The Basic Theorems of Natural Selection: a Naive Approach John R
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Fitness Maximization Jonathan Birch
Fitness maximization Jonathan Birch To appear in The Routledge Handbook of Evolution & Philosophy, ed. R. Joyce. Adaptationist approaches in evolutionary ecology often take it for granted that natural selection maximizes fitness. Consider, for example, the following quotations from standard textbooks: The majority of analyses of life history evolution considered in this book are predicated on two assumptions: (1) natural selection maximizes some measure of fitness, and (2) there exist trade- offs that limit the set of possible [character] combinations. (Roff 1992: 393) The second assumption critical to behavioral ecology is that the behavior studied is adaptive, that is, that natural selection maximizes fitness within the constraints that may be acting on the animal. (Dodson et al. 1998: 204) Individuals should be designed by natural selection to maximize their fitness. This idea can be used as a basis to formulate optimality models [...]. (Davies et al. 2012: 81) Yet there is a long history of scepticism about this idea in population genetics. As A. W. F. Edwards puts it: [A] naive description of evolution [by natural selection] as a process that tends to increase fitness is misleading in general, and hill-climbing metaphors are too crude to encompass the complexities of Mendelian segregation and other biological phenomena. (Edwards 2007: 353) Is there any way to reconcile the adaptationist’s image of natural selection as an engine of optimality with the more complex image of its dynamics we get from population genetics? This has long been an important strand in the controversy surrounding adaptationism.1 Yet debate here has been hampered by a tendency to conflate various different ways of thinking about maximization and what it entails. -
1 "Principles of Phylogenetics: Ecology
"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200 Spring 2016 University of California, Berkeley D.D. Ackerly March 7, 2016. Phylogenetics and Adaptation What is to be explained? • What is the evolutionary history of trait x that we see in a lineage (homology) or multiple lineages (homoplasy) - adaptations as states • Is natural selection the primary evolutionary process leading to the ‘fit’ of organisms to their environment? • Why are some traits more prevalent (occur in more species): number of origins vs. trait- dependent diversification rates (speciation – extinction) Some high points in the history of the adaptation debate: 1950s • Modern Synthesis of Genetics (Dobzhansky), Paleontology (Simpson) and Systematics (Mayr, Grant) 1960s • Rise of evolutionary ecology – synthesis of ecology with strong adaptationism via optimality theory, with little to no history; leads to Sociobiology in the 70s • Appearance of cladistics (Hennig) 1972 • Eldredge and Gould – punctuated equilibrium – argue that Modern Synthesis can’t explain pervasive observation of stasis in fossil record; Gould focuses on development and constraint as explanations, Eldredge more on ecology and importance of migration to minimize selective pressure 1979 • Gould and Lewontin – Spandrels – general critique of adaptationist program and call for rigorous hypothesis testing of alternatives for the ‘fit’ between organism and environment 1980’s • Debate on whether macroevolution can be explained by microevolutionary processes • Comparative methods -
What Is a Recessive Allele?
What Is a Recessive Allele? WernerG. Heim ONE of the commonlymisunderstood and misin- are termedthe dominant[dominirende], and those terpreted concepts in elementary genetics is that which becomelatent in the processrecessive [reces- sive]. The expression"recessive" has been chosen of dominance and recessiveness of alleles. Many becausethe charactersthereby designated withdraw students in introductory courses perceive the idea or entirelydisappear in the hybrids,but nevertheless that the dominant form of a gene is somehow stron- reappear unchanged in their progeny ... (Mendel ger than the recessive form and, when they are 1950,p. 8) together in a heterozygote, the dominant allele sup- Two important concepts are presented here: (1) presses the action of the recessive one. This belief is Statements about dominance and recessiveness are Downloaded from http://online.ucpress.edu/abt/article-pdf/53/2/94/44793/4449229.pdf by guest on 27 September 2021 not only incorrectbut it can lead to a whole series of statements about the appearanceof characters,about further errors. Students, for example, often errone- what is seen or can be detected, not about the ously conclude that because the dominant allele is the underlying genetic situation; (2) The relationship stronger, it therefore ought to become more common between two alleles of a gene falls on a continuous in the course of evolution. scale from one of complete dominance and recessive- There are other common misconceptions, among ness to a complete lack thereof. In the latter case, the them that: expression of both alleles is seen in either of two ways 1) Dominance operates at the genotypic level. -
Basic Genetic Terms for Teachers
Student Name: Date: Class Period: Page | 1 Basic Genetic Terms Use the available reference resources to complete the table below. After finding out the definition of each word, rewrite the definition using your own words (middle column), and provide an example of how you may use the word (right column). Genetic Terms Definition in your own words An example Allele Different forms of a gene, which produce Different alleles produce different hair colors—brown, variations in a genetically inherited trait. blond, red, black, etc. Genes Genes are parts of DNA and carry hereditary Genes contain blue‐print for each individual for her or information passed from parents to children. his specific traits. Dominant version (allele) of a gene shows its Dominant When a child inherits dominant brown‐hair gene form specific trait even if only one parent passed (allele) from dad, the child will have brown hair. the gene to the child. When a child inherits recessive blue‐eye gene form Recessive Recessive gene shows its specific trait when (allele) from both mom and dad, the child will have blue both parents pass the gene to the child. eyes. Homozygous Two of the same form of a gene—one from Inheriting the same blue eye gene form from both mom and the other from dad. parents result in a homozygous gene. Heterozygous Two different forms of a gene—one from Inheriting different eye color gene forms from mom mom and the other from dad are different. and dad result in a heterozygous gene. Genotype Internal heredity information that contain Blue eye and brown eye have different genotypes—one genetic code. -
Phylogenetics: Recovering Evolutionary History COMP 571 Luay Nakhleh, Rice University
1 Phylogenetics: Recovering Evolutionary History COMP 571 Luay Nakhleh, Rice University 2 The Structure and Interpretation of Phylogenetic Trees unrooted, binary species tree rooted, binary species tree speciation (direction of descent) Flow of time ๏ six extant taxa or operational taxonomic units (OTUs) 3 The Structure and Interpretation of Phylogenetic Trees Phylogenetics-RecoveringEvolutionaryHistory - March 3, 2017 4 The Structure and Interpretation of Phylogenetic Trees In a binary tree on n taxa, how may nodes, branches, internal nodes and internal branches are there? How many unrooted binary trees on n taxa are there? How many rooted binary trees on n taxa are there? ๏ six extant taxa or operational taxonomic units (OTUs) 5 The Structure and Interpretation of Phylogenetic Trees polytomy Non-binary Multifuracting Partially resolved Polytomous ๏ six extant taxa or operational taxonomic units (OTUs) 6 The Structure and Interpretation of Phylogenetic Trees A polytomy in a tree can be resolved (not necessarily fully) in many ways, thus producing trees with higher resolution (including binary trees) A binary tree can be turned into a partially resolved tree by contracting edges In how many ways can a polytomy of degree d be resolved? Compatibility between two trees guarantees that one can back and forth between the two trees by means of node refinement and edge contraction Phylogenetics-RecoveringEvolutionaryHistory - March 3, 2017 7 The Structure and Interpretation of Phylogenetic Trees branch lengths have Additive no meaning tree Additive tree ultrametric rooted at an tree outgroup (molecular clock) 8 The Structure and Interpretation of Phylogenetic Trees bipartition (split) AB|CDEF clade cluster 11 clades (4 nontrivial) 9 bipartitions (3 nontrivial) How many nontrivial clades are there in a binary tree on n taxa? How many nontrivial bipartitions are there in a binary tree on n taxa? How many possible nontrivial clusters of n taxa are there? 9 The Structure and Interpretation of Phylogenetic Trees Species vs. -
Basic Genetic Concepts & Terms
Basic Genetic Concepts & Terms 1 Genetics: what is it? t• Wha is genetics? – “Genetics is the study of heredity, the process in which a parent passes certain genes onto their children.” (http://www.nlm.nih.gov/medlineplus/ency/article/002048. htm) t• Wha does that mean? – Children inherit their biological parents’ genes that express specific traits, such as some physical characteristics, natural talents, and genetic disorders. 2 Word Match Activity Match the genetic terms to their corresponding parts of the illustration. • base pair • cell • chromosome • DNA (Deoxyribonucleic Acid) • double helix* • genes • nucleus Illustration Source: Talking Glossary of Genetic Terms http://www.genome.gov/ glossary/ 3 Word Match Activity • base pair • cell • chromosome • DNA (Deoxyribonucleic Acid) • double helix* • genes • nucleus Illustration Source: Talking Glossary of Genetic Terms http://www.genome.gov/ glossary/ 4 Genetic Concepts • H describes how some traits are passed from parents to their children. • The traits are expressed by g , which are small sections of DNA that are coded for specific traits. • Genes are found on ch . • Humans have two sets of (hint: a number) chromosomes—one set from each parent. 5 Genetic Concepts • Heredity describes how some traits are passed from parents to their children. • The traits are expressed by genes, which are small sections of DNA that are coded for specific traits. • Genes are found on chromosomes. • Humans have two sets of 23 chromosomes— one set from each parent. 6 Genetic Terms Use library resources to define the following words and write their definitions using your own words. – allele: – genes: – dominant : – recessive: – homozygous: – heterozygous: – genotype: – phenotype: – Mendelian Inheritance: 7 Mendelian Inheritance • The inherited traits are determined by genes that are passed from parents to children. -
THE MUTATION LOAD in SMALL POPULATIONS HE Mutation Load
THE MUTATION LOAD IN SMALL POPULATIONS MOT00 KIMURAZ, TAKE0 MARUYAMA, and JAMES F. CROW University of Wisconsin, Madison, Wisconsin Received April 29, 1963 HE mutation load has been defined as the proportion by which the population fitness, or any other attribute of interest, is altered by recurrent mutation (MORTON,CROW, and MULLER1956; CROW1958). HALDANE(1937) and MULLER(1950) had earlier shown that this load is largely independent of the harmfulness of the mutant. As long as the selective disadvantage of the mutant is of a larger order of magnitude than the mutation rate and the heterozygote fitness is not out of the range of that of the homozygotes, the load (measured in terms of fitness) is equal to the mutation rate for a recessive mutant and approxi- mately twice the mutation rate for a dominant mutant. A detailed calculation of the value for various degrees of dominance has been given by KIMURA(1 961 ) . In all these studies it has been assumed that the population is so large and the conditions so stable that the frequency of a mutant gene is exactly determined by the mutation rates, dominance, and selection coefficients, with no random fluctuation. However, actual populations are finite and also there are departures from equilibrium conditions because of variations in the various determining factors. Our purpose is to investigate the effect of random drift caused by a finite population number. It would be expected that the load would increase in a small population because the gene frequencies would drift away from the equilibrium values. This was confirmed by our mathematical investigations, but two somewhat unexpected results emerged. -
Glossary/Index
Glossary 03/08/2004 9:58 AM Page 119 GLOSSARY/INDEX The numbers after each term represent the chapter in which it first appears. additive 2 allele 2 When an allele’s contribution to the variation in a One of two or more alternative forms of a gene; a single phenotype is separately measurable; the independent allele for each gene is inherited separately from each effects of alleles “add up.” Antonym of nonadditive. parent. ADHD/ADD 6 Alzheimer’s disease 5 Attention Deficit Hyperactivity Disorder/Attention A medical disorder causing the loss of memory, rea- Deficit Disorder. Neurobehavioral disorders character- soning, and language abilities. Protein residues called ized by an attention span or ability to concentrate that is plaques and tangles build up and interfere with brain less than expected for a person's age. With ADHD, there function. This disorder usually first appears in persons also is age-inappropriate hyperactivity, impulsive over age sixty-five. Compare to early-onset Alzheimer’s. behavior or lack of inhibition. There are several types of ADHD: a predominantly inattentive subtype, a predomi- amino acids 2 nantly hyperactive-impulsive subtype, and a combined Molecules that are combined to form proteins. subtype. The condition can be cognitive alone or both The sequence of amino acids in a protein, and hence pro- cognitive and behavioral. tein function, is determined by the genetic code. adoption study 4 amnesia 5 A type of research focused on families that include one Loss of memory, temporary or permanent, that can result or more children raised by persons other than their from brain injury, illness, or trauma. -
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 -
Practice Problems in Population Genetics
PRACTICE PROBLEMS IN POPULATION GENETICS 1. In a study of the Hopi, a Native American tribe of central Arizona, Woolf and Dukepoo (1959) found 26 albino individuals in a total population of 6000. This form of albinism is controlled by a single gene with two alleles: albinism is recessive to normal skin coloration. a) Why can’t you calculate the allele frequencies from this information alone? Because you can’t tell who might be a carrier just by looking. b) Calculate the expected allele frequencies and genotype frequencies if the population were in Hardy-Weinberg equilibrium. How many of the Hopi are estimated to be carriers of the recessive albino allele? If we assume that the population’s in H-W equilibrium, then the frequency of individuals with the albino genotype is the square of the frequency of the albino allele. In other words, freq (aa) = q2. Freq (aa) = 26/6000 = 0.0043333, and the square root of that is 0.0658, which is q, the frequency of the albino allele. The frequency of the normal allele is p, equal to 1 - q, so p = 0.934. We’d then predict that the frequency of Hopi who are homozygous normal (genotype AA) is p2, which is 0.873. In other words, 87.3% of the population, or an estimated 5238 people, should be homozygous normal. The frequency of carriers we’d predict to be 2pq, which is 0.123. So 12.3%, or 737 people, should be carriers of albinism, if the population is in H-W. 2. A wildflower native to California, the dwarf lupin (Lupinus nanus) normally bears blue flowers. -
BIOL 116 General Biology II Common Course Outline
South Central College BIOL 116 General Biology II Common Course Outline Course Information Description This course covers biology at the organismal. population and system level. It will emphasize organismal diversity, population and community ecology and ecosystems. Students will gain an understanding of how evolutionary advances have occurred among organisms within a kingdom due to natural selection. This course involves a weekly three hour lab. (prerequisites: Score of 86 or above on the Sentence Skills portion of the Accuplacer test or ENGL 0090 and score of 50 or above on College Level Math portion of the Accuplacer test or MATH 0085) MNTC area 3 Total Credits 4.00 Total Hours 80.00 Types of Instruction Instruction Type Credits Lecture Lab Pre/Corequisites Prerequisite Score of 50 or above on the College Level Math portion of the Accuplacer test or MATH 0085 Prerequisite Score of 86 or above on the Sentence Skills portion of the Accuplacer test or ENGL 0090 Course Competencies 1 Appreciate and explain the process of scientific discovery and methodology Learning Objectives List and describe the steps of the scientific method Demonstrate the process of scientific discovery in the lab 2 Develop the skills necessary to engage in the scientific method Learning Objectives Formulate a hypothesis based on observations Develop a method to test a hypothesis Collect and analyze data Interpret data and form a conclusion Communicate scientific findings Common Course Outline - Page 1 of 4 Monday, September 24, 2012 3:42 PM 3 Explain the theory of -
Evolutionary Forces: Generation X Simulation to Launch the Genx
Biol 303 1 Lecture Notes Evolutionary Forces: Generation X Simulation To launch the GenX software: 1. Right-click ‘My Computer’. 2. Click ‘Map Network Drive’ 3. Don’t worry about what drive letter is assigned in the upper part of the dialogue box that pops up. In the lower part, enter: \\hopper\labshare. You can probably get this without typing by clicking the little triangle on the right of the field. 4. Using Windows Explorer, Click on the Labshare folder, then on Biology 303 folder, then on the GenX icon to start. A. Recall from lecture: Evolution is a change over time in allele (gene) frequencies within a population. There are 4 main evolutionary forces: Mutation - new allele arises by physical change in structure of DNA Genetic drift - random change in allele frequency by chance, important mainly in small populations (remember that variance ↑ as sample size ↓) Isolation - two populations that exchange members (even just 1 disperser per generation) do not diverge genetically. Isolated populations can diverge due to drift or natural selection Natural selection - differential survival and reproduction of individuals with different phenotypes Also recall that a locus is fixed for a single allele if any allele reaches a frequency of one. When a population holds only one allele, evolution cannot occur (until an alternative allele arrives by mutation or immigration). B. Background for Generation X simulations: Generation X is a computer model of evolution. It allows you to alter the four evolutionary forces, either one at a time or in combination, and see the effect on genotype and allele frequencies.