Genetics Session 4 2016
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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 -
Lecture 9: Population Genetics
Lecture 9: Population Genetics Plan of the lecture I. Population Genetics: definitions II. Hardy-Weinberg Law. III. Factors affecting gene frequency in a population. Small populations and founder effect. IV. Rare Alleles and Eugenics The goal of this lecture is to make students familiar with basic models of population genetics and to acquaint students with empirical tests of these models. It will discuss the primary forces and processes involved in shaping genetic variation in natural populations (mutation, drift, selection, migration, recombination, mating patterns, population size and population subdivision). I. Population genetics: definitions Population – group of interbreeding individuals of the same species that are occupying a given area at a given time. Population genetics is the study of the allele frequency distribution and change under the influence of the 4 evolutionary forces: natural selection, mutation, migration (gene flow), and genetic drift. Population genetics is concerned with gene and genotype frequencies, the factors that tend to keep them constant, and the factors that tend to change them in populations. All the genes at all loci in every member of an interbreeding population form gene pool. Each gene in the genetic pool is present in two (or more) forms – alleles. Individuals of a population have same number and kinds of genes (except sex genes) and they have different combinations of alleles (phenotypic variation). The applications of Mendelian genetics, chromosomal abnormalities, and multifactorial inheritance to medical practice are quite evident. Physicians work mostly with patients and families. However, as important as they may be, genes affect populations, and in the long run their effects in populations have a far more important impact on medicine than the relatively few families each physician may serve. -
Hemizygous Or Haploid Sex Diploid Sex
9781405132770_4_002.qxd 1/19/09 2:22 PM Page 16 Table 2.1 Punnett square to predict genotype frequencies for loci on sex chromosomes and for all loci in males and females of haplo-diploid species. Notation in this table is based on birds where the sex chromosomes are Z and W (ZZ males and ZW females) with a diallelic locus on the Z chromosome possessing alleles A and a at frequencies p and q, respectively. In general, genotype frequencies in the homogametic or diploid sex are identical to Hardy–Weinberg expectations for autosomes, whereas genotype frequencies are equal to allele frequencies in the heterogametic or haploid sex. Hemizygous or haploid sex Diploid sex Genotype Gamete Frequency Genotype Gamete Frequency ZW Z-A p ZZ Z-A p Z-a q Z-a q W Expected genotype frequencies under random mating Homogametic sex Z-A Z-A p2 Z-A Z-a 2pq Z-a Z-a q2 Heterogametic sex Z-A W p Z-a W q ·· 9781405132770_4_002.qxd 1/19/09 2:22 PM Page 19 Table 2.2 Example DNA profile for three simple tandem repeat (STR) loci commonly used in human forensic cases. Locus names refer to the human chromosome (e.g. D3 means third chromosome) and chromosome region where the SRT locus is found. Locus D3S1358 D21S11 D18S51 Genotype 17, 18 29, 30 18, 18 ·· 9781405132770_4_002.qxd 1/19/092:22PMPage20 Table 2.3 Allele frequencies for nine STR loci commonly used in forensic cases estimated from 196 US Caucasians sampled randomly with respect to geographic location. -
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. -
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. -
Popgen7: Genetic Drift
PopGen7: Genetic Drift Sampling error Before taking on the notion of genetic drift in populations, let’s first take a look at sampling variation. Let’s consider the age-old coin tossing experiment. Assume a fair coin with p = ½. If you sample many times the most likely single outcome = ½ heads. The overall most likely outcome ≠ ½ heads. This is a binomial sampling problem. ⎛n⎞ k n−k P = ⎜ ⎟()()1/ 2 1/ 2 ⎝k ⎠ ⎛n⎞ n! ⎜ ⎟ = ⎝k ⎠ k!()n − k ! n is the number of flips k is the number of successes Let’s look at the probability of the following: k heads from n flips Probability k =5 from n = 10 0.246 k =6 from n = 10 0.205 So, the most likely single outcome is ½ heads (with p = 0.246), the overall likelihood of observing something other than ½ heads is higher (p = 1 – 0.246 = 0.754) The good news is that as we increase the sample size the likelihood of observing something very close to the expected frequency, E(p) = 0.5, goes up. The probability of a given frequency of heads from n flips of the coin is: N flips p <0.35 p = 0.35-0.45 p = 0.45-0.55 p = 0.55-0.65 p <0.65 variance 10 0.16 0.21 0.25 0.21 0.16 0.025 20 0.06 0.19 0.50 0.19 0.06 0.0125 50 0.002 0.16 0.68 0.16 0.002 0.005 It is clear that sample size N is important. -
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. -
Adaptation for Fitness Intense Crossfit Workouts Improve Your Fitness—But How? Dr
Adaptation for Fitness Intense CrossFit workouts improve your fitness—but how? Dr. Lon Kilgore explains how doing Grace can cause adaptive changes at the cellular level and result in improved performance. By Dr. Lon Kilgore Midwestern State University January 2010 Courtesy of the Faculty of Kinesiology Management, University of Manitoba and Recreation Courtesy of the Faculty Any study of exercise physiology must begin with an understanding of what it is we wish to know. Exercise physiology is an applied science, meaning it is intended to solve a problem. The problem needing solving is that we—you, me and our trainees—are not as physically fit as we could be. 1 of 6 Copyright © 2010 CrossFit, Inc. All Rights Reserved. Subscription info at http://journal.crossfit.com CrossFit is a registered trademark ‰ of CrossFit, Inc. Feedback to [email protected] Visit CrossFit.com Adaptation ... (continued) The solution that needs to be provided by our study Courtesy of the University of Montreal should be a defined means of improving fitness levels. The discipline of exercise physiology should provide us with an understanding of how the body adapts to exercise to make us more fit. We can begin that quest with a look at the work of one individual, Hans Selye, MD. Who Is Hans Selye and Why Do I Care? Adaptation is not a new concept. Friedrich Nietzsche’s quote, “That which does not kill us makes us stronger,” is a famous adage used in reference to the many challenges we face in life. The fact that it’s from the 1800s means we have known for hundreds of years that the human body, when presented with a sub-lethal physical, psycho- logical or chemical stress, can adapt to the source of stress, allowing the body to tolerate incrementally larger similar stresses. -
Phylogeny and Fitness of Vibrio Fischeri from the Light Organs of Euprymna Scolopes in Two Oahu, Hawaii Populations
The ISME Journal (2011), 1–11 & 2011 International Society for Microbial Ecology All rights reserved 1751-7362/11 www.nature.com/ismej ORIGINAL ARTICLE Phylogeny and fitness of Vibrio fischeri from the light organs of Euprymna scolopes in two Oahu, Hawaii populations Michael S Wollenberg and Edward G Ruby Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA The evolutionary relationship among Vibrio fischeri isolates obtained from the light organs of Euprymna scolopes collected around Oahu, Hawaii, were examined in this study. Phylogenetic reconstructions based on a concatenation of fragments of four housekeeping loci (recA, mdh, katA, pyrC) identified one monophyletic group (‘Group-A’) of V. fischeri from Oahu. Group-A V. fischeri strains could also be identified by a single DNA fingerprint type. V. fischeri strains with this fingerprint type had been observed to be at a significantly higher abundance than other strains in the light organs of adult squid collected from Maunalua Bay, Oahu, in 2005. We hypothesized that these previous observations might be related to a growth/survival advantage of the Group-A strains in the Maunalua Bay environments. Competition experiments between Group-A strains and non- Group-A strains demonstrated an advantage of the former in colonizing juvenile Maunalua Bay hosts. Growth and survival assays in Maunalua Bay seawater microcosms revealed a reduced fitness of Group-A strains relative to non-Group-A strains. From these results, we hypothesize that there may exist trade-offs between growth in the light organ and in seawater environments for local V. fischeri strains from Oahu. -
Phylogenetic Relatedness and the Determinants of Competitive Outcomes
Ecology Letters, (2014) 17: 836–844 doi: 10.1111/ele.12289 LETTER Phylogenetic relatedness and the determinants of competitive outcomes Abstract Oscar Godoy,1* Nathan J. B. Kraft2 Recent hypotheses argue that phylogenetic relatedness should predict both the niche differences and Jonathan M. Levine1,3 that stabilise coexistence and the average fitness differences that drive competitive dominance. These still largely untested predictions complicate Darwin’s hypothesis that more closely related 1 Department of Ecology Evolution species less easily coexist, and challenge the use of community phylogenetic patterns to infer com- & Marine Biology University of petition. We field parameterised models of competitor dynamics with pairs of 18 California annual California Santa Barbara, CA, plant species, and then related species’ niche and fitness differences to their phylogenetic distance. 93106, USA Stabilising niche differences were unrelated to phylogenetic distance, while species’ average fitness 2Department of Biology University showed phylogenetic structure. This meant that more distant relatives had greater competitive of Maryland College Park, MD, 20742, USA asymmetry, which should favour the coexistence of close relatives. Nonetheless, coexistence 3Institute of Integrative Biology proved unrelated to phylogeny, due in part to increasing variance in fitness differences with phylo- ETH Zurich Universitaetstrasse 16 genetic distance, a previously overlooked property of such relationships. Together, these findings Zurich, 8092, Switzerland question the expectation that distant relatives should more readily coexist. *Correspondence and present Keywords address: Oscar Godoy, Instituto de Annual plants, California grasslands, coexistence, community assembly, competitive responses, Recursos Naturales y Agrobiologıa demography, fitness, niches, trait conservatism. de Sevilla (IRNAS), CSIC, PO Box 1052, Sevilla E-41080, Spain. -
A Fundamental Relationship Between Genotype Frequencies and Fitnesses
Copyright Ó 2008 by the Genetics Society of America DOI: 10.1534/genetics.108.093518 A Fundamental Relationship Between Genotype Frequencies and Fitnesses Joseph Lachance1 Graduate Program in Genetics, Department of Ecology and Evolution, State University of New York, Stony Brook, New York 11794-5222 Manuscript received July 3, 2008 Accepted for publication August 7, 2008 ABSTRACT The set of possible postselection genotype frequencies in an infinite, randomly mating population is found. Geometric mean heterozygote frequency divided by geometric mean homozygote frequency equals two times the geometric mean heterozygote fitness divided by geometric mean homozygote fitness. The ratio of genotype frequencies provides a measure of genetic variation that is independent of allele frequencies. When this ratio does not equal two, either selection or population structure is present. Within-population HapMap data show population-specific patterns, while pooled data show an excess of homozygotes. HAT patterns of genetic variation are possible within the set of possible postselection genotype frequencies is W a population, and how does natural selection affect derived. Much like how the Hardy–Weinberg principle these patterns? R. A. Fisher remarked ‘‘it is often conve- describes population genetic states in the absence of nient to consider a natural population not so much as an selection, this novel equation describes population genetic aggregate of living individuals but as an aggregate of gene states in the presence of selection. In the context of ratios’’ (Fisher 1953, p. 515). This mathematical abstrac- genotype-frequency space, this is a multidimensional tion allows key questions in evolutionary genetics to be surface, the curvature of which is influenced by natural addressed.