DOCSLIB.ORG

Linkage Disequilibrium in Human Ribosomal Genes: Implications for Multigene Family Evolution

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Linkage Disequilibrium in Human Ribosomal Genes: Implications for Multigene Family Evolution Copyright 0 1988 by the Genetics Societyof America Linkage Disequilibrium in Human Ribosomal Genes: Implications for Multigene Family Evolution Peter Seperack,*” Montgomery Slatkin+ and Norman Arnheim*.* *Department of Biochemistry and Program in Cellular andDevelopmental Biology, State University of New York, Stony Brook, New York I 1794, ?Department of Zoology, University of California, Berkeley, California 94720, and *Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-0371 Manuscript received January8, 1988 Revised copy accepted April 2 1, 1988 ABSTRACT Members of the rDNA multigene family withina species do not evolve independently,rather, they evolve together in a concerted fashion.Between species, however, each multigenefamily does evolve independently indicating that mechanisms exist whichwill amplify and fix new mutations bothwithin populations and within species. In order to evaluate the possible mechanisms by which mutation, amplification and fixation occurwe have determined thelevel of linkage disequilibrium betweentwo polymorphic sites in human ribosomal genes in five racial groups and among individuals within two of these groups.The marked linkage disequilibriumwe observe within individuals suggeststhat sister chromatid exchangesare much more important than homologousor nonhomologous recombination events in the concerted evolution of the rDNA family and further that recent models of molecular drive may not apply to the evolution of the rDNA multigene family. HE human ribosomal gene family is composed of ferences among individualsin the geneticcomposition T approximately 400 members which arear- of the multigene family because they create linkage ranged in small tandem clusters on five pairs of chro- disequilibrium among different members of familythe mosomes (for reviews, see LONG and DAWID1980; (OHTA1980a, b;NAGYLAKI and PETES1982; SLATKIN WILSON1982). Each member (Figure 1) is approxi- 1986).Interactions between chromosomes break mately 45,000 bases in length. The spacerregion down linkage disequilibriumand reduce the extentof (NTS) which is adjacent to the coding region and differences among individuals. In the theory of “mo- transcription regulatory signals has no known func- lecular drive”(DOVER 1982) it has been suggestedthat tion. transposition, gene conversion, and unequal crossing There is already evidencethat the humanribosomal over are possibly more important than natural selec- gene family evolves in a concerted fashion. Individual tion for the evolution of multigene families because members of the family in humans are much more soon after a variant arises, molecular drive tends to similar to one another than they are to members of limit the amount of variation among individuals on the rDNA family in other primates (ARNHEIMet al. which natural selection can act. We will show here 1980).Several mechanisms havebeen proposed to that there are substantial differences among individ- explain the relative homogeneity of rDNA and other uals in the rDNA family which is consistent with the multigene families despitethe fact that individual idea that interactions within chromosomes are much family members would beexpected to accumulate morefrequent than interactions betweenchromo- mutations independently of the others (for reviews, somes and that natural selection could contribute to see ARNHEIM 1983;DOVER 1982). Gene conversion, frequency changes in newly arising variants. unequal crossing over, and natural selection could all account for concerted evolution in the rDNA family. MATERIALS AND METHODS Because rDNA is notinterspersed throughout the genome, transposition is probably notimportant. Samples and DNA analysis: ALLANC. WILSON(Univer- What is at present unknown is whether gene conver- sity of California, Berkeley) supplied the aborigine DNA sion and unequalcrossing over occur primarilywithin samples andHAIG KAZAZIAN (The Johns Hopkins University Medical School) provided the Asian Indian, black, Chinese a chromosome (ie., sister chromatidexchanges) or andMediterranean DNA. All DNA werederived from primarilybetween either homologous or nonho- unrelated individuals. DNA were digested with restriction mologous chromosomes. Frequent interactions within enzymes accordingto the manufacturer’s recommendations. chromosomes would tend to produce substantial dif- Gel electrophoresis,Southern transfer and hybridization with a 28s ribosomal DNA probewere carried out as I Present address: BRI-Basic Research Program, NCI-Frederick Cancer described previously (ARNHEIMet al., 1980). Research Facility, P. 0. Box B, Frederick, Maryland 21701. Quantitative determination of rDNA haplotype fre- Genetics 119: 943-949 (August, 1988) 944 P. Seperack, M.and Slatkin N. Arnheim quencies: After Southern transfer andhybridization the 1984; NEI and ROYCHOUDHURY1982; CANN,BROWN nitrocellulose filters were exposed for either 6, 18 and 48 and WILSON 1982; JOHNSON et al. 1983). The BglII hr or 18,48 and 96 hron XS-5 film (Kodak) without intensification. For each exposure each lane was scanned site most likely arose as a point mutationin one rDNA twice using a Zeineh SoftLaser scanning densitometer genethat contained aparticular length variant. (LKB) with a tungsten lamp. Peak heights (PH) for each Therefore, measuring the frequency of the BglII site fragment in each gel lane were measured and values for in association with the closely linked length variation duplicate scans were averaged. Deviations from linearity region within andamong populationscan directly seen in the three different exposures of the same gel (due to film saturation and detector saturation)were determined assess thetempo and mode of the mechanism of and corrected, based on exposure time. The frequency of concerted evolution. rDNA repeats in each band in each exposure was deter- Figure 1B shows diagramatically how a Southern mined as follows. The ratio of the peak heights (a,) for type blot of a BglII-Hind111 digest of human DNA can 1, 2 and 3 fragments relative to the constant bands in each reveal each of the 10 possible haplotypes that result lane was determined: fromthe combination of 5 lengthvariants a, = PH;/PHc. (LVO LV4)and the two formsof the BglII poly- The frequency of each band (F,) was then determined by morphism (+/-). Densitometric tracingsof these blots dividing the ratio of the peak height to the constant band can then be used to determine thefrequency of each of each fragment (ai)by the sum of all ratios of all bands in haplotype. each lane: The degree of linkage disequilibrium is measured E = a,/C a, by comparing the observed frequency of each haplo- 3 type with that expected if the two markers segregated Using this method we have corrected for variation be- independently in the population. To examinethe tween lanes due to loading errors and amount of probe degree of linkage disequilibrium in several popula- hybridization to differentially digestedDNA. The corrected tions we pooled DNA samples fromindividuals of frequencies for each band in each of the three different exposures were averaged to give the frequency for the bands each population. Altogether we examined 20 Austra- presented in Tables 1 and 2. lian aborigines (8000 genes), 14 Asian Indians (5600 genes), 17 individuals of African descent (6800 genes), RESULTS 16 Chinese (6400 genes) and 17 Mediterranean indi- viduals (6800 genes). All of the individuals used in The approximately 400 rDNA genes in any given this study were unrelated. The results are seen in human are notidentical. A number of DNA polymor- Figure 2. Table 1 summarizesthe percentagesof each phisms involving restriction enzyme sites and length haplotype in each population. In general the distri- variation have been described (ARNHEIMand SOUTH- bution of length variant haplotypesare approximately ERN 1977; KRYSTALand ARNHEIM 1979; LAVOLPE the same in all populations with some notable excep- et al. 1985; WILSONet al. 1982; KRYSTALet al. 198 1; tions. The LVO length variant is found only in aborig- HIGUCHIet al. 198 1; RANZANI, BERNINI andCRIPPA 1984; SEPERACKand ARNHEIM 1982).The locations ine, Mediterranean and Chinese populationswhile the of several of thesepolymorphisms are shown in Figure LV3 variant is twice as common in blacks as in the 1A. We used two of these polymorphisms, a length other populations. The number of genes containing variation region and a restriction enzyme site to ex- the BglII site also varies among these groups (Table amine for thefirst time the degreeof linkage disequi- 1). librium between markers in members of a multigene These data were used to calculate the extent of family. In higher primates the length variation region linkagedisequilibrium between lengthvariants and is found in humans, chimpanzeesand pygmy chimpan- the BglII polymorphism. Because LV2 is in relatively zees (ARNHEIMet al. 1980). The BglII restriction high frequency in all population samples, a convenient enzyme site polymorphism, however, is human spe- way to quantify the extent of linkage disequilibrium cific (SEPERACKand ARNHEIM1982) and its increase is obtained by pooling the frequencies of the other in frequency in populations or in individuals could length variants and using the standard measure for only result by the mechanisms responsible for con- two alleles at each of two loci, D’, which is the ratio certed evolution in general (ARNHEIM 1983; SEPER- of the actual disequilibrium to the maximum possible ACK and ARNHEIM1982). Itis difficult to estimate the given those allele
Load more

Recommended publications
  • The Effects of Natural Selection on Linkage Disequilibrium and Relative Fitness in Experimental Populations of Drosophila Melanogaster
    THE EFFECTS OF NATURAL SELECTION ON LINKAGE DISEQUILIBRIUM AND RELATIVE FITNESS IN EXPERIMENTAL POPULATIONS OF DROSOPHILA MELANOGASTER GRACE BERT CANNON] Department of Zoology, Washington University, St. Louis, Missouri Received April 16, 1963 process of natural selection may be studied in laboratory populations in '?to ways. First, the genetic changes which occur during the course of micro- evolutionary change can be followed and, second, accompanying this, the size of the populations can be measured. CARSON(1961 ) considers the relative size of a population to be an important measure of relative population fitness when com- paring genetically different populations of the same species under uniform en- vironmental conditions over a period of time. In the present experiment, the experimental procedure of CARSONwas utilized to study the effects of selection on certain gene combinations and to measure the level of relative population fitness reached during the microevolutionary process. Experimental populations were constructed with certain oligogenes in low fre- quency and in certain associations in order to provide a situation likely to be changed by natural selection. Specifically, oligogenes on the third chromosome were allowed to recombine freely with the homologous Oregon chromosome so that three separate blocks could be selected for introduction into homozygous Oregon populations. The introduction contained all five of the oligogenes. At intervals samples were re- moved from the populations and testcrossed to determine whether selection had favored the coupling or repulsion phases of these blocks. In addition, the fitness of the populations was measured. This paper will show first the changes in frequency of the various gene combi- nations which occurred in the three experimental populations.
    [Show full text]
  • Fisher's Fundamental Theorem of Natural Selection Steven A
    TREE vol. 7, no. 3, March 1992 Fisher's Fundamental Theorem of Natural Selection Steven A. Frank and Montgomery Slatkin relationship to Adaptive Land- scapes. We focus on three ques- tions: What did Fisher really mean by the Fundamental Theorem? is Fishes Fundamental Theorem of natural though it were governed by the Fisher's interpretation of the Fun- selection is one of the most widely cited average condition of the species or damental Theorem useful? Why was theories in evolutionary biology. Yet it has inter-breeding group' (Ref. 3, p. 58). Fisher misinterpreted, even though been argued that the standard interpret- Fisher also pointed out that he stated on many occasions that he ation of the theorem is very different from average fitness, measured by the was not talking about the average what Fisher meant to say. What Fisher intrinsic (malthusian) rate of in- fitness of a population? really meant can be illustrated by look- crease of a species, must fluctuate ing in a new way at a recent model for about zero (Ref. 4, pp. 41-45). What did Fisher really mean? the evolution of clutch size. Why Fisher Otherwise, if a species' rate of The standard interpretation of was misunderstood depends, in part, on the increase were consistently positive, the Fundamental Theorem is that contrasting views of evolution promoted by it would soon overrun the world, or natural selection increases the Fisher and Wright. if a species' rate of increase were average fitness of a population at a consistently negative, it would rate equal to the genetic variance in R.A.
    [Show full text]
  • The Role of Linkage Disequilibrium in the Evolution of Premating Isolation
    Heredity (2009) 102, 51–56 & 2009 Macmillan Publishers Limited All rights reserved 0018-067X/09 $32.00 www.nature.com/hdy SHORT REVIEW The role of linkage disequilibrium in the evolution of premating isolation MR Servedio Department of Biology, University of North Carolina, Chapel Hill, NC, USA The suggestion that speciation may often occur, or be such factors: one-allele versus two-allele mechanisms of completed, in the presence of gene flow has long been premating isolation, and the form of selection against hybrids contentious, due to an appreciation of the challenges to as it relates to its effect on the pathway between post- maintaining population- or species-specific gene combina- zygotic and prezygotic isolation. The goal of this discussion tions when gene flow is occurring. Linkage disequilibrium is not to thoroughly review these factors, but instead to between loci involved in postzygotic and premating isolation concentrate on aspects and implications of these solutions must often be built and maintained as the source of these that are currently underemphasized in the speciation species-specific genotypes. Here, I discuss proposed solu- literature. tions to facilitate the establishment and maintenance of Heredity (2009) 102, 51–56; doi:10.1038/hdy.2008.98; this linkage disequilibrium. I concentrate primarily on two published online 24 September 2008 Keywords: gene flow; recombination; reinforcement; speciation; sympatric speciation Introduction on the build-up of linkage disequilibrium between genes involved in premating and postzygotic isolation. Here, I There has been a long-standing emphasis in speciation discuss solutions that have been proposed to ease the research on describing conditions that may facilitate the conditions for speciation with gene flow.
    [Show full text]
  • Linkage Disequilibrium and Its Expectation in Human Populations
    Linkage Disequilibrium and Its Expectation in Human Populations John A. Sved School of Biological Sciences, University of Sydney, Australia inkage disequilibrium (LD), the association in popu- By the time that the possibility of LD mapping was Llations between genes at linked loci, has achieved realized (e.g., Ikonen, 1990) the terminology of LD a high degree of prominence in recent years, primar- was well established. Currently the term is increas- ily because of its use in identifying and cloning genes ingly used, with many thousands of PubMed of medical importance. The field has recently been references and over 100 Wikipedia references. Note reviewed by Slatkin (2008). The present article is also the confusion with ‘lethal dose’, ‘learning disabili- largely devoted to a review of the theory of LD in ties’ and other terms in literature searches involving populations, including historical aspects. the LD acronym. The chance of any more appropriate Keywords: linkage disequilibrium, linked identity-by- terminology seems to have passed, even if a simple descent, LD mapping, composite D, Hapmap and suitable term could be suggested. ‘Allelic associa- tion’ would seem a desirable term (e.g., Morton et al., 2001) but for the fact that the genes involved are, by definition, non-allelic. Other authors have preferred to The Terminology of LD use the term ‘gametic phase disequilibrium’ (e.g., It has been clear for many years that LD is prevalent Falconer & Mackay, 1996; Denniston, 2000) to take across much of the human genome (e.g., Conrad account of the possibility of LD between genes on dif- 2006), and presumably any other organism when it is ferent, a situation that can arise when many unlinked looked for (e.g., Farnir et al., 2000, in cattle).
    [Show full text]
  • Prediction of Identity by Descent Probabilities from Marker-Haplotypes Theo Meuwissen, Mike Goddard
    Prediction of identity by descent probabilities from marker-haplotypes Theo Meuwissen, Mike Goddard To cite this version: Theo Meuwissen, Mike Goddard. Prediction of identity by descent probabilities from marker-haplotypes. Genetics Selection Evolution, BioMed Central, 2001, 33 (6), pp.605-634. 10.1051/gse:2001134. hal-00894392 HAL Id: hal-00894392 https://hal.archives-ouvertes.fr/hal-00894392 Submitted on 1 Jan 2001 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Genet. Sel. Evol. 33 (2001) 605–634 605 © INRA, EDP Sciences, 2001 Original article Prediction of identity by descent probabilities from marker-haplotypes a; b Theo H.E. MEUWISSEN ∗, Mike E. GODDARD a Research Institute of Animal Science and Health, Box 65, 8200 AB Lelystad, The Netherlands b Institute of Land and Food Resources, University of Melbourne, Parkville Victorian Institute of Animal Science, Attwood, Victoria, Australia (Received 13 February 2001; accepted 11 June 2001) Abstract – The prediction of identity by descent (IBD) probabilities is essential for all methods that map quantitative trait loci (QTL). The IBD probabilities may be predicted from marker genotypes and/or pedigree information. Here, a method is presented that predicts IBD prob- abilities at a given chromosomal location given data on a haplotype of markers spanning that position.
    [Show full text]
  • Evolution at Multiple Loci
    Evolution at multiple loci • Linkage • Sex • Quantitative genetics Linkage • Linkage can be physical or statistical, we focus on physical - easier to understand • Because of recombination, Mendel develops law of independent assortment • But loci do not always assort independently, suppose they are close together on the same chromosome Haplotype - multilocus genotype • Contraction of ‘haploid-genotype’ – The genotype of a chromosome (gamete) • E.g. with two genes A and B with alleles A and a, and B and b • Possible haplotypes – AB; Ab; aB, ab • Will selection at the A locus affect evolution of the B locus? Chromosome (haplotype) frequency v. allele frequency • Example, suppose two populations have: – A allele frequency = 0.6, a allele frequency 0.4 – B allele frequency = 0.8, b allele frequency 0.2 • Are those populations identical? • Not always! Linkage (dis)equilibrium • Loci are in equilibrium if: – Proportion of B alleles found with A alleles is the same as b alleles found with A alleles; and • Loci in linkage disequilibrium if an allele at one locus is more likely to be found with a particular allele at another locus – E.g., B alleles more likely with A alleles than b alleles are with A alleles Equilibrium - alleles A locus, A allele p = 15/25 = 0.6 a allele q = 1-p = 0.4 B locus, B allele p = 20/25 = 0.8; b allele q = 1-p = 0.2 Equilibrium - haplotypes Allele B with allele A = 12; A without B = 3 times; AB 12/15 = 0.8 Allele B with allele a = 8; a without B = 2 times; aB 8/10 = 0.8 Equilibrium graphically Disequilibrium - alleles
    [Show full text]
  • Design and Analysis of Genetic Association Studies
    ection S ON Design and Analysis of Statistical Genetic Association Genetics Studies Hemant K Tiwari, Ph.D. Professor & Head Section on Statistical Genetics Department of Biostatistics School of Public Health Association Analysis • Linkage Analysis used to be the first step in gene mapping process • Closely located SNPs to disease locus may co- segregate due to linkage disequilibrium i.e. allelic association due to linkage. • The allelic association forms the theoretical basis for association mapping Linkage vs. Association • Linkage analysis is based on pedigree data (within family) • Association analysis is based on population data (across families) • Linkage analyses rely on recombination events • Association analyses rely on linkage disequilibrium • The statistic in linkage analysis is the count of the number of recombinants and non-recombinants • The statistical method for association analysis is “statistical correlation” between Allele at a locus with the trait Linkage Disequilibrium • Over time, meiotic events and ensuing recombination between loci should return alleles to equilibrium. • But, marker alleles initially close (genetically linked) to the disease allele will generally remain nearby for longer periods of time due to reduced recombination. • This is disequilibrium due to linkage, or “linkage disequilibrium” (LD). Linkage Disequilibrium (LD) • Chromosomes are mosaics Ancestor • Tightly linked markers Present-day – Alleles associated – Reflect ancestral haplotypes • Shaped by – Recombination history – Mutation, Drift Tishkoff
    [Show full text]
  • Linkage Disequilibrium Fine Mapping of Quantitative Trait Loci
    Genet. Sel. Evol. 35 (2003) 513–532 513 © INRA, EDP Sciences, 2003 DOI: 10.1051/gse:2003037 Original article Linkage disequilibrium fine mapping of quantitative trait loci: A simulation study a∗ b Jihad M. ABDALLAH , Bruno GOFFINET , b a Christine CIERCO-AYROLLES , Miguel PÉREZ-ENCISO a Station d’amélioration génétique des animaux, Institut national de la recherche agronomique, Auzeville BP 27, 31326 Castanet-Tolosan Cedex, France b Unité de biométrie et intelligence artificielle, Institut national de la recherche agronomique, Auzeville BP 27, 31326 Castanet-Tolosan Cedex, France (Received 27 June 2002; accepted 17 January 2003) Abstract – Recently, the use of linkage disequilibrium (LD) to locate genes which affect quantitative traits (QTL) has received an increasing interest, but the plausibility of fine mapping using linkage disequilibrium techniques for QTL has not been well studied. The main objectives of this work were to (1) measure the extent and pattern of LD between a putative QTL and nearby markers in finite populations and (2) investigate the usefulness of LD in fine mapping QTL in simulated populations using a dense map of multiallelic or biallelic marker loci. The test of association between a marker and QTL and the power of the test were calculated based on single- marker regression analysis. The results show the presence of substantial linkage disequilibrium with closely linked marker loci after 100 to 200 generations of random mating. Although the power to test the association with a frequent QTL of large effect was satisfactory, the power was low for the QTL with a small effect and/or low frequency. More powerful, multi-locus methods may be required to map low frequent QTL with small genetic effects, as well as combining both linkage and linkage disequilibrium information.
    [Show full text]
  • Unbiased Estimation of Linkage Disequilibrium from Unphased Data
    bioRxiv preprint doi: https://doi.org/10.1101/557488; this version posted August 8, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Unbiased estimation of linkage disequilibrium from unphased data * 2 Aaron P. Ragsdale and Simon Gravel 3 Department of Human Genetics, McGill University, Montreal, QC, Canada * 4 [email protected] 5 August 8, 2019 6 Abstract 7 Linkage disequilibrium is used to infer evolutionary history, to identify genomic regions under selection, 8 and to dissect the relationship between genotype and phenotype. In each case, we require accurate 9 estimates of linkage disequilibrium statistics from sequencing data. Unphased data present a challenge 10 because multi-locus haplotypes cannot be inferred exactly. Widely used estimators for the common statis- 2 2 11 tics r and D exhibit large and variable upward biases that complicate interpretation and comparison 12 across cohorts. Here, we show how to find unbiased estimators for a wide range of two-locus statistics, 2 13 including D , for both single and multiple randomly mating populations. These unbiased statistics are 14 particularly well suited to estimate effective population sizes from unlinked loci in small populations. We 15 develop a simple inference pipeline and use it to refine estimates of recent effective population sizes of 16 the threatened Channel Island Fox populations. 17 Introduction 18 Linkage disequilibrium (LD), the association of alleles between two loci, is informative about evolutionary 19 and biological processes.
    [Show full text]
  • Linkage Disequilibrium and Heterozygosity Modulate the Genetic Architecture of Human Complex Phenotypes
    bioRxiv preprint doi: https://doi.org/10.1101/705285; this version posted August 11, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Linkage Disequilibrium and Heterozygosity Modulate the Genetic Architecture of Human Complex Phenotypes Dominic Hollanda,b,∗, Oleksandr Freid, Rahul Desikanc, Chun-Chieh Fana,e,f, Alexey A. Shadrind, Olav B. Smelanda,d,g, Ole A. Andreassend,g, Anders M. Dalea,b,f,h aCenter for Multimodal Imaging and Genetics, University of California at San Diego, La Jolla, CA 92037, USA, bDepartment of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA, cDepartment of Radiology, University of California, San Francisco, San Francisco, CA 94158, USA, dNORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo 0424 Oslo, Norway, eDepartment of Cognitive Sciences, University of California at San Diego, La Jolla, CA 92093, USA, fDepartment of Radiology, University of California, San Diego, La Jolla, CA 92093, USA, gDivision of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway, hDepartment of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA, Abstract We propose an extended Gaussian mixture model for the distribution of causal effects of common single nucleotide polymorphisms (SNPs) for human complex phenotypes, taking into account linkage disequilibrium (LD) and heterozy- gosity (H), while also allowing for independent components for small and large effects. Using a precise methodology showing how genome-wide association studies (GWAS) summary statistics (z-scores) arise through LD with underlying causal SNPs, we applied the model to multiple GWAS.
    [Show full text]
  • Genetic Diversity and Fitness in Small Populations of Partially Asexual, Self
    Heredity (2010) 104, 482–492 & 2010 Macmillan Publishers Limited All rights reserved 0018-067X/10 $32.00 www.nature.com/hdy ORIGINAL ARTICLE Genetic diversity and fitness in small populations of partially asexual, self-incompatible plants M Navascue´s1,2, S Stoeckel3 and S Mariette4 1Unidad de Gene´tica, Centro de Investigacio´n Forestal, INIA, Carretera de La Corun˜a km 7.5, Madrid, Spain; 2E´ quipe E´ co-e´volution Mathe´matique, CNRS, UMR 7625 E´ cologie et E´ volution, Universite´ Pierre et Marie Curie & E´ cole Normale Supe´rieure, Paris, France; 3UMR Biology of Organisms and Populations applied to Plant Protection, INRA Agrocampus Rennes, Le Rheu, France and 4Unite´ de Recherche sur les Espe`ces Fruitie`res, INRA, Domaine de la Grande Ferrade, Villenave d’Ornon, France How self-incompatibility systems are maintained in plant S-locus. In addition, an excess of heterozygotes was present in populations is still a debated issue. Theoretical models predict the population, causing an increase in mutation load. This that self-incompatibility systems break down according to the heterozygote excess was enhanced by the self-incompatibility intensity of inbreeding depression and number of S-alleles. system in small populations. In addition, in highly asexual Other studies have explored the function of asexual reproduc- populations, individuals produced asexually had some fitness tion in the maintenance of self-incompatibility. However, the advantages over individuals produced sexually, because population genetics of partially asexual, self-incompatible sexual reproduction produces homozygotes of the deleterious populations are poorly understood and previous studies have allele, contrary to asexual reproduction. Our results suggest failed to consider all possible effects of asexual reproduction or that future research on the function of asexuality for the could only speculate on those effects.
    [Show full text]
  • Using the Variability of Linkage Disequilibrium Between Subpopulations to Infer Sweeps and Epistatic Selection in a Diverse Panel of Chickens
    Heredity (2016) 116, 158–166 & 2016 Macmillan Publishers Limited All rights reserved 0018-067X/16 www.nature.com/hdy ORIGINAL ARTICLE Using the variability of linkage disequilibrium between subpopulations to infer sweeps and epistatic selection in a diverse panel of chickens TM Beissinger1,2,3, M Gholami4, M Erbe4,5, S Weigend6, A Weigend6, N de Leon2,7, D Gianola3,8,9 and H Simianer4 A whole-genome scan for identifying selection acting on pairs of linked loci is proposed and implemented. The scan is based on ʹ2 ’ D IS, one of Ohta s 1982 measures of between-population linkage disequilibrium (LD). An approximate empirical null distribution for the statistic is suggested. Although the partitioning of LD into between-population components was originally used to ʹ2 fl investigate epistatic selection, we demonstrate that values of D IS may also be in uenced by single-locus selective sweeps with linkage but no epistasis. The proposed scan is implemented in a diverse panel of chickens including 72 distinct breeds genotyped at 538 298 single-nucleotide polymorphisms. In all, 1723 locus pairs are identified as putatively corresponding to a selective sweep or epistatic selection. These pairs of loci generally cluster to form overlapping or neighboring signals of selection. Known variants that were expected to have been under selection in the panel are identified, as well as an assortment of novel regions that have putatively been under selection in chickens. Notably, a promising pair of genes located 8 MB apart on fi ʹ2 chromosome 9 are identi ed based on D IS as demonstrating strong evidence of dispersive epistatic selection between populations.
    [Show full text]