Evolution Lecture Notes PDF

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Notes from the zoom lectures in 2020 for BIOL 351...

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Evolution Lecture Notes [email protected] Evolution: ● Evolution is the process that is responsible for the diversity of the living world ○ Diversity in function ● Why study evolution ○ Implicit example ■ Usefulness of model organisms, why should we be able to learn anything about ourselves from fruit flies or rats? ○ Explicit example ■ Using humans to learn about ourselves ○ Understanding of HIV, covid, others are significantly due to evolution ○ Theory? ■ Atomic theory ■ Quantum theory ■ Cell theory ■ Theory of plate tectonics ■ Germ theory of disease ● A theory in the same sense as these being theories ○ Organized facts and laws that are well reasoned ○ Metaphysical Naturalism: an extension of materialism ○ Methodological Naturalism: in order for science to work, we have to operate under the unwavering premise of naturalism ■ We cant resort to supernatural explanations for empirical observations, even though there may be something beyond nature, but that is not covered by science ■ Without this, we would just give up when we encounter something we don't understand ○ What is evolution? ■ Latin – to unfold or unroll ● Has many meanings in different contexts ■ Evolution is shorthand for “biological evolution” ● The change in heritable properties of populations of organisms across generations ○ Changes in allele frequencies throughout time ■ Challenges long-held views of the world ■ Change, not stasis, is the natural order of the living world ● Already accepted in geology ● Biology moved in this direction leading up to darwin ■ Biological phenomenon explained by mechanistic causes ■ History is a crucial part of understanding patterns in nature ■ Variation is a ubiquitous component of biological systems

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● Major break with platonic essentialism Evolutionary biology is the study of variation in nature There are constraints on biological evolution, it is not endless forms though, only myriad forms What is the interplay between deterministic and stochastic forces? ● Interaction among 4 basic forces of evolutionary genetics ● How random is the living world? Was any of the biodiversity inevitable Evolution is an ongoing process

Lecture 2: 2/16 ● Descent with modification ● Charles Darwin ○ Observed the environment, species, fossils and patterns of traits in domesticated animals ■ Wasn’t just him coming up with these ideas ○ Key components (1600s) ■ Academic recognition of what fossils are ■ Noticing and recording patterns in distributions of fossil marine animals in terrestrial rocks ■ Grew into stratigraphy ● Stratigraphy: study of layering of rocks in terms of chronology ○ Key components (late 1700s) ■ Started to link strata together across distance ● Noticed strata showed consistency in the fossils they hold ■ Strata can be identified across wide geographic ranges by “index fossils” ● Fossils that serve as diagnostics for particular geological periods ○ Key components (early 1800s) ■ Processes that have built and shaped geological strata are essentially the same as the processes we see at work today ■ The subtle, gradual nature of these processes indicates that earth must be extremely old ○ Uniformitarianism: natural laws observable around us now are also responsible for events in the past ■ “The present is the key to the past” ○ Broader view of the living world takes shape around the same time ○ Mid 1700s: Linnaeus ■ Father of taxonomy and binomial nomenclature ● Classified and named over 12,000 species of plants and animals ● Searched for divine plan in relationship among taxa ● Thought species immutable ■ Biogeography: the study of the distribution of species across space ● Observing regional differences among species led to thinking that species may not be immutable after all

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Late 1700s-Early 1800s: Lamarck ■ Described how traits of organisms are matched to their environments and habits ■ Thought that species change over time ● First to develop a theory on how organisms evolve ○ Lamarckism: change in organisms brought about by natural physical processes ■ Force of complexification (spontaneous generation) ■ Force of adaptation (acquired inheritance) ○ Key developments: Early 1800s ■ Paleontology couple biological and geological patterns ■ Important recognition of extinction ■ Geological history appeared to be characterized by waves of very different fauna ○ Darwin and HMS Beagle ■ Restless young man, joins the company of naval vessel at 22 ■ Circumnavigates the globe, giving a breath of perspective on the natural world ■ Inevitability ● This “view of life” was coming into focus anyways ○ Darwin was the first person, but he sat on his ideas for decades ● Alfred Russell Wallace independently arrived at the same conclusions ● Wallace was more eager to announce findings, so Darwin got his act together Mechanisms of Evolution ○ Biodiversity ■ Special creation ● Species are immutable ● Lineages do not diverge ● Species created separately ● Species are genealogically independent ■ Descent with modification ● Species change over time ● Gives rise to new species that share common ancestors ○ Do species change? ■ Scientific Experiments and Applied Breeding ■ Artificial selection: proves yes ■ Experiments allow us to test this under tightly controlled conditions ● Strong inferences, but often modest expected change ■ Experiments allow us to: ● Involve exposing populations to experimental conditions and measuring the heritable changes ○ Experimental ponds

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Sticklebacks (3 spine) and freshwater populations having better cold tolerance ■ Shift in cold tolerance after beginning them back into the lab (in just 3 generations 2.5°C better tolerance) ■ Long history of selective breeding of plants and animals gives the answer ■ Biogeographic/Paleontological evidence: “law of succession” ● Correspondence among fossil and extant faunas (and floras) in space ● Australian fossil mammals are marsupials, asian fossil mammals are placentals Transitional Fossils: we expect to find fossils with mixes of ancestral and novel traits ■ Not direct links, rather a representative of organisms that shared a common ancestor with group near branching point ● Some cases came with striking success ○ Gradual evolution of terrestrial ungulates to the whales we know today Homology: characteristics shares among organisms because they were inherited from a common ancestor ■ Called homologous traits ● Mammal limb bones ○ (human, horse, mole, dolphin, bat) ■ Also evident in vestigial structures ● A useless, rudimentary version of a trait that is functional in related taxa ● Pseudogenes: nonfunctional copies of coding genes ■ Atavistic traits ● Reappearance of ancestral traits in individuals ● Evidence of homology in developmental pathways ■ Homology of DNA and protein sequences ● Homologous genes are called orthologs ● Paralogs: homologous genes that diverges within a lineage ○ Forms the basis for modern phylogenetics ○ Proximal repeat found in Homo and Pan ■ Duplication occurred in a common ancestor ● Orthologs are genes in different species evolved from a common ancestral gene. Paralogs are gene copies created by a duplication event within the same genome. ■ Acquisition of mitochondria occurred before MRCA of all extant Eukaryotes

Lecture 3: ● The connectivity in the living world is not along a single trajectory

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○ Evolution is not a straight line Two broad components (pattern and process) ○ Common descent ○ Mechanism for how change arises over time Malthus: exponential and geometric ○ Compare arithmetical: for each generation, x offspring are added to population (y) ■ Growing by a NUMBER of 2 ○ Exponential: for each generation, x offspring per individual (y) are added to the population ■ Growing by a RATE of 2 ○ If population grows too fast there is a famine, which is backed by Darwin ■ Contributed to darwin’s ideas on mechanism Natural Selection ○ “Word model” based on testable postulates ■ Describing a model based on logic, that if true can conclude something about it ○ Remained controversial because both biology and math had to catch up ■ Mechanisms of inheritance ■ Analyzing variation in populations – statistics Number 1: ○ Populations are variable ○ Differ in: ■ Morphology ■ Color ■ Physiology ■ Behavior ○ Extends to human population Number 2: traits are heritable ○ Discrete generations: phenotypic distribution of the second generation is partially a function of the phenotypic parent ■ A rather complex thing in practice; not completely straightforward ■ Ex of complication: genetic dominance Number 3: variation in survivorship and reproductive success ○ Universally true in natural populations ■ Including both r and k strategy organisms ● R: investment optimized to greatest number of offspring ● K: investment optimized for care and developing of offspring Number 4: survivorship and reproductive success vary as a function of traits ○ Rates of mortality and reproductive success are not uniformly distributed across the population in regard to certain phenotypes ■ Individuals with certain phenotypes are more likely to survive and reproduce ○ High year to year and site to site variability

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■ Constant dynamic process Fitness ○ The extent to which an individual contributes to the survival of the next generation ■ Not survival of the fittest ○ Reproductive success ■ Survival → reproduction ○ Survival → mating success → fecundity (number of female offspring produced) ○ Mating success: competition, locating a mate, copulation, fertilization Exponential Growth Yt = y0 * xt ○ X = rate ○ T = time in generations ○ Y0 = population at time zero ○ Yt = population at time t 15 eggs each birth, 2 males:1female and how many grandchildren ○ Y0 is 1 female ○ X is 5 females per birth ○ T is 2 generations ○ Yt is 25 females ■ Yt x 3 to find total turtles since 2:1 Fitness is sometimes counterintuitive ○ The biggest, strongest, fastest are not necessarily the fittest Dung beetle males build tunnels for females and guard them Smaller beetles sneak into the tunnels and mate with the females ○ 2 strategies for reproductive fitness Selection acts on individuals, but individuals do not evolve; populations evolve Natural selection can not see into the future ○ Purely mathematical process that occurs in the current/parental generation ■ It will lag behind about a generation Selection acts on the variation existing in a given population it does not add new genetic variation ○ Novel phenotypes do evolve ■ Reshuffling of genetic variation ■ Natural selection in concert with two other evolutionary forces ● Mutation and migration Natural selection does not add genetic variation, it only cuts out or shifts genetic variation ○ Mutation can add genetic variation Perfection of Organisms ○ Evolution is constrained, and cannot optimize all traits simultaneously Complexity

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Selection does not favor complexity, life has increased in complexity over time but it is not from selection. Fitness can just as easily favor a loss of complexity ■ Loss of complexity is not de-evolution.. It is just regular evolution Gould’s “left wall of biocomplexity” ○ Frequency of occurrence decreases as complexity increases Being evolutionary advanced is subjective Darwin had many gaps in knowledge that prevented universal acceptance of natural selection The nature of novel variation ○ Commonality of mutation not appreciated until Drosophila work began in 1900s ○ Small changes vs “Saltation” jumping ■ Was evolution driven by catastrophic mutations leading to ‘hopeful monsters” The nature of inheritance ○ Mendel was active around the time Origin was published ○ His work remained obscure for decades ○ In the meantime, popular ideas about inheritance didn’t work well with Darwinian Selection ○ Blending inheritance ■ Genes combine over time to create a new gene ○ Debates ■ Mendelians and biometricians ■ Discrete trait and continuous traits (blended) Modern Synthesis ○ Restatement of the four postulates: ■ 1: variation among individuals results from mutations creating new allele arising and segregating in populations ■ 2: Principles of dominance ■ 3: Through differential survival or reproductive success, not all individuals contribute to the following generation ■ 4: The probability of contributing to the next generation varies as a function of individual’s genotypes

How Alleles are Transmitted: ● Gene: the discrete functional unit of heredity ○ A segment of DNA that contains a transcribed region and a cis regulatory region ● In evolution, we are interested in a heritable variation more broadly than just protein coding regions ● Genetic locus: a specified location in the chromosome / genome ● Alleles: variant forms of a genetic locus ○ A variant, a point mutation ● Genotype: the specific allelic composition of an individual – at one or more loci ● Mendel’s Laws of Inheritance ○ Segregation: homologous chromosomes separate during meiosis so that only one copy of each gene occurs in each gamete (one allele per locus) ■ Closest one to a “law” – diploid individual ● Each gamete will only have one copy of that locus ■ Diploid - replication - segregation 1 - segregation 2 ○ Independent assortment: allelic variation at different loci are passed to offspring independently ■ The probability of an allele being expressed is independent of the probability of another allele being expressed ■ P(Red and Orange) = P(R) x P(O) = P(R and O) ● This “law” fails with: ○ Linked genes ○ Recombination: generates haploid multilocus genotypes that are different from the parental gametes ■ Includes both kinds of genes from each parent and crossing over ■ Both parents’ genes are shown in the cells of the child ○ Linkage is any breakdown of the independent assortment ■ Alleles at different loci are inherited together more often than expected by chance ■ Often due to physical linkage ● Close proximity on the same chromosome leads to physical linkage ● The closer the loci, the higher the chance of physical linkage ● Punnett Squares ○ Shows frequencies of GENOTYPES not phenotypes ○ Aa, aA, AA, aa ○ Determines the frequency of genotypes in the next generation from the gamete pool of the mating pair ○ Producing Aabb zygote one way is mutually exclusive of the other (Ab, ab or ab, Ab) ○ Independent (AND statements) = multiply ○ Exclusive (OR statements) = add ● Interactions among alleles at a single locus

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Dominance: phenotypic effect of one allele takes charge over another allele at the same locus ■ (blood types A, B, over o) ■ Eye color (blue is recessive) ■ Has nothing to do with the prevalence of an allele in population ■ Co-dominance is very common ○ How does dominance happen? ■ Haploinsufficiency ● Dosage effects of a gene.. If you don’t have enough dosage of it then it cannot be expressed ■ Dominant negative ● Protein interactions Fitness can be a trait in the same way ○ Beneficial alleles can be dominant, recessive, or incompletely dominant in the system Epistasis: an effect of the interaction among multiple loci on a phenotype (or fitness) such that the joint effect differs from the sum of the loci taken separately

○ Interaction: plant height, low and high temperature and low N and high N ■ Basically synergism ○ You can predict the plant height at both low and high temperatures across both, because the effects are additive, there is no interaction ■ Do not need to know the temperature to know how much the plant will grow with high nitrogen ○ There is an interaction when the variables do not affect the two plants the same exact way.. The effect cannot be parallel ○ Think of it like an interaction between genes that make it not independent

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The rise cannot be parallel lines Can be done with phenotypes ■ Ex. 1:

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The contribution of each allele is independent of the rest of the genotype

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The contribution of a single allele is not independent of the other alleles, it is dependent on the D allele to know if it will actually change the height ○ Interaction occurs, epistasis Raw Materials for Evolution ○ How mutations come about ○ Phenotype: the measurable properties of an organism manifested throughout its life ■ Morphological, physiological, biochemical, behavioral ■ Phenotype includes the total set of these properties or traits, but usually only a subset of traits are questioned ○ What determines phenotypic variation? ■ Genetic variation ● Phenotypic differences among individuals are explained by allelic differences ○ If we know genotype, we can make strong PREDICTIONS about the phenotype, but no guarantee ● Things occurring solely at the molecular level ○ Ex. ■ Variation in human taste sensitivity ■ ABO blood types ■ Single gene chromosomal abnormalities or genetic diseases ■ Environmental variation

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Some organisms can have the same exact genome, but different phenotypes in different environments ○ Ex. ■ Daphnia ■ Gene x Environment interactions ● The PHENOTYPIC differences caused by alleles depend on the particular conditions, and vice versa ○ Can't know the effect without knowing the environment ○ Just because you are homozygous for a trait does not mean you will show that trait Phenotypic Plasticity: changes in the phenotype exhibited by the same genotype due to environmental differences ■ Not completely different phenotypes, just slight changes ● This is continuous, not discrete ● There are intermediate stages between the big/small ants ● red/blue individuals but there are purple ones too Polyphenism: DISCRETE phenotypic variation arising from the same genotype in different environments ■ Completely different phenotypes from the same genotype ● This is discrete, not continuous Gene-by-environment interactions ■ Phenotypic differences are driven by interactions between allelic variations and environmental conditions ● Interaction in the same sense as epistasis ● Genes have different effects in different environments Reaction norm: the relationship between the environment and values of a phenotypically plastic traits ■ Graph environment vs phenotype to see differences ■ Gene interaction occurs when different genotypes have different reaction norms ● Occurs when they are all the same under one environment, but different in another environment ○ Phenotypic expression when child abuse is not and is present ■ Development of serial killers? Would they be normal if they were not abused? ■ Often the target of natural selection ■ How phenotypically plastic traits evolve ● Ex. ○ Black strain of caterpillars (manduca) can turn green after a heat shock treatment ● A selection experiment can change the phenotype and alter the reaction norm

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Natural selection can make plastic traits and make them non-responsive to the environment ■ Pushing the inflection point of the reaction norm below the threshold, the trait will appear under any conditions ● Called genetic assimilation Mutation ○ Types: small to large ■ Point Mutations ● SNPS: single nucleotide polymorphisms ● Indels: small insertions and deletions of base pairs ○ Due to a combination of DNA damage and/or replication error ○ Can occur in a: ■ Coding genes: exons ■ Introns ■ Regulatory regions (promoters, suppressors) ■ Gene duplications ● Unequal crossing over ○ Meiotic error ● Retroposition ○ mRNA processed by viral or retrotransposon machinery and integrated back in the genome ■ Chromosomal rearrangements ● Inversions ○ Change in the order of genes due to double-stranded breaks and misaligned repairs ■ Visible in karyotypes ■ Strong role in evolutionary process, keeps sets of genes together ● Fissions/Fusions ○ (one chromosome breaking into two or two joining into one) ■ Dr...