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FOR EXAM 3- EVOLUTIONARY BIOLOGY-BIOL
Evolutionary Biology (BIOL 3306) Notes What is evolution? Adaptation, Change, Mutation, Selection “Change over time” (“Descent with modification”) Examples : biology (evolution, development, cancer), physics (solar system, stars, galaxies), culture (language, knowledge, fashion), technology (airplane, computer, communications). “Change in the heritable properties of populations of organisms over several generations” Examples: antibiotic resistance in bacteria, HIV disease progression, etc. Excludes development of an organism (ontogeny) and aging Excludes direct effects of changes in the environment (secular increase in human height) Includes cancer at the level of the population of cells that make up the tumor SARS - CoV-2 spike protein 2.5% of amino acids have changed in about 2 years Human - Chimpanzee divergence 0.6% of amino acids have changed in 6 million years The theory of evolution Changes that happen in populations “Beginning with one primitive species” “Branched out over time” “Natural selection” Evolution, speciation, natural selection, gradualism, common ancestry, other mechanisms. “Life on earth evolved gradually beginning with one primitive species - perhaps a self-replicating molecule - that lived more than 3.5 billion years ago; it then branched out over time, throwing off many new and diverse species; and the mechanism for most (but not all) of evolutionary change is natural selection.” - Coyne (2009) Why Evolution is True Why study evolution? “Nothing in biology makes sense except in the light of evolution … Without that light it becomes a pile of sundry facts; some of them interesting or curious, but making no meaningful picture as a whole.” - Dobzhansky (1973) Studying Evolution: Historical sketch Jean-Baptiste Lamarck - proposed a detailed theory of evolution in Philosophie zoologique (1809) and Histoire naturelle des Animus sans vertèbres (1815) Charles Lyell - attacks Lamarck’s views in Principles of Geology (1833)
Charles Darwin - sketches out his theory of evolution by natural selection and shows it to a few colleagues (1842) Robert Chamber s- anonymously publishes a popular defense of evolution: Vestiges of the Natural History of Creation (1844) Alfred Wallace - publishes a paper defending evolution (1855). He discovers natural selection, writes a paper about it, and sends it to Darwin (1858). What took so long? Lack of direct evidence Poor understanding of biology Uncertainty over the age of the earth The argument from design Lack of a plausible mechanism “Some species that appear in the fossil record are not alive today” Extinction Georges Cuvier (1769-1832) Was not a biologist, never believed in evolution. Established the legitimacy of extinct species “ If the earth is young, evolution is impossible.” James Ussher (1581-1656) Ussher estimated that the first day of creation began at nightfall preceding Sunday, October 23, 4004 BC (proleptic Julian calendar). Although there was plenty of evidence for evolution, there was no plausible process that could account for it in principle (a similar problem occurred with continental drift in geology) Jean-Baptiste Lamarck (1744-1829) Proposed that evolution was caused by: Use and disuse, direct effects of environment on organisms, inheritance of acquired characteristics, an inherent tendency towards higher complexity. Biography The study of finding what species reside in a certain area. Continental islands: sit on a continental shelf (e.g., Greenland, Great Britain, Ireland, Sicily, Barbados, Trinidad, Sumatra, Java, Tasmania, Falklands) Tend to be large, old, and close to a continent more often than far Oceanic islands: do not sit on a continental shelf and usually have a volcanic origin (e.g., Galapagos, Azores, Cape Verde, Aleutian Islands, Hawaii Islands, Mauritius, Marianas) Tend to be small, young, and farther from a continent more often than close Definitions Distribution: where (spatially) a species is found Composition: which species are found somewhere Diversity: number of species Abundance: number of individuals of a species Native: arrived in Hawaii by natural means
Exponential Growth Observed that organisms have an enormous reproductive capacity A population of Escherichia coli can double in size every 20 minutes. Thus, after 3- 4 days, the descendants of a single cell with outnumber the atoms in the universe. Why do species not “take over the universe”? Population eventually runs out of resources (food), which keeps it from being about to grow. If a population shows a high potential growth rate, and if resources and limited, then only a subset of the population will survive and reproduce (differential reproductive success) (“the struggle for existence” ) Charles Lyell (1797-1875) - “Scientific theories should invoke the cumulative effects of processes that can be observed in the present, not catastrophes or miracles.” Natural selection does not act directly on genotypes, but on phenotypic differences between them. We must take into account how genotypes interact with environments to specify phenotypes (phenotypic plasticity). Fitness (combination of survival, ability to reproduce) is a specific to a particular genotype in a particular environment (e.g., a SARS-CoV-2 genotype in a particular human host with a particular medical history). Has multiple components (e.g., mating success, probability of survival to reproductive age, lifespan, resistance to pathogens) Which of the following statements about species native of oceanic islands is true? They tend to be similar to species from the closest mainland. Natural Selection (cont.) Artificial Selection A human being picks (consciously or unconsciously) which individuals in the population will survive and/or reproduce Allows us to test experimentally whether natural selection can cause evolutionary change. Example: pigeon breeding (Darwin) Beylaev’s experiment: change in traits of foxes When foxes become more juvenil, the hormones that take part in their growth and appearance are decreased. Anthropogenic evolution Evolutionary change caused by human activity Experimental evolution Natural selection is allowed to operate under experimental conditions Example: Lenski experiment (Escherichia (E) coli)
Environmental change is not a component of natural selection. Two types of adaptation Developmental / physiological / behavioral Change of an individual organism over its lifetime that makes the organism better suited to its environment. (Example: hematocrit increase at high altitude, darkening of the skin following exposure to ultraviolet radiation) Evolutionary Change in the heritable properties of populations of organisms over several generations that makes the organisms better suited to their environments. (Example: light coat color in populations of oldfield mice living in the dune environment) What is an adaptation in an evolutionary sense? A trait is an adaptation if: It is beneficial in the current environment It evolved by natural selection for its current function (Example: light coat color populations of oldfield mice is an adaptation to the dune environment) What is an exaptation in an evolutionary sense? A trait is an exaptation if: It is beneficial in the current environment It evolved by natural selection for a function other than its current function (Example: feathers are thought to have evolved in dinosaurs for insulation before they were exapted for flight in birds) Limits to natural selection Physical constraints Correlation of body parts in different mammals Trade-offs Lenski experiment Thermal adaptation (20,000 generations) Antagonistic pleiotropy: mutation in one gene that affects multiple genes at once Essentially a genetic trade-off Genetic basis of thermal adaptation (2,000 generations) Lack of foresight Lack of genetic variation Natural selection cannot do much without genetic variation Changing environment (evolutionary arms race) HOMEWORK 2 QUESTIONS Which of the following statements is true about evolution by natural selection? Some individuals are better able to survive in a certain environment than others. Describes differential reproductive success. Which of the following is not required for natural selection to operate? Changes in the environment. Natural selection only requires 3 components: variation, inheritance, and differential reproductive success. Changes in the environment are not required. Indeed, the environment can, in principle, be
Deleterious: reduce fitness Neutral: do not affect fitness Beneficial: increase fitness A mutation that is synonymous has no effect on the sequence of a protein. Most mutations with effects on fitness are deleterious. Directed mutation Are mutations random? Mutations are not random in many ways ● Some mutations are more likely to occur than others (e.g., transitions occur more often than transversions) ● Some regions of the genome are more likely to mutate than others ● Radiation and certain chemicals increase the mutation rate ● Deleterious mutations are more common than beneficial mutations Do organisms know when and how to mutate? Luria and Delbruck experiment (1943) Environmental change - bacteriophage Evolution - susceptible - resistant Random mutation hypothesis Prior to exposure to the phage, random mutations cause a few susceptible cells to become resistant. Acquired inherited resistance hypothesis Exposure to the page induces resistance in a few cells. Undirected mutation hypothesis Prior to exposure to the page, random mutations cause a few susceptible cells to become resistant. Directed mutation hypothesis Exposure to the phage induces resistance in a few cells. Lederberg and Lederberg experiment (1952) Environmental challenge - presence of antibiotic Evolution - susceptible
- resistant The random / undirected mutation hypothesis has been vindicated repeatedly. Natural selection appears to act primarily on preexisting, random / undirected variation.
Phylogeny Branching relationships of populations as they give rise to multiple descendant populations over evolutionary time. Types of trees: ● Unrooted ● Rooted ● “Tree” ● “Ladder” ● “circular” What are the applications of phylogenetic trees? ● Rates of evolutionary change ● Origins of derived traits ● Patterns of adaptive evolution ● Classify diversity ● Coevolution and co-speciation ● Conservation biology ● Origins of novel pathogens How to read Phylogenies Time advances from the root to the leaves/tips Leaves/tips represent taxa (species, genera, classes, populations, variants) Interior nodes represent ancestral species undergoing speciation, represent common ancestors of descendants Carl von Linne ● (Carl Linneaus after he died) ● Sweden; 1707 - 1778 ● Zoologist, botanist, taxonomist, and physician Observed incredible diversity in nature ● Asked: What is the best way to organize this? ● Devised Systema Naturae - Linnean Taxonomy ● Hierarchical system of naming and categorization ● Binomial nomenclature ( Genus species ) Homoplasy: Trait is shared between two taxa even though they do not share common ancestor Homoplasy is more like analogous trait (but is NOT homology, which is a shared trait inherited by common ancestor) Synapomorphies can help resolve polytomies and build phylogenies
Genetic variation
Variation
If the individuals of a population differ from one another
Inheritance
If some of this variation is heritable
Differential reproductive success
If some of this variation influences the ability of individuals to survive and reproduce.
Count of G (genotype)
Number of G individuals
Frequency of G
Proportion of G individuals out of the total number of individuals (i.e., probability of finding G)
( same goes for A (alleles) )
Evolution
General definition
Change in heritable properties of populations of organisms over several generations
Population genetic definition
Change in the genotype frequencies (or allele frequencies) of populations of organisms
over several generations.
Equilibrium Allele and/or genotype frequencies remain constant from generation to generation. Types of equilibria Stable ● A marble at the bottom of a rounded cup represents a stable equilibrium. No matter where the marble moves, it will always come back to the bottom of the cup Unstable ● A marble balanced on top of a hill represents an unstable equilibrium. The slightest movement of the marble will cause the marble to roll down, or move away, which is representative of an unstable equilibrium. Unlikely to find a population in the state of an unstable equilibrium. Neutral ● A marble at rest on a flat, still surface represents a neutral equilibrium. No matter where on the surface the marble moves, it will be stable. Mixed
● A marble in a half-pipe represents a mixed equilibrium. It is neither stable, nor neutral, nor unstable. It has all aspects of every other form of equilibrium, but it is not any of those 3 forms of equilibrium. ○ Stable with respect to changes in genotype frequencies that do not change the allele frequencies ○ Neutral with respect to changes in genotype frequencies that change the allele frequencies, but preserve x’=p^2, y’=2pq, and z’=q^2. ○ Unstable with respect to all other changes in genotype frequencies Yule’s equilibrium ● Stable equilibrium Hardy-Weinberg equilibrium ● Mixed equilibrium ● Effect of dominance ○ Dominance, on its own, has no effect on the frequency of an allele Deviations from Hardy-Weinberg equilibrium Oi = observed count of genotype i Ei = expected count of genotype i [D.f. = k - j = 1] = number of degrees of freedom [k = 3] = number of genotypes [j = 2] = number of parameters used to calculate Ei (n and p) Goodness-of-fit test In the Goodness-of-fit test equation, a high value of X^2 indicates poor fit Probability (P) that a X^2 statistic at least as high as the critical value has occurred by chance alone. The population does not show a statistically significant deviation from HW equilibrium frequencies (P > 0.05) Assumptions about Hardy-Weingberg equilibrium ● Autosomal locus ● The genotype frequencies are equal in both sexes ● No migration ● The offspring replace the parents every generation (i.i., non-overlapping generations) ● Individuals mate at random with respect to genotype ● The population is infinitely large ● All genotypes have the same number of offspring and probability of survival (i.e., fitness) ● No mutation —
