UPGMA tree, built with the Reynolds' genetic distances, shows all six Northeast Asian cattle populations clustering into one group linked to the two European taurine breed. Interestingly, the two populations of the Mongol cattle are not closely related to each other. However, bootstrap values between the Northeast Asian taurine breeds, with the exception of the bootstrap value between Yanbian and Hanwoo, are relatively low, therefore the relationship between the Northeast Asian populations should be taken with caution. Fst values between the three Mongolian cattle populations are significant (P < 0.01), with the Govi Altay population being more differentiated from the North Hangay population than from the Khalkhun Golun breed (data not shown). Our data suggest that the traditional classification of Govi Altay and North Hangay populations as one breed, the Mongol cattle, should be revisited

  17. Highlighting nonlinear patterns in population genetics datasets

    KAUST Repository

    Alanis Lobato, Gregorio

    2015-01-30

    Detecting structure in population genetics and case-control studies is important, as it exposes phenomena such as ecoclines, admixture and stratification. Principal Component Analysis (PCA) is a linear dimension-reduction technique commonly used for this purpose, but it struggles to reveal complex, nonlinear data patterns. In this paper we introduce non-centred Minimum Curvilinear Embedding (ncMCE), a nonlinear method to overcome this problem. Our analyses show that ncMCE can separate individuals into ethnic groups in cases in which PCA fails to reveal any clear structure. This increased discrimination power arises from ncMCE\\'s ability to better capture the phylogenetic signal in the samples, whereas PCA better reflects their geographic relation. We also demonstrate how ncMCE can discover interesting patterns, even when the data has been poorly pre-processed. The juxtaposition of PCA and ncMCE visualisations provides a new standard of analysis with utility for discovering and validating significant linear/nonlinear complementary patterns in genetic data.

  18. Genetic differentiation between Atlantic salmon populations in the Windermere catchment

    OpenAIRE

    Hartley, S.E.; Pickering, A.D.

    1994-01-01

    Genetic analysis, using single locus probes for genomic DNA, revealed that the juvenile Atlantic salmon populations in the Rivers Leven, Rothay and Troutbeck were related but genetically distinct. This genetic differentiation is greater than might be expected (by comparison with other salmon populations in the UK) and it is recommended that no action is taken which might promote genetic exchange between the three rivers. Thus, future fisheries management practices should treat the salmon from...

  19. Head and neck paragangliomas: clinical and molecular genetic classification.

    Science.gov (United States)

    Offergeld, Christian; Brase, Christoph; Yaremchuk, Svetlana; Mader, Irina; Rischke, Hans Christian; Gläsker, Sven; Schmid, Kurt W; Wiech, Thorsten; Preuss, Simon F; Suárez, Carlos; Kopeć, Tomasz; Patocs, Attila; Wohllk, Nelson; Malekpour, Mahdi; Boedeker, Carsten C; Neumann, Hartmut P H

    2012-01-01

    Head and neck paragangliomas are tumors arising from specialized neural crest cells. Prominent locations are the carotid body along with the vagal, jugular, and tympanic glomus. Head and neck paragangliomas are slowly growing tumors, with some carotid body tumors being reported to exist for many years as a painless lateral mass on the neck. Symptoms depend on the specific locations. In contrast to paraganglial tumors of the adrenals, abdomen and thorax, head and neck paragangliomas seldom release catecholamines and are hence rarely vasoactive. Petrous bone, jugular, and tympanic head and neck paragangliomas may cause hearing loss. The internationally accepted clinical classifications for carotid body tumors are based on the Shamblin Class I-III stages, which correspond to postoperative permanent side effects. For petrous-bone paragangliomas in the head and neck, the Fisch classification is used. Regarding the molecular genetics, head and neck paragangliomas have been associated with nine susceptibility genes: NF1, RET, VHL, SDHA, SDHB, SDHC, SDHD, SDHAF2 (SDH5), and TMEM127. Hereditary HNPs are mostly caused by mutations of the SDHD gene, but SDHB and SDHC mutations are not uncommon in such patients. Head and neck paragangliomas are rarely associated with mutations of VHL, RET, or NF1. The research on SDHA, SDHAF2 and TMEM127 is ongoing. Multiple head and neck paragangliomas are common in patients with SDHD mutations, while malignant head and neck paraganglioma is mostly seen in patients with SDHB mutations. The treatment of choice is surgical resection. Good postoperative results can be expected in carotid body tumors of Shamblin Class I and II, whereas operations on other carotid body tumors and other head and neck paragangliomas frequently result in deficits of the cranial nerves adjacent to the tumors. Slow growth and the tendency of hereditary head and neck paragangliomas to be multifocal may justify less aggressive treatment strategies. PMID:22584701

  20. Head and neck paragangliomas: clinical and molecular genetic classification

    Directory of Open Access Journals (Sweden)

    Christian Offergeld

    2012-01-01

    Full Text Available Head and neck paragangliomas are tumors arising from specialized neural crest cells. Prominent locations are the carotid body along with the vagal, jugular, and tympanic glomus. Head and neck paragangliomas are slowly growing tumors, with some carotid body tumors being reported to exist for many years as a painless lateral mass on the neck. Symptoms depend on the specific locations. In contrast to paraganglial tumors of the adrenals, abdomen and thorax, head and neck paragangliomas seldom release catecholamines and are hence rarely vasoactive. Petrous bone, jugular, and tympanic head and neck paragangliomas may cause hearing loss. The internationally accepted clinical classifications for carotid body tumors are based on the Shamblin Class I-III stages, which correspond to postoperative permanent side effects. For petrous-bone paragangliomas in the head and neck, the Fisch classification is used. Regarding the molecular genetics, head and neck paragangliomas have been associated with nine susceptibility genes: NF1, RET, VHL, SDHA, SDHB, SDHC, SDHD, SDHAF2 (SDH5, and TMEM127. Hereditary HNPs are mostly caused by mutations of the SDHD gene, but SDHB and SDHC mutations are not uncommon in such patients. Head and neck paragangliomas are rarely associated with mutations of VHL, RET, or NF1. The research on SDHA, SDHAF2 and TMEM127 is ongoing. Multiple head and neck paragangliomas are common in patients with SDHD mutations, while malignant head and neck paraganglioma is mostly seen in patients with SDHB mutations. The treatment of choice is surgical resection. Good postoperative results can be expected in carotid body tumors of Shamblin Class I and II, whereas operations on other carotid body tumors and other head and neck paragangliomas frequently result in deficits of the cranial nerves adjacent to the tumors. Slow growth and the tendency of hereditary head and neck paragangliomas to be multifocal may justify less aggressive treatment strategies.

  1. Genetic Differentiation of Different Geographical Populations of Bemisia tabaci (Gennadius) Complex

    Institute of Scientific and Technical Information of China (English)

    CHU Dong; LIU Guo-xia; FAN Zhong-xue; TAO Yun-li; ZHANG You-jun

    2007-01-01

    Bemisia tabaci (Gennadius) is a species complex, which includes different geographical populations with genetic differentiation. The recent progress on the genetic differentiation of various geographical populations of B. tabaci complex was introduced. The genetic differentiation was further analyzed on the basis of the sequences of mtDNA COI and rDNA ITSl recorded in the world's GenBank. Five groups are defined on the basis of mtDNA COI and rDNA ITS1, including the Asia group, America group, Africa group, Australia group, and Biotype B/Mediterranean/Middle East/ Northern Africa/Biotype Ms group. There are several ungrouped geographical classifications, such as the Uganda population, Ivory Coast population, and Taiwan population. Geographical isolation may be the most important factor that contributed to the genetic differentiation of various geographical populations of B. tabaci. Many populations with biological advantages invaded new regions and caused severe economic losses within human activity. It is necessary to strengthen the research of B. tabaci biotype to prevent the spread of invaded populations and the invasion of potentially dangerous populations.

  2. Study on genetic coadaptability of wild quail populations in China

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Genetic coadaptability of wild Japanese quail, wild Common quail and Domestic quail populations in China was studied using 7 microsatellite DNA markers and Monte Carlo method to test genetic disequilibrium. The molecular effects of genetic coadaptability were analyzed through a new statistical model of neutral site. The results showed that genetic coadaptability dominated the genetic disequilibrium of the three quail populations, and totally 16.67%, 9.66% and 10.05% of non-allelic combinations were in the genetic disequilibrium in wild Japanese quail, wild Common quail and Domestic quail populations, respectively. Genetic coadaptability existed at almost all the tested sites. In the molecular point of view, genetic coadaptability plays an important role of keeping lots of polymorphisms in natural populations. Therefore, it is another key factor to the genetic disequilibrium in the population except for linkage. The results enrich the conceptions and connotations of genetic disequilibrium, and help us know more about genetic coadaptability and its effects, and lay a foundation of evaluation and protection of wild quail genetic resources in China.

  3. Genetic Differentiation between Geographically Distant Populations of DROSOPHILA MELANOGASTER

    OpenAIRE

    Rama S Singh; Hickey, Donal A; David, Jean

    1982-01-01

    We have studied allozyme variation at 26 gene loci in nine populations of Drosophila melanogaster originating on five different continents. The distant populations show significant genetic differentiation. However, only half of the loci studied have contributed to this differentiation; the other half show identical patterns in all populations. The genetic differentiation in North American, European and African populations is correlated with the major climatic differences between north and sou...

  4. Genetic diversity and genetic differentiation of natural populations of Pinus kesiya var. Langbinanensis

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Genetic diversity and genetic differentiation of natural populations of Pinus kesiya var. Langbinanensis were examined by means of electrophoresis technique. Analysis of 9 enzyme systems including 16 loci showed that all the three natural populations of the pine were high in genetic diversity but low in inter -population genetic differentiation. The proportion of polymorphic loci is 0.667 , with eachlocus holding 2.13 alleles, averagely. The average expected and obse rved heterozygosity was 0.288 and 0.197, respectively. The gene differentiation among populations was 0.052, but the mean genetic distance was only 0.015.

  5. Genetic Control of Mosquitoes: population suppression strategies

    Directory of Open Access Journals (Sweden)

    André Barretto Bruno Wilke

    2012-10-01

    Full Text Available Over the last two decades, morbidity and mortality from malaria and dengue fever among other pathogens are an increasing Public Health problem. The increase in the geographic distribution of vectors is accompanied by the emergence of viruses and diseases in new areas. There are insufficient specific therapeutic drugs available and there are no reliable vaccines for malaria or dengue, although some progress has been achieved, there is still a long way between its development and actual field use. Most mosquito control measures have failed to achieve their goals, mostly because of the mosquito's great reproductive capacity and genomic flexibility. Chemical control is increasingly restricted due to potential human toxicity, mortality in no target organisms, insecticide resistance, and other environmental impacts. Other strategies for mosquito control are desperately needed. The Sterile Insect Technique (SIT is a species-specific and environmentally benign method for insect population suppression, it is based on mass rearing, radiation mediated sterilization, and release of a large number of male insects. Releasing of Insects carrying a dominant lethal gene (RIDL offers a solution to many of the drawbacks of traditional SIT that have limited its application in mosquitoes while maintaining its environmentally friendly and species-specific utility. The self-limiting nature of sterile mosquitoes tends to make the issues related to field use of these somewhat less challenging than for self-spreading systems characteristic of population replacement strategies. They also are closer to field use, so might be appropriate to consider first. The prospect of genetic control methods against mosquito vectored human diseases is rapidly becoming a reality, many decisions will need to be made on a national, regional and international level regarding the biosafety, social, cultural and ethical aspects of the use and deployment of these vector control methods.

  6. Integrating genetic algorithm method with neural network for land use classification using SZ-3 CMODIS data

    Institute of Scientific and Technical Information of China (English)

    WANG Changyao; LUO Chengfeng; LIU Zhengjun

    2005-01-01

    This paper presents a methodology on land use mapping using CMODIS (Chinese Moderate Resolution Imaging Spectroradiometer ) data on-board SZ-3 (Shenzhou 3) spacecraft. The integrated method is composed of genetic algorithm (GA) for feature extraction and neural network classifier for land use classification. In the data preprocessing, a moment matching method was adopted to reuse classification was obtained. To generate a land use map, the three layers back propagation neural network classifier is used for training the samples and classification. Compared with the Maximum Likelihood classification algorithm, the results show that the accuracy of land use classification is obviously improved by using our proposed method, the selected band number in the classification process is reduced,and the computational performance for training and classification is improved. The result also shows that the CMODIS data can be effectively used for land use/land cover classification and change monitoring at regional and global scale.

  7. Extreme genetic diversity in asexual grass thrips populations.

    Science.gov (United States)

    Fontcuberta García-Cuenca, A; Dumas, Z; Schwander, T

    2016-05-01

    The continuous generation of genetic variation has been proposed as one of the main factors explaining the maintenance of sexual reproduction in nature. However, populations of asexual individuals may attain high levels of genetic diversity through within-lineage diversification, replicate transitions to asexuality from sexual ancestors and migration. How these mechanisms affect genetic variation in populations of closely related sexual and asexual taxa can therefore provide insights into the role of genetic diversity for the maintenance of sexual reproduction. Here, we evaluate patterns of intra- and interpopulation genetic diversity in sexual and asexual populations of Aptinothrips rufus grass thrips. Asexual A. rufus populations are found throughout the world, whereas sexual populations appear to be confined to few locations in the Mediterranean region. We found that asexual A. rufus populations are characterized by extremely high levels of genetic diversity, both in comparison with their sexual relatives and in comparison with other asexual species. Migration is extensive among asexual populations over large geographic distances, whereas close sexual populations are strongly isolated from each other. The combination of extensive migration with replicate evolution of asexual lineages, and a past demographic expansion in at least one of them, generated high local clone diversities in A. rufus. These high clone diversities in asexual populations may mimic certain benefits conferred by sex via genetic diversity and could help explain the extreme success of asexual A. rufus populations. PMID:26864612

  8. Molecular population genetics of Dioscorea tokore, a wild yam species

    International Nuclear Information System (INIS)

    High levels of genetic diversity have been found in natural populations of the wild yam species Dioscorea tokoro. Genetic diversity was measured by investigating: (1) the allozyme allele frequenzies; (2) the nucleotide difference in haplotypes of the Pgi locus; and (3) microsatellite variation. Most of the genetic diversity was found to reside within each population and the diversity caused by population differentiation appeared to be small. The implications of the results for yam genetic conservation are discussed. (author). 21 refs, 1 fig., 3 tabs

  9. Population genetic diversity and fitness in multiple environments

    Directory of Open Access Journals (Sweden)

    McGreevy Thomas J

    2010-07-01

    Full Text Available Abstract Background When a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations to adapt to altered environments. However, it is not clear how much genetic diversity within populations may be lost before populations are put at significant risk. Development of tools to evaluate this relationship would be a valuable contribution to conservation biology. To address these issues, we have created an experimental system that uses laboratory populations of an estuarine crustacean, Americamysis bahia with experimentally manipulated levels of genetic diversity. We created replicate cultures with five distinct levels of genetic diversity and monitored them for 16 weeks in both permissive (ambient seawater and stressful conditions (diluted seawater. The relationship between molecular genetic diversity at presumptive neutral loci and population vulnerability was assessed by AFLP analysis. Results Populations with very low genetic diversity demonstrated reduced fitness relative to high diversity populations even under permissive conditions. Population performance decreased in the stressful environment for all levels of genetic diversity relative to performance in the permissive environment. Twenty percent of the lowest diversity populations went extinct before the end of the study in permissive conditions, whereas 73% of the low diversity lines went extinct in the stressful environment. All high genetic diversity populations persisted for the duration of the study, although population sizes and reproduction were reduced under stressful environmental conditions. Levels of fitness varied more among replicate low diversity populations than among replicate populations with high genetic diversity. There was a significant correlation

  10. Genetic diversity of natural Hepatacodium miconioides populations in Zhejiang Province

    Institute of Scientific and Technical Information of China (English)

    LI Junmin; JIN Zexin

    2006-01-01

    Hepatacodium miconioides is the Class Ⅱ protected plant species in China.This paper studies the genetic diversity and differentiation of its nine natural populations in Zhejiang Province by using random amplified polymorphic DNA (RAPD) technique.Twelve random primers were selected in the amplification,and 164 repetitive loci were produced.The percentage of polymorphic loci in each H.miconioides population ranged from 14.60% to 27.44%,with an average of 20.73%.Among the test populations,Kuochangshan had the highest percentage of polymorphic loci,Simingshan took the second place,and Guanyinping had the lowest percentage.As estimated by Shannon index,the genetic diversity within H.miconioides populations accounted for 27.28% of the total genetic diversity,while that among H.miconioides populations accounted for 72.72%.The genetic differentiation among H.miconioides populations as estimated by Nei index was 0.715,7.This figure was generally consistent with that estimated by Shannon index,i.e.,the genetic differentiation among populations was relatively high,but that within populations was relatively low.The gene flow among H.miconioides populations was relatively low (0.198,7),and the genetic similarity ranged from 0.655,7 to 0.811,9,with an average of 0.730,6.The highest genetic distance among populations was 0.422,9,while the lowest was 0.208,3.All the results showed that there was a distinct genetic differentiation among H.miconioides populations.The genetic distance matrix of nine test populations was calculated using this method,and the clustering analysis was made using the unweighted pair group method with arithmetic mean (UPGMA).The cluster analysis suggested that the ninepopulations of H.miconioides in Zhejiang Province could be divided into two groups,the eastern Zhejiang group and the western Zhejiang group.

  11. GENETICS OF INDO-EUROPEAN POPULATIONS: THE PAST, THE FUTURE

    OpenAIRE

    Balanovsky, Oleg; Utevska, Olga; Balanovska, Elena

    2013-01-01

    We describe our experience of comparing genetic and linguistic data in relation to the Indo-European problem. Our recent comparison of the genetic variation with lexicostatistical data on North Caucasian populations identified the parallel evolution of genes and languages; one can say that history of the populations was reflected in the linguistic and the genetic mirrors. For other linguistic families one can also expect this similarity, though it could be blurred by elite dominance and other...

  12. Multiscale modeling for classification of SAR imagery using hybrid EM algorithm and genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    Xianbin Wen; Hua Zhang; Jianguang Zhang; Xu Jiao; Lei Wang

    2009-01-01

    A novel method that hybridizes genetic algorithm (GA) and expectation maximization (EM) algorithm for the classification of syn-thetic aperture radar (SAR) imagery is proposed by the finite Gaussian mixtures model (GMM) and multiscale autoregressive (MAR)model. This algorithm is capable of improving the global optimality and consistency of the classification performance. The experiments on the SAR images show that the proposed algorithm outperforms the standard EM method significantly in classification accuracy.

  13. A Modified Decision Tree Algorithm Based on Genetic Algorithm for Mobile User Classification Problem

    OpenAIRE

    Dong-sheng Liu; Shu-jiang Fan

    2014-01-01

    In order to offer mobile customers better service, we should classify the mobile user firstly. Aimed at the limitations of previous classification methods, this paper puts forward a modified decision tree algorithm for mobile user classification, which introduced genetic algorithm to optimize the results of the decision tree algorithm. We also take the context information as a classification attributes for the mobile user and we classify the context into public context and private context cla...

  14. Population genetics of Glossina fuscipes fuscipes in Uganda

    International Nuclear Information System (INIS)

    Full text: Tsetse flies (Glossina ssp) transmit human and animal trypanosomoses, which exert considerable economic impact and constrain development in parts of Africa where the disease is endemic or epidemic. Laboratory and field research have demonstrated differences in behaviour, susceptibility to infection and vector capacity among tsetse sub-populations. The role of genetics in determining genetic variation and levels of population isolation in different disease foci has been demonstrated. Population genetic studies using methods that reveal genetic variation can generate data and information about genetic diversity and differentiation. Allozyme markers provide one method to study genetic variation in insects. However, studies on tsetse using this method have revealed little polymorphism in tsetse populations. An alternative approach is direct DNA-PCR based analysis. This involves the use of DNA markers such as Random Amplified Polymorphic DNA (RAPD), which provide a quick and relatively inexpensive method of generating comparative genetic data. Alternatively, microsatellite DNA markers are used to estimate genetic variation within and among tsetse populations. The present project will investigate the genetic diversity within and between Glossina fuscipes fuscipes sub-populations in Uganda. Tsetse (G. f. fuscipes) will be sampled in selected districts of Iganga, Kamuli, Tororo, Soroti, Wakiso, Lira and Moyo. The DNA from G. f. fuscipes will be isolated using the Chelex 100 procedure. The isolated DNA will be genotyped at several microsatellite loci followed by analyses of variability and differentiation. (author)

  15. How Ebola impacts genetics of Western lowland gorilla populations.

    Directory of Open Access Journals (Sweden)

    Pascaline J Le Gouar

    Full Text Available BACKGROUND: Emerging infectious diseases in wildlife are major threats for both human health and biodiversity conservation. Infectious diseases can have serious consequences for the genetic diversity of populations, which could enhance the species' extinction probability. The Ebola epizootic in western and central Africa induced more than 90% mortality in Western lowland gorilla population. Although mortality rates are very high, the impacts of Ebola on genetic diversity of Western lowland gorilla have never been assessed. METHODOLOGY/PRINCIPAL FINDINGS: We carried out long term studies of three populations of Western lowland gorilla in the Republic of the Congo (Odzala-Kokoua National Park, Lossi gorilla sanctuary both affected by Ebola and Lossi's periphery not affected. Using 17 microsatellite loci, we compared genetic diversity and structure of the populations and estimate their effective size before and after Ebola outbreaks. Despite the effective size decline in both populations, we did not detect loss in genetic diversity after the epizootic. We revealed temporal changes in allele frequencies in the smallest population. CONCLUSIONS/SIGNIFICANCE: Immigration and short time elapsed since outbreaks could explain the conservation of genetic diversity after the demographic crash. Temporal changes in allele frequencies could not be explained by genetic drift or random sampling. Immigration from genetically differentiated populations and a non random mortality induced by Ebola, i.e., selective pressure and cost of sociality, are alternative hypotheses. Understanding the influence of Ebola on gorilla genetic dynamics is of paramount importance for human health, primate evolution and conservation biology.

  16. Hybrid Model Based on Genetic Algorithms and SVM Applied to Variable Selection within Fruit Juice Classification

    Science.gov (United States)

    Fernandez-Lozano, C.; Canto, C.; Gestal, M.; Andrade-Garda, J. M.; Rabuñal, J. R.; Dorado, J.; Pazos, A.

    2013-01-01

    Given the background of the use of Neural Networks in problems of apple juice classification, this paper aim at implementing a newly developed method in the field of machine learning: the Support Vector Machines (SVM). Therefore, a hybrid model that combines genetic algorithms and support vector machines is suggested in such a way that, when using SVM as a fitness function of the Genetic Algorithm (GA), the most representative variables for a specific classification problem can be selected. PMID:24453933

  17. Hybrid Model Based on Genetic Algorithms and SVM Applied to Variable Selection within Fruit Juice Classification

    Directory of Open Access Journals (Sweden)

    C. Fernandez-Lozano

    2013-01-01

    Full Text Available Given the background of the use of Neural Networks in problems of apple juice classification, this paper aim at implementing a newly developed method in the field of machine learning: the Support Vector Machines (SVM. Therefore, a hybrid model that combines genetic algorithms and support vector machines is suggested in such a way that, when using SVM as a fitness function of the Genetic Algorithm (GA, the most representative variables for a specific classification problem can be selected.

  18. Hybrid Model Based on Genetic Algorithms and SVM Applied to Variable Selection within Fruit Juice Classification

    OpenAIRE

    C. Fernandez-Lozano; Canto, C.; Gestal, M.; Andrade-Garda, J. M.; Rabuñal, J. R.; Dorado, J.; Pazos, A.

    2013-01-01

    Given the background of the use of Neural Networks in problems of apple juice classification, this paper aim at implementing a newly developed method in the field of machine learning: the Support Vector Machines (SVM). Therefore, a hybrid model that combines genetic algorithms and support vector machines is suggested in such a way that, when using SVM as a fitness function of the Genetic Algorithm (GA), the most representative variables for a specific classification problem can be selected.

  19. Population demographics and genetic diversity in remnant and translocated populations of sea otters

    Science.gov (United States)

    Bodkin, J.L.; Ballachey, B.E.; Cronin, M.A.; Scribner, K.T.

    1999-01-01

    The effects of small population size on genetic diversity and subsequent population recovery are theoretically predicted, but few empirical data are available to describe those relations. We use data from four remnant and three translocated sea otter (Enhydra lutris) populations to examine relations among magnitude and duration of minimum population size, population growth rates, and genetic variation. Metochondrial (mt)DNA haplotype diversity was correlated with the number of years at minimum population size (r = -0.741, p = 0.038) and minimum population size (r = 0.709, p = 0.054). We found no relation between population growth and haplotype diversity, altough growth was significantly greater in translocated than in remnant populations. Haplotype diversity in populations established from two sources was higher than in a population established from a single source and was higher than in the respective source populations. Haplotype frequencies in translocated populations of founding sizes of 4 and 28 differed from expected, indicating genetic drift and differential reproduction between source populations, whereas haplotype frequencies in a translocated population with a founding size of 150 did not. Relations between population demographics and genetic characteristics suggest that genetic sampling of source and translocated populations can provide valuable inferences about translocations.

  20. Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides

    Science.gov (United States)

    Teixeira, Marcus M.

    2016-01-01

    During the past 20 years, a general picture of the genetic diversity and population structure of Coccidioides, the causal agent of coccidioidomycosis (Valley fever), has emerged. The genus consists of 2 genetically diverse species, C. immitis and C. posadasii, each of which contains 1 or more distinct populations with limited gene flow. Genotypic data indicate that C. immitis is divided into 2 subpopulations (central and southern California populations) and C. posadasii is divided into 3 subpopulations (Arizona, Mexico, and Texas/South America populations). However, admixture within and among these populations and the current paucity of environmental isolates limit our understanding of the population genetics of Coccidioides. We assessed population structure of Coccidioides in Arizona by analyzing 495 clinical and environmental isolates. Our findings confirm the population structure as previously described and indicate a finer scale population structure in Arizona. Environmental isolates appear to have higher genetic diversity than isolates from human patients. PMID:27191589

  1. Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides.

    Science.gov (United States)

    Teixeira, Marcus M; Barker, Bridget M

    2016-06-01

    During the past 20 years, a general picture of the genetic diversity and population structure of Coccidioides, the causal agent of coccidioidomycosis (Valley fever), has emerged. The genus consists of 2 genetically diverse species, C. immitis and C. posadasii, each of which contains 1 or more distinct populations with limited gene flow. Genotypic data indicate that C. immitis is divided into 2 subpopulations (central and southern California populations) and C. posadasii is divided into 3 subpopulations (Arizona, Mexico, and Texas/South America populations). However, admixture within and among these populations and the current paucity of environmental isolates limit our understanding of the population genetics of Coccidioides. We assessed population structure of Coccidioides in Arizona by analyzing 495 clinical and environmental isolates. Our findings confirm the population structure as previously described and indicate a finer scale population structure in Arizona. Environmental isolates appear to have higher genetic diversity than isolates from human patients. PMID:27191589

  2. Detailed genetic structure of European bitterling populations in Central Europe

    Directory of Open Access Journals (Sweden)

    Veronika Bartáková

    2015-11-01

    Full Text Available The European bitterling (Rhodeus amarus is a small cyprinid fish whose populations declined markedly between 1950 and 1980. However, its range currently expands, partly due to human-assisted introductions. We determined the genetic variability and detailed spatial structure among bitterling populations in Central Europe and tested alternative hypotheses about colonization of this area. Twelve polymorphic microsatellite loci on a large sample of 688 individuals had been used to analyse genetic variability and population structure. Samples originated from 27 localities with emphasis on area of the Czech Republic where three major sea drainages (Black, Baltic, and Northern Sea meet. Highly variable level of intrapopulation genetic variability had generally been detected and a recent decrease in numbers (“bottleneck” had been indicated by genetic data among six populations. High level of interpopulation differentiation was identified even within the basins. There was a significant role of genetic drift and indications of low dispersal ability of R. amarus. Surprisingly, the Odra River was inhabited by two distinct populations without any genetic signatures of a secondary contact. Czech part of the Odra (Baltic basin was colonized from the Danubian refugium (similarly to adjacent Danubian basin rivers including the Morava, while Polish part of the Odra was genetically similar to the populations in the Vistula River (Baltic basin, that has been colonized by a different (Eastern phylogeographic lineage of R. amarus. Most Czech R. amarus populations were colonized from the Danubian refugium, suggesting potential for a human-mediated colonization of the Odra or Elbe Rivers by R. amarus. One Elbe basin population was genetically mixed from the two (Danubian and Eastern phylogeographic lineages. In general the Czech populations of R. amarus were genetically stable except for a single population which has probably been recently introduced. This research

  3. Using population genetic analyses to understand seed dispersal patterns

    Science.gov (United States)

    Hamrick, J. L.; Trapnell, Dorset W.

    2011-11-01

    Neutral genetic markers have been employed in several ways to understand seed dispersal patterns in natural and human modified landscapes. Genetic differentiation among spatially separated populations, using biparentally and maternally inherited genetic markers, allows determination of the relative historical effectiveness of pollen and seed dispersal. Genetic relatedness among individuals, estimated as a function of spatial separation between pairs of individuals, has also been used to indirectly infer seed dispersal distances. Patterns of genetic relatedness among plants in recently colonized populations provide insights into the role of seed dispersal in population colonization and expansion. High genetic relatedness within expanding populations indicates original colonization by a few individuals and population expansion by the recruitment of the original colonists' progeny; low relatedness should occur if population growth results primarily from continuous seed immigration from multiple sources. Parentage analysis procedures can identify maternal parents of dispersed fruits, seeds, or seedlings providing detailed descriptions of contemporary seed dispersal patterns. With standard parent-pair analyses of seeds or seedlings, problems can arise in distinguishing the maternal parent. However, the use of maternal DNA from dispersed fruits or seed coats allows direct identification of maternal individuals and, as a consequence, the distance and patterns of seed dispersal and deposition. Application of combinations of these approaches provides additional insights into the role seed dispersal plays in the genetic connectivity between populations in natural and disturbed landscapes.

  4. A rangewide population genetic study of trumpeter swans

    Science.gov (United States)

    Oyler-McCance, S.J.; Ransler, F.A.; Berkman, L.K.; Quinn, T.W.

    2007-01-01

    For management purposes, the range of naturally occurring trumpeter swans (Cygnus buccinator) has been divided into two populations, the Pacific Coast Population (PP) and the Rocky Mountain Population (RMP). Little is known about the distribution of genetic variation across the species' range despite increasing pressure to make difficult management decisions regarding the two populations and flocks within them. To address this issue, we used rapidly evolving genetic markers (mitochondrial DNA sequence and 17 nuclear microsatellite loci) to elucidate the underlying genetic structure of the species. Data from both markers revealed a significant difference between the PP and RMP with the Yukon Territory as a likely area of overlap. Additionally, we found that the two populations have somewhat similar levels of genetic diversity (PP is slightly higher) suggesting that the PP underwent a population bottleneck similar to a well-documented one in the RMP. Both genetic structure and diversity results reveal that the Tri-State flock, a suspected unique, non-migratory flock, is not genetically different from the Canadian flock of the RMP and need not be treated as a unique population from a genetic standpoint. Finally, trumpeter swans appear to have much lower mitochondrial DNA variability than other waterfowl studied thus far which may suggest a previous, species-wide bottleneck. ?? 2007 Springer Science+Business Media, Inc.

  5. The genetic structure of Nautilus pompilius populations surrounding Australia and the Philippines.

    Science.gov (United States)

    Williams, Rachel C; Jackson, Benjamin C; Duvaux, Ludovic; Dawson, Deborah A; Burke, Terry; Sinclair, William

    2015-07-01

    Understanding the distribution of genetic diversity in exploited species is fundamental to successful conservation. Genetic structure and the degree of gene flow among populations must be assessed to design appropriate strategies to prevent the loss of distinct populations. The cephalopod Nautilus pompilius is fished unsustainably in the Philippines for the ornamental shell trade and has limited legislative protection, despite the species' recent dramatic decline in the region. Here, we use 14 microsatellite markers to evaluate the population structure of N. pompilius around Australia and the Philippines. Despite their relative geographical proximity, Great Barrier Reef individuals are genetically isolated from Osprey Reef and Shark Reef in the Coral Sea (FST  = 0.312, 0.229, respectively). Conversely, despite the larger geographical distances between the Philippines and west Australian reefs, samples display a small degree of genetic structure (FST  = 0.015). Demographic scenarios modelled using approximate Bayesian computation analysis indicate that this limited divergence is not due to contemporary gene flow between the Philippines and west Australia. Instead, present-day genetic similarity can be explained by very limited genetic drift that has occurred due to large average effective population sizes that persisted at both locations following their separation. The lack of connectivity among populations suggests that immigrants from west Australia would not facilitate natural recolonization if Philippine populations were fished to extinction. These data help to rectify the paucity of information on the species' biology currently inhibiting their conservation classification. Understanding population structure can allow us to facilitate sustainable harvesting, thereby preserving the diversity of genetically distinct stocks. PMID:26033519

  6. Role of population genetics in the sterile insect technique

    International Nuclear Information System (INIS)

    The detection and analysis of genetic variation in natural and laboratory populations are reviewed. The application of population genetic methods and theory can help to plan and evaluate the implementation of area-wide integrated pest management (AW-IPM) programmes that use the sterile insect technique (SIT). Population genetic studies can play an important role in estimating dispersal rates and thus gene flow among target populations, determining if sibling species exist, establishing the origin of outbreaks or reintroductions, and supporting the quality control of mass-reared colonies. The target's population history may be examined, in terms of 'bottlenecks', range fragmentations, and expansions. Genetic methods can be helpful in distinguishing wild insects from released sterile or substerile ones, and in ascertaining, together with mating cross-compatibility studies, the compatibility of mass-reared colonies with target wild insects. (author)

  7. Bacterial population genetics, evolution and epidemiology.

    OpenAIRE

    Spratt, B. G.; Maiden, M C

    1999-01-01

    Asexual bacterial populations inevitably consist of an assemblage of distinct clonal lineages. However, bacterial populations are not entirely asexual since recombinational exchanges occur, mobilizing small genome segments among lineages and species. The relative contribution of recombination, as opposed to de novo mutation, in the generation of new bacterial genotypes varies among bacterial populations and, as this contribution increases, the clonality of a given population decreases. In con...

  8. Isonymy and the genetic structure of Albanian populations.

    Science.gov (United States)

    Mikerezi, Ilia; Pizzetti, Paola; Lucchetti, Enzo; Ekonomi, Milva

    2003-12-01

    It is well known that in systems of surname transmission through the paternal line, surnames simulate neutral gene alleles belonging to the Y chromosome. This property of surnames was used to analyze the genetic structure of Albanian populations. Two large samples of surnames belonging to two different periods of time were analyzed. The analysis of indicators of population structure showed that geographical distance has an important effect on surname distribution. It seems that isolation by distance and genetic drift have been still important factors in the determination of the genetic structure of the Albanian population. PMID:14746137

  9. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    Directory of Open Access Journals (Sweden)

    Jian-Wei Zong

    Full Text Available Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777. According to the coefficient of genetic differentiation (Fst = 0.1215, genetic variation within the populations (87.85% were remarkably higher than among populations (12.15%. The average gene flow (Nm = 1.8080 significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080 among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km among populations (r = 0.419, P = 0.005, suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic

  10. Analysis of Distributed and Adaptive Genetic Algorithm for Mining Interesting Classification Rules

    Institute of Scientific and Technical Information of China (English)

    YI Yunfei; LIN Fang; QIN Jun

    2008-01-01

    Distributed genetic algorithm can be combined with the adaptive genetic algorithm for mining the interesting and comprehensible classification rules. The paper gives the method to encode for the rules, the fitness function, the selecting, crossover, mutation and migration operator for the DAGA at the same time are designed.

  11. Extensive genetic divergence among Diptychus maculatus populations in northwest China

    Science.gov (United States)

    Meng, Wei; Yang, Tianyan; Hai, Sa; Ma, Yanwu; Cai, Lingang; Ma, Xufa; Gao, Tianxiang; Guo, Yan

    2015-05-01

    D. maculates is a kind of specialized Schizothoracinae fish has been locally listed as a protected animal in Xinjiang Province, China. Ili River located in north of Tianshan Mountain and Tarim River located in north of Qinghai-Tibetan Plateau were two main distribution areas of this fish. To investigate the genetic diversity and genetic structure of D. maculates, four populations from Tarim River system and two populations from Ili River system were collected in this study. A 570-bp sequence of the control region was obtained for 105 specimens. Twenty-four haplotypes were detected from six populations, only Kunes River population and Kashi River population shared haplotypes with each other. For all the populations examined, the haplotype diversity ( h) was 0.904 8±0.012 6, nucleotide diversity (π) was 0.027 9±0.013 9, and the average number of pairwise nucleotide differences ( k) was 15.878 3±7.139 1. The analysis of molecular variance (AMOVA) showed that 86.31% of the total genetic variation was apportioned among populations, and the variation within sampled populations was 13.69%. Genetic differences among sampled populations were highly significant. F st statistical test indicated that all populations were significantly divergent from each other ( P<0.01). The largest F st value was between Yurungkash River population and Muzat River population, while the smallest F st value was between Kunes River population and Kashi River population. NJ phylogenetic tree of D-loop haplotypes revealed two main clades. The neutrality test and mismatch distribution analysis suggested that the fish had went through a recent population expansion. The uplift of Tianshan Mountain and movement of Qinghai-Tibetan Plateau might contribute to the wide genetic divergence of D. maculates in northwest China.

  12. Review of Image Classification Techniques Based on LDA, PCA and Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Mukul Yadav

    2014-02-01

    Full Text Available Image classification is play an important role in security surveillance in current scenario of huge Amount of image data base. Due to rapid change of feature content of image are major issues in classification. The image classification is improved by various authors using different model of classifier. The efficiency of classifier model depends on feature extraction process of traffic image. For the feature extraction process various authors used a different technique such as Gabor feature extraction, histogram and many more method on extraction process for classification. We apply the FLDA-GA for improved the classification rate of content based image classification. The improved method used heuristic function genetic algorithm. In the form of optimal GA used as feature optimizer for FLDA classification. The normal FLDA suffered from a problem of core and outlier problem. The both side kernel technique improved the classification process of support vector machine.FLDA perform a better classification in compression of another binary multi-class classification. Directed acyclic graph applied a graph portion technique for the mapping of feature data. The mapping space of feature data mapped correctly automatically improved the voting process of classification.

  13. Noninvasive genetics provides insights into the population size and genetic diversity of an Amur tiger population in China.

    Science.gov (United States)

    Wang, Dan; Hu, Yibo; Ma, Tianxiao; Nie, Yonggang; Xie, Yan; Wei, Fuwen

    2016-01-01

    Understanding population size and genetic diversity is critical for effective conservation of endangered species. The Amur tiger (Panthera tigris altaica) is the largest felid and a flagship species for wildlife conservation. Due to habitat loss and human activities, available habitat and population size are continuously shrinking. However, little is known about the true population size and genetic diversity of wild tiger populations in China. In this study, we collected 55 fecal samples and 1 hair sample to investigate the population size and genetic diversity of wild Amur tigers in Hunchun National Nature Reserve, Jilin Province, China. From the samples, we determined that 23 fecal samples and 1 hair sample were from 7 Amur tigers: 2 males, 4 females and 1 individual of unknown sex. Interestingly, 2 fecal samples that were presumed to be from tigers were from Amur leopards, highlighting the significant advantages of noninvasive genetics over traditional methods in studying rare and elusive animals. Analyses from this sample suggested that the genetic diversity of wild Amur tigers is much lower than that of Bengal tigers, consistent with previous findings. Furthermore, the genetic diversity of this Hunchun population in China was lower than that of the adjoining subpopulation in southwest Primorye Russia, likely due to sampling bias. Considering the small population size and relatively low genetic diversity, it is urgent to protect this endangered local subpopulation in China. PMID:26663614

  14. Genetic Variation of Host Populations of Liriomyza sativae Blanchard

    Institute of Scientific and Technical Information of China (English)

    WANG Li-ping; DU Yu-zhou; HE Ya-ting; ZHENG Fu-shan; LU Zi-qiang

    2008-01-01

    In this study, partial sequences of the mitochondrial cytochrome oxidase subunit Ⅰ (mtDNA-COI) gene and the ribosomal internal transcribed spacer 1 (rDNA-ITS1) gene, isolated from five artificial populations of Liriomyza sativae (Diptera:Agromyzidae), were sequenced and compared, to analyze their genetic variation. Analysis of the mtDNA-CO1 gene showed that a low genetic variation was detected among the five populations and only five variable sites were found in the nucleotide sequences. Most of the observed variations that occurred within the populations were because of nucleotide transitions, whereas, the interpopulation variation was because of the differences in haplotype frequencies occurring among the host populations. Analysis of the rDNA-ITS1 gene revealed a small diversity in the five host populations. The trend of genetic differentiation in the host populations was consistent with the preference of L. sativae to the plant hosts.

  15. Population genetic characteristics of horse chestnut in Serbia

    Directory of Open Access Journals (Sweden)

    Ocokoljić Mirjana

    2013-01-01

    Full Text Available The general population genetic characteristics of cultivated horse chestnut trees excelling in growth, phenotype characteristics, type of inflorescence, productivity and resistance to the leafminer Cameraria ohridella Deschka and Dimić were analyzed in Serbia. The analyzed population genetic parameters point to fundamental differences in the genetic structure among the cultivated populations in Serbia. The study shows the variability in all properties among the populations and inter-individual variability within the populations. The variability and differential characteristics were assessed using statistical parameters, taking into account the satisfactory reflection of the hereditary potential. The assessed differences in the vitality and evolution potential of different populations can determine the methods of horse chestnut gene pool collection, reconstruction and improvement. [Projekat Ministarstva nauke Republike Srbije, br. 31041: Establishment of Wood Plantations Intended for a forestation of Serbia

  16. What is new in genetics and osteogenesis imperfecta classification?

    OpenAIRE

    2014-01-01

    OBJECTIVE: Literature review of new genes related to osteogenesis imperfecta (OI) and update of its classification. SOURCES: Literature review in the PubMed and OMIM databases, followed by selection of relevant references. SUMMARY OF THE FINDINGS: In 1979, Sillence et al. developed a classification of OI subtypes based on clinical features and disease severity: OI type I, mild, common, with blue sclera; OI type II, perinatal lethal form; OI type III, severe and progressively deformin...

  17. Text Classification using Association Rule with a Hybrid Concept of Naive Bayes Classifier and Genetic Algorithm

    CERN Document Server

    Kamruzzaman, S M; Hasan, Ahmed Ryadh

    2010-01-01

    Text classification is the automated assignment of natural language texts to predefined categories based on their content. Text classification is the primary requirement of text retrieval systems, which retrieve texts in response to a user query, and text understanding systems, which transform text in some way such as producing summaries, answering questions or extracting data. Now a day the demand of text classification is increasing tremendously. Keeping this demand into consideration, new and updated techniques are being developed for the purpose of automated text classification. This paper presents a new algorithm for text classification. Instead of using words, word relation i.e. association rules is used to derive feature set from pre-classified text documents. The concept of Naive Bayes Classifier is then used on derived features and finally a concept of Genetic Algorithm has been added for final classification. A system based on the proposed algorithm has been implemented and tested. The experimental ...

  18. Genetic structure of Daphnia galeata populations in Eastern China.

    Directory of Open Access Journals (Sweden)

    Wenzhi Wei

    Full Text Available This study presents the first examination of the genetic structure of Daphnia longispina complex populations in Eastern China. Only one species, D. galeata, was present across the eight investigated lakes; as identified by taxon assignment using allelic variation at 15 microsatellite loci. Three genetically differentiated D. galeata subgroups emerged independent of the type of statistical analysis applied. Thus, Bayesian clustering, discriminant analysis based on results from factorial correspondence analysis, and UPGMA clustering consistently showed that populations from two neighbouring lakes were genetically separated from a mixture of genotypes found in other lakes, which formed another two subgroups. Clonal diversity was high in all D. galeata populations, and most samples showed no deviation from Hardy-Weinberg equilibrium, indicating that clonal selection had little effect on the genetic diversity. Overall, populations did not cluster by geographical origin. Further studies will show if the observed pattern can be explained by natural colonization processes or by recent anthropogenic impact on predominantly artificial lakes.

  19. Genetic Variation Within and Among Populations of Delmarva Fox Squirrels

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The objective of this study was to provide important information about genetic variation in populations of the Delmarva Fox Squirrel in the context of a more...

  20. GENETIC DRIFT IN POPULATIONS OF LARESTAN FARS PROVICE, IRAN

    OpenAIRE

    M. Saadat; P. Amirshahi; Farhud

    1999-01-01

    A total of 2519 blood samples were collected from five distinct populations of Larestan, in Fars province, in Iran (Lar, Gerash, Khour, Latifi and Berake) were examined for ABO and Rh blood groups. The gene frequencies obtained from these samples were compared with the hitherto reported corresponding data from other populations of Fars province to determine the genetic structure of the Larestan populations as a whole. The effects of natural selection, migration and size of populations on the ...

  1. Extensive genetic divergence among Diptychus maculatus populations in northwest China

    Science.gov (United States)

    Meng, Wei; Yang, Tianyan; Hai, Sa; Ma, Yanwu; Cai, Lingang; Ma, Xufa; Gao, Tianxiang; Guo, Yan

    2015-05-01

    D. maculates is a kind of specialized Schizothoracinae fish has been locally listed as a protected animal in Xinjiang Province, China. Ili River located in north of Tianshan Mountain and Tarim River located in north of Qinghai-Tibetan Plateau were two main distribution areas of this fish. To investigate the genetic diversity and genetic structure of D. maculates, four populations from Tarim River system and two populations from Ili River system were collected in this study. A 570-bp sequence of the control region was obtained for 105 specimens. Twenty-four haplotypes were detected from six populations, only Kunes River population and Kashi River population shared haplotypes with each other. For all the populations examined, the haplotype diversity ( h) was 0.904 8±0.012 6, nucleotide diversity (π) was 0.027 9±0.013 9, and the average number of pairwise nucleotide differences ( k) was 15.878 3±7.139 1. The analysis of molecular variance (AMOVA) showed that 86.31% of the total genetic variation was apportioned among populations, and the variation within sampled populations was 13.69%. Genetic differences among sampled populations were highly significant. F st statistical test indicated that all populations were significantly divergent from each other ( PChina.

  2. Genetic structure in four West African population groups

    Directory of Open Access Journals (Sweden)

    Chen Guanjie

    2005-06-01

    Full Text Available Abstract Background Africa contains the most genetically divergent group of continental populations and several studies have reported that African populations show a high degree of population stratification. In this regard, it is important to investigate the potential for population genetic structure or stratification in genetic epidemiology studies involving multiple African populations. The presences of genetic sub-structure, if not properly accounted for, have been reported to lead to spurious association between a putative risk allele and a disease. Within the context of the Africa America Diabetes Mellitus (AADM Study (a genetic epidemiologic study of type 2 diabetes mellitus in West Africa, we have investigated population structure or stratification in four ethnic groups in two countries (Akan and Gaa-Adangbe from Ghana, Yoruba and Igbo from Nigeria using data from 372 autosomal microsatellite loci typed in 493 unrelated persons (986 chromosomes. Results There was no significant population genetic structure in the overall sample. The smallest probability is associated with an inferred cluster of 1 and little of the posterior probability is associated with a higher number of inferred clusters. The distribution of members of the sample to inferred clusters is consistent with this finding; roughly the same proportion of individuals from each group is assigned to each cluster with little variation between the ethnic groups. Analysis of molecular variance (AMOVA showed that the between-population component of genetic variance is less than 0.1% in contrast to 99.91% for the within population component. Pair-wise genetic distances between the four ethnic groups were also very similar. Nonetheless, the small between-population genetic variance was sufficient to distinguish the two Ghanaian groups from the two Nigerian groups. Conclusion There was little evidence for significant population substructure in the four major West African ethnic groups

  3. Computer simulations: tools for population and evolutionary genetics

    OpenAIRE

    Hoban, Sean; Bertorelle, Giorgio; Gaggiotti, Oscar E

    2012-01-01

    Computer simulations are excellent tools for understanding the evolutionary and genetic consequences of complex processes whose interactions cannot be analytically predicted. Simulations have traditionally been used in population genetics by a fairly small community with programming expertise, but the recent availability of dozens of sophisticated, customizable software packages for simulation now makes simulation an accessible option for researchers in many fields. The in silico genetic data...

  4. How Ebola Impacts Genetics of Western Lowland Gorilla Populations

    OpenAIRE

    Le Gouar, Pascaline; Vallet, Dominique; David, Laetitia; Bermejo, Magdalena; Gatti, Sylvain; Levréro, Florence; Petit, Eric; Ménard, Nelly

    2009-01-01

    Background: Emerging infectious diseases in wildlife are major threats for both human health and biodiversity conservation. Infectious diseases can have serious consequences for the genetic diversity of populations, which could enhance the species' extinction probability. The Ebola epizootic in western and central Africa induced more than 90% mortality in Western lowland gorilla population. Although mortality rates are very high, the impacts of Ebola on genetic diversity of Western lowland go...

  5. Genetics of Type 2 Diabetes: the Power of Isolated Populations.

    Science.gov (United States)

    Andersen, Mette Korre; Pedersen, Casper-Emil Tingskov; Moltke, Ida; Hansen, Torben; Albrechtsen, Anders; Grarup, Niels

    2016-07-01

    Type 2 diabetes (T2D) affects millions of people worldwide. Improving the understanding of the underlying mechanisms and ultimately improving the treatment strategies are, thus, of great interest. To achieve this, identification of genetic variation predisposing to T2D is important. A large number of variants have been identified in large outbred populations, mainly from Europe and Asia. However, to elucidate additional variation, isolated populations have a number of advantageous properties, including increased amounts of linkage disequilibrium, and increased probability for presence of high frequency disease-associated variants due to genetic drift. Collectively, this increases the statistical power to detect association signals in isolated populations compared to large outbred populations. In this review, we elaborate on why isolated populations are a powerful resource for the identification of complex disease variants and describe their contributions to the understanding of the genetics of T2D. PMID:27189761

  6. Population Genetic Structure of Aedes fluviatilis (Diptera: Culicidae).

    Science.gov (United States)

    Multini, Laura Cristina; Wilke, André Barretto Bruno; Suesdek, Lincoln; Marrelli, Mauro Toledo

    2016-01-01

    Although Aedes fluviatilis is an anthropophilic mosquito found abundantly in urban environments, its biology, epidemiological potential and genetic characteristics are poorly understood. Climate change and urbanization processes that result in environmental modifications benefit certain anthropophilic mosquito species such as Ae. fluviatilis, greatly increasing their abundance in urban areas. To gain a better understanding of whether urbanization processes modulate the genetic structure of this species in the city of São Paulo, we used eight microsatellite loci to genetically characterize Ae. fluviatilis populations collected in nine urban parks in the city of São Paulo. Our results show that there is high gene flow among the populations of this species, heterozygosity deficiency and low genetic structure and that the species may have undergone a recent population expansion. There are two main hypotheses to explain these findings: (i) Ae. fluviatilis populations have undergone a population expansion as a result of urbanization; and (ii) as urbanization of the city of São Paulo occurred recently and was quite intense, the structuring of these populations cannot be observed yet, apart from in the populations of Ibirapuera and Piqueri parks, where the first signs of structuring have appeared. We believe that the expansion found in Ae. fluviatilis populations is probably correlated with the unplanned urbanization of the city of São Paulo, which transformed green areas into urbanized areas, as well as the increasing population density in the city. PMID:27598889

  7. Host genetics and population structure effects on parasitic disease

    Science.gov (United States)

    Williams-Blangero, Sarah; Criscione, Charles D.; VandeBerg, John L.; Correa-Oliveira, Rodrigo; Williams, Kimberly D.; Subedi, Janardan; Kent, Jack W.; Williams, Jeff; Kumar, Satish; Blangero, John

    2012-01-01

    Host genetic factors exert significant influences on differential susceptibility to many infectious diseases. In addition, population structure of both host and parasite may influence disease distribution patterns. In this study, we assess the effects of population structure on infectious disease in two populations in which host genetic factors influencing susceptibility to parasitic disease have been extensively studied. The first population is the Jirel population of eastern Nepal that has been the subject of research on the determinants of differential susceptibility to soil-transmitted helminth infections. The second group is a Brazilian population residing in an area endemic for Trypanosoma cruzi infection that has been assessed for genetic influences on differential disease progression in Chagas disease. For measures of Ascaris worm burden, within-population host genetic effects are generally more important than host population structure factors in determining patterns of infectious disease. No significant influences of population structure on measures associated with progression of cardiac disease in individuals who were seropositive for T. cruzi infection were found. PMID:22312056

  8. Interplay of population genetics and dynamics in the genetic control of mosquitoes

    OpenAIRE

    Alphey, Nina; Bonsall, Michael B.

    2014-01-01

    Some proposed genetics-based vector control methods aim to suppress or eliminate a mosquito population in a similar manner to the sterile insect technique. One approach under development in Anopheles mosquitoes uses homing endonuclease genes (HEGs)—selfish genetic elements (inherited at greater than Mendelian rate) that can spread rapidly through a population even if they reduce fitness. HEGs have potential to drive introduced traits through a population without large-scale sustained releases...

  9. Toward a Better Understanding of Population Genetics: Pop!World--A Virtual, Inquiry-Based Tool for Teaching Population Genetics

    Science.gov (United States)

    Poulin, Jessica; Ramamurthy, Bina; Dittmar, Katharina

    2013-01-01

    Population genetics is fundamental to understanding evolutionary theory, and is taught in most introductory biology/evolution courses. Many students are unaware that understanding this topic requires pertinent knowledge

  10. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.

    Science.gov (United States)

    Khanshour, Anas; Conant, Eleanore; Juras, Rytis; Cothran, Ernest Gus

    2013-01-01

    The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations. PMID:23450090

  11. Genetic variation in natural honeybee populations, Apis mellifera capensis

    Science.gov (United States)

    Hepburn, Randall; Neumann, Peter; Radloff, Sarah E.

    2004-09-01

    Genetic variation in honeybee, Apis mellifera, populations can be considerably influenced by breeding and commercial introductions, especially in areas with abundant beekeeping. However, in southern Africa apiculture is based on the capture of wild swarms, and queen rearing is virtually absent. Moreover, the introduction of European subspecies constantly failed in the Cape region. We therefore hypothesize a low human impact on genetic variation in populations of Cape honeybees, Apis mellifera capensis. A novel solution to studying genetic variation in honeybee populations based on thelytokous worker reproduction is applied to test this hypothesis. Environmental effects on metrical morphological characters of the phenotype are separated to obtain a genetic residual component. The genetic residuals are then re-calculated as coefficients of genetic variation. Characters measured included hair length on the abdomen, width and length of wax plate, and three wing angles. The data show for the first time that genetic variation in Cape honeybee populations is independent of beekeeping density and probably reflects naturally occurring processes such as gene flow due to topographic and climatic variation on a microscale.

  12. Population screening for genetic susceptibility to disease.

    OpenAIRE

    Clarke, A.

    1995-01-01

    Genetic screening for susceptibility to common diseases, such as the common cancers, cardiovascular disease, and diabetes, may soon be technically feasible. Commercial interests should not be allowed to introduce such screening before proper evaluation or without adequate counselling and support. The evaluation of such testing should include psychosocial and medical outcomes and outcomes for those given low risks as well as high risks. These tests may distract attention away from environmenta...

  13. Population genetic structure in natural and reintroduced beaver (Castor fiber populations in Central Europe

    Directory of Open Access Journals (Sweden)

    Kautenburger, R.

    2008-12-01

    Full Text Available Castor fiber Linnaeus, 1758 is the only indigenous species of the genus Castor in Europe and Asia. Due to extensive hunting until the beginning of the 20th century, the distribution of the formerly widespread Eurasian beaver was dramatically reduced. Only a few populations remained and these were in isolated locations, such as the region of the German Elbe River. The loss of genetic diversity in small or captive populations throughgenetic drift and inbreeding is a severe conservation problem. However, the reintroduction of beaver populations from several regions in Europe has shown high viability and populations today are growing fast. In the present study we analysed the population genetic structure of a natural and two reintroduced beaver populations in Germany and Austria. Furthermore, we studied the genetic differentiation between two beaver species, C. fiber and the American beaver (C. canadensis, using RAPD (Random Amplified Polymorphic DNA as a genetic marker. The reintroduced beaver populations of different origins and the autochthonous population of the Elbe River showed a similar low genetic heterogeneity. There was an overall high genetic similarity in the species C. fiber, and no evidence was found for a clear subspecific structure in the populations studied.

  14. Classification Methods for High-Dimensional Genetic Data

    Czech Academy of Sciences Publication Activity Database

    Kalina, Jan

    2014-01-01

    Roč. 34, č. 1 (2014), s. 10-18. ISSN 0208-5216 Institutional support: RVO:67985807 Keywords : multivariate statistics * classification analysis * shrinkage estimation * dimension reduction * data mining Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 0.646, year: 2014

  15. Dynamic Change of Genetic Diversity in Conserved Populations with Different Initial Genetic Architectures

    Institute of Scientific and Technical Information of China (English)

    LU Yun-feng; LI Hong-wei; WU Ke-liang; WU Chang-xin

    2013-01-01

    Maintenance and management of genetic diversity of farm animal genetic resources (AnGR) is very important for biological, socioeconomical and cultural significance. The core concern of conservation for farm AnGR is the retention of genetic diversity of conserved populations in a long-term perspective. However, numerous factors may affect evolution of genetic diversity of a conserved population. Among those factors, the genetic architecture of conserved populations is little considered in current conservation strategies. In this study, we investigated the dynamic changes of genetic diversity of conserved populations with two scenarios on initial genetic architectures by computer simulation in which thirty polymorphic microsatellite loci were chosen to represent genetic architecture of the populations with observed heterozygosity (Ho) and expected heterozygosity (He), observed and mean effective number of alleles (Ao and Ae), number of polymorphic loci (NP) and the percentage of polymorphic loci (PP), number of rare alleles (RA) and number of non-rich polymorphic loci (NRP) as the estimates of genetic diversity. The two scenarios on genetic architecture were taken into account, namely, one conserved population with same allele frequency (AS) and another one with actual allele frequency (AA). The results showed that the magnitude of loss of genetic diversity is associated with genetic architecture of initial conserved population, the amplitude of genetic diversity decline in the context AS was more narrow extent than those in context AA, the ranges of decline of Ho and Ao were about 4 and 2 times in AA compared with that in AS, respectively, the occurrence of first monomorphic locus and the time of change of measure NP in scenario AA is 20 generations and 23 generations earlier than that in scenario AS, respectively. Additionally, we found that NRP, a novel measure proposed by our research group, was a proper estimate for monitoring the evolution of genetic diversity

  16. Wilhelm Ludwig and his contributions to population genetics.

    Science.gov (United States)

    Antonovics, J

    1990-03-01

    This article reviews the life and work of the German biologist Wilhelm Ludwig (1901-1959), whose contributions to population genetics have been largely ignored. Ludwig's work was a rich tapestry of population biology, spanning investigations into population growth, biological asymmetries, sex ratio, and paternity analysis. He was ahead of his time in explicitly combining the theory of population ecology and population genetics. His classic paper on annidation showed the possibility of population differentiation in the face of gene flow, and his early studies demonstrated the importance of selection in evolutionary change. Much of his work spanned the period of the Second World War in Germany, and interesting questions remain about his life during this turbulent period. PMID:21232329

  17. Population Structure and Cryptic Relatedness in Genetic Association Studies

    OpenAIRE

    Astle, William; Balding, David J.

    2010-01-01

    We review the problem of confounding in genetic association studies, which arises principally because of population structure and cryptic relatedness. Many treatments of the problem consider only a simple ``island'' model of population structure. We take a broader approach, which views population structure and cryptic relatedness as different aspects of a single confounder: the unobserved pedigree defining the (often distant) relationships among the study subjects. Kinship is therefore a cent...

  18. Genetic analysis in the Collaborative Cross breeding population

    Energy Technology Data Exchange (ETDEWEB)

    Philip, Vivek [University of Tennessee, Knoxville (UTK); Sokoloff, Greta [ORNL; Ackert-Bicknell, Cheryl [Jackson Laboratory, The, Bar Harbor, ME; Striz, Martin [University of Kentucky, Lexington; Branstetter, Lisa R [ORNL; Beckmann, Melissa [ORNL; Spence, Jason S [ORNL; Jackson, Barbara L [ORNL; Galloway, Leslie D [ORNL; Barker, Gene [ORNL; Wymore, Ann M [Oak Ridge National Laboratory (ORNL); Hunsicker, Patricia R [ORNL; Durtschi, David W [University of Kentucky, Lexington; Shaw, Ginger S [University of Kentucky, Lexington; Shinpock, Sarah G [ORNL; Manly, Kenneth F [University of Kentucky, Lexington; Miller, Darla R [ORNL; Donahue, Kevin [University at Buffalo, NY; Culiat, Cymbeline T [ORNL; Churchill, Gary A [Jackson Laboratory, The, Bar Harbor, ME; Lariviere, William R [University of Pittsburgh; Palmer, Abraham [University of Chicago; O' Hara, Bruce [University of Kentucky; Voy, Brynn H [ORNL; Chesler, Elissa J [ORNL

    2011-01-01

    Genetic reference populations in model organisms are critical resources for systems genetic analysis of disease related phenotypes. The breeding history of these inbred panels may influence detectable allelic and phenotypic diversity. The existing panel of common inbred strains reflects historical selection biases, and existing recombinant inbred panels have low allelic diversity. All such populations may be subject to consequences of inbreeding depression. The Collaborative Cross (CC) is a mouse reference population with high allelic diversity that is being constructed using a randomized breeding design that systematically outcrosses eight founder strains, followed by inbreeding to obtain new recombinant inbred strains. Five of the eight founders are common laboratory strains, and three are wild-derived. Since its inception, the partially inbred CC has been characterized for physiological, morphological, and behavioral traits. The construction of this population provided a unique opportunity to observe phenotypic variation as new allelic combinations arose through intercrossing and inbreeding to create new stable genetic combinations. Processes including inbreeding depression and its impact on allelic and phenotypic diversity were assessed. Phenotypic variation in the CC breeding population exceeds that of existing mouse genetic reference populations due to both high founder genetic diversity and novel epistatic combinations. However, some focal evidence of allele purging was detected including a suggestive QTL for litter size in a location of changing allele frequency. Despite these inescapable pressures, high diversity and precision for genetic mapping remain. These results demonstrate the potential of the CC population once completed and highlight implications for development of related populations. Supplementary material consists of Supplementary Table 1 Phenotypic means, variances, ranges and heritabilities for all traits and generations, Supplementary Table

  19. Genetic diversity in Chilean populations of rainbow trout, Oncorhynchus mykiss

    Directory of Open Access Journals (Sweden)

    Claudia B Cárcamo

    2015-03-01

    Full Text Available The rainbow trout Oncorhynchus mykiss, was first introduced in Chile between 1905 and 1920 and is currently widely distributed in Chile from Antofagasta (23°S to Patagonia (55°S. The broad range of the geographic and climatic distributions of this species in Chile offers a unique opportunity to study the effect of naturalization of an introduced species on its genetic variability. It is of particular importance to observe the genetic variability of populations in the northern range of this species distribution, in a transition zone where a Mediterranean-type climate changes to an arid climate. The present study analyzed allozymic variability and distribution within and between populations of O. mykiss from the river basins of Elqui and Limari rivers, and six culture strains, using starch-gel protein electrophoresis. Populations were found to be in Hardy-Weinberg equilibrium and the average values of He (0.045, polymorphism (13.9% and allele per locus (1.19 are similar to rainbow trout in its native distributional range. About 77.8% of the genetic variability was within population, similar to the variability reported for wild populations in the northern hemisphere. However, a marked genetic differentiation between wild populations was also found. This is likely to be the consequence of initial founder effects followed by subsequent introgression of resident populations caused by reseeding with trout of different origins in both basins.

  20. Classification of hyperspectral remote sensing images based on simulated annealing genetic algorithm and multiple instance learning

    Institute of Scientific and Technical Information of China (English)

    高红民; 周惠; 徐立中; 石爱业

    2014-01-01

    A hybrid feature selection and classification strategy was proposed based on the simulated annealing genetic algorithm and multiple instance learning (MIL). The band selection method was proposed from subspace decomposition, which combines the simulated annealing algorithm with the genetic algorithm in choosing different cross-over and mutation probabilities, as well as mutation individuals. Then MIL was combined with image segmentation, clustering and support vector machine algorithms to classify hyperspectral image. The experimental results show that this proposed method can get high classification accuracy of 93.13%at small training samples and the weaknesses of the conventional methods are overcome.

  1. Automated Feature Design for Time Series Classification by Genetic Programming

    OpenAIRE

    Harvey, Dustin Yewell

    2014-01-01

    Time series classification (TSC) methods discover and exploit patterns in time series and other one-dimensional signals. Although many accurate, robust classifiers exist for multivariate feature sets, general approaches are needed to extend machine learning techniques to make use of signal inputs. Numerous applications of TSC can be found in structural engineering, especially in the areas of structural health monitoring and non-destructive evaluation. Additionally, the fields of process contr...

  2. Genetic Diversity among Ancient Nordic Populations

    DEFF Research Database (Denmark)

    Melchior, Linea; Lynnerup, Niels; Siegismund, Hans R;

    2010-01-01

    locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the...... ancient Danes (average 13%) than among extant Danes and Scandinavians ( approximately 2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type "diluted" by later immigration events. Interestingly, the two Neolithic...... samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300-3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for...

  3. Genetical pressures and social organization in small mammal populations

    International Nuclear Information System (INIS)

    Inherited variation is often useful for detecting and measuring ecological pressures in natural populations. For example, changes in allele and genotypic frequencies at the gene locus controlling the haemoglobin β chain in Mus musculus samples trapped on an isolated Welsh island have provided information about different mechanisms of death at different times of year and about the influence of social structure on genetical constitution. Notwithstanding, considerable caution has to be exercised in interpreting genetical changes, since detectable varients are often no more than linked markers of physiologically important gene loci, while habitat, deme, or ageing differences may be obscured in pooled data, such as are represented by concepts like overall allozymic heterozygosity. For these reasons, genetical studies on wild populations are likely to be most profitable when the contribution of individual genes to physiological or behavioral traits can be analyzed; it is at this level that genetics and ecology properly complement each other

  4. Genetic diversity among ancient Nordic populations.

    Directory of Open Access Journals (Sweden)

    Linea Melchior

    Full Text Available Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13% than among extant Danes and Scandinavians (approximately 2.5% as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type "diluted" by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300-3,500 YBP was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

  5. Genetic affinities between endogamous and inbreeding populations of Uttar Pradesh

    Directory of Open Access Journals (Sweden)

    Borkar Minal

    2007-04-01

    Full Text Available Abstract Background India has experienced several waves of migration since the Middle Paleolithic. It is believed that the initial demic movement into India was from Africa along the southern coastal route, approximately 60,000–85,000 years before present (ybp. It has also been reported that there were two other major colonization which included eastward diffusion of Neolithic farmers (Elamo Dravidians from Middle East sometime between 10,000 and 7,000 ybp and a southern dispersal of Indo Europeans from Central Asia 3,000 ybp. Mongol entry during the thirteenth century A.D. as well as some possible minor incursions from South China 50,000 to 60,000 ybp may have also contributed to cultural, linguistic and genetic diversity in India. Therefore, the genetic affinity and relationship of Indians with other world populations and also within India are often contested. In the present study, we have attempted to offer a fresh and immaculate interpretation on the genetic relationships of different North Indian populations with other Indian and world populations. Results We have first genotyped 20 tetra-nucleotide STR markers among 1800 north Indian samples of nine endogamous populations belonging to three different socio-cultural strata. Genetic distances (Nei's DA and Reynold's Fst were calculated among the nine studied populations, Caucasians and East Asians. This analysis was based upon the allelic profile of 20 STR markers to assess the genetic similarity and differences of the north Indian populations. North Indians showed a stronger genetic relationship with the Europeans (DA 0.0341 and Fst 0.0119 as compared to the Asians (DA 0.1694 and Fst – 0.0718. The upper caste Brahmins and Muslims were closest to Caucasians while middle caste populations were closer to Asians. Finally, three phylogenetic assessments based on two different NJ and ML phylogenetic methods and PC plot analysis were carried out using the same panel of 20 STR markers and 20

  6. Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

    DEFF Research Database (Denmark)

    Pham, L. D.; Do, Duy Ngoc; Nam, L. Q.;

    2014-01-01

    alleles (MNA = 10.1), gene diversity (He = 0.82), allele richness (5.33) and number of private alleles (10). Thirteen percentage of the total genetic variation observed was due to differences among populations. The neighbour-joining dendrogram obtained from Nei's standard genetic distance differentiated...

  7. A Quantitative Test of Population Genetics Using Spatio-Genetic Patterns in Bacterial Colonies

    OpenAIRE

    Korolev, Kirill; Xavier, Joao; Foster, Kevin; Nelson, David R.

    2011-01-01

    It is widely accepted that population-genetics theory is the cornerstone of evolutionary analyses. Empirical tests of the theory, however, are challenging because of the complex relationships between space, dispersal, and evolution. Critically, we lack quantitative validation of the spatial models of population genetics. Here we combine analytics, on- and off-lattice simulations, and experiments with bacteria to perform quantitative tests of the theory. We study two bacterial species, the gut...

  8. Genetic diversity of Sardinian goat population based on microsatellites

    Directory of Open Access Journals (Sweden)

    A. Carta

    2010-01-01

    Full Text Available During the last century, the selection for production traits of the main livestock species has led to a reduction in number of local populations with consequent loss of genetic variability. In Sardinia, the genetic improvement strategy has been based on selection for the local pure breed in sheep, whereas in the other species (cattle, swine and goat, an often unplanned crossbreeding with improved breeds has been applied.

  9. Genetic variability and viral seroconversion in an outcrossing vertebrate population

    OpenAIRE

    Matthew E. Gompper; Monello, Ryan J.; Eggert, Lori S.

    2010-01-01

    Inverse correlations between genetic variability and parasitism are important concerns for conservation biologists. We examined correlations between neutral genetic variability and the presence of antibodies to canine distemper virus (CDV) and feline parvovirus (FPV) in a free-ranging population of raccoons. Over 3 years there was a strong relationship between age and seroprevalence rates. Most young animals were seronegative to CDV and FPV, but the oldest age class was greater than 80 per ce...

  10. Genetic Structure of Daphnia galeata Populations in Eastern China

    OpenAIRE

    Wenzhi Wei; Sabine Gießler; Justyna Wolinska; Xiaolin Ma; Zhong Yang; Wei Hu; Mingbo Yin

    2015-01-01

    This study presents the first examination of the genetic structure of Daphnia longispina complex populations in Eastern China. Only one species, D. galeata, was present across the eight investigated lakes; as identified by taxon assignment using allelic variation at 15 microsatellite loci. Three genetically differentiated D. galeata subgroups emerged independent of the type of statistical analysis applied. Thus, Bayesian clustering, discriminant analysis based on results from factorial corres...

  11. Controlling bloat : individual and population based approaches in genetic programming

    OpenAIRE

    Silva, Sara Guilherme Oliveira da

    2008-01-01

    Genetic Programming (GP) is the automated learning of computer programs. Basically a search process, it is capable of solving complex problems by evolving populations of computer programs, using Darwinian evolution and Mendelian genetics as inspiration. Theoretically, GP can solve any problem whose candidate solutions can be measured and compared, making it a widely applicable technique. Furthermore, the solutions found by GP are usually provided in a format that users can understand and modi...

  12. Spread of pedigree versus genetic ancestry in spatially distributed populations

    OpenAIRE

    Kelleher, J; Etheridge, AM; Véber, A.; Barton, NH

    2016-01-01

    Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are s...

  13. Quasispecies theory in the context of population genetics

    Directory of Open Access Journals (Sweden)

    Wilke Claus O

    2005-08-01

    Full Text Available Abstract Background A number of recent papers have cast doubt on the applicability of the quasispecies concept to virus evolution, and have argued that population genetics is a more appropriate framework to describe virus evolution than quasispecies theory. Results I review the pertinent literature, and demonstrate for a number of cases that the quasispecies concept is equivalent to the concept of mutation-selection balance developed in population genetics, and that there is no disagreement between the population genetics of haploid, asexually-replicating organisms and quasispecies theory. Conclusion Since quasispecies theory and mutation-selection balance are two sides of the same medal, the discussion about which is more appropriate to describe virus evolution is moot. In future work on virus evolution, we would do good to focus on the important questions, such as whether we can develop accurate, quantitative models of virus evolution, and to leave aside discussions about the relative merits of perfectly equivalent concepts.

  14. The population genetics of synthetic lethals.

    Science.gov (United States)

    Phillips, P C; Johnson, N A

    1998-09-01

    Synthetic lethals are variants at different loci that have little or no effect on viability singly but cause lethality in combination. The importance of synthetic lethals and, more generally, of synthetic deleterious loci (SDL) has been controversial. Here, we derive the expected frequencies for SDL under a mutation-selection balance for the complete haploid model and selected cases of the diploid model. We have also obtained simple approximations that demonstrate good fit to exact solutions based on numerical iterations. In the haploid case, equilibrium frequencies of carrier haplotypes (individuals with only a single mutation) are comparable to analogous single-locus results, after allowing for the effects of linkage. Frequencies in the diploid case, however, are much higher and more comparable to the square root of the single-locus results. In particular, when selection operates only on the double-mutant homozygote and linkage is not too tight, the expected frequency of the carriers is approximately the quartic root of the ratio between the mutation rate and the selection coefficient of the synthetics. For a reasonably wide set of models, the frequencies of carriers can be on the order of a few percent. The equilibrium frequencies of these deleterious alleles can be relatively high because, with SDL, both dominance and epistasis act to shield carriers from exposure to selection. We also discuss the possible role of SDL in maintaining genetic variation and in hybrid breakdown. PMID:9725860

  15. Genetic Diversity and Population Structure of Theileria annulata in Oman.

    Directory of Open Access Journals (Sweden)

    Salama Al-Hamidhi

    Full Text Available Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle.Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman.We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia. A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075,

  16. Temporal genetic stability of Stegomyia aegypti (= Aedes aegypti) populations.

    Science.gov (United States)

    Gloria-Soria, A; Kellner, D A; Brown, J E; Gonzalez-Acosta, C; Kamgang, B; Lutwama, J; Powell, J R

    2016-06-01

    The mosquito Stegomyia aegypti (= Aedes aegypti) (Diptera: Culicidae) is the primary vector of viruses that cause yellow fever, dengue and Chikungunya fever. In the absence of effective vaccines, the reduction of these diseases relies on vector control strategies. The success of these strategies is tightly linked to the population dynamics of target populations. In the present study, 14 collections from St. aegypti populations separated by periods of 1-13 years were analysed to determine their temporal genetic stability. Although temporal structure is discernible in most populations, the degree of temporal differentiation is dependent on the population and does not obscure the geographic structure of the various populations. The results suggest that performing detailed studies in the years prior to and after population reduction- or modification-based control interventions at each target field site may be useful in assessing the probability of success. PMID:26744174

  17. Genetic affinities of the Jewish populations of India

    Science.gov (United States)

    Chaubey, Gyaneshwer; Singh, Manvendra; Rai, Niraj; Kariappa, Mini; Singh, Kamayani; Singh, Ashish; Pratap Singh, Deepankar; Tamang, Rakesh; Selvi Rani, Deepa; Reddy, Alla G.; Kumar Singh, Vijay; Singh, Lalji; Thangaraj, Kumarasamy

    2016-01-01

    Due to the lack of written records or inscription, the origin and affiliation of Indian Jewish populations with other world populations remain contentious. Previous genetic studies have found evidence for a minor shared ancestry of Indian Jewish with Middle Eastern (Jewish) populations. However, these studies (relied on limited individuals), haven’t explored the detailed temporal and spatial admixture process of Indian Jewish populations with the local Indian populations. Here, using large sample size with combination of high resolution biparental (autosomal) and uniparental markers (Y chromosome and mitochondrial DNA), we reconstructed genetic history of Indian Jewish by investigating the patterns of genetic diversity. Consistent with the previous observations, we detected minor Middle Eastern specific ancestry component among Indian Jewish communities, but virtually negligible in their local neighbouring Indian populations. The temporal test of admixture suggested that the first admixture of migrant Jewish populations from Middle East to South India (Cochin) occurred during fifth century. Overall, we concluded that the Jewish migration and admixture in India left a record in their genomes, which can link them to the ‘Jewish Diaspora’. PMID:26759184

  18. Genetic affinities of the Jewish populations of India.

    Science.gov (United States)

    Chaubey, Gyaneshwer; Singh, Manvendra; Rai, Niraj; Kariappa, Mini; Singh, Kamayani; Singh, Ashish; Pratap Singh, Deepankar; Tamang, Rakesh; Selvi Rani, Deepa; Reddy, Alla G; Kumar Singh, Vijay; Singh, Lalji; Thangaraj, Kumarasamy

    2016-01-01

    Due to the lack of written records or inscription, the origin and affiliation of Indian Jewish populations with other world populations remain contentious. Previous genetic studies have found evidence for a minor shared ancestry of Indian Jewish with Middle Eastern (Jewish) populations. However, these studies (relied on limited individuals), haven't explored the detailed temporal and spatial admixture process of Indian Jewish populations with the local Indian populations. Here, using large sample size with combination of high resolution biparental (autosomal) and uniparental markers (Y chromosome and mitochondrial DNA), we reconstructed genetic history of Indian Jewish by investigating the patterns of genetic diversity. Consistent with the previous observations, we detected minor Middle Eastern specific ancestry component among Indian Jewish communities, but virtually negligible in their local neighbouring Indian populations. The temporal test of admixture suggested that the first admixture of migrant Jewish populations from Middle East to South India (Cochin) occurred during fifth century. Overall, we concluded that the Jewish migration and admixture in India left a record in their genomes, which can link them to the 'Jewish Diaspora'. PMID:26759184

  19. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

    Institute of Scientific and Technical Information of China (English)

    Jiandong YANG; Zhihe ZHANG; Fujun SHEN; Xuyu YANG; Liang ZHANG; Limin CHEN; Wenping ZHANG; Qing ZHU; Rong HOU

    2011-01-01

    Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species.Tangjiahe Nature Reserve (NR) is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China.Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation.Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population.The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve.Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations.All individuals from the same subpopulation were assigned to one cluster.This indicates high gene flow between subpopulations.F statistic analyses revealed a low Fls-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR.Additionally,our data show a high level of genetic diversity for the Tangjiahe population.Mean allele number (A),Allelic richness (AR) and mean expected heterozygosity (HE) for the Tangiiahe population was 5.9,5.173 and 0.703,respectively.This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6):717-724,2011].

  20. Population genetic structure of Bombus terrestris in Europe: Isolation and genetic differentiation of Irish and British populations.

    Science.gov (United States)

    Moreira, António S; Horgan, Finbarr G; Murray, Tomás E; Kakouli-Duarte, Thomais

    2015-07-01

    The genetic structure of the earth bumblebee (Bombus terrestris L.) was examined across 22 wild populations and two commercially reared populations using eight microsatellite loci and two mitochondrial genes. Our study included wild bumblebee samples from six populations in Ireland, one from the Isle of Man, four from Britain and 11 from mainland Europe. A further sample was acquired from New Zealand. Observed levels of genetic variability and heterozygosity were low in Ireland and the Isle of Man, but relatively high in continental Europe and among commercial populations. Estimates of Fst revealed significant genetic differentiation among populations. Bayesian cluster analysis indicated that Irish populations were highly differentiated from British and continental populations, the latter two showing higher levels of admixture. The data suggest that the Irish Sea and prevailing south westerly winds act as a considerable geographical barrier to gene flow between populations in Ireland and Britain; however, some immigration from the Isle of Man to Ireland was detected. The results are discussed in the context of the recent commercialization of bumblebees for the European horticultural industry. PMID:25958977

  1. Comparative phylogeography and population genetics within Buteo lineatus reveals evidence of distinct evolutionary lineages

    Science.gov (United States)

    Hull, J.M.; Strobel, Bradley N.; Boal, C.W.; Hull, A.C.; Dykstra, C.R.; Irish, A.M.; Fish, A.M.; Ernest, H.B.

    2008-01-01

    Traditional subspecies classifications may suggest phylogenetic relationships that are discordant with evolutionary history and mislead evolutionary inference. To more accurately describe evolutionary relationships and inform conservation efforts, we investigated the genetic relationships and demographic histories of Buteo lineatus subspecies in eastern and western North America using 21 nuclear microsatellite loci and 375-base pairs of mitochondrial control region sequence. Frequency based analyses of mitochondrial sequence data support significant population distinction between eastern (B. l. lineatus/alleni/texanus) and western (B. l. elegans) subspecies of B. lineatus. This distinction was further supported by frequency and Bayesian analyses of the microsatellite data. We found evidence of differing demographic histories between regions; among eastern sites, mitochondrial data suggested that rapid population expansion occurred following the end of the last glacial maximum, with B. l. texanus population expansion preceding that of B. l. lineatus/alleni. No evidence of post-glacial population expansion was detected among western samples (B. l. elegans). Rather, microsatellite data suggest that the western population has experienced a recent bottleneck, presumably associated with extensive anthropogenic habitat loss during the 19th and 20th centuries. Our data indicate that eastern and western populations of B. lineatus are genetically distinct lineages, have experienced very different demographic histories, and suggest management as separate conservation units may be warranted. ?? 2008 Elsevier Inc. All rights reserved.

  2. Genetic hitchhiking in a subdivided population of Mytilus edulis

    Directory of Open Access Journals (Sweden)

    David Patrice

    2008-05-01

    Full Text Available Abstract Background Few models of genetic hitchhiking in subdivided populations have been developed and the rarity of empirical examples is even more striking. We here provide evidences of genetic hitchhiking in a subdivided population of the marine mussel Mytilus edulis. In the Bay of Biscay (France, a patch of M. edulis populations happens to be separated from its North Sea conspecifics by a wide region occupied only by the sister species M. galloprovincialis. Although genetic differentiation between the two M. edulis regions is largely non-significant at ten marker loci (average FST~0.007, a strong genetic differentiation is observed at a single locus (FST = 0.25. We validated the outlier status of this locus, and analysed DNA sequence polymorphism in order to identify the nature of the selection responsible for the unusual differentiation. Results We first showed that introgression of M. galloprovincialis alleles was very weak in both populations and did not significantly affect their differentiation. Secondly, we observed the genetic signature of a selective sweep within both M. edulis populations in the form of a star-shaped clade of alleles. This clade was nearly fixed in the North Sea and was segregating at a moderate frequency in the Bay of Biscay, explaining their genetic differentiation. Incomplete fixation reveals that selection was not direct on the locus but that the studied sequence recombined with a positively selected allele at a linked locus while it was on its way to fixation. Finally, using a deterministic model we showed that the wave of advance of a favourable allele at a linked locus, when crossing a strong enough barrier to gene flow, generates a step in neutral allele frequencies comparable to the step observed between the two M. edulis populations at the outlier locus. In our case, the position of the barrier is now materialised by a large patch of heterospecific M. galloprovincialis populations. Conclusion High FST

  3. The genetics of the dystonias – a review based on the new classification of the dystonias

    Directory of Open Access Journals (Sweden)

    Carlos Henrique F. Camargo

    2015-04-01

    Full Text Available The definition and classification of the dystonias was recently revisited. In the new 2013 classification, the dystonias are subdivided in terms of their etiology according to whether they are the result of pathological changes or structural damage, have acquired causes or are inherited. As hereditary dystonias are clinically and genetically heterogeneous, we sought to classify them according to the new recently defined criteria. We observed that although the new classification is still the subject of much debate and controversy, it is easy to use in a logical and objective manner with the inherited dystonias. With the discovery of new genes, however, it remains to be seen whether the new classification will continue to be effective.

  4. Improving melanoma classification by integrating genetic and morphologic features.

    OpenAIRE

    Amaya Viros; Jane Fridlyand; Juergen Bauer; Konstantin Lasithiotakis; Claus Garbe; Daniel Pinkel; Bastian, Boris C.

    2008-01-01

    Editors' Summary Background. Skin cancers—the most commonly diagnosed cancers worldwide—are usually caused by exposure to ultraviolet (UV) radiation in sunlight. UV radiation damages the DNA in skin cells and can introduce permanent genetic changes (mutations) into the skin cells that allow them to divide uncontrollably to form a tumor, a disorganized mass of cells. Because there are many different cell types in the skin, there are many types of skin cancer. The most dangerous type—melanoma—d...

  5. Can small wildlife conservancies maintain genetically stable populations of large mammals? Evidence for increased genetic drift in geographically restricted populations of Cape buffalo in East Africa

    DEFF Research Database (Denmark)

    Heller, R; Okello, J B A; Siegismund, H

    2010-01-01

    populations, the level of genetic differentiation found here is comparable to that among pan-African populations. Overall, correlations between conservancy area and indices of genetic diversity suggest buffalo populations inhabiting small parks are showing signs of genetic erosion, stressing the need for more...

  6. Genetic substructure of Kuwaiti population reveals migration history.

    Directory of Open Access Journals (Sweden)

    Osama Alsmadi

    Full Text Available The State of Kuwait is characterized by settlers from Saudi Arabia, Iran, and other regions of the Arabian Peninsula. The settlements and subsequent admixtures have shaped the genetics of Kuwait. High prevalence of recessive disorders and metabolic syndromes (that increase risk of diabetes is seen in the peninsula. Understanding the genetic structure of its population will aid studies designed to decipher the underlying causes of these disorders. In this study, we analyzed 572,366 SNP markers from 273 Kuwaiti natives genotyped using the illumina HumanOmniExpress BeadChip. Model-based clustering identified three genetic subgroups with different levels of admixture. A high level of concordance (Mantel test, p=0.0001 for 9999 repeats was observed between the derived genetic clusters and the surname-based ancestries. Use of Human Genome Diversity Project (HGDP data to understand admixtures in each group reveals the following: the first group (Kuwait P is largely of West Asian ancestry, representing Persians with European admixture; the second group (Kuwait S is predominantly of city-dwelling Saudi Arabian tribe ancestry, and the third group (Kuwait B includes most of the tent-dwelling Bedouin surnames and is characterized by the presence of 17% African ancestry. Identity by Descent and Homozygosity analyses find Kuwait's population to be heterogeneous (placed between populations that have large amount of ROH and the ones with low ROH with Kuwait S as highly endogamous, and Kuwait B as diverse. Population differentiation FST estimates place Kuwait P near Asian populations, Kuwait S near Negev Bedouin tribes, and Kuwait B near the Mozabite population. FST distances between the groups are in the range of 0.005 to 0.008; distances of this magnitude are known to cause false positives in disease association studies. Results of analysis for genetic features such as linkage disequilibrium decay patterns conform to Kuwait's geographical location at the nexus

  7. Genetic diversity and population differentiation of natural populations of Sclerotinia sclerotiorum on lentils in eastern Washington.

    Science.gov (United States)

    Genetic diversity and population differentiation of natural populations of Sclerotinia sclerotiorum on lentils in eastern Washington. X. Wang and W. Chen. Washington State University, Pullman, WA, and USDA-ARS, Pullman, WA 99163 Sclerotinia sclerotiorum is the causal agent of white mold on lentils....

  8. Genetic Characterization of Human Populations: From ABO to a Genetic Map of the British People

    Science.gov (United States)

    Bodmer, Walter

    2015-01-01

    From 1900, when Landsteiner first described the ABO blood groups, to the present, the methods used to characterize the genetics of human populations have undergone a remarkable development. Concomitantly, our understanding of the history and spread of human populations across the earth has become much more detailed. As has often been said, a better understanding of the genetic relationships among the peoples of the world is one of the best antidotes to racial prejudices. Such an understanding provides us with a fascinating, improved insight into our origins as well as with valuable information about population differences that are of medical relevance. The study of genetic polymorphisms has been essential to the analysis of the relationships between human populations. The evolution of methods used to study human polymorphisms and the resulting contributions to our understanding of human health and history is the subject of this Perspectives. PMID:25657345

  9. Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

    Directory of Open Access Journals (Sweden)

    Moritz Robin FA

    2003-05-01

    Full Text Available Abstract The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca and Pitiusas (Ibiza and Formentera, which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.

  10. Genetic studies of medfly populations and related species

    International Nuclear Information System (INIS)

    Multilocus enzyme electrophoresis (MLEE) and random amplified polymorphic DNA were used to detect genetic markers in Ceratitis capitata. The authors employed both types of markers (1) to study the genome organization of the medfly, (2) to determine the level of intraspecific genetic diversity, and (3) to understand the evolution of the geographical populations. Sterility and high mutation rates in interstrain crosses were observed in C. capitata, reminiscent of hybrid dysgenesis in Drosophila, and may represent the activation of mobile elements, useful for medfly transformation. The biochemical, genetic and molecular characterization of the enzyme alcohol dehydrogenase clarified the peculiarity of this selectable system, compared with that of Drosophila, and revealed a surprisingly high sequence variability in medfly populations. The phylogenetic relationships between C. capitata and other Tephritidae species of economic importance were analysed by the MLEE approach. (author)

  11. Genetic polymorphism of milk proteins in some Bos genus populations

    Directory of Open Access Journals (Sweden)

    A.M. Guastella

    2011-03-01

    Full Text Available In cattle the analysis of the genetic polymorphism of milk proteins provides an effective tool both to characterize the genetic diversity and to improve the efficiency of selection for specific production traits. Four genes, αS1-casein (CSN1S1, β-casein (CSN2, κ-casein (CSN3 and β-lactoglobulin (BLG have showed a high level of genetic polymorphism and are candidate to play a role in selection programmes in order to improve milk production. In this work three Bos genus populations, one taurine breed autochthonous of South-East of Sicily (Modicana and two Bos indicus populations (Azaouak and Gudali reared in Niger and Cameroon, respectively,..........

  12. Spread of pedigree versus genetic ancestry in spatially distributed populations.

    Science.gov (United States)

    Kelleher, J; Etheridge, A M; Véber, A; Barton, N H

    2016-04-01

    Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ∼t rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models. PMID:26546979

  13. Acceptance of genetic testing in a general population

    DEFF Research Database (Denmark)

    Aro, A R; Hakonen, A; Hietala, M;

    1997-01-01

    The aim of the study was to analyze effects of age, education and gender on acceptance of genetic testing. Subjects, n = 1967 aged 15-69, were a stratified random sample of the Finnish population. One thousand, one hundred and sixty nine subjects, 530 men and 639 women, returned the questionnaire....... The majority of the respondents approved of the availability of genetic testing. Young, aged 15-24, were more favourable towards testing and more willing to undergo suggested tests, but they were also more worried than others about the misuse of test results. Men aged 45-69 with only basic education...... were more in favour of mandatory genetic testing than other respondents. Respondents with university education were more critical towards genetic testing and expressed their worry about eugenics more often than other education groups. In conclusion, there are age, education and gender related...

  14. How allocation of individuals depends on genetic differences among populations

    Energy Technology Data Exchange (ETDEWEB)

    Smouse, P.E. (Univ. of Michigan, Ann Arbor, MI); Spielman, R.S.

    1976-10-10

    Several different subsets of eight codominant loci were used to allocate single individuals to one of seven South American Indian populations. Three different levels of biological organization were investigated: tribes, village-clusters within a single tribe, and villages within a single cluster. The proportion of correct allocation increased with the number of genetic markers used and with the average genetic distance among the populations. Using all eight loci, the correct allocation percentage to villages, clusters and tribes was 20.69%, 34.88% and 56.96%, respectively. A theoretical relationship was given which approximately predicts correct allocation fraction, on the basis of the number of groups and the average genetic distance between them. Using allelic frequency data from the literature, this relationship was used to predict 87% correct allocation for a set of racial groups, including Amerindians, Eskimoes, Japanese, Scandinavians, Bantus, Australian Aborigines and Polynesians. The results indicate that allelic frequency differences among populations collectively permit allocation of individuals to the correct population with substantial reliability, and that the differences among human populations are therefore large, relative to differences within.

  15. Accurate crop classification using hierarchical genetic fuzzy rule-based systems

    Science.gov (United States)

    Topaloglou, Charalampos A.; Mylonas, Stelios K.; Stavrakoudis, Dimitris G.; Mastorocostas, Paris A.; Theocharis, John B.

    2014-10-01

    This paper investigates the effectiveness of an advanced classification system for accurate crop classification using very high resolution (VHR) satellite imagery. Specifically, a recently proposed genetic fuzzy rule-based classification system (GFRBCS) is employed, namely, the Hierarchical Rule-based Linguistic Classifier (HiRLiC). HiRLiC's model comprises a small set of simple IF-THEN fuzzy rules, easily interpretable by humans. One of its most important attributes is that its learning algorithm requires minimum user interaction, since the most important learning parameters affecting the classification accuracy are determined by the learning algorithm automatically. HiRLiC is applied in a challenging crop classification task, using a SPOT5 satellite image over an intensively cultivated area in a lake-wetland ecosystem in northern Greece. A rich set of higher-order spectral and textural features is derived from the initial bands of the (pan-sharpened) image, resulting in an input space comprising 119 features. The experimental analysis proves that HiRLiC compares favorably to other interpretable classifiers of the literature, both in terms of structural complexity and classification accuracy. Its testing accuracy was very close to that obtained by complex state-of-the-art classification systems, such as the support vector machines (SVM) and random forest (RF) classifiers. Nevertheless, visual inspection of the derived classification maps shows that HiRLiC is characterized by higher generalization properties, providing more homogeneous classifications that the competitors. Moreover, the runtime requirements for producing the thematic map was orders of magnitude lower than the respective for the competitors.

  16. Chronic irradiation as an ecological factor affecting genetic population structure

    International Nuclear Information System (INIS)

    Genetic structure of two Centaurea scabiosa L. populations was studied by frequency distribution of leucine aminopeptidase (LAP) locus genotypes. The experimental population has been growing under conditions of chronic irradiation, with the dose per generation amounting to 1.2 to 25.5 Gy. In it, mutational variants are observed with a frequency of 5.4.10(-3)-4.5.10(-2) per generation (as compared to control population frequency at 5.4.10(-4)). Indexes for heterozygosity, mean number of genotypes, and effective number of alleles were higher in the experimental population. Segregation analysis revealed no differences in viability in the control population, and all genotypic combinations were found to be nearly neutral. In the experimental population, however, significant differences in relative viability of the genotypes were disclosed. The relative viability of heterozygotes for mutant allele C' was nearly maximum, while heterozygotes for other mutant alleles showed minimum viability. We reach the conclusion that the differences in genetic structure of the populations under investigation can be explained by the chronic irradiation factor that brought out differences in adaptability of both normal and mutant genotypes. The suggestion is that intra-locus interactions of the C' allele with normal alleles determine plant resistance to a wide range of unfavorable environmental conditions

  17. Population structure and genetic diversity of moose in Alaska.

    Science.gov (United States)

    Schmidt, Jennifer I; Hundertmark, Kris J; Bowyer, R Terry; McCracken, Kevin G

    2009-01-01

    Moose (Alces alces) are highly mobile mammals that occur across arboreal regions of North America, Europe, and Asia. Alaskan moose (Alces alces gigas) range across much of Alaska and are primary herbivore consumers, exerting a prominent influence on ecosystem structure and functioning. Increased knowledge gained from population genetics provides insights into their population dynamics, history, and dispersal of these unique large herbivores and can aid in conservation efforts. We examined the genetic diversity and population structure of moose (n = 141) with 8 polymorphic microsatellites from 6 regions spanning much of Alaska. Expected heterozygosity was moderate (H(E) = 0.483-0.612), and private alleles ranged from 0 to 6. Both F(ST) and R(ST) indicated significant population structure (P moose from the Yakutat and Tetlin regions versus all other moose, with slight substructure observed among the second population. Estimates of dispersal differed between analytical approaches, indicating a high level of historical or current gene flow. Mantel tests indicated that isolation-by-distance partially explained observed structure among moose populations (R(2) = 0.45, P moose in Alaska with population expansion from interior Alaska westward toward the coast. PMID:18836148

  18. Change in genetic size of small-closed populations: lessons from a domestic mammal population

    Directory of Open Access Journals (Sweden)

    Farhad Ghafouri-Kesbi

    2010-01-01

    Full Text Available The aim of this study was to monitor changes in genetic size of a small-closed population of Iranian Zandi sheep, by using pedigree information from animals born between 1991 and 2005. The genetic size was assessed by using measures based on the probability of identity-by-descend of genes (coancestry, f, and effective population size, Ne, as well as measures based on probability of gene origin (effective number of founders, f e, effective number of founder genomes, f g, and effective number of non-founder genomes, f ne. Average coancestry, or the degree of genetic similarity of individuals, increased from 0.81% to 1.44% during the period 1993 to 2005, at the same time that Ne decreased from 263 to 93. The observed trend for f e was irregular throughout the experiment in a way that f e was 68, 87, 77, 92, and 80 in 1993, 1996, 1999, 2002, and 2005, respectively. Simultaneously, f g, the most informative effective number, decreased from 61 to 35. The index of genetic diversity (GD which was obtained from estimates of f g,decreased about 2% throughout the period studied. In addition, a noticeable reduction was observed in the estimates of f ne from 595 in 1993 to 61 in 2005. The higher than 1 ratio of f e to f g indicated the presence of bottlenecks and genetic drift in the development of this population of Zandi sheep. From 1993 to 1999, f ne was much higher than f e, thereby indicating that with respect to loss of genetic diversity, the unequal contribution of founders was more important than the random genetic drift in non-founder generations. Subsequently, random genetic drift in non-founder generations was the major reason for f e> f ne. The minimization of average coancestry in new reproductive individuals was recommended as a means of preserving the population against a further loss in genetic diversity.

  19. Population genetics of non-genetic traits: Evolutionary roles of stochasticity in gene expression

    KAUST Repository

    Mineta, Katsuhiko

    2015-05-01

    The role of stochasticity in evolutionary genetics has long been debated. To date, however, the potential roles of non-genetic traits in evolutionary processes have been largely neglected. In molecular biology, growing evidence suggests that stochasticity in gene expression (SGE) is common and that SGE has major impacts on phenotypes and fitness. Here, we provide a general overview of the potential effects of SGE on population genetic parameters, arguing that SGE can indeed have a profound effect on evolutionary processes. Our analyses suggest that SGE potentially alters the fate of mutations by influencing effective population size and fixation probability. In addition, a genetic control of SGE magnitude could evolve under certain conditions, if the fitness of the less-fit individual increases due to SGE and environmental fluctuation. Although empirical evidence for our arguments is yet to come, methodological developments for precisely measuring SGE in living organisms will further advance our understanding of SGE-driven evolution.

  20. Genetic affinities of the central Indian tribal populations.

    Directory of Open Access Journals (Sweden)

    Gunjan Sharma

    Full Text Available BACKGROUND: The central Indian state Madhya Pradesh is often called as 'heart of India' and has always been an important region functioning as a trinexus belt for three major language families (Indo-European, Dravidian and Austroasiatic. There are less detailed genetic studies on the populations inhabited in this region. Therefore, this study is an attempt for extensive characterization of genetic ancestries of three tribal populations, namely; Bharia, Bhil and Sahariya, inhabiting this region using haploid and diploid DNA markers. METHODOLOGY/PRINCIPAL FINDINGS: Mitochondrial DNA analysis showed high diversity, including some of the older sublineages of M haplogroup and prominent R lineages in all the three tribes. Y-chromosomal biallelic markers revealed high frequency of Austroasiatic-specific M95-O2a haplogroup in Bharia and Sahariya, M82-H1a in Bhil and M17-R1a in Bhil and Sahariya. The results obtained by haploid as well as diploid genetic markers revealed strong genetic affinity of Bharia (a Dravidian speaking tribe with the Austroasiatic (Munda group. The gene flow from Austroasiatic group is further confirmed by their Y-STRs haplotype sharing analysis, where we determined their founder haplotype from the North Munda speaking tribe, while, autosomal analysis was largely in concordant with the haploid DNA results. CONCLUSIONS/SIGNIFICANCE: Bhil exhibited largely Indo-European specific ancestry, while Sahariya and Bharia showed admixed genetic package of Indo-European and Austroasiatic populations. Hence, in a landscape like India, linguistic label doesn't unequivocally follow the genetic footprints.

  1. Population genetics of atta sexdens rubropilosa (hymenoptera: formicidae)

    OpenAIRE

    Belizário Cantagalli, Liriana; Aparecida Mangolin, Claudete; Colla Ruvolo Takasusuki, Maria Claudia

    2013-01-01

    The genetic variability of Atta sexdens rubropilosa leaf-cutting ants collected from five brazilian localities was evaluated with PCR-RAPD technique. We used 15 primers producing 148 fragments of which 123 (83,11 %) contained polymorphisms. The estimated Shannon index was 0.3836 ± 0.2335 showing that these ants possess high genetic diversity. The GST value was 0,2372 and PT = 0,184, indicating that the analyzed populations are moderately differentiated and 82 % of the variation obtained occur...

  2. Exhaustive search for conservation networks of populations representing genetic diversity.

    Science.gov (United States)

    Diniz-Filho, J A F; Diniz, J V B P L; Telles, M P C

    2016-01-01

    Conservation strategies routinely use optimization methods to identify the smallest number of units required to represent a set of features that need to be conserved, including biomes, species, and populations. In this study, we provide R scripts to facilitate exhaustive search for solutions that represent all of the alleles in networks with the smallest possible number of populations. The script also allows other variables to be added to describe the populations, thereby providing the basis for multi-objective optimization and the construction of Pareto curves by averaging the values in the solutions. We applied this algorithm to an empirical dataset that comprised 23 populations of Eugenia dysenterica, which is a tree species with a widespread distribution in the Cerrado biome. We observed that 15 populations would be necessary to represent all 249 alleles based on 11 microsatellite loci, and that the likelihood of representing all of the alleles with random networks is less than 0.0001. We selected the solution (from two with the smallest number of populations) obtained for the populations with a higher level of climatic stability as the best strategy for in situ conservation of genetic diversity of E. dysenterica. The scripts provided in this study are a simple and efficient alternative to more complex optimization methods, especially when the number of populations is relatively small (i.e., <25 populations). PMID:26909939

  3. Genetic Diversity and Genetic Structure of Different Types of Natural Populations in Osmanthus fragrans Lour. and the Relationships with Sex Ratio, Population Structure, and Geographic Isolation

    Science.gov (United States)

    Hu, Shaoqing; Wu, Shuai; Wang, Yiguang; Zhang, Yuanyan

    2014-01-01

    Osmanthus fragrans Lour., an evergreen small tree, has the rare sexual system of androdioecy (coexistence of males and hermaphrodites), once with wide-spread natural distribution in the areas of the South Yangzi river basin. However, due to excessive human utilization, natural distribution became fragmented and the number and size of natural populations reduced sharply. With four different types of natural populations from the same region as research object, we aim to provide a comparative analysis on the relationships among genetic diversity, sexual system, population structure and size, and geographic isolation by ISSR. In genetic parameters of Ne, He, and I, the LQGC population had the highest value and the LQZGQ population had the lowest value. These indicated that LQGC population showed the highest genetic diversity, followed by QDH and JN population, and LQZGQ population exhibited the lowest genetic diversity. Genetic diversity in populations is closely related to population structure, reproduction mode, and sex ratio. However, there seems to be no obvious correlation between genetic diversity and population size. The results of AMOVA showed that genetic variations mostly occurred within populations. It indicates that no significant genetic differentiation among populations occurs, and geographic isolation has no significant effect on genetic diversity. PMID:25436228

  4. Hitchhiker's guide to genetic diversity in socially structured populations

    Institute of Scientific and Technical Information of China (English)

    L.S.PREMO

    2012-01-01

    When selection increases the frequency of a beneficial gene substitution it can also increase the frequencies of linked neutral alleles through a process called genetic hitchhiking.A model built to investigate reduced genetic diversity in Pleistocene hominins shows that genetic hitchhiking can have a strong effect on neutral diversity in the presence of culturally mediated migration.Under conditions in which genetic and cultural variants are transmitted symmetrically,neutral genes may also hitchhike to higher frequencies on the coattails of adaptive cultural traits through a process called cultural hitchhiking.Cultural hitchhiking has been proposed to explain why some species of matrilineal whales display relatively low levels of mitochondrial DNA diversity,and it may be applicable to humans as well.This paper provides a critical review of recent models of both types of hitchhiking in socially structured populations.The models' assumptions and predictions are compared and discussed in the hope that studies of reduced genetic diversity in humans might improve our understanding of reduced genetic diversity in other species,and vice versa [Current Zoology 58 (1):287-297,2012].

  5. Gene Flow and Genetic Diversity of a Broadcast-Spawning Coral in Northern Peripheral Populations

    OpenAIRE

    Yuichi Nakajima; Akira Nishikawa; Akira Iguchi; Kazuhiko Sakai

    2010-01-01

    Recently, reef-building coral populations have been decreasing worldwide due to various disturbances. Population genetic studies are helpful for estimating the genetic connectivity among populations of marine sessile organisms with metapopulation structures such as corals. Moreover, the relationship between latitude and genetic diversity is informative when evaluating the fragility of populations. In this study, using highly variable markers, we examined the population genetics of the broadca...

  6. Classification method for heterogeneity in monoclonal cell population

    Science.gov (United States)

    Aburatani, S.; Tashiro, K.; Kuhara, S.

    2015-09-01

    Monoclonal cell populations are known to be composed of heterogeneous subpopulations, thus complicating the data analysis. To gain clear insights into the mechanisms of cellular systems, biological data from a homogeneous cell population should be obtained. In this study, we developed a method based on Latent Profile Analysis (LPA) combined with Confirmatory Factor Analysis (CFA) to divide mixed data into classes, depending on their heterogeneity. In general cluster analysis, the number of measured points is a constraint, and thereby the data must be classified into fewer groups than the number of samples. By our newly developed method, the measured data can be divided into groups depending on their latent effects, without constraints. Our method is useful to clarify all types of omics data, including transcriptome, proteome and metabolic information.

  7. Genetic Characterization and Classification of Human and Animal Sapoviruses

    Science.gov (United States)

    Oka, Tomoichiro; Lu, Zhongyan; Phan, Tung; Delwart, Eric L.; Saif, Linda J.; Wang, Qiuhong

    2016-01-01

    Sapoviruses (SaVs) are enteric caliciviruses that have been detected in multiple mammalian species, including humans, pigs, mink, dogs, sea lions, chimpanzees, and rats. They show a high level of diversity. A SaV genome commonly encodes seven nonstructural proteins (NSs), including the RNA polymerase protein NS7, and two structural proteins (VP1 and VP2). We classified human and animal SaVs into 15 genogroups (G) based on available VP1 sequences, including three newly characterized genomes from this study. We sequenced the full length genomes of one new genogroup V (GV), one GVII and one GVIII porcine SaV using long range RT-PCR including newly designed forward primers located in the conserved motifs of the putative NS3, and also 5' RACE methods. We also determined the 5’- and 3’-ends of sea lion GV SaV and canine GXIII SaV. Although the complete genomic sequences of GIX-GXII, and GXV SaVs are unavailable, common features of SaV genomes include: 1) “GTG” at the 5′-end of the genome, and a short (9~14 nt) 5′-untranslated region; and 2) the first five amino acids (M [A/V] S [K/R] P) of the putative NS1 and the five amino acids (FEMEG) surrounding the putative cleavage site between NS7 and VP1 were conserved among the chimpanzee, two of five genogroups of pig (GV and GVIII), sea lion, canine, and human SaVs. In contrast, these two amino acid motifs were clearly different in three genogroups of porcine (GIII, GVI and GVII), and bat SaVs. Our results suggest that several animal SaVs have genetic similarities to human SaVs. However, the ability of SaVs to be transmitted between humans and animals is uncertain. PMID:27228126

  8. A modified decision tree algorithm based on genetic algorithm for mobile user classification problem.

    Science.gov (United States)

    Liu, Dong-sheng; Fan, Shu-jiang

    2014-01-01

    In order to offer mobile customers better service, we should classify the mobile user firstly. Aimed at the limitations of previous classification methods, this paper puts forward a modified decision tree algorithm for mobile user classification, which introduced genetic algorithm to optimize the results of the decision tree algorithm. We also take the context information as a classification attributes for the mobile user and we classify the context into public context and private context classes. Then we analyze the processes and operators of the algorithm. At last, we make an experiment on the mobile user with the algorithm, we can classify the mobile user into Basic service user, E-service user, Plus service user, and Total service user classes and we can also get some rules about the mobile user. Compared to C4.5 decision tree algorithm and SVM algorithm, the algorithm we proposed in this paper has higher accuracy and more simplicity. PMID:24688389

  9. Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus

    OpenAIRE

    Furlan, Elise; Stoklosa, J; Griffiths, J.; Gust, N; Ellis, R.; Huggins, R. M.; WEEKS, A. R.

    2012-01-01

    Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, ...

  10. Reconstructing the Population Genetic History of the Caribbean

    Science.gov (United States)

    Moreno-Estrada, Andrés; Gravel, Simon; Zakharia, Fouad; McCauley, Jacob L.; Byrnes, Jake K.; Gignoux, Christopher R.; Ortiz-Tello, Patricia A.; Martínez, Ricardo J.; Hedges, Dale J.; Morris, Richard W.; Eng, Celeste; Sandoval, Karla; Acevedo-Acevedo, Suehelay; Norman, Paul J.; Layrisse, Zulay; Parham, Peter; Martínez-Cruzado, Juan Carlos; Burchard, Esteban González; Cuccaro, Michael L.; Martin, Eden R.; Bustamante, Carlos D.

    2013-01-01

    The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse—which today is reflected by shorter, older ancestry tracts—consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse—reflected by longer, younger tracts—is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub

  11. Genetic Algorithm Optimized Back Propagation Neural Network for Knee Osteoarthritis Classification

    Directory of Open Access Journals (Sweden)

    Jian WeiKoh

    2014-10-01

    Full Text Available Osteoarthritis (OA is the most common form of arthritis that caused by degeneration of articular cartilage, which function as shock absorption cushion in our joint. The most common joints that infected by osteoarthritis are hand, hip, spine and knee. Knee osteoarthritis is the focus in this study. These days, Magnetic Resonance Imaging (MRI technique is widely applied in diagnosis the progression of osteoarthritis due to the ability to display the contrast between bone and cartilage. Traditionally, interpretation of MR image is done manually by physicians who are very inconsistent and time consuming. Hence, automated classifier is needed for minimize the processing time of classification. In this study, genetic algorithm optimized neural network technique is used for the knee osteoarthritis classification. This classifier consists of 4 stages, which are feature extraction by Discrete Wavelet Transform (DWT, training stage of neural network, testing stage of neural network and optimization stage by Genetic Algorithm (GA. This technique obtained 98.5% of classification accuracy when training and 94.67% on testing stage. Besides, classification time is reduced by 17.24% after optimization of the neural network.

  12. Into the depth of population genetics: pattern of structuring in mesophotic red coral populations

    Science.gov (United States)

    Costantini, Federica; Abbiati, Marco

    2016-03-01

    Deep-sea reef-building corals are among the most conspicuous invertebrates inhabiting the hard-bottom habitats worldwide and are particularly susceptible to human threats. The precious red coral ( Corallium rubrum, L. 1758) has a wide bathymetric distribution, from shallow up to 800 m depth, and represents a key species in the Mediterranean mesophotic reefs. Several studies have investigated genetic variability in shallow-water red coral populations, while geographic patterns in mesophotic habitats are largely unknown. This study investigated genetic variability of C. rubrum populations dwelling between 55 and 120 m depth, from the Ligurian to the Ionian Sea along about 1500 km of coastline. A total of 18 deep rocky banks were sampled. Colonies were analyzed by means of a set of microsatellite loci and the putative control region of the mitochondrial DNA. Collected data were compared with previous studies. Both types of molecular markers showed high genetic similarity between populations within the northern (Ligurian Sea and Tuscan Archipelago) and the southern (Tyrrhenian and Ionian seas) study areas. Variability in habitat features between the sampling sites did not affect the genetic variability of the populations. Conversely, the patchy distribution of suitable habitats affected populations' connectivity within and among deep coral banks. Based on these results and due to the emphasis on red coral protection in the Mediterranean Sea by international institutions, red coral could be promoted as a `focal species' to develop management plans for the conservation of deep coralligenous reefs, a reservoir of marine biodiversity.

  13. A Novel Training Algorithm of Genetic Neural Networks and Its Application to Classification

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    First of all, this paper discusses the drawbacks of multilayer perceptron (MLP), which is trained by the traditional back propagation (BP) algorithm and used in a special classification problem. A new training algorithm for neural networks based on genetic algorithm and BP algorithm is developed. The difference between the new training algorithm and BP algorithm in the ability of nonlinear approaching is expressed through an example, and the application foreground is illustrated by an example.

  14. Population genetic segmentation of MHC-correlated perfume preferences.

    Science.gov (United States)

    Hämmerli, A; Schweisgut, C; Kaegi, M

    2012-04-01

    It has become difficult to find a matching perfume. An overwhelming number of 300 new perfumes launch each year, and marketing campaigns target pre-defined groups based on gender, age or income rather than on individual preferences. Recent evidence for a genetic basis of perfume preferences, however, could be the starting point for a novel population genetic approach to better match perfumes with people's preferences. With a total of 116 participants genotyped for alleles of three loci of the major histocompatibility complex (MHC), the aim of this study was to test whether common MHC alleles could be used as genetic markers to segment a given population into preference types. Significant deviations from random expectations for a set of 10 common perfume ingredients indicate how such segmentation could be achieved. In addition, preference patterns of participants confronted with images that contained a sexual communication context significantly differed in their ratings for some of the scents compared with participants confronted with images of perfume bottles. This strongly supports the assumption that genetically correlated perfume preferences evolved in the context of sexual communication. The results are discussed in the light of perfume customization. PMID:22084926

  15. Logistic regression protects against population structure in genetic association studies

    OpenAIRE

    Setakis, Efrosini; Stirnadel, Heide; Balding, David J.

    2006-01-01

    We conduct an extensive simulation study to compare the merits of several methods for using null (unlinked) markers to protect against false positives due to cryptic substructure in population-based genetic association studies. The more sophisticated “structured association” methods perform well but are computationally demanding and rely on estimating the correct number of subpopulations. The simple and fast “genomic control” approach can lose power in certain scenarios. We find that procedur...

  16. Spontaneous genetic clustering in populations of competing organisms

    International Nuclear Information System (INIS)

    We introduce and analyse an individual-based evolutionary model, in which a population of genetically diverse organisms compete with each other for limited resources. Through theoretical analysis and stochastic simulations, we show that the model exhibits a pattern-forming instability which is highly amplified by the effects of demographic noise, leading to the spontaneous formation of genotypic clusters. This mechanism supports the thesis that stochasticity has a central role in the formation and coherence of species. (paper)

  17. Evolutionary Reconstruction and Population Genetics Analysis of Aurora Kinases

    OpenAIRE

    Balu Kamaraj; Ambuj Kumar; Rituraj Purohit

    2013-01-01

    BACKGROUND: Aurora kinases belong to the highly conserved kinase family and play a vital role in cell cycle regulation. The structure and function of these kinases are inter-related and sometimes they also act as substitutes in case of knockdown of other aurora kinases. METHOD: In this work we carried out the evolutionary reconstruction and population genetic studies of aurora kinase proteins. Substitution saturation test, CAI (Codon adaptation index), gene expression and RSCU (Relative synon...

  18. Population genetics of the frog-killing fungus Batrachochytrium dendrobatidis

    OpenAIRE

    Morgan, Jess A T; Vance T Vredenburg; Rachowicz, Lara J.; Knapp, Roland A; Stice, Mary J.; Tunstall, Tate; Bingham, Rob E.; Parker, John M.; Longcore, Joyce E.; Moritz, Craig; Briggs, Cheryl J.; Taylor, John W.

    2007-01-01

    Global amphibian decline by chytridiomycosis is a major environmental disaster that has been attributed to either recent fungal spread or environmental change that promotes disease. Here, we present a population genetic comparison of Batrachochytrium dendrobatidis isolates from an intensively studied region of frog decline, the Sierra Nevada of California. In support of a novel pathogen, we find low diversity, no amphibian-host specificity, little correlation between fungal genotype and geogr...

  19. Genetic Predisposition for Dermal Problems in Hexavalent Chromium Exposed Population

    OpenAIRE

    Priti Sharma; Vipin Bihari; Agarwal, Sudhir K.; Goel, Sudhir K.

    2012-01-01

    We studied the effect of genetic susceptibility on hexavalent chromium induced dermal adversities. The health status of population was examined from the areas of Kanpur (India) having the elevated hexavalent chromium levels in groundwater. Blood samples were collected for DNA isolation to conduct polymorphic determination of genes, namely: NQO1 (C609T), hOGG1 (C1245G), GSTT1, and GSTM1 (deletion). Symptomatic exposed subjects (n = 38) were compared with asymptomatic exposed subjects (n = 108)...

  20. Population genetic studies in Northeastern Atlantic minke whales

    OpenAIRE

    Berube, M.; Skaug, Hans Julius; Andersen, Liselotte W.; Haug, Tore; Øien, Nils

    2007-01-01

    Minke whales are the most abundance species of baleen whales in the North Atlantic. As part of current management of minke whales in Norwegian and adjacent waters, a DNA-register have been established. The register ensures that samples are taken of each animal caught under the Norwegian catch quota, and that a DNA-profile is established and stored in a database from each individual whale. Previous studies have indicated that genetic population sub-structure exists within the North Atlantic, b...

  1. Integrating genetic data and population viability analyses for the identification of harbour seal (Phoca vitulina) populations and management units

    DEFF Research Database (Denmark)

    Olsen, Morten Tange; Andersen, Liselotte Wesley; Dietz, Rune;

    2014-01-01

    present a novel approach, integrating genetic, life-history and demographic data to identify populations and management units in southern Scandinavian harbour seals. First, 15 microsatellite markers and model- and distance-based genetic clustering methods were used to determine the population genetic...... structure in harbour seals. Second, we used harbour seal demographic and life-history data to conduct population viability analyses (PVAs) in the VORTEX simulation model in order to determine whether the inferred genetic units could be classified as management units according to Lowe and Allendorf's (2010......) "population viability criterion" for demographic independence. The genetic analyses revealed fine-scale population structuring in southern Scandinavian harbour seals and pointed to the existence of six genetic units. The PVAs indicated that the census population size of each of these genetic units...

  2. Complex genetic origin of Indian populations and its implications

    Indian Academy of Sciences (India)

    Rakesh Tamang; Lalji Singh; Kumarasamy Thangaraj

    2012-11-01

    Indian populations are classified into various caste, tribe and religious groups, which altogether makes them very unique compared to rest of the world. The long-term firm socio-religious boundaries and the strict endogamy practices along with the evolutionary forces have further supplemented the existing high-level diversity. As a result, drawing definite conclusions on its overall origin, affinity, health and disease conditions become even more sophisticated than was thought earlier. In spite of these challenges, researchers have undertaken tireless and extensive investigations using various genetic markers to estimate genetic variation and its implication in health and diseases. We have demonstrated that the Indian populations are the descendents of the very first modern humans, who ventured the journey of out-of-Africa about 65,000 years ago. The recent gene flow from east and west Eurasia is also evident. Thus, this review attempts to summarize the unique genetic variation among Indian populations as evident from our extensive study among approximately 20,000 samples across India.

  3. Prospects for vector control through genetic manipulation of populations.

    Science.gov (United States)

    Craig, G B

    1963-01-01

    Since the development of insecticide-resistance and the consequent partial failure of the chemical approach to the control of disease vectors, interest in the biological approach has re-awakened. An aspect of the latter approach that is of great current interest is "autocidal control"-that is, the use of insects for their own destruction. This paper discusses the various ways in which genetic mechanisms can be used to bring about the destruction of harmful insects, with special reference to those of medical importance. The author considers that the prospects for the genetic control of vector species are good, but stresses that before genetic methods can be applied on a field scale certain requirements must be met. For example, genetic technology must be expanded, a firm background of genetic knowledge of vector species must be built up, a great deal more information about vector ecology, particularly population dynamics, must be acquired, and techniques for the mass production of vector insects under controlled conditions must be developed. PMID:20604180

  4. Expanding the population genetic perspective of cnidarian-Symbiodinium symbioses.

    Science.gov (United States)

    Santos, Scott R

    2014-09-01

    The modern synthesis was a seminal period in the biological sciences, establishing many of the core principles of evolutionary biology that we know today. Significant catalysts were the contributions of R.A. Fisher, J.B.S. Haldane and Sewall Wright (and others) developing the theoretical underpinning of population genetics, thus demonstrating adaptive evolution resulted from the interplay of forces such as natural selection and mutation within groups of individuals occupying the same space and time (i.e. a population). Given its importance, it is surprising that detailed population genetic data remain lacking for numerous organisms vital to many ecosystems. For example, the coral reef ecosystem is well recognized for its high biodiversity and productivity, numerous ecological services and significant economic and societal values (Moberg & Folke 1999;Cinner 2014). Many coral reef invertebrates form symbiotic relationships with single-celled dinoflagellates within the genus Symbiodinium Freudenthal (Taylor 1974), with hosts providing these (typically) intracellular symbionts with by-products of metabolism and in turn receiving photosynthetically fixed carbon capable of meeting hosts' respiratory demands (Falkowski et al. 1984; Muscatine et al. 1984). Unfortunately, the health and integrity of the coral reef ecosystem has been significantly and negatively impacted by onslaughts like anthropogenic eutrophication and disease in addition to global climate change, with increased incidences of 'bleaching' events (characterized as the loss of photosynthetic pigments from the algal cell or massive reduction of Symbiodinium density from hosts' tissue) and host mortality leading to staggering declines in geographic coverage (Bruno & Selig 2007) that have raised questions on the viability of this ecosystem as we know it (Bellwood et al. 2004; Parmesan 2006). One avenue towards anticipating the future of the coral reef ecosystem is by developing a broader and deeper

  5. Population genetic structure in the paddyfield warbler (Acrocephalus agricola Jerd.)

    Institute of Scientific and Technical Information of China (English)

    Pavel ZEHTINDJIEV; Mihaela ILIEVA; Bengt HANSSON; Olga OPARINA; Mihail OPARIN; Staffan BENSCH

    2011-01-01

    Population genefc structure was studied in paddyfield warblers Acrocephalus agricola breeding in NE Bulgaria, SE Russia and S Kazakhstan. We were particularly interested in the degree of genetic differentiation and gene flow of the Bulgarian population due to its geographical isolation, recent origin and unique migratory strategy. Analyses of mitochondrial DNA (mtDNA) showed that there was no divergence between Bulgarian and Russian populations (FST = 0.007), whereas those in Kazakhstan differed significantly from the European breeding populations (Russia: FST = 0.058; Bulgaria: Fsr = 0.114). The degree of differentiation between populations at nuclear markers (five microsatellite loci; FsT ≈ 0) was weaker than for mtDNA. We suggest that this relatively weak differentiation over the range of this species reflects a recent postglacial expansion, and results from mismatch distribution analyses and Fu's Fs tests are in agreement. Preservation of small and geographically isolated populations which may contain individuals with unique adaptive traits, such as the studied Bulgarian population of paddyfield warbler,is valuable for the long-term conservation of expanding migratory bird species.

  6. Genetic variation and population structure of interleukin genes among seven ethnic populations from Karnataka, India

    Indian Academy of Sciences (India)

    Srilakshmi M. Raj; Diddahally R. Govindaraju; Ranajit Chakraborty

    2007-12-01

    The extent of genetic variation and the degree of genetic differentiation among seven ethnic populations from Karnataka, India (Bunt, Havyak, Iyengar, Lingayath, Smartha, Vaishya, Vokkaliga), was investigated using four single nucleotide polymorphisms (SNPs: IL-1A 4845, IL-1B 3954, IL-1B 511 and IL-1RA 2018) of the interleukin gene cluster. Allele frequencies varied by threefold among these populations, which also differed for gene diversity and heterozygosity levels. The average degree of population subdivision among these castes was low ($F_{ST} = 0.02$). However, pair-wise interpopulation differentiation ranged from 0–7%, indicating no detectable differentiation to moderate differentiation between specific populations. The results of phylogenetic analysis based on genetic distances between populations agreed with known social and cultural data on these ethnic groups. Variation in the allele frequencies, as well as differentiation, may be attributed to differential selection and demographic factors including consanguinity among the ethnic groups. Information on the distribution of functionally relevant polymorphisms among ethnic populations may be important towards developing community medicine and public health policies.

  7. Factors affecting the exchange of genetic material between Nordic and US Holstein populations

    DEFF Research Database (Denmark)

    Buch, Line Hjortø; Sørensen, A.C.; Lassen, Jan;

    2009-01-01

    assumptions made in the simulation study, especially the genetic correlations between traits. A more similar relative weighting of the index traits across populations did not change total genetic gain in the Nordic Holstein population. The possibility of exchanging genetic material with the US Holstein...... population size is of greater importance than differences in trait definitions and relative weighting of the index traits for the advantage of exchanging genetic material between the Nordic and the US Holstein populations. The possibility of exchanging genetic material with the Nordic Holstein population did......, importation of genetic material from Nordic Holsteins may slow down the deterioration of animal health and reproduction in US Holsteins...

  8. Population Abundance and Genetic Structure of Black Bears in Coastal North Carolina and Virginia Using Noninvasive Genetic Techniques.

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Master thesis on the population abundance and genetic structure of black bears in coastal North Carolina and Virginia using noninvasive genetic technigues on...

  9. Whole mitochondrial genome genetic diversity in an Estonian population sample.

    Science.gov (United States)

    Stoljarova, Monika; King, Jonathan L; Takahashi, Maiko; Aaspõllu, Anu; Budowle, Bruce

    2016-01-01

    Mitochondrial DNA is a useful marker for population studies, human identification, and forensic analysis. Commonly used hypervariable regions I and II (HVI/HVII) were reported to contain as little as 25% of mitochondrial DNA variants and therefore the majority of power of discrimination of mitochondrial DNA resides in the coding region. Massively parallel sequencing technology enables entire mitochondrial genome sequencing. In this study, buccal swabs were collected from 114 unrelated Estonians and whole mitochondrial genome sequences were generated using the Illumina MiSeq system. The results are concordant with previous mtDNA control region reports of high haplogroup HV and U frequencies (47.4 and 23.7% in this study, respectively) in the Estonian population. One sample with the Northern Asian haplogroup D was detected. The genetic diversity of the Estonian population sample was estimated to be 99.67 and 95.85%, for mtGenome and HVI/HVII data, respectively. The random match probability for mtGenome data was 1.20 versus 4.99% for HVI/HVII. The nucleotide mean pairwise difference was 27 ± 11 for mtGenome and 7 ± 3 for HVI/HVII data. These data describe the genetic diversity of the Estonian population sample and emphasize the power of discrimination of the entire mitochondrial genome over the hypervariable regions. PMID:26289416

  10. Genetic divergence between Melipona quadrifasciata Lepeletier (Hymenoptera, Apidae populations

    Directory of Open Access Journals (Sweden)

    Mara Garcia Tavares

    2013-01-01

    Full Text Available Melipona quadrifasciata is a stingless bee widely found throughout the Brazilian territory, with two recognized subspecies, M. quadrifasciata anthidioides, that exhibits interrupted metasomal stripes, and M. quadrifasciata quadrifasciata, with continuous metasomal stripes. This study aimed to estimate the genetic variability of these subspecies. For this purpose, 127 colonies from 15 Brazilian localities were analyzed, using nine species-specific microsatellite primers. At these loci, the number of alleles ranged from three to 15 (mean: 7.2, and the observed heterozygosity (Ho ranged from 0.03-0.21, while the expected heterozygosity (He ranged from 0.23-0.47. The genetic distances among populations ranged from 0.03-0.45. The F ST multilocus value (0.23 indicated that the populations sampled were structured, and the clustering analysis showed the formation of two subgroups and two more distant populations. The first group contained the subspecies M. quadrifasciata quadrifasciata, and the other, the subspecies M. quadrifasciata anthidioides and the two M. quadrifasciata populations with continuous metasomal stripes from northern Minas Gerais. These results confirmed that the yellow metasomal stripes alone are not a good means for correctly identifying the different subspecies of M. quadrifasciata.

  11. Classification

    Science.gov (United States)

    Clary, Renee; Wandersee, James

    2013-01-01

    In this article, Renee Clary and James Wandersee describe the beginnings of "Classification," which lies at the very heart of science and depends upon pattern recognition. Clary and Wandersee approach patterns by first telling the story of the "Linnaean classification system," introduced by Carl Linnacus (1707-1778), who is…

  12. Modified Multi-Population Genetic Algorithm for Yeast Fed-batch Cultivation Parameter Identification

    Directory of Open Access Journals (Sweden)

    Angelova M.

    2009-12-01

    Full Text Available In this work, a modified multi-population genetic algorithm is developed for the purpose of parameter identification of fermentation process model. Modified multi-population genetic algorithm is similar to the multi-population one and its development is instigated by modified genetic algorithm, similar to simple one. A comparison of four types of genetic algorithms, namely simple, modified, multipopulation and modified multi-population is presented for parameter identification of a fed-batch cultivation of Saccharomyces cerevisiae

  13. Clinical and Pharmacogenomic Implications of Genetic Variation in a Southern Ethiopian Population

    OpenAIRE

    Tekola-Ayele, Fasil; Adeyemo, Adebowale; Aseffa, Abraham; Hailu, Elena; Finan, Chris; Davey, Gail; Rotimi, Charles N.; Newport, Melanie J.

    2014-01-01

    Africa is home to genetically diverse human populations. We compared the genetic structure of the Wolaita ethnic population from southern Ethiopia (WETH, n=120) with HapMap populations using genome-wide variants. We investigated allele frequencies of 443 clinically and pharmacogenomically relevant genetic variants in WETH compared to HapMap populations. We found that WETH were genetically most similar to the Kenya Maasai and least similar to the Japanese in HapMap. Variant alleles associated ...

  14. Strategies to work with HLA data in human populations for histocompatibility, clinical transplantation, epidemiology and population genetics: HLA-NET methodological recommendations.

    Science.gov (United States)

    Sanchez-Mazas, A; Vidan-Jeras, B; Nunes, J M; Fischer, G; Little, A-M; Bekmane, U; Buhler, S; Buus, S; Claas, F H J; Dormoy, A; Dubois, V; Eglite, E; Eliaou, J F; Gonzalez-Galarza, F; Grubic, Z; Ivanova, M; Lie, B; Ligeiro, D; Lokki, M L; da Silva, B Martins; Martorell, J; Mendonça, D; Middleton, D; Voniatis, D Papioannou; Papasteriades, C; Poli, F; Riccio, M E; Vlachou, M Spyropoulou; Sulcebe, G; Tonks, S; Nevessignsky, M Toungouz; Vangenot, C; van Walraven, A-M; Tiercy, J-M

    2012-12-01

    HLA-NET (a European COST Action) aims at networking researchers working in bone marrow transplantation, epidemiology and population genetics to improve the molecular characterization of the HLA genetic diversity of human populations, with an expected strong impact on both public health and fundamental research. Such improvements involve finding consensual strategies to characterize human populations and samples and report HLA molecular typings and ambiguities; proposing user-friendly access to databases and computer tools and defining minimal requirements related to ethical aspects. The overall outcome is the provision of population genetic characterizations and comparisons in a standard way by all interested laboratories. This article reports the recommendations of four working groups (WG1-4) of the HLA-NET network at the mid-term of its activities. WG1 (Population definitions and sampling strategies for population genetics' analyses) recommends avoiding outdated racial classifications and population names (e.g. 'Caucasian') and using instead geographic and/or cultural (e.g. linguistic) criteria to describe human populations (e.g. 'pan-European'). A standard 'HLA-NET POPULATION DATA QUESTIONNAIRE' has been finalized and is available for the whole HLA community. WG2 (HLA typing standards for population genetics analyses) recommends retaining maximal information when reporting HLA typing results. Rather than using the National Marrow Donor Program coding system, all ambiguities should be provided by listing all allele pairs required to explain each genotype, according to the formats proposed in 'HLA-NET GUIDELINES FOR REPORTING HLA TYPINGS'. The group also suggests taking into account a preliminary list of alleles defined by polymorphisms outside the peptide-binding sites that may affect population genetic statistics because of significant frequencies. WG3 (Bioinformatic strategies for HLA population data storage and analysis) recommends the use of programs capable

  15. Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus.

    Science.gov (United States)

    Furlan, Elise; Stoklosa, J; Griffiths, J; Gust, N; Ellis, R; Huggins, R M; Weeks, A R

    2012-04-01

    Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (H(E)= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed. PMID:22837830

  16. Molecular Genetic Variation in a Clonal Plant Population of Leymus chinensis (Trin.) Tzvel.

    Institute of Scientific and Technical Information of China (English)

    Yu-Sheng WANG; Li-Ming ZHAO; Hua WANG; Jie WANG; Da-Ming HUANG; Rui-Min HONG; Xiao-Hua TENG; Nakamura MIKI

    2005-01-01

    Randomly amplified polymorphic DNA (RAPD) analysis was used to investigate the genetic variation among populations, between populations, and within populations, relationships between genetic distance and geographic distance, and the molecular variation and population size. The effects of geographic and genetic distances, as well as of genetic differentiation and population size, on genetic variations of Leymus chinensis (Trin.) Tzvel. are discussed. The present study showed that there was significant RAPD variation between the Baicheng region population and the Daqing region population, with a molecular variance of 6.35% (P < 0.04), and for differentiation among area populations of the Daqing region, with a molecular variance of 8.78% (P < 0.002). A 21.06% RAPD variation among all 16 populations among two regions was found (P < 0.001), as well as 72.59% variation within populations (P < 0.001). Molecular variation within populations was significantly different among 16 populations.

  17. Population Structure and Genetic Relationships of Melia Taxa in China Assayed with Sequence-Related Amplified Polymorphism (SRAP Markers

    Directory of Open Access Journals (Sweden)

    Boyong Liao

    2016-04-01

    Full Text Available The uncertainty about whether, in China, the genus Melia (Meliaceae consists of one species (M. azedarach Linnaeus or two species (M. azedarach and M. toosendan Siebold & Zuccarini remains to be clarified. Although the two putative species are morphologically distinguishable, genetic evidence supporting their taxonomic separation is lacking. Here, we investigated the genetic diversity and population structure of 31 Melia populations across the natural distribution range of the genus in China. We used sequence-related amplified polymorphism (SRAP markers and obtained 257 clearly defined bands amplified by 20 primers from 461 individuals. The polymorphic loci (P varied from 35.17% to 76.55%, with an overall mean of 58.24%. Nei’s gene diversity (H ranged from 0.13 to 0.31, with an overall mean of 0.20. Shannon’s information index (I ranged from 0.18 to 0.45, with an average of 0.30. The genetic diversity of the total population (Ht and within populations (Hs was 0.37 ± 0.01 and 0.20 ± 0.01, respectively. Population differentiation was substantial (Gst = 0.45, and gene flow was low. Of the total variation, 31.41% was explained by differences among putative species, 19.17% among populations within putative species, and 49.42% within populations. Our results support the division of genus Melia into two species, which is consistent with the classification based on the morphological differentiation.

  18. Aquifer response to recharge-discharge phenomenon: inference from well hydrographs for genetic classification

    Science.gov (United States)

    Mukherjee, Arunangshu; Gupta, Anita; Ray, Ranjan Kumar; Tewari, Dinesh

    2015-05-01

    The continuous groundwater level data emanating from a high-frequency automatic water level recorder installed in a purpose-built piezometer provides a true hydrograph. Analyses of such hydrographs fairly reflect the aquifer character and can be used to draw inference for genetic classification of hard rock aquifers. The signature shape of annual water level fluctuation curve (annual cycle) of a piezometer is due to the specific character of the aquifer and the way it responds to the recharge-discharge phenomenon. The pattern of annual cycle remains identical year after year, although its magnitude may vary with the annual quantum of recharge-discharge. Lithology of the aquifer does not control the shape of the curve. Based on the crest and trough shape, the hard rock aquifers of Peninsular India, where the monsoonal pattern of rainfall occurs, have been classified into genetic groups. It is also found that the nature of the aquifer can be determined by visual comparison of apparent line thickness of the hydrograph, where thin lines denote unconfined aquifer and the apparently thicker lines correspond to confining condition. The response of an aquifer to a pumping event can be identified and separated by its pattern. Thus, the aquifer classification can be automated by adopting the proposed classification scheme.

  19. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa

    Directory of Open Access Journals (Sweden)

    Khulekhani Sedwell Khanyile

    2015-02-01

    Full Text Available Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterised and utilized. Surveys that can reveal a population’s genetic structure and provide an insight into its demographic history will give valuable information to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n =146, Malawi (n =30 and Zimbabwe (n =136 were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29-0.36, was observed between SNP markers that were less than 10kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK and 0.24 (VD at SNP marker interval of 500kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective population

  20. Genetic Diversity of Eight Domestic Goat Populations Raised in Turkey

    Science.gov (United States)

    Bulut, Zafer; Kurar, Ercan; Ozsensoy, Yusuf; Altunok, Vahdettin; Nizamlioglu, Mehmet

    2016-01-01

    The objective of this study was to determine the intra- and intergenetic diversities of eight different goat populations in Turkey including Hair, Angora, Kilis, Yayladag, Shami, Honamli, Saanen, and Alpine. A total of 244 DNA samples were genotyped using 11 microsatellites loci. The genetic differentiation between breeds was considerable as a result of the statistically significant (P 0.05). Heterozygosity values ranged between 0.62 and 0.73. According to the structure and assignment test, Angora and Yayladag goats were assigned to the breed they belong to, while other breeds were assigned to two or more different groups. Because this study for the first time presented genetic data on the Yayladag goat, results of structure analysis and assigned test suggest that further analyses are needed using additional and different molecular markers. PMID:27092309

  1. Genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV)

    DEFF Research Database (Denmark)

    Snow, M.; Bain, N.; Black, J.;

    2004-01-01

    The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders this the...... most comprehensive molecular epidemiological study of marine VHSV conducted to date. Phylogenetic analysis of nucleoprotein gene sequences confirmed the existence of the 4 major genotypes previously identified based on N- and subsequent G-gene based analyses. The range of Genotype I included subgroups...... of isolates associated with rainbow trout aquaculture (Genotype la) and those from the Baltic marine environment (Genotype Ib) to emphasise the relatively close genetic relationship between these isolates. The existence of an additional genotype circulating within the Baltic Sea (Genotype II) was...

  2. Population genetics of foxtail millet and its wild ancestor

    Directory of Open Access Journals (Sweden)

    Wang Yongfang

    2010-10-01

    Full Text Available Abstract Background Foxtail millet (Setaria italica (L. P. Beauv., one of the most ancient domesticated crops, is becoming a model system for studying biofuel crops and comparative genomics in the grasses. However, knowledge on the level of genetic diversity and linkage disequilibrium (LD is very limited in this crop and its wild ancestor, green foxtail (Setaria viridis (L. P. Beauv.. Such information would help us to understand the domestication process of cultivated species and will allow further research in these species, including association mapping and identification of agricultural significant genes involved in domestication. Results In this study, we surveyed DNA sequence for nine loci across 50 accessions of cultivated foxtail millet and 34 of its wild progenitor. We found a low level of genetic diversity in wild green foxtail (θ = 0.0059, θ means Watterson's estimator of θ. Despite of a 55% loss of its wild diversity, foxtail millet still harbored a considerable level of diversity (θ = 0.0027 when compared to rice and sorghum (θ = 0.0024 and 0.0034, respectively. The level of LD in the domesticated foxtail millet extends to 1 kb, while it decayed rapidly to a negligible level within 150 bp in wild green foxtail. Using coalescent simulation, we estimated the bottleneck severity at k = 0.6095 when ρ/θ = 1. These results indicated that the domestication bottleneck of foxtail millet was more severe than that of maize but slightly less pronounced than that of rice. Conclusions The results in this study establish a general framework for the domestication history of foxtail millet. The low level of genetic diversity and the increased level of LD in foxtail millet are mainly caused by a population bottleneck, although gene flow from foxtail millet to green foxtail is another factor that may have shaped the pattern of genetic diversity of these two related gene pools. The knowledge provided in this study will benefit future population

  3. Genetic Variation A mong European Lophodermium piceae Populations - Preliminary Results

    Directory of Open Access Journals (Sweden)

    MÜLLER, Michael M.

    2007-01-01

    Full Text Available Lophodermium piceae is a common needle endophyte of Norway spruce (Picea abies. The aim of the present study was to examine the degree of differentiation within and among European populations separated by various distances and geographical obstacles. For this purpose, populations (including > 10 isolates/subpopulation were collected along a north-south transect stretching from the northern timberline in Finnish Lapland to the southern border of the distribution area of Norway spruce in northern Italy. Differentiation between L. piceae populations was determined from DNA sequences of three genetic markers. One of the markers was the internal transcribed spacer (ITS of the ribosomal DNA and the other two (LP1 and LP2 were based on sequence characterized amplified regions (SCAR designed for L. piceae. Preliminary results including sequences of Finnish, Swiss and Italian isolates show low differentiation among populations. According to analysis of molecular variance the among population variation was 1%, 5% and 0% in ITS, LP1 and LP2 markers, respectively.

  4. A WebGIS system for relating genetic soil classification of China to soil taxonomy

    Science.gov (United States)

    Shi, Xuezheng; Yang, Guoxiang; Yu, Dongsheng; Xu, Shengxiang; Warner, Eric D.; Petersen, Gary W.; Sun, Weixia; Zhao, Yongcun; Easterling, William E.; Wang, Hongjie

    2010-06-01

    Soil classification is the basis for the exchange of soil science research results and the foundation for the application of modern soil resource management methods. A WebGIS-based system designed to relate genetic soil classification of China (GSCC) to soil taxonomy (ST) was developed to enhance global cooperation and to support communication between China and the other countries on important agricultural and environmental issues. The system has a Browse Server (B/S) structure and exploits the 1:1,000,000 soil databases of China using WebGIS functionality. This paper describes the application of the WebGIS system for easily accessing cross-reference information between GSCC to ST. First, we describe the three-level B/S structure of the system. The cross-reference methodologies, referenceability and maximum referenceability, are then explained and applied at three geographic scales (i.e. nation, region and pedon). Finally, three sub-modules based on the supported scales are described and illustrated with application scenarios to familiarize users with the inquiry system and its usage. The main advantage of the system is that it considers statistical similarity in the spatial distributions between the two different classification systems. Users with limited knowledge are able to obtain soil cross-reference information using an intuitive interface, which supports query, visualization and analysis via a web browser at the most detailed level. The inquiry system benefits the development of soil classification science and international academic exchange.

  5. Feasibility of Genetic Algorithm for Textile Defect Classification Using Neural Network

    Directory of Open Access Journals (Sweden)

    Md. Tarek Habib

    2012-07-01

    Full Text Available The global market for textile industry is highly competitive nowadays. Quality control in production process in textile industry has been a key factor for retaining existence in such competitive market. Automated textile inspection systems are very useful in this respect, because manual inspection is time consuming and not accurate enough. Hence, automated textile inspection systems have been drawing plenty of attention of the researchers of different countries in order to replace manual inspection. Defect detection and defect classification are the two major problems that are posed by the research of automated textile inspection systems. In this paper, we perform an extensive investigation on the applicability of genetic algorithm (GA in the context of textile defect classification using neural network (NN. We observe the effect of tuning different network parameters and explain the reasons. We empirically find a suitable NN model in the context of textile defect classification. We compare the performance of this model with that of the classification models implemented by others.

  6. National population-based biobanks for genetic research.

    Science.gov (United States)

    Swede, Helen; Stone, Carol L; Norwood, Alyssa R

    2007-03-01

    Clinical practice guidelines derived from genetic research using population-based biobanks could dramatically change the nature of personal and public health medicine. Centralized population-based biobanks have been established or proposed in at least nine countries to date, and many lessons have been learned from these landmark developments. Scientific and governmental leaders in the United States are currently contemplating pending federal legislation regarding the establishment of centralized and networked biobanks. Public health practitioners and clinical care providers may be called on to serve pronounced planning roles at the state level. Possible responsibilities include: formulating legislation, gathering public comment, reviewing research proposals, and developing procedures for informed consent, participant withdrawal, and confidentiality protection. State health agencies may also need to create and/or administer banking facilities. Proper planning may ensure that individual rights are protected while research benefits are maximized. PMID:17413418

  7. Quantifying population genetic differentiation from next-generation sequencing data

    DEFF Research Database (Denmark)

    Fumagalli, Matteo; Vieira, Filipe G.; Korneliussen, Thorfinn Sand;

    2013-01-01

    method for quantifying population genetic differentiation from next-generation sequencing data. In addition, we present a strategy to investigate population structure via Principal Components Analysis. Through extensive simulations, we compare the new method herein proposed to approaches based......Over the last few years, new high-throughput DNA sequencing technologies have dramatically increased speed and reduced sequencing costs. However, the use of these sequencing technologies is often challenged by errors and biases associated with the bioinformatical methods used for analyzing the data....... In particular, the use of naïve methods to identify polymorphic sites and infer genotypes can inflate downstream analyses. Recently, explicit modeling of genotype probability distributions has been proposed as a method for taking genotype call uncertainty into account. Based on this idea, we propose a novel...

  8. Genetic Bee Colony (GBC) algorithm: A new gene selection method for microarray cancer classification.

    Science.gov (United States)

    Alshamlan, Hala M; Badr, Ghada H; Alohali, Yousef A

    2015-06-01

    Naturally inspired evolutionary algorithms prove effectiveness when used for solving feature selection and classification problems. Artificial Bee Colony (ABC) is a relatively new swarm intelligence method. In this paper, we propose a new hybrid gene selection method, namely Genetic Bee Colony (GBC) algorithm. The proposed algorithm combines the used of a Genetic Algorithm (GA) along with Artificial Bee Colony (ABC) algorithm. The goal is to integrate the advantages of both algorithms. The proposed algorithm is applied to a microarray gene expression profile in order to select the most predictive and informative genes for cancer classification. In order to test the accuracy performance of the proposed algorithm, extensive experiments were conducted. Three binary microarray datasets are use, which include: colon, leukemia, and lung. In addition, another three multi-class microarray datasets are used, which are: SRBCT, lymphoma, and leukemia. Results of the GBC algorithm are compared with our recently proposed technique: mRMR when combined with the Artificial Bee Colony algorithm (mRMR-ABC). We also compared the combination of mRMR with GA (mRMR-GA) and Particle Swarm Optimization (mRMR-PSO) algorithms. In addition, we compared the GBC algorithm with other related algorithms that have been recently published in the literature, using all benchmark datasets. The GBC algorithm shows superior performance as it achieved the highest classification accuracy along with the lowest average number of selected genes. This proves that the GBC algorithm is a promising approach for solving the gene selection problem in both binary and multi-class cancer classification. PMID:25880524

  9. Genetic admixture and population substructure in Guanacaste Costa Rica.

    Directory of Open Access Journals (Sweden)

    Zhaoming Wang

    Full Text Available The population of Costa Rica (CR represents an admixture of major continental populations. An investigation of the CR population structure would provide an important foundation for mapping genetic variants underlying common diseases and traits. We conducted an analysis of 1,301 women from the Guanacaste region of CR using 27,904 single nucleotide polymorphisms (SNPs genotyped on a custom Illumina InfiniumII iSelect chip. The program STRUCTURE was used to compare the CR Guanacaste sample with four continental reference samples, including HapMap Europeans (CEU, East Asians (JPT+CHB, West African Yoruba (YRI, as well as Native Americans (NA from the Illumina iControl database. Our results show that the CR Guanacaste sample comprises a three-way admixture estimated to be 43% European, 38% Native American and 15% West African. An estimated 4% residual Asian ancestry may be within the error range. Results from principal components analysis reveal a correlation between genetic and geographic distance. The magnitude of linkage disequilibrium (LD measured by the number of tagging SNPs required to cover the same region in the genome in the CR Guanacaste sample appeared to be weaker than that observed in CEU, JPT+CHB and NA reference samples but stronger than that of the HapMap YRI sample. Based on the clustering pattern observed in both STRUCTURE and principal components analysis, two subpopulations were identified that differ by approximately 20% in LD block size averaged over all LD blocks identified by Haploview. We also show in a simulated association study conducted within the two subpopulations, that the failure to account for population stratification (PS could lead to a noticeable inflation in the false positive rate. However, we further demonstrate that existing PS adjustment approaches can reduce the inflation to an acceptable level for gene discovery.

  10. Low genetic differentiation in a sedentary bird: house sparrow population genetics in a contiguous landscape

    OpenAIRE

    Kekkonen, J; Seppä, P.; Hanski, I K; Jensen, H; Väisänen, R A; Brommer, J. E.

    2010-01-01

    The house sparrow Passer domesticus has been declining in abundance in many localities, including Finland. We studied the genetic diversity and differentiation of the house sparrow populations across Finland in the 1980s, at the onset of the species' decline in abundance. We genotyped 472 adult males (the less dispersive sex) from 13 locations in Finland (covering a range of 400 × 800 km) and one in Sweden (Stockholm) for 13 polymorphic microsatellite markers. Our analysis of Finnish ringing ...

  11. Genetic variation and population genetic structure of Rhizophora apiculata (Rhizophoraceae) in the Greater Sunda Islands, Indonesia using microsatellite markers.

    Science.gov (United States)

    Yahya, Andi Fadly; Hyun, Jung Oh; Lee, Jae Ho; Kim, Yong Yul; Lee, Kyung Mi; Hong, Kyung Nak; Kim, Seung-Chul

    2014-03-01

    Genetic variations within and among Rhizophora apiculata populations in the Greater Sunda Islands of Indonesia were studied using microsatellite markers. The study found 38 alleles on five loci in 15 populations. The observed (H(o)) and expected (H(e)) heterozygosity values are 0.338 and 0.378, respectively. Inbreeding effect from self-pollination might explain its heterozygote deficiency. Population genetic differentiation (F(ST) = 0.381) was similar to other mangrove species. The genetic diversity of R. apiculata populations along the coastline inside the archipelago (e.g., Buleleng, Donggala, Mamuju, and Takalar) was higher than those of population along the coastline outside the archipelago, especially northern Sumatra populations (i.e., Langkat, Tapanuli Tengah, Dumai, and Padang). The isolation by distances and sea currents directions as well as their connectivity might affect the gene flow and genetic exchange. The more isolated with fewer connections by sea currents, the smaller gene flow and genetic exchange observed between populations. The higher genetic exchange, on the contrary, occurred when population location was closer to the meeting point of the sea currents. The study also showed that the patterns of sea current movement seemed to have influence genetic clustering of populations which fell into three main groups (Sunda Shelf Mangroves) and one isolated population (New Guinea Mangroves). PMID:24323307

  12. Reappraisal of phylogenetic status and genetic diversity analysis of Asian population of Lentinula edodes

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Phylogenetic relationship within the Lentinula genus is constructed based on the sequenced ITS fragments of the 60Chinese wild L. edodes isolates and the sequence data of 48 isolates of different species from other districts downloaded from the GenBank. The 108 isolates of Lentinula genus are divided into two branches and seven groups, one branch and two groups in the New World, and the other branch and five groups in the Old World, and the isolates clustering of different groups corresponds obviously with the classification of the morphological species. Asian isolates are partitioned in group Ⅰ and Ⅴ, two of the five groups of the Old World,by which the germplasm resources status represented is of great importance shown by the phylogenetic analysis. Group V which fills up the blank of geographic distribution has become one of the mainstream groups with an increased isolate number, while group Ⅰ has a tendency to dissimilate into two subgroups (Ia and Ib) with a huge isolate quantity and a coverage of most tested districts, suggesting that China (or Asia) is an important genetic diversity center of the natural population of Lentinula genus. Genetic analysis of Asian isolates based on groups Ia, Ib and group V indicates that the diversity of the east coastal-land, northwestern highland and southwestern China and Himalayas districts is the most plentiful, which is the three priorities in diversity protection of Asian Lentinula population.

  13. Population structure and genetic diversity of the perennial medicinal shrub Plumbago

    OpenAIRE

    Panda, Sayantan; Naik, Dhiraj; Kamble, Avinash

    2015-01-01

    Knowledge of the natural genetic variation and structure in a species is important for developing appropriate conservation strategies. As genetic diversity analysis among and within populations of Plumbago zeylanica remains unknown, we aimed (i) to examine the patterns and levels of morphological and genetic variability within/among populations and ascertain whether these variations are dependent on geographical conditions; and (ii) to evaluate genetic differentiation and population structure...

  14. Population genetic structure in gadoid fish with focus on Atlantic cod Gadus morhua

    OpenAIRE

    Guðni Magnús Eiríksson 1970

    2015-01-01

    In the present study genetic variation and population genetic structure in spawning Atlantic cod, Gadus morhua, around Iceland was examined. Earlier research on population genetic structure in cod has not been conclusive and the use of different molecular methods have shown different patterns. It is important to determine why different methods show different patterns in order to describe the population genetic structure in cod. In the present study both microsatellite DNA variation and mitoch...

  15. Genetic variability of inflammatory genes in the Brazilian population.

    Science.gov (United States)

    dos Santos, Marcelo; Stur, Elaine; Maia, Lucas Lima; Agostini, Lidiane Pignaton; Peterle, Gabriela Tonini; Mendes, Suzanny Oliveira; Tajara, Eloiza Helena; de Carvalho, Marcos Brasilino; Louro, Iúri Drumond; Silva-Conforti, Adriana Madeira Álvares

    2013-11-01

    Inflammatory gene variants have been associated with several diseases, including cancer, diabetes, vascular diseases, neurodegenerative diseases, arthritis, and others. Therefore, determining the population genetic composition of inflammation-related genes can be useful for the determination of general risk, prognostic and therapeutic strategies to prevent or cure specific diseases. We have aimed to identify polymorphism genotype frequencies in genes related to the inflammatory response in the Brazilian population, namely, IκBL -62AT, IκBL -262CT, tumor necrosis factors alpha (TNFa) -238GA, TNFa -308GA, lymphotoxin-alpha (LTa) +80AC, LTa +252AG, FAS -670AG, and FASL -844TC, considering the white, black, and Pardo ethnicities of the São Paulo State. Our results suggest that the Brazilian population is under a miscegenation process at the current time, since some genotypes are not in the Hardy-Weinberg equilibrium. In addition, we conclude that the Pardo ethnicity is derived from a complex mixture of ethnicities, including the native Indian population. PMID:23909556

  16. Genetic structure of natural populations: Final technical report

    International Nuclear Information System (INIS)

    We determined the LD50 for individuals with any one of four genetic constitutions. The LD50 was in kR units (S and F refer to the two common alleles found in natural populations and N is a mull allele) S/S 5.31, F/F 4.61, S/F 4.19, N/N 3.16. These results are as expected under the hypothesis the SOD is involved in radio-resistance and the degree of protection is a function of SOD specific activity. S codes for an allozyme that has the highest in vitro specific activity while N reduces the amount of enzyme to 3.5% of the normal level. Natural selection experiments in population cages were carried out for 13 generations. In control populations, the frequency of the S allele decreases from the initial frequency of 0.50 to an equilibrium value 0.1 to 0.2 in about 10 generations. In populations with the larvae receiving 4 KR in each generation, s reaches an equilibrium frequency of 0.6; when the irradiation was no longer applied, the frequency of S started declining, eventually reaching 0.1 to 0.2. These results corroborate the hypothesis that SOD protects against irradiation and that the degree of protection is correlated by the in vitro specific activity of the allozymes. 29 refs., 4 tabs

  17. Reference benchmarks relating to great groups of genetic soil classification of China with soil taxonomy

    Institute of Scientific and Technical Information of China (English)

    SHI Xuezheng; YU Dongsheng; SUN Weixia; WANG Hongjie; ZHAO Qiguo; GONG Zitong

    2004-01-01

    Soil classification forms the basis for the exchange and extension of research findings in soil science and for the modernization of management of soil resources. This paper systematically reviews the compatibility of the genetic soil classification of China (GSCC) and soil taxonomy (ST).This includes a study of the evolution and consummation of the GSCC and assessment of the databases and methods of the study. Using the "Soil Species of China (six volumes)"and some provincial soil species as the basic material, the authors gathered information from 2540 soil species. Based on the key described in ST, the 2540 soil species were taxonomically classified into corresponding soil orders, suborders,great groups and subgroups and then matched with corresponding map units in the 1: 1000000 digital soil map of China. Using the high-level classification units of the two soil classification systems, and the attributes of each soil species,the sizes of distribution areas were mapped. The soil distribution results were analyzed and compared statistically. The reference compatibility between the great groups used in GSCC system and the soil orders of the ST is discussed. It is believed that 20 great groups display maximum referencibility >95% and 15 great groups depict maximum referencibility in the range of 70%-95%, which can be cited as reference benchmarks. The remaining 25 great groups are less compatible (with maximum referencibility <70%) and need further study, or require referencing at lower classification levels or at a regional level to help to improve the accuracy of the reference.

  18. Management of Thyroid Nodular Disease: Current Cytopathology Classifications and Genetic Testing.

    Science.gov (United States)

    Kuo, Lindsay E; Kelz, Rachel R

    2016-01-01

    Preoperative diagnosis and operative planning for patients with thyroid nodules has improved over the last decade. The Bethesda criteria for cytopathologic classification of thyroid nodule aspirate has enhanced communication between pathologists and clinicians. Multiple genetic tests, including molecular markers and the Afirma gene expression classifier, have been developed and validated. The tests, along with clinical and radiologic information, are most useful in the setting of indeterminate cytology. The development of an updated diagnostic and treatment algorithm incorporating all available tests will help standardize the management of patients with nodular thyroid disease and reduce variation and inefficiencies in care. PMID:26610771

  19. Population genetics of the Chilean frog Batrachyla Leptopus (Leptodactylidae

    Directory of Open Access Journals (Sweden)

    J.R. Formas

    2000-03-01

    Full Text Available Electrophoretic variation of proteins encoded by 14 loci was analyzed in eight (five continental and three insular populations of the Chilean leptodactylid frog Batrachyla leptopus. The overall proportion of polymorphic loci was estimated to be 18.7% and the average number of alleles per locus, 1.2, while observed and expected heterozygosities were 1.7 and 5.1%, respectively. The estimated coefficient of genetic identity was 0.940; the corresponding figure for genetic distance was 0.063. F-statistics analysis showed a total inbreeding coefficient (Fit of 0.855 and high levels of genetic subdivision (Fst = 0.596 as well as of inbreeding within populations (Fis = 0.640. However, there was only a moderate level of genetic differentiation (Fst = 0.181 between the insular group of populations and the continental group.A variação eletroforética de proteínas codificadas por 14 loci foi analisada em oito populações (5 continentais e 3 insulares da rã leptodactilídea chilena Batrachyla leptopus. A proporção geral de loci polimórficos foi estimada como sendo de 18,7% e o número médio de alelos por loco, 1,2, enquanto que as heterozigosidades observada e esperada foram 1,7 e 5,1%, respectivamente. O coeficiente esperado de identidade genética foi 0,940; o número correspondente para a distância genética foi 0,063. A análise estatística F mostrou um coeficiente de endogamia total (Fit de 0,855 e altos níveis de subdivisão genética (Fst = 0,596, assim como de endogamia dentro das populações (Fis = 0,640. Contudo, houve apenas um nível moderado de diferenciação genética (Fst = 0,181 entre o grupo insular de populações e o grupo continental.

  20. Genetic Signature of Anthropogenic Population Collapse in Orang-utans.

    Directory of Open Access Journals (Sweden)

    2006-01-01

    Full Text Available Great ape populations are undergoing a dramatic decline, which is predicted to result in their extinction in the wild from entire regions in the near future. Recent findings have particularly focused on African apes, and have implicated multiple factors contributing to this decline, such as deforestation, hunting, and disease. Less well-publicised, but equally dramatic, has been the decline in orang-utans, whose distribution is limited to parts of Sumatra and Borneo. Using the largest-ever genetic sample from wild orang-utan populations, we show strong evidence for a recent demographic collapse in North Eastern Borneo and demonstrate that this signature is independent of the mutation and demographic models used. This is the first demonstration that genetic data can detect and quantify the effect of recent, human-induced deforestation and habitat fragmentation on an endangered species. Because current demographic collapses are usually confounded by ancient events, this suggests a much more dramatic decline than demographic data alone and emphasises the need for major conservation efforts.

  1. Genetic signature of anthropogenic population collapse in orang-utans.

    Directory of Open Access Journals (Sweden)

    Benoît Goossens

    2006-02-01

    Full Text Available Great ape populations are undergoing a dramatic decline, which is predicted to result in their extinction in the wild from entire regions in the near future. Recent findings have particularly focused on African apes, and have implicated multiple factors contributing to this decline, such as deforestation, hunting, and disease. Less well-publicised, but equally dramatic, has been the decline in orang-utans, whose distribution is limited to parts of Sumatra and Borneo. Using the largest-ever genetic sample from wild orang-utan populations, we show strong evidence for a recent demographic collapse in North Eastern Borneo and demonstrate that this signature is independent of the mutation and demographic models used. This is the first demonstration that genetic data can detect and quantify the effect of recent, human-induced deforestation and habitat fragmentation on an endangered species. Because current demographic collapses are usually confounded by ancient events, this suggests a much more dramatic decline than demographic data alone and emphasises the need for major conservation efforts.

  2. Estimates of genetic variability in mutated population of triticum aestivum

    International Nuclear Information System (INIS)

    M2 populations of four cultivars of Mexican origin (Mexipak-65, Nayab, Pak-70 and 6134 x C-271) and two locally bred cultivars (H-68 and C-591) of bread wheat, triticum aestivum (2n = 6x = AA BB DD) derived from six irradiation treatments (gamma rays 60sub(Co); 10, 15 and 20 kR and fast neutrons; 300, 600 and 900 RADS) were critically examined for spike length, spikelets per spike, grains per spike and grain yield. Genotypes varied significantly (p>=0.01) for all the characters. Irradiation treatment were instrumental in creating significant variability for all the characters, indicating that varieties did not perform uniformly across different gamma rays as well as fast neutron treatments. In the M2 generation there was a considerable increase in variance for all the four metrical traits. Comparisons were made between controls and treated populations. Mutagenic treatments shifted the mean values mostly towards the negative direction, but the shift was not unidirectional nor equally effective for all the characters. The differences in mean values and the nature of variability observed in M2 indicated a possible preference of selection M3 generation. In general, estimates of genetic variability and heritability (b.s) increased with increasing doses of gamma rays and fast neutrons. Genetic advance also exhibited similar trend. The observed variability can be utilized in the evolution of new varieties. (authors)

  3. 基于粗集分类和遗传算法的知识库集成方法%The Methods of Knowledge Database Integration Based on the Rough Set Classification and Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    郭平; 程代杰

    2003-01-01

    As the base of intelligent system, it is very important to guarantee the consistency and non-redundancy of knowledge in knowledge database. Since the variety of knowledge sources, it is necessary to dispose knowledge with redundancy, inclusion and even contradiction during the integration of knowledge database. This paper researches the integration method based on the multi-knowledge database. Firstly, it finds out the inconsistent knowledge sets between the knowledge databases by rough set classification and presents one method eliminating the inconsistency by test data. Then, it regards consistent knowledge sets as the initial population of genetic calculation and constructs a genetic adaptive function based on accuracy, practicability and spreadability of knowledge representation to carry on the genetic calculation. Lastly, classifying the results of genetic calculation reduces the knowledge redundancy of knowledge database. This paper also presents a frameworkfor knowledge database integration based on the rough set classification and genetic algorithm.

  4. Genetic polymorphisms and skin aging: the identification of population genotypic groups holds potential for personalized treatments

    Directory of Open Access Journals (Sweden)

    Naval J

    2014-07-01

    Full Text Available Jordi Naval,1 Vicente Alonso,1,2 Miquel Angel Herranz11Genocosmetics Lab, Barcelona, Spain; 2Dermatology Unit, Hospital Nisa 9 de Octubre, Valencia, SpainIntroduction: Skin changes are among the most visible signs of aging. Skin properties such as hydration, elasticity, and antioxidant capacity play a key role in the skin aging process. Skin aging is a complex process influenced by heritable and environmental factors. Recent studies on twins have revealed that up to 60% of the skin aging variation between individuals can be attributed to genetic factors, while the remaining 40% is due to non-genetic factors. Recent advances in genomics and bioinformatics approaches have led to the association of certain single nucleotide polymorphisms (SNPs to skin properties. Our aim was to classify individuals based on an ensemble of multiple polymorphisms associated with certain properties of the skin for providing personalized skin care and anti-aging therapies.Methods and results: We identified the key proteins and SNPs associated with certain properties of the skin that contribute to skin aging. We selected a set of 13 SNPs in gene coding for these proteins which are potentially associated with skin aging. Finally, we classified a sample of 120 female volunteers into ten clusters exhibiting different skin properties according to their genotypic signature.Conclusion: This is the first study that describes the actual frequency of genetic polymorphisms and their distribution in clusters involved in skin aging in a Caucasian population. Individuals can be divided into genetic clusters defined by genotypic variables. These genotypic variables are linked with polymorphisms in one or more genes associated with certain properties of the skin that contribute to a person's perceived age. Therefore, by using this classification, it is possible to characterize human skin care and anti-aging needs on the basis of an individual's genetic signature, thus opening the door

  5. Natural Selection and Genetic Drift: Neutral and adaptive genetic variability of hatchery versus wild populations in brown trout Salmo trutta

    Directory of Open Access Journals (Sweden)

    Tamara Schenekar

    2015-11-01

    Full Text Available Genetic drift and natural selection are two of the major forces shaping the genetic makeup of a population. Genetic drift reduces genetic variability due to the random loss of alleles during the transition from one generation to the next one. The smaller the population, the stronger genetic drift is. Natural selection favors the spread of specific alleles within a population over time, namely those alleles that are beneficial in the specific environment of this population. Individuals that carry alleles that are less advantageous have a lower probability to survive and reproduce. For establishing a captive population, very often, only a small number of individuals are taken and the number breeding individuals used to maintain the population is limited, thus increasing the amount of genetic drift. On the other hand, the drastically different environment in captivity (artificial diet, higher individual density, altered pathogen pressure, etc. may favor alleles that are maladaptive for individuals when they are released back in the wild, e.g. for stocking measures. We screened both, neutral and adaptive genetic markers, in order to assess the relative importance of genetic drift and selection pressure on wild and hatchery populations of Austrian brown trout. We confirm a strong positive selection pressure on an adaptive locus of the Major histocompatibility Complex (MHC, whereas the signal of this selection pressure was more pronounced in hatchery populations. This may either stem from stronger genetic drift in wild populations due to smaller effective population sizes or a stronger directional selection in these wild populations, whereby only particular genetic variants proved to be adaptive in each specific environment. Therefore, the alleles arising from the hatchery selection regime may be detrimental in the wild, which can lead to lower survival rates of stocked fish in wild environments.

  6. Genetic Study of Population Mixture and Its Role in Human History

    OpenAIRE

    Moorjani, Priya

    2013-01-01

    Mixture between populations is an evolutionary process that shapes genetic variation. Intermixing between groups of distinct ancestries creates mosaics of chromosomal segments inherited from multiple ancestral populations. Studying populations of mixed ancestry (admixed populations) is of special interest in population genetics as it not only provides insights into the history of admixed groups but also affords an opportunity to reconstruct the history of the ancestral populations, some of wh...

  7. Extracting classification rules from an informatic security incidents repository by genetic programming

    Directory of Open Access Journals (Sweden)

    Carlos Javier Carvajal Montealegre

    2015-04-01

    Full Text Available This paper describes the data mining process to obtain classification rules over an information security incident data collection, explaining in detail the use of genetic programming as a mean to model the incidents behavior and representing such rules as decision trees. The described mining process includes several tasks, such as the GP (Genetic Programming approach evaluation, the individual's representation and the algorithm parameters tuning to upgrade the performance. The paper concludes with the result analysis and the description of the rules obtained, suggesting measures to avoid the occurrence of new informatics attacks. This paper is a part of the thesis work degree: Information Security Incident Analytics by Data Mining for Behavioral Modeling and Pattern Recognition (Carvajal, 2012.

  8. Genetic population structure of sympatric and allopatric populations of Baltic ciscoes (Coregonus albula complex, Teleostei, Coregonidae

    Directory of Open Access Journals (Sweden)

    Nitz Barbara

    2010-03-01

    Full Text Available Abstract Background Teleost fishes of the Coregonidae are good model systems for studying postglacial evolution, adaptive radiation and ecological speciation. Of particular interest is whether the repeated occurrence of sympatric species pairs results from in-situ divergence from a single lineage or from multiple invasions of one or more different lineages. Here, we analysed the genetic structure of Baltic ciscoes (Coregonus albula complex, examining 271 individuals from 8 lakes in northern Germany using 1244 polymorphic AFLP loci. Six lakes had only one population of C. albula while the remaining two lakes had C. albula as well as a sympatric species (C. lucinensis or C. fontanae. Results AFLP demonstrated a significant population structure (Bayesian θB = 0.22. Lower differentiation between allopatric (θB = 0.028 than sympatric (0.063-0.083 populations contradicts the hypothesis of a sympatric origin of taxa, and there was little evidence for stocking or ongoing hybridization. Genome scans found only three loci that appeared to be under selection in both sympatric population pairs, suggesting a low probability of similar mechanisms of ecological segregation. However, removal of all non-neutral loci decreased the genetic distance between sympatric pairs, suggesting recent adaptive divergence at a few loci. Sympatric pairs in the two lakes were genetically distinct from the six other C. albula populations, suggesting introgression from another lineage may have influenced these two lakes. This was supported by an analysis of isolation-by-distance, where the drift-gene flow equilibrium observed among allopatric populations was disrupted when the sympatric pairs were included. Conclusions While the population genetic data alone can not unambiguously uncover the mode of speciation, our data indicate that multiple lineages may be responsible for the complex patterns typically observed in Coregonus. Relative differences within and among lakes raises

  9. Genetic Relationship of Wickham and IRRDB 1981 Rubber Population Based on RAPD Markers Analysis

    Directory of Open Access Journals (Sweden)

    FETRINA OKTAVIA

    2011-03-01

    Full Text Available Rubber hand pollination in Indonesian Rubber Research Institute program currently uses Wickham population which genetic analysis showed that genetic diversity of this population is narrow. The development of breeding activity has made the genetic base narrower by inbreeding. In order to solve this problem can use a new genetic resource that is the rubber germplasm IRRDB 1981 population. The genetic relationship between these populations is important to choose parents to avoid closely related genotypes in hand pollination. Therefore RAPD analysis was carried out using four selected primers i.e. OPH-03, OPH-05, OPH-18 and OPN-06. The result showed that Wickham and IRRDB 1981 population were separated into two different big groups with genetic similarity value of 0.64, and those big groups were separated further into many small sub groups with some genetic similarity level. The genetic similarity matrix showed that Wickham and IRRDB 1981 population has a range of genetic similarity 0.37– 0.98. The highest genetic similarity was found between RRIM 600 and PN 621, while the lowest was between BPM 1 and RRIC 100. Value in this matrix showed the genetic diversity between each clone. Based on this result, rubber genotypes of Wickham population could be crossed with genotypes of IRRDB 1981 population by choosing genotypes that have low genetic similarity.

  10. A review of the diverse genetic disorders in the Lebanese population: highlighting the urgency for community genetic services

    OpenAIRE

    Nakouzi, Ghunwa; Kreidieh, Khalil; Yazbek, Soha

    2014-01-01

    The review lists the genetic diseases reported in Lebanese individuals, surveys genetic programs and services, and highlights the absence of basic genetic health services at the individual and community level. The incidence of individual diseases is not determined, yet the variety of genetic diseases reported is tremendous, most of which follow autosomal recessive inheritance reflecting the social norms in the population, including high rates of consanguinity, which favor the increase in inci...

  11. Evolving Neural Network Using Variable String Genetic Algorithm for Color Infrared Aerial Image Classification

    Institute of Scientific and Technical Information of China (English)

    FU Xiaoyang; P E R Dale; ZHANG Shuqing

    2008-01-01

    Coastal wetlands are characterized by complex patterns both in their geomorphic and ecological features.Besides field observations,it is necessary to analyze the land cover of wetlands through the color infrared (CIR) aerial photography or remote sensing image.In this paper,we designed an evolving neural network classifier using variable string genetic algorithm (VGA) for the land cover classification of CIR aerial image.With the VGA,the classifier that we designed is able to evolve automatically the appropriate number of hidden nodes for modeling the neural network topology optimally and to find a near-optimal set of connection weights globally.Then,with backpropagation algorithm (BP),it can find the best connection weights.The VGA-BP classifier,which is derived from hybrid algorithms mentioned above,is demonstrated on CIR images classification effectively.Compared with standard classifiers,such as Bayes maximum-likelihood classifier,VGA classifier and BP-MLP (multi-layer perception) classifier,it has shown that the VGA-BP classifier can have better performance on highly resolution land cover classification.

  12. A Template Matching Approach to Classification of QAM Modulation using Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Negar ahmadi

    2009-11-01

    Full Text Available The automatic recognition of the modulation format of a detected signal, the intermediate step between signal detection and demodulation, is a major task of an intelligent receiver, with various civilian and military applications. Obviously, with no knowledge of the transmitted data and many unknown parameters at the receiver, such as the signal power, carrier frequency and phase offsets, timing information, etc., blind identification of the modulation is a difficult task. This becomes even more challenging in real-world. In this paper modulation classification for QAM is performed by Genetic Algorithm followed by Template matching, considering the constellation of the received signal. In addition this classification finds the decision boundary of the signal which is critical information for bit detection. I have proposed and implemented a technique that casts modulation recognition into shape recognition. Constellation diagram is a traditional and powerful tool for design and evaluation of digital modulations. The simulation results show the capability of this method for modulation classification with high accuracy and appropriate convergence in the presence of noise.

  13. Vascular bone tumors: a proposal of a classification based on clinicopathological, radiographic and genetic features

    Energy Technology Data Exchange (ETDEWEB)

    Errani, Costantino [Istituto Ortopedico Rizzoli, Ortopedia Generale, Orthopaedic Service, Bagheria (Italy); Struttura Complessa Ortopedia Generale, Dipartimento Rizzoli-Sicilia, Bagheria, PA (Italy); Vanel, Daniel; Gambarotti, Marco; Alberghini, Marco [Istituto Ortopedico Rizzoli, Pathology Service, Bologna (Italy); Picci, Piero [Istituto Ortopedico Rizzoli, Laboratory for Cancer Research, Bologna (Italy); Faldini, Cesare [Istituto Ortopedico Rizzoli, Ortopedia Generale, Orthopaedic Service, Bagheria (Italy)

    2012-12-15

    The classification of vascular bone tumors remains challenging, with considerable morphological overlap spanning across benign to malignant categories. The vast majority of both benign and malignant vascular tumors are readily diagnosed based on their characteristic histological features, such as the formation of vascular spaces and the expression of endothelial markers. However, some vascular tumors have atypical histological features, such as a solid growth pattern, epithelioid change, or spindle cell morphology, which complicates their diagnosis. Pathologically, these tumors are remarkably similar, which makes differentiating them from each other very difficult. For this rare subset of vascular bone tumors, there remains considerable controversy with regard to the terminology and the classification that should be used. Moreover, one of the most confusing issues related to vascular bone tumors is the myriad of names that are used to describe them. Because the clinical behavior and, consequently, treatment and prognosis of vascular bone tumors can vary significantly, it is important to effectively and accurately distinguish them from each other. Upon review of the nomenclature and the characteristic clinicopathological, radiographic and genetic features of vascular bone tumors, we propose a classification scheme that includes hemangioma, hemangioendothelioma, angiosarcoma, and their epithelioid variants. (orig.)

  14. Vascular bone tumors: a proposal of a classification based on clinicopathological, radiographic and genetic features

    International Nuclear Information System (INIS)

    The classification of vascular bone tumors remains challenging, with considerable morphological overlap spanning across benign to malignant categories. The vast majority of both benign and malignant vascular tumors are readily diagnosed based on their characteristic histological features, such as the formation of vascular spaces and the expression of endothelial markers. However, some vascular tumors have atypical histological features, such as a solid growth pattern, epithelioid change, or spindle cell morphology, which complicates their diagnosis. Pathologically, these tumors are remarkably similar, which makes differentiating them from each other very difficult. For this rare subset of vascular bone tumors, there remains considerable controversy with regard to the terminology and the classification that should be used. Moreover, one of the most confusing issues related to vascular bone tumors is the myriad of names that are used to describe them. Because the clinical behavior and, consequently, treatment and prognosis of vascular bone tumors can vary significantly, it is important to effectively and accurately distinguish them from each other. Upon review of the nomenclature and the characteristic clinicopathological, radiographic and genetic features of vascular bone tumors, we propose a classification scheme that includes hemangioma, hemangioendothelioma, angiosarcoma, and their epithelioid variants. (orig.)

  15. Cytochrome P450 genetic polymorphisms of Mexican indigenous populations.

    Science.gov (United States)

    Sosa-Macías, Martha; Llerena, Adrián

    2013-01-01

    This review focuses on the genetic polymorphisms of the cytochrome P450 (CYP) genes in Mexican indigenous populations, who are a part of the wide ethnic diversity of this country. These native groups have a particular historical trajectory that is different from the Mexican Mestizos. This variability may be reflected in the frequency distribution of polymorphisms in the CYP genes that encode enzymes involved in the metabolism of drugs and other xenobiotics. Therefore, these polymorphisms may affect drug efficacy and safety in indigenous populations in Mexico. The present study aimed to analyze the prevalence of CYP polymorphisms in indigenous Mexicans and to compare the results with studies in Mexican Mestizos. Because the extrapolation of pharmacogenetic data from Mestizos is not applicable to the majority of indigenous groups, pharmacogenetic studies directed at indigenous populations need to be developed. The Amerindians analyzed in this study showed a low phenotypic (CYP2D6) and genotypic (CYP2D6, CYP2C9) diversity, unlike Mexican Mestizos. The frequency of polymorphisms in the CYP1A1, CYP2C19, CYP2E1, and CYP3A4 genes was more similar among the Amerindians and Mexican Mestizos, with the exception of the CYP1A2 gene, whose *1F variant frequency in Mexican Amerindians was the highest described to date. PMID:24145057

  16. Relevant genetic differentiation among Brazilian populations of Anastrepha fraterculus (Diptera, Tephritidae)

    Science.gov (United States)

    Manni, Mosè; Lima, Kátia Manuela; Guglielmino, Carmela Rosalba; Lanzavecchia, Silvia Beatriz; Juri, Marianela; Vera, Teresa; Cladera, Jorge; Scolari, Francesca; Gomulski, Ludvik; Bonizzoni, Mariangela; Gasperi, Giuliano; Silva, Janisete Gomes; Malacrida, Anna Rodolfa

    2015-01-01

    Abstract We used a population genetic approach to detect the presence of genetic diversity among six populations of Anastrepha fraterculus across Brazil. To this aim, we used Simple Sequence Repeat (SSR) markers, which may capture the presence of differentiative processes across the genome in distinct populations. Spatial analyses of molecular variance were used to identify groups of populations that are both genetically and geographically homogeneous while also being maximally differentiated from each other. The spatial analysis of genetic diversity indicates that the levels of diversity among the six populations vary significantly on an eco-geographical basis. Particularly, altitude seems to represent a differentiating adaptation, as the main genetic differentiation is detected between the two populations present at higher altitudes and the other four populations at sea level. The data, together with the outcomes from different cluster analyses, identify a genetic diversity pattern that overlaps with the distribution of the known morphotypes in the Brazilian area. PMID:26798258

  17. Genetic Background and Population Genetics of Hungarian Brown Trout Populations Using PCR-RFLP and Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Ágnes Ősz

    2015-12-01

    4 University of West Hungary, Mosonmagyaróvár Vár 2., 9200 Mosonmagyaróvár, Hungary Based on the analyses of the mitochondrial DNA of several European brown trout populations, five evolutionary lineages of brown trout were indentified (Atlantic, Danubian, Mediterranean, Adriatic, Marble. The species is bred primarily for stock enhancement of natural waters, however the most hatchery-maintained broodstocks originate from the Atlantic lineage. Due to the hydrogeography of Hungary our stocks should theoretically belong to the Danubian lineage; however, this has not been investigated earlier by genetic studies. For our genetic analysis, 702 fin clips were collected from two brown trout broodstocks (Lillafüred and Szilvásvárad as well as populations of natural streams (Bán, Jósva, Kemence, Apátkút, Bittva and Kölöntés in Hungary. Sequencing of the control region in mitochondrial DNA, three PCR-RFLP (mitochondrial DNA control region, lactate dehydrogenase and somatolactin genes and five microsatellite markers were used to distinguish between Danubian and Atlantic lineages of brown trout. The proportion of the mitochondrial haplotype of the Danubian lineage was low, with the exception of the Apátkúti, Kölöntés streams and Szilvásvárad broodstock. Analyses of nuclear PCR-RFLP and microsatellites markers showed various distributions of alleles characteristic of the Atlantic or Danubian lineages, although the Atlantic genotype has dominated in all population. In case of the analyses of microsatellites the polymorphism varied greatly at all locations. In addition we found several alleles that were not described earlier in other populations. Those alleles probably would be typical of Hungarian brown trout populations. Overall the populations were effectively in Hardy-Weinberg equilibrium for both PCR-RFLP and microsatellite markers. The remarkably high proportion of allochthonous Atlantic alleles in the analyzed sites is a clear indicator of the import

  18. Detection of genetic polymorphism in the populations of brinjal shoot and fruit borer, Leucinodes orbonalis (Guenee).

    Science.gov (United States)

    Karthikeyan, K A M; Vijayakumar, I; Murali, P; Suresh, P; Janarthanan, S

    2005-06-01

    In the present study six different populations of L. orbonalis were collected and subjected to analysis of genetic variability in terms of carboxylesterase isozyme pattern and DNA polymorphism using RAPD-PCR. Pattern of carboxylesterase revealed a similar isozyme cluster in the populations namely, sivaganga (population-3), dindigal (population-4), virudhunagar (population-5) and coimbatore (population-6). Similarly, the populations of L. orbonalis recorded 3 distinct randomly amplified polymorphic DNA markers in all populations grouped above. This pattern of genetic variability in the populations was also supported by the analysis of the similarity indices and UPGMA dendrogram. PMID:15991581

  19. Effect of population size on genetic variation levels in Capparis spinosa (Capparaceae detected by RAPDs

    Directory of Open Access Journals (Sweden)

    Houshang Nosrati

    2012-07-01

    Full Text Available Background: The population size of plants affects on population genetic variation. Materials and Methods: We studied the impact of population size on genetic variation in populations of Capparis spinosa (caper, Capparaceae using RAPDs in East Azerbaijan (Iran. Within-population genetic diversity was estimated based on Nei`s and Shanonn`s diversity using Popgen, and genetic similarity among the populations was studied from a UPGMA dendrogram based the matrix of Nei’s distances obtained through SHAN. Difference in the level genetic variation between small-sized and large-sized populations was tested using Mann-Whitney U test, and correlation between geographical and genetic distances among populations was examined by Pearson test (SPSS, 11.3. Total genetic variation was partitioned into within and among populations based on AMOVA using Arlequin. Results: The polymorphism levels of RAPDs bands among the populations ranged from 48.8% to 81.4%, and within-population Nei’s diversity varied from 0.1667 to 0.2630. Genetic variation in small-sized populations (0.1667 to 0.1809 was significantly lower than the variations in large-sized populations (0.2158 -0.2630 (N= 7, P0.674, Pearson correlation test. Conclusions: Population size has a dramatic impact on its genetic diversity. The results revealed that fragmentation of caper population in the study region has most likely occurred recently. The low genetic diversity revealed within caper populations indicates high risk of extinction and suggests that urgent conservation action is needed to recover diversity in these populations.

  20. Examination of the Genetic Connectedness of Various Hungarian Pig Populations

    Directory of Open Access Journals (Sweden)

    László Csató

    2004-12-01

    Full Text Available Authors analysed field test data (collected and owned by the National Institute for Agricultural Quality Control between 1994-1999 of various pig breeds (Belgian Landrace, Duroc, Pietrain, and constructions (Duroc × Belgian Landrace, Belgian Landrace × Hampshire, Pietrain × Hampshire, Pietrain × Duroc, the D and E-lines of the Ka-Hyb hybrid pig. Gilts are kept in groups up to 25 pigs while boars are raised in smaller groups up to 15 on an ad libitum feeding regime. In the field test three ultrasonic back fat measurements are taken from boars and gilts between 80 and 110 kg at the middle of the spinal chord (shoulder, mid-back, loin. Average back fat thickness is calculated as the average of these three measurements. Heritability of average back fat depth was estimated using the REML method. The estimates varied between 0.12-0.51 depending on the genotype. The existence of genetic ties between the herds of the various pig populations was measured through the use of boars across the herds. Concerning the Belgian Landrace breed and the E-line of the Ka-Hyb hybrid pig no genetic ties were found, which means that the boars of these populations were only used within the herds. On the other hand week connections (5-14% were found for the other genotypes. Boars having been used in two or more herds showed more reliable breeding values (lower prediction error variance than those animals, which had progeny in one herd only. Based on the results authors suggested the exclusive application of the BLUP method in the Hungarian pig evaluation.

  1. Genetic diversity, population structure and Wolbachia infection status in a worldwide sample of Drosophila melanogaster and D. simulans populations.

    Directory of Open Access Journals (Sweden)

    Rudi L Verspoor

    Full Text Available Drosophila melanogaster and its close relatives have been extremely important model species in the development of population genetic models that serve to explain patterns of diversity in natural populations, a major goal of evolutionary biology. A detailed picture of the evolutionary history of these species is beginning to emerge, as the relative importance of forces including demographic changes and natural selection is established. A continuing aim is to characterise levels of genetic diversity in a large number of populations of these species, covering a wide geographic area. We have used collections from five previously un-sampled wild populations of D. melanogaster and two of D. simulans, across three continents. We estimated levels of genetic diversity within, and divergence between, these populations, and looked for evidence of genetic structure both between ancestral and derived populations, and amongst derived populations. We also investigated the prevalence of infection with the bacterial endosymbiont Wolbachia. We found that D. melanogaster populations from Sub-Saharan Africa are the most diverse, and that divergence is highest between these and non-Sub-Saharan populations. There is strong evidence for structuring of populations between Sub-Saharan Africa and the rest of the world, and some evidence for weak structure amongst derived populations. Populations from Sub-Saharan Africa also differ in the prevalence of Wolbachia infection, with very low levels of infection compared to populations from the rest of the world.

  2. The Genetic Structure of Wild Orobanche cumana Wallr. (Orobanchaceae Populations in Eastern Bulgaria Reflects Introgressions from Weedy Populations

    Directory of Open Access Journals (Sweden)

    Rocío Pineda-Martos

    2014-01-01

    Full Text Available Orobanche cumana is a holoparasitic plant naturally distributed from central Asia to south-eastern Europe, where it parasitizes wild Asteraceae species. It is also an important parasitic weed of sunflower crops. The objective of this research was to investigate genetic diversity, population structure, and virulence on sunflower of O. cumana populations parasitizing wild plants in eastern Bulgaria. Fresh tissue of eight O. cumana populations and mature seeds of four of them were collected in situ on wild hosts. Genetic diversity and population structure were studied with SSR markers and compared to weedy populations. Two main gene pools were identified in Bulgarian populations, with most of the populations having intermediate characteristics. Cross-inoculation experiments revealed that O. cumana populations collected on wild species possessed similar ability to parasitize sunflower to those collected on sunflower. The results were explained on the basis of an effective genetic exchange between populations parasitizing sunflower crops and those parasitizing wild species. The occurrence of bidirectional gene flow may have an impact on wild populations, as new physiological races continuously emerge in weedy populations. Also, genetic variability of wild populations may favour the ability of weedy populations to overcome sunflower resistance mechanisms.

  3. Population dynamics of a natural red deer population over 200 years detected via substantial changes of genetic variation.

    Science.gov (United States)

    Hoffmann, Gunther Sebastian; Johannesen, Jes; Griebeler, Eva Maria

    2016-05-01

    Most large mammals have constantly been exposed to anthropogenic influence over decades or even centuries. Because of their long generation times and lack of sampling material, inferences of past population genetic dynamics, including anthropogenic impacts, have only relied on the analysis of the structure of extant populations. Here, we investigate for the first time the change in the genetic constitution of a natural red deer population over two centuries, using up to 200-year-old antlers (30 generations) stored in trophy collections. To the best of our knowledge, this is the oldest DNA source ever used for microsatellite population genetic analyses. We demonstrate that government policy and hunting laws may have strong impacts on populations that can lead to unexpectedly rapid changes in the genetic constitution of a large mammal population. A high ancestral individual polymorphism seen in an outbreeding population (1813-1861) was strongly reduced in descendants (1923-1940) during the mid-19th and early 20th century by genetic bottlenecks. Today (2011), individual polymorphism and variance among individuals is increasing in a constant-sized (managed) population. Differentiation was high among periods (F ST > ***); consequently, assignment tests assigned individuals to their own period with >85% probability. In contrast to the high variance observed at nuclear microsatellite loci, mtDNA (D-loop) was monomorphic through time, suggesting that male immigration dominates the genetic evolution in this population. PMID:27096075

  4. The effect of the last glacial age on speciation and population genetic structure of the endangered Ethiopian wolf (Canis simensis).

    Science.gov (United States)

    Gottelli, Dada; Marino, Jorgelina; Sillero-Zubiri, Claudio; Funk, Stephan M

    2004-08-01

    During the last glacial age, Afro-alpine habitats were widespread across the highlands of Ethiopia. A wolf-like canid ancestor is thought to have colonized this expanding habitat and given rise to a new species that was remarkably well adapted to the high altitude environment: the Ethiopian wolf Canis simensis. Here, we address the timing of genetic divergence and examine population genetic history and structure by investigating the distribution of mitochondrial DNA (mtDNA) sequence variation. The pattern of mtDNA variation and geographical distribution indicate an initial population expansion, probably immediately after divergence from the wolf-like ancestor, around 100,000 years ago. The partition of mtDNA haplotypes that followed was most likely the result of habitat reduction and fragmentation at the onset of deglaciation approximately 15,000 years ago. Phylogenetic and geographical associations suggest that the most likely genetic partitioning corresponds to three mountain areas, Arsi/Bale, Wollo/Shoa and Simien/Mt. Guna. Although there is a degree of clustering of haplotypes from both sides of the Rift Valley, the lack of reciprocal monophyly does not support the taxonomic classification of two subspecies. This study highlights the importance of populations north of the Rift Valley for the maintenance of genetic variability within the species and has consequent implications for conservation. PMID:15245401

  5. Application of ILO classification to a population without industrial exposure: findings to be differentiated from pneumoconiosis

    International Nuclear Information System (INIS)

    The International Labour Office (ILO) classification for radiographs of pneumoconiosis is a standard means of assessing the presence or absence of pneumoconiosis in workers exposed to mineral dusts. Using this classification, 200 admission chest radiographs were reviewed on hospitalized patients in an urban university medical center to determine the prevalence and possible significance of ''small opacities'' in a population without known industrial exposure. Seventy-one men and 129 women were screened with the mean age of 44.2 years (range, 15-84). Thirty-six (18%) of the 200 patients had small opacities at profusion level 1/0 or greater, and this constituted the ''positive radiographs'' group. Twenty-two patients (11%) with positive radiographs had no documentable dust exposure or other specific medical etiology that would explain the presence of their lung opacities. The high prevalence of small opacities in ''normal'' older individuals has important implications in the assessment of patients with suspected pneumoconiosis

  6. Population structure, genetic variation and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance

    Directory of Open Access Journals (Sweden)

    Mallikarjuna Rao eKovi

    2015-11-01

    Full Text Available Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF] and 27 of Unselected [US] from the second generation of the two divergently selected populations and an unselected control population were genotyped using 278 genome-wide SNPs derived from Lolium perenne L. transcriptome sequence. Our studies showed that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two Fst outlier methods; finite island model (fdist by LOSITAN and hierarchical structure model using ARLEQUIN detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation and abiotic stress and might be the potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

  7. Sampling strategy for wild soybean (Glycine soja) populations based on their genetic diversity and fine-scale spatial genetic structure

    Institute of Scientific and Technical Information of China (English)

    ZHU Weiyue; ZHOU Taoying; ZHONG Ming; LU Baorong

    2007-01-01

    A total of 892 individuals sampled from a wild soybean population in a natural reserve near the Yellow River estuary located in Kenli of Shandong Province (China) were investigated.Seventeen SSR (simple sequence repeat) primer pairs from cultivated soybeans were used to estimate the genetic diversity of the population and its variation pattern versus changes of the sample size (sub-samples),in addition to investigating the fine-scale spatial genetic structure within the population.The results showed relatively high genetic diversity of the population with the mean value of allele number (A) being 2.88,expected heterozygosity (He) 0.431,Shannon diversity index (/) 0.699,and percentage of polymorphic loci (P) 100%.Sub-samples of different sizes (ten groups) were randomly drawn from the population and their genetic diversity was calculated by computer simulation.The regression model of the four diversity indexes with the change of sample sizes was computed.As a result,27-52 individuals can reach 95% of total genetic variability of the population.Spatial autocorrelation analysis revealed that the genetic patch size of this wild soybean population is about 18 m.The study provided a scientific basis for the sampling strategy of wild soybean populations.

  8. Evolutionary reconstruction and population genetics analysis of aurora kinases.

    Directory of Open Access Journals (Sweden)

    Balu Kamaraj

    Full Text Available BACKGROUND: Aurora kinases belong to the highly conserved kinase family and play a vital role in cell cycle regulation. The structure and function of these kinases are inter-related and sometimes they also act as substitutes in case of knockdown of other aurora kinases. METHOD: In this work we carried out the evolutionary reconstruction and population genetic studies of aurora kinase proteins. Substitution saturation test, CAI (Codon adaptation index, gene expression and RSCU (Relative synonymous codon usage values were computed for all the three aurora kinases. Linear regression method was used to check the dependency of gene expression on their CAI values. RESULTS: The results suggested that aurora-B and aurora-C has shown convergence in their evolutionary pathway. Moreover, the aurora-A I57V mutation showed high penetrance in human population and exist at very high frequency (84.4% when compared to the native residue (15.6%. The mutation showed notable range of functional gain and seemed to be promising for the evolution of aurora-A function. Mutant allele might also become a challenging prospect for understanding the pattern of evolution followed by cell cycle kinases. CONCLUSION: The overall result suggested that the aurora-A is currently under the evolutionary transition and to determine the functional significance of the mutation further investigation are required.

  9. Genealogical data in population medical genetics: field guidelines

    Directory of Open Access Journals (Sweden)

    Fernando A. Poletta

    2014-01-01

    Full Text Available This is a guide for fieldwork in Population Medical Genetics research projects. Data collection, handling, and analysis from large pedigrees require the use of specific tools and methods not widely familiar to human geneticists, unfortunately leading to ineffective graphic pedigrees. Initially, the objective of the pedigree must be decided, and the available information sources need to be identified and validated. Data collection and recording by the tabulated method is advocated, and the involved techniques are presented. Genealogical and personal information are the two main components of pedigree data. While the latter is unique to each investigation project, the former is solely represented by gametic links between persons. The triad of a given pedigree member and its two parents constitutes the building unit of a genealogy. Likewise, three ID numbers representing those three elements of the triad is the record field required for any pedigree analysis. Pedigree construction, as well as pedigree and population data analysis, varies according to the pre-established objectives, the existing information, and the available resources.

  10. The Druze: a population genetic refugium of the Near East.

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    Liran I Shlush

    Full Text Available BACKGROUND: Phylogenetic mitochondrial DNA haplogroups are highly partitioned across global geographic regions. A unique exception is the X haplogroup, which has a widespread global distribution without major regions of distinct localization. PRINCIPAL FINDINGS: We have examined mitochondrial DNA sequence variation together with Y-chromosome-based haplogroup structure among the Druze, a religious minority with a unique socio-demographic history residing in the Near East. We observed a striking overall pattern of heterogeneous parental origins, consistent with Druze oral tradition, together with both a high frequency and a high diversity of the mitochondrial DNA (mtDNA X haplogroup within a confined regional subpopulation. Furthermore demographic modeling indicated low migration rates with nearby populations. CONCLUSIONS: These findings were enabled through the use of a paternal kindred based sampling approach, and suggest that the Galilee Druze represent a population isolate, and that the combination of a high frequency and diversity of the mtDNA X haplogroup signifies a phylogenetic refugium, providing a sample snapshot of the genetic landscape of the Near East prior to the modern age.

  11. Does population size affect genetic diversity? A test with sympatric lizard species.

    Science.gov (United States)

    Hague, M T J; Routman, E J

    2016-01-01

    Genetic diversity is a fundamental requirement for evolution and adaptation. Nonetheless, the forces that maintain patterns of genetic variation in wild populations are not completely understood. Neutral theory posits that genetic diversity will increase with a larger effective population size and the decreasing effects of drift. However, the lack of compelling evidence for a relationship between genetic diversity and population size in comparative studies has generated some skepticism over the degree that neutral sequence evolution drives overall patterns of diversity. The goal of this study was to measure genetic diversity among sympatric populations of related lizard species that differ in population size and other ecological factors. By sampling related species from a single geographic location, we aimed to reduce nuisance variance in genetic diversity owing to species differences, for example, in mutation rates or historical biogeography. We compared populations of zebra-tailed lizards and western banded geckos, which are abundant and short-lived, to chuckwallas and desert iguanas, which are less common and long-lived. We assessed population genetic diversity at three protein-coding loci for each species. Our results were consistent with the predictions of neutral theory, as the abundant species almost always had higher levels of haplotype diversity than the less common species. Higher population genetic diversity in the abundant species is likely due to a combination of demographic factors, including larger local population sizes (and presumably effective population sizes), faster generation times and high rates of gene flow with other populations. PMID:26306730

  12. High Genetic Diversity in Geographically Remote Populations of Endemic and Widespread Coral Reef Angelfishes (genus: Centropyge)

    OpenAIRE

    Munday, Philip L.; Jones, Geoffrey P.; Hobbs, Jean-Paul A.; Lynne van Herwerden; Jerry, Dean R.

    2013-01-01

    In the terrestrial environment, endemic species and isolated populations of widespread species have the highest rates of extinction partly due to their low genetic diversity. To determine if this pattern holds in the marine environment, we examined genetic diversity in endemic coral reef angelfishes and isolated populations of widespread species. Specifically, this study tested the prediction that angelfish (genus: Centropyge) populations at Christmas and Cocos Islands have low genetic divers...

  13. Population genetics of the sugarcane borer Diatraea saccharalis (Fabr.) (Lepidoptera: Crambidae)

    OpenAIRE

    Denise Alves Lopes; Liriana Belizário Cantagalli; Ana Lucia Paz Barateiro Stuchi; Claudete Aparecida Mangolin; Maria Claudia Colla Ruvolo-Takasusuki

    2014-01-01

    Diatraea saccharalis is the principal pest of sugarcane in Brazil and is found throughout the sugarcane crop. Information about its population genetics is scarce, but population genetic analysis is of particular importance as a basis for a successful pest control program. Pest control requires a constant evaluation of genetic variability so that appropriate strategies can be employed. In this study, the structure of D. saccharalis populations in sugarcane crops was analyzed with PCR-RAPD (Pol...

  14. Population genetic differences along a latitudinal cline between original and recently colonized habitat in a butterfly.

    OpenAIRE

    Sofie Vandewoestijne; Hans Van Dyck

    2010-01-01

    BACKGROUND: Past and current range or spatial expansions have important consequences on population genetic structure. Habitat-use expansion, i.e. changing habitat associations, may also influence genetic population parameters, but has been less studied. Here we examined the genetic population structure of a Palaeartic woodland butterfly Pararge aegeria (Nymphalidae) which has recently colonized agricultural landscapes in NW-Europe. Butterflies from woodland and agricultural landscapes differ ...

  15. Genetic Diversity Analysis of Lates calcarifer (Bloch 1790) in Captive and Wild Populations Using RAPD Markers

    OpenAIRE

    Muthusamy RAJASEKAR; Muthusamy THANGARAJ; Thathiredypalli R. BARATHKUMAR; Jayachandran SUBBURAJ; Kaliyan MUTHAZHAGAN

    2012-01-01

    Lates calcarifer (Bloch 1790) is one of the major economically important cultivable fish species in India. In this study, three populations of L. calcarifer was selected to assess the genetic diversity. Of which, two wild (Mudaslodai, Muthupettai) and one captive (Mutukadu) population. The genetic diversity of three populations of this species was studied using Random Amplified Polymorphic DNA (RAPD) markers. Ten random primers were used for the assessment of their genetic diversity and const...

  16. Population genetics of drifting (Calanus spp.) and resident (Acartia clausi) plankton in Norwegian fjords

    Digital Repository Service at National Institute of Oceanography (India)

    Bucklin, A.; Kaartvedt, S.; Guarnieri, M.; Goswami, U.

    isolation and restricted gene flow (Wright, 1969). Conversely, genetic homogenization of the species’ population reflects high rates of exchange among populations. We have used population genetic analysis to provide some insight into the degree to which... genetics of drifting (Calanus spp.) and resident (Acartia clausi) plankton in Norwegian fjords A.Bucklin 1,2 , S.Kaartvedt 3 , M.Guarnieri 1 and U.Goswami 4 1 Ocean Process Analysis Laboratory and 2 Department of Zoology, University of New Hampshire...

  17. Alu repeats as markers for human population genetics

    Energy Technology Data Exchange (ETDEWEB)

    Batzer, M.A.; Alegria-Hartman, M. [Lawrence Livermore National Lab., CA (United States); Bazan, H. [Louisiana State Univ., New Orleans, LA (United States). Medical Center] [and others

    1993-09-01

    The Human-Specific (HS) subfamily of Alu sequences is comprised of a group of 500 nearly identical members which are almost exclusively restricted to the human genome. Individual subfamily members share an average of 97.9% nucleotide identity with each other and an average of 98.9% nucleotide identity with the HS subfamily consensus sequence. HS Alu family members are thought to be derived from a single source ``master`` gene, and have an average age of 2.8 million years. We have developed a Polymerase Chain Reaction (PCR) based assay using primers complementary to the 5 in. and 3 in. unique flanking DNA sequences from each HS Alu that allows the locus to be assayed for the presence or absence of an Alu repeat. Individual HS Alu sequences were found to be either monomorphic or dimorphic for the presence or absence of each repeat. The monomorphic HS Alu family members inserted in the human genome after the human/great ape divergence (which is thought to have occurred 4--6 million years ago), but before the radiation of modem man. The dimorphic HS Alu sequences inserted in the human genome after the radiation of modem man (within the last 200,000-one million years) and represent a unique source of information for human population genetics and forensic DNA analyses. These sites can be developed into Dimorphic Alu Sequence Tagged Sites (DASTS) for the Human Genome Project as well. HS Alu family member insertion dimorphism differs from other types of polymorphism (e.g. Variable Number of Tandem Repeat [VNTR] or Restriction Fragment Length Polymorphism [RFLP]) because individuals share HS Alu family member insertions based upon identity by descent from a common ancestor as a result of a single event which occurred one time within the human population. The VNTR and RFLP polymorphisms may arise multiple times within a population and are identical by state only.

  18. Classification of Atrial Septal Defect and Ventricular Septal Defect with Documented Hemodynamic Parameters via Cardiac Catheterization by Genetic Algorithms and Multi-Layered Artificial Neural Network

    Directory of Open Access Journals (Sweden)

    Mustafa Yıldız

    2012-08-01

    Full Text Available Introduction: We aimed to develop a classification method to discriminate ventricular septal defect and atrial septal defect by using severalhemodynamic parameters.Patients and Methods: Forty three patients (30 atrial septal defect, 13 ventricular septal defect; 26 female, 17 male with documentedhemodynamic parameters via cardiac catheterization are included to study. Such parameters as blood pressure values of different areas,gender, age and Qp/Qs ratios are used for classification. Parameters, we used in classification are determined by divergence analysismethod. Those parameters are; i pulmonary artery diastolic pressure, ii Qp/Qs ratio, iii right atrium pressure, iv age, v pulmonary arterysystolic pressure, vi left ventricular sistolic pressure, vii aorta mean pressure, viii left ventricular diastolic pressure, ix aorta diastolicpressure, x aorta systolic pressure. Those parameters detected from our study population, are uploaded to multi-layered artificial neuralnetwork and the network was trained by genetic algorithm.Results: Trained cluster consists of 14 factors (7 atrial septal defect and 7 ventricular septal defect. Overall success ratio is 79.2%, andwith a proper instruction of artificial neural network this ratio increases up to 89%.Conclusion: Parameters, belonging to artificial neural network, which are needed to be detected by the investigator in classical methods,can easily be detected with the help of genetic algorithms. During the instruction of artificial neural network by genetic algorithms, boththe topology of network and factors of network can be determined. During the test stage, elements, not included in instruction cluster, areassumed as in test cluster, and as a result of this study, we observed that multi-layered artificial neural network can be instructed properly,and neural network is a successful method for aimed classification.

  19. Comparative population genetic analysis of brackish- and freshwater populations of Eurasian perch (Perca fluviatilis L.: implication for fish forensics.

    Directory of Open Access Journals (Sweden)

    Lilian Pukk

    2015-11-01

    Full Text Available Understanding the genetic population structure of commercially important fish species is crucial for developing biologically sound management and conservation strategies. Genetic information can be also useful for fighting against illegal fishing and fish trade. Here, we studied commercially important brackish and freshwater populations of Eurasian perch (Perca fluviatilis L. in Estonia, to describe the genetic divergence among populations and evaluate the power of 16 microsatellite markers to assign individual fish and group of fish to their population of origin. To do so, a total of 785 individuals caught from 13 different sites in the Baltic Sea and four locations in Lake Peipus were analyzed. We found significant differences in genetic diversity between brackish and freshwater populations with Baltic Sea samples showing slightly lower allelic richness and heterozygosity compared to Lake Peipus. We also observed moderate genetic differentiation among populations (overall FST=0.034. Individual self-assignment tests assigned large proportion of individuals correctly back to freshwater or coastal origin (Lake Peipus: 87.1%; Baltic Sea: 89.4%. Also, when evaluating the origin of group of individuals, it was possible to identify the origin of the brackish and freshwater fish groups with very high confidence (log 10 LR > 2 when sample size was larger than 15. Our results demonstrate the power of highly variable genetic markers separating two commercially most important Eurasian perch stocks in Estonia and the usefulness of assignment tests to successfully identify the genetic origin of fish.

  20. Genetic diversity and population structure of Sitodiplosis mosellana in Northern China.

    Directory of Open Access Journals (Sweden)

    Yun Duan

    Full Text Available The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups, broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (F ST = 0.117 between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (F ST = 0.116, Nm = 1.89 than those in the eastern group (F ST = 0.049, Nm = 4.91. Genetic distance between populations was positively and significantly correlated with geographic distance (r = 0.56, P<0.001. The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs.

  1. Population genetic evidence for cold adaptation in European Drosophila melanogaster populations.

    Science.gov (United States)

    Božičević, Vedran; Hutter, Stephan; Stephan, Wolfgang; Wollstein, Andreas

    2016-03-01

    We studied Drosophila melanogaster populations from Europe (the Netherlands and France) and Africa (Rwanda and Zambia) to uncover genetic evidence of adaptation to cold. We present here four lines of evidence for genes involved in cold adaptation from four perspectives: (i) the frequency of SNPs at genes previously known to be associated with chill-coma recovery time (CCRT), startle reflex (SR) and resistance to starvation stress (RSS) vary along environmental gradients and therefore among populations; (ii) SNPs of genes that correlate significantly with latitude and altitude in African and European populations overlap with SNPs that correlate with a latitudinal cline from North America; (iii) at the genomewide level, the top candidate genes are enriched in gene ontology (GO) terms that are related to cold tolerance; (iv) GO enriched terms from North American clinal genes overlap significantly with those from Africa and Europe. Each SNP was tested in 10 independent runs of Bayenv2, using the median Bayes factors to ascertain candidate genes. None of the candidate genes were found close to the breakpoints of cosmopolitan inversions, and only four candidate genes were linked to QTLs related to CCRT. To overcome the limitation that we used only four populations to test correlations with environmental gradients, we performed simulations to estimate the power of our approach for detecting selection. Based on our results, we propose a novel network of genes that is involved in cold adaptation. PMID:26558479

  2. Trapped in the extinction vortex? Strong genetic effects in a declining vertebrate population

    Directory of Open Access Journals (Sweden)

    Larsson Mikael

    2010-02-01

    Full Text Available Abstract Background Inbreeding and loss of genetic diversity are expected to increase the extinction risk of small populations, but detailed tests in natural populations are scarce. We combine long-term population and fitness data with those from two types of molecular markers to examine the role of genetic effects in a declining metapopulation of southern dunlins Calidris alpina schinzii, an endangered shorebird. Results The decline is associated with increased pairings between related individuals, including close inbreeding (as revealed by both field observations of parentage and molecular markers. Furthermore, reduced genetic diversity seems to affect individual fitness at several life stages. Higher genetic similarity between mates correlates negatively with the pair's hatching success. Moreover, offspring produced by related parents are more homozygous and suffer from increased mortality during embryonic development and possibly also after hatching. Conclusions Our results demonstrate strong genetic effects in a rapidly declining population, emphasizing the importance of genetic factors for the persistence of small populations.

  3. Genetic variability and bottleneck detection of four Tricholoma matsutake populations from northeastern and southwestern China.

    Science.gov (United States)

    Zeng, Dong-Fang; Chen, Bin

    2015-08-01

    The excessive commercial collection of matsutake mushrooms can lead to extreme reduction of population size, which may cause genetic bottleneck and decrease genetic diversity of Tricholoma matsutake. Here, six polymorphic microsatellite loci markers were used to examine the genetic diversity of four natural T. matsutake populations from two main producing regions of China. The minimum combinations of four loci were able to discriminate total 86 sampled individuals with distinctive multilocus genotypes. Our analysis of molecular variance (AMOVA) revealed that about 80% and 20% of the overall genetic variation were respectively partitioned within and among populations. The principal-coordinate analyses (PCA) distinguished the four tested populations into three genetic clusters, each of which was correlated with respective endemic host plants on a geographical basis. The AMOVA, PCA and pairwise population FST estimates consistently displayed the same genetic divergence patterns and spatial structure of T. matsutake mediated by host plants in China. The significant heterozygosity excesses demonstrated that a recent genetic bottleneck occurred in each population tested. The complementary M-ratio test indicated past genetic bottleneck events over longer periods. Only four individuals were identified as putative first generation migrants within northeastern China, which implies restricted interpopulation gene flow in T. matsutake. We discuss that the significant genetic differentiation among populations of T. matsutake is most likely a function of host adaptation, host specificity, genetic bottleneck, limited dispersal and habitat fragmentation. PMID:25682708

  4. Genetic consequences of the action of ionizing radiations on natural populations after the Kyshtym accident

    International Nuclear Information System (INIS)

    The object of the present review is to consider some problems in radiation genetics of natural populations and to reveal problems which are of key importance, in the author's opinion, in monitoring irradiated natural populations. (author)

  5. Binary Image Classification: A Genetic Programming Approach to the Problem of Limited Training Instances.

    Science.gov (United States)

    Al-Sahaf, Harith; Zhang, Mengjie; Johnston, Mark

    2016-01-01

    In the computer vision and pattern recognition fields, image classification represents an important yet difficult task. It is a challenge to build effective computer models to replicate the remarkable ability of the human visual system, which relies on only one or a few instances to learn a completely new class or an object of a class. Recently we proposed two genetic programming (GP) methods, one-shot GP and compound-GP, that aim to evolve a program for the task of binary classification in images. The two methods are designed to use only one or a few instances per class to evolve the model. In this study, we investigate these two methods in terms of performance, robustness, and complexity of the evolved programs. We use ten data sets that vary in difficulty to evaluate these two methods. We also compare them with two other GP and six non-GP methods. The results show that one-shot GP and compound-GP outperform or achieve results comparable to competitor methods. Moreover, the features extracted by these two methods improve the performance of other classifiers with handcrafted features and those extracted by a recently developed GP-based method in most cases. PMID:25700148

  6. A Multiobjective Genetic Programming-Based Ensemble for Simultaneous Feature Selection and Classification.

    Science.gov (United States)

    Nag, Kaustuv; Pal, Nikhil R

    2016-02-01

    We present an integrated algorithm for simultaneous feature selection (FS) and designing of diverse classifiers using a steady state multiobjective genetic programming (GP), which minimizes three objectives: 1) false positives (FPs); 2) false negatives (FNs); and 3) the number of leaf nodes in the tree. Our method divides a c -class problem into c binary classification problems. It evolves c sets of genetic programs to create c ensembles. During mutation operation, our method exploits the fitness as well as unfitness of features, which dynamically change with generations with a view to using a set of highly relevant features with low redundancy. The classifiers of i th class determine the net belongingness of an unknown data point to the i th class using a weighted voting scheme, which makes use of the FP and FN mistakes made on the training data. We test our method on eight microarray and 11 text data sets with diverse number of classes (from 2 to 44), large number of features (from 2000 to 49 151), and high feature-to-sample ratio (from 1.03 to 273.1). We compare our method with a bi-objective GP scheme that does not use any FS and rule size reduction strategy. It depicts the effectiveness of the proposed FS and rule size reduction schemes. Furthermore, we compare our method with four classification methods in conjunction with six features selection algorithms and full feature set. Our scheme performs the best for 380 out of 474 combinations of data sets, algorithm and FS method. PMID:25769178

  7. Genetic resources of teak (Tectona grandis Linn. f.)—strong genetic structure among natural populations

    OpenAIRE

    Hansen, Ole K.; Changtragoon, Suchitra; Ponoy, Bundit; Kjær, Erik D.; Minn, Yazar; Finkeldey, Reiner; Nielsen, Knud B.; Graudal, Lars

    2015-01-01

    Twenty-nine provenances of teak (Tectona grandis Linn. f.) representing the full natural distribution range of the species were genotyped with microsatellite DNA markers to analyse genetic diversity and population genetic structure. Provenances originating from the semi-moist east coast of India had the highest genetic diversity while provenances from Laos showed the lowest. In the eastern part of the natural distribution area, comprising Myanmar, Thailand and Laos, there was a strong clinal ...

  8. Population genetic structure of urban malaria vector Anopheles stephensi in India.

    Science.gov (United States)

    Sharma, Richa; Sharma, Arvind; Kumar, Ashwani; Dube, Madhulika; Gakhar, S K

    2016-04-01

    Malaria is a major public health problem in India because climatic condition and geography of India provide an ideal environment for development of malaria vector. Anopheles stephensi is a major urban malaria vector in India and its control has been hampered by insecticide resistance. In present study population genetic structure of A. stephensi is analyzed at macro geographic level using 13 microsatellite markers. Significantly high genetic differentiation was found in all studied populations with differentiation values (FST) ranging from 0.0398 to 0.1808. The geographic distance was found to be playing a major role in genetic differentiation between different populations. Overall three genetic pools were observed and population of central India was found to be coexisting in two genetic pools. High effective population size (Ne) was found in all the studied populations. PMID:26777030

  9. A review of the diverse genetic disorders in the Lebanese population: highlighting the urgency for community genetic services.

    Science.gov (United States)

    Nakouzi, Ghunwa; Kreidieh, Khalil; Yazbek, Soha

    2015-01-01

    The review lists the genetic diseases reported in Lebanese individuals, surveys genetic programs and services, and highlights the absence of basic genetic health services at the individual and community level. The incidence of individual diseases is not determined, yet the variety of genetic diseases reported is tremendous, most of which follow autosomal recessive inheritance reflecting the social norms in the population, including high rates of consanguinity, which favor the increase in incidence of these diseases. Genetic services including all activities for the diagnosis, care, and prevention of genetic diseases at community level are extremely inadequate. Services are limited to some clinical and laboratory diagnostic services with no genetic counseling. These services are localized within the capital thus preventing their accessibility to high-risk communities. Screening programs, which are at the core of public health prevention services, are minimal and not nationally mandated. The absence of adequate genetic services is attributed to many factors undermining the importance of genetic diseases and their burden on society, the most important of which is genetic illiteracy at all levels of the population, including high-risk families, the general public, and most importantly health care providers and public health officials. Thus, a country like Lebanon, where genetic diseases are expected to be highly prevalent, is in utmost need for community genetics services. Strategies need to be developed to familiarize public health officials and medical professionals with medical genetics leading to a public health infrastructure that delivers community genetics services for the prevention and care of genetic disorders at community level. PMID:25261319

  10. Genetic structure of Mesoamerican populations of Big-leaf mahogany (Swietenia macrophylla) inferred from microsatellite analysis.

    Science.gov (United States)

    Novick, Rachel Roth; Dick, Christopher W; Lemes, Maristerra R; Navarro, Carlos; Caccone, Adalgisa; Bermingham, Eldredge

    2003-11-01

    While microsatellites have been used to examine genetic structure in local populations of Neotropical trees, genetic studies based on such high-resolution markers have not been carried out for Mesoamerica as a whole. Here we assess the genetic structure of the Mesoamerican mahogany Swietenia macrophylla King (big-leaf mahogany), a Neotropical tree species recently listed as endangered in CITES which is commercially extinct through much of its native range. We used seven variable microsatellite loci to assess genetic diversity and population structure in eight naturally established mahogany populations from six Mesoamerican countries. Measures of genetic differentiation (FST and RST) indicated significant differences between most populations. Unrooted dendrograms based on genetic distances between populations provide evidence of strong phylogeographic structure in Mesoamerican mahogany. The two populations on the Pacific coasts of Costa Rica and Panama were genetically distant from all the others, and from one another. The remaining populations formed two clusters, one comprised of the northern populations of Mexico, Belize and Guatemala and the other containing the southern Atlantic populations of Nicaragua and Costa Rica. Significant correlation was found between geographical distance and all pairwise measures of genetic divergence, suggesting the importance of regional biogeography and isolation by distance in Mesoamerican mahogany. The results of this study demonstrate greater phylogeographic structure than has been found across Amazon basin S. macrophylla. Our findings suggest a relatively complex Mesoamerican biogeographic history and lead to the prediction that other Central American trees will show similar patterns of regional differentiation. PMID:14629370

  11. Microsatellite markers reveal genetic divergence among wild and cultured populations of Chinese sucker Myxocyprinus asiaticus.

    Science.gov (United States)

    Cheng, W W; Wang, D Q; Wang, C Y; Du, H; Wei, Q W

    2016-01-01

    Studies of genetic diversity and genetic population structure are critical for the conservation and management of endangered species. The Chinese sucker Myxocyprinus asiaticus is a vulnerable monotypic species in China, which is at a risk of decline owing to fluctuations in effective population size and other demographic and environmental factors. We screened 11 microsatellite loci in 214 individuals to assess genetic differentiation in both wild and cultured populations. The single extant wild population had a higher number of alleles (13) than the cultured populations (average 7.3). High levels of genetic diversity, expressed as observed and expected heterozygosity (HO = 0.771, HE = 0.748, respectively), were found in both wild and cultured populations. We also report significant differentiation among wild and cultured populations (global FST = 0.023, P < 0.001). Both STRUCTURE analysis and neighbor-joining tree revealed three moderately divergent primary genetic clusters: the wild Yangtze population and the Sichuan population were each identified as an individual cluster, with the remaining populations clustered together. Twenty-two samples collected from the Yangtze River were assigned to the cultured population, demonstrating the efficacy of artificial propagation to avoid drastic reduction in the population size of M. asiaticus. These genetic data support the endangered status of the M. asiaticus and have implications for conservation management planning. PMID:27173283

  12. Genetic Diversity, Population Structure and Wolbachia Infection Status in a Worldwide Sample of Drosophila melanogaster and D. simulans Populations

    OpenAIRE

    Verspoor, Rudi L.; Haddrill, Penelope R

    2011-01-01

    Drosophila melanogaster and its close relatives have been extremely important model species in the development of population genetic models that serve to explain patterns of diversity in natural populations, a major goal of evolutionary biology. A detailed picture of the evolutionary history of these species is beginning to emerge, as the relative importance of forces including demographic changes and natural selection is established. A continuing aim is to characterise levels of genetic dive...

  13. Gene flow and genetic diversity of a broadcast-spawning coral in northern peripheral populations.

    Directory of Open Access Journals (Sweden)

    Yuichi Nakajima

    Full Text Available Recently, reef-building coral populations have been decreasing worldwide due to various disturbances. Population genetic studies are helpful for estimating the genetic connectivity among populations of marine sessile organisms with metapopulation structures such as corals. Moreover, the relationship between latitude and genetic diversity is informative when evaluating the fragility of populations. In this study, using highly variable markers, we examined the population genetics of the broadcast-spawning coral Acropora digitifera at 19 sites in seven regions along the 1,000 km long island chain of Nansei Islands, Japan. This area includes both subtropical and temperate habitats. Thus, the coral populations around the Nansei Islands in Japan are northern peripheral populations that would be subjected to environmental stresses different from those in tropical areas. The existence of high genetic connectivity across this large geographic area was suggested for all sites (F(ST < or = 0.033 although small but significant genetic differentiation was detected among populations in geographically close sites and regions. In addition, A. digitifera appears to be distributed throughout the Nansei Islands without losing genetic diversity. Therefore, A. digitifera populations in the Nansei Islands may be able to recover relatively rapidly even when high disturbances of coral communities occur locally if populations on other reefs are properly maintained.

  14. Genetic diversity and population structure of cucumber (Cucumis sativus L.)

    Science.gov (United States)

    Understanding genetic variation in germplasm collection is essential for the conservation and their efficient use in plant breeding. Cucumber is an important vegetable crop worldwide. Previous studies revealed a low genetic diversity in cucumber, but detailed insights into the crop’s genetic structu...

  15. Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl.

    Directory of Open Access Journals (Sweden)

    Martina Temunović

    Full Text Available Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM. We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.

  16. Constructivisms from a genetic point of view: a critical classification of current tendencies.

    Science.gov (United States)

    Sánchez, José Carlos; Loredo, José Carlos

    2009-12-01

    In this paper, we propose a critical classification of contemporary constructivist orientations. Our fundamental theoretical reference is the notion of genesis, understood as the construction of reality in a way that is neither relativist nor positivist-realist. We identify a nucleus of classic, genetic constructivism that revolves around the ideas of Baldwin, Piaget and Vygotsky and discuss two tendencies that distort the spirit of that nucleus: objectivism and subjectivism. Objectivism rules out the psychological, constructive activity of the subject, subordinating (or just reducing) it to objective structures either from nature (like genetic endowment or neural functioning), or from culture (like language or social practices). Subjectivism completely detaches the objectivity of knowledge from its construction on the part of the subject, reducing it to the mere product of individual interest, view, or irrationality. Thus, subjectivism is the non-constructive way to conceive the subject. Then, we attempt to show the dialectics that exists between these two tendencies and the scope of our criteria by analysing a representative (non exhaustive) group of authors who are defined as constructivists or who bring important elements to the debate about constructivism. PMID:19306117

  17. Population genetics of Y-chromosome STRs in a population of Northern Greeks.

    Science.gov (United States)

    Kovatsi, Leda; Saunier, Jessica L; Irwin, Jodi A

    2009-12-01

    Seventeen Y STR loci were typed in a population sample of 191 unrelated male individuals from Northern Greece. Haplotypes are presented for the following loci: DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438 and DYS448. The overall haplotype diversity was 0.9992. This database study provides significant additional information for the application of Y-chromosomal STRs to forensic identification efforts in Greece by nearly doubling both the number of individuals and the number of Y-loci typed from Greek populations. These samples have been previously typed for autosomal STRs [L. Kovatsi, T.J. Parsons, R.S. Just, J.A. Irwin, Genetic variation for 15 autosomal STR loci (PowerPlex 16) in a population sample from northern Greece, Forensic Sci. Int. 159 (2006) 61-63] and the mitochondrial DNA control region [J. Irwin, J. Saunier, K. Strouss, C. Paintner, T. Diegoli, K. Sturk, L. Kovatsi, A. Brandstatter, M.A. Cariolou, W. Parson, T.J. Parsons, Mitochondrial control region sequences from northern Greece and Greek Cypriots, Int. J. Legal Med. 122 (2008) 87-89]. PMID:19948315

  18. Strategies to work with HLA data in human populations for histocompatibility, clinical transplantation, epidemiology and population genetics

    DEFF Research Database (Denmark)

    Sanchez-Mazas, A; Vidan-Jeras, B; Nunes, J M;

    2012-01-01

    outcome is the provision of population genetic characterizations and comparisons in a standard way by all interested laboratories. This article reports the recommendations of four working groups (WG1-4) of the HLA-NET network at the mid-term of its activities. WG1 (Population definitions and sampling......HLA-NET (a European COST Action) aims at networking researchers working in bone marrow transplantation, epidemiology and population genetics to improve the molecular characterization of the HLA genetic diversity of human populations, with an expected strong impact on both public health...... and fundamental research. Such improvements involve finding consensual strategies to characterize human populations and samples and report HLA molecular typings and ambiguities; proposing user-friendly access to databases and computer tools and defining minimal requirements related to ethical aspects. The overall...

  19. Genetic characterisation and social structure of the East Scotland population of bottlenose dolphins (Tursiops truncatus)

    OpenAIRE

    Islas, Valentina

    2010-01-01

    The Eastern Scottish population of bottlenose dolphins (Tursiops truncatus) is the northernmost population of this species. The resident core of this population consists of 120 to 150 different individuals. This small size and its geographical isolation from other populations raises questions about its viability and whether the population has behavioural patterns that differ from those common to other populations of the same species. Microsatellite genetic diversity was low ...

  20. Genetic and phenotypic correlations of quantitative traits in two long-term randomly mated soybean populations

    Science.gov (United States)

    The genetic effects of long term random mating and natural selection aided by genetic male sterility (gms) were evaluated in two soybean [Glycine max (L.) Merr.] populations designated: RSII and RSIII. These populations were evaluated in the field at three locations each with two replications. Genot...

  1. Analysis of Quantitative Traits in Two Long-Term Randomly Mated Soybean Populations I. Genetic Variances

    Science.gov (United States)

    The genetic effects of long term random mating and natural selection aided by genetic male sterility were evaluated in two soybean [Glycine max (L.) Merr.] populations: RSII and RSIII. Population means, variances, and heritabilities were estimated to determine the effects of 26 generations of random...

  2. Genetic structure of Anopheles gambiae populations on islands in northwestern Lake Victoria, Uganda

    Directory of Open Access Journals (Sweden)

    Coulibaly Mamadou B

    2005-12-01

    Full Text Available Abstract Background Alternative means of malaria control are urgently needed. Evaluating the effectiveness of measures that involve genetic manipulation of vector populations will be facilitated by identifying small, genetically isolated vector populations. The study was designed to use variation in microsatellite markers to look at genetic structure across four Lake Victoria islands and two surrounding mainland populations and for evidence of any restriction to free gene flow. Methods Four Islands (from 20–50 km apart and two surrounding mainland populations (96 km apart were studied. Samples of indoor resting adult mosquitoes, collected over two consecutive years, were genotyped at microsatellite loci distributed broadly throughout the genome and analysed for genetic structure, effective migration (Nem and effective population size (Ne. Results Ne estimates showed island populations to consist of smaller demes compared to the mainland ones. Most populations were significantly differentiated geographically, and from one year to the other. Average geographic pair-wise FST ranged from 0.014–0.105 and several pairs of populations had Ne m Conclusion These island populations are significantly genetically differentiated. Differences reoccurred over the study period, between the two mainland populations and between each other. This appears to be the product of their separation by water, dynamics of small populations and local adaptation. With further characterisation these islands could become possible sites for applying measures evaluating effectiveness of control by genetic manipulation.

  3. Microsatellite genetic diversity and differentiation of native and introduced grass carp populations in three continents

    Science.gov (United States)

    Chapman, Duane C.; Chen, Qin; Wang, Chenghui; Zhao, Jinlian; Lu, Guoqing; Zsigmond, Jeney; Li, Sifa

    2012-01-01

    Grass carp (Ctenopharyngodon idella), a freshwater species native to China, has been introduced to about 100 countries/regions and poses both biological and environmental challenges to the receiving ecosystems. In this study, we analyzed genetic variation in grass carp from three introduced river systems (Mississippi River Basin in US, Danube River in Hungary, and Tone River in Japan) as well as its native ranges (Yangtze, Pearl, and Amur Rivers) in China using 21 novel microsatellite loci. The allelic richness, observed heterozygosity, and within-population gene diversity were found to be lower in the introduced populations than in the native populations, presumably due to the small founder population size of the former. Significant genetic differentiation was found between all pairwise populations from different rivers. Both principal component analysis and Bayesian clustering analysis revealed obvious genetic distinction between the native and introduced populations. Interestingly, genetic bottlenecks were detected in the Hungarian and Japanese grass carp populations, but not in the North American population, suggesting that the Mississippi River Basin grass carp has experienced rapid population expansion with potential genetic diversification during the half-century since its introduction. Consequently, the combined forces of the founder effect, introduction history, and rapid population expansion help explaining the observed patterns of genetic diversity within and among both native and introduced populations of the grass carp.

  4. Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis

    Institute of Scientific and Technical Information of China (English)

    QIAO Hongjin; LIU Xiangquan; ZHANG Xijia; JIANG Haibin; WANG Jiying; ZHANG Limin

    2013-01-01

    Amplified fragment length polymorphisms (AFLP) markers were developed to assess the genetic variation of populations and clones of Rhopilema esculentum Kishinouye (Scyphozoa,Rhizostomatidae).One hundred and seventy-nine loci from 56 individuals of two hatchery populations and two wild populations were genotyped with five primer combinations.The polymorphic ratio,Shannon's diversity index and average heterozygosity were 70.3%,0.346 and 0.228 for the white hatchery population,74.3%,0.313,and 0.201 for the red hatchery population,79.3%,0.349,and 0.224 for the Jiangsu wild population,and 74.9%,0.328 and 0.210 for the Penglai wild population,respectively.Thus,all populations had a relatively high level of genetic diversity.A specific band was identified that could separate the white from the red hatchery population.There was 84.85% genetic differentiation within populations.Individual cluster analysis using unweighted pair-group method with arithmetic mean (UPGMA) suggested that hatchery populations and wild populations could be divided.For the hatchery populations,the white and red populations clustered separately; however,for the wild populations,Penglai and Jiangsu populations clustered together.The genetic diversity at the clone level was also determined.Our data suggest that there are relatively high genetic diversities within populations but low genetic differentiation between populations,which may be related to the long-term use of germplasm resources from Jiangsu Province for artificial seeding and releasing.These findings will benefit the artificial seeding and conservation of the germplasm resources.

  5. Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis

    Science.gov (United States)

    Qiao, Hongjin; Liu, Xiangquan; Zhang, Xijia; Jiang, Haibin; Wang, Jiying; Zhang, Limin

    2013-03-01

    Amplified fragment length polymorphisms (AFLP) markers were developed to assess the genetic variation of populations and clones of Rhopilema esculentum Kishinouye (Scyphozoa, Rhizostomatidae). One hundred and seventy-nine loci from 56 individuals of two hatchery populations and two wild populations were genotyped with five primer combinations. The polymorphic ratio, Shannon's diversity index and average heterozygosity were 70.3%, 0.346 and 0.228 for the white hatchery population, 74.3%, 0.313, and 0.201 for the red hatchery population, 79.3%, 0.349, and 0.224 for the Jiangsu wild population, and 74.9%, 0.328 and 0.210 for the Penglai wild population, respectively. Thus, all populations had a relatively high level of genetic diversity. A specific band was identified that could separate the white from the red hatchery population. There was 84.85% genetic differentiation within populations. Individual cluster analysis using unweighted pair-group method with arithmetic mean (UPGMA) suggested that hatchery populations and wild populations could be divided. For the hatchery populations, the white and red populations clustered separately; however, for the wild populations, Penglai and Jiangsu populations clustered together. The genetic diversity at the clone level was also determined. Our data suggest that there are relatively high genetic diversities within populations but low genetic differentiation between populations, which may be related to the long-term use of germplasm resources from Jiangsu Province for artificial seeding and releasing. These findings will benefit the artificial seeding and conservation of the germplasm resources.

  6. Human genetic variation database, a reference database of genetic variations in the Japanese population

    Science.gov (United States)

    Higasa, Koichiro; Miyake, Noriko; Yoshimura, Jun; Okamura, Kohji; Niihori, Tetsuya; Saitsu, Hirotomo; Doi, Koichiro; Shimizu, Masakazu; Nakabayashi, Kazuhiko; Aoki, Yoko; Tsurusaki, Yoshinori; Morishita, Shinichi; Kawaguchi, Takahisa; Migita, Osuke; Nakayama, Keiko; Nakashima, Mitsuko; Mitsui, Jun; Narahara, Maiko; Hayashi, Keiko; Funayama, Ryo; Yamaguchi, Daisuke; Ishiura, Hiroyuki; Ko, Wen-Ya; Hata, Kenichiro; Nagashima, Takeshi; Yamada, Ryo; Matsubara, Yoichi; Umezawa, Akihiro; Tsuji, Shoji; Matsumoto, Naomichi; Matsuda, Fumihiko

    2016-01-01

    Whole-genome and -exome resequencing using next-generation sequencers is a powerful approach for identifying genomic variations that are associated with diseases. However, systematic strategies for prioritizing causative variants from many candidates to explain the disease phenotype are still far from being established, because the population-specific frequency spectrum of genetic variation has not been characterized. Here, we have collected exomic genetic variation from 1208 Japanese individuals through a collaborative effort, and aggregated the data into a prevailing catalog. In total, we identified 156 622 previously unreported variants. The allele frequencies for the majority (88.8%) were lower than 0.5% in allele frequency and predicted to be functionally deleterious. In addition, we have constructed a Japanese-specific major allele reference genome by which the number of unique mapping of the short reads in our data has increased 0.045% on average. Our results illustrate the importance of constructing an ethnicity-specific reference genome for identifying rare variants. All the collected data were centralized to a newly developed database to serve as useful resources for exploring pathogenic variations. Public access to the database is available at http://www.genome.med.kyoto-u.ac.jp/SnpDB/. PMID:26911352

  7. Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study

    Directory of Open Access Journals (Sweden)

    Flávio de Oliveira Francisco

    2013-01-01

    Full Text Available Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.

  8. ESTIMATES OF GENETIC VARIANCE COMPONENT OF AN EQUILIBRIUM POPULATION OF CORN

    OpenAIRE

    Hamirul Hadini; Nasrullah; Taryono .; Panjisakti Basunanda

    2015-01-01

    There are abundant maize populations in Hardy-Weinberg equilibrium, which can be used as source of gene to develop either a hybrid variety or an open pollinated variety. Genetic parameters of a population, such as additive genetic variance and variance due to dominance which can be estimated using North Carolina Design I, were used to decide a breeding method to be applied. The objectives of this research were to estimate the genetic variance component of important quantitative traits in an e...

  9. Size of genetic bottlenecks leading to virus fitness loss is determined by mean initial population fitness.

    OpenAIRE

    Novella, I S; Elena, S F; Moya, A.; Domingo, E; Holland, J J

    1995-01-01

    Genetic bottlenecks are important events in the genetic diversification of organisms and colonization of new ecological niches. Repeated bottlenecking of RNA viruses often leads to fitness losses due to the operation of Muller's ratchet. Herein we use vesicular stomatitis virus to determine the transmission population size which leads to fitness decreases of virus populations. Remarkably, the effective size of a genetic bottleneck associated with fitness loss is greater when the fitness of th...

  10. Divergence between phenotypic and genetic variation within populations of a common herb across Europe

    OpenAIRE

    Villellas, Jesús; Berjano, Enrique Regina; Terrab, Anass; García González, María Begoña

    2014-01-01

    Analyzing the pattern and causes of phenotypic and genetic variation within and among populations might help to understand life history variability in plants, and to predict their responses to changing environmental conditions. Here we compare phenotypic variation and genetic diversity of the widespread herb Plantago coronopus across Europe, and evaluate their relationship with environmental and geographical factors. Genetic diversity was estimated in 18 populations from molecular markers wit...

  11. Consequences of genetic erosion on fitness and phenotypic plasticity in European tree frog populations (Hyla arborea).

    OpenAIRE

    Luquet E.; Léna J.P.; David P; Joly P.; Lengagne T.; Perrin N.; Plénet S.

    2011-01-01

    The detrimental effects of genetic erosion on small isolated populations are widely recognized contrary to their interactions with environmental changes. The ability of genotypes to plastically respond to variability is probably essential for the persistence of these populations. Genetic erosion impact may be exacerbated if inbreeding affects plastic responses or if their maintenance were at higher phenotypic costs. To understand the interplay 'genetic erosion-fitness-phenotypic plasticity', ...

  12. Attitudes toward genetic testing among the general population and relatives of patients with a severe genetic disease

    DEFF Research Database (Denmark)

    Hietala, M; Hakonen, A; Aro, A R;

    1995-01-01

    In the present study we explore the attitudes of the Finnish population toward genetic testing by conducting a questionnaire study of a stratified sample of the population as well as of family members of patients with a severe hereditary disease, aspartylglucosaminuria (AGU). The questionnaire ev...

  13. Quantitative measurement of retinal ganglion cell populations via histology-based random forest classification.

    Science.gov (United States)

    Hedberg-Buenz, Adam; Christopher, Mark A; Lewis, Carly J; Fernandes, Kimberly A; Dutca, Laura M; Wang, Kai; Scheetz, Todd E; Abràmoff, Michael D; Libby, Richard T; Garvin, Mona K; Anderson, Michael G

    2016-05-01

    The inner surface of the retina contains a complex mixture of neurons, glia, and vasculature, including retinal ganglion cells (RGCs), the final output neurons of the retina and primary neurons that are damaged in several blinding diseases. The goal of the current work was two-fold: to assess the feasibility of using computer-assisted detection of nuclei and random forest classification to automate the quantification of RGCs in hematoxylin/eosin (H&E)-stained retinal whole-mounts; and if possible, to use the approach to examine how nuclear size influences disease susceptibility among RGC populations. To achieve this, data from RetFM-J, a semi-automated ImageJ-based module that detects, counts, and collects quantitative data on nuclei of H&E-stained whole-mounted retinas, were used in conjunction with a manually curated set of images to train a random forest classifier. To test performance, computer-derived outputs were compared to previously published features of several well-characterized mouse models of ophthalmic disease and their controls: normal C57BL/6J mice; Jun-sufficient and Jun-deficient mice subjected to controlled optic nerve crush (CONC); and DBA/2J mice with naturally occurring glaucoma. The result of these efforts was development of RetFM-Class, a command-line-based tool that uses data output from RetFM-J to perform random forest classification of cell type. Comparative testing revealed that manual and automated classifications by RetFM-Class correlated well, with 83.2% classification accuracy for RGCs. Automated characterization of C57BL/6J retinas predicted 54,642 RGCs per normal retina, and identified a 48.3% Jun-dependent loss of cells at 35 days post CONC and a 71.2% loss of RGCs among 16-month-old DBA/2J mice with glaucoma. Output from automated analyses was used to compare nuclear area among large numbers of RGCs from DBA/2J mice (n = 127,361). In aged DBA/2J mice with glaucoma, RetFM-Class detected a decrease in median and mean nucleus size

  14. Clonal structure and high genetic diversity at peripheral populations of Sorbus torminalis (L. Crantz.

    Directory of Open Access Journals (Sweden)

    Jankowska-Wroblewska S

    2016-05-01

    Full Text Available Knowing the level of genetic diversity and structure in marginal plant populations is essential for managing their genetic resources. This is particularly important for rare scattered tree species, such as Sorbus torminalis (L. Crantz. We investigated the genetic diversity and its spatial distribution in peripheral populations of S. torminalis. As the species is known to reproduce vegetatively, we also evaluated clonal structure within populations. Using 13 nuclear microsatellite loci designed in two multiplexes, we genotyped 172 individuals revealing the existence of 100 distinct genotypes. Number of ramets per genotype was variable across populations with an average of 1.72. Examples of somaclonal variation at particular loci were detected. Measures of genetic diversity of the total sample were relatively high (mean allelic richness AR = 10.293; expected heterozygosity He = 0.756, as compared to other S. torminalis populations. We noticed a slightly negative inbreeding coefficient (FIS = -0.029 indicating a small excess of heterozygotes, which is typical for self-incompatible plants. Genetic differentiation among populations was low (FST = 0.048, but Bayesian clustering methods revealed the existence of three distinct genetic clusters only in part related to population structure. Significant spatial genetic structure within populations was also detected (Sp = 0.0125 indicating fine-scale pattern of isolation by distance. Our study demonstrated that peripheral populations of S. torminalis may exhibit relatively high levels of genetic diversity despite the existence of vegetative propagation. Nevertheless, if the studied or similar populations are expected to be utilized as seed sources for ex-situ or in-situ conservation purposes, the existence of clonal structure and spatial genetic structure must be taken into account in order to avoid excessive sampling of the same or closely related genets.

  15. Low Genetic Diversity in Melanaphis sacchari Aphid Populations at the Worldwide Scale

    OpenAIRE

    Nibouche, Samuel; Fartek, Benjamin; Mississipi, Stelly; Delatte, Hélène; Reynaud, Bernard; Costet, Laurent

    2014-01-01

    Numerous studies have examined the genetic diversity and genetic structure of invading species, with contrasting results concerning the relative roles of genetic diversity and phenotypic plasticity in the success of introduced populations. Increasing evidence shows that asexual lineages of aphids are able to occupy a wide geographical and ecological range of habitats despite low genetic diversity. The anholocyclic aphid Melanaphis sacchari is a pest of sugarcane and sorghum which originated i...

  16. Population Genetic Structure of a Widespread Bat-Pollinated Columnar Cactus.

    Science.gov (United States)

    Bustamante, Enriquena; Búrquez, Alberto; Scheinvar, Enrique; Eguiarte, Luis Enrique

    2016-01-01

    Bats are the main pollinators and seed dispersers of Stenocereus thurberi, a xenogamous columnar cactus of northwestern Mexico and a good model to illustrate spatial dynamics of gene flow in long-lived species. Previous studies in this cactus showed differences among populations in the type and abundance of pollinators, and in the timing of flowering and fruiting. In this study we analyzed genetic variability and population differentiation among populations. We used three primers of ISSR to analyze within and among populations genetic variation from eight widely separated populations of S. thurberi in Sonora, Mexico. Sixty-six out of 99 of the ISSR bands (P = 66.7%) were polymorphic. Total heterozygosity for all populations sampled revealed high genetic diversity (Hsp = 0.207, HBT = 0.224). The AMOVA showed that most of the genetic variation was within populations (80.5%). At the species level, estimates of population differentiation, θ = 0.175 and θB = 0.194, indicated moderate gene flow among populations. The absence of a significant correlation between genetic and geographic distances indicated little isolation by geographic distance. The large genetic variation and diversity found in S. thurberi is consistent with its open reproductive system and the high mobility of bats, a major pollinator. However, small changes in number or kind of pollinators and seed dispersal agents, in the directionality of migratory routes, and/or in the timing of flowering and fruiting among populations, can critically affect gene flow dynamics. PMID:27015281

  17. Assessing genetic diversity of wild populations of Japanese flounder using AFLP markers

    Institute of Scientific and Technical Information of China (English)

    XU Xiaofei; ZHANG Quanqi; WANG Zhigang; QI Jie; ZHANG Zhifeng; BAO Zhenmin; Heisuke Nakagawa

    2006-01-01

    Amplified fragment length polymorphism (AFLP) analysis was used to evaluate the genetic diversity of four wild geographical populations of Japanese flounder (Paralichthys olivaceus). A total of 775 loci (58.32% of which was polymorphic) in the range between 100 and 1 300 base pairs were detected from 110 individuals using seven primer combinations. The percentage of polymorphic loci detected by single primer combination for each population was calculated, ranging from 19.59% to 53.33%. Genetic similarities within and among the populations were calculated from the binary matrices of presence - absence. Phylogenetic tree of four populations was constructed by using the UPGMA method using PHYLIP Version 3.5. According to intrapopulation genetic similarities, CW population displayed the highest genetic diversity value and KY population had the lowest genetic diversity value.The distance between CW and CF populations was the farthest, which was possibly resulted from the farthest distance of Weihai of Shandong and Fujian of China compared with the geographical distance between other locations of populations. The subpopulation differentiation value ( Gst ) is 0.356 5, showing a certain extent of differentiation among the four geographical populations. AFLP technology was confirmed to be an effective tool to assess within- and among-population genetic diversity of Japanese flounder. The present survey provided significant insights for research in the Japanese flounder breeding program.

  18. Population Genetic Structure of a Widespread Bat-Pollinated Columnar Cactus

    Science.gov (United States)

    Bustamante, Enriquena; Búrquez, Alberto; Scheinvar, Enrique; Eguiarte, Luis Enrique

    2016-01-01

    Bats are the main pollinators and seed dispersers of Stenocereus thurberi, a xenogamous columnar cactus of northwestern Mexico and a good model to illustrate spatial dynamics of gene flow in long-lived species. Previous studies in this cactus showed differences among populations in the type and abundance of pollinators, and in the timing of flowering and fruiting. In this study we analyzed genetic variability and population differentiation among populations. We used three primers of ISSR to analyze within and among populations genetic variation from eight widely separated populations of S. thurberi in Sonora, Mexico. Sixty-six out of 99 of the ISSR bands (P = 66.7%) were polymorphic. Total heterozygosity for all populations sampled revealed high genetic diversity (Hsp = 0.207, HBT = 0.224). The AMOVA showed that most of the genetic variation was within populations (80.5%). At the species level, estimates of population differentiation, θ = 0.175 and θB = 0.194, indicated moderate gene flow among populations. The absence of a significant correlation between genetic and geographic distances indicated little isolation by geographic distance. The large genetic variation and diversity found in S. thurberi is consistent with its open reproductive system and the high mobility of bats, a major pollinator. However, small changes in number or kind of pollinators and seed dispersal agents, in the directionality of migratory routes, and/or in the timing of flowering and fruiting among populations, can critically affect gene flow dynamics. PMID:27015281

  19. Genetic effect of transportation infrastructure on roe deer populations (Capreolus capreolus).

    Science.gov (United States)

    Kuehn, Ralph; Hindenlang, Karin E; Holzgang, Otto; Senn, Josef; Stoeckle, Bernhard; Sperisen, Christoph

    2007-01-01

    Anthropogenic transportation infrastructure is a major factor of habitat fragmentation leading to genetic population fragmentation in wildlife. Assessing and understanding the impact of this deterministic factor on genetic diversity and divergence of populations is crucial to appraise the viability of wildlife populations in fragmented landscapes. In this study, the roe deer is used as an example species for the assessment of genetic differentiation of populations separated by an anthropogenic barrier. In order to detect genetic discontinuities, we screened 12 polymorphic microsatellites on 222 individuals out of 11 roe deer populations that were sampled on the east and the westside of a fenced motorway in Central Switzerland. The interaction between landscape structure and microevolutionary processes such as gene flow and drift were assessed and evaluated by different population genetic methods like F-statistics, Mantel test, spatial autocorrelation analyses, Monmonier algorithm, and principal component analysis in conjunction with geographic information system data (synthesis map). We revealed an influence of the transportation infrastructure on genetic divergence of the roe deer population examined, but no impact on genetic diversity was detected. Based on the achieved genetic findings, recommendations for management implementation were made. PMID:17170074

  20. Genetic Diversity of Three Aristichthys nobilis Populations and One Inbreeding Stock

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Genetic diversity of three Aristichthys nobilis populations and one inbreeding stock was studied using random amplified polymorphic DNA(RAPD)method. Materials of natural populations were collected from two counties of Guangxi Province, Hengxian (NH) and Shanglin (NS) and one city of Hubei Province, Wuhan city.(NW). Shanglin and Hengxian's river system respectively belongs to Qianjiang and Yujiang River, two tributaries confluencing to Xunjiang River, main tributary of Xijiang River, which is the biggest tributary of the Zhujiang River system, and Wuhan's water system belongs to the Yangtse River system. The inbreeding stock (RS) was the more than 10 generation descendant by brother-sister mating system whose parents were collected from Shanglin. The results showed that the genetic variety of individuals of RS was very low (0.105 4), whereas that of natural populations was relatively high,which from high to low was 0.158 1 (NW), 0.132 0 (NH) and 0.110 5 (NS). As an index for genetic distance pair-wise populations, the genetic variety between populations was studied, which characterized the genetic distance between populations. The genetic distance of NW and NH, NW and NS, NW and RS were respectively high, whereas that of NH and NS, NS and RS, NH and RS was low. Chi-test(χ2) and the analysis of the genetic variety pair-wise populations was taken as efficient approach for studying population difference.

  1. Population genetic differences along a latitudinal cline between original and recently colonized habitat in a butterfly.

    Directory of Open Access Journals (Sweden)

    Sofie Vandewoestijne

    Full Text Available BACKGROUND: Past and current range or spatial expansions have important consequences on population genetic structure. Habitat-use expansion, i.e. changing habitat associations, may also influence genetic population parameters, but has been less studied. Here we examined the genetic population structure of a Palaeartic woodland butterfly Pararge aegeria (Nymphalidae which has recently colonized agricultural landscapes in NW-Europe. Butterflies from woodland and agricultural landscapes differ in several phenotypic traits (including morphology, behavior and life history. We investigated whether phenotypic divergence is accompanied by genetic divergence between populations of different landscapes along a 700 km latitudinal gradient. METHODOLOGY/PRINCIPAL FINDINGS: Populations (23 along the latitudinal gradient in both landscape types were analyzed using microsatellite and allozyme markers. A general decrease in genetic diversity with latitude was detected, likely due to post-glacial colonization effects. Contrary to expectations, agricultural landscapes were not less diverse and no significant bottlenecks were detected. Nonetheless, a genetic signature of recent colonization is reflected in the absence of clinal genetic differentiation within the agricultural landscape, significantly lower gene flow between agricultural populations (3.494 than between woodland populations (4.183, and significantly higher genetic differentiation between agricultural (0.050 than woodland (0.034 pairwise comparisons, likely due to multiple founder events. Globally, the genetic data suggest multiple long distance dispersal/colonization events and subsequent high intra- and inter-landscape gene flow in this species. Phosphoglucomutase deviated from other enzymes and microsatellite markers, and hence may be under selection along the latitudinal gradient but not between landscape types. Phenotypic divergence was greater than genetic divergence, indicating directional

  2. Novel Microsatellite Loci Variation and Population Genetics within Leafy Seadragons, Phycodurus eques

    OpenAIRE

    Shawn Larson; Catherine Ramsey; Deborah Tinnemore; Chris Amemiya

    2014-01-01

    Novel leafy seadragon (Phycodurus eques) microsatellite loci were developed via standard cloning techniques and tested for use in population genetics studies. Six out of a total of twelve microsatellites tested were usable for population analysis. Seadragon samples from Western Australia (N = 6), Southern Australia (N = 11), and a captive group (N = 11) were analyzed. Here, we present leafy seadragon microsatellite primer sequences for all 12 loci and population genetics statistics for the si...

  3. Assessing White’s Classification of Pregestational Diabetes in a Contemporary Diabetic Population

    Science.gov (United States)

    Bennett, Stevie N.; Tita, Alan; Owen, John; Biggio, Joseph R.; Harper, Lorie M.

    2016-01-01

    Objective To assess the validity of White’s classification, including the role of chronic hypertension, in a contemporary diabetic population. Methods We performed a retrospective cohort study of all singleton pregnancies with preexisting diabetes mellitus from 2008 to 2013. Adverse outcomes were compared across classes B, C, D and vascular disease (R, F, H) and further stratified by the presence or absence of chronic hypertension. Outcomes examined were a composite perinatal outcome (stillbirth, neonatal death, shoulder dystocia, birth injury, seizures, requiring chest compressions or intubation at delivery, blood pressure support), small for gestational age (SGA), large for gestational age (LGA), macrosomia, shoulder dystocia, preterm delivery preeclampsia, and cesarean delivery. Results Of the 475 patients, the 1980 White’s classification was significantly associated with SGA, LGA, macrosomia, preterm delivery, preeclampsia, and cesarean (p ≤ 0.01). Within each White’s class based on age or time since diagnosis alone, hypertension was significantly associated with a higher incidence of preeclampsia in class B (16% without hypertension versus 32% with hypertension, p < 0.01) and C (22% vs. 40%, p = 0.04), SGA in C (4.7% vs. 21%, p < 0.01), preterm delivery in B (25% vs. 46%, p < 0.01) and C (35% vs. 58%, p = 0.01), and the composite neonatal outcome in B (7.9% vs. 17%, p = 0.03). The incidence of adverse outcomes in classes B and C with hypertension resembles the incidence of adverse outcomes in those with diabetes one class higher. Conclusion The 1980 White’s classification system, taking into consideration the presence of chronic hypertension, remains a useful system for counseling pregestational diabetic women regarding adverse pregnancy outcomes. PMID:25932851

  4. Genetic distances between the Utah Mormons and related populations.

    OpenAIRE

    McLellan, T; Jorde, L.B.; Skolnick, M H

    1984-01-01

    Gene frequency data, consisting of six red cell antigen loci, nine electrophoretic systems, and HLA-A and -B are reported for the Utah Mormon population. These are compared statistically to gene frequencies from at U.S. population, 13 European populations, and seven populations from three religious isolates. The Mormon gene frequencies are similar to those of their northern European ancestors. This is explained by the large founding size of the Mormon population and high rates of gene flow. I...

  5. The Genetic Structure of Wild Orobanche cumana Wallr. (Orobanchaceae) Populations in Eastern Bulgaria Reflects Introgressions from Weedy Populations

    OpenAIRE

    Rocío Pineda-Martos; Pujadas-Salvà, Antonio J.; Fernández-Martínez, José M.; Kiril Stoyanov; Leonardo Velasco; Begoña Pérez-Vich

    2014-01-01

    Orobanche cumana is a holoparasitic plant naturally distributed from central Asia to south-eastern Europe, where it parasitizes wild Asteraceae species. It is also an important parasitic weed of sunflower crops. The objective of this research was to investigate genetic diversity, population structure, and virulence on sunflower of O. cumana populations parasitizing wild plants in eastern Bulgaria. Fresh tissue of eight O. cumana populations and mature seeds of four of them were collected in s...

  6. Extensive genetic diversity, unique population structure and evidence of genetic exchange in the sexually transmitted parasite Trichomonas vaginalis.

    Directory of Open Access Journals (Sweden)

    Melissa D Conrad

    Full Text Available Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes.Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2 differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages.Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease.

  7. Population genetic structure of Rhizoctonia solani AG 3-PT from potatoes in South Africa.

    Science.gov (United States)

    Muzhinji, Norman; Woodhall, James W; Truter, Mariette; van der Waals, Jacquie E

    2016-05-01

    Rhizoctonia solani AG 3-PT is an important potato pathogen causing significant yield and quality losses in potato production. However, little is known about the levels of genetic diversity and structure of this pathogen in South Africa. A total of 114 R. solani AG 3-PT isolates collected from four geographic regions were analysed for genetic diversity and structure using eight microsatellite loci. Microsatellite analysis found high intra-population genetic diversity, population differentiation and evidence of recombination. A total of 78 multilocus genotypes were identified with few shared among populations. Low levels of clonality (13-39 %) and high levels of population differentiation were observed among populations. Most of the loci were in Hardy-Weinberg equilibrium and all four populations showed evidence of a mixed reproductive mode of both clonality and recombination. The PCoA clustering method revealed genetically distinct geographic populations of R. solani AG 3-PT in South Africa. This study showed that populations of R. solani AG 3-PT in South Africa are genetically differentiated and disease management strategies should be applied accordingly. This is the first study of the population genetics of R. solani AG 3-PT in South Africa and results may help to develop knowledge-based disease management strategies. PMID:27109367

  8. Optimization of genomic selection training populations with a genetic algorithm

    Science.gov (United States)

    In this article, we derive a computationally efficient statistic to measure the reliability of estimates of genetic breeding values for a fixed set of genotypes based on a given training set of genotypes and phenotypes. We adopt a genetic algorithm scheme to find a training set of certain size from ...

  9. Population genetic variation in the tree fern Alsophila spinulosa (Cyatheaceae: effects of reproductive strategy.

    Directory of Open Access Journals (Sweden)

    Ting Wang

    Full Text Available BACKGROUND: Essentially all ferns can perform both sexual and asexual reproduction. Their populations represent suitable study objects to test the population genetic effects of different reproductive systems. Using the diploid homosporous fern Alsophila spinulosa as an example species, the main purpose of this study was to assess the relative impact of sexual and asexual reproduction on the level and structure of population genetic variation. METHODOLOGY/PRINCIPAL FINDINGS: Inter-simple sequence repeats analysis was conducted on 140 individuals collected from seven populations (HSG, LCH, BPC, MPG, GX, LD, and ZHG in China. Seventy-four polymorphic bands discriminated a total of 127 multilocus genotypes. Character compatibility analysis revealed that 50.0 to 70.0% of the genotypes had to be deleted in order to obtain a tree-like structure in the data set from populations HSG, LCH, MPG, BPC, GX, and LD; and there was a gradual decrease of conflict in the data set when genotypes with the highest incompatibility counts were successively deleted. In contrast, in population ZHG, only 33.3% of genotypes had to be removed to achieve complete compatibility in the data set, which showed a sharp decline in incompatibility upon the deletion of those genotypes. All populations examined possessed similar levels of genetic variation. Population ZHG was not found to be more differentiated than the other populations. CONCLUSIONS/SIGNIFICANCE: Sexual recombination is the predominant source of genetic variation in most of the examined populations of A. spinulosa. However, somatic mutation contributes most to the genetic variation in population ZHG. This change of the primary mode of reproduction does not cause a significant difference in the population genetic composition. Character compatibility analysis represents an effective approach to separate the role of sexual and asexual components in shaping the genetic pattern of fern populations.

  10. The Impact of Evolutionary Driving Forces on Human Complex Diseases: A Population Genetics Approach.

    Science.gov (United States)

    Saeb, Amr T M; Al-Naqeb, Dhekra

    2016-01-01

    Investigating the molecular evolution of human genome has paved the way to understand genetic adaptation of humans to the environmental changes and corresponding complex diseases. In this review, we discussed the historical origin of genetic diversity among human populations, the evolutionary driving forces that can affect genetic diversity among populations, and the effects of human movement into new environments and gene flow on population genetic diversity. Furthermore, we presented the role of natural selection on genetic diversity and complex diseases. Then we reviewed the disadvantageous consequences of historical selection events in modern time and their relation to the development of complex diseases. In addition, we discussed the effect of consanguinity on the incidence of complex diseases in human populations. Finally, we presented the latest information about the role of ancient genes acquired from interbreeding with ancient hominids in the development of complex diseases. PMID:27313952

  11. The Impact of Evolutionary Driving Forces on Human Complex Diseases: A Population Genetics Approach

    Directory of Open Access Journals (Sweden)

    Amr T. M. Saeb

    2016-01-01

    Full Text Available Investigating the molecular evolution of human genome has paved the way to understand genetic adaptation of humans to the environmental changes and corresponding complex diseases. In this review, we discussed the historical origin of genetic diversity among human populations, the evolutionary driving forces that can affect genetic diversity among populations, and the effects of human movement into new environments and gene flow on population genetic diversity. Furthermore, we presented the role of natural selection on genetic diversity and complex diseases. Then we reviewed the disadvantageous consequences of historical selection events in modern time and their relation to the development of complex diseases. In addition, we discussed the effect of consanguinity on the incidence of complex diseases in human populations. Finally, we presented the latest information about the role of ancient genes acquired from interbreeding with ancient hominids in the development of complex diseases.

  12. Genetic structure analysis of Eufriesea violacea (Hymenoptera, Apidae populations from southern Brazilian Atlantic rainforest remnants

    Directory of Open Access Journals (Sweden)

    Silvia H. Sofia

    2005-09-01

    Full Text Available Random amplified polymorphic DNA (RAPD markers were used to analyze the genetic structure of Eufriesea violacea populations in three fragments (85.47, 832.58 and 2800 ha of Atlantic rainforest located in the north of the Brazilian state of Paraná. A total of twelve primers produced 206 loci, of which 129 were polymorphic (95% criterion. The proportions of polymorphic loci in each population ranged from 57.28% to 59.2%, revealing very similar levels of genetic variability in the groups of bees from each fragment. Unbiased genetic distances between groups ranged from 0.0171 to 0.0284, the smallest genetic distance occurring between bees from the two larger fragments. These results suggest that the E. violacea populations from the three fragments have maintained themselves genetically similar to native populations of this species originally present in northern Paraná.

  13. Genetic diversity and population structure of endangered Aquilaria malaccensis revealed potential for future conservation

    Indian Academy of Sciences (India)

    Pradeep Singh; Akshay Nag; Rajni Parmar; Sneha Ghosh; Brijmohan Singh Bhau; Ram Kumar Sharma

    2015-12-01

    The endangered Aquilaria malaccensis, is an important plant with high economic values. Characterization of genetic diversity and population structure is receiving tremendous attention for effective conservation of genetic resources. Considering important repositories of biological diversity, the genetic relationships of 127 A. malaccensis accessions from 10 home gardens of three states of northeast India were assessed using amplified fragment length polymorphism (AFLP). Of the 1153 fragments amplified with four AFLP primer combinations, 916 (79.4%) were found to be polymorphic. Polymorphic information content (PIC) and marker index (MI) of each primer combination correlate significantly with the number of genotypes resolved. Overall, a high genetic diversity (avg. 71.85%) was recorded. Further, high gene flow (m : 3.37), low genetic differentiation (ST : 0.069) and high within population genetic variation (93%) suggests that most of the genetic diversity is restricted within population. Neighbour joining (NJ), principal coordinate analysis (PCoA) and Bayesian-based STRUCTURE grouped all the accessions in two clusters with significant intermixing between populations, therefore, revealed that two genetically distinct gene pools are operating in the A. malaccensis populations cultivated in home gardens. Based on the various diversity inferences, five diverse populations (JOH, FN, HLF, DHM and ITN) were identified, which can be potentially exploited to develop conservation strategies for A. malaccensis.

  14. Mathematical and descriptive classification of variations in dental arch shape in an Australian aborigine population.

    Science.gov (United States)

    McKee, J K; Molnar, S

    1988-01-01

    The ability to describe dental arch shape is necessary for biomechanical studies of occlusion as well as for anthropological studies of human and primate dental variation. A mathematical method of describing and classifying human dental arch shape was used to assess the nature of individual variability. The method involved the calculation of a series of third-degree polynomials which were fitted to coordinate points along the dental arcade. The slopes of the polynomials, evaluated at these coordinate points, provided a multivariate description of shape, independent of arch size. Graphic representations of arch shape could be constructed from the polynomial equations. These mathematical techniques were used in association with multivariate and univariate statistics to explore the types of variability in dental arch shape among a population of Australian aborigines. The results illustrated the ambiguities of conventional subjective classifications. PMID:3256297

  15. Genetic diversity of natural and planted populations of Tsoongiodendron odorum from the Nanling Mountains

    Directory of Open Access Journals (Sweden)

    Xueqin Wu

    2013-01-01

    Full Text Available Ex situ conservation, complementary to in situ conservation, plays an important role in preservation and recovery of endangered species. Tsoongiodendron odorum is a relic species that was listed in the Second Grade of the List of Wild Plants Under State Protection (First Batch in China. For protection of its genetic diversity, ex situ conservation populations have been established and managed outside of natural habitats in several nature reserves since 1980. However, only dozens of individuals are currently saved from each planted population. To assess the actual protective effectiveness of these planted populations, we detected and compared the genetic diversity of three planted populations from Nanling Mountains with four natural populations using ISSR markers. Overall, we detected 362 total ISSR discernible bands with 16 ISSR primers, of which 301 were polymorphic. The percentage of polymorphic bands (P was 83.2%. At the populationlevel, the percent of polymorphic bands ranged from 37.9% to 62.2%, with an average value of 53.1%. This result showed that T. odorum had high genetic diversity both at population and species levels. However, the percentage of polymorphic bands and Shannon information index (I of ex situ conservation populations (66.6% and 0.2990 were much lower than those of natural populations (80.9% and 0.3629. We deduced that there was a narrow genetic base for plantations of T. odorum. Population structure analysis revealed that three planted populations could be collected from the same wild population (i.e., YK population. The genetic variation of four natural populations (GST=0.2495 showed that there was significant isolation among populations, which would limit gene flow and population differentiation among populations. We present suggestions on regulating seed collection from different natural habitats to establish planted populations and strengthening research on the reproductive biology of T. odorum.

  16. Genetic variability and population structure of Plasmodium falciparum parasite populations from different malaria ecological regions of Kenya.

    Science.gov (United States)

    Ingasia, Luicer A; Cheruiyot, Jelagat; Okoth, Sheila Akinyi; Andagalu, Ben; Kamau, Edwin

    2016-04-01

    Transmission intensity, movement of human and vector hosts, biogeographical features, and malaria control measures are some of the important factors that determine Plasmodium falciparum parasite genetic variability and population structure. Kenya has different malaria ecologies which might require different disease intervention methods. Refined parasite population genetic studies are critical for informing malaria control and elimination strategies. This study describes the genetic diversity and population structure of P. falciparum parasites from the different malaria ecological zones in Kenya. Twelve multi-locus microsatellite (MS) loci previously described were genotyped in 225 P. falciparum isolates collected between 2012 and 2013 from five sites; three in lowland endemic regions (Kisumu, Kombewa, and Malindi) and two in highland, epidemic regions (Kisii and Kericho). Parasites from the lowland endemic and highland epidemic regions of western Kenya had high genetic diversity compared to coastal lowland endemic region of Kenya [Malindi]. The Kenyan parasites had a mean genetic differentiation index (FST) of 0.072 (p=0.011). The multi-locus genetic analysis of the 12 MS revealed all the parasites had unique haplotypes. Significant linkage disequilibrium (LD) was observed in all the five parasite populations. Kisumu had the most significant index of association values (0.16; partemether-lumefantrine is important in refining the spread of drug resistant strains and malaria transmission for more effective control and eventual elimination of malaria in Kenya. PMID:26472129

  17. Analysis of genetic distribution and population genetic structure of the MyoD gene in 10 pig breeds

    Institute of Scientific and Technical Information of China (English)

    Li ZHU; Xuewei LI; Surong SHUAI; Mingzhou LI; Fangqiong LI; Lei CHEN

    2008-01-01

    Restriction fragment length polymorphism (RFLP) data was applied to analyze the distribution of the MyoD gene in 10 pig breeds and pig breed crosses.The population genetic information about genetic distribution,variation,and heterozygosity of the MyoD gene in different breed populations were analyzed.Based on the allele frequency,genetic distance and evolution distance among each breed populations were calculated and Unweighted Pair Group Method with Arithmetic mean (UPGMA) phylogenetic tree was gained based on the evolution distances between populations.The results indicated that the distribution of the MyoD genotype kept in Hardy-Weinberg equilibrium in most tested groups but not in Duroc (D) and Duroc × (Landrance × Yorkshire)(DLY) population.Generally,the genetic diversity of the MyoD gene was abundant and these tested breed populations had high genetic variations.The evolution of the MyoD gene was under natural selection pressure.On the phylogenetic tree,10 pig breeds were divided into 4 clusters.The first cluster consisted of four breeds developed from Landrace.The second cluster was two indigenous Chinese pig breeds.The third cluster was three breeds developed from Duroc.The fourth cluster was a Tibetan pig breed.The constitution of the topology of the phylogenetic tree was consistent with the breeding history of each pig breed.From this experiment,we can conclude that some RFLP data obtained from functional gene can be used in the genetic deviation research between some closely related species or between different populations in certain species.

  18. Genetic diversity of 38 insertion-deletion polymorphisms in Jewish populations.

    Science.gov (United States)

    Ferragut, J F; Pereira, R; Castro, J A; Ramon, C; Nogueiro, I; Amorim, A; Picornell, A

    2016-03-01

    Population genetic data of 38 non-coding biallelic autosomal indels are reported for 466 individuals, representing six populations with Jewish ancestry (Ashkenazim, Mizrahim, Sephardim, North African, Chuetas and Bragança crypto-Jews). Intra-population diversity and forensic parameters values showed that this set of indels was highly informative for forensic applications in the Jewish populations studied. Genetic distance analysis demonstrated that this set of markers efficiently separates populations from different continents, but does not seem effective for molecular anthropology studies in Mediterranean region. Finally, it is important to highlight that although the genetic distances between Jewish populations were small, significant differences were observed for Chuetas and Bragança Jews, and therefore, specific databases must be used for these populations. PMID:26610303

  19. The population genetic structure of vectors and our understanding of disease epidemiology

    Directory of Open Access Journals (Sweden)

    McCoy K.D.

    2008-09-01

    Full Text Available Understanding and predicting disease epidemiology relies on clear knowledge about the basic biology of the organisms involved. Despite the key role that arthropod vectors play in disease dynamics and detailed mechanistic work on the vectorpathogen interface, little information is often available about how these populations function under natural conditions. Population genetic studies can help fill this void by providing information about the taxonomic status of species, the spatial limits of populations, and the nature of gene flow among populations. Here, I briefly review different types of population genetic structure and some recent examples of where this information has provided key elements for understanding pathogen transmission in tick-borne systems.

  20. Genetic monitoring of natural drosophila populations in radiation contaminated regions of Belarus

    International Nuclear Information System (INIS)

    The genetic monitoring of natural Drosophila melanogaster populations inhabiting regions of Belarus with different levels of contamination after the reactor accidents at the Chernobylsk NPP (Vetka and Svetilovichi villages) as compared with populations from the Berezinsky biosphere reserve (the control area) is carried out. The dominant and recessive lethal mutations levels and the genetic structure of populations are analyzed for frequencies of F- and S-alleles of alcohol dehydrogenase,glycerinophosphate dehydrogenase and superoxidase dismutase loci. Populations inhabiting contamination regions demonstrate higher frequency of lethal mutations and higher heterozygosity than those from the control area. The nonspecific adaptation of Drosophila populations from contaminated villages of the Gomel region is reveled

  1. Influence of anti-filarial chemotherapy strategies on the genetic structure of Wuchereria bancrofti populations

    Directory of Open Access Journals (Sweden)

    Dhamodharan Ramasamy

    2011-03-01

    Full Text Available Lymphatic filarial (LF parasites have been under anti-filarial drug pressure for more than half a century. Currently, annual mass drug administration (MDA of diethylcarbamazine (DEC or ivermectin in combination with albendazole (ALB have been used globally to eliminate LF. Long-term chemotherapies exert significant pressure on the genetic structure of parasitic populations. We investigated the genetic variation among 210 Wuchereria bancrofti populations that were under three different chemotherapy strategies, namely MDA with DEC alone (group I, n = 74, MDA with DEC and ALB (group II, n = 60 and selective therapy (ST with DEC (group III, n = 34 to understand the impact of these three drug regimens on the parasite genetic structure. Randomly amplified polymorphic DNA profiles were generated for the three groups of parasite populations; the gene diversity, gene flow and genetic distance values were determined and phylogenetic trees were constructed. Analysis of these parameters indicated that parasite populations under ST with a standard dose of DEC (group III were genetically more diverse (0.2660 than parasite populations under MDA with DEC alone (group I, H = 0.2197 or with DEC + ALB (group II, H = 0.2317. These results indicate that the MDA may reduce the genetic diversity of W. bancrofti populations when compared to the genetic diversity of parasite populations under ST.

  2. Genetic diversity and population structure of Bretschneidera sinensis, an endangered species

    Directory of Open Access Journals (Sweden)

    Gangbiao Xu

    2013-11-01

    Full Text Available Amounts and distribution of intraspecific genetic variation provide benchmarks for developing conservation strategies. Bretschneidera sinensis is a monotypic relic species listed in the First Grade of the List of Wild Plants Under State Protection (First Batch in China. We examined the genetic diversity and genetic structure of 219 B. sinensis individuals sampled from 15 natural populations distributed in Hunan, Jiangxi, Guangdong, Guangxi, and Guizhou using inter-simple sequence repeat (ISSR markers generated by seven ISSR primers. The percentage of polymorphic bands (PPB at the species and population level was 74.42% and 38.06%, respectively. Shannon’s index (I of phenotypic diversity at the species and population level was 0.3630 and 0.2081, respectively, and Nei’s genetic diversity (He at the species and population level was 0.2397 and 0.1405, respectively. These results indicate that B. sinensis contains relatively high levels of genetic diversity. Analysis of molecular variance (AMOVA and estimates of the coefficient of genetic differentiation based on phenotypic diversity index also indicated high levels of population subdivision (GST = 0.2973; FST = 0.4267 in the species. Analysis of the ISSR data using UPGMA further revealed that populations were genetically clustered into two groups, while a Mantel test showed that genetic divergence was significantly correlated with geographical distance among populations (Mantel test; r = 0.3096, P = 0.008. We conclude from our results that B. sinensis is not endangered due to low evolutionary potential stemming from low genetic diversity, but by habitat destruction coupled with a low reproductive capacity, poor adaptability and weak competitiveness. The Mt. Yangming, Mt. Mangshan, Ruyang, and Mt. Bamianshan populations of the species with higher genetic diversity should be given priority for conservation, and inbreeding depression monitoring should be conducted.

  3. Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation

    Directory of Open Access Journals (Sweden)

    Thomas Meredith M

    2009-10-01

    Full Text Available Abstract Background Developing a greater understanding of population genetic structure in lowland tropical plant species is highly relevant to our knowledge of increasingly fragmented forests and to the conservation of threatened species. Specific studies are particularly needed for taxa whose population dynamics are further impacted by human harvesting practices. One such case is the fishtail or xaté palm (Chamaedorea ernesti-augusti of Central America, whose wild-collected leaves are becoming progressively more important to the global ornamental industry. We use microsatellite markers to describe the population genetics of this species in Belize and test the effects of climate change and deforestation on its recent and historical effective population size. Results We found high levels of inbreeding coupled with moderate or high allelic diversity within populations. Overall high gene flow was observed, with a north and south gradient and ongoing differentiation at smaller spatial scales. Immigration rates among populations were more difficult to discern, with minimal evidence for isolation by distance. We infer a tenfold reduction in effective population size ca. 10,000 years ago, but fail to detect changes attributable to Mayan or contemporary deforestation. Conclusion Populations of C. ernesti-augusti are genetically heterogeneous demes at a local spatial scale, but are widely connected at a regional level in Belize. We suggest that the inferred patterns in population genetic structure are the result of the colonization of this species into Belize following expansion of humid forests in combination with demographic and mating patterns. Within populations, we hypothesize that low aggregated population density over large areas, short distance pollen dispersal via thrips, low adult survival, and low fruiting combined with early flowering may contribute towards local inbreeding via genetic drift. Relatively high levels of regional connectivity

  4. Quantifying spatial genetic structuring in mesophotic populations of the precious coral Corallium rubrum.

    Science.gov (United States)

    Costantini, Federica; Carlesi, Lorenzo; Abbiati, Marco

    2013-01-01

    While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58-118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations. PMID:23646109

  5. Quantifying spatial genetic structuring in mesophotic populations of the precious coral Corallium rubrum.

    Directory of Open Access Journals (Sweden)

    Federica Costantini

    Full Text Available While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58-118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations.

  6. Prevalence and impacts of genetically engineered feedstuffs on livestock populations.

    Science.gov (United States)

    Van Eenennaam, A L; Young, A E

    2014-10-01

    Globally, food-producing animals consume 70 to 90% of genetically engineered (GE) crop biomass. This review briefly summarizes the scientific literature on performance and health of animals consuming feed containing GE ingredients and composition of products derived from them. It also discusses the field experience of feeding GE feed sources to commercial livestock populations and summarizes the suppliers of GE and non-GE animal feed in global trade. Numerous experimental studies have consistently revealed that the performance and health of GE-fed animals are comparable with those fed isogenic non-GE crop lines. United States animal agriculture produces over 9 billion food-producing animals annually, and more than 95% of these animals consume feed containing GE ingredients. Data on livestock productivity and health were collated from publicly available sources from 1983, before the introduction of GE crops in 1996, and subsequently through 2011, a period with high levels of predominately GE animal feed. These field data sets, representing over 100 billion animals following the introduction of GE crops, did not reveal unfavorable or perturbed trends in livestock health and productivity. No study has revealed any differences in the nutritional profile of animal products derived from GE-fed animals. Because DNA and protein are normal components of the diet that are digested, there are no detectable or reliably quantifiable traces of GE components in milk, meat, and eggs following consumption of GE feed. Globally, countries that are cultivating GE corn and soy are the major livestock feed exporters. Asynchronous regulatory approvals (i.e., cultivation approvals of GE varieties in exporting countries occurring before food and feed approvals in importing countries) have resulted in trade disruptions. This is likely to be increasingly problematic in the future as there are a large number of "second generation" GE crops with altered output traits for improved livestock

  7. Genetic Polymorphisms of Nine X-STR Loci in Four Population Groups from Inner Mongolia, China

    Institute of Scientific and Technical Information of China (English)

    Qiao-Fang Hou; Bin Yu; Sheng-Bin Li

    2007-01-01

    Nine short tandem repeat (STR) markers on the X chromosome (DXS101, DXS6789, DXS6799, DXS6804, DXS7132, DXS7133, DXS7423, DXS8378, and HPRTB) were analyzed in four population groups (Mongol, Ewenki, Oroqen, and Daur) from Inner Mongolia, China, in order to learn about the genetic diversity, forensic suitability, and possible genetic affinities of the populations. Frequency estimates, Hardy-Weinberg equilibrium, and other parameters of forensic interest were computed. The results revealed that the nine markers have a moderate degree of variability in the population groups. Most heterozygosity values for the nine loci range from 0.480 to 0.891, and there are evident differences of genetic variability among the populations. A UPGMA tree constructed on the basis of the generated data shows very low genetic distance betweent Mongol and Han (Xi'an) populations. Our results based on genetic distance analysis are consistent with the results of earlier studies based on linguistics and the immigration history and origin of these populations. The minisatellite loci on the X chromosome studied here are not only useful in showing significant genetic variation between the populations, but also are suitable for human identity testing among Inner Mongolian populations.

  8. Genetic polymorphism of milk proteins in some Bos genus populations

    OpenAIRE

    A. M. Guastella; G. D'Urso; G. Tirella; Budelli, E; S. Bordonaro; Marletta, D

    2011-01-01

    In cattle the analysis of the genetic polymorphism of milk proteins provides an effective tool both to characterize the genetic diversity and to improve the efficiency of selection for specific production traits. Four genes, αS1-casein (CSN1S1), β-casein (CSN2), κ-casein (CSN3) and β-lactoglobulin (BLG) have showed a high level of genetic polymorphism and are candidate to play a role in selection programmes in order to improve milk production. In this work three Bos genu...

  9. Estimation of genetic parameters and genetic trends for weight and body measurements at birth in sheep populations in Thailand

    OpenAIRE

    China Supakorn; Winai Pralomkarn; Suwit Anothaisinthawee

    2013-01-01

    The main objective of this study was to estimate the genetic parameters and genetic trends for birth weight (BW),heart girth (HG), and body length (BL) at birth of sheep populations in Thailand. Data were collected during 1998 to 2011 fromfour livestock research and testing stations. Fixed effect testing showed that sex, herd, contemporary group and breed groupgreatly influenced on the investigated traits (P

  10. Genetic structure and demographic history of brown trout ( Salmo trutta ) populations from the southern Balkans

    DEFF Research Database (Denmark)

    Apostolidis, A.P.; Madeira, M.J.; Hansen, Michael Møller;

    2008-01-01

    1. The present study was designed to characterize the genetic structure of brown trout (Salmo trutta) populations from the southern Balkans and to assess the spread of non-native strains and their introgression into native trout gene pools. We analysed polymorphism at nine microsatellite loci in...... seven supposedly non-admixed and three stocked brown trout populations. 2. The analyses confirmed the absence of immigration and extraordinarily strong genetic differentiation among the seven non-introgressed populations in parallel with low levels of intrapopulation genetic variability. In contrast...

  11. Population genetic strucutre of annual Nothobranchius fishes in southern Mozambique

    Czech Academy of Sciences Publication Activity Database

    Bartáková, Veronika; Bryja, Josef; Polačik, Matej; Blažek, Radim; Reichard, Martin

    Liege: Université de Liege, 2012. s. 15. [European Congress of Ichthyology /14./. 03.07.2012-08.07.2012, Liege] Institutional support: RVO:68081766 Keywords : genetic structure * Nothobranchius * Mozambique Subject RIV: EG - Zoology

  12. Preliminary Report on Seaside Sparrow Population Genetics Project

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This is a preliminary report on a genetic variation study that was conducted at St. Vincent National Wildlife Refuge. Blood samples were taken from 57 Seaside...

  13. A cat's tale: the impact of genetic restoration on Florida panther population dynamics and persistence.

    Science.gov (United States)

    Hostetler, Jeffrey A; Onorato, David P; Jansen, Deborah; Oli, Madan K

    2013-05-01

    1. Genetic restoration has been suggested as a management tool for mitigating detrimental effects of inbreeding depression in small, inbred populations, but the demographic mechanisms underlying population-level responses to genetic restoration remain poorly understood. 2. We studied the dynamics and persistence of the endangered Florida panther Puma concolor coryi population and evaluated the potential influence of genetic restoration on population growth and persistence parameters. As part of the genetic restoration programme, eight female Texas pumas P. c. stanleyana were released into Florida panther habitat in southern Florida in 1995. 3. The overall asymptotic population growth rate (λ) was 1.04 (5th and 95th percentiles: 0.95-1.14), suggesting an increase in the panther population of approximately 4% per year. Considering the effects of environmental and demographic stochasticities and density-dependence, the probability that the population will fall below 10 panthers within 100 years was 0.072 (0-0.606). 4. Our results suggest that the population would have declined at 5% per year (λ = 0.95; 0.83-1.08) in the absence of genetic restoration. Retrospective life table response experiment analysis revealed that the positive effect of genetic restoration on survival of kittens was primarily responsible for the substantial growth of the panther population that would otherwise have been declining. 5. For comparative purposes, we also estimated probability of quasi-extinction under two scenarios - implementation of genetic restoration and no genetic restoration initiative - using the estimated abundance of panthers in 1995, the year genetic restoration was initiated. Assuming no density-dependence, the probability that the panther population would fall below 10 panthers by 2010 was 0.098 (0.002-0.332) for the restoration scenario and 0.445 (0.032-0.944) for the no restoration scenario, providing further evidence that the panther population would have faced a

  14. Analysis of the genetic diversity and differentiation of Fenneropenaeus penicillatus populations using AFLP technology

    Institute of Scientific and Technical Information of China (English)

    ZHANG Guiling; CAO Yuanyu; LI Zhongbao; CHEN Jin; ZHAO Binli; LEI Guanggao; WANG Zhanlin

    2012-01-01

    Fenneropenaeus penicillatus (redtail shrimp) is an important marine commercial animal in China.Recently,its resources have been depleted rapidly as a result of,for example,over-exploitation and environmental degradation of spawning grounds.Therefore,we analyzed the genetic diversity and differentiation of nine wild populations of F.penicillatus of China (Ningde,Lianjiang,Putian,Xiamen,Quanzhou,Zhangpu,Dongshan,Nanao,and Shenzhen populations) by amplified fragment length polymorphism (AFLP) technology,to provide genetic information necessary for resource protection,rejuvenation,artificial breeding,and sustainable use of the resource.Eight AFLP primer pairs were used for amplification,and 508 bands were detected among the populations.The results show that the percentage of polymorphic loci (P) ranged from 41.34% to 63.58%; the Nei's gene diversity (H) of the populations was 0.119 4-0.230 5; and Sharnon's Information Index (I) was 0.184 1-0.342 5.These genetic data indicate that the genetic diversity of F.penicillatus was high.The genetic differentiation coefficient (Gsr=0.216 2) and gene flow (Nm=1.812 4) show that there was a high level of genetic differentiation and a moderate level of gene flow among populations.More studies on the genetic differentiation mechanism of F.penicillatus along the south-eastern coast of China need to be conducted to find more effective scientific protection strategies for the conservation ofF.penicillatus genetic resources.

  15. Business Analysis and Decision Making Through Unsupervised Classification of Mixed Data Type of Attributes Through Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Rohit Rastogi

    2014-01-01

    Full Text Available Grouping or unsupervised classification has variety of demands in which the major one is the capability of the chosen clustering approach to deal with scalability and to handle the mixed variety of data set. There are variety of data sets like categorical/nominal, ordinal, binary (symmetric or asymmetric, ratio and interval scaled variables. In the present scenario, latest approaches of unsupervised classification are Swarm Optimization based, Customer Segmentation based, Soft Computing methods like Fuzzy Based and GA based, Entropy Based methods and hierarchical approaches. These approaches have two serious bottlenecks…Either they are hybrid mathematical techniques or large computation demanding which increases their complexity and hence compromises with accuracy. It is very easy to compare and analyze that unsupervised classification by Genetic Algorithm is feasible, suitable and efficient for high-dimensional data sets with mixed data values that are obtained from real life results, events and happenings.

  16. Genetic Diversity in Jatropha curcas Populations in the State of Chiapas, Mexico

    Directory of Open Access Journals (Sweden)

    Miguel Salvador-Figueroa

    2011-10-01

    Full Text Available Jatropha curcas L. has become an important source of oil production for biodiesel fuel. Most genetic studies of this plant have been conducted with Asian and African accessions, where low diversity was encountered. There are no studies of this kind focusing in the postulated region of origin. Therefore, five populations of J. curcas were studied in the state of Chiapas, Mexico, using amplified fragment length polymorphism (AFLP markers. One hundred and fifty-two useful markers were obtained: overall polymorphism = 81.18% and overall Nei’s genetic diversity (He = 0.192. The most diverse population was the Border population [He: 0.245, Shanon’s information index (I: 0.378]. A cluster analysis revealed the highest dissimilarity coefficient (0.893 yet to be reported among accessions. An analysis of molecular variance (AMOVA revealed that the greatest variation is within populations (87.8%, followed by the variation among populations (7.88%. The PhiST value (0.121 indicated moderate differentiation between populations. However, a spatial AMOVA (SAMOVA detected a stronger genetic structure of populations, with a PhiST value of 0.176. To understand the fine structure of populations, an analysis of data with Bayesian statistics was conducted with software Structure©. The number of genetic populations (K was five, with mixed ancestry in most individuals (genetic migrants, except in the Soconusco, where there was a tiny fraction of fragments from other populations. In contrast, SAMOVA grouped populations in four units. To corroborate the above findings, we searched for possible genetic barriers, determining as the main barrier that separating the Border from the rest of the populations. The results are discussed based on the possible ancestry of populations.

  17. SSR-based identification of genetic groups within European populations of Tuber aestivum Vittad.

    Science.gov (United States)

    Molinier, Virginie; Murat, Claude; Peter, Martina; Gollotte, Armelle; De la Varga, Herminia; Meier, Barbara; Egli, Simon; Belfiori, Beatrice; Paolocci, Francesco; Wipf, Daniel

    2016-02-01

    Tuber species are ectomycorrhizal ascomycetes establishing relationships with different host trees and forming hypogeous fruiting bodies known as truffles. Among Tuber species, Tuber aestivum Vittad. has a wide distributional range being found naturally all over Europe. Here, we performed large-scale population genetic analyses in T. aestivum to (i) investigate its genetic diversity at the European scale, (ii) characterize its genetic structure and test for the presence of ecotypes and (iii) shed light into its demographic history. To reach these goals, 230 ascocarps from different populations were genotyped using 15 polymorphic simple sequence repeat markers. We identified 181 multilocus genotypes and four genetic groups which did not show a clear geographical separation; although, one of them was present exclusively in Southeast France, Italy and Spain. Fixation index values between pairs of genetic groups were generally high and ranged from 0.29 to 0.45. A significant deficit of heterozygosity indicated a population expansion instead of a recent population bottleneck, suggesting that T. aestivum is not endangered in Europe, not even in Mediterranean regions. Our study based on a large-scale population genetic analysis suggests that genetically distinct populations and likely ecotypes within T. aestivum are present. In turn, this study paves the way to future investigations aimed at addressing the biological and/or ecological factors that have concurred in shaping the population genetic structure of this species. Present results should also have implications for the truffle market since defining genetic markers are now possible at least for some specific T. aestivum genetic groups. PMID:26070448

  18. Genetic Variation among 11 Abies concolor Populations Based on Allozyme Analysis

    Institute of Scientific and Technical Information of China (English)

    Zhang Jin-feng; Li Hui; Dong Jian-sheng; Wang Jun-hui

    2005-01-01

    In order to obtain information on the genetic structure of Abies concolor and the genetic variation among 11 populations introduced from America to China, allozyme analysis based on starch gel electrophoresis technology was used. 24 loci of 10allozyme systems were mensurated, and the genetic structure and genetic diversity of the 11 populations of A. concolor evaluated.The results show that the genetic variation among is significant, and the genetic variation within A. concolor populations is more important. In contrast with other conifers, the variation of A. concolor is above the average level of conifers, and higher than the same level ofAbies. The percentage of polymorphic loci (P) was 62.5%, the number of alleles per locus (A) 2.08, the number of effective alleles per locus (Ae) was 1.37, the expected heterozygosity (H) 0.204, and the Shannon information index (I) 0.351 7. There is a short genetic distance (D=0.061) and a low gene flow (Nm=0.839 4) among the 11 introduced populations of A. concolor with high genetic variation. The genetic differentiation coefficient (Gst) was 0.229 5, which is higher than that of the mean in Abies or Pinus.

  19. Genetic ecotoxicology II: population genetic structure in mosquito fish exposed in situ to radionuclides

    International Nuclear Information System (INIS)

    DNA polymorphism in mosquito fish (Gambusia affinis), as revealed by RAPD (randomly amplified polymorphic DNA) and allozyme analysis, was compared to relative amounts of DNA strand breakage in blood and liver tissues. Mosquito fish were exposed to radionuclide contamination in situ and to X-rays in the laboratory. The types of RAPD metrics used were the number of RAPD bands per individual and the frequency of certain RAPD bands. In a previous study, it was noted that in some instances the number of RAPD bands and the frequency of certain RAPD bands were elevated in radionuclide-contaminated sites relative to reference sites. In the present study, it was found that the median molecular length (MML) of the DNA (which is inversely proportional to the amount of DNA strand breakage) was correlated in several cases to the number of RAPD bands per individual. In addition, for those RAPD bands that occurred at a higher frequency in mosquito fish from radionuclide-contaminated sites, DNA strand breakage was often lower for those fish with than without these RAPD bands. RAPD data obtained on mosquito fish exposed to X-rays in the laboratory paralleled those from the field. Furthermore, analysis showed that heterozygotes for the allozyme locus nucleoside phosphorylase were more prevalent in radionuclide-contaminated sites and had fewer DNA strand breaks than did homozygotes. These results provide additional evidence that changes in population genetic structure of mosquito fish exposed to a genotoxicant (radiation) can be detected at the DNA level

  20. Genetic population structure and call variation in a passerine bird, the satin bowerbird, Ptilonorhynchus violaceus.

    Science.gov (United States)

    Nicholls, J A; Austin, J J; Moritz, C; Goldizen, A W

    2006-06-01

    Geographic variation in vocalizations is widespread in passerine birds, but its origins and maintenance remain unclear. One hypothesis to explain this variation is that it is associated with geographic isolation among populations and therefore should follow a vicariant pattern similar to that typically found in neutral genetic markers. Alternatively, if environmental selection strongly influences vocalizations, then genetic divergence and vocal divergence may be disassociated. This study compared genetic divergence derived from 11 microsatellite markers with a metric of phenotypic divergence derived from male bower advertisement calls. Data were obtained from 16 populations throughout the entire distribution of the satin bowerbird, an Australian wet-forest-restricted passerine. There was no relationship between call divergence and genetic divergence, similar to most other studies on birds with learned vocalizations. Genetic divergence followed a vicariant model of evolution, with the differentiation of isolated populations and isolation-by-distance among continuous populations. Previous work on Ptilonorhynchus violaceus has shown that advertisement call structure is strongly influenced by the acoustic environment of different habitats. Divergence in vocalizations among genetically related populations in different habitats indicates that satin bowerbirds match their vocalizations to the environment in which they live, despite the homogenizing influence of gene flow. In combination with convergence of vocalizations among genetically divergent populations occurring in the same habitat, this shows the overriding importance that habitat-related selection can have on the establishment and maintenance of variation in vocalizations. PMID:16892977

  1. Genetic Programming for the Generation of Crisp and Fuzzy Rule Bases in Classification and Diagnosis of Medical Data

    DEFF Research Database (Denmark)

    Dounias, George; Tsakonas, Athanasios; Jantzen, Jan;

    2002-01-01

    This paper demonstrates two methodologies for the construction of rule-based systems in medical decision making. The first approach consists of a method combining genetic programming and heuristic hierarchical rule-base construction. The second model is composed by a strongly-typed genetic...... programming system for the generation of fuzzy rule-based systems. Two different medical domains are used to evaluate the models. The first field is the diagnosis of subtypes of Aphasia. Two models for crisp rule-bases are presented. The first one discriminates between four major types and the second attempts...... the classification between all common types. A third model consisted of a GP-generated fuzzy rule-based system is tested on the same domain. The second medical domain is the classification of Pap-Smear Test examinations where a crisp rule-based system is constructed. Results denote the effectiveness of the proposed...

  2. A Hybrid Machine Learning Method for Fusing fMRI and Genetic Data: Combining both Improves Classification of Schizophrenia

    Directory of Open Access Journals (Sweden)

    Honghui Yang

    2010-10-01

    Full Text Available We demonstrate a hybrid machine learning method to classify schizophrenia patients and healthy controls, using functional magnetic resonance imaging (fMRI and single nucleotide polymorphism (SNP data. The method consists of four stages: (1 SNPs with the most discriminating information between the healthy controls and schizophrenia patients are selected to construct a support vector machine ensemble (SNP-SVME. (2 Voxels in the fMRI map contributing to classification are selected to build another SVME (Voxel-SVME. (3 Components of fMRI activation obtained with independent component analysis (ICA are used to construct a single SVM classifier (ICA-SVMC. (4 The above three models are combined into a single module using a majority voting approach to make a final decision (Combined SNP-fMRI. The method was evaluated by a fully-validated leave-one-out method using 40 subjects (20 patients and 20 controls. The classification accuracy was: 0.74 for SNP-SVME, 0.82 for Voxel-SVME, 0.83 for ICA-SVMC, and 0.87 for Combined SNP-fMRI. Experimental results show that better classification accuracy was achieved by combining genetic and fMRI data than using either alone, indicating that genetic and brain function representing different, but partially complementary aspects, of schizophrenia etiopathology. This study suggests an effective way to reassess biological classification of individuals with schizophrenia, which is also potentially useful for identifying diagnostically important markers for the disorder.

  3. Genetic analysis of a Sicilian population using 15 short tandem repeats.

    Science.gov (United States)

    Calò, C M; Garofano, L; Mameli, A; Pizzamiglio, M; Vona, G

    2003-04-01

    The genetic structure of the population of Alia (Sicily, Italy) was analyzed using 15 short tandem repeats: TPOX, D2S1338, D3S1358, FIBRA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D19S433, and D21S11. Two of these markers, D2S1338 and D19S433, have never before been used in research on population genetics and only recently have they been put to use in forensic medicine. Results of the analysis underline the genetic isolation of the Alia population and show it to be a recent bottleneck as a consequence of a cholera epidemic in 1837. While comparing the Alia population with other populations from Sicily, a genetic heterogeneity within Sicily was uncovered, thus confirming previous results obtained from the analysis of classical markers. This heterogeneity underlines the existence of genetic boundaries within the island. Comparisons with other Italian, Mediterranean, and European populations highlight the differentiation of the Sicilian population, reflecting the presence of a genetic boundary that separates Sicily from northern and central Italy and from the western Mediterranean basin. PMID:12943156

  4. Comparative population genetics of mimetic Heliconius butterflies in an endangered habitat; Brazil's Atlantic Forest

    Directory of Open Access Journals (Sweden)

    Cardoso Márcio Z

    2011-01-01

    Full Text Available Abstract Background Brazil's Atlantic Forest is a biodiversity hotspot endangered by severe habitat degradation and fragmentation. Habitat fragmentation is expected to reduce dispersal among habitat patches resulting in increased genetic differentiation among populations. Here we examined genetic diversity and differentiation among populations of two Heliconius butterfly species in the northern portion of Brazil's Atlantic Forest to estimate the potential impact of habitat fragmentation on population connectivity in butterflies with home-range behavior. Results We generated microsatellite, AFLP and mtDNA sequence data for 136 Heliconius erato specimens from eight collecting locations and 146 H. melpomene specimens from seven locations. Population genetic analyses of the data revealed high levels of genetic diversity in H. erato relative to H. melpomene, widespread genetic differentiation among populations of both species, and no evidence for isolation-by-distance. Conclusions These results are consistent with the hypothesis that the extensive habitat fragmentation along Brazil's Atlantic Forest has reduced dispersal of Heliconius butterflies among neighboring habitat patches. The results also lend support to the observation that fine-scale population genetic structure may be common in Heliconius. If such population structure also exists independent of human activity, and has been common over the evolutionary history of Heliconius butterflies, it may have contributed to the evolution of wing pattern diversity in the genus.

  5. Genetic Variability and Structuring of Arctic Charr (Salvelinus alpinus Populations in Northern Fennoscandia.

    Directory of Open Access Journals (Sweden)

    Takahito Shikano

    Full Text Available Variation in presumably neutral genetic markers can inform us about evolvability, historical effective population sizes and phylogeographic history of contemporary populations. We studied genetic variability in 15 microsatellite loci in six native landlocked Arctic charr (Salvelinus alpinus populations in northern Fennoscandia, where this species is considered near threatened. We discovered that all populations were genetically highly (mean FST ≈ 0.26 differentiated and isolated from each other. Evidence was found for historical, but not for recent population size bottlenecks. Estimates of contemporary effective population size (Ne ranged from seven to 228 and were significantly correlated with those of historical Ne but not with lake size. A census size (NC was estimated to be approximately 300 individuals in a pond (0.14 ha, which exhibited the smallest Ne (i.e. Ne/NC = 0.02. Genetic variability in this pond and a connected lake is severely reduced, and both genetic and empirical estimates of migration rates indicate a lack of gene flow between them. Hence, albeit currently thriving, some northern Fennoscandian populations appear to be vulnerable to further loss of genetic variability and are likely to have limited capacity to adapt if selection pressures change.

  6. Population expansions shared among coexisting bacterial lineages are revealed by genetic evidence.

    Science.gov (United States)

    Avitia, Morena; Escalante, Ana E; Rebollar, Eria A; Moreno-Letelier, Alejandra; Eguiarte, Luis E; Souza, Valeria

    2014-01-01

    Comparative population studies can help elucidate the influence of historical events upon current patterns of biodiversity among taxa that coexist in a given geographic area. In particular, comparative assessments derived from population genetics and coalescent theory have been used to investigate population dynamics of bacterial pathogens in order to understand disease epidemics. In contrast, and despite the ecological relevance of non-host associated and naturally occurring bacteria, there is little understanding of the processes determining their diversity. Here we analyzed the patterns of genetic diversity in coexisting populations of three genera of bacteria (Bacillus, Exiguobacterium, and Pseudomonas) that are abundant in the aquatic systems of the Cuatro Cienegas Basin, Mexico. We tested the hypothesis that a common habitat leaves a signature upon the genetic variation present in bacterial populations, independent of phylogenetic relationships. We used multilocus markers to assess genetic diversity and (1) performed comparative phylogenetic analyses, (2) described the genetic structure of bacterial populations, (3) calculated descriptive parameters of genetic diversity, (4) performed neutrality tests, and (5) conducted coalescent-based historical reconstructions. Our results show a trend of synchronic expansions across most populations independent of both lineage and sampling site. Thus, we provide empirical evidence supporting the analysis of coexisting bacterial lineages in natural environments to advance our understanding of bacterial evolution beyond medical or health-related microbes. PMID:25548732

  7. Population expansions shared among coexisting bacterial lineages are revealed by genetic evidence

    Directory of Open Access Journals (Sweden)

    Morena Avitia

    2014-12-01

    Full Text Available Comparative population studies can help elucidate the influence of historical events upon current patterns of biodiversity among taxa that coexist in a given geographic area. In particular, comparative assessments derived from population genetics and coalescent theory have been used to investigate population dynamics of bacterial pathogens in order to understand disease epidemics. In contrast, and despite the ecological relevance of non-host associated and naturally occurring bacteria, there is little understanding of the processes determining their diversity. Here we analyzed the patterns of genetic diversity in coexisting populations of three genera of bacteria (Bacillus, Exiguobacterium, and Pseudomonas that are abundant in the aquatic systems of the Cuatro Cienegas Basin, Mexico. We tested the hypothesis that a common habitat leaves a signature upon the genetic variation present in bacterial populations, independent of phylogenetic relationships. We used multilocus markers to assess genetic diversity and (1 performed comparative phylogenetic analyses, (2 described the genetic structure of bacterial populations, (3 calculated descriptive parameters of genetic diversity, (4 performed neutrality tests, and (5 conducted coalescent-based historical reconstructions. Our results show a trend of synchronic expansions across most populations independent of both lineage and sampling site. Thus, we provide empirical evidence supporting the analysis of coexisting bacterial lineages in natural environments to advance our understanding of bacterial evolution beyond medical or health-related microbes.

  8. [Genetic variability in captive populations of Crocodylus moreletii (Crocodylia: Crocodylidae) using microsatellites markers].

    Science.gov (United States)

    Serna-Lagunes, Ricardo; González, Dolores; Díaz-Rivera, Pablo

    2012-03-01

    Crocodylus moreletii, an extinction threatened species, represents an emblem for tropical ecosystems in Mexico. Surprisingly, there is a lack of information about their genetic constitution, which should be evaluated for a proper management ex situ and for making decisions on the release of crocodiles into natural habitats. The aim of this study was to characterize and compare the genetic variability of four populations of C. moreletii (two wild versus two born ex situ). Through PCR were amplified seven microsatellite polymorphic loci, however a heterozygote deficit, diminished by the presence of null alleles, was found in the populations (average Ho=0.02). The AMOVA indicated that the highest proportion of genetic variability is within populations, and a limited genetic differentiation among populations (average F(ST)=0.03), probably due to high inbreeding index (average F(IS)=0.97). When comparing the genetic variability between and within other crocodilian species, we found that in C. moreletii is well below those reported. We concluded that the limited genetic variability in ex situ born populations is probably due to a founder effect derived from the social structure of their progenitors, and by the bottleneck effect, inferred by the limited effective population size, that historically characterizes their natural distribution in wild populations. PMID:22458236

  9. Population Bottlenecks Increase Additive Genetic Variance But Do Not Break a Selection Limit in Rainforest Drosophila

    DEFF Research Database (Denmark)

    van Heerwaarden, Belinda; Willi, Yvonne; Kristensen, Torsten N; Hoffmann, Ary A

    2008-01-01

    desiccation resistance in the rain forest-restricted fly Drosophila bunnanda. After one generation of single-pair mating, additive genetic variance for desiccation resistance increased to a significant level, on average higher than for the control lines. Line crosses revealed that both dominance and epistatic......According to neutral quantitative genetic theory, population bottlenecks are expected to decrease standing levels of additive genetic variance of quantitative traits. However, some empirical and theoretical results suggest that, if nonadditive genetic effects influence the trait, bottlenecks may...... actually increase additive genetic variance. This has been an important issue in conservation genetics where it has been suggested that small population size might actually experience an increase rather than a decrease in the rate of adaptation. Here we test if bottlenecks can break a selection limit for...

  10. Assessing Genetic Diversity Based on Gliadin Proteins in Aegilops cylindrica Populations from Northwest of Iran

    Directory of Open Access Journals (Sweden)

    Toraj KHABIRI

    2013-02-01

    Full Text Available Wild wheat progenitors served as a valuable gene pool in breeding perspectives. In this respect, gliadins could be an important tool in assessing genetic variability as protein markers. Thus, genetic diversity of gliadin protein patterns in seventeen populations of Aegilops cylindrica collected from northwest of Iran were investigated using acid polyacrylamide gel electrophoresis. Results showed that the highest number of bands in the electrophoregrams were related to the ω type of geliadins. Conversely, the lowest number of bands were pertained to the β type of gliadins. Genetic diversity between populations was greater than within population variation. Assessment of total variation for the three gliadin types indicated that the highest total variation was related to β type while, the lowest one was belonged to ω type. Cluster analysis using complete linkage method divided populations into two separated groups in which genetic diversity does not follow from geographical distribution.

  11. Parallel Genetic and Phenotypic Evolution of DNA Superhelicity in Experimental Populations of Escherichia coli

    DEFF Research Database (Denmark)

    Crozat, Estelle; Winkworth, Cynthia; Gaffé, Joël;

    2010-01-01

    20,000 generations, parallel increases in DNA supercoiling were observed in ten populations. The genetic changes associated with the increased supercoiling were examined in one population, and beneficial mutations in the genes topA (encoding topoisomerase I) and fis (encoding a histone-like protein......) were identified. To elucidate the molecular basis and impact of these changes, we quantified the level of genetic, phenotypic, and molecular parallelism linked to DNA supercoiling in all 12 evolving populations. First, sequence determination of DNA topology-related loci revealed strong genetic...... resulting phenotypic effects. Third, artificially increasing DNA supercoiling in one of the two populations that lacked DNA topology changes led to a significant fitness increase. The high levels of molecular and genetic parallelism, targeting a small subset of the many genes involved in DNA supercoiling...

  12. Harbour porpoises (Phocoena phocoena in the North Atlantic: Distribution and genetic population structure

    Directory of Open Access Journals (Sweden)

    Liselotte Wesley Andersen

    2013-10-01

    Full Text Available The known geographical distribution (based on ship surveys, aerial surveys, incidental sightings, stranding and bycatch data and the population genetic structure obtained from mitochondria DNA and nuclear DNA (isozymes and microsatellites data analyses of the harbour porpoise in the North Atlantic have recently been reviewed and revised by the International Whaling Commission. The present review builds on these documents by integrating more recent genetic and distributional studies. Studies of the genetic structure of harbour porpoise populations tend to be concentrated in areas where samples are available which coincide with areas where incidental or directed catches or stranding take place. Nevertheless, recently, several genetic studies on the population structure have been able to reveal a more comprehensive picture of the harbour porpoise population structure in the Northwest and Northeast Atlantic, although not all areas have been subjected to analyses.

  13. jPopGen Suite: population genetic analysis of DNA polymorphism from nucleotide sequences with errors

    OpenAIRE

    Liu, Xiaoming

    2012-01-01

    1. Next-generation sequencing (NGS) is being increasingly used in ecological and evolutionary studies. Though promising, NGS is known to be error-prone. Sequencing error can cause significant bias for population genetic analysis of a sequence sample.

  14. Marine landscapes and population genetic structure of herring ( Clupea harengus L.) in the Baltic Sea

    DEFF Research Database (Denmark)

    Jørgensen, H.B.H.; Hansen, Michael Møller; Bekkevold, Dorte;

    2005-01-01

    Numerically small but statistically significant genetic differentiation has been found in many marine fish species despite very large census population sizes and absence of obvious barriers to migrating individuals. Analyses of morphological traits have previously identified local spawning groups...

  15. Dissecting the genetic structure and admixture of four geographical Malay populations

    OpenAIRE

    Lian Deng; Boon-Peng Hoh; Dongsheng Lu; Woei-Yuh Saw; Rick Twee-Hee Ong; Anuradhani Kasturiratne; H Janaka de Silva; Bin Alwi Zilfalil; Norihiro Kato; Wickremasinghe, Ananda R; Yik-Ying Teo; Shuhua Xu

    2015-01-01

    The Malay people are an important ethnic composition in Southeast Asia, but their genetic make-up and population structure remain poorly studied. Here we conducted a genome-wide study of four geographical Malay populations: Peninsular Malaysian Malay (PMM), Singaporean Malay (SGM), Indonesian Malay (IDM) and Sri Lankan Malay (SLM). All the four Malay populations showed substantial admixture with multiple ancestries. We identified four major ancestral components in Malay populations: Austrones...

  16. Subpopulation genetic structure of a plant panmictic population of Castanea sequinii as revealed by microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    WANG Ying; KANG Ming; HUANG Hongwen

    2007-01-01

    Castanea squinii Dode,an endemic tree widely distributed in China,plays an important role both in chestnut breeding and forest ecosystem function.The spatial genetic structure within and among populations is an important part of the evolutionary and ecological genetic dynamics of natural populations,and can provide insights into effective conservation of genetic resources.In the present study,the spatial genetic structure of a panmictic natural population of C.sequinii in the Dabie Mountain region was investigated using microsatellite markers.Nine prescreened microsatellite loci generated 29-33 alleles each,and were used for spatial autocorrelation analysis.Based on Moran's I coefficient,a panmictic population of C.sequinii in the Dabie Mountain region was found to be lacking a spatial genetic structure.These results suggest that a high pollen-mediated gene flow among subpopulations counteract genetic drift and/or genetic differentiation and plays an important role in maintaining a random and panmictic population structure in C.sequinii populations.Further,a spatial genetic structure was detected in each subpopulation's scale (0.228 km),with all three subpopulations showing significant fine-scale structure.The genetic variation was found to be nonrandomly distributed within 61 m in each subpopulation (Moran's I positive values).Although Moran's I values varied among the different subpopulations,Moran's I in all the three subpopulations reached the expected values with an increase in distances,suggesting a generally patchy distribution in the subpopulations.The fine-scale structure seems to reflect restricted seed dispersal and microenvironment selection in C.sequinii.These results have important implications for understanding the evolutionary history and ecological process of the natural population of C.sequinii and provide baseline data for formulating a conservation strategy of Castanea species.

  17. At the interface of phylogenetics and population genetics, the phylogeography of Dirca occidentalis (Thymelaeaceae).

    Science.gov (United States)

    Graves, William R; Schrader, James A

    2008-11-01

    Dirca occidentalis is a rare shrub indigenous to only six counties near the San Francisco Bay in California, United States. We used intersimple sequence repeat (ISSR) markers and automated genotyping to probe 29 colonies of D. occidentalis from four geographically disjunct populations (East Bay, North Bay, Salmon Creek, and Peninsula) and used methods of phylogenetics and population genetics to model variation across the species. Results show that the four disjunct populations are genetically isolated and have undergone divergence. Phylogenetic analyses indicate that the East Bay population was the first to diverge, followed by the North Bay, then the Salmon Creek and Peninsula populations. This order of divergence suggests an intriguing natural history for D. occidentalis that is explained by the dynamic geological and climatic history of the Bay Area. Spatial genetic structure detected for the species suggests an interaction of four factors: limited seed dispersal, clonal regeneration, distances traveled by pollinators, and genetic isolation of the four populations. Genetic diversity within the North Bay and Salmon Creek populations is low, indicating poor ecological fitness and risk of decline. ISSRs resolved phylogeographic structure within D. occidentalis, results unattainable with ITS methods, and the integration of tools of phylogenetics and population biology led to an enhanced understanding of this endemic species. PMID:21628153

  18. Genetic diversity between and within populations of Handroanthus heptaphyllus (Vell. Mattos using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Neide Tomita Mori

    2012-03-01

    Full Text Available Handroanthus heptaphyllus (Vell. Mattos, popularly known as ipê-roxo, is a species of the family Bignoneaceae much appreciated for its beauty, excellent quality wood which is used for making medicinal products and also in reforestation programs of degraded areas, as well as landscaping and restoration. The aim of this study was to investigate the genetic diversity between and within populations of H. heptaphyllus using microsatellite markers. The 192 seedlings were produced from seeds collected on 30 trees into the two populations of natural forest fragments in Botucatu region, São Paulo, Brazil. Eight microsatellite loci were analyzed, with allelic polymorphism varying from six alleles for locus TAU22 to 14 alleles for loci TAU12, TAU30, and TAU31, with an expected mean number of alleles per locus (Ae of 4.9. The mean expected heterozygosity (He for the two populations was 0.785, the mean observed heterozygosity (Ho was 0.609, and the fixation index (F was low between populations, with a mean of 0.222. The gene differentiation between the two populations (Gst was 0.100. We concluded that the higher genetic diversity is within populations; therefore, as far as germplasm collection programs in Botucatu region are concerned, it is recommended that a larger sampling of individuals should be considered within populations, thereby providing good genetic representativeness. The populations have enough genetic diversity to support genetic improvement and germplasm preservation programs.

  19. Population genetic structure of peninsular Malaysia Malay sub-ethnic groups.

    Directory of Open Access Journals (Sweden)

    Wan Isa Hatin

    Full Text Available Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis. To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia.

  20. Population genetic structure of peninsular Malaysia Malay sub-ethnic groups.

    Science.gov (United States)

    Hatin, Wan Isa; Nur-Shafawati, Ab Rajab; Zahri, Mohd-Khairi; Xu, Shuhua; Jin, Li; Tan, Soon-Guan; Rizman-Idid, Mohammed; Zilfalil, Bin Alwi

    2011-01-01

    Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia. PMID:21483678

  1. Unreliable Populations: A Classification of Types of Unreliability in Kepler Exoplanet Catalogs

    Science.gov (United States)

    Bryson, Steve; Mullally, Fergal

    2015-12-01

    Exoplanet occurrence rate estimates based on Kepler data suffer from the problem of reliability: Objects in the catalog may be due to false alarms (FAs), spurious detections of non-transit-like signals; or false positives (FPs), detection of transit-like signals that are not due to planets orbiting the observed star. The computation of the true occurrence rate requires knowledge of the rate of FPs and FAs, which can be very difficult to determine on a planet-by-planet basis, particularly at the low signal levels expected in the Earth-Sun analog regime. Some occurrence rate estimates treat reliability as a population, assuming that the reliability rate depends on planet period and radius.We present a classification of types of FAs and FPs in terms of their underlying cause. These include astrophysical FPs such as eclipsing binaries (grazing or blended) and FAs due to stellar variability. We give particular emphasis to instrumental FAs, which can be due to a variety of causes. Our classification emphasizes that different classes of FAs, and to a lesser extent FPs, can be strongly dependent on position or time of observation. For example, the likelihood of background eclipsing binary FPs depends strongly on Galactic latitude. Some types of instrumental FAs occur only on particular locations on the focal plane or at particular observation times such as near strong instrument thermal transients. These dependencies imply that care should be taken when treating FP/FA rates as functions of only planet period and radius.The Kepler mission provides various reliability diagnostics at the Exoplanet Archive. We discuss how these diagnostics relate to our classification scheme, and find that while FPs are well covered, instrumental FAs have poor coverage. At low signal-to-noise ratios these diagnostics provide little information, so the reliability rate for small planets in long-period orbits is less well known and may be high. We describe upcoming studies by the Kepler team

  2. Genetic polymorphisms of pharmacogenomic VIP variants in the Uygur population from northwestern China

    OpenAIRE

    Wang, Li; Aikemu, Ainiwaer; Yibulayin, Ayiguli; Du, Shuli; Geng, Tingting; Wang, Bo; Zhang, Yuan; Jin, Tianbo; Yang, Jie

    2015-01-01

    Background Drug response variability observed amongst patients is caused by the interaction of both genetic and non-genetic factors, and frequencies of functional genetic variants are known to vary amongst populations. Pharmacogenomic research has the potential to help with individualized treatments. We have not found any pharmacogenomics information regarding Uygur ethnic group in northwest China. In the present study, we genotyped 85 very important pharmacogenetic (VIP) variants (selected f...

  3. Genetic diversity and population structure of Korean and Chinese soybean [Glycine max (L.) Merr.] accessions

    Science.gov (United States)

    Korean and Chinese cultivated soybean [Glycine max (L.) Merr.] populations are major soybean gene pools. Information has been reported comparing genetic diversity between soybeans from the two countries using an unequal number of accessions and only 6 to 35 genetic markers. This study compares diffe...

  4. Microgeographic and Temporal Genetic Differentiation in Natural Populations of DROSOPHILA SUBOBSCURA

    OpenAIRE

    Cabrera, V M; González, A M; M Hernández; Larruga, J. M.; Martell, M

    1985-01-01

    Evidence of microgeographic and temporal genetic differentiation in natural populations of Drosophila subobscura is presented. The alcohol dehydrogenease locus was used as a genetic marker. Behavioral differences among the sexes and genotypes may explain these observations, although the molecular basis remains obscure.

  5. Genetic variances, trends and mode of inheritance for hip and elbow dysplasia in Finnish dog populations

    NARCIS (Netherlands)

    Mäki, K.; Groen, A.F.; Liinamo, A.E.; Ojala, M.

    2002-01-01

    The aims of this study were to assess genetic variances, trends and mode of inheritance for hip and elbow dysplasia in Finnish dog populations. The influence of time-dependent fixed effects in the model when estimating the genetic trends was also studied. Official hip and elbow dysplasia screening r

  6. Population genetic dynamics of an invasion reconstructed from the sediment egg bank.

    Science.gov (United States)

    Möst, Markus; Oexle, Sarah; Marková, Silvia; Aidukaite, Dalia; Baumgartner, Livia; Stich, Hans-Bernd; Wessels, Martin; Martin-Creuzburg, Dominik; Spaak, Piet

    2015-08-01

    Biological invasions are a global issue with far-reaching consequences for single species, communities and whole ecosystems. Our understanding of modes and mechanisms of biological invasions requires knowledge of the genetic processes associated with successful invasions. In many instances, this information is particularly difficult to obtain as the initial phases of the invasion process often pass unnoticed and we rely on inferences from contemporary population genetic data. Here, we combined historic information with the genetic analysis of resting eggs to reconstruct the invasion of Daphnia pulicaria into Lower Lake Constance (LLC) in the 1970s from the resting egg bank in the sediments. We identified the invader as 'European D. pulicaria' originating from meso- and eutrophic lowland lakes and ponds in Central Europe. The founding population was characterized by extremely low genetic variation in the resting egg bank that increased considerably over time. Furthermore, strong evidence for selfing and/or biparental inbreeding was found during the initial phase of the invasion, followed by a drop of selfing rate to low levels in subsequent decades. Moreover, the increase in genetic variation was most pronounced during early stages of the invasion, suggesting additional introductions during this period. Our study highlights that genetic data covering the entire invasion process from its beginning can be crucial to accurately reconstruct the invasion history of a species. We show that propagule banks can preserve such information enabling the study of population genetic dynamics and sources of genetic variation in successful invasive populations. PMID:26122166

  7. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population

    Science.gov (United States)

    Genetic variants responsible for susceptibility to obesity and its comorbidities among Hispanic children have not been identified. The VIVA LA FAMILIA Study was designed to genetically map childhood obesity and associated biological processes in the Hispanic population. A genome-wide association stu...

  8. Range-wide population genetic structure of the Pipistrellus pipistrellus complex based on microsatellites

    Czech Academy of Sciences Publication Activity Database

    Bryja, Josef; Fornůsková, Alena; Horáček, I.; Benda, P.; Hulva, P.

    Cluj-Napoca: Babeş-Bolyai University, 2008 - (Hutson, A.; Lina, P.). s. 35 [European Bat Research Symposium /11./. 18.08.2008-22.08.2008, Cluj-Napoca] Institutional research plan: CEZ:AV0Z60930519 Keywords : bats * microsatellites * population genetic structure Subject RIV: EB - Genetics ; Molecular Biology http://www.ebrs2008.org/docs/EBRS_2008_Abstracts.pdf

  9. Do hatchery-reared sea urchins pose a threat to genetic diversity in wild populations?

    Science.gov (United States)

    Segovia-Viadero, M; Serrão, E A; Canteras-Jordana, J C; Gonzalez-Wangüemert, M

    2016-04-01

    In salmonids, the release of hatchery-reared fish has been shown to cause irreversible genetic impacts on wild populations. However, although responsible practices for producing and releasing genetically diverse, hatchery-reared juveniles have been published widely, they are rarely implemented. Here, we investigated genetic differences between wild and early-generation hatchery-reared populations of the purple sea urchin Paracentrotus lividus (a commercially important species in Europe) to assess whether hatcheries were able to maintain natural levels of genetic diversity. To test the hypothesis that hatchery rearing would cause bottleneck effects (that is, a substantial reduction in genetic diversity and differentiation from wild populations), we compared the levels and patterns of genetic variation between two hatcheries and four nearby wild populations, using samples from both Spain and Ireland. We found that hatchery-reared populations were less diverse and had diverged significantly from the wild populations, with a very small effective population size and a high degree of relatedness between individuals. These results raise a number of concerns about the genetic impacts of their release into wild populations, particularly when such a degree of differentiation can occur in a single generation of hatchery rearing. Consequently, we suggest that caution should be taken when using hatchery-reared individuals to augment fisheries, even for marine species with high dispersal capacity, and we provide some recommendations to improve hatchery rearing and release practices. Our results further highlight the need to consider the genetic risks of releasing hatchery-reared juveniles into the wild during the establishment of restocking, stock enhancement and sea ranching programs. PMID:26758187

  10. Influence of anti-filarial chemotherapy strategies on the genetic structure of Wuchereria bancrofti populations

    OpenAIRE

    Dhamodharan Ramasamy; Hoti Sugeerappa Laxmanappa; Rohit Sharma; Manoj Kumar Das

    2011-01-01

    Lymphatic filarial (LF) parasites have been under anti-filarial drug pressure for more than half a century. Currently, annual mass drug administration (MDA) of diethylcarbamazine (DEC) or ivermectin in combination with albendazole (ALB) have been used globally to eliminate LF. Long-term chemotherapies exert significant pressure on the genetic structure of parasitic populations. We investigated the genetic variation among 210 Wuchereria bancrofti populations that were under three different che...

  11. Population genetics of the westernmost distribution of the glaciations-surviving black truffle Tuber melanosporum.

    Science.gov (United States)

    García-Cunchillos, Iván; Sánchez, Sergio; Barriuso, Juan José; Pérez-Collazos, Ernesto

    2014-04-01

    The black truffle (Tuber melanosporum Vittad.) is an important natural resource due to its relevance as a delicacy in gastronomy. Different aspects of this hypogeous fungus species have been studied, including population genetics of French and Italian distribution ranges. Although those studies include some Spanish populations, this is the first time that the genetic diversity and genetic structure of the wide geographical range of the natural Spanish populations have been analysed. To achieve this goal, 23 natural populations were sampled across the Spanish geographical distribution. ISSR technique demonstrated its reliability and capability to detect high levels of polymorphism in the species. Studied populations showed high levels of genetic diversity (h N  = 0.393, h S  = 0.678, Hs = 0.418), indicating a non threatened genetic conservation status. These high levels may be a consequence of the wide distribution range of the species, of its spore dispersion by animals, and by its evolutionary history. AMOVA analysis showed a high degree of genetic structure among populations (47.89%) and other partitions as geographical ranges. Bayesian genetic structure analyses differentiated two main Spanish groups separated by the Iberian Mountain System, and showed the genetic uniqueness of some populations. Our results suggest the survival of some of these populations during the last glaciation, the Spanish southern distribution range perhaps surviving as had occurred in France and Italy, but it is also likely that specific northern areas may have acted as a refugia for the later dispersion to other calcareous areas in the Iberian Peninsula and probably France. PMID:24272144

  12. Social and genetic interactions drive fitness variation in a free-living dolphin population

    OpenAIRE

    Frère, C H; Krützen, M; J. Mann; Connor, R C; Bejder, L; Sherwin, W B

    2010-01-01

    The evolutionary forces that drive fitness variation in species are of considerable interest. Despite this, the relative importance and interactions of genetic and social factors involved in the evolution of fitness traits in wild mammalian populations are largely unknown. To date, a few studies have demonstrated that fitness might be influenced by either social factors or genes in natural populations, but none have explored how the combined effect of social and genetic parameters might inter...

  13. Characterization of genetic diversity of native 'Ancho' chili populations of Mexico using microsatellite markers

    OpenAIRE

    Rocío Toledo-Aguilar; Higinio López-Sánchez; Amalio Santacruz-Varela; Ernestina Valadez-Moctezuma; Pedro A López; Víctor H Aguilar-Rincón; Víctor A González-Hernández; Humberto Vaquera-Huerta

    2016-01-01

    'Ancho' type chilis (Capsicum annuum L. var. annuum) are an important ingredient in the traditional cuisine of Mexico and so are in high demand. It includes six native sub-types with morphological and fruit color differences. However, the genetic diversity of the set of these sub­types has not been determined. The objective of this study was to characterize the genetic diversity of native Mexican ancho chili populations using microsatellites and to determine the relationship among these popul...

  14. Evaluation of the population structure and genetic diversity of Plasmodium falciparum in southern China

    OpenAIRE

    Wei, Guiying; Zhang, Lili; Yan, He; Zhao, Yuemeng; Hu, Jingying; Pan, Weiqing

    2015-01-01

    Background Yunnan and Hainan provinces are the two major endemic regions for Plasmodium falciparum malaria in China. However, few studies have investigated the characteristics of this parasite. Therefore, this study aimed to evaluate the genetic diversity and population structure of P. falciparum to predict the geographic origin of falciparum malaria. Methods Thirteen highly polymorphic microsatellite loci were studied to estimate the genetic diversity and population structure of 425 P. falci...

  15. Genetic Diversity and Population Structure of Rice Pathogen Ustilaginoidea virens in China

    OpenAIRE

    Sun, Xianyun; Kang, Shu; Zhang, Yongjie; Tan, Xinqiu; Yu, Yufei; He, Haiyong; Zhang, Xinyu; Liu, Yongfeng; Wang, Shu; Sun, Wenxian; Cai, Lei; Li, Shaojie

    2013-01-01

    Rice false smut caused by the fungal pathogen Ustilaginoidea virens is becoming a destructive disease throughout major rice-growing countries. Information about its genetic diversity and population structure is essential for rice breeding and efficient control of the disease. This study compared the genome sequences of two U . virens isolates. Three SNP-rich genomic regions were identified as molecular markers that could be used to analyze the genetic diversity and population structure of U ....

  16. Breast cancer risk assessment using genetic variants and risk factors in a Singapore Chinese population

    OpenAIRE

    Lee, Charmaine Pei Ling; Irwanto, Astrid; Salim, Agus; Yuan, Jian-Min; Liu, Jianjun; Koh, Woon Puay; Hartman, Mikael

    2014-01-01

    Introduction Genetic variants for breast cancer risk identified in genome-wide association studies (GWAS) in Western populations require further testing in Asian populations. A risk assessment model incorporating both validated genetic variants and established risk factors may improve its performance in risk prediction of Asian women. Methods A nested case-control study of female breast cancer (411 cases and 1,212 controls) within the Singapore Chinese Health Study was conducted to investigat...

  17. Genomic sweep and potential genetic rescue during limiting environmental conditions in an isolated wolf population

    OpenAIRE

    Adams, Jennifer R.; Vucetich, Leah M.; Hedrick, Philip W.; Rolf O Peterson; Vucetich, John A.

    2011-01-01

    Genetic rescue, in which the introduction of one or more unrelated individuals into an inbred population results in the reduction of detrimental genetic effects and an increase in one or more vital rates, is a potentially important management tool for mitigating adverse effects of inbreeding. We used molecular techniques to document the consequences of a male wolf (Canis lupus) that immigrated, on its own, across Lake Superior ice to the small, inbred wolf population in Isle Royale National P...

  18. Genetic variation in Danish populations of Erysiphe graminis f.sp. hordei: estimation of gene diversity and effective population size using RFLP data

    DEFF Research Database (Denmark)

    Damgaard, C.; Giese, Nanna Henriette

    1996-01-01

    Genetic variation of the barley powdery mildew fungus (Erysiphe graminis f.sp. hordei) was estimated in three Danish local populations. Genetic variation was estimated from the variation amongst clones of Egh, and was therefore an estimate of the maximum genetic variation in the local populations...

  19. Population genetic structure and demographic history of the black fly vector, Simulium nodosum in Thailand.

    Science.gov (United States)

    Chaiyasan, P; Pramual, P

    2016-09-01

    An understanding of the genetic structure and diversity of vector species is crucial for effective control and management. In this study, mitochondrial DNA sequences were used to examine the genetic structure, diversity and demographic history of a black fly vector, Simulium nodosum Puri (Diptera: Simuliidae), in Thailand. A total of 145 sequences were obtained from 10 sampling locations collected across geographical ranges in the country. Low genetic diversity was found in populations of S. nodosum that could be explained by the recent population history of this species. Demographic history analysis revealed a signature of demographic expansion dating back to only 2600-5200 years ago. Recent population expansion in S. nodosum possibly followed an increase in agriculture that enabled its hosts', humans and domestic animals, densities to increase. Alternatively, the Thai populations could be a derivative of an older expansion event in the more northern populations. Mitochondrial DNA genealogy revealed no genetically divergent lineages, which agrees with the previous cytogenetic study. Genetic structure analyses found that only 27% of the pairwise comparisons were significantly different. The most likely explanation for the pattern of genetic structuring is the effect of genetic drift because of recent colonization. PMID:27245148

  20. Detecting genetic isolation in human populations: a study of European language minorities.

    Directory of Open Access Journals (Sweden)

    Marco Capocasa

    Full Text Available The identification of isolation signatures is fundamental to better understand the genetic structure of human populations and to test the relations between cultural factors and genetic variation. However, with current approaches, it is not possible to distinguish between the consequences of long-term isolation and the effects of reduced sample size, selection and differential gene flow. To overcome these limitations, we have integrated the analysis of classical genetic diversity measures with a bayesian method to estimate gene flow and have carried out simulations based on the coalescent. Combining these approaches, we first tested whether the relatively short history of cultural and geographical isolation of four "linguistic islands" of the Eastern Alps (Lessinia, Sauris, Sappada and Timau had left detectable signatures in their genetic structure. We then compared our findings to previous studies of European population isolates. Finally, we explored the importance of demographic and cultural factors in shaping genetic diversity among the groups under study. A combination of small initial effective size and continued genetic isolation from surrounding populations seems to provide a coherent explanation for the diversity observed among Sauris, Sappada and Timau, which was found to be substantially greater than in other groups of European isolated populations. Simulations of micro-evolutionary scenarios indicate that ethnicity might have been important in increasing genetic diversity among these culturally related and spatially close populations.

  1. Application of AFLP markers for population genetic study on half-smooth tongue sole Cynoglossus semilaevis

    Institute of Scientific and Technical Information of China (English)

    LIU Yunguo; LI Junfeng; YE Naihao

    2011-01-01

    The genetic diversity of wild and hatchery populations of half-smooth tongue sole Cynoglossus semilaevis, based on observation of amplified fragment length polymorphism (AFLP) was described. Two hundred individuals from four wild populations, Laizhou (LZ), Weihai (WH), Qingdao (QD), Rizhao (RZ), and one hatchery population, Mingbo (MB), were screened using eight different AFLP primer combinations. A total of 384 loci were screened in the five studied populations. 48.4%, 51.3%,50.7%, 49.3% and 45.8% of these loci were polymorphic among the individuals tested in the LZ, WH,QD, RZ and MB populations, respectively. The number of polymorphic loci detected by single primer combinations ranged from 17 to 35. The average heterozygosity of the LZ, WH, QD, RZ and MB populations was 0.072, 0.093, 0.092, 0.090 and 0.063, respectively. The WH population showed the highest genetic diversity in terms of total number of AFLP bands, total number of polymorphic bands,average heterozygosity and percentage of low frequency (0-0.2) polymorphic loci among all the populations,while the LZ population was the lowest among the wild populations. Compared with the wild populations,the hatchery population showed a low genetic viability.

  2. Use of Genetic Effects and Genotype by Environmental Interactions for the Classification of Mexican Races of Maize

    Science.gov (United States)

    Cervantes, Tarcicio S.; Goodman, Major M.; Casas, Eduardo D.; Rawlings, John O.

    1978-01-01

    To examine the questions of whether the additive and dominance effects present for morphological characters in racial crosses are of sufficient consistency and magnitude to allow such genetic effects to be used for racial classification, we used a diallel experiment among the 25 well-defined Mexican races of maize, which include the ancestral stocks of most commercial and genetic maize types. With such an experiment, genetic effects and genotype by environmental interactions for one or more characters can be used to measure genetic and adaptational or environmental similarity. We used average parental effects (general combining abilities), specific effects, and genotype by environmental effects of 21 characters from the diallel (grown at three locations) to group the Mexican races of maize. The groupings based upon average genetic effects and upon genotype by environmental interactions are more satisfactory than groupings based upon specific effects. The standard errors for genetic distances based upon specific (largely dominance) effects seem to be too high for practical use. Principal components analyses of the same data suggest a similar conclusion.—The groupings based upon average genetic effects are in general agreement with previous studies, with the exception of Maíz Dulce, which is grouped with the Cónicos, rather than being isolated from the other Mexican races of maize. PMID:17248866

  3. Critical fitness collapse in three-dimensional spatial population genetics

    Science.gov (United States)

    Lavrentovich, Maxim O.

    2015-05-01

    If deleterious mutations near a fitness maximum in a spatially distributed population are sufficiently frequent or detrimental, the population can undergo a fitness collapse, similarly to the Muller's ratchet effect in well-mixed populations. Recent studies of 1D habitats (e.g. the frontier of a 2D range expansion) have shown that the onset of the fitness collapse is described by a directed percolation phase transition with its associated critical exponents. We consider population fitness collapse in 3D range expansions with both inflating and fixed-size frontiers (applicable to, e.g. expanding and treadmilling spherical tumors, respectively). We find that the onset of fitness collapse in these two cases obeys different scaling laws, and that competition between species at the frontier leads to a deviation from directed percolation scaling. As in 2D range expansions, inflating frontiers modify the critical behavior by causally disconnecting well-separated portions of the population.

  4. Population genetics of the Eastern Hellbender (Cryptobranchus alleganiensis alleganiensis across multiple spatial scales.

    Directory of Open Access Journals (Sweden)

    Shem D Unger

    Full Text Available Conservation genetics is a powerful tool to assess the population structure of species and provides a framework for informing management of freshwater ecosystems. As lotic habitats become fragmented, the need to assess gene flow for species of conservation management becomes a priority. The eastern hellbender (Cryptobranchus alleganiensis alleganiensis is a large, fully aquatic paedamorphic salamander. Many populations are experiencing declines throughout their geographic range, yet the genetic ramifications of these declines are currently unknown. To this end, we examined levels of genetic variation and genetic structure at both range-wide and drainage (hierarchical scales. We collected 1,203 individuals from 77 rivers throughout nine states from June 2007 to August 2011. Levels of genetic diversity were relatively high among all sampling locations. We detected significant genetic structure across populations (Fst values ranged from 0.001 between rivers within a single watershed to 0.218 between states. We identified two genetically differentiated groups at the range-wide scale: 1 the Ohio River drainage and 2 the Tennessee River drainage. An analysis of molecular variance (AMOVA based on landscape-scale sampling of basins within the Tennessee River drainage revealed the majority of genetic variation (∼94-98% occurs within rivers. Eastern hellbenders show a strong pattern of isolation by stream distance (IBSD at the drainage level. Understanding levels of genetic variation and differentiation at multiple spatial and biological scales will enable natural resource managers to make more informed decisions and plan effective conservation strategies for cryptic, lotic species.

  5. Genetic population structure of Tectura paleacea: implications for the mechanisms regulating population structure in patchy coastal habitats.

    Directory of Open Access Journals (Sweden)

    Emina Begovic

    Full Text Available The seagrass limpet Tectura paleacea (Gastropoda; Patellogastropoda belongs to a seagrass obligate lineage that has shifted from the Caribbean in the late Miocene, across the Isthmus of Panama prior to the closing of the Panamanian seaway, and then northward to its modern Baja California - Oregon distribution. To address whether larval entrainment by seagrass beds contributes to population structuring, populations were sampled at six California/Oregon localities approximately 2 degrees latitude apart during two post-settlement periods in July 2002 and June 2003. Partial cytochrome oxidase b (Cytb sequences were obtained from 20 individuals (10 per year from each population in order to determine the levels of population subdivision/connectivity. From the 120 individuals sequenced, there were eighty-one unique haplotypes, with the greatest haplotype diversity occurring in southern populations. The only significant genetic break detected was consistent with a peri-Point Conception (PPC biogeographic boundary while populations north and south of Point Conception were each panmictic. The data further indicate that populations found south of the PPC biogeographic boundary originated from northern populations. This pattern of population structure suggests that seagrass patches are not entraining the larvae of T. paleacea by altering flow regimes within their environment; a process hypothesized to produce extensive genetic subdivision on fine geographic scales. In contrast to the haplotype data, morphological patterns vary significantly over very fine geographic scales that are inconsistent with the observed patterns of genetic population structure, indicating that morphological variation in T. paleacea might be attributed to differential ecophenotypic expression in response to local habitat variability throughout its distribution. These results suggest that highly localized conservation efforts may not be as effective as large-scale conservation

  6. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations.

    Science.gov (United States)

    Santure, Anna W; Poissant, Jocelyn; De Cauwer, Isabelle; van Oers, Kees; Robinson, Matthew R; Quinn, John L; Groenen, Martien A M; Visser, Marcel E; Sheldon, Ben C; Slate, Jon

    2015-12-01

    Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long-term studies across Europe and consequently are considered an ecological 'model organism'. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long-term study populations of great tits-one in the Netherlands and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population-specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population-specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free-living populations. PMID:26661500

  7. Genetic relationship and population structure of three Indian local chicken populations as revealed by mtDNA D-loop.

    Science.gov (United States)

    Sahu, P K; Das, B; Sahoo, L; Senapati, S; Nayak, G D

    2016-07-01

    The genetic information obtained from the mitochondrial DNA D-loop region has paramount importance in understanding the evolution of closely related individuals, and designing proper breeding or conservation plans. The present study was conducted using partial D-loop sequences of three local poultry populations from Odisha, India. The partial D-loop sequences were found to be highly polymorphic having 164 polymorphic sites with 89 singletons and 75 parsimony informative sites. Furthermore, 25 insertion and deletion sites were observed. High genetic diversity was observed within three local chicken populations. Highest genetic difference was observed between Gujuri and Kalua population (0.2230) followed by Gujuri and Hansli (0.199) and Kalua with Hansli (0.166). The pairwise mismatch distribution showed that all populations are of constant size over time. Phylogenetic tree analysis indicated that the said three populations were close to the referred population of China, Sri Lanka, Indonesia and Japan than Aseel and Kadaknath (Indian native breeds). PMID:26162050

  8. Modelling the loss of genetic diversity in vole populations in a spatially and temporally varying environment

    DEFF Research Database (Denmark)

    Topping, Christopher John; Østergaard, Siri; Pertoldi, Cino; Bach, Lars Arve

    2003-01-01

    habitat availability and their influence on vole behaviour. Interaction between spatial and temporal dynamics altered the ratio of effective population size to census size. This indicates an altered reproductive potential, crucial in conservation biology applications. However, when the loss of...... genetically explicit individual-based model (IBM) coupled to a dynamic landscape model was used to obtain measures for the genetic status of simulated vole populations. The rate of loss of expected heterozygosity (He) was calculated for simulated populations using two levels of spatial and temporal...... heterogeneity. Results showed that both spatial and temporal heterogeneity exerted an influence on the rate of loss of genetic diversity, but the precise effect was a balance between the effects of population sub-structuring, the frequency of founder effects and population size. These were in turn related to...

  9. MONITORING OF GENETIC DIVERSITY IN FARMED DEER POPULATIONS USING MICROSATELLITE MARKERS

    Directory of Open Access Journals (Sweden)

    Pavol Bajzík

    2011-12-01

    Full Text Available Deer (Cervidaei belong to the most important species used as farmed animals. We focused on assesing the genetic diversity among five deer populations. Analysis has been performed on a total of 183 animals originating from Czech Republic, Hungary, New Zealand, Poland and Slovak Republic. Genetic variability were investigated using 8 microsatellite markers used in deer. Statistical data of all populations we obtained on the basis of Nei statistics, using by POWERMARKER 3.23 programme. Graphical view of relationships among populations and individuals in the populations was obtained using the Dendroscope software. Molecular genetic data combinated with evaluation in statistical programmes could lead to a complex view of populations and diffrences among them.doi:10.5219/172

  10. Genetic Investigations Using Immuno-biochemical Markers in a Maramureş Brown Cattle Population

    Directory of Open Access Journals (Sweden)

    Nicoleta Isfan

    2011-05-01

    Full Text Available The study of the genetic markers and identifying new markers involves an increasing number of research projects in the fields of genetics of immunology, biochemical genetics, molecular genetics, quantity genetics and the genetic improvement of animals. Some studies on genes frequency determining the red cells specificity and for whey hemoglobin are approached in the present report. In this way, some blood factors, most of them belonging to B system (the most complex system in cattle have been evidenced. The lowest gene frequency was present in K factor (7%, and highest one in, O1, G’ , W and F1 (100%. In addition to basic importance on knowledge and determination of cattle population genetic structure for studied protein loci, another theme proposed to correlate hemoglobin type with some traits of economical importance: milk yield, fat and protein content, fat and protein yield. Higher performance was recorded by HbA/HbA individuals.

  11. Genetic diversity and differentiation of mud crab Scylla serrata populations from southeastern China

    Institute of Scientific and Technical Information of China (English)

    LI Zhongbao; LI Shaojing; WANG Guizhong

    2004-01-01

    The genetic diversity and differentiation of 6 mud crab Scylla serrata populations from southeastern China are investigated using allozyme electrophoresis. The mean number of alleles per locus population is 1.3 ± 0.1; the percentage of polymorphic loci per population is 27.3; the observed heterozygosity ranges from ( 0.195 ± 0.083)to ( 0.241 ± 0.090) and the expected heterozygosity ranges from ( 0.105 ± 0.043 ) to ( 0.131 ± 0.047 ). The coefficient of gene differentiation among populations is low (Fst =0.032), indicating that only 3.2 % of the total genetic diversity comes from inter-population, while the remaining 96.8 % comes from intra-population differences.The genetic distance among populations is 0.000~0.008 (the average is 0.002). Gene flow among the populations is large (Nm= 7.56).Genetic structure is very similar among 6 Scylla serrata populations.

  12. Population genetics of 14 ethnic groups using phenotypic data from VNTR loci.

    Science.gov (United States)

    Balazs, I

    1993-01-01

    Population genetic studies were performed using five VNTR loci (D2S44, D4S163, D14S13, D17S79, D18S27). The populations examined were Caucasian (Australia, Brazil and U.S.A.), Australian aborigine, Chinese, Amerindian (Cheyenne, Maya, Navajo, Pima, Tobas/Wicnis), North American Black, North American Hispanic (California, Miami, New York, Texas). The overall size range of the alleles for these loci, in PstI-digested DNA, was the same in all populations. The major difference among populations was the relative frequency of particular groups of alleles. These differences were small among similar ethnic groups, while sometimes varying several fold among some of the more distinct populations. However, groups of alleles that were rare in the major ethnic groups (Caucasian, Black, Chinese) were also rare in the other populations. The frequency databases generated by typing individuals for 4 loci were used to compare the random DNA profile frequencies among populations. The results show that the estimated frequency of any 4 locus profile is very low in all populations examined (e.g., median value < 10(-8)). Analysis of relative genetic similarity among populations was used to create the most likely clustering of these ethnic groups. Results show an uncanny similarity between the clusters generated and genetic distance measurements obtained with traditional calculations of conventional genetic markers. PMID:8104559

  13. Quantitative genetics of functional characters in Drosophila melanogaster populations subjected to laboratory selection

    Indian Academy of Sciences (India)

    Henrique Teotónio; Margarida Matos; Michael R. Rose

    2004-12-01

    What are the genetics of phenotypes other than fitness, in outbred populations? To answer this question, the quantitative-genetic basis of divergence was characterized for outbred Drosophila melanogaster populations that had previously undergone selection to enhance characters related to fitness. Line-cross analysis using first-generation and second-generation hybrids from reciprocal crosses was conducted for two types of cross, each replicated fivefold. One type of cross was between representatives of the ancestral population, a set of five populations maintained for several hundred generations on a two-week discrete-generation life cycle and a set of five populations adapted to starvation stress. The other type of cross was between the same set of ancestral-representative populations and another set of five populations selected for accelerated development from egg to egg. Developmental time from egg to eclosion, starvation resistance, dry body weight and fecundity at day 14 from egg were fit to regression models estimating single-locus additive and dominant effects, maternal and paternal effects, and digenic additive and dominance epistatic effects. Additive genetic variation explained most of the differences between populations, with additive maternal and cytoplasmic effects also commonly found. Both within-locus and between-locus dominance effects were inferred in some cases, as well as one instance of additive epistasis. Some of these effects may have been caused by linkage disequilibrium. We conclude with a brief discussion concerning the relationship of the genetics of population differentiation to adaptation.

  14. Genetic variability for morphological parameters in F2 segregating populations of rice

    International Nuclear Information System (INIS)

    This study was conducted to evaluate genetic variation among four parents and their 12 F2 populations for various morphological attributes at The University of Agriculture, Peshawar during 2012 rice crop growing season. Significant variation among the genotypes was manifested for all the traits studied. F /sub 2/ population Kashmir-Basmati/Kangni-27 manifested minimum days to heading (100) while the F /sub 2/ population Dilrosh/Kashmir-Basmati took minimum days to maturity (135). F /sub 2/ population Kashmir-Basmati /Dilrosh had the longest panicles (29.5 cm) while F /sub 2/ population Dilrosh/ Kashmir-Basmati excelled for number of primary (12.4) and secondary (35.9) branches panicle-1. Maximum broad sense heritability for panicle length (0.85), number of primary branches (0.87) and secondary branches (0.93) panicle-1 was observed for F /sub 2/ populations Kashmir-Basmati/Dilrosh, Dilrosh/Kangni-27 and Kashmir-Basmati/TN-1, respectively. F/sub 2/ population Kashmir-Basmati /Dilrosh showed the highest genetic advance for panicle length (22 percentage). F /sub 2/ population Dilrosh/Kangni-27 manifested maximum genetic advance (34.7 percentage) for primary branches panicle-1 while TN-1/ Kashmir-Basmati revealed the highest value (48.8 percentage) of genetic advance for secondary branches panicle-1. The above mentioned segregating populations on account of better performance for maturity and panicle traits could be advanced further to develop desirable recombinant inbred lines and rice cultivars. (author)

  15. Genetic Diversity Analysis of Lates calcarifer (Bloch 1790 in Captive and Wild Populations Using RAPD Markers

    Directory of Open Access Journals (Sweden)

    Muthusamy RAJASEKAR

    2012-08-01

    Full Text Available Lates calcarifer (Bloch 1790 is one of the major economically important cultivable fish species in India. In this study, three populations of L. calcarifer was selected to assess the genetic diversity. Of which, two wild (Mudaslodai, Muthupettai and one captive (Mutukadu population. The genetic diversity of three populations of this species was studied using Random Amplified Polymorphic DNA (RAPD markers. Ten random primers were used for the assessment of their genetic diversity and construction of the dendrogram. A total of 589 scorable bands were obtained, 93.12% of them were polymorphic. The Nei�s gene diversity (H of two wild populations were more (0.0504 � 0.0670 and 0.0519 � 0.0953 than the captive population (0.0489 � 0.0850. The clustering pattern obtained by UPGMA method emphasized the wild populations were clustered in one clade and captive population was deviated into another clade. This study proved that RAPD analysis has the ability to discriminate L. calcarifer populations. Further molecular studies, comprising a higher number of molecular tools are still required to precisely evaluate the genetic structure of all seabass populations along the Indian coast.

  16. Genetic structure and diversity of three Colombian southwest afrodescendent populations using 8 STR's

    International Nuclear Information System (INIS)

    To estimate the diversity, structure and genetic flow in three Colombian southwest afrodescendent populations (Buenaventura, Mulalo y Tumaco), the alleles revealed by 8 autosomal STR's were analyzed in 78 no-related individuals, by the use of PCR and comparison with specific allelic ladders for every system resolved by polyacrylamide gel (8%). the results were compared with 2 Amerindian populations (Awa-Kuaikier and Coyaima) and 2 mixed Colombian populations (Valle del Cauca and Cauca). For the afrodescendent and Amerindian populations was found moderate diversity (h between 0.768±0.414 and 0.796±0.424), in contrast, the mixed population showed higher rates (>0.803), which is probably caused by mixing with Amerindians, that also can explain the high endogamy seen in mixed populations. The AMOVA exhibited moderate genetic structure between the afrodescendent populations (FST= 0.098; p<0.05), but higher between the three ethnical groups compared (FST=0.26723; p<0.05). The closer genetics distances are in favor of Tumaco and Buenaventura, supported for the migration rate found (34.298), which was the same inside of Amerindian and mixed populations. Maybe, because Mulalo is a closed isolated population, its differences in front others afrodescendent populations are explained. The neighbor-joining tree showed nearest relations among Amerindian and mixed populations, furthermore, the ancestral character for the afrodescendents. That sustains the idea of genetic flow maintained between the 3 ethnical groups, principally between Amerindian and mixed populations, supported because the genetic differences, migration rates and Amerindian matrilineality reported in the literature

  17. Genetic variation within and among naturally regenerating populations of alder (Alnus glutinosa

    Directory of Open Access Journals (Sweden)

    Leon Mejnartowicz

    2011-04-01

    Full Text Available To assess the inter- and intrapopulation genetic variation in the filial generation (F1 of alder (Alnus glutinosa (L. Gaertn., 11 naturally regenerated populations were analysed. Their parental populations (P, represent the whole Polish territory and belong to three phytosociological associations with alder: typical alder swamp forest Carici elongatae-Alnetum (Ce-A; alder riparian forest Circaeo-Alnetum (C-A; and ash-elm riparian forest Fraxino-Ulmetum (F-U. F1 populations are grown in a common-garden experiment (provenance trial. Genotyping of individual trees has been carried out by analysis in a bud tissue allele frequency in the 21 isozyme putative loci of 10 enzymes. Differences between populations in respect to the level of genetic diversity were not high. Genetic diversity measured as the number of effective alleles per locus was the highest (Ne = 1.65 in population Wińsko originating from F-U (where also the inbreeding coefficient was the highest, F = 0.429, and the lowest (Ne = 1.48 in population Sławki from Ce-A. In all investigated populations, observed heterozygosity (Ho = 20% was lower than expected from H-W equilibrium (He = 29%. The highest genetic variation expressed as percentage of polymorphic loci (77.3% was observed in the offspring populations from Ce-A, and the smallest (69.9% in the populations originating from F-U. It seems that the low genetic differentiation between populations is probably connected with long-distance seed dispersal via river systems. Alder seed can be transported over long distances thanks to periodical flooding. There is some gene flow between alder populations, with about 2.5 immigrants successfully entering a population per generation (Nm = 2.55. The level of population subdivision within A. glutinosa was low (Fst = 0.089. There was no significant genetic differentiation between populations from different phytosociological associations. Mantel test exhibited no significant correlation (r = 0

  18. Clinical and pharmacogenomic implications of genetic variation in a Southern Ethiopian population.

    Science.gov (United States)

    Tekola-Ayele, F; Adeyemo, A; Aseffa, A; Hailu, E; Finan, C; Davey, G; Rotimi, C N; Newport, M J

    2015-02-01

    Africa is home to genetically diverse human populations. We compared the genetic structure of the Wolaita ethnic population from Southern Ethiopia (WETH, n=120) with HapMap populations using genome-wide variants. We investigated allele frequencies of 443 clinically and pharmacogenomically relevant genetic variants in WETH compared with HapMap populations. We found that WETH were genetically most similar to the Kenya Maasai and least similar to the Japanese in HapMap. Variant alleles associated with increased risk of adverse reactions to drugs used for treating tuberculosis (rs1799929 and rs1495741 in NAT2), thromboembolism (rs7294, rs9923231 and rs9934438 in VKORC1), and HIV/AIDS and solid tumors (rs2242046 in SLC28A1) had significantly higher frequencies in WETH compared with African ancestry HapMap populations. Our results illustrate that clinically relevant pharmacogenomic loci display allele frequency differences among African populations. We conclude that drug dosage guidelines for important global health diseases should be validated in genetically diverse African populations. PMID:25069476

  19. Structure and genetic diversity of natural Brazilian pepper populations (Schinus terebinthifolius Raddi).

    Science.gov (United States)

    Álvares-Carvalho, S V; Duarte, J F; Santos, T C; Santos, R M; Silva-Mann, R; Carvalho, D

    2016-01-01

    In the face of a possible loss of genetic diversity in plants due the environmental changes, actions to ensure the genetic variability are an urgent necessity. The extraction of Brazilian pepper fruits is a cause of concern because it results in the lack of seeds in soil, hindering its distribution in space and time. It is important to address this concern and explore the species, used by riparian communities and agro-factories without considering the need for keeping the seeds for natural seed banks and for species sustainability. The objective of this study was to evaluate the structure and the genetic diversity in natural Brazilian pepper populations (Schinus terebinthifolius Raddi). Twenty-two alleles in 223 individuals were identified from eight forest remnants located in the states of Minas Gerais, Espírito Santo, and Sergipe. All populations presented loci in Hardy-Weinberg equilibrium deviation. Four populations presented six combinations of loci in linkage disequilibrium. Six exclusive alleles were detected in four populations. Analysis of molecular variance showed the absence of diversity between regions and that between the populations (GST) was 41%. Genetic diversity was structured in seven clusters (ΔK7). Brazilian pepper populations were not structured in a pattern of isolation by distance and present genetic bottleneck. The populations São Mateus, Canastra, Barbacena, and Ilha das Flores were identified as management units and may support conservation projects, ecological restoration and in implementation of management plans for Brazilian pepper in the State of Sergipe. PMID:27323193

  20. Spatial and temporal dynamics of the genetic organization of small mammal populations

    International Nuclear Information System (INIS)

    A functional population is a group of organisms and their offspring that contributes to a common gene pool within a certain area and time period. It is also the unit of evolution and should be viewed both in quantitative and qualitative terms. Selection, drift, dispersal, and mutation can alter the composition of populations. Spatial heterogeneity in allele frequencies argues for a conceptual model that has a series of relatively small populations semi-isolated from one another. Because of the relatively high levels of genetic variability characteristic of most mammalian species, significant amounts of gene flow between these spatially subdivided populations must occur when longer time periods are considered. Fluctuations in the genetic structure of populations seem to be important in altering the fitness of the individuals within the populations. The interaction of populations through gene flow is important in changing the levels of intrapopulational genetic variability. Populations can be characterized as existing on a continuum from relatively stable to unstable numbers and by other associated changes in their characteristics. Temporal changes in allele frequency occur in a variety of mammals. Conceptually, a species can be viewed as a series of dynamic populations that vary in numbers and quality in both a spatial and temporal context even over short distances and time periods. Short term changes in the quality of individuals in a population can be important in altering the short term dynamics of a population

  1. Genetic gain in dairy cattle populations is increased using sexed semen in commercial herds

    DEFF Research Database (Denmark)

    Sørensen, Morten Kargo; Andersen, Jakob Voergaard; Pedersen, Louise Dybdahl;

    2011-01-01

    100 cows each. Each year 50 young bulls (YB), 10 active sires and 215 BD were selected on best linear unbiased prediction estimated breeding values by truncation selection across the simulated population, and the YB were tested within the population. Use of sexed semen alone gave a positive increase...... annual genetic gain by 1.8–2.5% compared with schemes without sexed semen and MOET on all BD. Performing MOET on all BD enables selection of offspring with high Mendelian deviations, which increase the annual genetic gain. Use of sexed semen decreased the genetic lag between the sires and the CD by 12...

  2. Morphological and genetic divergence in Swedish postglacial stickleback (Pungitius pungitius populations

    Directory of Open Access Journals (Sweden)

    Englund Göran

    2011-10-01

    Full Text Available Abstract Background An important objective of evolutionary biology is to understand the processes that govern phenotypic variation in natural populations. We assessed patterns of morphological and genetic divergence among coastal and inland lake populations of nine-spined stickleback in northern Sweden. Coastal populations are either from the Baltic coast (n = 5 or from nearby coastal lakes (n = 3 that became isolated from the Baltic Sea ( Results Coastal populations showed little variation in 11 morphological traits and had longer spines per unit of body length than inland populations. Inland populations were larger, on average, and showed greater morphological variation than coastal populations. A principal component analysis (PCA across all populations revealed two major morphological axes related to spine length (PC1, 47.7% variation and body size (PC2, 32.9% variation. Analysis of PCA scores showed marked similarity in coastal (Baltic coast and coastal lake populations. PCA scores indicate that inland populations with predators have higher within-group variance in spine length and lower within-group variance in body size than inland populations without predators. Estimates of within-group PST (a proxy for QST from PCA scores are similar to estimates of FST for coastal lake populations but PST >FST for Baltic coast populations. PST >FST for PC1 and PC2 for inland predator and inland no predator populations, with the exception that PST FST for body size in inland populations lacking predators. Conclusions Baltic coast and coastal lake populations show little morphological and genetic variation within and between groups suggesting that these populations experience similar ecological conditions and that time since isolation of coastal lakes has been insufficient to demonstrate divergent morphology in coastal lake populations. Inland populations, on the other hand, showed much greater morphological and genetic variation characteristic of long

  3. Genetic diversity affects the strength of population regulation in a marine fish.

    Science.gov (United States)

    Johnson, D W; Freiwald, J; Bernardi, G

    2016-03-01

    Variation is an essential feature of biological populations, yet much of ecological theory treats individuals as though they are identical. This simplifying assumption is often justified by the perception that variation among individuals does not have significant effects on the dynamics of whole populations. However, this perception may be skewed by a historic focus on studying single populations. A true evaluation of the extent to which among-individual variation affects the dynamics of populations requires the study of multiple populations. In this study, we examined variation in the dynamics of populations of a live-bearing, marine fish (black surfperch; Embiotoca jacksoni). In collaboration with an organization of citizen scientists (Reef Check California), we were able to examine the dynamics of eight populations that were distributed throughout approximately 700 km of coastline, a distance that encompasses much of this species' range. We hypothesized that genetic variation within a local population would be related to the intensity of competition and to the strength of population regulation. To test this hypothesis, we examined whether genetic diversity (measured by the diversity of mitochondrial DNA haplotypes) was related to the strength of population regulation. Low-diversity populations experienced strong density dependence in population growth rates and population sizes were regulated much more tightly than they were in high-diversity populations. Mechanisms that contributed to this pattern include links between genetic diversity, habitat use, and spatial crowding. On average, low-diversity populations used less of the available habitat and exhibited greater spatial clustering (and more intense competition) for a given level of density (measured at the scale of the reef). Although the populations we studied also varied with respect to exogenous characteristics (habitat complexity, densities of predators, and interspecific competitors), none of these

  4. Genetic structure of honeybee populations from southern Brazil and Uruguay

    OpenAIRE

    Nilza Maria Diniz; Ademilson Espencer Egea Soares,; Walter Steve Sheppard; Marco Antonio Del Lama

    2003-01-01

    Apis mellifera scutellata was introduced to Brazil in 1956 and Africanized honeybee populations have now spread from Argentina to the southwestern United States. Temperate climatic restrictions seem to be a natural limit to Africanized honeybee expansion around parallels 35° to 40° SL. We used allozyme loci (Mdh-1 and Hk-1) and mtDNA haplotypes to characterize honeybee populations in southern Brazil and Uruguay and define a possible transition area between Africanized and European bees. Sampl...

  5. Consultants Group Meeting on Genetic Sexing and Population Genetics of Screwworms. Working Material

    International Nuclear Information System (INIS)

    A Thematic Plan on SIT for Screwworms developed in 1999 by IPC and TC identified certain R and D bottlenecks to the expansion of this technology into new agricultural areas. This consultant's meeting was held to review these conclusions and to advise the Agency on the need, or otherwise, of initiating a CRP to address the bottlenecks identified in the Thematic Plan. In 2001 it is expected that the New World Screwworm, Cochliomyia hominivorax, will have been eradicated from all of Central America, including Panama where a sterile release barrier will be established to prevent re-invasion from South America. This barrier will need to be maintained indefinitely with its associated costs. The use of an all-male strain in the production facility would have very positive impact on the cost/benefit analysis of the programme. The Director of the Screwworm Programme in Central America made this point very strongly during the Thematic Plan discussions and at a subsequent technical meeting in Tuxtla Gutierrez. Interest to expand the programme into South America is now being shown by certain countries in the region where the economic feasibility of implementing an SIT programme might depend on producing sterile flies more economically and here again the use of a genetic sexing strain could play an important role. For the Old World Screwworm, Chrysomya bezziana the Australian authorities have just completed a successful small field trial of the SIT in Malaysia and it is proposed that more extensive field tests be carried out in the region. For both the New World Screwworm in South America and the Old World Screwworm, in Asia there is virtually no information regarding the population structure in relation to the implementation of an SIT programme. Is the Old World Screwworm a single species over its very wide distribution and are the populations of New World Screwworm in South America the same as in Central America and related to each other? Are the populations isolated? These

  6. Spatial genetic structure and mitochondrial DNA phylogeography of Argentinean populations of the grasshopper Dichroplus elongatus.

    Directory of Open Access Journals (Sweden)

    Natalia Rosetti

    Full Text Available Many grasshopper species are considered of agronomical importance because they cause damage to pastures and crops. Comprehension of pest population dynamics requires a clear understanding of the genetic diversity and spatial structure of populations. In this study we report on patterns of genetic variation in the South American grasshopper Dichroplus elongatus which is an agricultural pest of crops and forage grasses of great economic significance in Argentina. We use Direct Amplification of Minisatellite Regions (DAMD and partial sequences of the cytochrome oxydase 1 (COI mitochondrial gene to investigate intraspecific structure, demographic history and gene flow patterns in twenty Argentinean populations of this species belonging to different geographic and biogeographic regions. DAMD data suggest that, although genetic drift and migration occur within and between populations, measurable relatedness among neighbouring populations declines with distance and dispersal over distances greater than 200 km is not typical, whereas effective gene flow may occur for populations separated by less than 100 km. Landscape analysis was useful to detect genetic discontinuities associated with environmental heterogeneity reflecting the changing agroecosystem. The COI results indicate the existence of strong genetic differentiation between two groups of populations located at both margins of the Paraná River which became separated during climate oscillations of the Middle Pleistocene, suggesting a significant restriction in effective dispersion mediated by females and large scale geographic differentiation. The number of migrants between populations estimated through mitochondrial and DAMD markers suggest that gene flow is low prompting a non-homogeneous spatial structure and justifying the variation through space. Moreover, the genetic analysis of both markers allows us to conclude that males appear to disperse more than females, reducing the chance of the

  7. Genetic structure and phylogenetic relationships of Colombian Trypanosoma cruzi populations as determined by schizodeme and isoenzyme markers.

    Science.gov (United States)

    Jaramillo, N; Moreno, J; Triana, O; Arcos-Burgos, M; Muñoz, S; Solari, A

    1999-12-01

    Twenty-four Trypanosoma cruzi stocks isolated from vectors and from human and Didelphis marsupialis hosts from highly separated sylvatic localities in Colombia were characterized by isoenzyme and schizodeme analyses. The stocks were collected primarily from sylvatic ecotopes representing areas of low, moderate, and high endemicity for Chagas' diseases in Colombia. Parasites were characterized mainly by schizodeme analysis with the restriction enzyme Eco RI and the isoenzyme analysis was performed at 10 genetic loci. These analyses demonstrated an agreement between the classifications based on the isoenzyme analysis and on the restriction fragment length polymorphism patterns obtained with the Colombian stocks. There is clear evidence of demic subdivision between the eastern (E) and western (W) stocks separated by the Andean Mountains and Magdalena River, which is likely due to the geographic isolation generated by these topographic features. Heterozygosity estimates indicate that the E group could be more ancient than the W group. As was postulated in a previous study, these results are also compatible with the existence of a clonal population structure in Colombian sylvatic T. cruzi. Evidence presented here failed to demonstrate a correlation between the degree of endemy and genetic clustering. Finally, schizodeme and isoenzymatic analyses comparing Colombian T. cruzi stocks with others from Chile confirm that Colombian isolates are genetically related to zymodeme 1 and distant from zymodeme 2. PMID:10674683

  8. Genetic Drift Suppresses Bacterial Conjugation in Spatially Structured Populations

    Science.gov (United States)

    Freese, Peter D.; Korolev, Kirill S.; Jiménez, José I.; Chen, Irene A.

    2014-02-01

    Conjugation is the primary mechanism of horizontal gene transfer that spreads antibiotic resistance among bacteria. Although conjugation normally occurs in surface-associated growth (e.g., biofilms), it has been traditionally studied in well-mixed liquid cultures lacking spatial structure, which is known to affect many evolutionary and ecological processes. Here we visualize spatial patterns of gene transfer mediated by F plasmid conjugation in a colony of Escherichia coli growing on solid agar, and we develop a quantitative understanding by spatial extension of traditional mass-action models. We found that spatial structure suppresses conjugation in surface-associated growth because strong genetic drift leads to spatial isolation of donor and recipient cells, restricting conjugation to rare boundaries between donor and recipient strains. These results suggest that ecological strategies, such as enforcement of spatial structure and enhancement of genetic drift, could complement molecular strategies in slowing the spread of antibiotic resistance genes.

  9. Low genetic diversity and minimal population substructure in the endangered Florida manatee: implications for conservation

    Science.gov (United States)

    Tucker, Kimberly Pause; Hunter, Margaret E.; Bonde, Robert K.; Austin, James D.; Clark, Ann Marie; Beck, Cathy A.; McGuire, Peter M.; Oli, Madan K.

    2012-01-01

    Species of management concern that have been affected by human activities typically are characterized by low genetic diversity, which can adversely affect their ability to adapt to environmental changes. We used 18 microsatellite markers to genotype 362 Florida manatees (Trichechus manatus latirostris), and investigated genetic diversity, population structure, and estimated genetically effective population size (Ne). The observed and expected heterozygosity and average number of alleles were 0.455 ± 0.04, 0.479 ± 0.04, and 4.77 ± 0.51, respectively. All measures of Florida manatee genetic diversity were less than averages reported for placental mammals, including fragmented or nonideal populations. Overall estimates of differentiation were low, though significantly greater than zero, and analysis of molecular variance revealed that over 95% of the total variance was among individuals within predefined management units or among individuals along the coastal subpopulations, with only minor portions of variance explained by between group variance. Although genetic issues, as inferred by neutral genetic markers, appear not to be critical at present, the Florida manatee continues to face demographic challenges due to anthropogenic activities and stochastic factors such as red tides, oil spills, and disease outbreaks; these can further reduce genetic diversity of the manatee population.

  10. Genetic variability in captive populations of the stingless bee Tetragonisca angustula.

    Science.gov (United States)

    Santiago, Leandro R; Francisco, Flávio O; Jaffé, Rodolfo; Arias, Maria C

    2016-08-01

    Low genetic variability has normally been considered a consequence of animal husbandry and a major contributing factor to declining bee populations. Here, we performed a molecular analysis of captive and wild populations of the stingless bee Tetragonisca angustula, one of the most commonly kept species across South America. Microsatellite analyses showed similar genetic variability between wild and captive populations However, captive populations showed lower mitochondrial genetic variability. Male-mediated gene flow, transport and division of nests are suggested as the most probable explanations for the observed patterns of genetic structure. We conclude that increasing the number of colonies kept through nest divisions does not negatively affect nuclear genetic variability, which seems to be maintained by small-scale male dispersal and human-mediated nest transport. However, the transport of nests from distant localities should be practiced with caution given the high genetic differentiation observed between samples from western and eastern areas. The high genetic structure verified is the result of a long-term evolutionary process, and bees from distant localities may represent unique evolutionary lineages. PMID:27305916

  11. Coupling genetic and ecological-niche models to examine how past population distributions contribute to divergence.

    Science.gov (United States)

    Knowles, L Lacey; Carstens, Bryan C; Keat, Marcia L

    2007-06-01

    Understanding the impact of climate-induced distributional shifts on species divergence, like those accompanying the Pleistocene glacial cycles [1, 2], requires tools that explicitly incorporate the geographic configuration of past distributions into analyses of genetic differentiation. Depending on the historical distribution of species, genetic differences may accumulate among ancestral source populations, but there is long-standing debate whether displacements into glacial refugia promoted divergence. Here we integrate coalescent-based genetic models [3, 4] with ecological-niche modeling [5, 6] to generate expectations for patterns of genetic variation based on an inferred past distribution of a species. Reconstruction of the distribution of a montane grasshopper species during the last glacial maximum suggests that Melanoplus marshalli populations from the sky islands of Colorado and Utah were likely colonized from multiple ancestral source populations. The genetic analyses provide compelling evidence that the historical distribution of M. marshalli-namely, spatial separation of multiple refugia-was conducive to genetic differentiation. The coupling of genetic and ecological-niche modeling provides a new and flexible tool for integrating paleoenvironmental details into species-specific predictions of population structure that can increase our understanding of why the glacial cycles promoted speciation in some taxa and yet inhibited diversification in others [7, 8]. PMID:17475496

  12. Behavior of different numerical schemes for population genetic drift problems

    OpenAIRE

    Chen, Minxin; Liu, Chun; Xu, Shixin; Yue, Xingye; Zhang, Ran

    2014-01-01

    In this paper, we focus on numerical methods for the genetic drift problems, which is governed by a degenerated convection-dominated parabolic equation. Due to the degeneration and convection, Dirac singularities will always be developed at boundary points as time evolves. In order to find a \\emph{complete solution} which should keep the conservation of total probability and expectation, three different schemes based on finite volume methods are used to solve the equation numerically: one is ...

  13. Genetic relationships within Czech sika and red deer populations

    Czech Academy of Sciences Publication Activity Database

    Barančeková, Miroslava; Krojerová-Prokešová, Jarmila; Vallo, Peter; Voloshina, I. V.; Igota, H.; Koubek, Petr

    Moscow : IUGB, 2009, s. 1-6. ISBN 978-5-7035-2118-2. [IUGB Congress /29./. Moscow (RU), 17.08.2009-22.08.2009] R&D Projects: GA ČR GA524/09/1569; GA MŠk LC06073 Institutional research plan: CEZ:AV0Z60930519 Keywords : sika deer * red deer Subject RIV: EB - Genetics ; Molecular Biology http://www.iugb-moscow2009.ru/cd/docs/ps/M.Barancekova.pdf

  14. Genetic diversity of macauba from natural populations of Brazil

    OpenAIRE

    da Conceição, Léo Duc Haa Carson Schwartzhaupt; Antoniassi, Rosemar; Junqueira, Nilton Tadeu Vilela; Braga, Marcelo Fideles; de Faria-Machado, Adelia Ferreira; Rogério, Joice Barbosa; Duarte, Iara Duprat; Bizzo, Humberto Ribeiro

    2015-01-01

    Background The macauba has been identified as the most promising native species for the production of vegetable oil and biomass. Several studies confirm its potential for numerous purposes (liquid and solid biofuels, food, cosmetics and pharmaceuticals), but this Brazilian biodiversity resource has been little explored, and work aimed at their domestication and genetic improvement are relatively recent. This study consisted of a multivariate approach to levels of trans fatty acids, oil yield ...

  15. Multi Population Hybrid Genetic Algorithms for University Course Timetabling Problem

    Directory of Open Access Journals (Sweden)

    Leila Jadidi

    2012-06-01

    Full Text Available University course timetabling is one of the important and time consuming issues that each University is involved with it at the beginning of each. This problem is in class of NP-hard problem and is very difficult to solve by classic algorithms. Therefore optimization techniques are used to solve them and produce optimal or near optimal feasible solutions instead of exact solutions. Genetic algorithms, because of multidirectional search property of them, are considered as an efficient approach for solving this type of problems. In this paper three new hybrid genetic algorithms for solving the university course timetabling problem (UCTP are proposed: FGARI, FGASA and FGATS. In proposed algorithms, fuzzy logic is used to measure violation of soft constraints in fitness function to deal with inherent uncertainly and vagueness involved in real life data. Also, randomized iterative local search, simulated annealing and tabu search are applied, respectively, to improve exploitive search ability and prevent genetic algorithm to be trapped in local optimum. The experimental results indicate that the proposed algorithms are able to produce promising results for the UCTP.

  16. Multi Population Hybrid Genetic Algorithms for University Course Timetabling

    Directory of Open Access Journals (Sweden)

    Mehrnaz Shirani LIRI

    2012-08-01

    Full Text Available University course timetabling is one of the important and time consuming issues that each University is involved with at the beginning of each university year. This problem is in class of NP-hard problem and is very difficult to solve by classic algorithms. Therefore optimization techniques are used to solve them and produce optimal or almost optimal feasible solutions instead of exact solutions. Genetic algorithms, because of their multidirectional search property, are considered as an efficient approach for solving this type of problems. In this paper three new hybrid genetic algorithms for solving the university course timetabling problem (UCTP are proposed: FGARI, FGASA and FGATS. In the proposed algorithms, fuzzy logic is used to measure violation of soft constraints in fitness function to deal with inherent uncertainty and vagueness involved in real life data. Also, randomized iterative local search, simulated annealing and tabu search are applied, respectively, to improve exploitive search ability and prevent genetic algorithm to be trapped in local optimum. The experimental results indicate that the proposed algorithms are able to produce promising results for the UCTP

  17. Microsatellite based genetic diversity and population structure of the endangered Spanish Guadarrama goat breed

    Directory of Open Access Journals (Sweden)

    Jurado Juan J

    2009-09-01

    Full Text Available Abstract Background Assessing genetic biodiversity and population structure of minor breeds through the information provided by neutral molecular markers, allows determination of their extinction risk and to design strategies for their management and conservation. Analysis of microsatellite loci is known to be highly informative in the reconstruction of the historical processes underlying the evolution and differentiation of animal populations. Guadarrama goat is a threatened Spanish breed which actual census (2008 consists of 3057 females and 203 males distributed in 22 populations more or less isolated. The aim of this work is to study the genetic status of this breed through the analysis of molecular data from 10 microsatellites typed in historic and actual live animals. Results The mean expected heterozygosity across loci within populations ranged from 0.62 to 0.77. Genetic differentiation measures were moderate, with a mean FST of 0.074, GST of 0.081 and RST of 0.085. Percentages of variation among and within populations were 7.5 and 92.5, respectively. Bayesian clustering analyses pointed out a population subdivision in 16 clusters, however, no correlation between geographical distances and genetic differences was found. Management factors such as the limited exchange of animals between farmers (estimated gene flow Nm = 3.08 mostly due to sanitary and social constraints could be the major causes affecting Guadarrama goat population subdivision. Conclusion Genetic diversity measures revealed a good status of biodiversity in the Guadarrama goat breed. Since diseases are the first cause affecting the census in this breed, population subdivision would be an advantage for its conservation. However, to maintain private alleles present at low frequencies in such small populations minimizing the inbreeding rate, it would necessitate some mating designs of animals carrying such alleles among populations. The systematic use of molecular markers will

  18. Genetic diversity and population structure of the Guinea pig (Cavia porcellus, Rodentia, caviidae in Colombia

    Directory of Open Access Journals (Sweden)

    William Burgos-Paz

    2011-01-01

    Full Text Available The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven production zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allelic richness ranging from 3.0 to 6.56, and observed heterozygosity (Ho from 0.33 to 0.60, with a deficit in heterozygous individuals. Although statistically significant (p < 0.05, genetic differentiation between population pairs was found to be low. Genetic distance, as well as clustering of guinea-pig lines and populations, coincided with the historical and geographical distribution of the populations. Likewise, high genetic identity between improved and native lines was established. An analysis of group probabilistic assignment revealed that each line should not be considered as a genetically homogeneous group. The findings corroborate the absorption of native genetic material into the improved line introduced into Colombia from Peru. It is necessary to establish conservation programs for native-line individuals in Nariño, and control genealogical and production records in order to reduce the inbreeding values in the populations.

  19. Population Genetic Structure of the Endangered Kaiser's Mountain Newt, Neurergus kaiseri (Amphibia: Salamandridae.

    Directory of Open Access Journals (Sweden)

    Hossein Farasat

    Full Text Available Species often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in an endemic and critically endangered stream breeding mountain newt, Neurergus kaiseri, within its entire range in southwestern Iran. We identified two geographic regions based on phylogenetic relationships using Bayesian inference and maximum likelihood of 779 bp mtDNA (D-loop in 111 individuals from ten of twelve known breeding populations. This analysis revealed a clear divergence between northern populations, located in more humid habitats at higher elevation, and southern populations, from drier habitats at lower elevations regions. From seven haplotypes found in these populations none was shared between the two regions. Analysis of molecular variance (AMOVA of N. kaiseri indicates that 94.03% of sequence variation is distributed among newt populations and 5.97% within them. Moreover, a high degree of genetic subdivision, mainly attributable to the existence of significant variance among the two regions is shown (θCT = 0.94, P = 0.002. The positive and significant correlation between geographic and genetic distances (r = 0.61, P = 0.002 following controlling for environmental distance suggests an important influence of geographic divergence of the sites in shaping the genetic variation and may provide tools for a possible conservation based prioritization policy for the endangered species.

  20. Population genetic analysis and trichothecene profiling of Fusarium graminearum from wheat in Uruguay.

    Science.gov (United States)

    Pan, D; Mionetto, A; Calero, N; Reynoso, M M; Torres, A; Bettucci, L

    2016-01-01

    Fusarium graminearum sensu stricto (F. graminearum s.s.) is the major causal agent of Fusarium head blight of wheat worldwide, and contaminates grains with trichothecene mycotoxins that cause serious threats to food safety and animal health. An important aspect of managing this pathogen and reducing mycotoxin contamination of wheat is knowledge regarding its population genetics. Therefore, isolates of F. graminearum s.s. from the major wheat-growing region of Uruguay were analyzed by amplified fragment length polymorphism assays, PCR genotyping, and chemical analysis of trichothecene production. Of the 102 isolates identified as having the 15-ADON genotype via PCR genotyping, all were DON producers, but only 41 strains were also 15-ADON producers, as determined by chemical analysis. The populations were genotypically diverse but genetically similar, with significant genetic exchange occurring between them. Analysis of molecular variance indicated that most of the genetic variability resulted from differences between isolates within populations. Multilocus linkage disequilibrium analysis suggested that the isolates had a panmictic population genetic structure and that there is significant recombination occurs in F. graminearum s.s. In conclusion, tour findings provide the first detailed description of the genetic structure and trichothecene production of populations of F. graminearum s.s. from Uruguay, and expands our understanding of the agroecology of F. graminearum and of the correlation between genotypes and trichothecene chemotypes. PMID:26985955

  1. An investigation of the statistical power of neutrality tests based on comparative and population genetic data

    DEFF Research Database (Denmark)

    Zhai, Weiwei; Nielsen, Rasmus; Slatkin, Montgomery

    2009-01-01

    In this report, we investigate the statistical power of several tests of selective neutrality based on patterns of genetic diversity within and between species. The goal is to compare tests based solely on population genetic data with tests using comparative data or a combination of comparative...... and population genetic data. We show that in the presence of repeated selective sweeps on relatively neutral background, tests based on the d(N)/d(S) ratios in comparative data almost always have more power to detect selection than tests based on population genetic data, even if the overall level of divergence...... is low. Tests based solely on the distribution of allele frequencies or the site frequency spectrum, such as the Ewens-Watterson test or Tajima's D, have less power in detecting both positive and negative selection because of the transient nature of positive selection and the weak signal left by negative...

  2. Ethical considerations of population screening for late-onset genetic disease.

    Science.gov (United States)

    Golden-Grant, K; Merritt, J L; Scott, C R

    2015-12-01

    Population-based genetic screening has been a mainstay of public health in the United States for many years. The goal of genetic screening is to identify individuals at increased risk for treatable diseases. The evolution of genetic testing to include multi-disease panels allows for new screening applications which challenge the traditional model of clinical genetics care by the identification of late-onset disorders in an asymptomatic fetus, child, or adult. We present two unique examples of individuals referred to a biochemical genetics clinic due to the detection of late-onset Pompe disease by population-based screening modalities. We review early experiences in counseling and management of pre-symptomatic individuals and highlight some of the primary ethical factors warranting consideration as we enter the era of genomic medicine. PMID:25677830

  3. Uncovering the genetic history of the present-day greenlandic population

    DEFF Research Database (Denmark)

    Moltke, Ida; Fumagalli, Matteo; Korneliussen, Thorfinn Sand; Crawford, Jacob E; Bjerregaard, Peter; Jørgensen, Marit E; Grarup, Niels; Gulløv, Hans Christian; Linneberg, Allan René; Pedersen, Oluf Borbye; Hansen, Torben; Nielsen, Rasmus; Albrechtsen, Anders

    2015-01-01

    Because of past limitations in samples and genotyping technologies, important questions about the history of the present-day Greenlandic population remain unanswered. In an effort to answer these questions and in general investigate the genetic history of the Greenlandic population, we analyzed...

  4. Erythropoietin in the General Population : Reference Ranges and Clinical, Biochemical and Genetic Correlates

    NARCIS (Netherlands)

    Grote Beverborg, Niels; Verweij, Niek; Klip, IJsbrand T.; van der Wal, Haye H.; Voors, Adriaan A.; van Veldhuisen, Dirk J.; Gansevoort, Ron T.; Bakker, Stephan J. L.; van der Harst, Pim; van der Meer, Peter

    2015-01-01

    Background Although erythropoietin has been used for decades in the treatment of anemia, data regarding endogenous levels in the general population are scarce. Therefore, we determined erythropoietin reference ranges and its clinical, biochemical and genetic associations in the general population. M

  5. Population genetic diversity of sesarmid crab (Perisesarma bidens) in China based on mitochondrial DNA.

    Science.gov (United States)

    Zhou, Haolang; Xu, Jingming; Yang, Mingliu; Wu, Bin; Yan, Bing; Xiong, Yingze

    2016-09-01

    The population genetic diversity of Perisesarma bidens in China was investigated using 627 bp fragment of mtDNA COI gene sequence. A total of 186 individuals were collected from ten localities over most of the species' range and 31 different haplotypes were obtained. The most frequent haplotype was Hap2, which was shared in all ten localities (132 individuals), whereas most haplotypes were rare and existed in only one or two individuals. Haplotype diversity (h) and nucleotide diversity (π) ranged from 0.338 to 0.731 and from 0.00058 to 0.00278, respectively, which represented a moderate level of haplotype diversity and a low level of nucleotide diversity. The genetic distance ranged from 0.0006 to 0.0028 within populations and from 0.0006 to 0.0023 between populations. An analysis of molecular variance and conventional population statistics (FST) revealed a low level of genetic differentiation among ten populations (FST = -0.00439, p > 0.05), indicating that no significant population genetic structure existed in populations from the East China Sea and South China Sea. Both mismatch distribution and neutrality tests implied a recent population expansion event for the sesarmid crab species in the late Pleistocene. PMID:25693695

  6. Estimates of genetic parameters for kyphosis in two crossbred swine populations

    Science.gov (United States)

    Genetic parameters for degree of kyphosis were estimated from a Duroc-Landrace F2 population (n = 316) and from a composite population (Line C) composed of Duroc, Large White, and two sources of Landrace (n = 1,552). Live presentation did not indicate kyphosis in pigs or sows. Degree of kyphosis was...

  7. Microsatellite analysis reveals genetically distinct populations of red pine (Pinus resinosa, Pinaceae).

    Science.gov (United States)

    Boys, Jacquelyn; Cherry, Marilyn; Dayanandan, Selvadurai

    2005-05-01

    Red pine (Pinus resinosa Ait.) is an ecologically and economically important forest tree species of northeastern North America and is considered one of the most genetically depauperate conifer species in the region. We have isolated and characterized 13 nuclear microsatellite loci by screening a partial genomic library with di-, tri-, and tetranucleotide repeat oligonucleotide probes. In an analysis of over 500 individuals representing 17 red pine populations from Manitoba through Newfoundland, five polymorphic microsatellite loci with an average of nine alleles per locus were identified. The mean expected and observed heterozygosity values were 0.508 and 0.185, respectively. Significant departures from Hardy-Weinberg equilibrium with excess homozygosity indicating high levels of inbreeding were evident in all populations studied. The population differentiation was high with 28-35% of genetic variation partitioned among populations. The genetic distance analysis showed that three northeastern (two Newfoundland and one New Brunswick) populations are genetically distinct from the remaining populations. The coalescence-based analysis suggests that "northeastern" and "main" populations likely became isolated during the most recent Pleistocene glacial period, and severe population bottlenecks may have led to the evolution of a highly selfing mating system in red pine. PMID:21652464

  8. SNP identification, verification, and utility for population genetics in a non-model genus

    Directory of Open Access Journals (Sweden)

    Bustamante Carlos D

    2010-04-01

    Full Text Available Abstract Background By targeting SNPs contained in both coding and non-coding areas of the genome, we are able to identify genetic differences and characterize genome-wide patterns of variation among individuals, populations and species. We investigated the utility of 454 sequencing and MassARRAY genotyping for population genetics in natural populations of the teleost, Fundulus heteroclitus as well as closely related Fundulus species (F. grandis, F. majalis and F. similis. Results We used 454 pyrosequencing and MassARRAY genotyping technology to identify and type 458 genome-wide SNPs and determine genetic differentiation within and between populations and species of Fundulus. Specifically, pyrosequencing identified 96 putative SNPs across coding and non-coding regions of the F. heteroclitus genome: 88.8% were verified as true SNPs with MassARRAY. Additionally, putative SNPs identified in F. heteroclitus EST sequences were verified in most (86.5% F. heteroclitus individuals; fewer were genotyped in F. grandis (74.4%, F. majalis (72.9%, and F. similis (60.7% individuals. SNPs were polymorphic and showed latitudinal clinal variation separating northern and southern populations and established isolation by distance in F. heteroclitus populations. In F. grandis, SNPs were less polymorphic but still established isolation by distance. Markers differentiated species and populations. Conclusions In total, these approaches were used to quickly determine differences within the Fundulus genome and provide markers for population genetic studies.

  9. Global population genetic structure and biogeography of the oceanic copepods Eucalanus hyalinus and E. spinifer

    DEFF Research Database (Denmark)

    Goetze, Erica

    2005-01-01

    Although theory dictates that limited gene flow between populations is a necessary precursor to speciation under allopatric and parapatric models, it is currently unclear how genetic differentiation between conspecific populations can arise in open-ocean plankton species. I examined two recently ...

  10. Population genetics at three spatial scales of a rare sponge living in fragmented habitats

    Directory of Open Access Journals (Sweden)

    Uriz Maria J

    2010-01-01

    Full Text Available Abstract Background Rare species have seldom been studied in marine habitats, mainly because it is difficult to formally assess the status of rare species, especially in patchy benthic organisms, for which samplings are often assumed to be incomplete and, thus, inappropriate for establishing the real abundance of the species. However, many marine benthic invertebrates can be considered rare, due to the fragmentation and rarity of suitable habitats. Consequently, studies on the genetic connectivity of rare species in fragmented habitats are basic for assessing their risk of extinction, especially in the context of increased habitat fragmentation by human activities. Sponges are suitable models for studying the intra- and inter-population genetic variation of rare invertebrates, as they produce lecitotrophic larvae and are often found in fragmented habitats. Results We investigated the genetic structure of a Mediterranean sponge, Scopalina lophyropoda (Schmidt, using the allelic size variation of seven specific microsatellite loci. The species can be classified as "rare" because of its strict habitat requirements, the low number of individuals per population, and the relatively small size of its distribution range. It also presents a strong patchy distribution, philopatric larval dispersal, and both sexual and asexual reproduction. Classical genetic-variance-based methods (AMOVA and differentiation statistics revealed that the genetic diversity of S. lophyropoda was structured at the three spatial scales studied: within populations, between populations of a geographic region, and between isolated geographic regions, although some stochastic gene flow might occur among populations within a region. The genetic structure followed an isolation-by-distance pattern according to the Mantel test. However, despite philopatric larval dispersal and fission events in the species, no single population showed inbreeding, and the contribution of clonality to the

  11. Unexpectedly low rangewide population genetic structure of the imperiled eastern box turtle Terrapene c. carolina.

    Directory of Open Access Journals (Sweden)

    Steven J A Kimble

    Full Text Available Rangewide studies of genetic parameters can elucidate patterns and processes that operate only over large geographic scales. Herein, we present a rangewide population genetic assessment of the eastern box turtle Terrapene c. carolina, a species that is in steep decline across its range. To inform conservation planning for this species, we address the hypothesis that disruptions to demographic and movement parameters associated with the decline of the eastern box turtle has resulted in distinctive genetic signatures in the form of low genetic diversity, high population structuring, and decreased gene flow. We used microsatellite genotype data from (n = 799 individuals from across the species range to perform two Bayesian population assignment approaches, two methods for comparing historical and contemporary migration among populations, an evaluation of isolation by distance, and a method for detecting barriers to gene flow. Both Bayesian methods of population assignment indicated that there are two populations rangewide, both of which have maintained high levels of genetic diversity (HO = 0.756. Evidence of isolation by distance was detected in this species at a spatial scale of 300-500 km, and the Appalachian Mountains were identified as the primary barrier to gene flow across the species range. We also found evidence for historical but not contemporary migration between populations. Our prediction of many, highly structured populations across the range was not supported. This may point to cryptic contemporary gene flow, which might in turn be explained by the presence of rare transients in populations. However these data may be influenced by historical signatures of genetic connectivity because individuals of this species can be long-lived.

  12. Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

    Science.gov (United States)

    Greenbaum, Gili; Templeton, Alan R; Bar-David, Shirli

    2016-04-01

    Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition's modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of

  13. Patterns of genetic and reproductive traits differentiation in Mainland vs. Corsican populations of bumblebees.

    Directory of Open Access Journals (Sweden)

    Thomas Lecocq

    Full Text Available Populations on islands often exhibit lower levels of genetic variation and ecomorphological divergence compared to their mainland relatives. While phenotypic differentiation in characters, such as size or shape among insular organisms, has been well studied, insular differentiation in quantitative reproductive traits involved in chemical communication has received very little attention to date. Here, we investigated the impact of insularity on two syntopic bumblebee species pairs: one including species that are phylogenetically related (Bombus terrestris and B. lucorum, and the other including species that interact ecologically (B. terrestris and its specific nest inquiline B. vestalis. For each bumblebee species, we characterized the patterns of variation and differentiation of insular (Corsican vs. mainland (European populations (i with four genes (nuclear and mitochondrial, 3781 bp and (ii in the chemical composition of male marking secretions (MMS, a key trait for mate attraction in bumblebees, by gas chromatography-mass spectrometry (GC-MS. Our results provide evidence for genetic differentiation in Corsican bumblebees and show that, contrary to theoretical expectations, island populations of bumblebees exhibit levels of genetic variation similar to the mainland populations. Likewise, our comparative chemical analyses of MMS indicate that Corsican populations of bumblebees are significantly differentiated from the mainland yet they hold comparative levels of within-population MMS variability compared to the mainland. Therefore, insularity has led Corsican populations to diverge both genetically and chemically from their mainland relatives, presumably through genetic drift, but without a decrease of genetic diversity in island populations. We hypothesize that MMS divergence in Corsican bumblebees was driven by a persistent lack of gene flow with mainland populations and reinforced by the preference of Corsican females for sympatric (Corsican

  14. Unexpectedly low rangewide population genetic structure of the imperiled eastern box turtle Terrapene c. carolina.

    Science.gov (United States)

    Kimble, Steven J A; Rhodes, O E; Williams, Rod N

    2014-01-01

    Rangewide studies of genetic parameters can elucidate patterns and processes that operate only over large geographic scales. Herein, we present a rangewide population genetic assessment of the eastern box turtle Terrapene c. carolina, a species that is in steep decline across its range. To inform conservation planning for this species, we address the hypothesis that disruptions to demographic and movement parameters associated with the decline of the eastern box turtle has resulted in distinctive genetic signatures in the form of low genetic diversity, high population structuring, and decreased gene flow. We used microsatellite genotype data from (n = 799) individuals from across the species range to perform two Bayesian population assignment approaches, two methods for comparing historical and contemporary migration among populations, an evaluation of isolation by distance, and a method for detecting barriers to gene flow. Both Bayesian methods of population assignment indicated that there are two populations rangewide, both of which have maintained high levels of genetic diversity (HO = 0.756). Evidence of isolation by distance was detected in this species at a spatial scale of 300-500 km, and the Appalachian Mountains were identified as the primary barrier to gene flow across the species range. We also found evidence for historical but not contemporary migration between populations. Our prediction of many, highly structured populations across the range was not supported. This may point to cryptic contemporary gene flow, which might in turn be explained by the presence of rare transients in populations. However these data may be influenced by historical signatures of genetic connectivity because individuals of this species can be long-lived. PMID:24647580

  15. Genetic and morphometric differences between yellowtail snapper (Ocyurus chrysurus, Lutjanidae populations of the tropical West Atlantic

    Directory of Open Access Journals (Sweden)

    Anderson V. Vasconcellos

    2008-01-01

    Full Text Available Populations of Ocyurus chrysurus were compared genetically and morphometrically along the West Atlantic coast to test the null hypothesis of population homogeneity in the area. Brazilian populations were found to be differentiated in shape (canonical variates analysis; F[48,515] = 10.84, p < 0.0001. Analyses of mitochondrial DNA sequences (663 bp of the control region did not show any differences between Brazilian populations but could detect differences between Brazilian and Caribbean (Belize populations. The samples from Pernambuco differed significantly from the other Brazilian populations in allozyme frequencies (11 loci; F ST = 0.167; p < 0.05, but this may have resulted from the small number of samples analysed for that population. Sequence variation of Belize samples departed from neutral expectations (Fu's FS = -8.88; p < 0.001. A mismatch distribution analysis points to an ancient population expansion in that area. We conclude that the genetic data do not allow the rejection of the null hypothesis of panmixia for Brazilian yellowtail snapper populations which should be treated as a single genetic stock, with a latitudinal gradient on their morphology which probably results from phenotypic plasticity. On the other hand, there is a severe restriction to gene flow between O. chrysurus populations from the Caribbean and from the southwestern Atlantic.

  16. Genetic diversity of Quercus glandulifera var. brevipetiolata populations in three forest communities with different succession stages

    Institute of Scientific and Technical Information of China (English)

    Junmin LI; Zexin JIN; Qiping GU; Wenyan LOU

    2009-01-01

    In order to understand the relationship between population succession and its genetic behavior, random amplified polymorphic DNA (RAPD) technique was used to analyze the genetic diversity of Quercu glandulifera var.brevipetiolata populations in three forest communities with different succession stages (coniferous forest, coniferous and broad-leaved mixed forest, evergreen broad-leaved forest). The results showed that 145 repetitive loci were produced in 60 individuals of Q. glandulifera using 11 primers, among which 120 loci were polymorphic, and the total percentage of polymorphic loci was 82.76% with an average of 64.14%. Estimated by the Shannon information index, the total genetic diversity of the three populations was 0.4747, with an average of 0.3642, while it was 0.3234, with an average of 0.2484, judged from the Nei index. Judged from percentage of polymorphic loci,Shannon inform at ion index and Nei index, the genetic diversity followed a decreasing order: coniferous forest >broad-leaved mixed forest > evergreen broad-leaved for-est. Analysis of molecular variance (AMOVA) showed that 69.73% of the genetic variance existed within populations and 30.27% of the genetic variance existed among popu-lations. The coefficient of gene differentiation (Gst) was 0.2319 and the gene flow (Nm) was 1.6539. The mean of genetic identity among populations of Q. glandulifera was 0.8501 and the mean of genetic distance was 0.1626. The genetic identity between the Q. glandulifera population in the coniferous forest and that in the coniferous and broad-leaved mixed forest was the highest. UPGMA cluster analysis based on Nei's genetic distance showed that the population in the coniferous forest gathered with that in the coniferous and broad-leaved mixed forest firstly, then with that in the evergreen broad-leaved forest. The genetic structure of Q. glandulifera was not only characteristic of the biological characteristics of this species, but was also influenced by the

  17. Polygyny and strong genetic structuring within an isolated population of the wood ant Formica rufa

    Directory of Open Access Journals (Sweden)

    Wouter Dekoninck

    2014-12-01

    Full Text Available Social structuring of populations within some Formica species exhibits considerable variation going from monodomous and monogynous populations to polydomous, polygynous populations. The wood ant species Formica rufa appears to be mainly monodomous and monogynous throughout most of its distribution area in central and northern Europe. Only occasionally it was mentioned that F. rufa can have both polygynous and monogynous colonies in the same geographical region. We studied an isolated polydomous F. rufa population in a deciduous mixed forest in the north-west of Belgium. The level of polydomy within the colonies varied from monodomous to 11 nests per colony. Our genetic analysis of eight variable microsatellites suggest an oligo- to polygynous structure for at least the major part of the sampled nests. Relatedness amongst nest mate workers varies considerable within the population and colonies but confirms in general a polygynous structure. Additionally high genetic diversity (e.g. up to 8 out of 11 alleles per nest for the most variable locus and high within nest genetic variance (93% indicate that multiple queens contribute to the gene pool of workers of the same nest. Moreover significant genetic structuring among colonies indicates that gene flow between colonies is restricted and that exchange of workers between colonies is very limited. Finally we explain how possible factors as budding and the absence of Serviformica can explain the differences in genetic structure within this polygynous F. rufa population.

  18. Broad-scale Population Genetics of the Host Sea Anemone, Heteractis magnifica

    KAUST Repository

    Emms, Madeleine

    2015-12-01

    Broad-scale population genetics can reveal population structure across an organism’s entire range, which can enable us to determine the most efficient population-wide management strategy depending on levels of connectivity. Genetic variation and differences in genetic diversity on small-scales have been reported in anemones, but nothing is known about their broad-scale population structure, including that of “host” anemone species, which are increasingly being targeted in the aquarium trade. In this study, microsatellite markers were used as a tool to determine the population structure of a sessile, host anemone species, Heteractis magnifica, across the Indo-Pacific region. In addition, two rDNA markers were used to identify Symbiodinium from the samples, and phylogenetic analyses were used to measure diversity and geographic distribution of Symbiodinium across the region. Significant population structure was identified in H. magnifica across the Indo-Pacific, with at least three genetic breaks, possibly the result of factors such as geographic distance, geographic isolation and environmental variation. Symbiodinium associations were also affected by environmental variation and supported the geographic isolation of some regions. These results suggests that management of H. magnifica must be implemented on a local scale, due to the lack of connectivity between clusters. This study also provides further evidence for the combined effects of geographic distance and environmental distance in explaining genetic variance.

  19. Genetic diversity in Scots pine populations along a radiation exposure gradient

    Energy Technology Data Exchange (ETDEWEB)

    Geras' kin, Stanislav A., E-mail: stgeraskin@gmail.com; Volkova, Polina Yu.

    2014-10-15

    Polymorphisms of antioxidant enzymes were studied in the endosperm and embryos of seeds from Scots pine populations inhabiting sites in the Bryansk region of Russia radioactively contaminated as a result of the Chernobyl accident. Chronic radiation exposure at dose rates from 0.8 μGy/h led to a significant increase in the rate of enzymatic loci mutations. The main parameters of genetic variability of the affected Scots pine populations had considerably higher values than those from the reference site. Changes in the genetic makeup of Scots pine populations were observed at dose rates greater than 10.4 μGy/h. However, the higher mutation rate had no effect on the activities of antioxidant enzymes. - Highlights: • Polymorphism of antioxidant enzymes was studied in affected Scots pine populations. • Genetic processes in affected Scots pine populations increase genetic diversity. • Chronic exposure at dose rates from 0.8 μGy/h lead to increasing of mutation rates. • Changes in population genetic structure were observed at dose rates from 10.4 μGy/h. • The higher rate of mutations had no effect on antioxidant enzymes activities.

  20. Genetic Diversity Evaluation of Maize Recurrent Selection Population with RAPD Marker

    Institute of Scientific and Technical Information of China (English)

    Liu Xunjia; Zheng Yonglian; Liu Jilin

    2000-01-01

    The genetic diversity of maize populations Wuxi (W) from Southwest China, BSSS9(B) from America, Mohuangjiu (M) from Mexico, WBMC0 synthesized by W, B, M as main parents,WBMC1 one cycle selected from WBMC0 were evaluated by RAPD molecular marker. The results showed that :(1) Totally 89 fragments (loci) were amplified by 15 10-mar random primers, the proportion of polymorphic loci were W 76. 4%, B 75. 3%, M 79. 8%,WBMC0 85. 4% and WBMC1 92. 1% respectively; (2) The mean gene heterozygosity based on 89 loci was W 0. 285, B 0. 252, M 0. 296, WBMC0 0. 327 and WBMC1 0. 346; (3) The mean genetic distance based on 89 loci were W 0. 2533, B 0. 2246, M 0. 2481, WBMC0 0. 3006 and WBMC1 0. 3119; (4) The genotypic mean numbers amplified by 15 primers were W 9.1, B 7.8, M 8.5, WBMC0 10. 1 and WBMC1 10. All indexes indicated that the synthesized maize population were more polymorphic than the parent populations in DNA level. One cycle selection did not reduce the variation. The new conception of "genotypic diversity" (the number of genotypes in a population) was provided to describe the genetic diversity for any population being equilibrium or unequilibrium in genetics. The principle and technical system were discussed for evaluating genetic variation of recurrent selection population using RAPD molecular marker.

  1. Genetic diversity in Scots pine populations along a radiation exposure gradient

    International Nuclear Information System (INIS)

    Polymorphisms of antioxidant enzymes were studied in the endosperm and embryos of seeds from Scots pine populations inhabiting sites in the Bryansk region of Russia radioactively contaminated as a result of the Chernobyl accident. Chronic radiation exposure at dose rates from 0.8 μGy/h led to a significant increase in the rate of enzymatic loci mutations. The main parameters of genetic variability of the affected Scots pine populations had considerably higher values than those from the reference site. Changes in the genetic makeup of Scots pine populations were observed at dose rates greater than 10.4 μGy/h. However, the higher mutation rate had no effect on the activities of antioxidant enzymes. - Highlights: • Polymorphism of antioxidant enzymes was studied in affected Scots pine populations. • Genetic processes in affected Scots pine populations increase genetic diversity. • Chronic exposure at dose rates from 0.8 μGy/h lead to increasing of mutation rates. • Changes in population genetic structure were observed at dose rates from 10.4 μGy/h. • The higher rate of mutations had no effect on antioxidant enzymes activities

  2. Analysis of genetic structure and relationship among nine indigenous Chinese chicken populations by the Structure program

    Indian Academy of Sciences (India)

    H. F. Li; W. Han; Y. F. Zhu; J. T. Shu; X. Y. Zhang; K. W. Chen

    2009-08-01

    The multi-locus model-based clustering method Structure program was used to infer the genetic structure of nine indigenous Chinese chicken (Gallus gallus) populations based on 16 microsatellite markers. Twenty runs were carried out at each chosen value of predefined cluster numbers $(K)$ under admixture model. The Structure program properly inferred the presence of genetic structure with 0.999 probabilities. The genetic structure not only indicated that the nine kinds of chicken populations were defined actually by their locations, phenotypes or culture, but also reflected the underlying genetic variations. At $K = 2$, nine chicken populations were divided into two main clusters, one light-body type, including Chahua chicken (CHA), Tibet chicken (TIB), Xianju chicken (XIA), Gushi chicken (GUS) and Baier chicken (BAI); and the other heavy-body type, including Beijing You chicken (YOU), Xiaoshan chicken (XIA), Luyuan chicken (LUY) and Dagu chicken (DAG). GUS and DAG were divided into independent clusters respectively when equaled 4, 5, or 6. XIA and BIA chicken, XIA and LUY chicken, TIB and CHA chicken still clustered together when equaled 6, 7, and 8, respectively. These clustering results were consistent with the breeding directions of the nine chicken populations. The Structure program also identified migrants or admixed individuals. The admixed individuals were distributed in all the nine chicken populations, while migrants were only distributed in TIB, XIA and LUY populations. These results indicated that the clustering analysis using the Structure program might provide an accurate representation of the genetic relationship among the breeds.

  3. Inbreeding rate and genetic structure of cat populations in Poland.

    Science.gov (United States)

    Mucha, S; Wolc, A; Gradowska, A; Szwaczkowski, T

    2011-02-01

    The objective of the study was to analyze effective population size and inbreeding level in populations of cat breeds registered in the Polish Studbook. The Association of Purebred Cat Breeders in Poland provided access to pedigrees of 26725 cats from seven breeds. The most frequent breed was Persian, however increasing tendency in numbers of registered animals from other breeds was recorded in later years. Although the percentage of inbred individuals was increasing over time, mating of close relatives was avoided by most of the breeders, and the average inbreeding coefficient exceeded 5% only for Siberian and Russian breeds. Current analysis suggests that the Polish pedigree cat populations are not threatened by negative effects of inbreeding. PMID:21128045

  4. A genetic algorithm based wrapper feature selection method for classification of hyperspectral images using support vector machine

    Science.gov (United States)

    Zhuo, Li; Zheng, Jing; Li, Xia; Wang, Fang; Ai, Bin; Qian, Junping

    2008-10-01

    The high-dimensional feature vectors of hyper spectral data often impose a high computational cost as well as the risk of "over fitting" when classification is performed. Therefore it is necessary to reduce the dimensionality through ways like feature selection. Currently, there are two kinds of feature selection methods: filter methods and wrapper methods. The former kind requires no feedback from classifiers and estimates the classification performance indirectly. The latter kind evaluates the "goodness" of selected feature subset directly based on the classification accuracy. Many experimental results have proved that the wrapper methods can yield better performance, although they have the disadvantage of high computational cost. In this paper, we present a Genetic Algorithm (GA) based wrapper method for classification of hyper spectral data using Support Vector Machine (SVM), a state-of-art classifier that has found success in a variety of areas. The genetic algorithm (GA), which seeks to solve optimization problems using the methods of evolution, specifically survival of the fittest, was used to optimize both the feature subset, i.e. band subset, of hyper spectral data and SVM kernel parameters simultaneously. A special strategy was adopted to reduce computation cost caused by the high-dimensional feature vectors of hyper spectral data when the feature subset part of chromosome was designed. The GA-SVM method was realized using the ENVI/IDL language, and was then tested by applying to a HYPERION hyper spectral image. Comparison of the optimized results and the un-optimized results showed that the GA-SVM method could significantly reduce the computation cost while improving the classification accuracy. The number of bands used for classification was reduced from 198 to 13, while the classification accuracy increased from 88.81% to 92.51%. The optimized values of the two SVM kernel parameters were 95.0297 and 0.2021, respectively, which were different from the

  5. Founder effects and genetic population structure of brown trout (Salmo trutta) in a Danish river system

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Mensberg, Karen-Lise Dons

    1996-01-01

    The influence of founder effects on the genetic population structure of brown trout (Salmo trutta) was studied in a small Danish river system. Samples of trout from seven locations were analysed by allozyme electrophoresis and mitochondrial DNA restriction fragment length polymorphism analysis. For...... comparison, allozyme data from other Danish trout populations and mtDNA data from two hatchery strains were included. Genetic differentiation among populations was found to be small but significant. Pairwise tests for homogeneity of allele and haplotype frequencies between samples showed that significance...

  6. Genetic structure of European populations of Salmo salar L (Atlantic salmon) inferred from mitochondrial DNA

    DEFF Research Database (Denmark)

    Eg Nielsen, Einar; Hansen, Michael Møller; Loeschcke, V.

    1996-01-01

    analyses of the NADH dehydrogenase 1 segment, employing four endonucleases. Significant genetic differentiation was observed among populations. A hierarchical analysis of the distribution of the mtDNA variability revealed that only a small part was distributed among geographical groups within the study......The genetic relationships between the only natural population of Atlantic salmon (Salmo salar L.) in Denmark and seven other European salmon populations were studied using RFLP analysis of PCR amplified mitochondrial DNA segments. Six different haplotypes were detected by restriction enzyme...

  7. Population genetics of the malaria vector Anopheles aconitus in China and Southeast Asia

    OpenAIRE

    Chen, Bin; Harbach, Ralph E.; Walton, Catherine; He, Zhengbo; Zhong, Daibin; Yan, Guiyun; Butlin, Roger K.

    2012-01-01

    Anopheles aconitus is a well-known vector of malaria and is broadly distributed in the Oriental Region, yet there is no information on its population genetic characteristics. In this study, the genetic differentiation among populations was examined using 140 mtDNA COII sequences from 21 sites throughout southern China, Myanmar, Vietnam, Thailand, Laos and Sri Lanka. The population in Sri Lanka has characteristic rDNA D3 and ITS2, mtDNA COII and ND5 haplotypes, and may be considered a distinct...

  8. Genetic Diversity of Maize Populations Developed by Two Kinds of Recurrent Selection Methods Investigated with SSR Markers

    Institute of Scientific and Technical Information of China (English)

    LI Lu-jiang; YANG Ke-cheng; PAN Guang-tang; RONG Ting-zhao

    2008-01-01

    Two cycles of biparental mass selection (MS) and one cycle of half-sib-S3 family combining selection (HS-S3) for yield were carried out in 2 synthetic maize populations P4C0 and P5C0 synchronously.The genetic diversity of 8 maize populations,including both the basic populations and their developed populations,were evaluated by 30 SSR primers.On the 30 SSR loci,a total of 184 alleles had been detected in these populations.At each locus,the number of alleles varied from 2 to 14,with an average of 6.13.The number and ratio of polymorphic loci in both the basic populations were higher than those of their developed populations,respectively.There was nearly no difference after MS but decreased after HS-S3 in both the basic populations in the mean gene heterozygosity.The mean genetic distance changed slightly after MS but decreased in a bigger degree after HS-S3 in both the basic populations.Analyses on the distribution of genetic distances showed that the ranges of the genetic distance were wider after MS and most of the genetic distances in populations developed by HS-S3 were smaller than those in both the basic populations.The number of genotypes increased after MS but decreased after HS-S3 in both the basic populations.The genetic diversity of intra-population was much more than genetic diversity of inter-population in both the basic populations.All these indexes demonstrated that the genetic diversity of populations after MS was similar to their basic populations,and the genetic diversity was maintained during MS,whereas the genetic diversity of populations decreased after HS-S3.This result indicated that heterogeneity between some of the individuals in the developed populations increased after MS,whereas the populations become more homozygotic after HS-S3.

  9. Genetic variation in time and space : Microsatellite analysis of extinct and extant populations of Atlantic salmon

    DEFF Research Database (Denmark)

    Eg Nielsen, Einar; Hansen, Michael Møller; Loeschcke, V.

    1999-01-01

    rivers that covered a time span of up to 76 years. These results suggest that salmon populations evolve as semi- independent units connected by modest amounts of gene flow. Additionally, a clear association between geographic and genetic distance was found. This relationship has otherwise been difficult....... Variation at six microsatellite loci was studied. Tests for differentiation among populations and among time series within populations showed that population structure was stable over time. This was also confirmed by a neighbor-joining dendrogram which showed a clear clustering of samples from individual...... to establish in several recent studies. The discrepancy may be due to impact of human activities on the genetic structure of present populations, whereas old samples represent populations in a more unaffected state. However, other explanations related to differences in the sampling of past and...

  10. Population Genetics of Franciscana Dolphins (Pontoporia blainvillei): Introducing a New Population from the Southern Edge of Their Distribution.

    Science.gov (United States)

    Gariboldi, María Constanza; Túnez, Juan Ignacio; Dejean, Cristina Beatriz; Failla, Mauricio; Vitullo, Alfredo Daniel; Negri, María Fernanda; Cappozzo, Humberto Luis

    2015-01-01

    Due to anthropogenic factors, the franciscana dolphin, Pontoporia blainvillei, is the most threatened small cetacean on the Atlantic coast of South America. Four Franciscana Management Areas have been proposed: Espiritu Santo to Rio de Janeiro (FMA I), São Paulo to Santa Catarina (FMA II), Rio Grande do Sul to Uruguay (FMA III), and Argentina (FMA IV). Further genetic studies distinguished additional populations within these FMAs. We analyzed the population structure, phylogeography, and demographic history in the southernmost portion of the species range. From the analysis of mitochondrial DNA control region sequences, 5 novel haplotypes were found, totalizing 60 haplotypes for the entire distribution range. The haplotype network did not show an apparent phylogeographical signal for the southern FMAs. Two populations were identified: Monte Hermoso (MH) and Necochea (NC)+Claromecó (CL)+Río Negro (RN). The low levels of genetic variability, the relative constant size over time, and the low levels of gene flow may indicate that MH has been colonized by a few maternal lineages and became isolated from geographically close populations. The apparent increase in NC+CL+RN size would be consistent with the higher genetic variability found, since genetic diversity is generally higher in older and expanding populations. Additionally, RN may have experienced a recent split from CL and NC; current high levels of gene flow may be occurring between the latter ones. FMA IV would comprise four franciscana dolphin populations: Samborombón West+Samborombón South, Cabo San Antonio+Buenos Aires East, NC+CL+Buenos Aires Southwest+RN and MH. Results achieved in this study need to be taken into account in order to ensure the long-term survival of the species. PMID:26221960

  11. Learning with Admixture: Modeling, Optimization, and Applications in Population Genetics

    DEFF Research Database (Denmark)

    Cheng, Jade Yu

    2016-01-01

    including population splits, effective population sizes, gene flow, etc. Since joining the CoalHMM development team in 2014, I have mainly contributed in two directions: 1) improving optimizations through heuristic-based evolutionary algorithms and 2) modeling of historical admixture events. Ohana, meaning...... data. Ohana's admixture module is based on classical structure modeling but uses new optimization subroutines through quadratic programming, which outperform the current state-of-the-art software in both speed and accuracy. Ohana presents a new method for phylogenetic tree inference using Gaussian...

  12. Population genetics of an ecosystem-defining reef coral Pocillopora damicornis in the Tropical Eastern Pacific.

    Directory of Open Access Journals (Sweden)

    David J Combosch

    Full Text Available BACKGROUND: Coral reefs in the Tropical Eastern Pacific (TEP are amongst the most peripheral and geographically isolated in the world. This isolation has shaped the biology of TEP organisms and lead to the formation of numerous endemic species. For example, the coral Pocillopora damicornis is a minor reef-builder elsewhere in the Indo-West Pacific, but is the dominant reef-building coral in the TEP, where it forms large, mono-specific stands, covering many hectares of reef. Moreover, TEP P. damicornis reproduces by broadcast spawning, while it broods mostly parthenogenetic larvae throughout the rest of the Indo-West Pacific. Population genetic surveys for P. damicornis from across its Indo-Pacific range indicate that gene flow (i.e. larval dispersal is generally limited over hundreds of kilometers or less. Little is known about the population genetic structure and the dispersal potential of P. damicornis in the TEP. METHODOLOGY: Using multilocus microsatellite data, we analyzed the population structure of TEP P. damicornis among and within nine reefs and test for significant genetic structure across three geographically and ecologically distinct regions in Panama. PRINCIPAL FINDINGS/CONCLUSIONS: We detected significant levels of population genetic structure (global R(ST = 0.162, indicating restricted gene flow (i.e. larvae dispersal, both among the three regions (R(RT = 0.081 as well as within regions (R(SR = 0.089. Limited gene flow across a distinct environmental cline, like the regional upwelling gradient in Panama, indicates a significant potential for differential adaptation and population differentiation. Individual reefs were characterized by unexpectedly high genet diversity (avg. 94%, relatively high inbreeding coefficients (global F(IS = 0.183, and localized spatial genetic structure among individuals (i.e. unique genets over 10 m intervals. These findings suggest that gene flow is limited in TEP P. damicornis

  13. Genetic divergence among geographical populations of the migratory locust in China

    Institute of Scientific and Technical Information of China (English)

    ZHANG Minzhao; KANG Le

    2005-01-01

    The random amplified polymorphic DNA (RAPD) technique was used to examine genetic divergence and interrelations of 11 geographical populations of the migratory locust in China, and the role of spatial separation in the population differentiations. AMOVA analysis of genetic variations in all the populations indicated greater within- (79.55%) than among-population variability (20.45%), and that there were significant differentiations among the populations; 11 populations were divided into four regional groups, with significantly greater variability within (82.99%) than among the groups (17.01%), and there existed apparent regional differentiations. Paired comparisons showed significantly greater variability within- than between-groups, indicating significant differentiations between populations of different regional groups. Of all the pairwise comparisons, Hainan and Tibetan groups displayed the greatest differentiation, with the difference between the two groups being seven folds of that between populations within the groups; the least differentiations were exhibited between the groups of Hainan, Xinjiang, and Inner Mongolia, with the differences between groups being only half of the differences between populations within the groups. Mantel tests of the genetic and spatial distances showed that the two matrices were significantly correlated (p<0.01), indicating that the geographical isolation played an important role in the differentiations of the geographical populations of the migratory locusts. Cluster analysis divided all populations into four major groups: Xinjiang and Inner Mongolia group, the Great Plains of North China (the Yellow River and Huai River Plains) group, Hainan group, and Tibet group. Principal component analysis (PCA) supported the division of populations based on the cluster analysis. However, analysis of individuals clustered the locusts into five populations: Xinjiang and Inner Mongolia, Hami in Xinjiang, the Great Plains of North China

  14. Genetic and cytogenetic structure of wild lemon grass (Elionurus muticus populations

    Directory of Open Access Journals (Sweden)

    Thanise Nogueira Füller

    2015-12-01

    Full Text Available Elionurus muticus is a native aromatic grass from the Pampa biome that produces an essential oil that is rich in citral. Despite the importance of citral, few studies have examined this species. The aims of this work were to evaluate the genetic structure and to characterize cytogenetically natural populations collected from Brazil. Genetic characterization was performed using AFLP markers, and cytogenetics assessed the chromosome number, karyotype and meiosis. The studied populations had genetic variability, especially within populations, indicating the possibility of selecting plants with relevant characters. High variability also suggests the preferential occurrence of outcrossing in natural populations. Regular meiosis was observed in the cytogenetic analysis with chromosome number 2n=20. The karyotype of the species is presented for the first time, with the karyotype formula 3sm + 4a + 1saSAT.

  15. Genetic structure of European populations of Salmo salar L (Atlantic salmon) inferred from mitochondrial DNA

    DEFF Research Database (Denmark)

    Eg Nielsen, Einar; Hansen, Michael Møller; Loeschcke, V.

    1996-01-01

    The genetic relationships between the only natural population of Atlantic salmon (Salmo salar L.) in Denmark and seven other European salmon populations were studied using RFLP analysis of PCR amplified mitochondrial DNA segments. Six different haplotypes were detected by restriction enzyme...... analyses of the NADH dehydrogenase 1 segment, employing four endonucleases. Significant genetic differentiation was observed among populations. A hierarchical analysis of the distribution of the mtDNA variability revealed that only a small part was distributed among geographical groups within the study...... area. No correlation was found between genetic and geographic distance among populations. The effective migration of females (Nm)(F) among rivers was estimated to be approximately one per generation...

  16. Characterization of new microsatellite loci for population genetic studies in the Smooth Cauliflower Coral (Stylophora sp.)

    KAUST Repository

    Banguera-Hinestroza, E.

    2013-01-09

    A total of one hundred microsatellites loci were selected from the draft genome of Stylophora pistillata and evaluated in previously characterized samples of Stylophora cf pistillata from the Red Sea. 17 loci were amplified successfully and tested in 24 individuals from samples belonging to a single population from the central region of the Red Sea. The number of alleles ranged from 3 to 15 alleles per locus, while observed heterozygosity ranged from 0. 292 to 0. 95. Six of these loci showed significant deviations from Hardy-Weinberg equilibrium (HWE) expectations, and 4/136 paired loci comparisons suggested linkage disequilibrium after Bonferroni corrections. After excluding loci with significant HWE deviation and evidence of null alleles, average genetic diversity over loci in the population studied (N = 24, Nloci = 11) was 0. 701 ± 0. 380. This indicates that these loci can be used effectively to evaluate genetic diversity and undertake population genetics studies in Stylophora sp. populations. 2013 The Author(s).

  17. Dynamics of genetic processes in chronically irradiated populations of small mammals

    International Nuclear Information System (INIS)

    The distinctive features of dynamics of mutagenesis in mammalian populations under chronic low-intensive irradiation were first revealed. The main of them is gradual increase in mutability in somatic cells and embryonal lethality during series of irradiated generations of animals (bank vole - Clethrionomys glareolus). The data obtained strongly suggest that there are oppositely directed processes in natural populations after irradiation of more than 20 generations of animals: on the one hand, accumulation of mutations (genetic load of populations) and pre-mutation events which increase genome instability of germ and somatic cells in consecutive generations of animals, and on the other, formation of genetic radio adaptation through better functioning protection systems. In this period of micro evolution in chronically irradiated populations, the frequencies of genetic damages could be higher if the radiation adaptation doesn't form. (authors)

  18. Genetic Variation of Three Populations of Indian Frog (Hoplobatrachus tigerinus Revealed by Allozyme Marker

    Directory of Open Access Journals (Sweden)

    M. Belal Hossain

    2012-01-01

    Full Text Available The Indian bullfrog, Hoplobatrachus tigerinus plays a significant role in maintaining the natural balance in the ecosystems. It plays an important role in controlling the various agricultural pests because of its omnivorous feeding habit. The aim of the present study is to know the genetic variation of H. tigerinus in three natural habitats. Samples collected from three districts of Bangladesh were analyzed with five enzymes (MDH, LDH, GPI, PGM and EST in CA 6.1 buffer system for their genetic variation. Four polymorphic loci (Mdh-1, Est-1, Gpi-1 and Pgm were interpretable in muscle with starch gel electrophoresis. Among the 5 presumptive loci, the mean proportion of polymorphic loci was observed 80, 80 and 60% in Rangpur, Khulna and Mymensingh populations, respectively. The highest mean number of allele per locus and mean proportion of heterozygous loci per individual were observed in the Rangpur population. The average observed heterozygosity (Ho was 0.163 and expected heterozygosity (He was 0.469. In pair-wise analysis, comparatively higher Nm value (5.507 was estimated between the Rangpur and Khulna populations corresponding lower level of FST value (0.043. The UPGMA dendrogram showed two clusters among the three Indian bullfrog populations. Rangpur and Khulna populations formed one cluster while Mymensingh population formed another cluster. The Mymensingh population separated from Rangpur and Khulna by a genetic distance of 0.177 whereas, the Khulna population is different from the Rangpur population by the genetic distance of 0.052. The results suggested that the considerable genetic variation is maintained among the natural H. tigerinus populations.

  19. The Use of Genetics for the Management of a Recovering Population: Temporal Assessment of Migratory Peregrine Falcons in North America

    OpenAIRE

    Johnson, Jeff A; Sandra L Talbot; Sage, George K.; Kurt K Burnham; Brown, Joseph W.; Maechtle, Tom L.; William S Seegar; Yates, Michael A.; Bud Anderson; David P Mindell

    2010-01-01

    BACKGROUND: Our ability to monitor populations or species that were once threatened or endangered and in the process of recovery is enhanced by using genetic methods to assess overall population stability and size over time. This can be accomplished most directly by obtaining genetic measures from temporally-spaced samples that reflect the overall stability of the population as given by changes in genetic diversity levels (allelic richness and heterozygosity), degree of population differentia...

  20. Genetic adaptation to metal stress by natural populations of Daphnia longispina

    OpenAIRE

    Lopes, Isabel; Baird, Donald J; Ribeiro, Rui

    2006-01-01

    Loss of genetic diversity in natural populations as a result of chemical contamination has been reported in some studies. Here, four field populations of Daphnia longispina, two from sites historically impacted by acid mine drainage (AMD) and two from reference sites, were used to address four objectives: (1) identify differences in sensitivity between the stressed and reference populations; (2) distinguish between the components responsible for those differences (environmental influence vs g...

  1. High genetic diversity in a small population: the case of Chilean blue whales

    OpenAIRE

    Torres-Florez, Juan P; Hucke-Gaete, Rodrigo; Rosenbaum, Howard; Christian C Figueroa

    2014-01-01

    It is generally assumed that species with low population sizes have lower genetic diversities than larger populations and vice versa. However, this would not be the case for long-lived species with long generation times, and which populations have declined due to anthropogenic effects, such as the blue whale (Balaenoptera musculus). This species was intensively decimated globally to near extinction during the 20th century. Along the Chilean coast, it is estimated that at least 4288 blue whale...

  2. Genetic structure of marine Borrelia garinii and population admixture with the terrestrial cycle of Lyme borreliosis

    OpenAIRE

    Gomez-Diaz, E.; Boulinier, T.; Sertour, N.; Cornet, M.; Ferquel, E.; McCoy, Karen

    2011-01-01

    Despite the importance of population structure for the epidemiology of pathogenic bacteria, the spatial and ecological heterogeneity of these populations is often poorly characterized. Here, we investigated the genetic diversity and population structure of the Lyme borreliosis (LB) spirochaete Borrelia garinii in its marine cycle involving colonial seabirds and different host races of the seabird tick Ixodes uriae. Multilocus sequence analyses (MLSA) on eight chromosomal and two plasmid loci ...

  3. Genetics analysis of 38 STR loci in Uygur population from Southern Xinjiang of China.

    Science.gov (United States)

    Yuan, Li; Liu, Haibo; Liao, Qinxiang; Xu, Xu; Chen, Wen; Hao, Shicheng

    2016-05-01

    The allele frequencies and statistical parameters of 38 autosomal short tandem repeat (STR) loci were analyzed in the Uygur population from Southern Xinjiang of China with 290 unrelated individuals. The results show these 38 STR loci have high or medium power of discrimination and probabilities of exclusion. All loci are in Hardy-Weinberg equilibrium. The genetic distances between the Uygur population and other Chinese populations were also estimated. PMID:26438047

  4. Lack of Population Genetic Structuring in Ocelots (Leopardus pardalis) in a Fragmented Landscape

    OpenAIRE

    Figueiredo, Marina G.; Marcelo Cervini; Fernando P. Rodrigues; Eduardo Eizirik; Fernando C. C. Azevedo; Laury Cullen; Peter G. Crawshaw; Pedro M. Galetti

    2015-01-01

    Habitat fragmentation can promote patches of small and isolated populations, gene flow disruption between those populations, and reduction of local and total genetic variation. As a consequence, these small populations may go extinct in the long-term. The ocelot (Leopardus pardalis), originally distributed from Texas to southern Brazil and northern Argentina, has been impacted by habitat fragmentation throughout much of its range. To test whether habitat fragmentation has already induced gene...

  5. Population expansions shared among coexisting bacterial lineages are revealed by genetic evidence

    OpenAIRE

    Morena Avitia; Escalante, Ana E.; Rebollar, Eria A.; Alejandra Moreno-Letelier; Eguiarte, Luis E.; Valeria Souza

    2014-01-01

    Comparative population studies can help elucidate the influence of historical events upon current patterns of biodiversity among taxa that coexist in a given geographic area. In particular, comparative assessments derived from population genetics and coalescent theory have been used to investigate population dynamics of bacterial pathogens in order to understand disease epidemics. In contrast, and despite the ecological relevance of non-host associated and naturally occurring bacteria, there ...

  6. Molecular and Quantitative Genetic Differentiation in European Populations of Silene latifolia (Caryophyllaceae)

    OpenAIRE

    Jolivet, Céline; Bernasconi, Giorgina

    2009-01-01

    Background and Aims: Among-population differentiation in phenotypic traits and allelic variation is expected as a consequence of isolation, drift, founder effects and local selection. Therefore, investigating molecular and quantitative genetic divergence is a pre-requisite for studies of local adaptation in response to selection under variable environmental conditions. Methods: Among- and within-population variation were investigated in six geographically separated European populations of t...

  7. Bacterial Genetic Signatures of Human Social Phenomena among M. tuberculosis from an Aboriginal Canadian Population

    OpenAIRE

    Pepperell, Caitlin; Hoeppner, Vernon H.; Lipatov, Mikhail; Wobeser, Wendy; Schoolnik, Gary K.; Feldman, Marcus W.

    2009-01-01

    Despite a widespread global distribution and highly variable disease phenotype, there is little DNA sequence diversity among isolates of Mycobacterium tuberculosis. In addition, many regional population genetic surveys have revealed a stereotypical structure in which a single clone, lineage, or clade makes up the majority of the population. It is often assumed that dominant clones are highly adapted, that is, the overall structure of M. tuberculosis populations is the result of positive selec...

  8. Population genetics, diversity and spread of virulence in Toxoplasma gondii

    Science.gov (United States)

    Globally, an estimated third of the human population harbors infection with Toxoplasma gondii, a single-celled eukaryotic parasite belonging to the phylum Apicomplexa (Dubey, 2010). Most infected persons are unaware of, and evidently unharmed by, the parasite cysts established in their muscles and/...

  9. Population genetics of Sargassum horneri (Fucales, Phaeophyta) in China revealed by ISSR and SRAP markers

    Science.gov (United States)

    Yu, Shenhui; Chong, Zhuo; Zhao, Fengjuan; Yao, Jianting; Duan, Delin

    2013-05-01

    Sargassum horneri is a common brown macro-alga that is found in the inter-tidal ecosystems of China. To investigate the current status of seaweed resources and provide basic data for its sustainable development, ISSR (inter simple sequence repeat) and SRAP (sequence related amplified polymorphism) markers were used to analyze the population genetics among nine natural populations of S. horneri. The nine studied populations were distributed over 2 000 km from northeast to south China. The percentage of polymorphic loci P % (ISSR, 99.44%; SRAP, 100.00%), Nei's genetic diversity H (ISSR, 0.107-0.199; SRAP, 0.100-0.153), and Shannon's information index I (ISSR, 0.157-0.291; SRAP, 0.148-0.219) indicated a fair amount of genetic variability among the nine populations. Moreover, the high degree of gene differentiation G st (ISSR, 0.654; SRAP, 0.718) and low gene flow N m (ISSR, 0.265; SRAP, 0.196) implied that there was significant among-population differentiation, possibly as a result of habitat fragmentation. The matrices of genetic distances and fixation indices ( F st) among the populations correlated well with their geographical distribution (Mantel test R =0.541 5, 0.541 8; P =0.005 0, 0.002 0 and R =0.728 6, 0.641 2; P =0.001 0, 0.001 0, respectively); the Rongcheng population in the Shandong peninsula was the only exception. Overall, the genetic differentiation agreed with the geographic isolation. The fair amount of genetic diversity that was revealed in the S. horneri populations in China indicated that the seaweed resources had not been seriously affected by external factors.

  10. Hierarchical spatial genetic structure in a distinct population segment of greater sage-grouse

    Science.gov (United States)

    Oyler-McCance, Sara J.; Casazza, Michael L.; Fike, Jennifer A.; Coates, Peter S.

    2014-01-01

    Greater sage-grouse (Centrocercus urophasianus) within the Bi-State Management Zone (area along the border between Nevada and California) are geographically isolated on the southwestern edge of the species’ range. Previous research demonstrated that this population is genetically unique, with a high proportion of unique mitochondrial DNA (mtDNA) haplotypes and with significant differences in microsatellite allele frequencies compared to populations across the species’ range. As a result, this population was considered a distinct population segment (DPS) and was recently proposed for listing as threatened under the U.S. Endangered Species Act. A more comprehensive understanding of the boundaries of this genetically unique population (where the Bi-State population begins) and an examination of genetic structure within the Bi-State is needed to help guide effective management decisions. We collected DNA from eight sampling locales within the Bi-State (N = 181) and compared those samples to previously collected DNA from the two most proximal populations outside of the Bi-State DPS, generating mtDNA sequence data and amplifying 15 nuclear microsatellites. Both mtDNA and microsatellite analyses support the idea that the Bi-State DPS represents a genetically unique population, which has likely been separated for thousands of years. Seven mtDNA haplotypes were found exclusively in the Bi-State population and represented 73 % of individuals, while three haplotypes were shared with neighboring populations. In the microsatellite analyses both STRUCTURE and FCA separate the Bi-State from the neighboring populations. We also found genetic structure within the Bi-State as both types of data revealed differences between the northern and southern part of the Bi-State and there was evidence of isolation-by-distance. STRUCTURE revealed three subpopulations within the Bi-State consisting of the northern Pine Nut Mountains (PNa), mid Bi-State, and White Mountains (WM) following a

  11. Effects of traffic pollution on the genetic structure of Poa annua L.populations

    Institute of Scientific and Technical Information of China (English)

    LI Ning; CHEN Xiao-yong; SHEN Lang; LI Yuan-yuan; CAI Yue-wei

    2004-01-01

    The genetic composition of Poa annua L. populations with a series of traffic pollution was studied by starch electrophoresis. Five enzyme systems were stained. The results showed that: (1) Traffic pollution can dramatically change genotypic frequencies at some loci of P. annua populations. Significant deviations from Hardy-Weinberg equilibrium were observed on loci Fe-1 and Me due to the excess of heterozygote in some populations. (2) The effective number of alleles per locus, and the observed and expected heterozygosity were higher in the pollution series than in the clear control site(Botanic Park population), but the increase was not related with the pollution extent. (3) Most genetic variation was found within populations, and only 6.21% was among populations of the polluted series. Slightly higher differentiation(FST=7.98%) was observed when the control population was included. (4) The calculated gene flow(Nm) is 2.8841 per generation. The mean of genetic identity is 0.9864 and the genetic distance average to 0.0138.

  12. Catastrophic floods may pave the way for increased genetic diversity in endemic artesian spring snail populations.

    Directory of Open Access Journals (Sweden)

    Jessica Worthington Wilmer

    Full Text Available The role of disturbance in the promotion of biological heterogeneity is widely recognised and occurs at a variety of ecological and evolutionary scales. However, within species, the impact of disturbances that decimate populations are neither predicted nor known to result in conditions that promote genetic diversity. Directly examining the population genetic consequences of catastrophic disturbances however, is rarely possible, as it requires both longitudinal genetic data sets and serendipitous timing. Our long-term study of the endemic aquatic invertebrates of the artesian spring ecosystem of arid central Australia has presented such an opportunity. Here we show a catastrophic flood event, which caused a near total population crash in an aquatic snail species (Fonscochlea accepta endemic to this ecosystem, may have led to enhanced levels of within species genetic diversity. Analyses of individuals sampled and genotyped from the same springs sampled both pre (1988-1990 and post (1995, 2002-2006 a devastating flood event in 1992, revealed significantly higher allelic richness, reduced temporal population structuring and greater effective population sizes in nearly all post flood populations. Our results suggest that the response of individual species to disturbance and severe population bottlenecks is likely to be highly idiosyncratic and may depend on both their ecology (whether they are resilient or resistant to disturbance and the stability of the environmental conditions (i.e. frequency and intensity of disturbances in which they have evolved.

  13. Population genetic structure of Sisyrinchium micranthum Cav. (Iridaceae) in Itapuã State Park, Southern Brazil.

    Science.gov (United States)

    Tacuatiá, Luana Olinda; Eggers, Lilian; Kaltchuk-Santos, Eliane; Souza-Chies, Tatiana T

    2012-01-01

    Sisyrinchium micranthum Cav. is a member of the family Iridaceae, which is distributed over the American continent. In Brazil, this species is found, not only in disturbed areas and coastal regions, but is also very common in urban centers, such as public parks, during the spring. Chromosome counts for North American specimens are 2n = 32 and 2n = 48, whereas in southern Brazil, there is a polyploidy series with three chromosome numbers, 2n = 16, 2n = 32, and 2n = 48. Population analyses using DNA molecular markers are inexistent for this species, in spite of its wide distribution and morphological variation. To study the genetic population structure of S. micranthum, five natural populations were accessed in a conservation park within the Atlantic Rain Forest Biome in southern Brazil. Here, the chromosome numbers 2n = 16 and 2n = 48 had already been described. Molecular analysis showed that the populations are highly structured with low gene flow among them. The population with 2n = 48 was genetically less variable than and distinct from the other populations. Population genetics in relation to cytogenetic data provided new insights regarding the genetic diversification and mating system of S. micranthum. PMID:22481881

  14. Genetic evidence for an origin of the Armenians from Bronze Age mixing of multiple populations.

    Science.gov (United States)

    Haber, Marc; Mezzavilla, Massimo; Xue, Yali; Comas, David; Gasparini, Paolo; Zalloua, Pierre; Tyler-Smith, Chris

    2016-06-01

    The Armenians are a culturally isolated population who historically inhabited a region in the Near East bounded by the Mediterranean and Black seas and the Caucasus, but remain under-represented in genetic studies and have a complex history including a major geographic displacement during World War I. Here, we analyse genome-wide variation in 173 Armenians and compare them with 78 other worldwide populations. We find that Armenians form a distinctive cluster linking the Near East, Europe, and the Caucasus. We show that Armenian diversity can be explained by several mixtures of Eurasian populations that occurred between ~3000 and ~2000 bce, a period characterized by major population migrations after the domestication of the horse, appearance of chariots, and the rise of advanced civilizations in the Near East. However, genetic signals of population mixture cease after ~1200 bce when Bronze Age civilizations in the Eastern Mediterranean world suddenly and violently collapsed. Armenians have since remained isolated and genetic structure within the population developed ~500 years ago when Armenia was divided between the Ottomans and the Safavid Empire in Iran. Finally, we show that Armenians have higher genetic affinity to Neolithic Europeans than other present-day Near Easterners, and that 29% of Armenian ancestry may originate from an ancestral population that is best represented by Neolithic Europeans. PMID:26486470

  15. Genetic diversity in mesoamerican populations of mahogany (Swietenia macrophylla), assessed using RAPDs.

    Science.gov (United States)

    Gillies, A C; Navarro, C; Lowe, A J; Newton, A C; Hernández, M; Wilson, J; Cornelius, J P

    1999-12-01

    Swietenia macrophylla King, a timber species native to tropical America, is threatened by selective logging and deforestation. To quantify genetic diversity within the species and monitor the impact of selective logging, populations were sampled across Mesoamerica, from Mexico to Panama, and analysed for RAPD DNA variation. Ten decamer primers generated 102 polymorphic RAPD bands and pairwise distances were calculated between populations according to Nei, then used to construct a radial neighbour-joining dendrogram and examine intra- and interpopulation variance coefficients, by analysis of molecular variation (AMOVA). Populations from Mexico clustered closely together in the dendrogram and were distinct from the rest of the populations. Those from Belize also clustered closely together. Populations from Panama, Guatemala, Costa Rica, Nicaragua and Honduras, however, did not cluster closely by country but were more widely scattered throughout the dendrogram. This result was also reflected by an autocorrelation analysis of genetic and geographical distance. Genetic diversity estimates indicated that 80% of detected variation was maintained within populations and regression analysis demonstrated that logging significantly decreased population diversity (P = 0.034). This study represents one of the most wide-ranging surveys of molecular variation within a tropical tree species to date. It offers practical information for the future conservation of mahogany and highlights some factors that may have influenced the partitioning of genetic diversity in this species across Mesoamerica. PMID:10651917

  16. Genetic diversity and landscape genetic structure of otter (Lutra lutra) populations in Europe

    Czech Academy of Sciences Publication Activity Database

    Mucci, N.; Arrendal, J.; Ansorge, H.; Bailey, M.; Bodner, M.; Delibes, M.; Ferrando, A.; Fournier, P.; Fournier, C.; Godoy, J. A.; Hájková, Petra; Hauer, S.; Heggberget, T. M.; Heidecke, D.; Kirjavainen, H.; Krueger, H.-H.; Kvaloy, K.; Lafontaine, L.; Lanszki, J.; Lemarchand, C.; Liukko, U.-M.; Loeschcke, V.; Ludwig, G.; Madsen, A. B.; Mercier, L.; Ozolins, J.; Paunovic, M.; Pertoldi, C.; Piriz, A.; Prigioni, C.; Santos-Reis, M.; Luis, T. S.; Stjernberg, T.; Schmid, H.; Suchentrunk, F.; Teubner, J.; Tornberg, R.; Zinke, O.; Randi, E.

    2010-01-01

    Roč. 11, č. 2 (2010), s. 583-599. ISSN 1566-0621 R&D Projects: GA AV ČR KJB600930804; GA MŽP SP/2D4/16/08 Grant ostatní: European Science Foundation(XE) ConGen program Institutional research plan: CEZ:AV0Z60930519 Keywords : Eurasian otter * Mitochondrial DNA * Microsatellites * Bayesian clustering * Spatial genetic structure * Landscape genetics Subject RIV: EG - Zoology Impact factor: 1.255, year: 2010

  17. RAPD-based assessment of genetic diversity among annual caraway (Carum carvi populations

    Directory of Open Access Journals (Sweden)

    Bochra Laribi

    2011-06-01

    Full Text Available Genetic variability and differentiation among five annual caraway (Carum carvi populations originating from Tunisia, Germany and Egypt were examined for the first time. Random Amplified Polymorphic DNA (RAPD marker data were obtained and analysed with respect to genetic diversity, population structure and gene flow. Fourteen primers generated a total of 136 discernible and reproducible bands across the analyzed populations, out of which 56 were polymorphic. The UPGMA cluster analysis permitted the discrimination of all the genotypes and their sorting into 3 main groups. German and Egyptian caraway populations diverged significantly from Tunisian ones. Population clustering was made dependently from geographic origin. This has been further explained at the DNA level as we were able to select a set of RAPD fingerprints unique to each of the studied populations. Furthermore, dimensional graph derived from factorial analysis of RAPD frequency data, allowed significant grouping of the genotypes into five sub-plots, representing each one population. Shannon’s index values showed that variation ranks between rather than within populations. These results indicated that considerable genetic differences among C. carvi populations were registered.

  18. Genetics of breast cancer: Applications to the Mexican population

    Directory of Open Access Journals (Sweden)

    Elad Ziv

    2011-10-01

    Full Text Available Breast cancer research has yielded several important results including the strong susceptibility genes,BRCA1 and BRCA2 and more recently 19 genes and genetic loci that confer a more moderate risk.The pace of discovery is accelerating as genetic technology and computational methods improve. These discoveries will change the way that breast cancer risk is understood in Mexico over the next few decades.La investigación en cáncer de mama ha dado varios resultados importantes incluyendo los genes fuertemente susceptibles, BRCA1 y BRCA2, y más recientemente 19 genes y loci genéticos que confieren un riesgo moderado. El ritmo de los descubrimientos se acelera conforme mejora la tecnología y métodos computacionales.Estosdescubrimientoscambiarán la forma en que la investigación del cáncer es comprendida en México en las próximas décadas.

  19. Radiation-sensitive genetically susceptible pediatric sub-populations

    Energy Technology Data Exchange (ETDEWEB)

    Kleinerman, Ruth A. [National Cancer Institute, NIH, DHHS, Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, Rockville, MD (United States)

    2009-02-15

    Major advances in pediatric cancer treatment have resulted in substantial improvements in survival. However, concern has emerged about the late effects of cancer therapy, especially radiation-related second cancers. Studies of childhood cancer patients with inherited cancer syndromes can provide insights into the interaction between radiation and genetic susceptibility to multiple cancers. Children with retinoblastoma (Rb), neurofibromatosis type 1 (NF1), Li-Fraumeni syndrome (LFS), and nevoid basal cell carcinoma syndrome (NBCCS) are at substantial risk of developing radiation-related second and third cancers. A radiation dose-response for bone and soft-tissue sarcomas has been observed in hereditary Rb patients, with many of these cancers occurring in the radiation field. Studies of NF1 patients irradiated for optic pathway gliomas have reported increased risks of developing another cancer associated with radiotherapy. High relative risks for second and third cancers were observed for a cohort of 200 LFS family members, especially children, possibly related to radiotherapy. Children with NBCCS are very sensitive to radiation and develop multiple basal cell cancers in irradiated areas. Clinicians following these patients should be aware of their increased genetic susceptibility to multiple primary malignancies enhanced by sensitivity to ionizing radiation. (orig.)

  20. Biomarkers of genetic damage in human populations exposed to pesticides

    International Nuclear Information System (INIS)

    The effect of pesticides on human, animal and environmental health has been cause of concern in the scientific community for a long time. Numerous studies have reported that pesticides are not harmless and that their use can lead to harmful biological effects in the medium and long term, in exposed human and animals, and their offspring. The importance of early detection of genetic damage is that it allows us to take the necessary measures to reduce or eliminate the exposure to the deleterious agent when damage is still reversible, and thus to prevent and to diminish the risk of developing tumors or other alterations. In this paper we reviewed the main concepts in the field, the usefulness of genotoxicity studies and we compiled studies performed during the last twenty years on genetic monitoring of people occupationally exposed to pesticides. we think that genotoxicity tests, including that include chromosomal aberrations, micronucleus, sister chromatid exchanges and comet assays, should be considered as essential tools in the implementation of complete medical supervision for people exposed to potential environmental pollutants, particularly for those living in the same place as others who were others have already developed some type of malignancy. This action is particularly important at early stages to prevent the occurrence of tumors, especially from environmental origins.

  1. Impact of nonrandom mating on genetic variance and gene flow in populations with mass selection.

    Science.gov (United States)

    Sánchez, Leopoldo; Woolliams, John A

    2004-01-01

    The mechanisms by which nonrandom mating affects selected populations are not completely understood and remain a subject of scientific debate in the development of tractable predictors of population characteristics. The main objective of this study was to provide a predictive model for the genetic variance and covariance among mates for traits subjected to directional selection in populations with nonrandom mating based on the pedigree. Stochastic simulations were used to check the validity of this model. Our predictions indicate that the positive covariance among mates that is expected to result with preferential mating of relatives can be severely overpredicted from neutral expectations. The covariance expected from neutral theory is offset by an opposing covariance between the genetic mean of an individual's family and the Mendelian sampling term of its mate. This mechanism was able to predict the reduction in covariance among mates that we observed in the simulated populations and, in consequence, the equilibrium genetic variance and expected long-term genetic contributions. Additionally, this study provided confirmatory evidence on the postulated relationships of long-term genetic contributions with both the rate of genetic gain and the rate of inbreeding (deltaF) with nonrandom mating. The coefficient of variation of the expected gene flow among individuals and deltaF was sensitive to nonrandom mating when heritability was low, but less so as heritability increased, and the theory developed in the study was sufficient to explain this phenomenon. PMID:15020441

  2. Genetic diversity, population structure and association analysis in cut chrysanthemum (Chrysanthemum morifolium Ramat.).

    Science.gov (United States)

    Li, Pirui; Zhang, Fei; Chen, Sumei; Jiang, Jiafu; Wang, Haibin; Su, Jiangshuo; Fang, Weimin; Guan, Zhiyong; Chen, Fadi

    2016-06-01

    Characterizing the genetic diversity present in a working set of plant germplasm can contribute to its effective management and genetic improvement. The cut flower chrysanthemum (Chrysanthemum morifolium Ramat.) is an economically important ornamental species. With the repeated germplasm exchange and intensive breeding activities, it remains a major task in genetic research. The purpose of the present study was to characterize the genetic diversity and the population structure of a worldwide collection of 159 varieties, and to apply an association mapping approach to identify DNA-based markers linked to five plant architecture traits and six inflorescence traits. The genotyping demonstrated that there was no lack of genetic diversity in the collection and that pair-wise kinship values were relatively low. The clustering based on a Bayesian model of population structure did not reflect known variation in either provenance or inflorescence type. A principal coordinate analysis was, however, able to discriminate most of the varieties according to both of these criteria. About 1 in 100 marker pairs exhibited a degree of linkage disequilibrium. The association analysis identified a number of markers putatively linked to one or more of the traits. Some of these associations were robust over two seasons. The findings provide an in-depth understanding of genetic diversity and population structure present in cut flower chrysanthemum varieties, and an insight into the genetic control of plant architecture and inflorescence-related traits. PMID:26780102

  3. Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Thomas L Turner

    2011-03-01

    Full Text Available Body size is a classic quantitative trait with evolutionarily significant variation within many species. Locating the alleles responsible for this variation would help understand the maintenance of variation in body size in particular, as well as quantitative traits in general. However, successful genome-wide association of genotype and phenotype may require very large sample sizes if alleles have low population frequencies or modest effects. As a complementary approach, we propose that population-based resequencing of experimentally evolved populations allows for considerable power to map functional variation. Here, we use this technique to investigate the genetic basis of natural variation in body size in Drosophila melanogaster. Significant differentiation of hundreds of loci in replicate selection populations supports the hypothesis that the genetic basis of body size variation is very polygenic in D. melanogaster. Significantly differentiated variants are limited to single genes at some loci, allowing precise hypotheses to be formed regarding causal polymorphisms, while other significant regions are large and contain many genes. By using significantly associated polymorphisms as a priori candidates in follow-up studies, these data are expected to provide considerable power to determine the genetic basis of natural variation in body size.

  4. Microsatellite based genetic structure of regional transboundary Istrian sheep breed populations in Croatia and Slovenia

    Directory of Open Access Journals (Sweden)

    Beatriz Gutierrez-Gil

    2015-02-01

    Full Text Available Istrian dairy sheep is a local breed essential for the identity and development of the Northern- Adriatic karstic region through high-quality products, primarily the hard sheep artisanal cheese. Border changes fragmented the initial Istrian dairy sheep population in three genetically isolated sub-populations in Italy (1000 animals, Slovenia (1150 animals and Croatia (2500 animals. Due to the drastic reduction of their population sizes and fragmentation, the populations in Croatia and Slovenia are included in governmentally supported conservation programs. The initial subpopulation in Italy was restored after near extinction with stock from Slovenia, and is used today in meat production. The aim of this study was to provide an initial understanding of the current genetic structure and distribution of the genetic variability that exists in Istrian sheep by analysing individuals sampled in two regional groups of Istrian sheep from Croatia and Slovenia. Cres island sheep and Lika pramenka sheep were used as out-groups for comparison. Genetic differentiation was analysed using factorial correspondence analysis and structure clustering over 26 microsatellite loci for a total of 104 sheep belonging to three breeds from Croatia and Slovenia. Factorial correspondence analysis and clustering-based structure analysis both showed three distinct populations: Lika pramenka sheep, Cres island sheep and Istrian sheep. We did not find a marked genetic divergence of the regional groups of Istrian sheep. Istrian sheep regional group from Slovenia showed lower genetic variability compared to the one from Croatia. Variability and structure information obtained in this study considered alongside with socio-cultural-contexts and economic goals for the Istrian sheep reared in Croatia and Slovenia indicate that the cross-border exchange of genetic material of animals carrying private alleles among populations would maintain these alleles at low frequencies and minimize

  5. A general population genetic framework for antagonistic selection that accounts for demography and recurrent mutation.

    Science.gov (United States)

    Connallon, Tim; Clark, Andrew G

    2012-04-01

    Antagonistic selection--where alleles at a locus have opposing effects on male and female fitness ("sexual antagonism") or between components of fitness ("antagonistic pleiotropy")--might play an important role in maintaining population genetic variation and in driving phylogenetic and genomic patterns of sexual dimorphism and life-history evolution. While prior theory has thoroughly characterized the conditions necessary for antagonistic balancing selection to operate, we currently know little about the evolutionary interactions between antagonistic selection, recurrent mutation, and genetic drift, which should collectively shape empirical patterns of genetic variation. To fill this void, we developed and analyzed a series of population genetic models that simultaneously incorporate these processes. Our models identify two general properties of antagonistically selected loci. First, antagonistic selection inflates heterozygosity and fitness variance across a broad parameter range--a result that applies to alleles maintained by balancing selection and by recurrent mutation. Second, effective population size and genetic drift profoundly affect the statistical frequency distributions of antagonistically selected alleles. The "efficacy" of antagonistic selection (i.e., its tendency to dominate over genetic drift) is extremely weak relative to classical models, such as directional selection and overdominance. Alleles meeting traditional criteria for strong selection (N(e)s > 1, where N(e) is the effective population size, and s is a selection coefficient for a given sex or fitness component) may nevertheless evolve as if neutral. The effects of mutation and demography may generate population differences in overall levels of antagonistic fitness variation, as well as molecular population genetic signatures of balancing selection. PMID:22298707

  6. Hierarchical genetic analysis of German cockroach (Blattella germanica populations from within buildings to across continents.

    Directory of Open Access Journals (Sweden)

    Edward L Vargo

    Full Text Available Understanding the population structure of species that disperse primarily by human transport is essential to predicting and controlling human-mediated spread of invasive species. The German cockroach (Blattella germanica is a widespread urban invader that can actively disperse within buildings but is spread solely by human-mediated dispersal over longer distances; however, its population structure is poorly understood. Using microsatellite markers we investigated population structure at several spatial scales, from populations within single apartment buildings to populations from several cities across the U.S. and Eurasia. Both traditional measures of genetic differentiation and Bayesian clustering methods revealed increasing levels of genetic differentiation at greater geographic scales. Our results are consistent with active dispersal of cockroaches largely limited to movement within a building. Their low levels of genetic differentiation, yet limited active spread between buildings, suggests a greater likelihood of human-mediated dispersal at more local scales (within a city than at larger spatial scales (within and between continents. About half the populations from across the U.S. clustered together with other U.S. populations, and isolation by distance was evident across the U.S. Levels of genetic differentiation among Eurasian cities were greater than those in the U.S. and greater than those between the U.S. and Eurasia, but no clear pattern of structure at the continent level was detected. MtDNA sequence variation was low and failed to reveal any geographical structure. The weak genetic structure detected here is likely due to a combination of historical admixture among populations and periodic population bottlenecks and founder events, but more extensive studies are needed to determine whether signatures of global movement may be present in this species.

  7. Hierarchical genetic analysis of German cockroach (Blattella germanica) populations from within buildings to across continents.

    Science.gov (United States)

    Vargo, Edward L; Crissman, Jonathan R; Booth, Warren; Santangelo, Richard G; Mukha, Dmitry V; Schal, Coby

    2014-01-01

    Understanding the population structure of species that disperse primarily by human transport is essential to predicting and controlling human-mediated spread of invasive species. The German cockroach (Blattella germanica) is a widespread urban invader that can actively disperse within buildings but is spread solely by human-mediated dispersal over longer distances; however, its population structure is poorly understood. Using microsatellite markers we investigated population structure at several spatial scales, from populations within single apartment buildings to populations from several cities across the U.S. and Eurasia. Both traditional measures of genetic differentiation and Bayesian clustering methods revealed increasing levels of genetic differentiation at greater geographic scales. Our results are consistent with active dispersal of cockroaches largely limited to movement within a building. Their low levels of genetic differentiation, yet limited active spread between buildings, suggests a greater likelihood of human-mediated dispersal at more local scales (within a city) than at larger spatial scales (within and between continents). About half the populations from across the U.S. clustered together with other U.S. populations, and isolation by distance was evident across the U.S. Levels of genetic differentiation among Eurasian cities were greater than those in the U.S. and greater than those between the U.S. and Eurasia, but no clear pattern of structure at the continent level was detected. MtDNA sequence variation was low and failed to reveal any geographical structure. The weak genetic structure detected here is likely due to a combination of historical admixture among populations and periodic population bottlenecks and founder events, but more extensive studies are needed to determine whether signatures of global movement may be present in this species. PMID:25020136

  8. Population genetics of Trypanosoma brucei rhodesiense: clonality and diversity within and between foci.

    Directory of Open Access Journals (Sweden)

    Craig W Duffy

    2013-11-01

    Full Text Available African trypanosomes are unusual among pathogenic protozoa in that they can undergo their complete morphological life cycle in the tsetse fly vector with mating as a non-obligatory part of this development. Trypanosoma brucei rhodesiense, which infects humans and livestock in East and Southern Africa, has classically been described as a host-range variant of the non-human infective Trypanosoma brucei that occurs as stable clonal lineages. We have examined T. b. rhodesiense populations from East (Uganda and Southern (Malawi Africa using a panel of microsatellite markers, incorporating both spatial and temporal analyses. Our data demonstrate that Ugandan T. b. rhodesiense existed as clonal populations, with a small number of highly related genotypes and substantial linkage disequilibrium between pairs of loci. However, these populations were not stable as the dominant genotypes changed and the genetic diversity also reduced over time. Thus these populations do not conform to one of the criteria for strict clonality, namely stability of predominant genotypes over time, and our results show that, in a period in the mid 1990s, the previously predominant genotypes were not detected but were replaced by a novel clonal population with limited genetic relationship to the original population present between 1970 and 1990. In contrast, the Malawi T. b. rhodesiense population demonstrated significantly greater diversity and evidence for frequent genetic exchange. Therefore, the population genetics of T. b. rhodesiense is more complex than previously described. This has important implications for the spread of the single copy T. b. rhodesiense gene that allows human infectivity, and therefore the epidemiology of the human disease, as well as suggesting that these parasites represent an important organism to study the influence of optional recombination upon population genetic dynamics.

  9. Intraspecific genetic admixture and the morphological diversification of an estuarine fish population complex.

    Science.gov (United States)

    Dodson, Julian J; Bourret, Audrey; Barrette, Marie France; Turgeon, Julie; Daigle, Gaétan; Legault, Michel; Lecomte, Frédéric

    2015-01-01

    The North-east American Rainbow smelt (Osmerus mordax) is composed of two glacial races first identified through the spatial distribution of two distinct mtDNA lineages. Contemporary breeding populations of smelt in the St. Lawrence estuary comprise contrasting mixtures of both lineages, suggesting that the two races came into secondary contact in this estuary. The overall objective of this study was to assess the role of intraspecific genetic admixture in the morphological diversification of the estuarine rainbow smelt population complex. The morphology of mixed-ancestry populations varied as a function of the relative contribution of the two races to estuarine populations, supporting the hypothesis of genetic admixture. Populations comprising both ancestral mtDNA races did not exhibit intermediate morphologies relative to pure populations but rather exhibited many traits that exceeded the parental trait values, consistent with the hypothesis of transgressive segregation. Evidence for genetic admixture at the level of the nuclear gene pool, however, provided only partial support for this hypothesis. Variation at nuclear AFLP markers revealed clear evidence of the two corresponding mtDNA glacial races. The admixture of the two races at the nuclear level is only pronounced in mixed-ancestry populations dominated by one of the mtDNA lineages, the same populations showing the greatest degree of morphological diversification and population structure. In contrast, mixed-ancestry populations dominated by the alternate mtDNA lineage showed little evidence of introgression of the nuclear genome, little morphological diversification and little contemporary population genetic structure. These results only partially support the hypothesis of transgressive segregation and may be the result of the differential effects of natural selection acting on admixed genomes from different sources. PMID:25856193

  10. Dualities in population genetics: a fresh look with new dualities

    CERN Document Server

    Carinci, Gioia; Giberti, Claudio; Redig, Frank

    2013-01-01

    We apply our general method of duality, introduced in [Giardina', Kurchan, Redig, J. Math. Phys. 48, 033301 (2007)], to models of population dynamics. The classical dualities between forward and ancestral processes can be viewed as a change of representation in the classical creation and annihilation operators, both for diffusions dual to coalescents of Kingman's type, as well as for models with finite population size. Next, using SU(1,1) raising and lowering operators, we find new dualities between the Wright-Fisher diffusion with $d$ types and the Moran model, both in presence and absence of mutations. These new dualities relates two forward evolutions. From our general scheme we also identify self-duality of the Moran model.

  11. Genetic and phenotypic differentiation of an Andean intermediate altitude population

    OpenAIRE

    Eichstaedt, Christina A; Antão, Tiago; Cardona, Alexia; Pagani, Luca; Kivisild, Toomas; Mormina, Maru

    2015-01-01

    Highland populations living permanently under hypobaric hypoxia have been subject of extensive research because of the relevance of their physiological adaptations for the understanding of human health and disease. In this context, what is considered high altitude is a matter of interpretation and while the adaptive processes at high altitude (above 3000 m) are well documented, the effects of moderate altitude (below 3000 m) on the phenotype are less well established. In this study, we compar...

  12. The effect of recurrent floods on genetic composition of marble trout populations.

    Directory of Open Access Journals (Sweden)

    José Martin Pujolar

    Full Text Available A changing global climate can threaten the diversity of species and ecosystems. We explore the consequences of catastrophic disturbances in determining the evolutionary and demographic histories of secluded marble trout populations in Slovenian streams subjected to weather extremes, in particular recurrent flash floods and debris flows causing massive mortalities. Using microsatellite data, a pattern of extreme genetic differentiation was found among populations (global F(ST of 0.716, which exceeds the highest values reported in freshwater fish. All locations showed low levels of genetic diversity as evidenced by low heterozygosities and a mean of only 2 alleles per locus, with few or no rare alleles. Many loci showed a discontinuous allele distribution, with missing alleles across the allele size range, suggestive of a population contraction. Accordingly, bottleneck episodes were inferred for all samples with a reduction in population size of 3-4 orders of magnitude. The reduced level of genetic diversity observed in all populations implies a strong impact of genetic drift, and suggests that along with limited gene flow, genetic differentiation might have been exacerbated by recurrent mortalities likely caused by flash flood and debris flows. Due to its low evolutionary potential the species might fail to cope with an intensification and altered frequency of flash flood events predicted to occur with climate change.

  13. Dispersal similarly shapes both population genetics and community patterns in the marine realm

    KAUST Repository

    Chust, Guillem

    2016-06-27

    Dispersal plays a key role to connect populations and, if limited, is one of the main processes to maintain and generate regional biodiversity. According to neutral theories of molecular evolution and biodiversity, dispersal limitation of propagules and population stochasticity are integral to shaping both genetic and community structure. We conducted a parallel analysis of biological connectivity at genetic and community levels in marine groups with different dispersal traits. We compiled large data sets of population genetic structure (98 benthic macroinvertebrate and 35 planktonic species) and biogeographic data (2193 benthic macroinvertebrate and 734 planktonic species). We estimated dispersal distances from population genetic data (i.e., FST vs. geographic distance) and from β-diversity at the community level. Dispersal distances ranked the biological groups in the same order at both genetic and community levels, as predicted by organism dispersal ability and seascape connectivity: macrozoobenthic species without dispersing larvae, followed by macrozoobenthic species with dispersing larvae and plankton (phyto- and zooplankton). This ranking order is associated with constraints to the movement of macrozoobenthos within the seabed compared with the pelagic habitat. We showed that dispersal limitation similarly determines the connectivity degree of communities and populations, supporting the predictions of neutral theories in marine biodiversity patterns.

  14. Feasibility of Genetic Algorithm for Textile Defect Classification Using Neural Network

    Directory of Open Access Journals (Sweden)

    Md. Tarek Habib

    2012-08-01

    Full Text Available The global market for textile industry is highly competitive nowadays. Quality control in productionprocess in textile industry has been a key factor for retaining existence in such competitive market.Automated textile inspection systems are very useful in this respect, because manual inspection is timeconsuming and not accurate enough. Hence, automated textile inspection systems have been drawing plentyof attention of the researchers of different countries in order to replace manual inspection. Defect detectionand defect classification are the two major problems that are posed by the research of automated textileinspection systems. In this paper, we perform an extensive investigation on the applicability of geneticalgorithm (GA in the context of textile defect classification using neural network (NN. We observe theeffect of tuning different network parameters and explain the reasons. We empirically find a suitable NNmodel in the context of textile defect classification. We compare the performance of this model with that ofthe classification models implemented by others.

  15. Genetic diversity and population structure of an important wild berry crop.

    Science.gov (United States)

    Zoratti, Laura; Palmieri, Luisa; Jaakola, Laura; Häggman, Hely

    2015-01-01

    The success of plant breeding in the coming years will be associated with access to new sources of variation, which will include landraces and wild relatives of crop species. In order to access the reservoir of favourable alleles within wild germplasm, knowledge about the genetic diversity and the pop