Gene Flow and Population Structure in a Rmeria Maritima
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Allele Frequency–Based and Polymorphism-Versus
View metadata, citation and similar papers at core.ac.uk brought to you by CORE Allele Frequency–Based and Polymorphism-Versus- provided by PubMed Central Divergence Indices of Balancing Selection in a New Filtered Set of Polymorphic Genes in Plasmodium falciparum Lynette Isabella Ochola,1 Kevin K. A. Tetteh,2 Lindsay B. Stewart,2 Victor Riitho,1 Kevin Marsh,1 and David J. Conway*,2 1Kenya Medical Research Institute, Centre for Geographic Medicine Research Coast, Kilifi, Kenya 2Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom *Corresponding author: E-mail: [email protected], [email protected]. Associate editor: John H. McDonald Research article Abstract Signatures of balancing selection operating on specific gene loci in endemic pathogens can identify candidate targets of naturally acquired immunity. In malaria parasites, several leading vaccine candidates convincingly show such signatures when subjected to several tests of neutrality, but the discovery of new targets affected by selection to a similar extent has been slow. A small minority of all genes are under such selection, as indicated by a recent study of 26 Plasmodium falciparum merozoite- stage genes that were not previously prioritized as vaccine candidates, of which only one (locus PF10_0348) showed a strong signature. Therefore, to focus discovery efforts on genes that are polymorphic, we scanned all available shotgun genome sequence data from laboratory lines of P. falciparum and chose six loci with more than five single nucleotide polymorphisms per kilobase (including PF10_0348) for in-depth frequency–based analyses in a Kenyan population (allele sample sizes .50 for each locus) and comparison of Hudson–Kreitman–Aguade (HKA) ratios of population diversity (p) to interspecific divergence (K) from the chimpanzee parasite Plasmodium reichenowi. -
Microevolution and the Genetics of Populations Microevolution Refers to Varieties Within a Given Type
Chapter 8: Evolution Lesson 8.3: Microevolution and the Genetics of Populations Microevolution refers to varieties within a given type. Change happens within a group, but the descendant is clearly of the same type as the ancestor. This might better be called variation, or adaptation, but the changes are "horizontal" in effect, not "vertical." Such changes might be accomplished by "natural selection," in which a trait within the present variety is selected as the best for a given set of conditions, or accomplished by "artificial selection," such as when dog breeders produce a new breed of dog. Lesson Objectives ● Distinguish what is microevolution and how it affects changes in populations. ● Define gene pool, and explain how to calculate allele frequencies. ● State the Hardy-Weinberg theorem ● Identify the five forces of evolution. Vocabulary ● adaptive radiation ● gene pool ● migration ● allele frequency ● genetic drift ● mutation ● artificial selection ● Hardy-Weinberg theorem ● natural selection ● directional selection ● macroevolution ● population genetics ● disruptive selection ● microevolution ● stabilizing selection ● gene flow Introduction Darwin knew that heritable variations are needed for evolution to occur. However, he knew nothing about Mendel’s laws of genetics. Mendel’s laws were rediscovered in the early 1900s. Only then could scientists fully understand the process of evolution. Microevolution is how individual traits within a population change over time. In order for a population to change, some things must be assumed to be true. In other words, there must be some sort of process happening that causes microevolution. The five ways alleles within a population change over time are natural selection, migration (gene flow), mating, mutations, or genetic drift. -
Gene Flow by Pollen Into Small Populations
Proc. Natl. Acad. Sci. USA Vol. 86, pp. 9044-9047, November 1989 Population Biology Gene flow by pollen into small populations: Data from experimental and natural stands of wild radish (Raphanus sativus/spatial isolation/interpopulation mating) NORMAN C. ELLSTRANDt, B. DEVLINt, AND DIANE L. MARSHALL§ Department of Botany and Plant Sciences and Program in Genetics, University of California, Riverside, CA 92521-0124 Communicated by R. W. Allard, August 14, 1989 (received for review August 18, 1988) ABSTRACT Gene flow can have an especially strong im- much from population to population, whether it varies within pact on the evolution of small populations. However, empirical a population over a season, and whether it varies with spatial studies on the actual rates and patterns of gene flow into small isolation from the nearest conspecific. More data are needed populations are few. Thus, we sought to measure gene flow into that focus more closely on a number ofpopulations ofa single small populations of wild radish, Raphanus sativus. We found species. significant differences in gene flow receipt among experimental Therefore, we selected wild radish, Raphanus sativus L. populations and within those populations over a season. A (Brassicaceae), to measure patterns of gene flow by pollen maximum-likelihood estimate revealed that almost all of the into small populations. This species is especially suitable for gene flow into these synthetic populations had its origin in both experimental and descriptive gene flow studies because relatively distant (>650 m), large natural populations rather it is a common outcrossing weed in southern California (8), than the proximal (255400 m), small synthetic populations. -
Intro Forensic Stats
Popstats Unplugged 14th International Symposium on Human Identification John V. Planz, Ph.D. UNT Health Science Center at Fort Worth Forensic Statistics From the ground up… Why so much attention to statistics? Exclusions don’t require numbers Matches do require statistics Problem of verbal expression of numbers Transfer evidence Laboratory result 1. Non-match - exclusion 2. Inconclusive- no decision 3. Match - estimate frequency Statistical Analysis Focus on the question being asked… About “Q” sample “K” matches “Q” Who else could match “Q" partial profile, mixtures Match – estimate frequency of: Match to forensic evidence NOT suspect DNA profile Who is in suspect population? So, what are we really after? Quantitative statement that expresses the rarity of the DNA profile Estimate genotype frequency 1. Frequency at each locus Hardy-Weinberg Equilibrium 2. Frequency across all loci Linkage Equilibrium Terminology Genetic marker variant = allele DNA profile = genotype Database = table that provides frequency of alleles in a population Population = some assemblage of individuals based on some criteria for inclusion Where Do We Get These Numbers? 1 in 1,000,000 1 in 110,000,000 POPULATION DATA and Statistics DNA databases are needed for placing statistical weight on DNA profiles vWA data (N=129) 14 15 16 17 18 19 20 freq 14 9 75 15 3 0 6 16 19 1 1 46 17 23 1 14 9 72 18 6 0 3 10 4 31 19 6 1 7 3 2 2 23 20 0 0 0 3 2 0 0 5 258 Because data are not available for every genotype possible, We use allele frequencies instead of genotype frequencies to estimate rarity. -
Saving Our Tree HUMAN GENETICS
HIGHLIGHTS EVOLUTION IN BRIEF Saving our tree HUMAN GENETICS Identification of a gene responsible for familial For several years, evolutionary biolo- Wolff–Parkinson–White syndrome. gists interested in gene flow between species have been investigating and Gollob, M. H. et al. N. Engl. J. Med. 344, 1823–1831 (2001) debating a controversial issue: the hor- Wolff–Parkinson–White (WPW) syndrome is an inherited heart izontal exchange of genes between dis- defect associated with arrhythmia, cardiac arrest and sudden death. tantly related species, its extent and Gollob et al. studied two large families with autosomal-dominant possible adaptive significance. WPW syndrome, and used a positional candidate-gene approach to Horizontal gene transfer (HGT) is an identify the causative gene, which encodes a regulatory subunit of important evolutionary force in appears in a cluster of bacterial AMP-activated protein kinase. This finding should shed light on prokaryotes, as their life cycles facilitate sequences, then the vertebrate gene the mechanisms that lead to heart arrhythmias. the exchange of genes between even was probably horizontally transferred distantly related species. However, this from bacteria. Conversely, if all GENETIC NETWORKS is trickier in multicellular organisms, eukaryotic sequences cluster together, in which the fixation of horizontally then HGT has probably not occurred Ordering genes in a flagella pathway by analysis of transferred genes can only occur if as this grouping is most parsimo- expression kinetics from living bacteria. they are transmitted through the germ niously explained by vertebrates hav- Kalir, S. et al. Science 292, 2080–2083 (2001) line. It was therefore surprising when ing acquired the sequence by descent the International Human Genome through other eukaryotes. -
Allele Frequency Difference AFD–An Intuitive Alternative to FST for Quantifying Genetic Population Differentiation
G C A T T A C G G C A T genes Opinion Allele Frequency Difference AFD–An Intuitive Alternative to FST for Quantifying Genetic Population Differentiation Daniel Berner Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland; [email protected]; Tel.: +41-(0)-61-207-03-28 Received: 21 February 2019; Accepted: 12 April 2019; Published: 18 April 2019 Abstract: Measuring the magnitude of differentiation between populations based on genetic markers is commonplace in ecology, evolution, and conservation biology. The predominant differentiation metric used for this purpose is FST. Based on a qualitative survey, numerical analyses, simulations, and empirical data, I here argue that FST does not express the relationship to allele frequency differentiation between populations generally considered interpretable and desirable by researchers. In particular, FST (1) has low sensitivity when population differentiation is weak, (2) is contingent on the minor allele frequency across the populations, (3) can be strongly affected by asymmetry in sample sizes, and (4) can differ greatly among the available estimators. Together, these features can complicate pattern recognition and interpretation in population genetic and genomic analysis, as illustrated by empirical examples, and overall compromise the comparability of population differentiation among markers and study systems. I argue that a simple differentiation metric displaying intuitive properties, the absolute allele frequency difference AFD, provides a valuable alternative to FST. I provide a general definition of AFD applicable to both bi- and multi-allelic markers and conclude by making recommendations on the sample sizes needed to achieve robust differentiation estimates using AFD. -
The Allele Frequency Spectrum in Genome-Wide Human Variation Data Reveals Signals of Differential Demographic History in Three Large World Populations
Copyright 2004 by the Genetics Society of America The Allele Frequency Spectrum in Genome-Wide Human Variation Data Reveals Signals of Differential Demographic History in Three Large World Populations Gabor T. Marth,1 Eva Czabarka, Janos Murvai and Stephen T. Sherry National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 Manuscript received April 15, 2003 Accepted for publication September 4, 2003 ABSTRACT We have studied a genome-wide set of single-nucleotide polymorphism (SNP) allele frequency measures for African-American, East Asian, and European-American samples. For this analysis we derived a simple, closed mathematical formulation for the spectrum of expected allele frequencies when the sampled populations have experienced nonstationary demographic histories. The direct calculation generates the spectrum orders of magnitude faster than coalescent simulations do and allows us to generate spectra for a large number of alternative histories on a multidimensional parameter grid. Model-fitting experiments using this grid reveal significant population-specific differences among the demographic histories that best describe the observed allele frequency spectra. European and Asian spectra show a bottleneck-shaped history: a reduction of effective population size in the past followed by a recent phase of size recovery. In contrast, the African-American spectrum shows a history of moderate but uninterrupted population expansion. These differences are expected to have profound consequences for the design of medical association studies. The analytical methods developed for this study, i.e., a closed mathematical formulation for the allele frequency spectrum, correcting the ascertainment bias introduced by shallow SNP sampling, and dealing with variable sample sizes provide a general framework for the analysis of public variation data. -
Gene Flow 1 6 James Mallet
Gene Flow 1 6 James Mallet Calton Laboratory, Department of Biology, Univetsity College London, 4 Stephenson Way, London NWI 2HE, UK What is Gene Flow? 'Gene flow' means the movement of genes. In some cases, small fragments of DNA may pass from one individual directly into the germline of another, perhaps transduced by a pathogenic virus or other vector, or deliberately via a human transgenic manipulation. However, this kind of gene flow, known as horizontal gene transfer, is rare. Most of the time, gene flow is caused by the movement or dispersal of whole organisms or genomes from one popula- tion to another. After entering a new population, immigrant genomes may become incorporated due to sexual reproduction or hybridization, and will be gradually broken up by recombination. 'Genotype flow' would therefore be a more logical term to indicate that the whole genome is moving at one time. The term 'gene flow' is used probably because of an implicit belief in abundant recombination, and because most theory is still based on simple single locus models: it does not mean that genes are transferred one at a time. The fact that gene flow is usually caused by genotype flow has important consequences for its measurement, as we shall see. Two Meanings of 'Gene Flow' We are often taught that 'dispersal does not necessarily lead to gene flow'. The term 'gene flow' is then being used in the sense of a final state of the population, i.e. successful establishment of moved genes. This disagrees somewhat with a more straightforward interpretation of gene flow as actual EICAR International 2001. -
Guide to Interpreting Genomic Reports: a Genomics Toolkit
Guide to Interpreting Genomic Reports: A Genomics Toolkit A guide to genomic test results for non-genetics providers Created by the Practitioner Education Working Group of the Clinical Sequencing Exploratory Research (CSER) Consortium Genomic Report Toolkit Authors Kelly East, MS, CGC, Wendy Chung MD, PhD, Kate Foreman, MS, CGC, Mari Gilmore, MS, CGC, Michele Gornick, PhD, Lucia Hindorff, PhD, Tia Kauffman, MPH, Donna Messersmith , PhD, Cindy Prows, MSN, APRN, CNS, Elena Stoffel, MD, Joon-Ho Yu, MPh, PhD and Sharon Plon, MD, PhD About this resource This resource was created by a team of genomic testing experts. It is designed to help non-geneticist healthcare providers to understand genomic medicine and genome sequencing. The CSER Consortium1 is an NIH-funded group exploring genomic testing in clinical settings. Acknowledgements This work was conducted as part of the Clinical Sequencing Exploratory Research (CSER) Consortium, grants U01 HG006485, U01 HG006485, U01 HG006546, U01 HG006492, UM1 HG007301, UM1 HG007292, UM1 HG006508, U01 HG006487, U01 HG006507, R01 HG006618, and U01 HG007307. Special thanks to Alexandria Wyatt and Hugo O’Campo for graphic design and layout, Jill Pope for technical editing, and the entire CSER Practitioner Education Working Group for their time, energy, and support in developing this resource. Contents 1 Introduction and Overview ................................................................ 3 2 Diagnostic Results Related to Patient Symptoms: Pathogenic and Likely Pathogenic Variants . 8 3 Uncertain Results -
Biological Invasions at the Gene Level VIEWPOINT Rémy J
Diversity and Distributions, (Diversity Distrib.) (2004) 10, 159–165 Blackwell Publishing, Ltd. BIODIVERSITY Biological invasions at the gene level VIEWPOINT Rémy J. Petit UMR Biodiversité, Gènes et Ecosystèmes, 69 ABSTRACT Route d’Arcachon, 33612 Cestas Cedex, France Despite several recent contributions of population and evolutionary biology to the rapidly developing field of invasion biology, integration is far from perfect. I argue here that invasion and native status are sometimes best discussed at the level of the gene rather than at the level of the species. This, and the need to consider both natural (e.g. postglacial) and human-induced invasions, suggests that a more integrative view of invasion biology is required. Correspondence: Rémy J. Petit, UMR Key words Biodiversité, Gènes et Ecosystèmes, 69 Route d’Arcachon, 33612 Cestas Cedex, France. Alien, genetic assimilation, gene flow, homogenization, hybridization, introgression, E-mail: [email protected] invasibility, invasiveness, native, Quercus, Spartina. the particular genetic system of plants. Although great attention INTRODUCTION has been paid to the formation of new hybrid taxa, introgression Biological invasions are among the most important driving more often results in hybrid swarms or in ‘genetic pollution’, forces of evolution on our human-dominated planet. According which is best examined at the gene level. Under this perspective, to Myers & Knoll (2001), distinctive features of evolution now translocations of individuals and even movement of alleles include a homogenization of biotas, a proliferation of opportunistic within a species’ range (e.g. following selective sweeps) should species, a decline of biodisparity (the manifest morphological equally be recognized as an important (if often cryptic) and physiological variety of biotas), and increased rates of speci- component of biological invasions. -
Divergence, Gene Flow, and Speciation in Eight Lineages of Trans‐Beringian Birds
Received: 2 May 2019 | Revised: 22 July 2020 | Accepted: 27 July 2020 DOI: 10.1111/mec.15574 ORIGINAL ARTICLE Divergence, gene flow, and speciation in eight lineages of trans-Beringian birds Jessica F. McLaughlin1,2 | Brant C. Faircloth3 | Travis C. Glenn4 | Kevin Winker1 1University of Alaska Museum, Fairbanks, AK, USA Abstract 2Sam Noble Oklahoma Museum of Natural Determining how genetic diversity is structured between populations that span the History, Norman, OK, USA divergence continuum from populations to biological species is key to understanding 3Department of Biological Sciences and Museum of Natural Science, Louisiana State the generation and maintenance of biodiversity. We investigated genetic divergence University, Baton Rouge, LA, USA and gene flow in eight lineages of birds with a trans-Beringian distribution, where 4 Department of Environmental Health Asian and North American populations have likely been split and reunited through Science and Institute of Bioinformatics, University of Georgia, Athens, GA, USA multiple Pleistocene glacial cycles. Our study transects the speciation process, in- cluding eight pairwise comparisons in three orders (ducks, shorebirds and passer- Correspondence Kevin Winker, University of Alaska Museum, ines) at population, subspecies and species levels. Using ultraconserved elements 907 Yukon Drive, Fairbanks, AK 99775, USA. (UCEs), we found that these lineages represent conditions from slightly differentiated Email: [email protected] populations to full biological species. Although allopatric speciation is considered Funding information the predominant mode of divergence in birds, all of our best divergence models in- National Science Foundation, Grant/Award Number: DEB-1242267-1242241-1242260 cluded gene flow, supporting speciation with gene flow as the predominant mode in Beringia. -
G14TBS Part II: Population Genetics
G14TBS Part II: Population Genetics Dr Richard Wilkinson Room C26, Mathematical Sciences Building Please email corrections and suggestions to [email protected] Spring 2015 2 Preliminaries These notes form part of the lecture notes for the mod- ule G14TBS. This section is on Population Genetics, and contains 14 lectures worth of material. During this section will be doing some problem-based learning, where the em- phasis is on you to work with your classmates to generate your own notes. I will be on hand at all times to answer questions and guide the discussions. Reading List: There are several good introductory books on population genetics, although I found their level of math- ematical sophistication either too low or too high for the purposes of this module. The following are the sources I used to put together these lecture notes: • Gillespie, J. H., Population genetics: a concise guide. John Hopkins University Press, Baltimore and Lon- don, 2004. • Hartl, D. L., A primer of population genetics, 2nd edition. Sinauer Associates, Inc., Publishers, 1988. • Ewens, W. J., Mathematical population genetics: (I) Theoretical Introduction. Springer, 2000. • Holsinger, K. E., Lecture notes in population genet- ics. University of Connecticut, 2001-2010. Available online at http://darwin.eeb.uconn.edu/eeb348/lecturenotes/notes.html. • Tavar´eS., Ancestral inference in population genetics. In: Lectures on Probability Theory and Statistics. Ecole d'Et´esde Probabilit´ede Saint-Flour XXXI { 2001. (Ed. Picard J.) Lecture Notes in Mathematics, Springer Verlag, 1837, 1-188, 2004. Available online at http://www.cmb.usc.edu/people/stavare/STpapers-pdf/T04.pdf Gillespie, Hartl and Holsinger are written for non-mathematicians and are easiest to follow.