Evolution and Natural Selection Lecture Notes PDF

➔​ Learning objectives for lecture L1: Intro ➔​ Describe 4 reasons why understanding evolution is important ➔​ Understand how evolutionary theory can be used as a tool to make predictions about biological questions ​ Evolution is important for: ○​ Our understanding of life...

➔​ Learning objectives for lecture L1: Intro ➔​ Describe 4 reasons why understanding evolution is important ➔​ Understand how evolutionary theory can be used as a tool to make predictions about biological questions ​ Evolution is important for: ○​ Our understanding of life ​ Life started ~3 to 3.5 billion years ago from a single self-replicating molecule ○​ Conservation ○​ Agriculture ​ Artificial selection and domestication ​ Pest management ○​ Humans ​ Health and medicine ​ Understanding ourselves ​ The predictive power of evolutionary biology ○​ Evolutionary mindset is like a toolbox - theories (“tools”) can be used to generate and test hypotheses related to biological questions (“fix things”) ​ Comparative approaches in biology ○​ Comparative studies between species can be powerful because: ​ Much of life on earth faces similar survival problems and evolution can deal with them in a similar way ​ The more similar to the survival problem = the more powerful the comparison ​ At some point, all species on Earth shared a common ancestor ​ Eusocial vertebrate ○​ Richard Alexander’s prediction ​ Nest ​ 1) safe ​ 2) expandable ​ 3) in or near an abundance of food ​ 4) food should be obtained with little risk ​ Animal ​ 5) completely subterranean ​ 6) a mammal ​ 7) rodent ○​ since many of them nest underground ​ 8) primary food would be large underground roots and tubers ​ 9) predators deterred by heroic acts of one or few individuals ​ 10) live in wet-dry tropics  ○​ Plants there are more likely to produce large roots and tubers that store water and nutrients to help them survive the dry periods ​ 11) soil would be hard clay ○​ Otherwise, it would be unsafe from digging predators ​ 12) open woodland or scrubs of Africa ​ Naked Mole Rat = only known eusocial vertebrate L2: History of Evolution ➔​ Learn the 2 major principles of Lamarck’s theory of evolution (and understand why they are flawed) ➔​ Describe the major pieces of evidence that led Darwin to his theory of natural selection, as well as his three postulates of natural selection ➔​ Define biological evolution from a modern perspective, and list the five major mechanisms of evolution ​ Theory of special creation ○​ Species do not change through time ○​ Species were created independently of one another ○​ Species were created recently ○​ The mechanism of all life: ​ The divine intervention of God ​ People: ○​ Erasmus Darwin (1731-1802) ​ Charles Darwin grandfather ​ Examine animal traits and suggest they were related somehow ​ However, there was no convincing evidence as to why these relationships may exist ○​ Jean-Baptiste Lamarck (1744-1829) ​ Failed to describe mechanism of evolution correctly but recognized importance of inheritance and modification of traits over time ​ Lamarckian Evolution ​ Inheritance of acquired characteristics ○​ This is somewhat consistent with modern understanding of Epigenetics now ​ Epigenetics = non-nucleotide changes in DNA that can modify gene expression ​ Epigenetic changes can be modified and erased. While it can be inherited it is not an Evolutionary mechanism  ​ Organisms have tendency to advance to higher forms ○​ Charles Darwin (1809-1882) ​ Found passion in being a naturalist after he was pressured to be a doctor by his father due to poor grades and trained to be a priest ​ The most important event in his life he considered to be the Voyage of the HMS Beagle (1831-1836) ​ The Galapagos Islands ○​ Most species there not found anywhere else in the world ○​ Group of volcanic islands near the equator that he hypothesized had been colonized by organisms that arrived from South America. They diversified through Natural Selection and new species arose ​ Darwin's Finches ○​ The variation in beak shape in the various finches across the island appeared perfectly specialized for consumption of the primary food source the birds on each island ○​ Hypothesis: All had a common ancestor and diversified due to natural selection ​ Darwin's definition of evolution = "Descent with Modification” ​ Origin of Species (1859) ○​ Book Summarizing Darwin's evidence ​ knowledge of geology and "deep time” ​ breeding of domestic pigeons ​ natural observations during the Beagle and throughout his life ○​ was hesitant to publish until a letter from Alfred Wallace who had similar ideas prompted him to ​ 3 Conditions of Natural Selection ​ Natural Selections: differential survival and reproduction of individuals due to differences in traits ○​ Individuals within the population must vary in phenotypic traits ○​ At Least some of the variation must have a genetic basis (it is heritable) ○​ variation must influence reproductive success in terms of survival or reproduction ​ Darwin's theory of sexual selection ​ It is a mode of natural selection in relation to Sex ( reproductive success) ○​ males & females of same species differ  ○​ certain species have traits that have no survival benefit and can be costly for survival ​ Modern Synthesis of Evolutionary Biology (1920s-1950s) ○​ mathematics to synthesize our early understanding of genetics and inheritance with Darwin's description of evolution ○​ Modern definition of evolution: change in frequency of alleles in a Population over time ​ Change in allele frequency over time due to 5 major mechanisms of evolution ​ Natural selection ​ Sexual Selection ​ mutations ​ Gene flow (migration) ​ Genetic drift ○​ Led to realization that multiple mechanisms can cause evolutionary change ​ Major Contributions to the Modern Synthesis ○​ R.A. Fisher: Demonstrated the importance of genetic variation in evolution ○​ Sewall Wright: Demonstrated the relative roles of selection and genetic drift depending on population sizes ○​ J.B.S. Haldane: Devised mathematical theories of natural and artificial selection ​ Population genetics ○​ Calculating frequency of alleles in population and using information about evolutionary mechanisms action on the population to predict how those frequencies may change ○​ Recall: “Hardy-Weinberg Equilibrium” = no evolutionary mechanisms are at play = allele frequencies do not change ​ Evolutionary biology today ○​ Is highly interdisciplinary endeavor ○​ Most biologists recognize its importance in understanding ecology, genetics, physiology, health, and more ​ 10 Fundamental Principles of Evolution ○​ Genes store the info underlying heritable characteristics ○​ Phenotype = genes + environment ○​ Acquired characteristics are not genetically inherited ○​ Mutation is the origin of all heritable variations ○​ Evolution is a population-level process ○​ Evolutionary potential of a population is a direct function of the amount of generic variation ○​ Changes in allele/genotype frequency occur as a result of five mechanisms: mutation, selection, non-random mating, genetic drift, and dispersal  ○​ Populations are groups of interbreeding individuals ○​ Speciation is the origin of two or more species from a single common ancestor ○​ All organisms form a great tree of life descent from a single common ancestor L3: Natural History and Evidence of Evolution ➔​ Explain four major milestones spanning from the origin of life, to life on Earth today ➔​ Describe the scientific evidence that supports the theory of evolution from the perspective of: ◆​ The fossil record ◆​ Homology ◆​ Direct observation ◆​ Biogeography ​ Initial milestones: ○​ ~13.7 billion years ago: “Big Bang” and expansion of the universe ○​ ~4.6 billion years ago: formation of solar systems and Earth ○​ ~4 billion years ag: formation of Earth’s oceans ​ Timeline (image provided in lecture) ○​ Origin of life ​ Chemical physical processes on early Earth may have produced very simple cells through a sequence of stages: ​ Abiotic synthesis of small organic molecules ​ Joining of these small molecules into macromolecules ​ Packaging of molecules into protocells ​ Origin of self-replicating molecules ○​ Origin of single-celled organisms ​ Single-celled Organisms ​ ~3.5-3.7 bya: earliest direct evidence of life = stromatolites ○​ Stromatolites: layered rocks that form when prokaryotes bind thin films of sediment together ​ Primary producers ​ ~3.0 bys: ancestors of modern cyanobacteria (blue0green algae) lived on the Earth ​ Oxygen (photosynthesis byproduct) saturated the water and began to fill the atmosphere (the “oxygen revolution”) ​ Evolution of eukaryotic cells ​ ~1.8 bya ​ Compared to prokaryotes, characterized by a membrane-bound nucleus and more organelles ○​ Particularly the mitochondria and chloroplasts, which are thought to have arose via endosymbiosis  ○​ Origin of multicellular organisms ​ Multicellular eukaryotes (plants, animals, and fungi) = ~1.2 bya ​ Compared to unicellular organisms, ​ Multicellular organisms = can divide labor into specialized tasks such as movement, digestion, reproduction ○​ Competitive edge led to evolution of the vast diversity of multicellular life we see today ○​ Colonization of land ​ The oxygen revolution transformed the planet and paved the way for colonization of land ​ ~500 mya ago = plants colonized land, followed shortly later by animals ​ Evidence for evolution ​ Theory = an explanation that is broader in scope than a hypothesis, generates new hypotheses, and is supported by a large body of evidence ○​ The fossil record ​ What is it? ​ Remains or traces of organisms from the past ​ Often found in sedimentary rock, appears in layers of strata ​ Can provide evidence of the existence of extinct organisms, and give us a snapshot of evolutionary changes over time ​ “Holes” in the fossil record ​ Fossil record has many “holes” because only some organisms are likely to be preserved and under specific conditions ○​ Ex: lived where sediments were deposited, possess “hard” parts, present in large # ​ Transitional fossils ​ Fossilized remains of organisms that exhibit traits common to an ancestral group and its derived descendant group ​ Can help “link” together the relationships between living organisms (the oldest human fossil dates to ~3000,000 yrs ago) ○​ Tiktaalik (Big freshwater fish) ​ ~375 million yrs. Early ancestor of amphibians, reptiles, birds, and mammals ○​ Archaeopteryx (Ancient wing) ​ ~145 million yrs. Transition between dinosaurs and birds ○​ Ambulocetus (Walking whale) ​ Mammals diversified after dinosaurs went extinct (~65 mya)  ​ Ambilocetus is the transition between land mammals and whales (~50 mya) ○​ Homology ​ What is it? ​ Homology = similarities in structure and function and traits and their underlying genes = due to descent from common ancestry ​ Characteristics present in ancestral organism might be altered by natural selection in its descendants but they once shared the same form ​ As a result = we often observe similar characteristics between species that are closely related on the tree of life ​ Homology in structure ​ ~180 mya all living mammals on Earth shared a common ancestor ​ Limbs of various mammals, although used for different functions, are homologous in their underlying anatomical structure ​ Homology in genes ​ Homology and evolution of new characteristics ​ New characteristics appear throughout the tree of life ​ The key point: all descendants from that point onwards may possess some homologous version of that trait ○​ Direct Observation ​ What is it? ​ In species that have short generation cycles, we can observe and document that process of evolution in real-life ​ Has been observed both in natural settings and the lab ​ Ex: Peppered moth and the rapid adaptive evolution ​ During Industrial Revolution in England: soot from pollution caused many trees to turn black = white morphs were no longer camouflaged on many trees ​ Dark morphs 1848 was 2% then in 1895 was 95% ○​ Study found that birds were the main predator and factor driving this rapid evolution ​ Evolution of drug-resistant bacteria ​ Found/seen ○​ S. aureus is a species of bacteria that is usually harmless but some variants are dangerous pathogens ​ Following the use and discovery of penicillin as antibiotic in 1943 = strains of bacteria were resistant to penicillin began to pop up  ​ 1959 = doctors began using the antibiotic methicillin instead and within 2 yrs methicillin resistant strains began to appear ​ Long-Term Evolution experiment (LTEE) ○​ Every day the cultures are propagated ○​ Every 75 days (500 generations) samples are frozen away ○​ Mean fitness, relative to the ancestor, is estimated using the mixed-population samples ○​ Simple experiment has lead to approximately 300 papers in some of the most prestigious journals, earning Lenski the nickname “The Man Who Bottled Evolution” ○​ Biogeography ​ Is the study of geographic distribution of species ​ Earth’s continents were formerly united as a single large continent, but drifted apart over many years ​ Distribution of fossils and living species accurately reflects the historic movement of these continents ​ Ex: similarity of fossils in parts of South America and Africa is consistent with the idea that they were formerly attached L4: Phylogeny ➔​ Read a simple phylogenetic tree to infer evolutionary relatedness, and identify the evolution of homologous and analogous traits ➔​ Understand 3 common misconceptions related to reading phylogenetic trees, and be able to identity independent clades on a tree ➔​ Describe how phylogenetic trees are constructed, and understand how parsimony is used to resolve competing phylogenetic hypotheses ​ Systematics ○​ Systematics = study of diversification of life across time, and the evolutionary relationships between them ○​ Two major components: ​ Taxonomy = naming and classification of species ​ Species are grouped in increasingly broad categories ​ From broad to narrow ○​ Domain -> kingdom -> phylum -> class -> order -> family -> genus -> species ​ Binomial Nomenclature ○​ The 2 naming system ○​ Genetic name: ​ Indicates the genus the organism belongs to  ○​ Specific name: ​ Distinguishes the species within the genus ​ About 1.8 million species were identified and named but new ones identified each year ○​ 3 domains of life ​ Prokaryotes ​ Bacteria ​ Archaea ​ Eukaryotes ​ Eukaryota ​ Phylogenetics = evolutionary relationships between species ​ Phylogenetic tree: ○​ Used to form hypotheses about species relationships ○​ It is a branching diagram that represents a hypothesis about the evolutionary history of a group of organisms through time ​ Homologeous vs analogous traits ○​ Homologous ​ Traits that are similar traits that have the same evolutionary origin ○​ Analogous ​ Traits with similar functions that have different evolutionary origins - also referred to as homoplasy (usually when referring to form, rather than function) ○​ Ex: wing evolution is analogous but evolution of 4 limbs is homologous ​ Cleaning up some common misconceptions ○​ Phylogenetic trees can be drawn in different ways but communicate the same thing ○​ Trees and even entire clades can be rotated and communicate the same thing ○​ The terminal ends of phylogenetic trees aren’t linear and don’t represent any sort of “progression” ​ How are trees constructed? ○​ Character = a heritable aspect of organisms that can be compared across taxa ○​ Synapomorphy = derived form of a trait that is shared by a group of related species ○​ To construct a tree ​ we need to compare the presence/absence of various synapomorphies across species we think are closely related ​ Remember that every tree is a hypothesis ​ Character evolved twice = example of homoplasy ​ Same character evolved in two lineages that do not share common ancestor = convergent evolution ​ Rely on the gain and subsequent loss of a trait = evolutionary reversal ​ How do we choose? ​ Parsimony = one heuristic approach for evaluating hypotheses; good enough but not the optimum ○​ Believes the simplest explanation tends to be the correct one (fewest # of evolutionary steps) ​ Equally parsimonious outcomes ○​ Instead of deciding on one arbitrarily we combine the trees into a consensus tree ​ If tree disagrees with relationships of few animals = polytomy ​ More data must be collected to resolve polymies L5: Mutation and Genetic Variation ➔​ Define mutation, and explain why it is considered to be the source of all genetic variation ➔​ List and describe 3 major types of mutations at the DNA level and explain how they can potentially affect phenotypes ➔​ Describe Mendel’s law of segregation and law of dominance, and explain how they relate to the expression and inheritance of specific gene variants (alleles) ➔​ Explain how environmental effects and gene interactions add complexity to Mendel’s basic view of inheritance ​ Definitions ○​ Evolution ​ A change in the frequency of an allele or genotype in a population over time ○​ Gene ​ A distinct sequence of heritable DNA ○​ Allele ​ Unique copy of a gene (or gene variant) ○​ Genotype ​ The genetic constitution of an organism (the allele(s) the organism has) ○​ Phenotype ​ The observable expression of a trait (ex: eye color, aggression) ○​ Phenotypic evolution ​ A change in the frequency of alleles, resulting in a change in the distribution of phenotypic traits in a population ​ DNA structure and function ○​ DNA ​ DNA or deoxyribonucleic acid is the molecule that encodes the genome ​ Composed of 4 monomers (bases) ​ Base pairs: G-C and A-T ​ Function: ​ To provide a stable and reliable template for the production of RNA and ultimately proteins ○​ Gene expression ​ All expressed biological traits (phenotypes) are influenced in part due to genetics and the environment ​ DNA inside the nucleus is transcribed into RNA ​ RNA is translated by ribosomes in the cell into protein ​ Each protein has a specific function that contributes to determine every trait expressed by an organism. This expression traits is called phenotype ​ Mutations  ○​ At the population level, a mutation is a novel genetic difference between parents and offspring (ex: mutations that have occurred in germline) ○​ A the molecular level, mutations represent a “mistake” that occurs during DNA replication ○​ Mutations arise randomly ○​ Genetic variation is required for natural selection to occur and mutations are the ultimate source of all variation ○​ Types of mutations: ​ Nucleotide level ​ Point mutations ○​ Change of a single base pair due to a substitution, insertion, or deletion ○​ Non-synonymous mutation ​ Can completely change the protein and its function ○​ Synonymous mutation ​ Has no effect at all ○​ It will cause effects at the protein and phenotype level ​ Chromosome level ​ Chromosome inversion ○​ Flipping of chromosome segment ○​ Typically has no individual consequences, but can influence recombination, and thisis the allele frequency in the next generation ​ Gene/chromosome/genome duplication ○​ Gene duplication ​ Duplication of a segment of DNA ​ Typically, this leads to two of the same proteins, allowing the extra to freely evolve into something with a new function ○​ Frequency of mutation types in humans ​ Somatic mutations ​ Mutations that occur in the cells that compose our bodies and are not heritable ​ Often the cause of many cancers ​ Germline mutations ​ Mutations that occur in our gametes and are heritable ○​ Mutations and fitness ​ Most mutations have negative or little effects on fitness ​ Beneficial mutations are rare but would be quickly picked up by selection ​ General Information:  ○​ Chromosomes ​ Diploid organisms have a homologous pair of each chromosome = means each individual has 2 copies of every gene ○​ Protein structures ​ Polymer composed of 20 different monomers (amino acids) ​ Approximately 100,000 proteins in the human body ​ Comprise most of the dry weight of cells - the “business end” of the cell, comprising cell structure and functions ​ Capable of forming complex structures that relate to the function - this is due to the fundamental properties of amino acids that constitute the primary structure ○​ Genetic recombination and meiosis ​ Genetic “reshuffling” ​ Occurs during meiosis ​ Two mechanisms ​ Crossing-over ​ Independent assortment ​ Linkage ​ Genes that are closer together on the same chromosome are more likely to be passed on to each other ​ How is DNA inherited? ○​ Mendel’s Law of Segregation ​ The 2 members of a gene pair (alleles) segregate from each other in the formation of gametes ​ So for every single gene, each parent contributes one of their two alleles ○​ Mendel’s Law of Dominance ​ Individuals can have two of the same alleles or two different ones ​ Homozygous ○​ Two copies of the same allele for a given gene ​ Heterozygous ○​ Two different alleles for a given gene ​ Different alleles are expressed in different ways depending on the number of copies ​ Dominant ○​ Always expressed, even with one copy only ​ Recessive ○​ Expressed = requires two copies present ○​ Some Mendelian traits in humans ​ wet/dry earwax  ​ Aversion to cilantro ​ Ability to smell the by-product of asparagusic acid (the chemical that smells in your pee after you eat asparagus) ○​ Modern view of genotype to phenotype ​ Mendel was correct but the current view is more complex ​ Phenotype = Interactions between multiple genes and alleles + environmental effects ​ Environmental effects ○​ Phenotypic plasticity ​ Refers to when genotypically idential individuals have different phenotypes due to environmental effects ​ Ex: Horned beetles either have horns or not, but this is determined by environmental circumstances experienced as a larva. Beetles experiencing malnutrition early do not reach the threshold size needed to grow horns ​ Polygenic effects ○​ In reality, most traits are polygenic ​ Polygenic =influenced by more than a single gene ○​ In general, the more genes involved, the more continuous the trait (also referred to as a quantitative trait) L6: SARS-CoV-2 Evolution ➔​ Describe the SARS-CoV-2 origin hypothesis of zoonotic spillover ➔​ Read a phylogenetic tree to describe the evolutionary history of the delta and omicron variants ➔​ Explain the concept of a host-pathogen arms race as it relates to the evolution of delta ➔​ Explain the concept of transmissibility-virulence trade-offs as it relates to the evolution of omicron ​ SARS-CoV-2 origins ​ Hidden Evolution: where was omicron? ○​ Isolated population ○​ Jumped to another animal then back to humans ○​ Immunocompromised individual ​ How is the public health impact of a virus characterized? ○​ 2 types of characterization: ​ Virulence ​ Severity or harmfulness of an infectious disease and its symptoms ​ Transmissibility ​ The ability for a pathogen to pass from one host to another ○​ The Spike (S) protein ​ Functions: ​ Cell entry ​ Immune evasion ​ 1273 amino acids and 3821 nucleotides ​ Mutations randomly arise and change the shape of the spike protein ​ Some of these changes resulted in functional phenotypes that make viruses more transmissible and Better at immune evasion ​ Viruses with these traits replicate in greater numbers and spread throughout the population of hosts and may become the dominant variant over time ​ Delta had 10 mutations on the S gene but Omicron (B1) had 37 ○​ The evolution of Delta ​ Evolution of immune evasion in Delta ​ The l452R changes a leucine to arginine on the receptor binding domain ○​ This is a substitution missense CUG (wildtype) to CGG ○​ The evolution of Omicron ​ Transmissibility ​ Original: wildtype ○​ R0 = 2-3  ​ Delta: ○​ R0 = ~5 ​ Omicron: ○​ R0 = ~7 ​ Virulence ​ During a period with mixed delta and omicron variant circulation, SARS-CoV-2 infections with presumed omicron variant infection were associated with substantially reduced risk of severe clinical endpoints and shorter durations of hospital stays ​ How is omicron different? Alternate cell entry ​ Omicron does not require TMPSS2 to cleave its spike protein and center the cell ​ Why omicron tends to stay out of the lungs ​ There is a lower expression of the TMPRSS2 enzyme in the upper airway compared to the lungs ​ How could this increase viral fitness? ​ If the virus remains in the upper airway, it may spread more easily through coughing and sneezing. ○​ More transmission means more replication ​ More replication = more viruses with the mutation that characterizes the omicron variant  ​ If infected individuals tend to experience less severe illness, this may increase their exposure to other people, ultimately resulting in increased transmission ​ Common omicron symptoms: ○​ Sore throat ○​ Runny nose ○​ Sneezing ​ Common Wildtype/Delta symptoms: ○​ Dry cough ○​ Shortness of breath ○​ Fever ○​ Loss of smell ○​ Host-pathogen arms race ​ As host gains immunity against a pathogen (by producing antibodies), the pathogens can only continue to infect new hosts if they evolve a new tactic to evade the resistance of the host ​ Once the pathogen acquires a new tactic, the host may require new antibodies to protect itself ​ Goes on and on = Antagonistic co-adapation ​ Why are viruses virulent? ○​ They benefit from virulence ​ Increased ability to invade tissues ○​ Cost of TOO much virulence ​ Decreased transmissibility ○​ Trade-off ​ Increase transmissible and decrease virulent ​ Viral Trade-Offs ​ Trade-off: ○​ A situation in which evolution cannot optimize the fitness associated with a specific trait without compromising the fitness associated with another  ​ In airborne viruses, too much virulence may begin to compromise transmissibility L7: Natural Selection I ➔​ Revisit and describe the three criteria for evolution by natural selection ➔​ Explain how we can describe selection across multiple scales (Ex: Gene, individual, group) ➔​ List and describe three forms of natural selection, and explain how they may change the distribution of traits in populations ​ Change of allele frequency over time: (5 major mechanisms of evolution) ○​ Natural selection ​ 3 conditions of natural selection: ​ 1. Individuals within the population must vary in phenotypic traits ○​ Variation: ​ Differences in quantifiable traits between individuals ​ Individuals vary in phenotypic traits within species ​ Variation provides the “raw material” for evolution ​ 2. At least some of the variation must have a genetic basis (ex: is ​ heritable) ○​ Heritability: ​ The proportion of variation in a trait that is due to genetic differences ​ We now know that genes are the mode of all inheritance ​ 3. This variation must influence reproductive success in terms of ​ survival or reproduction (ex: influence fitness) ○​ Fitness: survival and reproduction ​ Survival means nothing if successful reproduction cannot occur ​ But traits that increase survival typically improve reproductive success ○​ More opportunity ○​ Sexual selection ○​ Sexual selection  ○​ Mutations ○​ Gene flow (migration) ○​ Genetic drift ​ Natural selection ○​ Fitness: ​ A quantitative measure of reproductive success ○​ Natural selection ​ Differential survival and reproduction of individuals due to differences in traits (differential fitness) ○​ Adaptation ​ Increase the ability to survive and reproduce compared to individuals without the trait (increase fitness) ​ natural selection leads to the evolution of adaptations ○​ Natural selection can act at multiple levels: ​ On individuals ​ Darwin’s primary view: ○​ Natural selection acts on variation among individuals causing some to reproduce more than others ​ Refresher: ○​ Evolution acts on populations, not individuals ​ On genes ​ Dawkins proposed theidea that natural selection actson individual genes (most specifically alleles) -This is called the selfish gene hypothesis ​ Genes ‘compete’ to be passed on to the next generation ​ Does not reject Darwin's individual view, more so compliments it ​ Inclusive fitness and kin selection ○​ The concept of gene level selection was futher substantiated by WIlliam Hamilton and his model of inclusive fitness and kin selection ○​ Inclusive fitness: ​ the ability for an individual to pass on its genes to the next generation, taking into account genes shared by other kin(relatives) ○​ Kin selection theory has been applied to explain the evolution of traits that would be difficult to explain via individual-level selection alone, such as altruism ​ On groups ​ Natural selection opiates on traits above the gene and individual level, acting on average traits of the population  ○​ Acting for “the good of the species” ​ Theoretically possible but probably too weak to overpower individual selection ○​ Not much empirical evidence to support this hypothesis ​ Multilevel selection and the rise of human civilization ​ David Sloan Wilson, one of major and loud proponents for group-level selection has argued for multilevel selection theory ​ That is, our definition for inclusive fitness should include individuals, genes, and groups ​ He acknowledges that group-level might not always be a strong mechanism but can become relevant when dealing with highly social species that compete in groups ​ Selection ○​ Directional (positive) selection ​ Variants that are the most extreme in one direction of the mean are favored ​ ​ The selection causes directional changes in the evolution of a trait ​ ​ Ex: beak size in finishes after drought ​ In 1977, a drought on the island of Daphne Major changed the composition of plants (and thus seed availability) ​ This lead to the evolution of large beak size over the course of a year ○​ Stabilizing (purifying) selection ​ Variants closest to the mean value are favored  ​ ​ Selection prevents the changes to a trait by selecting against variants that deviate from the optimal value ​ ​ Ex: Goldenrod gall fly predation ​ Wasps target small galls ​ Birds target large galls ​ Leading to a selective advantage for medium galls ○​ Diversifying (divergent) selection ​ Variants on either extreme of the mean value are favored ​ ​ Selection causes a population to diverge into two directions ​ ​ Ex: Black-bellied seed cracker ​ Individuals specialize on either eating large or small seeds ​ Smith (1993) showed only juvelines with relative small are large beaks survived to adulthood L8: Natural selection II ➔​ Describe the concept of balancing selection and explain four ways genetic variation can be maintained in the face of directional selection ➔​ Describe how selection can be measured in natural populations and calculate selection differential ​ How and why is variation maintained in populations? ○​ Balance selection: ​ Any form of selection on its own or in conjunction with another evolutionary mechanism, that results in the maintenance of genetic variation ○​ Mutation selection balance ​ Although a minor evolutionary force, mutations are constantly introducing new variants into the population ​ When selection is weak it may contribute enough to maintain variation ​ Effects of mutation-selection balance ​ Mutations with small effects on fitness can take generations to eliminate - ○​ Mutation Load: ​ it is estimated that all individuals harbor hundreds of slightly deleterious mutations ​ Recessive alleles with large effects can persist in populations if they are rare ○​ Ex: more than 2000 different disease-causing alleles of the CFTR gene (which causes cystic fibrosis) have been identified ○​ Frequency-dependent selection ​ In some systems, individual fitness depends on the frequency of its genotype in the population ​ Positive: ​ The common genotype has the highest fitness (results in directional selection) ​ Negative: ​ The rarest genotype has the highest fitness (results in a form of balancing selection) ​ Pollinator selection and negative frequency-dependent selection  ​ Elderflower orchids provide no pollen reward for bees ​ As such, they quickly learn to avoid the most common color, leading to the positive selection for rare morphs and negative selection for common morphs ○​ Heterozygote advantage ​ Even if you have an allele that causes a phenotype with reduced fitness, this allele can be maintained if the heterozygous genotype is advantageous ​ Ex: imagine a gene with two alleles, X and Y ​ Even if the relative fitness of XX is 0.7 and YY is 0.1 ​ If XY is >0.7, then allele Y will be maintained in the population ​ Sickle cell anemia as a case of heterozygote advantage ​ A disorder resulting in abnormally shaped red blood cells with reduced ability for cells to carry oxygen ​ Occurs when a person possesses two dysfunctional copies of the β-globin gene (Ex: Recessive) ​ In areas where risk of contraction malaria is high, having one copy of this allele is beneficial (Ex: heterozygous advantage) ○​ Gene x environment interactions ​ Sometimes, fitness is determined by an interaction between genotype and environment ​ When this happens, two different genotypes can be maintained in these separate environments ​ GxE and disease risk  ​ Ex: many underlying variants that predispose one to various diseases may only result in disease in certain environments ​ Pair that with the fact that as a species, we are being exposed to novel environmental factors that our ancestors never faced, and this could explain why these genetic variants persist in populations in the first place ​ Measuring selection: ○​ Diversity in Darwin’s finches ​ Medium ground finch (Geospiza fortis) ​ Variation in beak size influences efficiency at eating different types of seeds ​ Beak size evolution ​ Beak size and beak depth are highly heritable ​ Hypothesis: Beak size affects how birds can eat seeds ​ Measured the sizes and hardness of all foods and quantified their abundance ​ Birds eat the same seeds under rainy season conditions but specialize on different seeds when food is scarce: Deep-billed birds eat hardy woody seeds more efficiently ​ Severe drought resulted in only harder, woody seeds available to birds ○​ Result: Large-beaked birds favored ○​ How do we measure natural selection? ​ Selection differential: ​ Measures the strength of selection  ​ It is the mean trait value of individuals that survive to reproduce after a selection event, minus the mean of the entire population before the event ​ s = x̄* - x̄ ​ Where s is the selection differential ​ x̄ is the mean trait value before the selection ​ x̄* is the mean value after selection ​ Natural selection is variable over time and can result in rapid evolutionary change ​ In some years, the selection on break size favored large beaks ​ In other years, selection favored smaller beaks, or selection on beak size was minimal ​ Key concepts: ○​ Beak size is strongly heritable and influences fitness ​ Natural selection can cause rapid change ○​ Long-term studies reveal fluctuation in the direction and strength of natural selection in real-time L9: Gene Flow and Genetic Drift ➔​ Define dispersal and gene flow and understand their effects on evolution ➔​ Define the concept of genetic drift, and explain three ways it can occur ➔​ Explain how genetic drift can lead to the change of allele frequencies in populations, and describe why its impact is greater in smaller populations ​ How can the frequency of alleles change over time? ○​ There are five major mechanisms of evolution ○​ Natural selection ○​ Sexual selection ○​ Mutations ○​ Gene flow (migration) ​ Dispersal and gene flow ​ Dispersal/migration: ○​ The physical movement of individuals from one population to another ​ Gene flow: ○​ The movement of alleles from one population to other ○​ ​ Therefore dispersal = gene flow, if the individuals form the dispersing population breed with the new population ​ Like mutation, gene flow can introduce variation into populations but it differs from mutation as its is not the origin of this variation ​ How does gene flow influence evolution? ​ In large populations with ample genetic variation, effect is usually small (selection remains dominant evolutionary force) ​ However, in small populations with low genetic variation, gene flow can influence the strength of selection ​ The strength of this effect depends on the amount of gene flow ○​ Low gene flow ​ Can rescue inbred populations from lack of genetic diversity ○​ Medium gene flow ​ A good source of new genetic variation, thus increasing the effeciency of natural selection ○​ High gene flow ​ Can swamp out variation and reduce selection  ○​ Genetic drift ​ Genetic drift ​ The random change of allele frequencies from generation to generation ​ Genetic drift acts on alleles with a neutral effect on fitness ​ Allees with a neutral effect on fitness ​ If selection is not acting on an allele, the change of its being passed on to the next generation is completely random. This “randomness” is determined by which gametes are passed onto the next generation ​ ​ Why does this drift occur ​ “Gametic sampling error” ○​ 1. If fitness effect is neutral... we may statistically expect the frequency to remain the same over time… ○​ 2. However, there is always a chance that we won’t get what is statistically expected! 1.​ 2. ​ If drift is only an evolutionary mechanism, a single allele will eventually become fixed in the population ​ The chance of an allele getting fixed is directly proportional to its starting frequency ​ Blue has a 66.6% chance of fixation, and red 33.3% ​ Now, blue has 83.3% chance of fixation and red 16.6% ​ Blue is fixed in the population  ​ ​ Drift can cause populations to follow unique evolutionary paths ​ ​ Evolution in small populations ○​ Compared to larger populations, in small populations, the effects of natural selection are weaker because of less genetic variation ○​ However, the effects of drift are often stronger, due to higher probability of an allele becoming fixed over time due to less genetic variation and greater gametic sampling error ​ What kind of events can rapidly reduce a population’s size? ​ Population bottle neck ○​ When a catastrophic event causes a large amount of individuals in a population to randomly die or stop reproducing and only a small amount of individuals make it through ○​ ​ Founder events ○​ When a new population is established by a small number of colonists ​ Many new human diseases can be explained in part by founder effects  ​ In Iceland, virtually all cases of breast cancer linked to BRCA2 mutations are due to a single specific mutation (999del5), suggesting that this mutation descended from a single common ancestor and then spread throughout the population ​ These events are types of genetic drift and increase the impact of drift by reducing a population’s size ​ Selection vs Drift ○​ Selection: ​ Alleles with highest fitness pass on most copies ​ Evolution is NOT random ​ Leads to evolution of adaptations ○​ Drift: ​ Alleles passed on influenced by chance events ​ Evolution is random ​ Cannot lead to the evolution of adaptations ​ Butts ​ Genetic Rescue Case Study ○​ Human intervention to rescue small, inbred populations negatively affected by artificially introducing gene flow ○​ Genetic rescue of the Florida panther ​ In the 1900s, the population nosedived due to hunting and habitat loss/fragmentation ​ The low population size led to a loss of genetic diversity due to drift and increased rates of inbreeding ​ By the 1990s, there were less than 30 Florida panthers left ​ To make matters worse, these individuals were of poor genetic quality and expressed traits such as poor sperm quality, kinked tails, and heart defects - the population was slated to go extinct ​ ​ In 1995, 8 female pumas from Texas (a different subspecies of the panther) were moved into Florida, introducing novel genetic variation into the population ​ By 2007, population grew to 102 and genetic variation increased ​ ​ Today, the species is still at risk, but genetic rescue efforts have greatly increased the heterozygosity and average fitness of individuals within the population ​