The Hill–Robertson Effect: Evolutionary Consequences of Weak Selection and Linkage in finite Populations
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Weak Selection Revealed by the Whole-Genome Comparison of the X Chromosome and Autosomes of Human and Chimpanzee
Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee Jian Lu and Chung-I Wu* Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 Communicated by Tomoko Ohta, National Institute of Genetics, Mishima, Japan, January 19, 2005 (received for review November 22, 2004) The effect of weak selection driving genome evolution has at- An alternative approach to measuring the extent and strength tracted much attention in the last decade, but the task of measur- of selection, both positive and negative, is to contrast the ing the strength of such selection is particularly difficult. A useful evolution of X-linked and autosomal genes (18, 19). If the fitness approach is to contrast the evolution of X-linked and autosomal effect of a mutation is (partially) recessive, then this effect can genes in two closely related species in a whole-genome analysis. If be more readily manifested on the X chromosome than on the the fitness effect of mutations is recessive, X-linked genes should autosomes (20). When the recessive mutations are still rare, they evolve more rapidly than autosomal genes when the mutations are will nonetheless be expressed in the hemizygous males of the XY advantageous, and they should evolve more slowly than autoso- system. On the other hand, autosomal mutations have to become mal genes when the mutations are deleterious. We found synon- sufficiently frequent to form homozygotes to be influenced by ymous substitutions on the X chromosome of human and chim- natural selection under random mating. Therefore, if recessive panzee to be less frequent than those on the autosomes. -
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. -
Population Size and the Rate of Evolution
Review Population size and the rate of evolution 1,2 1 3 Robert Lanfear , Hanna Kokko , and Adam Eyre-Walker 1 Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia 2 National Evolutionary Synthesis Center, Durham, NC, USA 3 School of Life Sciences, University of Sussex, Brighton, UK Does evolution proceed faster in larger or smaller popu- mutations occur and the chance that each mutation lations? The relationship between effective population spreads to fixation. size (Ne) and the rate of evolution has consequences for The purpose of this review is to synthesize theoretical our ability to understand and interpret genomic varia- and empirical knowledge of the relationship between tion, and is central to many aspects of evolution and effective population size (Ne, Box 1) and the substitution ecology. Many factors affect the relationship between Ne rate, which we term the Ne–rate relationship (NeRR). A and the rate of evolution, and recent theoretical and positive NeRR implies faster evolution in larger popula- empirical studies have shown some surprising and tions relative to smaller ones, and a negative NeRR implies sometimes counterintuitive results. Some mechanisms the opposite (Figure 1A,B). Although Ne has long been tend to make the relationship positive, others negative, known to be one of the most important factors determining and they can act simultaneously. The relationship also the substitution rate [5–8], several novel predictions and depends on whether one is interested in the rate of observations have emerged in recent years, causing some neutral, adaptive, or deleterious evolution. Here, we reassessment of earlier theory and highlighting some gaps synthesize theoretical and empirical approaches to un- in our understanding. -
Demography and Weak Selection Drive Patterns of Transposable Element Diversity in Natural Populations of Arabidopsis Lyrata
Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata Steven Lockton, Jeffrey Ross-Ibarra, and Brandon S. Gaut* Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 Edited by M. T. Clegg, University of California, Irvine, CA, and approved June 25, 2008 (received for review May 13, 2008) Transposable elements (TEs) are the major component of most approximately 6,000 TEs within the A. thaliana genome have been plant genomes, and characterizing their population dynamics is well characterized (4, 19). A. lyrata diverged from A. thaliana Ϸ5 key to understanding plant genome complexity. Yet there have million years ago (20) and has become a model system for plant been few studies of TE population genetics in plant systems. To molecular population genetics (21). A. lyrata is a predominantly study the roles of selection, transposition, and demography in self-incompatible, perennial species distributed across northern and shaping TE population diversity, we generated a polymorphism central Europe, Asia, and North America. A. lyrata consists of large, dataset for six TE families in four populations of the flowering stable populations, particularly in Central Europe where popula- plant Arabidopsis lyrata. The TE data indicated significant differ- tions are hypothesized to have served as Pleistocene refugia (21– entiation among populations, and maximum likelihood procedures 23). Importantly, Ross-Ibarra et al. (24) modeled the demographic suggested weak selection. For strongly bottlenecked populations, history of six natural A. lyrata populations based on single- the observed TE band-frequency spectra fit data simulated under nucleotide polymorphism (SNP) data from 77 nuclear genes. -
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. -
Joint Effects of Genetic Hitchhiking and Background Selection on Neutral Variation
Copyright 2000 by the Genetics Society of America Joint Effects of Genetic Hitchhiking and Background Selection on Neutral Variation Yuseob Kim and Wolfgang Stephan Department of Biology, University of Rochester, Rochester, New York 14627 Manuscript received December 7, 1999 Accepted for publication March 20, 2000 ABSTRACT Due to relatively high rates of strongly selected deleterious mutations, directional selection on favorable alleles (causing hitchhiking effects on linked neutral polymorphisms) is expected to occur while a deleteri- ous mutation-selection balance is present in a population. We analyze this interaction of directional selection and background selection and study their combined effects on neutral variation, using a three- locus model in which each locus is subjected to either deleterious, favorable, or neutral mutations. Average heterozygosity is measured by simulations (1) at the stationary state under the assumption of recurrent hitchhiking events and (2) as a transient level after a single hitchhiking event. The simulation results are compared to theoretical predictions. It is shown that known analytical solutions describing the hitchhiking effect without background selection can be modi®ed such that they accurately predict the joint effects of hitchhiking and background on linked, neutral variation. Generalization of these results to a more appro- priate multilocus model (such that background selection can occur at multiple sites) suggests that, in regions of very low recombination rates, stationary levels of nucleotide diversity are primarily determined by hitchhiking, whereas in regions of high recombination, background selection is the dominant force. The implications of these results on the identi®cation and estimation of the relevant parameters of the model are discussed. -
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. -
Codon Usage Bias in the Model Moss Physcomitrella Patens
GBE Selfing in Haploid Plants and Efficacy of Selection: Codon Usage Bias in the Model Moss Physcomitrella patens Pe´ ter Szo¨ve´nyi,1,* Kristian K. Ullrich,2,7 Stefan A. Rensing,2,3 Daniel Lang,4 Nico van Gessel,5 Hans K. Stenøien,6 Elena Conti,1 and Ralf Reski3,5 1Department of Systematic and Evolutionary Botany, University of Zurich, Switzerland 2Plant Cell Biology, Faculty of Biology, University of Marburg, Germany 3BIOSS—Centre for Biological Signalling Studies, University of Freiburg, Germany 4Plant Genome and Systems Biology, Helmholtz Zentrum Mu¨ nchen, German Research Center for Environmental Health, Neuherberg, Germany 5Plant Biotechnology, Faculty of Biology, University of Freiburg, Germany 6NTNU University Museum, Trondheim, Norway 7Present address: Max-Planck-Insitut fu¨ r Evolutionsbiologie, Plo¨n,Germany *Corresponding author: E-mail: [email protected]. Accepted: May 25, 2017 Data deposition: This project has been deposited at EMBL ENA under the accession PRJEB8683. Abstract A long-term reduction in effective population size will lead to major shift in genome evolution. In particular, when effective population size is small, genetic drift becomes dominant over natural selection. The onset of self-fertilization is one evolutionary event considerably reducing effective size of populations. Theory predicts that this reduction should be more dramatic in organ- isms capable for haploid than for diploid selfing. Although theoretically well-grounded, this assertion received mixed experimen- tal support. Here, we test this hypothesis by analyzing synonymous codon usage bias of genes in the model moss Physcomitrella patens frequently undergoing haploid selfing. In line with population genetic theory, we found that the effect of natural selection on synonymous codon usage bias is very weak. -
Recombination, Dominance and Selection on Amino Acid Polymorphism in the Drosophila Genome: Contrasting Patterns on the X and Fourth Chromosomes
Copyright 2003 by the Genetics Society of America Recombination, Dominance and Selection on Amino Acid Polymorphism in the Drosophila Genome: Contrasting Patterns on the X and Fourth Chromosomes Lea A. Sheldahl, Daniel M. Weinreich and David M. Rand1 Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912 Manuscript received December 14, 2002 Accepted for publication June 27, 2003 ABSTRACT Surveys of nucleotide polymorphism and divergence indicate that the average selection coefficient on Drosophila proteins is weakly positive. Similar surveys in mitochondrial genomes and in the selfing plant Arabidopsis show that weak negative selection has operated. These differences have been attributed to the low recombination environment of mtDNA and Arabidopsis that has hindered adaptive evolution through the interference effects of linkage. We test this hypothesis with new sequence surveys of proteins lying in low recombination regions of the Drosophila genome. We surveyed Ͼ3800 bp across four proteins at the tip of the X chromosome and Ͼ3600 bp across four proteins on the fourth chromosome in 24 strains of D. melanogaster and 5 strains of D. simulans. This design seeks to study the interaction of selection and linkage by comparing silent and replacement variation in semihaploid (X chromosome) and diploid (fourth chromosome) environments lying in regions of low recombination. While the data do indicate very low rates of exchange, all four gametic phases were observed both at the tip of the X and across the ϭ fourth chromosome. Silent variation is very low at the tip of the X ( S 0.0015) and on the fourth ϭ chromosome ( S 0.0002), but the tip of the X shows a greater proportional loss of variation than the fourth shows relative to normal-recombination regions. -
Genetic Linkage of the Huntington's Disease Gene to a DNA Marker James F
LE JOURNAL CANADIEN DES SCIENCES NEUROLOG1QUES SPECIAL FEATURE Genetic Linkage of the Huntington's Disease Gene to a DNA Marker James F. Gusella ABSTRACT: Recombinant DNA techniques have provided the means to generate large numbers of new genetic linkage markers. This technology has been used to identify a DNA marker that coinherits with the Huntington's Disease (HD) gene in family studies. The HD locus has thereby been mapped to human chromosome 4. The discovery of a genetic marker for the inheritance of HD has implications both for patient care and future research. The same approach holds considerable promise for the investigation of other genetic diseases, including Dystonia Musculorum Deformans. RESUME: Les techniques d'ADN recombine ont fourni le moyen de g£nerer un grand nombre de nouveux marqueurs a liason g6n£tique. Cette technologie a He employe" afin d'identifier un marqueur d'ADN qui co-herite avec le gene de la maladie de Huntington (MH) dans les etudes familiales. Le lieu du gene de la MH a ainsi 6te localise sur le chromosome humain numero 4. La d6couverte d'un marqueur g6n6tique pour I'her6dit6 de MH a des implications pour la soin de patients ainsi que pour la recherche dans le futur. La meme approche semble pleine de promesses pour l'investigation d'autres maladies g6ndtiques, incluant la dystonie musculaire deTormante. Can. J. Neurol. Sci. 1984; 11:421-425 Huntington's Disease currently no effective therapy to cure this devastating disease, Huntington's disease (HD) is a genetic neurodegenerative or to slow its inexorable progression. disorder first described by George Huntington in 1873 (Hunting ton, 1972;Hayden, 1981;Chaseetal., 1979). -
Linkage & Genetic Mapping in Eukaryotes
LinLinkkaaggee && GGeenneetticic MMaappppiningg inin EEuukkaarryyootteess CChh.. 66 1 LLIINNKKAAGGEE AANNDD CCRROOSSSSIINNGG OOVVEERR ! IInn eeuukkaarryyoottiicc ssppeecciieess,, eeaacchh lliinneeaarr cchhrroommoossoommee ccoonnttaaiinnss aa lloonngg ppiieeccee ooff DDNNAA – A typical chromosome contains many hundred or even a few thousand different genes ! TThhee tteerrmm lliinnkkaaggee hhaass ttwwoo rreellaatteedd mmeeaanniinnggss – 1. Two or more genes can be located on the same chromosome – 2. Genes that are close together tend to be transmitted as a unit Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 2 LinkageLinkage GroupsGroups ! Chromosomes are called linkage groups – They contain a group of genes that are linked together ! The number of linkage groups is the number of types of chromosomes of the species – For example, in humans " 22 autosomal linkage groups " An X chromosome linkage group " A Y chromosome linkage group ! Genes that are far apart on the same chromosome can independently assort from each other – This is due to crossing-over or recombination Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 3 LLiinnkkaaggee aanndd RRecombinationecombination Genes nearby on the same chromosome tend to stay together during the formation of gametes; this is linkage. The breakage of the chromosome, the separation of the genes, and the exchange of genes between chromatids is known as recombination. (we call it crossing over) 4 IndependentIndependent assortment:assortment: -
Detecting the Form of Selection from DNA Sequence Data
Outlook COMMENT Male:female mutation ratio muscular dystrophy, neurofibromatosis and retinoblast- outcome of further investigation, this unique transposition oma), there is a large male excess. So, I believe the evidence event and perhaps others like it are sure to provide impor- is convincing that the male base-substitution rate greatly tant cytogenetic and evolutionary insights. exceeds the female rate. There are a number of reasons why the historical Acknowledgements male:female mutation ratio is likely to be less than the I have profited greatly from discussions with my colleagues current one, the most important being the lower age of B. Dove, B. Engels, C. Denniston and M. Susman. My reproduction in the earliest humans and their ape-like greatest debt is to D. Page for a continuing and very fruitful ancestors. More studies are needed. But whatever the dialog and for providing me with unpublished data. References Nature 406, 622–625 6 Engels, W.R. et al. (1994) Long-range cis preference in DNA 1 Vogel, F. and Motulsky, A. G. (1997) Human Genetics: 4 Shimmin, L.C. et al. (1993) Potential problems in estimating homology search over the length of a Drosophila chromosome. Problems and Approaches. Springer-Verlag the male-to-female mutation rate ratio from DNA sequence Science 263, 1623–1625 2 Crow, J. F. (1997) The high spontaneous mutation rate: is it a data. J. Mol. Evol. 37, 160–166 7 Crow, J.F. (2000) The origins, patterns and implications of health risk? Proc. Natl. Acad. Sci. U. S. A. 94, 8380–8386 5 Richardson, C. et al.