Genetic Variation in Subdivided Populations and Conservation Genetics
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Adaptation from Standing Genetic Variation and from Mutation
Adaptation from standing genetic variation and from mutation Experimental evolution of populations of Caenorhabditis elegans Sara Carvalho Dissertation presented to obtain the Ph.D degree in Biology Instituto de Tecnologia Química e Biológica | Universidade Nova de Lisboa Oeiras, Janeiro, 2012 Adaptation from standing genetic variation and from mutation Experimental evolution of populations of Caenorhabditis elegans Sara Carvalho Dissertation presented to obtain the Ph.D degree in Evolutionary Biology Instituto de Tecnologia Química e Biológica | Universidade Nova de Lisboa Research work coordinated by: Oeiras, Janeiro, 2012 To all the people I love. Table of contents List of Figures 3 List of Tables 5 Acknowledgements 7 Abstract 9 Resumo 13 CHAPTER 1 – Introduction 17 1.1 And yet…it changes 18 1.1.2 Evolution and adaptation 19 1.1.3 Mutation and standing genetic variation 25 Mutation 26 Standing genetic variation 32 Mutation versus standing genetic variation 34 Genetic recombination among adaptive alleles 35 1.1.4 Other players in evolution 37 1.1.5 Evolution in the wild and in the lab 40 1.1.6 Objectives 43 1.2 Caenorhabditis elegans as a model for experimental evolution 45 1.2.1 Experimental populations of C. elegans 50 1.3 References 53 CHAPTER 2 – Adaptation from high levels of standing genetic 63 variation under different mating systems 2.1 Summary 64 2.2 Introduction 64 2.3 Materials and Methods 69 2.4 Results 84 2.5 Discussion 98 2.6 Acknowledgements 103 2.7 References 103 2.8 Supplementary information 110 1 CHAPTER 3 – Evolution -
Pliocene Origin, Ice Ages and Postglacial Population Expansion Have Influenced a Panmictic Phylogeography of the European Bee-Eater Merops Apiaster
diversity Article Pliocene Origin, Ice Ages and Postglacial Population Expansion Have Influenced a Panmictic Phylogeography of the European Bee-Eater Merops apiaster Carina Carneiro de Melo Moura 1,*, Hans-Valentin Bastian 2 , Anita Bastian 2, Erjia Wang 1, Xiaojuan Wang 1 and Michael Wink 1,* 1 Department of Biology, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany; [email protected] (E.W.); [email protected] (X.W.) 2 Bee-Eater Study Group of the DO-G, Geschwister-Scholl-Str. 15, 67304 Kerzenheim, Germany; [email protected] (H.V.B.); [email protected] (A.B.) * Correspondence: [email protected] (C.C.d.M.M.); [email protected] (M.W.) Received: 20 August 2018; Accepted: 26 December 2018; Published: 15 January 2019 Abstract: Oscillations of periods with low and high temperatures during the Quaternary in the northern hemisphere have influenced the genetic composition of birds of the Palearctic. During the last glaciation, ending about 12,000 years ago, a wide area of the northern Palearctic was under lasting ice and, consequently, breeding sites for most bird species were not available. At the same time, a high diversity of habitats was accessible in the subtropical and tropical zones providing breeding grounds and refugia for birds. As a result of long-term climatic oscillations, the migration systems of birds developed. When populations of birds concentrated in refugia during ice ages, genetic differentiation and gene flow between populations from distinct areas was favored. In the present study, we explored the current genetic status of populations of the migratory European bee-eater. -
Genetic Variation in Polyploid Forage Grass: Assessing the Molecular Genetic Variability in the Paspalum Genus Cidade Et Al
Genetic variation in polyploid forage grass: Assessing the molecular genetic variability in the Paspalum genus Cidade et al. Cidade et al. BMC Genetics 2013, 14:50 http://www.biomedcentral.com/1471-2156/14/50 Cidade et al. BMC Genetics 2013, 14:50 http://www.biomedcentral.com/1471-2156/14/50 RESEARCH ARTICLE Open Access Genetic variation in polyploid forage grass: Assessing the molecular genetic variability in the Paspalum genus Fernanda W Cidade1, Bianca BZ Vigna2, Francisco HD de Souza2, José Francisco M Valls3, Miguel Dall’Agnol4, Maria I Zucchi5, Tatiana T de Souza-Chies6 and Anete P Souza1,7* Abstract Background: Paspalum (Poaceae) is an important genus of the tribe Paniceae, which includes several species of economic importance for foraging, turf and ornamental purposes, and has a complex taxonomical classification. Because of the widespread interest in several species of this genus, many accessions have been conserved in germplasm banks and distributed throughout various countries around the world, mainly for the purposes of cultivar development and cytogenetic studies. Correct identification of germplasms and quantification of their variability are necessary for the proper development of conservation and breeding programs. Evaluation of microsatellite markers in different species of Paspalum conserved in a germplasm bank allowed assessment of the genetic differences among them and assisted in their proper botanical classification. Results: Seventeen new polymorphic microsatellites were developed for Paspalum atratum Swallen and Paspalum notatum Flüggé, twelve of which were transferred to 35 Paspalum species and used to evaluate their variability. Variable degrees of polymorphism were observed within the species. Based on distance-based methods and a Bayesian clustering approach, the accessions were divided into three main species groups, two of which corresponded to the previously described Plicatula and Notata Paspalum groups. -
Panmixia of European Eel in the Sargasso Sea
Molecular Ecology (2011) doi: 10.1111/j.1365-294X.2011.05011.x FROM THE COVER All roads lead to home: panmixia of European eel in the Sargasso Sea THOMAS D. ALS,*1 MICHAEL M. HANSEN,‡1 GREGORY E. MAES,§ MARTIN CASTONGUAY,– LASSE RIEMANN,**2 KIM AARESTRUP,* PETER MUNK,†† HENRIK SPARHOLT,§§ REINHOLD HANEL–– and LOUIS BERNATCHEZ*** *National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark, ‡Department of Biological Sciences, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark, §Laboratory of Animal Diversity and Systematics, Katholieke Universiteit Leuven, B-3000, Leuven, Belgium, –Institut Maurice-Lamontagne, Fisheries and Oceans Canada, PO Box 1000 Mont-Joli, QC G5H 3Z4, Canada, **Department of Natural Sciences, Linnaeus University, SE-39182 Kalmar, Sweden, ††National Institute of Aquatic Resources, Technical University of Denmark, DK-2920 Charlottenlund, Denmark, §§International Council for Exploration of the Sea, DK-1553 Copenhagen, Denmark, ––Institute of Fisheries Ecology, Johann Heinrich von Thu¨nen-Institut (vTI), Federal Research Institute for Rural Areas, Forestry and Fisheries, Palmaille 9, 22767 Hamburg, Germany, ***De´partement de Biologie, Institut de Biologie Inte´grative et des Syste`mes (IBIS), Pavillon Charles-Euge`ne-Marchand, 1030, Avenue de la Me´decine, Universite´ Laval, QC G1V 0A6, Canada Abstract European eels (Anguilla anguilla) spawn in the remote Sargasso Sea in partial sympatry with American eels (Anguilla rostrata), and juveniles are transported more than 5000 km back to the European and North African coasts. The two species have been regarded as classic textbook examples of panmixia, each comprising a single, randomly mating population. However, several recent studies based on continental samples have found subtle, but significant, genetic differentiation, interpreted as geographical or temporal heterogeneity between samples. -
Testing Local-Scale Panmixia Provides Insights Into the Cryptic Ecology, Evolution, and Epidemiology of Metazoan Animal Parasites
981 REVIEW ARTICLE Testing local-scale panmixia provides insights into the cryptic ecology, evolution, and epidemiology of metazoan animal parasites MARY J. GORTON†,EMILYL.KASL†, JILLIAN T. DETWILER† and CHARLES D. CRISCIONE* Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA (Received 14 December 2011; revised 15 February 2012; accepted 16 February 2012; first published online 4 April 2012) SUMMARY When every individual has an equal chance of mating with other individuals, the population is classified as panmictic. Amongst metazoan parasites of animals, local-scale panmixia can be disrupted due to not only non-random mating, but also non-random transmission among individual hosts of a single host population or non-random transmission among sympatric host species. Population genetics theory and analyses can be used to test the null hypothesis of panmixia and thus, allow one to draw inferences about parasite population dynamics that are difficult to observe directly. We provide an outline that addresses 3 tiered questions when testing parasite panmixia on local scales: is there greater than 1 parasite population/ species, is there genetic subdivision amongst infrapopulations within a host population, and is there asexual reproduction or a non-random mating system? In this review, we highlight the evolutionary significance of non-panmixia on local scales and the genetic patterns that have been used to identify the different factors that may cause or explain deviations from panmixia on a local scale. We also discuss how tests of local-scale panmixia can provide a means to infer parasite population dynamics and epidemiology of medically relevant parasites. -
Evolution Ofsenescence Under Positive Pleiotropy?
Why organisms age: Evolution ofsenescence under positive pleiotropy? Alexei A. Maklako, Locke Rowe and Urban Friberg Linköping University Post Print N.B.: When citing this work, cite the original article. Original Publication: Alexei A. Maklako, Locke Rowe and Urban Friberg, Why organisms age: Evolution ofsenescence under positive pleiotropy?, 2015, Bioessays, (37), 7, 802-807. http://dx.doi.org/10.1002/bies.201500025 Copyright: Wiley-VCH Verlag http://www.wiley-vch.de/publish/en/ Postprint available at: Linköping University Electronic Press http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-117545 1 Why organisms age: Evolution of senescence under positive pleiotropy? Alexei A. Maklakov1, Locke Rowe2 and Urban Friberg3,4 1Ageing Research Group, Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden 2 Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3G5, Canada 3Ageing Research Group, Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden 4IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden Corresponding author: Maklakov, A.A. ([email protected]) Keywords: Aging, life-history evolution, mutation accumulation, positive pleiotropy senescence 2 Abstract Two classic theories maintain that aging evolves either because of alleles whose deleterious effects are confined to late life or because of alleles with broad pleiotropic effects that increase early-life fitness at the expense of late-life fitness. However, empirical studies often reveal positive pleiotropy for fitness across age classes, and recent evidence suggests that selection on early-life fitness can decelerate aging and increase lifespan, thereby casting doubt on the current consensus. -
3 Further Challenges
3 Further Challenges Hamilton’s claim of the inevitability of senescence can be disproved even within his own framework. Furthermore, his framework has sev- eral limitations. In this chapter theoretical and empirical issues that weaken his approach as the main explanation for the evolution of senes- cence will be discussed. Building on Medawar [126] and Williams [212], Hamilton wrote the pioneering first chapter on the moulding of senes- cence. I draw two main conclusions. • First, Hamilton’s basic notion – that the age-pattern of mortality is an inverse function of the age-pattern of his indicator – is wrong. For both his indicator and the other indicators in Table 2.1 the relationship between the indicator and mortality is so complicated that sophisticated modeling is required. • Second, several theoretical arguments as well as the bulk of em- pirical findings suggest that mutation accumulation is of secondary importance in molding the age-trajectories of mortality across the varied species of life. The primary force appears to be adaptation, i.e. the concept that patterns of aging are a byproduct of optimiza- tion of trade-offs. Hence, deep understanding of the evolution of aging requires optimization modeling. 3.1 General Problem with All Indicators Because his indicator declines with age, Hamilton deduced that mor- tality must increase with age. The relationship between his indicator of selection pressure and the age-pattern of mortality is not a simple one, however. During development his indicator is constant, while mortality, 36 3 Further Challenges for many and perhaps all species, is falling. At post-reproductive ages his indicator is zero, while mortality, at least in humans, rises and then slowly levels off. -
Environmental Correlates of Genetic Variation in the Invasive and Largely Panmictic
bioRxiv preprint doi: https://doi.org/10.1101/643858; this version posted August 13, 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-NC-ND 4.0 International license. Hofmeister 1 1 Environmental correlates of genetic variation in the invasive and largely panmictic 2 European starling in North America 3 4 Running title: Starling genotype-environment associations 5 6 Natalie R. Hofmeister1,2*, Scott J. Werner3, and Irby J. Lovette1,2 7 8 1 Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, 9 Ithaca, NY 14853 10 2 Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, 159 11 Sapsucker Woods Road, Ithaca, NY 14850 12 3 United States Department of Agriculture, Animal and Plant Health Inspection Service, 13 Wildlife Services, National Wildlife Research Center, 4101 LaPorte Avenue, Fort Collins, CO 14 80521 15 *corresponding author: [email protected] 16 17 ABSTRACT 18 Populations of invasive species that colonize and spread in novel environments may 19 differentiate both through demographic processes and local selection. European starlings 20 (Sturnus vulgaris) were introduced to New York in 1890 and subsequently spread 21 throughout North America, becoming one of the most widespread and numerous bird 22 species on the continent. Genome-wide comparisons across starling individuals and 23 populations can identify demographic and/or selective factors that facilitated this rapid bioRxiv preprint doi: https://doi.org/10.1101/643858; this version posted August 13, 2020. -
Evolutionary Genetics
Evolutionary Genetics Ruben C. Arslan & Lars Penke Institute of Psychology Georg August University Göttingen Forthcoming in D. M. Buss (Ed.), Handbook of Evolutionary Psychology (2nd ed.). New York: Wiley. September 17, 2014 Corresponding author: Ruben C. Arslan Georg August University Göttingen Biological Personality Psychology and Psychological Assessment Georg Elias Müller Institute of Psychology Goßlerstr. 14 37073 Göttingen, Germany Tel.: +49 551 3920704 Email: [email protected] 1 Introduction When Charles Darwin developed the theory of evolution, he knew nothing about genetics. Hence, one of its biggest weaknesses was that Darwin had to base it on crude ideas of inheritance. Around the same time, Gregor Mendel discovered the laws of inheritance, but the scientific community initially failed to appreciate his work’s importance. It was only in the 1930’s that Dobzhansky, Fisher, Haldane, Wright, Mayr and others unified genetics and the theory of evolution in the ‘modern synthesis’. Still, the modern synthesis was built on a basic understanding of genetics, with genes merely being particulate inherited information. The basics of molecular genetics, like the structure of DNA, were not discovered until the 1950’s. When modern evolutionary psychology emerged from ethology and sociobiology in the late 1980’s, it had a strong emphasis on human universals, borne from both the assumption that complex adaptations are monomorphic (or sexually dimorphic) and have to go back to at least the last common ancestor of all humans, and the methodological proximity to experimental cognitive psychology, which tends to treat individual differences as statistical noise. As a consequence, genetic differences between people were marginalized in evolutionary psychology (Tooby & Cosmides, 1990). -
What Is a Population? an Empirical Evaluation of Some Genetic Methods for Identifying the Number of Gene Pools and Their Degree of Connectivity
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Publications, Agencies and Staff of the U.S. Department of Commerce U.S. Department of Commerce 2006 What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity Robin Waples NOAA, [email protected] Oscar Gaggiotti Université Joseph Fourier, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/usdeptcommercepub Waples, Robin and Gaggiotti, Oscar, "What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity" (2006). Publications, Agencies and Staff of the U.S. Department of Commerce. 463. https://digitalcommons.unl.edu/usdeptcommercepub/463 This Article is brought to you for free and open access by the U.S. Department of Commerce at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Publications, Agencies and Staff of the U.S. Department of Commerce by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Molecular Ecology (2006) 15, 1419–1439 doi: 10.1111/j.1365-294X.2006.02890.x INVITEDBlackwell Publishing Ltd REVIEW What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity ROBIN S. WAPLES* and OSCAR GAGGIOTTI† *Northwest Fisheries Science Center, 2725 Montlake Blvd East, Seattle, WA 98112 USA, †Laboratoire d’Ecologie Alpine (LECA), Génomique des Populations et Biodiversité, Université Joseph Fourier, Grenoble, France Abstract We review commonly used population definitions under both the ecological paradigm (which emphasizes demographic cohesion) and the evolutionary paradigm (which emphasizes reproductive cohesion) and find that none are truly operational. -
Worldwide Genetic Variation in Dopamine and Serotonin Pathway
American Journal of Medical Genetics Part B (Neuropsychiatric Genetics) 147B:1070–1075 (2008) Worldwide Genetic Variation in Dopamine and Serotonin Pathway Genes: Implications for Association Studies Michelle Gardner,1,2 Jaume Bertranpetit,1,2 and David Comas1,2* 1Unitat de Biologia Evolutiva, Universitat Pompeu Fabra, Doctor Aiguader, Barcelona, Spain 2CIBER Epidemiologı´a y Salud Pu´blica (CIBERESP), Barcelona, Spain The dopamine and serotonin systems are two of the most important neurotransmitter pathways in Please cite this article as follows: Gardner M, Bertran- the human nervous system and their roles in petit J, Comas D. 2008. Worldwide Genetic Variation controlling behavior and mental status are well in Dopamine and Serotonin Pathway Genes: Implica- accepted. Genes from both systems have been tions for Association Studies. Am J Med Genet widely implicated in psychiatric and behavioral Part B 147B:1070–1075. disorders, with numerous reports of associations and almost equally as numerous reports of the failure to replicate a previous finding of associa- tion. We investigate a set of 21 dopamine and serotonin genes commonly tested for association INTRODUCTION with psychiatric disease in a set of 39 worldwide The dopamine and serotonin systems are two of the major populations representing global genetic diversity neurotransmitter systems in humans. Dopamine affects brain to see whether the failure to replicate findings of processes that control both motor and emotional behavior and association may be explained by population based it is known to have a role in the brain’s reward mechanism differences in allele frequencies and linkage [Schultz, 2002]. Serotonin has a critical role in temperature disequilibrium (LD) in this gene set. -
1055.Full.Pdf
Copyright 1999 by the Genetics Society of America Evolution of Genetic Variability and the Advantage of Sex and Recombination in Changing Environments Reinhard BuÈrger Institut fuÈr Mathematik, UniversitaÈt Wien, A-1090 Wien, Austria and International Institute of Applied Systems Analysis, A-2361 Laxenburg, Austria Manuscript received February 22, 1999 Accepted for publication May 12, 1999 ABSTRACT The role of recombination and sexual reproduction in enhancing adaptation and population persistence in temporally varying environments is investigated on the basis of a quantitative-genetic multilocus model. Populations are ®nite, subject to density-dependent regulation with a ®nite growth rate, diploid, and either asexual or randomly mating and sexual with or without recombination. A quantitative trait is determined by a ®nite number of loci at which mutation generates genetic variability. The trait is under stabilizing selection with an optimum that either changes at a constant rate in one direction, exhibits periodic cycling, or ¯uctuates randomly. It is shown by Monte Carlo simulations that if the directional- selection component prevails, then freely recombining populations gain a substantial evolutionary advan- tage over nonrecombining and asexual populations that goes far beyond that recognized in previous studies. The reason is that in such populations, the genetic variance can increase substantially and thus enhance the rate of adaptation. In nonrecombining and asexual populations, no or much less increase of variance occurs. It is explored by simulation and mathematical analysis when, why, and by how much genetic variance increases in response to environmental change. In particular, it is elucidated how this change in genetic variance depends on the reproductive system, the population size, and the selective regime, and what the consequences for population persistence are.