BIO 354 Final Review PDF

BIO 354: Final Study Guide Learning Objectives Answered Unit 1: Natural Selection Lecture 1: History of Evolution Describe how evolution is both a pattern and a process ○ Pattern: Documented change of organisms on Earth over billions of years...

BIO 354: Final Study Guide Learning Objectives Answered Unit 1: Natural Selection Lecture 1: History of Evolution Describe how evolution is both a pattern and a process ○ Pattern: Documented change of organisms on Earth over billions of years ○ Process: Change in allele frequencies between generations Identify the major figures and their contributions to the development of evolutionary biology ○ Ancient Greeks: life emerged from the sea, life was “monster-like” Plato & Aristotle: Form matches function, life is unchanging ○ Natural Theology—William Paley Divine creator, perfect design, matches God ○ Carolus Linnaeus Modern Taxonomy, Classified “related” species into genera Describe how the ancient Greeks paved the way for modern evolutionary ideas ○ Basis of Evolutionary idea, Define uniformitarianism ○ James Hutton & Charles Lyell Unifomitarianism The Earth is very old, the processes that shape the world now have also shaped it in the past Describe the idea of inheritance of acquired traits, and explain why it is incorrect ○ Lamarck Species progress up a chain of complexity, organisms originate separately Inheritance of acquired characteristics—Changes to traits during lifetime are passed onto offspring List the major observations that Darwin made on the Beagle, and describe how they informed his theory of evolution, as laid out in Origin of Species ○ Darwin & Wallace Experienced a Changing Earth—Ancient Earth, Uniformitarianism Organisms can diversify in isolation (on islands) Lecture 2: The Tree of Life Identify different types of evidence that support common ancestry of species ○ Common Ancestry of Species: Organisms share fundamental characteristics because they—and their genes—have descended from a common ancestor in the distant past  Same genes in related species, chimps and other animals vs humans, genes being replaceable by other species’ genes and being functional Be able to describe possible relationships between present day taxa using phylogenetic trees, using the terms sister taxa and common ancestor ○ Two lineages are more closely related to each other than some other lineage if they share a more recent common ancestor ○ Sister species: the one most closely related to any given species Describe what a molecular clock is, and how they are used. ○ Molecular clock: a method used in molecular biology to estimate the time of divergence between two species or lineages based on the accumulation of genetic mutations over time. Compare and contrast species trees and gene trees Distinguish between orthologs and paralogs, given a gene tree and species tree ○ Homologs: Gene copies; share common ancestry ○ Paralogs: Gene copies that arise as a result of gene duplication Two bats w/ different gene forms ○ Orthologs: gene copies that arise as a result of speciation—OTHER species Bat vs. bunny Diagnose duplication vs. speciation events, and use the terms ortholog, paralog, homolog ○ Duplication (Paralog): Genes are within the same species and result from a duplication event that creates gene copies within that species. ○ Speciation (Ortholog): Genes are in different species that evolved from a common ancestral gene after a speciation event. Define homoplasy and describe how to recognize it ○ Homoplasy: Similarity that is not due to common ancestry. It is the result of independent evolution and can provide misleading evidence of phylogenetic relationships. CONVERGENCE EVOLUTION The presence of a trait not from its common ancestor  Evaluate evidence for homology versus convergence, given a phylogeny and trait mapping ○ Homology: Traits are homologous if they are inherited from a common ancestor, meaning the similarity is due to shared ancestry. ○ Convergence: Traits are convergent if they appear independently in unrelated species due to similar selective pressures, rather than common ancestry. Lecture 3: Natural Selection & Adaptation Compare and contrast evolution and adaptation ○ Adaptation: Feature that increases the fitness of organisms ○ Natural selection is the only mechanism of evolution that consistently leads to adaption; Not all evolution leads to adaptation List the requirements for natural selection ○ Natural Selection: Any consistent difference in fitness among phenotypically different classes of biological entities Variation in trait Trait is heritable (genetic basis) Different versions of trait have different reproductivve success Define fitness ○ Fitness: reproductive success, how many offspring are left to the next generation? Individuals: number of surviving offspring Genotypes: Avg. number of surviving offspring of individuals of a genotype Identify evidence for evolution, using real life examples such as the ground finches on Daphne Major ○ The finches had larger and thicker beaks during a drought because the smaller finches weren’t able to survive with the limited food source. Estimate fitness of an individual using reproduction data ○ The fitness of a plant % x Number of seeds produced Lecture 4: Mutation & Variation Identify major sources of genetic variation ○ Different alleles==different genotype and phenotype ○ Change in amino acids—mutations Point mutation: single base change Use the genetic code to evaluate the effect of mutations in protein-coding sequences ○ The genetic code is a set of rules that defines how sequences of nucleotides in DNA or RNA are translated into proteins. Point mutation: single base change Structural Mutation: affect more than one base pair  Transposible Elements: genes that can move around and insert themselves into other parts of the genome Describe the relationship between mutation and evolution, the typical selection coefficient of most mutations, and the meaning of the phrase "mutation is random" ○ Mutation is a fundamental mechanism of evolution. It introduces new genetic variations (alleles) into a population. These variations can then be acted upon by natural selection, genetic drift, and gene flow. ○ Selection coefficient (s) is a measure of the relative fitness of a genotype compared to the most fit genotype in a population ○ Not all mutations are equally likely, Mutations re random with respect to NEED Evaluate how physical distance between loci affects co-inheritance of variation ○ On the same chromosome, genes that are especially close to each other have lower recombination rates ○ Genes sitting near each other are more likely to be inherited together Lecture 5: Genetics & Evolution Calculate the allele and gene frequencies of a population # 𝑜𝑓 𝐴1 𝑎𝑙𝑙𝑒𝑙𝑒𝑠 ○ Frequency of alleles: 𝑡𝑜𝑡𝑎𝑙 𝑎𝑙𝑙𝑒𝑙𝑒𝑠 ○ 𝑝 + 𝑞 = 1, p=allele frequency, q=other alele frequency 2 2 ○ 𝑝 + 2𝑝𝑞 + 𝑞 = 1, p2=homozygous dominant genotype frequency, 2pq=heterozygous genotype frequency, q2=homozygous recessive genotype frequency ○ Frequency of genotypes: given the frequencies of parental allele frequencies Be able to predict genotype or allele frequencies using the Hardy Weinberg formulas and define characteristics of a population in H-W equilibrium ○ Hardy-Weinberg Principle—Null hypothesis  ○ Allele and genotype frequencies remain constant between generations when no evolution is occurring Assess whether a population is evolving based on allele and gene frequencies ○ If there is a c hange in allele frequencies between populations, evolution is likely happening Lecture 6: Fitness & Selection Compare and contrast relative and absolute fitness, and be able to calculate fitness of various genotypes ○ Absolute fitness: the number of offspring produced in a lifetime 𝑊 = (𝑝𝑟𝑜𝑏𝑎𝑏𝑖𝑙𝑖𝑡𝑦 𝑜𝑓 𝑠𝑢𝑟𝑣𝑖𝑣𝑎𝑙 𝑡𝑜 𝑚𝑎𝑡𝑢𝑟𝑖𝑡𝑦) × (𝑒𝑥𝑝𝑒𝑐𝑡𝑒𝑑 # 𝑜𝑓 𝑜𝑓𝑓𝑠𝑝𝑟𝑖𝑛𝑔) ○ Relative fitness: using the absolute fitness compared to another genotype fitness W11/W11=1, W12/W11=1+s, W22/W11=1 +2s s = strength of selection that favors the beneficial allele Calculate the rate of evolution for a trait where you know the allele frequency and selection coefficient ○ ∆𝑝 = 𝑠𝑝(1 − 𝑝) Compare and contrast purifying selection, positive selection, and balancing selection ○ Positive selection: beneficial allele increases,underdominance; purifying selection: deleterious allele decreases; balancing selection: maintains genetic variation, overdominance Describe mutation-selection balance ○ More common diseases are less severe with a higher mutation rate while other diseases are less common but more severe with a lower mutation rate Describe how genetic correlations can lead to the spread of alleles that are not beneficial ○ When two or more traits are inherited together due to shared genetic factors, such as linked genes or pleiotropy Compare and contrast hitchhiking and pleiotropy  ○ Hitchhiking: a second allele spreads due to linkage disequilibrium ○ Pleiotropy: when a gene loci affects multiple alleles Describe how overdominance and underdominance affect allele frequencies. ○ Heterozygote has the highest fitness: Overdominance ○ Heterozygote has the lowest fitness: Underdominance Calculate mean fitness of a population 𝑤11+𝑤12+𝑤22 ○ 𝑤= 3 Unit 2: Genetic Drift and Gene Flow, and Phenotypic Evolution Lecture 1: Genetic Drift Define the following terms: bottleneck event, genetic drift, coalescence, heterozygosity, founder effect, molecular clock, neutral mutation, synonymous substitution, nonsynonymous substitution ○ Genetic Drift: the change in frequency of an existing gene variant in the population due to random chance (pervasive force) ○ Founder Effect: an extreme form of genetic drift and is a bottleneck effect Increased incidence of normally rare and often deleterious alleles ○ Coalescence theory: Not all gene copies make it to the next generation, the population will be composed of one type of gene copy. the population will coalesce back in time to one single gene copy. ○ Describe how genetic drift and coalescence are related Consider the likely fate of a new mutation in a gamete. Describe how it is related to drift. ○ Smaller effective population sizes result in greater effects of drift. ○ More drift results in less genetic variation. Interpret simulations of genetic drift, with and without natural selection. ○ Drift causes populations that are initially identical to become different. ○ An allele can become fixed without the benefit of natural selection. Identify simulation parameters that determine the rate at which an allele is fixed or lost Identify simulation parameters that affect coalescence times Identify simulation parameters that affect changes in heterozygosity over time Compare and contrast census size and effective population size Describe how census size and effective population size are important for predicting the amount of genetic drift and resulting genetic variation in a population ○ Real population sizes are not constant. ○ The model assumes all genes contribute and are sampled at random—effective sex ratio may be unequal—some males contribute more and this makes the population size effectively smaller—sometimes very much smaller  ○ Model assumes Poisson distribution of family sizes—but some individuals over contribute more, others under contribute to the next generation Identify the factors that determine the effective population size Relate observed heterozygosity to effective population size ○ The heterozygosity of a population will tell us about the effective population size Be able to compare and contrast how genetic and environmental factors can influence a phenotype. Describe how quantitative traits are inherited differently from discrete traits Describe how the number of loci that encode for the same trait affect the distribution of the trait values in a population. Describe how the number of loci that encode for the same trait affect the magnitude that allele frequencies may affect genotype and phenotype frequencies. Apply the fitness function to quantitative traits Compare and contrast directional, stabilizing, and diversifying selection Describe how each of the above types of selection affects the mean and variance of traits Calculate the rate of evolution for quantitative traits Explain why many diseases can be thought of as quantitative traits Describe how genetic correlations can lead to trade-offs in quantitative traits Use data from common garden studies to determine whether phenotypic plasticity or genetic differences can explain differences in traits. Compare and contrast the effect of natural selection and gene flow on genetic variation between populations Define these terms: cline, Bergmann's rule, Local adaptation, gene flow, dispersal, FST Calculate the migration rate, and describe the effect of migration on changes in allele frequencies Describe what a high versus low FST means for two populations Describe how gene flow and natural selection work against each other when local conditions favor a particular allele Describe what determines the relative strength of the forces of evolution (mutation, gene flow, genetic drift, and natural selection) Unit 3: Sex and Speciation Lecture 1: What is a Species? Describe some of the species concepts and what they have in common Describe how speciation happens List features used to recognize the existence of a separate species  Explain the importance of barriers in the process of speciation Compare and contrast allopatric and sympatric speciation Recognize pre-zygotic and post-zygotic barriers, and provide examples of each Explain why genetic incompatibilities can arise from long-term genetic separation of populations Describe some ways that hybrids can be at a disadvantage Explain why allo- and auto-polyploidy can be described as “instant speciation” Identify the observation that led Darwin to his ideas about sexual selection Compare and contrast natural and sexual selection, and intersexual and intrasexual selection Relate parental investment to choosiness of mates in nature Explain how trade-offs, including elaborate secondary sexual characteristics,play a role in shaping traits via sexual selection List some of the strategies that males use in competition for mates Explain why females of some species are attracted to elaborate ornaments and sexual behaviors in males. Describe the runaway selection hypothesis, and contrast it with chase away selection List the benefits and costs of sexual reproduction compared with asexual reproduction Describe what facultative reproducers can teach us about the evolution of sexual reproduction Predict cases in which asexual reproduction would be favored because the benefits outweigh the costs Unit 4: Life History and Species Interactions Describe how antagonistic pleiotropy can limit or extend lifespan Describe the tradeoff between reproduction and survivorship Identify evidence that suggests that reproduction has a cost Use life history tables to examine different life history strategies and their effects on fitness. Define lx and mx, and calculate them Describe how changes in fecundity at different ages affect fitness Explain why all species don’t put all of their reproductive effort into the first generation Describe under what circumstances can changes in survivorship after the last age of reproduction affect fitness Identify the potential fitness benefits to each of the four main types of one-on-one interactions within a species (mutualistic, selfish, altruistic, spiteful) Identify potential fitness losses incurred by each of the four main types of one-on-one interactions. Contrast the level of selection implied in kin selection and group selection.  Provide an example of when fitness gain at one level results in a fitness loss at another level. Explain why the prisoner’s dilemma provides evidence against cooperation as an evolutionarily stable strategy Describe the requirements for reciprocal altruism to be a successful strategy Define kin selection Apply Hamilton’s Rule to determine whether cooperation may evolve in a given situation Describe how haplodiploid relationships relate to Hamilton’s Rule Describes the conflict between parents and between parents and offspring in terms of comparative effort and resource use Identify conditions that support the evolution of eusocial communities Describe the three (discussed) categories of interactions among different species (predator/prey, etc) Explain why predator and prey coevolution can be thought of as an evolutionary “arms” race, including examples of adaptations that have arisen Describe the differences among specific, diffuse, and escape-and-radiate coevolution Describe how competition can lead to character displacement Describe how mutualistic relationships between organisms can also involve conflict Unit 5: Molecular Evolution Identify how many genes and the size of the human genome Define these terms: pseudogene, neofunctionalization, subfunctionalization, transposable element Describe the DDC model and what it explains Describe how TE content affects genome size Relate gene density with TE density Explain why TEs contribute to adaptation or disease Describe the relationship between genome size, gene count, and organismal complexity List consequences of larger genome size Describe the hemoglobin gene cluster and how it demonstrates patterns of genome evolution Identify monophyletic groups in a phylogeny, and explain their evolutionary relationships. Define incomplete lineage sorting, and describe its consequence for understanding species relationships Describe a molecular clock and how to use it. Define these terms: allometry, y = bxa , heterochrony, paedomorphosis, heterotopy, epigenetic effects, homeotic mutations, co-option, genetic toolkit, reaction norm Describe how the Hox gene cluster illustrates patterns of developmental evolution  Examine genes and answer the question "how did these gene copies arise?" Examine reaction norms for different genotypes, and describe whether the effects of genotype and environment are independent or interact with each other. Define these terms: paraphyly, homoplasy, ortholog, inparalog, outparalog Given an alignment, evaluate the fit of the data to alternative trees using parsimony. Based on an optimal tree, determine which positions contain homoplasies. Given a gene tree and a species tree, evaluate how duplications and deletions can reconcile the fit of the gene tree to species tree. Using a reconciliation, distinguish between orthologs, inparalogs, and outparalogs. Unit 6: History of Life and Macroevolution Recognize that animal life arose very late in the history of the universe and the history of Earth Describe the major hypotheses surrounding the origin of life including the characteristics of the earth at the time. Match the approximate dates and eras to the 10 important events listed at the end of the history of life lecture Describe the lines of evidence that support our current understanding of how life has evolved Describe how the Cambrian explosion, Permian extinction, and K/Pg extinctions marked large changes in the predominant groups of life Recognize that the major transitions from Pangaea, to Laurasia and Gondwana, to modern continental positions mostly occurred during the Mesozoic era. Explain why the Mesozoic is referred to as the Reptile Age and the Cenozoic is referred to as the Mammal age. Define biogeography and provide some example questions that are addressed by this area of study Describe the early observations made by naturalists that were first studying biogeography Compare and contrast historical and ecological biogeography Correct the misconception that organisms are optimally adapted to wherever they are currently found Define the terms cosmopolitan, endemic, continuous distribution, and disjunct distribution Identify the occurrence of vicariance or dispersal, based on molecular, geologic, and fossil evidence Determine the relative importance of historical and ecological factors to explain current distributions of organisms Explain why barriers are ecologically specific, and how barriers can affect genetic variation within and between species  Describe the latitudinal biodiversity gradient, and the leading hypothesis explaining its formation Describe the leading hypotheses to explain why certain clades have more species than others Compare and contrast ecological opportunities and key adaptations as explanations for radiation Compare and contrast extinction and competitive displacement as mechanisms for radiation Define microevolution and macroevolution, and describe the processes that underlie these two concepts Explain why taxa names that describe monophyletic relationships are preferred by evolutionary biologists Explain why analyzing extinct species helps scientists describe differences among living species Describe how complex traits can evolve through many small steps Describe how novel traits can arise through changes in the expression of genes that are already present Describe how to identify periods of stasis within traits across generations Compare and contrast gradualism and punctuated equilibrium as patterns of evolution Unit 7: Humans and Evolution Define these terms: Neanderthal, Homo sapiens, Denisovan, introgression Describe the geographic pattern of human dispersal in very, very broad terms Identify the evidence for Human-Neanderthal-Denosivan introgression, in very broad terms Consider how the following concepts contribute to geographic patterns of human genetic variation: introgression (ch. 16), genetic drift (ch. 7), mutation (ch. 4), gene flow (ch. 8), dispersal (ch. 8), clines and isolation by distance (ch. 8), natural selection and adaptation (ch. 3). Describe how the amount of human genetic variation is geographically distributed. Describe how genetic variation is distributed geographically. Consider the size of difference in the genetic composition between humans from different geographic regions Compare and contrast ancestry and race, and choose which applies to biology Describe classic adaptive genetic variation cases among humans: lactose tolerance and malaria resistance. Identify misconceptions about human genetic variation, and describe why they are incorrect. Identify course concepts that provide the most compelling evidence for the ability of evolutionary theory to explain living organisms and their diversity  Identify examples where evolutionary biology is helpful to humans and society in very practical ways Explain why a low level of public acceptance of evolution might affect advancement of evidence-based medicine and policy in the United States. Describe how the tree of SARS-CoV2 genomes developed by Forster et al. might help us to understand the origin, transmission, and evolution of the virus Describe how an understanding of the evolution of SAR-CoV2 might help direct development and use of antiviral therapies and vaccines