Bio 304 1st EditionExam # 2 Study Guide Lectures: No class February 13 – snow dayLecture 1 (February 16)Chapter 5Variation is ubiquitous is all species and populations- Kinds of variations- Kinds of mutations- Rates of mutations- Mutation and fitness- Epigenetics Kinds of variation- Genetic- Environmental- Genotype by environment variationGenetic variation- Affects protein function- DNA – mRNA – Protein - Ex – liking different food is partly genetic Environmental variation- Upregulating of different genes - Ex – induced differences Genotype by environmental interactions- Allows phenotypic plasticity to evolve- Ex – temperature changing sex in animalsWhere does genetic variation come from?- How you define “variation”- Sexual reproduction = new combinations of existing alleles = new phenotypes- Only mutations = new alleles and genesKinds of mutations- Single base substitution/ insertion/deletion (point mutation)- Gene duplication- Chromosomal mutations- Genome duplicationsGene – segment of DNA that codes for RNA or protein productAllele – 1 of several versions of the same gene that differ in base sequenceLocus – identifiable location of a gene within a genomeLecture 2 (February 18) Point mutation (substitution)- Happens when a single base is substituted for another- 2 kinds transitions and transversions (transitions are more common)- Transitions are less likely to be fixed in DNA synthesisIndels (insertion or deletion) in coding regions may cause frame shift mutationsSingle base substitution may cause 1 amino acid in gene product (0 if synonymous)Insertion/ deletions change the reading frame and alter many amino acids in gene production2.1 mutations occur per genome per generationGene duplication- Unequal crossing overo Mistakes during meiosis- Retrotranspositionso – 40% of human genome represents remnants of transposonso Some very ancient, might have moved by horizontal gene transferSingle point mutations are more frequentDuplicated genes?- May retain original function- Can evolve novel functions- May be or become nonfunctional pseudogenesGene duplication by unequal crossing over- Recent event in monkeys – RNASE1 (defense against viruses (original)) and RNASE1B (digestion of leaf RNA (new))Duplicated genes complicate the concept of homology- Paralogs are homologous genes within a genome that were duplicated and then diverged in sequence by mutationso May or may not have same functiono Orthologs are homologous genes found in different species Generally have the same functionNew genes from scratcho Point mutations may turn non coding DNA into codingChromosome mutationo When a chromosome breaks, it is repaired incorrectlyo Inverts the gene sequence on chromosomeo Affects independent segregation of alleleso Can cause tight linkage of the inverted group of geneso In Heterozygous individuals, the only crossing over events that are valid are those that keep the entire inverted sequence togetherGenome duplicationo Involves duplication of entire nuclear genomeo Can arise from mistake during meiosiso Homologs do not separate during meiosis Io Or sister chromatids do not separate during meiosis IIo Common in plants : rare in animals - half of vascular plants spp.Lecture 3 (February 20)Genome duplication allows genetic innovationo Associated with increased speciation rateo Early diversity explosion in angiosperms?o High diversity of ray – finned fishesPoint mutations = change in single nucleotide base of DNAFitness effects of mutationso Usually neutral, some lethal, very little is betterEpigeneticso Non – genetic inheritance (no change in DNA nucleotide identity/order)o Ex – methylation on DNA can = phenotypic changeo Can be from environmento Can be maintained during DNA replication, so transferred parent to offspringo May last few or many generationsEpigenetic marks from environmental stressors may increase/decrease health of offspring across generationso War, genocide, abuse, famine?Measuring genetic diversityo Focus has been on identifying allelic diversityo How many alleles does a population have for a particular geneo Measured across many lociChapter 6Mendelian genetics in populations I: selection and mutationShould know:o Meiosis – independent assortment of chromosomes, and crossing overo Mendelian genetico Homologous chromosome, gene, allele, locusMendelian geneticso Predicts patterns of genetic inheritance within a family lineageo Alone, doesn’t tell us about patterns of genetic traits within a populationRules of probability1. Probability of 2 independent events occurring = product of individual probabilities2. Probability of either of 2 or more independent events occurring = sum of individual probabilitiesLecture 4 (February 23)A2+2AB+B2=1Hardy – Weinberg PrincipleIf all assumptions are met for A2+2AB+B2=1, then1. Allele frequencies will not change across a population2. Always 2 allelesThings that can change thiso Mutationo Drifto Selectiono MigrationHardy W. model is useful but nullIf assumptions not met1. Allele frequency will change2. Equation won’t workIn certain cases selection can drive genotype frequency away from H-W predicted proportions, even if frequencies are not changingCase study: spongy brain diseaseo Bovine spongiform encephalopathy in cows (mad cow)o Creutzfeldt-Jakob disease in humanso Same causative agent: prions (defective proteins that cause other proteins to become misfolded) o Can be spread human-human-animalo Met and val alleles, every victim had met/met genotypeo Spread by contact with contaminated tissueso Suspected mode of infection among Fore was ritual funereal cannibalismRead case studies in bookPredicted vs actual genotype frequencieso Met /met predicted .23, actual .22o Met /val predicted .5, actual .51o Val /val predicted .27, actual .26Lecture 5 (February 25)Evolution does not go to perfection – best genotype requires that some individuals die from lethal recessive allele frequencies (homologous) Selection favoring unstable allele frequency equilibriumo When either homozygote is equally fit, and heterozygotes are lethal, 1 allele will go fixation quickly, the other will go extincto Random with respect to which allele goes extinctSelection favoring homozygotes leads to unstable allele frequency equilibriao When 1 homozygote is more fit that the other, and heterozygotes are lethal, the equilibrium is still unstableo Most of the time, favored allele will be fixed. Not always. Frequency-dependent