Developmental Plasticity and the Origin of Species Differences
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Korunes Duke 0066D 14983.Pdf
How Linkage Disequilibrium and Recombination Shape Genetic Variation Within and Between Species by Katharine L Korunes University Program in Genetics and Genomics Duke University Date:_______________________ Approved: ___________________________ Mohamed Noor, Supervisor ___________________________ Mark Rausher, Chair ___________________________ Paul Magwene ___________________________ John Willis ___________________________ Jeff Sekelsky Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the University Program in Genetics and Genomics in the Graduate School of Duke University 2019 ABSTRACT How Linkage Disequilibrium and Recombination Shape Genetic Variation Within and Between Species by Katharine L Korunes University Program in Genetics and Genomics Duke University Date:_______________________ Approved: ___________________________ Mohamed Noor, Supervisor ___________________________ Mark Rausher, Chair ___________________________ Paul Magwene ___________________________ John Willis ___________________________ Jeff Sekelsky An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the University Program in Genetics and Genomics in the Graduate School of Duke University 2019 Copyright by Katharine L Korunes 2019 Abstract Meiotic recombination creates genetic diversity by shuffling combinations of alleles across loci, yet alleles at neighboring loci often remain non-randomly associated. This non-random association is -
A Role for Genetic Accommodation in Evolution? Christian Braendle1* and Thomas Flatt2
What the papers say A role for genetic accommodation in evolution? Christian Braendle1* and Thomas Flatt2 Summary lowered. Third, selection in the presence of the environmental Whether evolutionary change can occur by genetic factor enriches the previously cryptic alleles determining assimilation, or more generally by genetic accommoda- tion, remains controversial. Here we examine some of the the trait. Eventually, these alleles become so frequent that experimental evidence for both phenomena. Several the expression of the trait overcomes the higher threshold in experiments in Drosophila suggest that assimilation is the absence of the environmental stimulus.(9,20) Thus, genetic (1) possible, and a new paper shows that a color poly- assimilation transforms an environmentally induced (pheno- phenism in the tobacco hornworm, Manduca sexta, can typically plastic) trait into a phenotype which is stably evolve by genetic accommodation. We argue that genetic accommodation, including assimilation, is a plausible expressed without the eliciting environmental stimulus: the mechanism in evolution; however, more work is required genetically assimilated phenotype is no longer plastic, but to test how this mechanism acts and how often it is exhibits a genetically fixed response independent of the involved in evolutionary change. BioEssays 28:868– environmental conditions,(2,9,14,16) a phenomenon called 873, 2006. ß 2006 Wiley Periodicals, Inc. canalization.(20) Genetic assimilation is a special case of a more general Genetic assimilation and accommodation phenomenon, called genetic accommodation, most promi- (2–9) Whether the processes of genetic assimilation and nently proposed by Mary Jane West-Eberhard in 2003.(10) This (1,10) accommodation can explain evolutionary change and scenario of phenotypic evolution posits that (1) a mutation or phenotypic novelty is a controversial issue among evolutionary environmental change triggers the expression of a novel, herit- biologists (for example Refs 11–16). -
Degeneracy and Genetic Assimilation in RNA Evolution Reza Rezazadegan1* and Christian Reidys1,2
Rezazadegan and Reidys BMC Bioinformatics (2018) 19:543 https://doi.org/10.1186/s12859-018-2497-3 RESEARCH ARTICLE Open Access Degeneracy and genetic assimilation in RNA evolution Reza Rezazadegan1* and Christian Reidys1,2 Abstract Background: The neutral theory of Motoo Kimura stipulates that evolution is mostly driven by neutral mutations. However adaptive pressure eventually leads to changes in phenotype that involve non-neutral mutations. The relation between neutrality and adaptation has been studied in the context of RNA before and here we further study transitional mutations in the context of degenerate (plastic) RNA sequences and genetic assimilation. We propose quasineutral mutations, i.e. mutations which preserve an element of the phenotype set, as minimal mutations and study their properties. We also propose a general probabilistic interpretation of genetic assimilation and specialize it to the Boltzmann ensemble of RNA sequences. Results: We show that degenerate sequences i.e. sequences with more than one structure at the MFE level have the highest evolvability among all sequences and are central to evolutionary innovation. Degenerate sequences also tend to cluster together in the sequence space. The selective pressure in an evolutionary simulation causes the population to move towards regions with more degenerate sequences, i.e. regions at the intersection of different neutral networks, and this causes the number of such sequences to increase well beyond the average percentage of degenerate sequences in the sequence space. We also observe that evolution by quasineutral mutations tends to conserve the number of base pairs in structures and thereby maintains structural integrity even in the presence of pressure to the contrary. -
GSA Welcomes 2012 Board Members
7INTERs3PRING 4HE'3!2EPORTER winter s spring 2012 New Executive GSA Welcomes 2012 Board Members Director Now on Board The Genetics Society of America New Members of the GSA Board of welcomes four new members elected Directors Adam P. Fagen, by the general membership to the Ph.D., stepped in as 2012 GSA Board of Directors. The VICE PRESIDENT: GSA’s new Executive new members are: Michael Lynch Michael Lynch, Director beginning (Indiana University), who serves as Distinguished December 1, 2011. vice president in 2012 and as GSA Professor of Dr. Fagen previously president in 2013 and Marnie E. Biology, Class of was at the American Halpern (Carnegie Institution for 1954 Professor, Society of Plant Science); Mohamed Noor (Duke Department of Biologists (ASPB), University); and John Schimenti Biology, Indiana where he was the director of public (Cornell University), who will serve as University, continued on page nineteen directors. Bloomington. Dr. Lynch is a population and evolutionary biologist and a In addition to these elected officers, long-time member of GSA. Dr. Lynch 2012 Brenda J. Andrews (University of sees GSA as the home for geneticists Toronto), Editor-in-Chief of GSA’s who study a broad base of topics GSA Award journal, G3: Genes|Genomes|Genetics, and organisms, and as a forum Recipients which was first published online in where general discussion occurs, June 2011, becomes a member of the whether based on the principles Announced Board of Directors. The bylaws have of genetics, the most pressing historically included the GENETICS GSA is pleased to announce the issues within the discipline itself, or editor-in-chief on the Board and as a responses to societal concerns and/ 2012 recipients of its five awards result of a 2011 bylaw revision, the G3 for distinguished service in the or conflicts within applied genetics. -
Duke University Dissertation Template
Life History Tradeoffs and Genetic Variation for Social Behaviors in a Wild Primate Population by Emily McLean University Program in Genetics and Genomics Duke University Date:_______________________ Approved: ___________________________ Susan Alberts, Supervisor ___________________________ Mark Rausher, Chair ___________________________ Mohamed Noor ___________________________ Jenny Tung ___________________________ Elizabeth Archie Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the University Program in Genetics and Genomics of Duke University 2018 ABSTRACT Life History Tradeoffs and Genetic Variation for Social Behaviors in a Wild Primate Population by Emily McLean University Program in Genetics and Genomics Duke University Date:_______________________ Approved: ___________________________ Susan Alberts, Supervisor ___________________________ Mark Rausher, Chair ___________________________ Mohamed Noor ___________________________ Jenny Tung ___________________________ Elizabeth Archie An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the University Program in Genetics and Genomics in the Graduate School of Duke University 2018 Copyright by Emily McLean 2018 Abstract Understanding the genetic and environmental forces that contribute to phenotypic variation is a major goal of evolutionary biology. However, social living blurs the distinction between genes and environments because the social environment is (at least in part) determined by the genes of its members. Therefore, the genes that influence an individual’s phenotype are not limited to his own genes (direct genetic effects) but potentially include the genes of individuals in his social context (indirect genetic effects). Indirect genetic effects are thought to be of particular importance in the evolution of social behavior. Social living is a common phenotype in many animal taxa and is especially well-developed in non-human primates and humans. -
Coupling, Reinforcement, and Speciation Roger Butlin, Carole Smadja
Coupling, Reinforcement, and Speciation Roger Butlin, Carole Smadja To cite this version: Roger Butlin, Carole Smadja. Coupling, Reinforcement, and Speciation. American Naturalist, Uni- versity of Chicago Press, 2018, 191 (2), pp.155-172. 10.1086/695136. hal-01945350 HAL Id: hal-01945350 https://hal.archives-ouvertes.fr/hal-01945350 Submitted on 5 Dec 2018 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. Distributed under a Creative Commons Attribution| 4.0 International License vol. 191, no. 2 the american naturalist february 2018 Synthesis Coupling, Reinforcement, and Speciation Roger K. Butlin1,2,* and Carole M. Smadja1,3 1. Stellenbosch Institute for Advanced Study, Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa; 2. Department of Animal and Plant Sciences, The University of Sheffield, Sheffield S10 2TN, United Kingdom; and Department of Marine Sciences, University of Gothenburg, Tjärnö SE-45296 Strömstad, Sweden; 3. Institut des Sciences de l’Evolution, Unité Mixte de Recherche 5554 (Centre National de la Recherche Scientifique–Institut de Recherche pour le Développement–École pratique des hautes études), Université de Montpellier, 34095 Montpellier, France Submitted March 15, 2017; Accepted August 28, 2017; Electronically published December 15, 2017 abstract: During the process of speciation, populations may di- Introduction verge for traits and at their underlying loci that contribute barriers Understanding how reproductive isolation evolves is key fl to gene ow. -
MOHAMED NOOR Earl D
MOHAMED NOOR Earl D. McLean Professor and Chair, Department of Biology BIOGRAPHY Mohamed Noor wants to answer one of the greatest unsolved questions in biology: How constant evolutionary change produces the discontinuous groups known as species. As technology improves Dr. Noor’s work gets closer to the answer. Recently, his research team used fruit fly species to understand the causes and evolutionary [ Faculty Fellow through December 2017 ] consequences of variation in rates of genetic recombination. Now, his team is working to determine the genetic features and evolutionary EDUCATION processes that allow hybridizing species to persist. From reframing foundational principles of biology to applying modern approaches like Cornell University, Section of Genetics and whole-genome sequencing, Noor explores a wide range of scientific Development, Post-doc, 1996-98 topics to figure out what makes organisms similar and at the same University of Chicago, Ecology and Evolution, time unique. Ph.D., 1996 College of William and Mary, Biology, B.S., 1992 Dr. Noor’s innovative techniques are not limited to his research. He has developed a popular online course, “Introduction to Genetics and Evolution,” and uses the ‘flipped classroom” technique to deliver TOPICS traditional lecture material online so that his class can discuss the material the next day. This allows Noor to interact with his 400 students and to address specific topics during his precious class time. Genetics and evolution In 2012, Dr. Noor was the recipient of the ADUTA award for teaching Molecular evolution excellence, a student-nominated and selected award, given by the Evolution by natural selection Duke Alumni Association. -
Reproductive Isolation Between Two Species T. Freemani
Heredity72 (1994) 155—1 62 Received 14 June 1.993 Genetical Society of Great Britain Reproductive isolation between two species of flour beetles, Tribolium castaneum and T. freemani: variation within and among geographical populations of T castaneum MICHAEL J. WADE* & NORMAN A. JOHNSON Department of Ecology and Evolution, 1101 E. 57th Street, University of Chicago, Chicago, IL 60637,USA Tribolium casraneum and T freernani produce sterile hybrid progeny in reciprocal crosses. The reciprocal crosses differ significantly in the mean numbers of progeny, progeny sex ratios, hybrid male body size and male antennal and leg morphologies. These results suggest an effect of either the X chromosome or the cytoplasm on characteristics of F1 hybrids. In contrast, large X chromosome effects on morphological traits are not usually oberved in interspecific crosses among drosophilid flies. We also report large, significant differences in progeny numbers, body mass and degree of female bias in sex ratio between different geographic strains of T castaneum when mated in reciprocal crosses with T freemani. Sex ratio bias also varies significantly among matings within geographic strains of T castaneum. When T castaneum males are mated with T freemani females, but not in the reciprocal cross, the F1 sex ratio is female biased, uncorrelated with family size and ranges from 57.14 per cent to 72.23 per cent female, depending on the geographic strain of the T castaneum male. Keywords: hybridinviability, genetic variation,morphology, reproductive isolation, speciation, Tribolium sex that is most adversely affected. This rule applies to Introduction taxa in which males are the heterogametic sex (includ- Dobzhansky(1937),Mayr(1963) and others (Coyne et ing beetles) as well as in cases wherein females are the al., 1988; Coyne, 1992b; Wu & Davis, 1993) have heterogametic sex. -
The Evolution of Prezygotic Reproductive Isolation in The
Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2005 The evolution of prezygotic reproductive isolation in the Drosophila pseudoobscura subgroup Sheri Dixon Schully Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Schully, Sheri Dixon, "The ve olution of prezygotic reproductive isolation in the Drosophila pseudoobscura subgroup" (2005). LSU Doctoral Dissertations. 1001. https://digitalcommons.lsu.edu/gradschool_dissertations/1001 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. THE EVOLUTION OF PREZYGOTIC REPRODUCTIVE ISOLATION IN THE DROSOPHILA PSEUDOOBSCURA SUBGROUP A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences by Sheri Dixon Schully B.S., Louisiana State University, 2001 August 2005 DEDICATION I dedicate this dissertation to my parents, Lydia and Dale Dixon. My dad taught me the values of first-rate hard work. My mother has always made me feel that I could accomplish anything I put my mind and heart into. It has been her belief in me that has gotten me this far. ii ACKNOWLEDGEMENTS I would like to recognize and thank the people who made all of this work possible. First and foremost, I would like to express extreme gratitude to Mike Hellberg for his support and guidance. -
Dancing with DNA and Flirting with the Ghost of Lamarck
Biology and Philosophy (2007) 22:439–451 Ó Springer 2006 DOI 10.1007/s10539-006-9034-x Book review Dancing with DNA and flirting with the ghost of Lamarck MARY JANE WEST-EBERHARD Smithsonian Tropical Research Institute, c/o Escuela de Biologı´a, Cı`udad Unı`versitaria, Costa Rica (e-mail: [email protected]; phone: +506-228-0001; fax: +506-228-0001) Review of: Evolution in Four Dimensions, Eva Jablonka and Marion J. Lamb, 2005, MIT Press, Cambridge, Massachusetts Evolution in Four Dimensions, by Eva Jablonka and Marion Lamb, is a dis- armingly good-humored book that challenges the overly gene-centered ‘Neo- Darwinian’ (mid-20th-Century-Synthesis) view of evolution via selection on phenotypes affected by random changes in DNA. Their remedy, more palat- able by the end of the book than I expected at the beginning, is to propose that we revise and expand our ‘‘unidimensional’ vision of heredity. Heredity, they argue, occurs in four dimensions: genetic inheritance, the conventionally rec- ognized mode of inheritance via transmission of DNA; epigenetic inheritance, or transmission of non-genetic information from parental cells to daughter cells, as in the cytoplasm of an egg; behavioral inheritance, or cultural trans- mission of learned traits; and symbolic transmission of information by means of abstract representation, especially language in humans. All four modes of inheritance provide variants on which natural selection can act. Therefore they portray evolution as occurring in four dimensions, corresponding to the four dimensions of inheritance. The style of the book makes it accessible to an educated lay reader. The text has been unburdened by removal of bibliographic citations to a single section of notes at the end of the book, and by a series of dialogues with a make-believe Devil’s advocate named Ifcha Mistabra (in Aramaic, ‘‘The opposite conjecture’’), where the authors anticipate and answer potential confusions and objections to their main points. -
Clusters of Incompatible Genotypes Evolve with Limited Dispersal
ORIGINAL RESEARCH published: 22 April 2015 doi: 10.3389/fgene.2015.00151 Clusters of incompatible genotypes evolve with limited dispersal Erin L. Landguth 1*, Norman A. Johnson 2 and Samuel A. Cushman 3 1 Computational Ecology Laboratory, Division of Biological Sciences, University of Montana, Missoula, MT, USA, 2 Department of Biology, Department of Environmental Conservation, and Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA, USA, 3 Rocky Mountain Research Station, United States Forest Service, Flagstaff, AZ, USA Theoretical and empirical studies have shown heterogeneous selection to be the primary driver for the evolution of reproductively isolated genotypes in the absence of geographic barriers. Here, we ask whether limited dispersal alone can lead to the evolution of reproductively isolated genotypes despite the absence of any geographic barriers or heterogeneous selection. We use a spatially-explicit, individual-based, landscape genetics program to explore the influences of dispersal strategies on reproductive isolation. We simulated genetic structure in a continuously distributed population and across various dispersal strategies (ranging from short- to long-range individual Edited by: movement), as well as potential mate partners in entire population (ranging from 20 to Stéphane Joost, 5000 individuals). We show that short-range dispersal strategies lead to the evolution of École Polytechnique Fédérale de Lausanne, Switzerland clusters of reproductively isolated genotypes despite the absence of any geographic Reviewed by: barriers or heterogeneous selection. Clusters of genotypes that are reproductively Severine Vuilleumier, isolated from other clusters can persist when migration distances are restricted such University of Lausanne, Switzerland that the number of mating partners is below about 350 individuals. -
Genetic Assimilation: a Review of Its Potential Proximate Causes and Evolutionary Consequences
Annals of Botany Page 1 of 11 doi:10.1093/aob/mcv130, available online at www.aob.oxfordjournals.org REVIEW: PART OF A SPECIAL ISSUE ON DEVELOPMENTAL ROBUSTNESS AND SPECIES DIVERSITY Genetic assimilation: a review of its potential proximate causes and evolutionary consequences Ian M. Ehrenreich1,* and David W. Pfennig2,* 1Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA and 2Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA *For correspondence. E-mail [email protected] or [email protected] Downloaded from Received: 25 March 2015 Returned for revision: 7 May 2015 Accepted: 29 June 2015 Background Most, if not all, organisms possess the ability to alter their phenotype in direct response to changes in their environment, a phenomenon known as phenotypic plasticity. Selection can break this environmental sensi- tivity, however, and cause a formerly environmentally induced trait to evolve to become fixed through a process called genetic assimilation. Essentially, genetic assimilation can be viewed as the evolution of environmental http://aob.oxfordjournals.org/ robustness in what was formerly an environmentally sensitive trait. Because genetic assimilation has long been suggested to play a key role in the origins of phenotypic novelty and possibly even new species, identifying and characterizing the proximate mechanisms that underlie genetic assimilation may advance our basic understanding of how novel traits and species evolve. Scope This review begins by discussing how the evolution of phenotypic plasticity, followed by genetic assimila- tion, might promote the origins of new traits and possibly fuel speciation and adaptive radiation. The evidence implicating genetic assimilation in evolutionary innovation and diversification is then briefly considered.