Genomes and Genes
Summary: The discipline studying genetic composition of populations and effects of factors such as SELECTION (GENETICS), population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.
Publications300 found, 100 shown here
- Inference of population structure using multilocus genotype dataJ K Pritchard
Department of Statistics, University of Oxford, United Kingdom
Genetics 155:945-59. 2000..g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html...
- Inference of population structure using multilocus genotype data: linked loci and correlated allele frequenciesDaniel Falush
Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, Schumann Strasse 21 22, 10117 Berlin, Germany
Genetics 164:1567-87. 2003..The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu...
- Population structure and eigenanalysisNick Patterson
Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
PLoS Genet 2:e190. 2006..This means that we can predict the dataset size needed to detect structure...
- Bayesian coalescent inference of past population dynamics from molecular sequencesA J Drummond
Department of Zoology, University of Oxford, Oxford, United Kingdom
Mol Biol Evol 22:1185-92. 2005....
- Detecting the number of clusters of individuals using the software STRUCTURE: a simulation studyG Evanno
Department of Ecology and Evolution, Biology Building, University of Lausanne, CH 1015 Lausanne, Switzerland
Mol Ecol 14:2611-20. 2005The identification of genetically homogeneous groups of individuals is a long standing issue in population genetics. A recent Bayesian algorithm implemented in the software STRUCTURE allows the identification of such groups...
- Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency dataJ M Cornuet
Laboratoire Population, Genetique, Evolution, CNRS, Gif sur Yvette, France
Genetics 144:2001-14. 1996..The usefulness of these tests for conservation biology is discussed...
- A comparison of bayesian methods for haplotype reconstruction from population genotype dataMatthew Stephens
Department of Statistics, University of Washington, Seattle, WA 98195 4322, USA
Am J Hum Genet 73:1162-9. 2003..The new algorithm is included in the software package PHASE, version 2.0, available online (http://www.stat.washington.edu/stephens/software.html)...
- Generating samples under a Wright-Fisher neutral model of genetic variationRichard R Hudson
Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA
Bioinformatics 18:337-8. 2002..The samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models...
- A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phasePaul Scheet
Department of Statistics, University of Washington, Seattle, 98195 4322, USA
Am J Hum Genet 78:629-44. 2006..The methods described in this article are implemented in a software package, fastPHASE, which is available from the Stephens Lab Web site...
- Approximate Bayesian computation in population geneticsMark A Beaumont
School of Animal and Microbial Sciences, The University of Reading, Whiteknights, Reading RG6 6AJ, United Kingdom
Genetics 162:2025-35. 2002..The method is suited to complex problems that arise in population genetics, extending ideas developed in this setting by earlier authors...
- PowerMarker: an integrated analysis environment for genetic marker analysisKejun Liu
Bioinformatics Research Center, North Carolina State University Raleigh, 27695 7566, USA
Bioinformatics 21:2128-9. 2005..It accelerates the analysis lifecycle and enables users to maintain data integrity throughout the process. An ever-growing list of more than 50 different statistical analyses for genetic markers has been implemented in PowerMarker...
- Genes mirror geography within EuropeJohn Novembre
Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics, University of California Los Angeles, Los Angeles, California 90095, USA
Nature 456:98-101. 2008..In addition, the results are relevant to the prospects of genetic ancestry testing; an individual's DNA can be used to infer their geographic origin with surprising accuracy-often to within a few hundred kilometres...
- A new multipoint method for genome-wide association studies by imputation of genotypesJonathan Marchini
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
Nat Genet 39:906-13. 2007..A notable future use of our method will be to boost power by combining data from genome-wide scans that use different SNP sets...
- Signals of recent positive selection in a worldwide sample of human populationsJoseph K Pickrell
Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
Genome Res 19:826-37. 2009..Finally, we search for local adaptation between geographically close populations, and highlight several examples...
- GENECLASS2: a software for genetic assignment and first-generation migrant detectionS Piry
Centre de Biologie et de Gestion des Populations, INRA, Campus International de Baillarguet CS 30 016, F34988, Monferrier sur Lez CEDEX, France
J Hered 95:536-9. 2004..e., not a first-generation migrant) in the population where it was sampled. A user-friendly interface facilitates the treatment of large datasets...
- The incomplete natural history of mitochondriaJ William O Ballard
Department of Biological Sciences, University of Iowa, Iowa City, Iowa 52242, USA
Mol Ecol 13:729-44. 2004..Here we limelight mitochondrial ecology, sexually antagonistic selection, life-history evolution including ageing and disease, and the evolution of mitochondrial inheritance...
- Isolation by distance, web serviceJeffrey L Jensen
High Tech High, 2861 Womble Road, San Diego, CA 92106 6025, USA
BMC Genet 6:13. 2005..However, few software programs exist for estimating the degree of isolation by distance among populations, and they tend not to be user-friendly...
- Detecting immigration by using multilocus genotypesB Rannala
Department of Integrative Biology, University of California, Berkeley, CA 94720 3140, USA
Proc Natl Acad Sci U S A 94:9197-201. 1997..The test has power to detect immigrant ancestors, for these data, up to two generations in the past even though the overall differentiation of allele frequencies among populations is low...
- Soft sweeps: molecular population genetics of adaptation from standing genetic variationJoachim Hermisson
Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilians University Munich, Germany
Genetics 169:2335-52. 2005..We find that soft sweeps with weaker selective footprints are likely under both scenarios if the mutation rate and/or the selection coefficient is high...
- Molecular signatures of natural selectionRasmus Nielsen
Center for Bioinformatics and Department of Evolutionary Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
Annu Rev Genet 39:197-218. 2005..Particular attention is placed on issues relating to the analysis of large-scale genomic data sets...
- Population genomics of human gene expressionBarbara E Stranger
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nat Genet 39:1217-24. 2007..We also explore several methodologies that improve the current state of analysis of gene expression variation...
- The power and promise of population genomics: from genotyping to genome typingGordon Luikart
Laboratoire d Ecologie Alpine, Génomique des Populations et Biodiversit, CNRS UMR 5553, Universite Joseph Fourier, B P 53, F 38041 Grenoble, Cedex 9, France
Nat Rev Genet 4:981-94. 2003..However, the most useful contribution of the genomics model to population genetics will be improving inferences about population demography and evolutionary history.
- Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approachP Beerli
Department of Genetics, University of Washington, Seattle, WA 98195 7360, USA
Proc Natl Acad Sci U S A 98:4563-8. 2001..The algorithm converges to the estimates fairly quickly, even when the Markov chain is started from unfavorable parameters. The method was used to estimate gene flow in the Nile valley by using mtDNA data from three human populations...
- Genome-wide detection and characterization of positive selection in human populationsPardis C Sabeti
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
Nature 449:913-8. 2007....
- Identifying adaptive genetic divergence among populations from genome scansMark A Beaumont
School of Animal and Microbial Sciences, The University of Reading, Whiteknights, PO Box 228, Reading RG6 6AJ, UK
Mol Ecol 13:969-80. 2004..Neither method could reliably distinguish loci under balancing selection in our simulations, even when the selection coefficient is twenty times the migration rate...
- Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population geneticsJody Hey
Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08846, USA
Proc Natl Acad Sci U S A 104:2785-90. 2007..Several examples, including an application to the divergence of chimpanzee subspecies, are provided...
- Relative impact of nucleotide and copy number variation on gene expression phenotypesBarbara E Stranger
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Science 315:848-53. 2007..Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans...
- Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and powerDavid Paetkau
Department of Zoology and Entomology, University of Queensland, St Lucia, QLD 4072, Australia
Mol Ecol 13:55-65. 2004....
- Global variation in copy number in the human genomeRichard Redon
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nature 444:444-54. 2006..The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies...
- Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in AfricaSohini Ramachandran
Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 102:15942-7. 2005..Given this serial-founder scenario, the relationship between genetic and geographic distance allows us to derive bounds for the effects of drift and natural selection on human genetic variation...
- Detection of reduction in population size using data from microsatellite lociJ C Garza
Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
Mol Ecol 10:305-18. 2001..This method, and others like it, promises to be an important tool for the conservation and management of populations that are in need of intervention or recovery...
- How to track and assess genotyping errors in population genetics studiesA Bonin
Laboratoire d Ecologie Alpine, CNRS UMR 5553, Universite Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France
Mol Ecol 13:3261-73. 2004..every genetic data set includes some erroneous genotypes, but genotyping errors remain a taboo subject in population genetics, even though they might greatly bias the final conclusions, especially for studies based on individual ..
- Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple lociBruce Rannala
Department of Medical Genetics, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
Genetics 164:1645-56. 2003The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution...
- Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence dataAlexei J Drummond
School of Biological Sciences, University of Auckland 1001, Auckland, New Zealand
Genetics 161:1307-20. 2002..We illustrate some of the important features of this approach on a genealogy of HIV-1 envelope (env) partial sequences...
- Calibrating a coalescent simulation of human genome sequence variationStephen F Schaffner
Program in Medical and Population Genetics, The Broad Institute, Cambridge, Massachusetts 02139, USA
Genome Res 15:1576-83. 2005..We anticipate that this model, for which software is publicly available, and others like it will have numerous applications in empirical studies of human genetics...
- The population genetics of dN/dSSergey Kryazhimskiy
Biology Department, University of Pennsylvania, Philadelphia, PA, USA
PLoS Genet 4:e1000304. 2008..These results have significant implications for the interpretation of dN/dS measurements among population-genetic samples...
- Time dependency of molecular rate estimates and systematic overestimation of recent divergence timesSimon Y W Ho
Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, Oxford, United Kingdom
Mol Biol Evol 22:1561-8. 2005....
- Using genome scans of DNA polymorphism to infer adaptive population divergenceJay F Storz
Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA
Mol Ecol 14:671-88. 2005..Finally, I consider the evolutionary and functional insights that might be gained by conducting genome scans for loci involved in adaptive population divergence...
- Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approachP Beerli
Department of Genetics, University of Washington, Box 357360, Seattle, Washington 98195 7360, USA
Genetics 152:763-73. 1999..The estimates are as good as or better than those from an optimized FST-based measure. The program is available on the World Wide Web at http://evolution.genetics. washington.edu/lamarc.html/...
- What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivityRobin S Waples
Northwest Fisheries Science Center, Seattle, WA 98112 USA
Mol Ecol 15:1419-39. 2006..Some recent theoretical developments and continued advances in computational power provide hope that this situation may change in the future...
- A worldwide survey of haplotype variation and linkage disequilibrium in the human genomeDonald F Conrad
Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
Nat Genet 38:1251-60. 2006..Consequently, although the portability of tag SNPs based on the HapMap is reduced in low-LD Africans, the HapMap will be helpful for the design of genome-wide association mapping studies in nearly all human populations...
- Estimation of pairwise relatedness with molecular markersM Lynch
Department of Biology, University of Oregon, Eugene, Oregon 97403
Genetics 152:1753-66. 1999..Two examples are given in which the new estimators are applied to natural populations, one that reveals isolation-by-distance in an annual plant and the other that suggests a genetic basis for a coat color polymorphism in bears...
- A Markov chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype dataHong Gao
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
Genetics 176:1635-51. 2007..48-0.70)...
- Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiologyKarine Brudey
Unite de la Tuberculose et des Mycobacteries, Institut Pasteur de Guadeloupe, Guadeloupe
BMC Microbiol 6:23. 2006..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 ..
- Genetic structure of human populationsNoah A Rosenberg
Molecular and Computational Biology, 1042 West 36th Place DRB 289, University of Southern California, Los Angeles, CA 90089, USA
Science 298:2381-5. 2002..General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies...
- DNA barcoding: how it complements taxonomy, molecular phylogenetics and population geneticsMehrdad Hajibabaei
Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
Trends Genet 23:167-72. 2007..example, here we compare the goals and methods of DNA barcoding with those of molecular phylogenetics and population genetics, and suggest that DNA barcoding can complement current research in these areas by providing background ..
- The hidden side of invasions: massive introgression by local genesMathias Currat
Computational and Molecular Population Genetics Laboratory, Institute of Zoology, University of Bern, Baltzerstrasse 6, 3012 Berne, Switzerland
Evolution 62:1908-20. 2008..Our results imply that speciation genes can be identified by comparing genomes of interfertile native and invading species pairs...
- Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysisArnaud Estoup
Centre de Biologie et de Gestion des Populations, Campus International de Baillarguet, 34980 Montferrier Lez, France
Mol Ecol 11:1591-604. 2002..that homoplasy at microsatellite electromorphs does not represent a significant problem for many types of population genetics analyses realized by molecular ecologists, the large amount of variability at microsatellite loci often ..
- Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traitsJ R Stinchcombe
Department of Ecology and Evolutionary Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
Heredity (Edinb) 100:158-70. 2008..Specifically, we discuss advantages and limitations of each method and argue that a combination of the two provides a powerful approach to uncovering the molecular mechanisms responsible for adaptation...
- Enhanced Bayesian modelling in BAPS software for learning genetic structures of populationsJukka Corander
Department of Mathematics, Fänriksgatan 3B, Abo Akademi University, Abo, Finland
BMC Bioinformatics 9:539. 2008..However, the complexity of biological problems related to genetic structure analysis keeps increasing such that in many cases the current methods may provide either inappropriate or insufficient solutions...
- A standardized genetic differentiation measurePhilip W Hedrick
School of Life Sciences, Arizona State University, Tempe 85287 4501, USA
Evolution 59:1633-8. 2005....
- APE: Analyses of Phylogenetics and Evolution in R languageEmmanuel Paradis
Laboratoire de Paléontologie, Paléobiologie and Phylogénie, Institut des Sciences de l Evolution, Universite Montpellier II, F 34095 Montpellier cedex 05, France
Bioinformatics 20:289-90. 2004..APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes...
- pegas: an R package for population genetics with an integrated-modular approachEmmanuel Paradis
Institut de Recherche pour le Developpement, UR175 CAVIAR, BP 5095, 361 Rue Jean François Breton, F 34196 Montpellier Cédex 5, France
Bioinformatics 26:419-20. 2010..pegas emphasizes the need to further develop an integrated-modular approach for software dedicated to the analysis of population genetic data...
- Heterogeneous genomic differentiation between walking-stick ecotypes: "isolation by adaptation" and multiple roles for divergent selectionPatrik Nosil
Department of Zoology, University of British Columbia, Vancouver, BC, Canada
Evolution 62:316-36. 2008..They thus illustrate the varied and sometimes nonintuitive contributions of selection to heterogeneous genomic differentiation...
- Glacial refugia: hotspots but not melting pots of genetic diversityRemy J Petit
Institut National de la Recherche Agronomique, UMR Biodiversité, Génes et Ecosystémes, F 33612 Cestas, France
Science 300:1563-5. 2003..However, the genetically most diverse populations were not located in the south but at intermediate latitudes, a likely consequence of the admixture of divergent lineages colonizing the continent from separate refugia...
- Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPsC Phillips
Forensic Genetics Department, University of Santiago de Compostela, 15782, and Centro Nacional de Genotipado CeGen, Hospital Clinico Universitario, 15706 Galicia, Spain
Forensic Sci Int Genet 1:273-80. 2007..This study shows that by choosing SNPs exhibiting marked allele frequency differences between population-groups a practical forensic test for assigning the most likely ancestry can be achieved from a single multiplexed assay...
- Positive natural selection in the human lineageP C Sabeti
Broad Institute of MIT and Harvard, Cambridge, MA, USA
Science 312:1614-20. 2006....
- Comparison of Bayesian and maximum-likelihood inference of population genetic parametersPeter Beerli
School of Computational Science and Department of Biological Sciences, Florida State University, Tallahassee, FL 32306 4120, USA
Bioinformatics 22:341-5. 2006..Using simulated datasets, the Bayesian method generally fares better than the ML approach in accuracy and coverage, although for some values the two approaches are equal in performance...
- Perspective: Reproductive isolation caused by natural selection against immigrants from divergent habitatsPatrik Nosil
Department of Biosciences, Behavioural Ecology Research Group, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
Evolution 59:705-19. 2005..We hope that the formal recognition of immigrant inviability and our demonstration of its evolutionary importance will stimulate more explicit empirical studies of its contributions to speciation...
- Estimation of individual admixture: analytical and study design considerationsHua Tang
Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
Genet Epidemiol 28:289-301. 2005..g., simulations) not possible by Bayesian methods. Our simulation results demonstrate that inclusion of ancestral populations or their surrogates in the analysis is required by any method of IA estimation to obtain reasonable results...
- A simulated annealing approach to define the genetic structure of populationsI Dupanloup
Dipartimento di Biologia, Universita di Ferrara, Via L Borsari 46, 44100 Ferrara, Italy
Mol Ecol 11:2571-81. 2002....
- Molecular clocks: when times are a-changin'Simon Y W Ho
Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
Trends Genet 22:79-83. 2006..We conclude that many studies involving recent divergence events will need to be reconsidered...
- The speed of evolution and maintenance of variation in asexual populationsMichael M Desai
Department of Physics, Harvard University, Cambridge, MA 02138, USA
Curr Biol 17:385-94. 2007..We focus on the effects of such multiple mutations...
- Compensatory mutations, antibiotic resistance and the population genetics of adaptive evolution in bacteriaB R Levin
Department of Biology, Emory University, Atlanta, Georgia 30322, USA
Genetics 154:985-97. 2000....
- Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populationsRemy J Petit
INRA, UMR Biodiversity, Genes and Ecosystems, 69 route d Arcachon, F 33612 Cestas cedex, France
Mol Ecol 14:689-701. 2005....
- simuPOP: a forward-time population genetics simulation environmentBo Peng
Department of Statistics, Rice University, Houston, TX 77005, USA
Bioinformatics 21:3686-7. 2005simuPOP is a forward-time population genetics simulation environment...
- Most species are not driven to extinction before genetic factors impact themDerek Spielman
Key Centre for Biodiversity and Bioresources, Department of Biological Sciences, Macquarie University, Sydney NSW 2109, Australia
Proc Natl Acad Sci U S A 101:15261-4. 2004..Thus, most taxa are not driven to extinction before genetic factors affect them adversely...
- G(ST) and its relatives do not measure differentiationLou Jost
Via Runtun, Baños, Tungurahua, Ecuador
Mol Ecol 17:4015-26. 2008..These measures can be directly related to the migration and mutation rates of the finite-island model...
- Estimating local ancestry in admixed populationsSriram Sankararaman
Computer Science Deptartment, University of California, Berkeley, CA 94720, USA
Am J Hum Genet 82:290-303. 2008....
- Use of population isolates for mapping complex traitsL Peltonen
Department of Medical Genetics, University of Helsinki and National Public Health Institute, Finland
Nat Rev Genet 1:182-90. 2000..Despite the obvious genetic and environmental complications, geneticists have targeted several population isolates for mapping genes for complex diseases...
- Pattern of polymorphism after strong artificial selection in a domestication eventHideki Innan
Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
Proc Natl Acad Sci U S A 101:10667-72. 2004..These theoretical results are discussed in light of data collected from maize. Although the main focus of this article is on domestication, this model can also be generalized to describe selective sweeps from standing genetic variation...
- Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contactMarkus Pfenninger
Abteilung Okologie und Evolution, Zoologisches Institut der J W Goethe Universitat, Frankfurt Main, Germany
Evolution 56:1776-88. 2002..unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal...
- A note on exact tests of Hardy-Weinberg equilibriumJanis E Wigginton
Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
Am J Hum Genet 76:887-93. 2005..They have been implemented in freely available code that will be useful for quality assessment of genotype data and for the detection of genetic association or population stratification in very large data sets...
- The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virusRafael Sanjuan
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, P O Box 22085, 46071 Valencia, Spain
Proc Natl Acad Sci U S A 101:8396-401. 2004..The proportion of beneficial mutations was unexpectedly high. Beneficial effects followed a gamma distribution, with expected fitness increases of 1% for random mutations and 5% for preobserved mutations...
- Identifying the environmental factors that determine the genetic structure of populationsMatthieu Foll
Laboratoire d Ecologie Alpine LECA, UMR CNRS 5553, 38 041 Grenoble Cedex 09, France
Genetics 174:875-91. 2006..We also carry out a simulation study to investigate the performance of the method and find that it can correctly identify the factors that play a role in the structuring of genetic diversity under a wide range of scenarios...
- Estimating genetic parameters in natural populations using the "animal model"Loeske E B Kruuk
Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, Scotland, UK
Philos Trans R Soc Lond B Biol Sci 359:873-90. 2004....
- Twenty years of phylogeography: the state of the field and the challenges for the Southern HemisphereLuciano B Beheregaray
Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
Mol Ecol 17:3754-74. 2008..I expect the information and views presented here will assist in promoting international collaborative work in phylogeography and in guiding research efforts at both regional and global levels...
- Genome-wide identification of susceptibility alleles for viral infections through a population genetics approachMatteo Fumagalli
Scientific Institute IRCCS E Medea, Bioinformatic Lab, Bosisio Parini LC, Italy
PLoS Genet 6:e1000849. 2010....
- Reduced genetic variation and the success of an invasive speciesN D Tsutsui
Department of Biology 0116, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0116, USA
Proc Natl Acad Sci U S A 97:5948-53. 2000..Here we examine the behavior and population genetics of the invasive Argentine ant (Linepithema humile) in its native and introduced ranges, and we provide a ..
- Linkage disequilibrium decay and haplotype block structure in the pigAndreia J Amaral
Animal Breeding and Genomics Centre, Wageningen UR, 6700AH, Wageningen, The Netherlands
Genetics 179:569-79. 2008..Second, modern breeding programs increased the extent of LD in Europe and caused differences of LD between genomic regions. Large White, Landrace, and Duroc showed evidence of past introgression from Chinese breeds...
- A Bayesian approach to inferring population structure from dominant markersKent E Holsinger
Department of Ecology and Evolutionary Biology, U 3043, University of Connecticut, Storrs, CT 06269 3043, USA
Mol Ecol 11:1157-64. 2002..We illustrate the method with a reanalysis of RAPD data from 14 populations of a North American orchid, Platanthera leucophaea...
- Pathogen-driven selection and worldwide HLA class I diversityFranck Prugnolle
Theoretical and Molecular Population Genetics Group, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, United Kingdom
Curr Biol 15:1022-7. 2005..This is in good agreement with both previous immunological and genetic data suggesting that HLA B could be under a higher selective pressure from pathogens...
- Microsatellite null alleles and estimation of population differentiationMarie Pierre Chapuis
Centre de Biologie et de Gestion des Populations, Institut National pour la Recherche Agronomique, Campus International de Baillarguet, Montferrier Lez, France
Mol Biol Evol 24:621-31. 2007Microsatellite null alleles are commonly encountered in population genetics studies, yet little is known about their impact on the estimation of population differentiation...
- The pattern of polymorphism in Arabidopsis thalianaMagnus Nordborg
Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
PLoS Biol 3:e196. 2005..Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics...
- IBD (Isolation by Distance): a program for analyses of isolation by distanceA J Bohonak
Department of Biology, San Diego State University, San Diego, CA 92182 4614, USA
J Hered 93:153-4. 2002
- EMPOP--a forensic mtDNA databaseWalther Parson
Institute of Legal Medicine, Innsbruck Medical University Müllerstreet 44, 6020 Innsbruck, Austria
Forensic Sci Int Genet 1:88-92. 2007..EMPOP has been launched on 16 October 2006 and is since then available at http://www.empop.org...
- Perspective: models of speciation: what have we learned in 40 years?Sergey Gavrilets
Department of Ecology and Evolutionary Biology, Department of Mathematics, University of Tennessee, Knoxville, Tennessee 37996, USA
Evolution 57:2197-215. 2003..Sympatric speciation is promoted if costs of being choosy are small (or absent) and if linkage between the loci experiencing disruptive selection and those controlling assortative mating is strong...
- Case-control studies of association in structured or admixed populationsJ K Pritchard
Department of Statistics, University of Oxford, Oxford, OX1 3TG, United Kingdom
Theor Popul Biol 60:227-37. 2001..We discuss the statistical issues involved in the different approaches and present results from simulations comparing the relative performance of the methods under a range of models...
- Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plantsHilde Nybom
Balsgård Department of Crop Science, Swedish University of Agricultural Sciences, Fjälkestadsvägen 459, SE 291 94 Kristianstad, Sweden
Mol Ecol 13:1143-55. 2004..plants per population and number of scored microsatellite DNA alleles are correlated with some of the population genetics parameters...
- Correlation between genetic and geographic structure in EuropeOscar Lao
Department of Forensic Molecular Biology, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
Curr Biol 18:1241-8. 2008..By including the widely used CEPH from Utah (CEU) samples into our analysis, we could show that these individuals represent northern and western Europeans reasonably well, thereby confirming their assumed regional ancestry...
- Association mapping in structured populationsJ K Pritchard
Department of Statistics, University of Oxford, United Kingdom
Am J Hum Genet 67:170-81. 2000..It provides power comparable with the TDT in many settings and may substantially outperform it if there are conflicting associations in different subpopulations...
- LAMARC 2.0: maximum likelihood and Bayesian estimation of population parametersMary K Kuhner
Department of Genome Sciences Box 357730 University of Washington Seattle, 98195 7730, USA
Bioinformatics 22:768-70. 2006..It is available as portable source code and executables for all three major platforms...
- How can tsetse population genetics contribute to African trypanosomiasis control?Philippe Solano
Institut de Recherche pour le Développement IRD Centre International de Recherche pour l Elevage en zones Subhumides CIRDES, IRD UMR 177, CIRDES 01 BP 454 Bobo Dioulasso 01, Burkina Faso
Trends Parasitol 26:255-63. 2010..This review mainly focuses on population genetics of tsetse of the palpalis group, the main vectors of sleeping sickness, and reports recent results on ..
- Genomic hotspots for adaptation: the population genetics of MÃ¼llerian mimicry in Heliconius eratoBrian A Counterman
Department of Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
PLoS Genet 6:e1000796. 2010....
- A new approach to estimate parameters of speciation models with application to apesCeline Becquet
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
Genome Res 17:1505-19. 2007..Similarly, Eastern and Western gorillas and Sumatran and Bornean orangutans appear to have experienced gene flow since their splits approximately 90 and over 250 Kya, respectively...
- Bayesian analysis of population structure based on linked molecular informationJukka Corander
Department of Mathematics and Statistics, P O Box 68, University of Helsinki, 00014 Helsinki, Finland
Math Biosci 205:19-31. 2007..The advantages of incorporating the dependence due to linkage in the classification models are illustrated by analyses of both simulated data and real samples of Bacillus cereus...
- A simple and robust statistical test for detecting the presence of recombinationTrevor C Bruen
McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
Genetics 172:2665-81. 2006..The results suggest that phi(w) is one of the best approaches to distinguish recurrent mutation from recombination in a wide variety of circumstances...
- Mitochondrial DNA as a marker of molecular diversity: a reappraisalN Galtier
Institut des Sciences de l Evolution, Universite Montpellier 2, C N R S UMR 5554, Place E Bataillon, CC 64, 34195 Montpellier, France
Mol Ecol 18:4541-50. 2009..We critically evaluate the usage of mitochondrial DNA for species delineation and identification. Finally, we note the great potential of accumulating mtDNA data for evolutionary and functional analysis of the mitochondrial genome...
- Surfing during population expansions promotes genetic revolutions and structurationLaurent Excoffier
Computational and Molecular Population Genetics Lab, Institute of Zoology, University of Berne, Baltzerstrasse 6, Berne, Switzerland
Trends Ecol Evol 23:347-51. 2008..They also suggest that a single range expansion can create very complex patterns at neutral loci, mimicking adaptive processes and resembling postglacial segregation of clades from distinct refuge areas...
- Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interfaceGilles Guillot
Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, P O Box 1066 Blindern, 0316 Oslo, Norway
Bioinformatics 24:1406-7. 2008..We show by simulations that the presence of null alleles can affect the accuracy of inferences if not properly accounted for and that our algorithm improve signficantly their accuracy...
- Mitochondrial DNA structure in the Arabian PeninsulaKhaled K Abu-Amero
Mitochondrial Research Laboratory, Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
BMC Evol Biol 8:45. 2008....
- Demographics and phylogeography of hybrid speciationJARED STRASBURG; Fiscal Year: 2007..abstract_text> ..
- The Rate and Molecular Spectrum of Spontaneous MutationsMichael Lynch; Fiscal Year: 2009....
- Diverse implications of population structure for identifying human disease genesAlkes Price; Fiscal Year: 2008..unreadable] [unreadable] [unreadable]..
- Defining an Obesity QTL on Chromosome 3qXiaofeng Zhu; Fiscal Year: 2007..The methodologies applied have been used successfully to identify unique sequence variants in linkage peaks and to conduct fine mapping with specific physiologic candidate genes. ..
- Linkage Disequilibrium Methods For Complex Trait MappingJonathan Pritchard; Fiscal Year: 2007..The long term goal of this project is to develop statistical/computational tools and models of LD that can be of practical use to complex trait mapping community, and will contribute to cheaper and more effective studies. ..
- GENETICS OF SPECIATION IN DROSOPHILAEMANUEL HEY; Fiscal Year: 2001....
- Admixture Mapping Development and Testing in AA SLEMichael Seldin; Fiscal Year: 2009..abstract_text> ..
- STOCHASTIC PROCESSES IN POPULATION GENETICSWarren Ewens; Fiscal Year: 2005..Evolutionary population genetics theory has in large part considered one gene locus and random-mating populations...
- THERMODYNAMICS AND STRUCTURE OF POLYMERIZING ACTINSANDRA GREER; Fiscal Year: 2001..abstract_text> ..
- MA Admixture Mapping Development & Application to NIDDMMichael Seldin; Fiscal Year: 2008..Finally, the three strongest signals will be further investigated utilizing a dense set of SNPs in the putative susceptibility regions. [unreadable] [unreadable]..
- Epigenetic Variation and its Determinants in DepressionJames Potash; Fiscal Year: 2008..Results from the novel studies proposed in this application should shed light on the epigenetic mechanisms and gene-environment interactions that result in vulnerability to depression. ..
- The effects of natural selection and recombination on molecular variation in struMALCOLM SCHUG; Fiscal Year: 2008..Such knowledge is critical for understanding the mechanisms determining the distribution of genetic traits in natural populations, including human genetic diseases. [unreadable] [unreadable] [unreadable]..
- Genome-wide identification of cis-regulatory polymorphisms in S. cerevisiaeKevin Chen; Fiscal Year: 2008..The aim of this project is to develop and validate computational methods that can eventually be used to create a comprehensive catalogue of gene regulatory variation in the human genome. [unreadable] [unreadable] [unreadable]..
- MOLECULAR EPIDEMIOLOGY OF COLORECTAL CANCERStephen Gruber; Fiscal Year: 2008..abstract_text> ..
- An Imprinted Gene Cluster on Mouse Chromosome 12Jennifer Schmidt; Fiscal Year: 2008..abstract_text> ..
- TRANSGRESSIVE SEGREGATION, ADAPTATION, AND SPECIATIONLoren Rieseberg; Fiscal Year: 2008..The proposed work represents an important step toward understanding the contribution of hybridization to adaptive evolution and speciation. ..
- Population Genetics & Drug Dependence in Asian IsolatesJennifer Listman; Fiscal Year: 2007..g., admixed but genetically close European populations. [unreadable] [unreadable] [unreadable]..
- Mutation rate catastrophe: testing a novel theory for the extinction of clonal orPHILIP JOHN GERRISH; Fiscal Year: 2010....
- Working Models of HIV Persistence & EvolutionIGOR ROUZINE; Fiscal Year: 2008..At this stage of our research, we will put emphasis on follow-up tests of our models in collaborating groups and design of new tests of updated models. [unreadable] [unreadable] [unreadable]..
- Novel Statistical Methods for Human Gene MappingMICHAEL PHILIP EPSTEIN; Fiscal Year: 2010..Finally, this project will be opportunistic in identifying and addressing unforseen statistical problems arising in human gene mapping studies. ..
- Clinicians' Concepts of Racial/Ethnic Differences in the Management of Chronic IlLinda M Hunt; Fiscal Year: 2010....
- Genome-Wide Analysis of Adaptive Evolution in HumansJOSHUA MICHAEL AKEY; Fiscal Year: 2010..Research that increases our understanding of the evolutionary forces that shape patterns of human genetic variation will facilitate disease gene mapping studies. ..
- Molecular Genetics of Cadmium ToxicityDaniel W Nebert; Fiscal Year: 2010....
- Development and Implementation of Genome-wide Exome Re-sequencing for Medical GenStacey Gabriel; Fiscal Year: 2009....
- HYPERTENSION IN POPULATIONS OF WEST AFRICAN ORIGINRichard Cooper; Fiscal Year: 2008..The African diaspora creates a unique opportunity for these[unreadable] cross-cultural studies.[unreadable]..
- Adolescents at High Risk for Familial Bipolar DisorderJohn Nurnberger; Fiscal Year: 2009..The ethical implications of this research will be studied by examining the effects of participation and the effect on self-esteem due to high- risk status. ..
- Identifying human adaptations: theory and applicationsMolly Przeworski; Fiscal Year: 2009..Thus, the proposed research will generate new statistical tools for the detection of regions of functional importance and will identify the first set of candidates for human-specific adaptations in gene expression regulation. ..
- Population genomics of Streptococcus pyogenesDEBRA BESSEN; Fiscal Year: 2009..abstract_text> ..
- METHYLATION PROFILING AND RISK OF COLORECTAL CANCERHassan Ashktorab; Fiscal Year: 2007..These studies will help in the detection and _rofiling of genetic changes in the pathway of CRC in AA. ..
- Population structure in whole-genome disease scansDavid Reich; Fiscal Year: 2008..We believe our new techniques will provide near-optimal power, and will be computationally efficient. We intend to make all these tools publicly available for the scientific community. [unreadable] [unreadable] [unreadable] [unreadable]..
- Microarray Analyses of Polluted Natural PopulationsMARJORIE OLEKSIAK; Fiscal Year: 2008..These patterns will provide indices of pollutant exposure in other polluted populations. [unreadable] [unreadable] [unreadable]..
- Gene expression variation in geographically diverse human populationsJOSHUA MICHAEL AKEY; Fiscal Year: 2010..Research that increases our understanding of gene expression variation will facilitate disease gene mapping studies. ..
- GENOME WIDE ANALYSIS OF DNA COPY NUMBER BY ARRAYDaniel Pinkel; Fiscal Year: 2001..The combination of array CGH data with data from other sources, for example microarray measurements of mRNA expression. will provide an even more powerful window on the genetic events involved in cancer development and progression. ..
- Quantitative genomics of sexual dimorphismSergey Nuzhdin; Fiscal Year: 2005..We expect our results to have a profound impact on our understanding of the evolution of sexual dimorphism, and the role that sexual differentiation plays in the generation of phenotypic diversity. ..
- STUDIES OF GENOMIC IMPRINTING IN BIPOLAR DISORDERJames Potash; Fiscal Year: 2005....
- ROBUST LINKAGE METHODS FOR HUMAN PEDIGREE DATAKatrina Goddard; Fiscal Year: 2004..At the end of the project period, a comprehensive set of tools for model-free affected relative pair analysis will be available. ..
- DISEASE DYNAMICS FOLLOWING MULTIPLE VECTOR INTRODUCTIONSROBERT FLEISCHER; Fiscal Year: 2004..We will use isolates of P. relictum from America, Australia, and Hawaii, and also from sites to be determined by our results from the survey for the geographic origin of Hawaiian P. relictum...
- Collaborative Clinical Culture and Quality of CareSheldon Greenfield; Fiscal Year: 2003..The results of this study will provide insight into whether HCTs are associated with high staff morale and high quality of care. ..
- PHYSIOLOGICAL STRESS REACTIVITY AND PREGNANCY OUTCOMESPathik Wadhwa; Fiscal Year: 2002....
- EVOLUTION OF GROUP A STREPTOCOCCIDEBRA BESSEN; Fiscal Year: 2004..These sera will be tested to determine whether strain structure is determined by the immunogenicity of the emm and sof gene products. ..
- PHASE VARIATION IN SACCHAROMYCES CEREVISIAEJOHN MCCUSKER; Fiscal Year: 2003..The PHI genes will be introduced to the non-phase variable laboratory strain, 288c, in efforts to reconstruct phase variation. ..
- UCI-CFC Projects on School ReadinessJames Swanson; Fiscal Year: 2002....
- POLYMORPHISM/DIVERGENCE IN DROSOPHILA PATHOGEN DEFENSESAndrew Clark; Fiscal Year: 2002This is a proposal to investigate the molecular population genetics of bacteriocidal genes in Drosophila melanogaster. There are three components to the research plan...
- Cultural and Ethical Issues in Genetic Family StudiesNedal Arar; Fiscal Year: 2002..2) recruiters' perspective on family enrollment. (3) association of participants' responses with demographic characteristics. (4) ethnic differences in attitudes towards participation in GFS. ..
- Molecular Evolution of Resistance in Strep. pyogenesDEBRA BESSEN; Fiscal Year: 2005..GAS provide a sound model system for understanding the molecular evolution underlying the early stages of the emergence and global spread of antibiotic resistance. ..
- Using Third-Party Data in Pedigree and Subgroup AnalysesMORRIS FOSTER; Fiscal Year: 2005..Finally, we will examine the implications of third-party information from the perspectives of study participants. We will conduct this project in the contexts of actual clinical populations. ..
- African-American Haplotype Map Engagement and Follow-upMORRIS FOSTER; Fiscal Year: 2004..abstract_text> ..
- Development of SPR/MS protein array platformDobrin Nedelkov; Fiscal Year: 2007..abstract_text> ..
- MALDI-TOF to Analyze KIR Association with HIV DiseaseElizabeth Trachtenberg; Fiscal Year: 2006..Data from this study will be critical to future studies examining the functional significance of KIR gene expression in HIV disease. [unreadable] [unreadable]..
- Calcium ATPases in Apicomplexan Parasites as Potential DL Sibley; Fiscal Year: 2006..Knowledge gained through these studies may improve the ability to pharmacologically inhibit key calcium regulatory enzymes and hence block motility and invasion by this important group of parasites. ..
- CONCEPTS OF RACE & ETHNICITY IN GENETICS RESEARCHLinda Hunt; Fiscal Year: 2005..3) Explore how research findings and clinical experiences regarding the relevance of race and ethnicity are interpreted and applied by genetic scientists and clinicians. ..
- Linkage Disequilibrium: mapping and positional cloningNewton Morton; Fiscal Year: 2006..abstract_text> ..
- Bayesian methods for analyzing genetic diversityKENT HOLSINGER; Fiscal Year: 2006..Moreover, we develop refinements to existing user-friendly software implementing the methods we develop and make the software and the associated source code freely available under the GNU General Public license. ..
- Genetics of Attention Deficit-Hyperactivity DisorderJames Swanson; Fiscal Year: 2006..Genomic haplotypes", meaning haplo-specific genotypes at more than one locus, will be defined and tested for possible interactive roles among the genes. ..
- Analysis of Ethnic Admixture in Lung CancerJill Barnholtz Sloan; Fiscal Year: 2006..These projects will give me experience in developing methodology in statistical genetics and genetic epidemiology, while also helping me to better understand etiology of disease. ..
- Comparative Functional Genomics of Drosophila ObesityAndrew Clark; Fiscal Year: 2009..which particular genes and pathways are most relevant to variation in fat storage homeostasis, and by developing a systems biology approach to make inferences from data that span cellular, endocrine, and whole-organism attributes ..
- Inferring Multiple-SNP Disease Association with DNA Resequence DataRasmus Nielsen; Fiscal Year: 2010..These methods will also be extended to include prior information about molecular mechanisms of gene function, where available, as well as environmental contributions to disease risk. ..
- Molecular epidemiology of drug resistant malariaMIRIAM LAUFER; Fiscal Year: 2008..abstract_text> ..
- Molecular Genetics of Dengue Resistance in MosquitoesDavid Severson; Fiscal Year: 2008..abstract_text> ..
- Associating genetic variation to resistance to severe malaria in East AfricaDavid Reich; Fiscal Year: 2007..unreadable] [unreadable] [unreadable]..
- Building a Latino admixture map & pilot study to find Type 2 Diabetes riskDavid Reich; Fiscal Year: 2007..The study will also enable larger admixture mapping studies with many thousands of patients with Type 2 Diabetes, which we would like to pursue both in U.S. Latino and in Latin American populations. [unreadable] [unreadable] [unreadable]..
- PAHs: Balance of Detoxication vs Metabolic ActivationDaniel Nebert; Fiscal Year: 2009..dissemination of ingested BaP and will be informative in clinical studies in which we would determine which haplotypes of these three human genes might be associated with resistance vs. sensitivity to PAH-induced toxicity and cancer. ..
- RFLP MAPPING OF PLASMODIUM REFACTORY GENES IN MOSQUITOESDavid Severson; Fiscal Year: 2004..abstract_text> ..
- The Aedes aegypti Genome ProjectDavid Severson; Fiscal Year: 2003..The long range goal is to promote and foster collaboration between funding agencies to support an effort to sequence the entire A. aegypti genome. ..
- GENOTOXICITY IN CYP1A2 DEFICIENT TRANSGENIC MICEDaniel Nebert; Fiscal Year: 2002..S. population. ..
- CYP1A1 GENE AND ENVIRONMENTAL TOXICITYDaniel Nebert; Fiscal Year: 2005..abstract_text> ..