Glossary for Anth 3234: Genes, Health, and History
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Approximating Selective Sweeps
Approximating Selective Sweeps by Richard Durrett and Jason Schweinsberg Dept. of Math, Cornell U. Corresponding Author: Richard Durrett Dept. of Mathematics 523 Malott Hall Cornell University Ithaca NY 14853 Phone: 607-255-8282 FAX: 607-255-7149 email: [email protected] 1 ABSTRACT The fixation of advantageous mutations in a population has the effect of reducing varia- tion in the DNA sequence near that mutation. Kaplan, Hudson, and Langley (1989) used a three-phase simulation model to study the effect of selective sweeps on genealogies. However, most subsequent work has simplified their approach by assuming that the number of individ- uals with the advantageous allele follows the logistic differential equation. We show that the impact of a selective sweep can be accurately approximated by a random partition created by a stick-breaking process. Our simulation results show that ignoring the randomness when the number of individuals with the advantageous allele is small can lead to substantial errors. Key words: selective sweep, hitchhiking, coalescent, random partition, paintbox construction 2 When a selectively favorable mutation occurs in a population and is subsequently fixed (i.e., its frequency rises to 100%), the frequencies of alleles at closely linked loci are altered. Alleles present on the chromosome on which the original mutation occurred will tend to increase in frequency, and other alleles will decrease in frequency. Maynard Smith and Haigh (1974) referred to this as the ‘hitchhiking effect,’ because an allele can get a lift in frequency from selection acting on a neighboring allele. They considered a situation with a neutral locus with alleles A and a and a second locus where allele B has a fitness of 1 + s relative to b. -
Y-Chromosome Short Tandem Repeat, Typing Technology, Locus Information and Allele Frequency in Different Population: a Review
Vol. 14(27), pp. 2175-2178, 8 July, 2015 DOI:10.5897/AJB2015.14457 Article Number: 2E48C3F54052 ISSN 1684-5315 African Journal of Biotechnology Copyright © 2015 Author(s) retain the copyright of this article http://www.academicjournals.org/AJB Review Y-Chromosome short tandem repeat, typing technology, locus information and allele frequency in different population: A review Muhanned Abdulhasan Kareem1, Ameera Omran Hussein2 and Imad Hadi Hameed2* 1Babylon University, Centre of Environmental Research, Hilla City, Iraq. 2Department of Molecular Biology, Babylon University, Hilla City, Iraq. Received 29 January, 2015; Accepted 29 June, 2015 Chromosome Y microsatellites seem to be ideal markers to delineate differences between human populations. They are transmitted in uniparental and they are very sensitive for genetic drift. This review will highlight the importance of the Y- Chromosome as a tool for tracing human evolution and describes some details of Y-chromosomal short tandem repeat (STR) analysis. Among them are: microsatellites, amplification using polymerase chain reaction (PCR) of STRs, separation and detection and advantages of X-chromosomal microsatellites. Key words: Forensic, population, review, STR, Y- chromosome. INTRODUCTION Microsatellites are DNA regions with repeat units that are microsatellite, but repeats of five (penta-) or six (hexa-) 2 to 7 bp in length or most generally short tandem nucleotides are usually classified as microsatellites as repeats (STRs) or simple sequence repeats (SSRs) well. DNA can be used to study human evolution. (Ellegren, 2000; Imad et al., 2014). The classification of Besides, information from DNA typing is important for the DNA sequences is determined by the length of the medico-legal matters with polymorphisms leading to more core repeat unit and the number of adjacent repeat units. -
Population Genetic Considerations for Using Biobanks As International
Carress et al. BMC Genomics (2021) 22:351 https://doi.org/10.1186/s12864-021-07618-x REVIEW Open Access Population genetic considerations for using biobanks as international resources in the pandemic era and beyond Hannah Carress1, Daniel John Lawson2 and Eran Elhaik1,3* Abstract The past years have seen the rise of genomic biobanks and mega-scale meta-analysis of genomic data, which promises to reveal the genetic underpinnings of health and disease. However, the over-representation of Europeans in genomic studies not only limits the global understanding of disease risk but also inhibits viable research into the genomic differences between carriers and patients. Whilst the community has agreed that more diverse samples are required, it is not enough to blindly increase diversity; the diversity must be quantified, compared and annotated to lead to insight. Genetic annotations from separate biobanks need to be comparable and computable and to operate without access to raw data due to privacy concerns. Comparability is key both for regular research and to allow international comparison in response to pandemics. Here, we evaluate the appropriateness of the most common genomic tools used to depict population structure in a standardized and comparable manner. The end goal is to reduce the effects of confounding and learn from genuine variation in genetic effects on phenotypes across populations, which will improve the value of biobanks (locally and internationally), increase the accuracy of association analyses and inform developmental efforts. Keywords: Bioinformatics, Population structure, Population stratification bias, Genomic medicine, Biobanks Background individuals, families, communities and populations, ne- Association studies aim to detect whether genetic vari- cessitated genomic biobanks. -
Combinatorial Genomic Data Refute the Human Chromosome 2 Evolutionary Fusion and Build a Model of Functional Design for Interstitial Telomeric Repeats
The Proceedings of the International Conference on Creationism Volume 8 Print Reference: Pages 222-228 Article 32 2018 Combinatorial Genomic Data Refute the Human Chromosome 2 Evolutionary Fusion and Build a Model of Functional Design for Interstitial Telomeric Repeats Jeffrey P. Tomkins Institute for Creation Research Follow this and additional works at: https://digitalcommons.cedarville.edu/icc_proceedings Part of the Biology Commons, and the Genomics Commons DigitalCommons@Cedarville provides a publication platform for fully open access journals, which means that all articles are available on the Internet to all users immediately upon publication. However, the opinions and sentiments expressed by the authors of articles published in our journals do not necessarily indicate the endorsement or reflect the views of DigitalCommons@Cedarville, the Centennial Library, or Cedarville University and its employees. The authors are solely responsible for the content of their work. Please address questions to [email protected]. Browse the contents of this volume of The Proceedings of the International Conference on Creationism. Recommended Citation Tomkins, J.P. 2018. Combinatorial genomic data refute the human chromosome 2 evolutionary fusion and build a model of functional design for interstitial telomeric repeats. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. Whitmore, pp. 222–228. Pittsburgh, Pennsylvania: Creation Science Fellowship. Tomkins, J.P. 2018. Combinatorial genomic data refute the human chromosome 2 evolutionary fusion and build a model of functional design for interstitial telomeric repeats. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. Whitmore, pp. 222–228. Pittsburgh, Pennsylvania: Creation Science Fellowship. COMBINATORIAL GENOMIC DATA REFUTE THE HUMAN CHROMOSOME 2 EVOLUTIONARY FUSION AND BUILD A MODEL OF FUNCTIONAL DESIGN FOR INTERSTITIAL TELOMERIC REPEATS Jeffrey P. -
Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC
© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Gene Linkage and © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 4NOTGenetic FOR SALE OR DISTRIBUTIONMapping NOT FOR SALE OR DISTRIBUTION CHAPTER ORGANIZATION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR4.1 SALELinked OR alleles DISTRIBUTION tend to stay 4.4NOT Polymorphic FOR SALE DNA ORsequences DISTRIBUTION are together in meiosis. 112 used in human genetic mapping. 128 The degree of linkage is measured by the Single-nucleotide polymorphisms (SNPs) frequency of recombination. 113 are abundant in the human genome. 129 The frequency of recombination is the same SNPs in restriction sites yield restriction for coupling and repulsion heterozygotes. 114 fragment length polymorphisms (RFLPs). 130 © Jones & Bartlett Learning,The frequency LLC of recombination differs © Jones & BartlettSimple-sequence Learning, repeats LLC (SSRs) often NOT FOR SALE OR DISTRIBUTIONfrom one gene pair to the next. NOT114 FOR SALEdiffer OR in copyDISTRIBUTION number. 131 Recombination does not occur in Gene dosage can differ owing to copy- Drosophila males. 115 number variation (CNV). 133 4.2 Recombination results from Copy-number variation has helped human populations adapt to a high-starch diet. 134 crossing-over between linked© Jones alleles. & Bartlett Learning,116 LLC 4.5 Tetrads contain© Jonesall & Bartlett Learning, LLC four products of meiosis. -
A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome
PLoS BIOLOGY A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome Kun Tang1*, Kevin R. Thornton2, Mark Stoneking1 1 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, 2 Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America Genome-wide scanning for signals of recent positive selection is essential for a comprehensive and systematic understanding of human adaptation. Here, we present a genomic survey of recent local selective sweeps, especially aimed at those nearly or recently completed. A novel approach was developed for such signals, based on contrasting the extended haplotype homozygosity (EHH) profiles between populations. We applied this method to the genome single nucleotide polymorphism (SNP) data of both the International HapMap Project and Perlegen Sciences, and detected widespread signals of recent local selection across the genome, consisting of both complete and partial sweeps. A challenging problem of genomic scans of recent positive selection is to clearly distinguish selection from neutral effects, given the high sensitivity of the test statistics to departures from neutral demographic assumptions and the lack of a single, accurate neutral model of human history. We therefore developed a new procedure that is robust across a wide range of demographic and ascertainment models, one that indicates that certain portions of the genome clearly depart from neutrality. Simulations of positive selection showed that our tests have high power towards strong selection sweeps that have undergone fixation. Gene ontology analysis of the candidate regions revealed several new functional groups that might help explain some important interpopulation differences in phenotypic traits. -
Refining the Use of Linkage Disequilibrium As A
HIGHLIGHTED ARTICLE | INVESTIGATION Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps Guy S. Jacobs,*,†,1 Timothy J. Sluckin,* and Toomas Kivisild‡ *Mathematical Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, †Complexity Institute, Nanyang Technological University, Singapore 637723, and ‡Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, United Kingdom ORCID IDs: 0000-0002-4698-7758 (G.S.J.); 0000-0002-9163-0061 (T.J.S.); 0000-0002-6297-7808 (T.K.) ABSTRACT During a selective sweep, characteristic patterns of linkage disequilibrium can arise in the genomic region surrounding a selected locus. These have been used to infer past selective sweeps. However, the recombination rate is known to vary substantially along the genome for many species. We here investigate the effectiveness of current (Kelly’s ZnS and vmax) and novel statistics at inferring hard selective sweeps based on linkage disequilibrium distortions under different conditions, including a human-realistic demographic model and recombination rate variation. When the recombination rate is constant, Kelly’s ZnS offers high power, but is outperformed by a novel statistic that we test, which we call Za: We also find this statistic to be effective at detecting sweeps from standing variation. When recombination rate fluctuations are included, there is a considerable reduction in power for all linkage disequilibrium-based statistics. However, this can largely be reversed by appropriately controlling for expected linkage disequilibrium using a genetic map. To further test these different methods, we perform selection scans on well-characterized HapMap data, finding that all three statistics—vmax; Kelly’s ZnS; and Za—are able to replicate signals at regions previously identified as selection candidates based on population differentiation or the site frequency spectrum. -
Identification of Selective Sweeps, Major Genes, and Genotype by Diet Interactions Melanie D
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Theses and Dissertations in Animal Science Animal Science Department 12-2015 Genomic Analysis of Sow Reproductive Traits: Identification of Selective Sweeps, Major Genes, and Genotype by Diet Interactions Melanie D. Trenhaile University of Nebraska-Lincoln, [email protected] Follow this and additional works at: http://digitalcommons.unl.edu/animalscidiss Part of the Meat Science Commons Trenhaile, Melanie D., "Genomic Analysis of Sow Reproductive Traits: Identification of Selective Sweeps, Major Genes, and Genotype by Diet Interactions" (2015). Theses and Dissertations in Animal Science. 114. http://digitalcommons.unl.edu/animalscidiss/114 This Article is brought to you for free and open access by the Animal Science Department at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Theses and Dissertations in Animal Science by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. GENOMIC ANALYSIS OF SOW REPRODUCTIVE TRAITS: IDENTIFICATION OF SELECTIVE SWEEPS, MAJOR GENES, AND GENOTYPE BY DIET INTERACTIONS By Melanie Dawn Trenhaile A THESIS Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science Major: Animal Science Under the Supervision of Professor Daniel Ciobanu Lincoln, Nebraska December, 2015 GENOMIC ANALYSIS OF SOW REPRODUCTIVE TRAITS: IDENTIFICATION OF SELECTIVE SWEEPS, MAJOR GENES, AND GENOTYPE BY DIET INTERACTIONS Melanie D. Trenhaile, M.S. University of Nebraska, 2015 Advisor: Daniel Ciobanu Reproductive traits, such as litter size and reproductive longevity, are economically important. However, selection for these traits is difficult due to low heritability, polygenic nature, sex-limited expression, and expression late in life. -
Genetic Linkage Analysis
BASIC SCIENCE SEMINARS IN NEUROLOGY SECTION EDITOR: HASSAN M. FATHALLAH-SHAYKH, MD Genetic Linkage Analysis Stefan M. Pulst, MD enetic linkage analysis is a powerful tool to detect the chromosomal location of dis- ease genes. It is based on the observation that genes that reside physically close on a chromosome remain linked during meiosis. For most neurologic diseases for which the underlying biochemical defect was not known, the identification of the chromo- Gsomal location of the disease gene was the first step in its eventual isolation. By now, genes that have been isolated in this way include examples from all types of neurologic diseases, from neu- rodegenerative diseases such as Alzheimer, Parkinson, or ataxias, to diseases of ion channels lead- ing to periodic paralysis or hemiplegic migraine, to tumor syndromes such as neurofibromatosis types 1 and 2. Arch Neurol. 1999;56:667-672 With the advent of new genetic markers tin gene, diagnosis using flanking mark- and automated genotyping, genetic map- ers requires the analysis of several family ping can be conducted extremely rap- members. idly. Genetic linkage maps have been gen- erated for the human genome and for LINKAGE OF GENES model organisms and have provided the basis for the construction of physical maps When Mendel observed an “independent that permit the rapid mapping of disease assortment of traits” (Mendel’s second traits. law), he was fortunate to have chosen traits As soon as a chromosomal location that were not localized close to one an- for a disease phenotype has been estab- other on the same chromosome.1 Subse- lished, genetic linkage analysis helps quent studies revealed that many genes determine whether the disease pheno- were indeed linked, ie, that traits did not type is only caused by mutation in a assort or segregate independently, but that single gene or mutations in other genes traits encoded by these linked genes were can give rise to an identical or similar inherited together. -
Microdeletion of the Azfc Locus with High Frequency of Mosaicism 46,XY/47XYY in Cases of Non Obstructive Azoospermia in Eastern Population of India
Microdeletion of the AZFc locus with high frequency of mosaicism 46,XY/47XYY in cases of non obstructive azoospermia in eastern population of India A.K. Saxena and K. Aniket Department of Pathology/Lab Medicine, Molecular Cytogenetics Laboratory, All India Institute of Medical Sciences, Patna (Bihar), India Corresponding author: A.K. Saxena E-mail: [email protected] Genet. Mol. Res. 18 (2): gmr18349 Received May 07, 2019 Accepted June 06, 2019 Published June 18, 2019 DOI http://dx.doi.org/10.4238/gmr18349 ABSTRACT. The etiopathology of male infertility is highly complex, involving gene - environment interactions to regulate spermatogenesis. Consequently, genetic analysis becomes imperative for cases of non-obstructive azoospermia (NOA) to identify the causative factors. Cases (n = 111) of NOA referred to the cytogenetics and molecular genetics laboratory of the All India Institute of Medical Sciences in -Patna from 2013-2018 were subjected to 1) karyotyping using GTG bandings techniques, 2) fluorescence in situ hybridization (FISH) for the sex determining region (SRY), and 3) PCR based analysis of STS markers based on microdeletion of the Y- chromosome after isolation of genomic DNA from whole blood. A flow cytometer was used for a cell- kinetic and DNA methylation study after incorporation of 5-azacytidine (5- AzaC) (1.0 ug/mL) in lymphocyte culture. PCR products were analyzed on an agarose gel (1.5%) and bands were visualized on Gel Doc after ethidium bromide staining. Chromosomal abnormalities, including structural numerical variations, were observed in 14 of the karyotypes. Eight cases showed a 46,XY/47,XYY i.e. mosaic pattern; two cases 46, XY/45/XO; a single case with 47,XY +16; two cases with 46,X+ ring Y; a single case with 46,XY+dicentric in Genetics and Molecular Research 18 (2): gmr18349 ©FUNPEC-RP www.funpecrp.com.br A.K. -
Rapid Evolution of a Skin-Lightening Allele in Southern African Khoesan
Rapid evolution of a skin-lightening allele in southern African KhoeSan Meng Lina,1,2, Rebecca L. Siforda,b,3, Alicia R. Martinc,d,e,3, Shigeki Nakagomef, Marlo Möllerg, Eileen G. Hoalg, Carlos D. Bustamanteh, Christopher R. Gignouxh,i,j, and Brenna M. Henna,2,4 aDepartment of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, NY 11794; bThe School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287; cAnalytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114; dProgram in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141; eStanley Center for Psychiatric Research, Broad Institute, Cambridge, MA 02141; fSchool of Medicine, Trinity College Dublin, Dublin 2, Ireland; gDST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa; hDepartment of Genetics, Stanford University, Stanford, CA 94305; iColorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045; and jDepartment of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 Edited by Nina G. Jablonski, The Pennsylvania State University, University Park, PA, and accepted by Editorial Board Member C. O. Lovejoy October 18, 2018 (received for review February 2, 2018) Skin pigmentation is under strong directional selection in northern Amhara or another group who themselves are substantially European and Asian populations. The indigenous KhoeSan popula- admixed with Near Eastern people has been proposed (13, 14). -
A Genetic Map of Chromosome 11 Q. Including the Atopy Locus
Original Paper EurJ Hum Genet 1995;3:188-194 A.J. Sandforda A Genetic Map of Chromosome M.F. Moffat t* S.E. Danielsa 11 q. Including the Atopy Locus Y. Nakamura'0 GM. Lathropc J.M. Hopkind W.O.CM. Cooksona 1608202 a Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, UK; b Division of Biochemistry, Abstract Cancer Institute, Tokyo, Japan; Atopy is a common and genetically heterogeneous syndrome c CEPHB, Paris, France; and predisposing to allergic asthma and rhinitis. A locus linked to d Osier Chest Unit, Churchill Hospital, Oxford, UK the atopy phenotype has been shown to be present on chromo some llql2-13. Linkage has only been seen in maternally derived alleles. We have constructed a genetic linkage map of Key Words the region, using 15 markers to span approximately 27 cM, Atopy and integrate previously published maps. Under a model of Genetic map maternal inheritance, the atopy locus is placed within a 7-cM Linkage analysis interval between D11S480 and D11S451. The interval con Chromosome 11 tains the important candidate gene FCERIB. Introduction The linkage has been replicated in nuclear families [3], and has been independently con Atopy is a common familial syndrome firmed in extended Japanese families [4], and which underlies allergic asthma and rhinitis. Dutch asthmatic sib pairs [5]. All these posi It is characterised by immunoglobulin E re tive linkage results were seen in families with sponses to common aero-allergens such as severe symptomatic atopy. Linkage at this grass pollens or house dust mite. An atopy- locus is made more difficult because it is seen associated phenotype may be defined by mea predominately through maternal meioses [3- suring prick skin test responses to these aller 7], Linkage is also confounded by a high pop gens, by measuring specific IgE responses and ulation prevalence, and low penetrance in ear by estimating the total serum IgE.