BIOL 206 Midterm Notes PDF

**BIOL 206 Midterm Notes** Lecture: [**Zoom Link**](https://queensu.zoom.us/j/99222678258?pwd=YTg1S01ZdnlHeWpsNW1kWmJRQ0trdz09#success) ------------------ **W1 Lecture 1** ------------------ Evolution is a change through time (over generations) - - Is evolution by natural selection \...

**BIOL 206 Midterm Notes** Lecture: [**Zoom Link**](https://queensu.zoom.us/j/99222678258?pwd=YTg1S01ZdnlHeWpsNW1kWmJRQ0trdz09#success) ------------------ **W1 Lecture 1** ------------------ Evolution is a change through time (over generations) - - Is evolution by natural selection \"just a theory\"? No, it is a mathematical inevitability. A misconception is that a theory is a hunch, a vague guess, or just a speculation. A scientific theory, on the other hand, is an overarching set of principles or mechanisms that govern the natural world, based on repeated confirmation through observation and experiment. The theory of evolution is a testable, unifying theory, applied at all levels. Evolution by Natural Selection 1. individuals within a population vary phenotypically 2. phenotypic variation is at least partially heritable 3. individuals vary in lifetime reproductive success 4. variation in survival/reproduction is non-random with respect to phenotype In an example question, the reason why students were taller in 1997 compared to 1914 was due to the fact that access to food and better diet meant people were able to grow taller. Evolutionary theory is a framework to understand the natural world. Evolutionary biology explains both adaptations and diversity, and natural selection is the central tenet. ------------------ **W1 Lecture 2** ------------------ **PART 1** The theory of evolution involved two controversial ideas. One was a concept of a changing universe, replacing the view of a static world. Another was a phenomenon with no purpose, which replaced the view that the causes of all phenomena had to have a purpose. *Early Ideas of Evolution* - Earth formed according to the laws of physics and chemistry (older than previously thought) - Life emerged as distinct types, and transformed when the environment changes - Paleontology provided evidence that life changed. Fossils resemble, but are not exactly the same as modern species. Many past species have since become extinct Charles Darwin and Alfred Russel Wallace co-discover the chief mechanism of evolution (natural selection). Darwin's ideas on evolution came from exploration and voyage on the H.M.S. Beage around the world for 5 years. Made numerous observations and collections of plants, animals, and fossils. He returned to England and spent the rest of his life developing his ideas, conducting experiments, and writing books. The Origin of Species believed that all organisms have descended with modification from common ancestors (all species share common ancestry), and that the major agent of modification is natural selection operating on variation among individuals (provided a mechanism!!). Textbooks tell a "Western" view of this history, where there are missing narratives. **PART 2** Phylogeny is similar to a family tree. It is a way of grouping organisms and patterns of descent. Reading a phylogenetic tree must be read from derived to ancestral (read right to left). Most closely related share the most recent common ancestor. Trees imply evolutionary groupings and shared ancestry/history. ------------------ **W1 Lecture 3** ------------------ Phylogenetic trees are hypotheses about relationships between taxa. They are constantly reevaluated when new data becomes available. Statistical models help researchers sift through modular evidence to determine the best hypothesis or hypotheses that explain the data Each nucleotide is potentially an informative character, but homoplasy is common (only four possible character states, thus, the probability that separate lineages independently arrive at the same charter state can be high). Genes differ in rates of evolution. Slowly evolving genes are useful for distantly related species, and rapidly evolving genes are useful for closely related lineages. Estimating phylogenies is complicated due to homoplasy. This could be due to repeated evolution of a trait (convergent evolution), or even the loss of a trait. With a good molecular phylogeny, we can mark phenotypes. *Example: The Evolution of Tetrapods* Construction of phylogenies in real time is useful for disease epidemiology. Phylogenetic evidence is useful for all sorts of questions, historical origins, trait evolution, and even forensics **Definitions from readings :** 1. A *taxon* (plural, taxa) refers to groups of organisms that a taxonomist judges to be cohesive units, such as species or orders. 2. *Taxonomy* is the science of describing, naming, and classifying species of living or fossil organisms. 3. *Carolus Linnaeus* is considered the founder of modern taxonomy because his system for grouping organisms into a nested hierarchy is still in use today (although many of the groupings he proposed are not). 4. *Uniformitarianism* is the idea that the natural laws observable around us now are also responsible for events in the past. One part of this view, for example, is the idea that Earth has been shaped by the cumulative action of gradual processes like sediment deposition and erosion. 5. A *theory* is an overarching set of mechanisms or principles that explain major aspects of the natural world. Theories are supported by many different kinds of evidence and experimental results. Modern science is dominated by theories. 6. A *hypothesis* is a tentative explanation for an observation, phenomenon, or scientific problem that can be tested by further investigation or experimentation. 7. *Homology* refers to the similarity of characteristics resulting from shared ancestry. 8. A *homologous characteristic* is similar in two or more species because it is inherited from a common ancestor. 9. *Descent with modification* refers to the passing of traits from parents to offspring. Darwin recognized that, over time, this process could account for gradual change in species' traits and homology. 10. *Natural selection* is a mechanism that can lead to adaptive evolution, whereby differences in the phenotypes of individuals cause some of them to survive and reproduce more effectively than others. 11. *Artificial selection* is the selective breeding of animals and plants to encourage the occurrence of desirable traits. Individuals with preferred characteristics are mated or cross-pollinated with other individuals having similar traits. 12. An *adaptation* is an inherited aspect of an individual that allows it to outcompete other members of the same population that lack the trait (or that have a different version of the trait). Adaptations are traits that have evolved through the mechanism of natural selection. 13. A *branch* is a lineage evolving through time that connects successive speciation or other branching events. 14. *Phylogeny* is a visual representation of the evolutionary history of populations, genes, or species. 15. A *node* is a point in a phylogeny where a lineage splits (a speciation event or other branching event, such as the formation of subspecies). 16. A *tip* is the terminal end of an evolutionary tree, representing species, molecules, or populations being compared. 17. An *internal node* is a node that occurs within a phylogeny and represents ancestral populations or species. 18. A *clade* is a single "branch" in the tree of life; each clade represents an organism and all of its descendants. 19. A *taxon* (plural, taxa) is a group of organisms that a taxonomist judges to be a cohesive taxonomic unit, such as a species or order. 20. *Monophyletic* describes a group of organisms that form a clade. 21. *Polyphyletic* describes a taxonomic group that does not share an immediate common ancestor and therefore does not form a clade. 22. *Paraphyletic* describes a group of organisms that share a common ancestor, although the group does not include all the descendants of that common ancestor. 23. A *character* is a heritable aspect of organisms that can be compared across taxa. 24. *Synapomorphy* is a derived form of a trait that is shared by a group of related species (that is, one that evolved in the immediate common ancestor of the group and was inherited by all of its descendants). 25. An *outgroup* is a group of organisms (for example, a species) that is outside of the monophyletic group being considered. In phylogenetic studies, outgroups can be used to infer the ancestral states of characters. 26. *Homoplasy* describes a character state similarity not due to shared descent (for example, produced by convergent evolution or evolutionary reversal). 27. *Convergent evolution* is the independent origin of similar traits in separate evolutionary lineages. 28. *Evolutionary reversal* describes the reversion of a derived character state to a form resembling its ancestral state. 29. *Parsimony* is a principle that guides the selection of the most compelling hypothesis among several choices. The hypothesis requiring the fewest assumptions or steps is usually (but not always) best. In cladistics, scientists search for the tree topology with the least number of character-state changes---the most parsimonious. 30. *Polytomy* describes an internal node of a phylogeny with more than two branches (that is, the order in which the branchings occurred is not resolved). 31. A *microsatellite* is a noncoding stretch of DNA containing a string of short (one to six base pairs), repeated segments. The number of repetitive segments can be highly polymorphic, and for this reason microsatellites are valuable genetic characters for comparing populations and for assigning relatedness among individuals (DNA fingerprinting). ------------------ **W2 Lecture 1** ------------------ **PART 1** Evolution requires genetic variation. This variation can come from mutation, recombination, gene flow, and hybridization. Mutation is the ULTIMATE source of genetic variation (introduces novel variation). Different kinds of mutations affect different number of bases: Not all mutations affect proteins, which will ultimately affect phenotypes. Also, NOT all DNA is coding, and the same DNA can make different proteins. Redundancy in the genetic code is used to translate RNA to proteins. Non-coding regions make up most of the genome. Non-coding regions include RNA genes, pseudogenes, and transposable elements ("jumping genes"). Transposable elements give rise to the many different colours of corn kernels. Mutation is an unstoppable phenomenon, despite cellular mechanisms to correct errors during DNA replication. Mutation is not directed by the organism or the environment. It is instead random with respect to effects on fitness (but the ones that persist are not random!). Rates of mutation depends on the type of mutation, and also varies among genes. Recombination occurs during meiosis, and generates variation. During prophase one, chromosomes recombine. Independent assortment ensures novel combinations of alleles. Recombination and independent assortment during meiosis generates enormous diversity (ie. in humans, n=23 chromosomes, 2^23^ = \>8 million possible gamete combinations!). Most genetic variability results from sexual reproduction. In any given generation, input from mutation is very small. **PART 2** Discrete phenotypic variation often is caused by single-locus polymorphisms (ie. Mendel). To the left is how to calculate different frequencies (ie. phenotype, genotype, allele) for a given population of organisms. The life cycle is about opportunities for change. ------------------ **W2 Lecture 2** ------------------ Evolution can be defined as a change in allele frequencies through time. All genotypes make an equivalent number of gametes, and go into a big pool for mating.  1. 2. 3. 4. 5. Allele frequencies in a population ALWAYS sum to one, regardless of if it is in H-W equilibrium or not. There are some interesting implications of HWE. allele frequencies sum to 1, and genotype frequencies sum to 1. For every set of allele frequencies, there is a set of expected genotype frequencies. Rare alleles are primarily found in heterozygotes (when q is very small, q^2^ is even smaller). When a mutation arises, it is rare, and almost always in the heterozygous form. The amount of heterozygosity is maximized when the allele frequencies are intermediate. 2pq has a maximum value of 0.5 when p = q = 0.5. H~e~ = 2pq = "expected heterozygosity" *Do we find HWE in nature? -* YES! One generation of random mating returns to HWE. It is a very robust and useful expression. Mating is mostly random with respect to genotype at most loci. 1. 2. 3. There are essentially two types of scenarios: 1. Given phenotype frequencies and some information about dominance/recessive/additive. Asked to calculate genotype frequencies if the population is in HWE. a. Calculate p and q b. use expected frequencies to find the genotypes 2. Given the number of individuals with each genotype, asked whether the population is in HW equilibrium. c. Write out observed genotype frequencies d. Use observed genotype frequencies to calculate allele frequencies (p and q) e. Now use HW equilibrium (ie. p?, 2pq, q2) to calculate the expected genotype frequencies IF the population was at HWE. f. Compare the OBSERVED to EXPECTED frequencies. If same then not evolving, if different then evolving. +-----------------------------------+-----------------------------------+ | Example for Scenario 1: | Example for Scenario | | | 2: | +-----------------------------------+-----------------------------------+ Violation of the HW expectation means one of the original HWE assumptions is not holding true. Common mistakes include: 1. Assuming a population is in HWE because both p and q equal 0.5 OR Assuming a population is not in HWE because p and q are really different (e.g. p=0.1, q=0.9). The allele frequencies can take on any value (as long as they add to 1), what is important is whether the observed genotype frequencies are equal to the expected genotype frequencies: AA=p^2^, Aa=2pq, aa=q^2^ 2. Calculating the genotype frequencies: AA=p^2^, Aa=2pq, aa=q^2^ and then saying that the population is in HWE because it sums to 1. It has to sum to one! That is just a check that your math is correct. You need to compare observed to expected. Technically, you would want to use a X^2^ test to see if observed and expected counts differ significantly. For X^2^ tests you use counts not frequencies. In this course, we will use a rough estimate - ie. if the frequencies are different by 0.05 or more (ie. 0.9 vs. 0.85) we will call them different. ------------------ **W2 Lecture 3** ------------------ Allele frequency performs a "random walk" (ie. it drifts). Alleles are lost more rapidly in small populations. The changes are also less predictable in small populations. In a huge population, changes are more minor. Rare alleles are more likely to be lost in a population bottleneck. The probability of loss of allele in a bottleneck (one round of sampling): P~loss~ = (11 - p)^2N^ *Properties of Genetic Drift:* - The direction of change in allele frequency can not be predicted - One allele will eventually be fixed, other eliminated: genetic drift tends to remove genetic variation - The probability that a particular allele will eventually become fixed (or lost) is proportional to its frequency in the population Heterozygosity can be used to measure genetic variation. For a locus with two alleles, the expected heterozygosity is 2pq. It has a maximum value of 0.5 when p=q=0.5. The amount of heterozygosity is maximized when the allele frequencies are intermediate. A [loss of genetic] variation results *within* populations (because one allele will eventually be lost or fixed). [Genetic divergence] results *between* populations (populations become more different by chance). Drift causes evolution (ie. allele frequencies change), but not adaptive evolution. ------------------ **W3 Lecture 1** ------------------ **PART 1** Evolution requires genetic variation. This variation can come from mutation, recombination, gene flow, and hybridization. Mutation is the ULTIMATE source of genetic variation (introduces novel variation). Different kinds of mutations affect different number of bases: Not all mutations affect proteins, which will ultimately affect phenotypes. Also, NOT all DNA is coding, and the same DNA can make different proteins. Redundancy in the genetic code is used to translate RNA to proteins. Non-coding regions make up most of the genome. Non-coding regions include RNA genes, pseudogenes, and transposable elements ("jumping genes"). Transposable elements give rise to the many different colours of corn kernels. Mutation is an unstoppable phenomenon, despite cellular mechanisms to correct errors during DNA replication. Mutation is not directed by the organism or the environment. It is instead random with respect to effects on fitness (but the ones that persist are not random!). Rates of mutation depends on the type of mutation, and also varies among genes. Recombination occurs during meiosis, and generates variation. During prophase one, chromosomes recombine. Independent assortment ensures novel combinations of alleles. Recombination and independent assortment during meiosis generates enormous diversity (ie. in humans, n=23 chromosomes, 2^23^ = \>8 million possible gamete combinations!). Most genetic variability results from sexual reproduction. In any given generation, input from mutation is very small. **PART 2** Discrete phenotypic variation often is caused by single-locus polymorphisms (ie. Mendel). To the left is how to calculate different frequencies (ie. phenotype, genotype, allele) for a given population of organisms. The life cycle is about opportunities for change. ------------------ **W3 Lecture 2** ------------------ Evolution can be defined as a change in allele frequencies through time. All genotypes make an equivalent number of gametes, and go into a big pool for mating. 1. 2. 3. 4. 5. Allele frequencies in a population ALWAYS sum to one, regardless of if it is in H-W equilibrium or not. There are some interesting implications of HWE. allele frequencies sum to 1, and genotype frequencies sum to 1. For every set of allele frequencies, there is a set of expected genotype frequencies. Rare alleles are primarily found in heterozygotes (when q is very small, q^2^ is even smaller). When a mutation arises, it is rare, and almost always in the heterozygous form. The amount of heterozygosity is maximized when the allele frequencies are intermediate. 2pq has a maximum value of 0.5 when p = q = 0.5. H~e~ = 2pq = "expected heterozygosity" *Do we find HWE in nature? -* YES! One generation of random mating returns to HWE. It is a very robust and useful expression. Mating is mostly random with respect to genotype at most loci. 1. 2. 3. There are essentially two types of scenarios: 1. Given phenotype frequencies and some information about dominance/recessive/additive. Asked to calculate genotype frequencies if the population is in HWE. a. Calculate p and q b. use expected frequencies to find the genotypes 2. Given the number of individuals with each genotype, asked whether the population is in HW equilibrium. c. Write out observed genotype frequencies d. Use observed genotype frequencies to calculate allele frequencies (p and q) e. Now use HW equilibrium (ie. p?, 2pq, q2) to calculate the expected genotype frequencies IF the population was at HWE. f. Compare the OBSERVED to EXPECTED frequencies. If same then not evolving, if different then evolving. +-----------------------------------+-----------------------------------+ | Example for Scenario 1: | Example for Scenario 2: | | | | |  | | +-----------------------------------+-----------------------------------+ Violation of the HW expectation means one of the original HWE assumptions is not holding true. Common mistakes include: 1. Assuming a population is in HWE because both p and q equal 0.5 OR Assuming a population is not in HWE because p and q are really different (e.g. p=0.1, q=0.9). The allele frequencies can take on any value (as long as they add to 1), what is important is whether the observed genotype frequencies are equal to the expected genotype frequencies: AA=p^2^, Aa=2pq, aa=q^2^ 2. Calculating the genotype frequencies: AA=p^2^, Aa=2pq, aa=q^2^ and then saying that the population is in HWE because it sums to 1. It has to sum to one! That is just a check that your math is correct. You need to compare observed to expected. Technically, you would want to use a X^2^ test to see if observed and expected counts differ significantly. For X^2^ tests you use counts not frequencies. In this course, we will use a rough estimate - ie. if the frequencies are different by 0.05 or more (ie. 0.9 vs. 0.85) we will call them different. ------------------ **W3 Lecture 3** ------------------ Allele frequency performs a "random walk" (ie. it drifts). Alleles are lost more rapidly in small populations. The changes are also less predictable in small populations. In a huge population, changes are more minor. Rare alleles are more likely to be lost in a population bottleneck. The probability of loss of allele in a bottleneck (one round of sampling): P~loss~ = (11 - p)^2N^ *Properties of Genetic Drift:* - The direction of change in allele frequency can not be predicted - One allele will eventually be fixed, other eliminated: genetic drift tends to remove genetic variation - The probability that a particular allele will eventually become fixed (or lost) is proportional to its frequency in the population Heterozygosity can be used to measure genetic variation. For a locus with two alleles, the expected heterozygosity is 2pq. It has a maximum value of 0.5 when p=q=0.5. The amount of heterozygosity is maximized when the allele frequencies are intermediate. A [loss of genetic] variation results *within* populations (because one allele will eventually be lost or fixed). [Genetic divergence] results *between* populations (populations become more different by chance). Drift causes evolution (ie. allele frequencies change), but not adaptive evolution. ------------------ **W4 Lecture 1** ------------------ **PART 1** Under random mating, all combinations are equally probable. With ASSORTATIVE MATING, like genotypes preferentially make with like genotypes. Under both inbreeding and assortative mating, genotypes mate preferentially with like genotypes. The difference is that INBREEDING acts on the whole genome simultaneously, unlike assortative mating, which only acts on the loci associated with those trait(s).  There are two events required for gene flow : gene movement (movement of individuals, or movement of their gametes), AND gene establishment (survival or reproduction) *How do we measure migration (gene flow)?* - *Direct Methods* - eg. mark-recapture studies in natural populations. For many organisms, this is NOT a realistic option - *Indirect Methods -* eg. molecular marker variation Gene flow over longer distance and longer times is inferred from genetic structure/genetic differentiation - When populations differ in allele frequencies, they are 'genetically differentiated' - When two adjacent populations are genetically differentiated, we know that gene flow has NOT homogenized them Differentiation is measures with F~ST~ \[recall that F = reduced H~OBS~ due to nonrandom mating compared to H~EXP~ (2*pq*)\] *Quantifying Population Subdivision with F~ST~ -* F~ST~ measures variation in allele frequencies among populations. F~ST~ ranged from 0-1. It compares the average expected heterozygosity of individual subpopulations (S) to the total expected heterozygosity if the subpopulations are combined (T) Steps for example include calculating 2*pq* for each sub population, and then find the mean. This is the average heterozygosity in the subpopulations (H~S~). Now, calculate the total expected heterozygosity if the subpopulations were homogenized (H~T~). calculate mean p, calculate mean q, and then calculate the heterozygosity you would get in the total sample. (p~mean~ = 0.5, q~mean~ = 0.5, 2*p*~mean~*q*~mean~ = 0.5 = H~T~ \| [\$F\_{\\text{ST}} = 1\\ - \\frac{H\_{S}}{H\_{T}}\$]{.math.inline} [\$= 1\\ - \\frac{mean(2pq)}{{2p}\_{\\text{mean}}q\_{\\text{mean}}}\$]{.math.inline} [\$\\ = 1\\ - \\frac{0.5}{0.5}\$]{.math.inline} [  = 1 ]{.math.inline} High heterozygosity means high genetic variation. Inbreeding will remove heterozygosity. **PART 2** A founder effect causes genetic drift. Allele frequencies among colonists are not representative of the source population. Population subdivision causes some level of inbreeding (reduced mate pool, more alleles are identical by descent) (ie. Tay-Sachs disease in Ashkenazi Jewish). Average heterozygosity is a really useful metric for quantifying the degree of inbreeding and the amount of population structure. Selection could also affect average heterozygosity; so often use noncoding (neutral) loci for tests above.  *Describing Genetic Variation* - [In Populations] - number of alleles at a locus. Frequency of alleles at a locus (*p, q -* if only 2, then p + q = 1). Frequency of genotypes at a locus, under HWE *Mutation -* ALWAYS increases variation, and introduces new variants, represented as µ, and changes both p and q. Most new mutations are deleterious. There will always be a slow influx of mutations, whether an allele newly arisen by mutation persists depends on the strength of selection. *Drift* - allele frequencies change from one generation to the next as a result of sampling error. The probability that any allele will be fixed is equal to its current frequency. Drift REDUCES variation (or heterozygosity) within populations. Effective population size is driven by the effects of drift. *Selection -* fitness is survival x fecundity, and selection acts on relative fitness. Genotype frequencies can change from before selection to after selection. Allele frequencies can change from before selection to after selection. Dominant/additive/recessive changes the effect of selection on an allele. Types of selection include directional, heterozygote advantage, heterozygote disadvantage, negative frequency dependent, and positive frequency dependent. *Non-Random Mating: Inbreeding -* mating among relatives. Allele frequencies don\'t change, heterozygotes are less frequent than expected. Identity by descent: *F* - probability that two alleles chosen at random are identical by descent. *F*, inbreeding coefficient, measures departure from HWE expectations for heterozygosity. *Population Subdivision -* you could still have HWE within each subdivision. *F~ST~* measures the degree of departure from HWE in subpopulations relative to the total population. Heterozygote deficiency when subpopulations are combined into a single population. Can use this to estimate the amount of migration (low *F~ST~* means lots of migration, and high *F~ST~* means low migration)