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Variation Hereditary Information !! DNA !! !! In nearly all Complementary !! !! G-C A-T 1! Replication !! DNA Polymerase !! It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material. !! Watson and Crick, 1953 Towards a phenotype !! The central “dogma” !! DNA -> RNA -> Protein 2! The Code ! tell me two things !! Codons in triplets !! 1) !! 2) What is mutation? !! Changes in base pair sequence !! May be silent – when? 3! What is mutation? !! Changes in base pair sequence !! May be silent – or not What is mutation? !! What we see !! !! Strong phenotypic effects What we don’t see Subtle phenotypic effects !! Synonymous substitutions !! 4! What is mutation? !! What we see !! !! Nature 463, 864-867 (2010) Strong phenotypic effects What we don’t see Subtle phenotypic effects !! Synonymous substitutions !! Transitions vs. Transversions !! Some changes are more likely than others !! !! Purines (A, G) more likely to be exchanged with each other than with a pyrimidine (C, T) Pyrimidines (C, T) more likely to be exchanged with each other than with a purine (A, G) 5! Mutation rates vary !! RNA Polymerase Tradeoff between speed and accuracy !! !! Repair !! Also varies A few questions !! Do you think variation in accuracy and repair is ! Heritable? !! A potential cause of differential success? !! Would differential success influence future generations? !! 6! What will happen if ! Variation + !! Variation heritable + !! Differential Success + !! Differential representation in the next generation? !! What will happen if ! Variation + !! Variation heritable + !! Differential Success + !! Differential representation in the next generation? !! Evolution by Natural Selection !! !! What does “Fit” mean? 7! Aren’t all mutations deleterious? !! As the source of adaptive variability, then, mutations (and orthodox evolution theories) fail completely. As a source of "negative variability," however, mutations serve only too well. Basing their thinking on what we observe of mutations and their net effect (genetic burden), creationists use mutations to help explain the existence of disease, genetic defects, and other examples of "negative variation" within species. !! Institute for Creation Research Aren’t all mutations deleterious? !! Why are most mutations either ! Neutral, or !! Deleterious? !! 8! Aren’t all mutations deleterious? !! Why are most mutations either ! Neutral, or !! Deleterious? !! When would it be favorable to have a high mutation rate? !! What does this imply? !! Sources of new genes !! Retrotranspositions Processed RNA transcribed back !! E.g. Jumping Genes !! !! Unequal Crossing over 9! Gene duplication pretty common !! Ortholog !! !! Same gene, same locus, different species Paralogs Copy of gene at different locus !! Can give rise to gene families !! E.g. Globin genes !! Why would this be important evolutionarily? !! What happens with multiple copies? !! Loss of function/transcription !! !! Maintain original function !! !! Pseudogenes E.g. rRNA One copy develops new functions The joys of redundancy!!! !! Globin is a nice example !! 10! Gene duplication pretty common Inversions !! Can create supergenes !! Genes that are tightly linked and are transmitted as a block 11! Polyploidy and its consequences Speciation – More later !! Innovation and diversity? !! Polyploidy and its consequences Speciation – More later !! Innovation and diversity? !! 12! Polyploidy and its consequences !! Science. 2011 Sep 2;333(6047):1257. doi: 10.1126/science.1207205. Epub 2011 Aug 18. Recently formed polyploid plants diversify at lower rates. Mayrose I, Zhan SH, Rothfels CJ, Magnuson-Ford K, Barker MS, Rieseberg LH, Otto SP. Abstract !! Polyploidy, the doubling of genomic content, is a widespread feature, especially among plants, yet its macroevolutionary impacts are contentious. Traditionally, polyploidy has been considered an evolutionary dead end, whereas recent genomic studies suggest that polyploidy has been a key driver of macroevolutionary success. Fission and fusion !! Given this phylogeny, what do you think happened? 13! Genetic Variation in populations !! Expectation – Purifying selection !! What would this mean? Diversity in populations !! Heterozygosity !! !! What proportion of genes are heterozygous in an average individual? What would you expect? 14! Genetic Variation in populations Expectation – Purifying selection !! Observation (60’s) – Lots of variation !! Variation – Why so much? Two Ideas: !! 1) !! !! 2) 15! Evolutionary Mechanisms Null models, Selection, and Mutation Population Genetics Some History !! Darwin and Mendel 16! Population Genetics Some History !! Wright, Haldane, and Fisher Hardy-Weinberg as a null model Terms Allele frequency: The proportion of total alleles composed of a particular allele. E.g. for two alleles !! Genotypic frequency: Proportion of the total number of individuals composed of a particular genotype. E.g. For two alleles !! f(AA) = (# AA)/(total number of individuals) !! f(Aa) = (# Aa)/(total number of individuals) !! f(aa) = (# aa)/(total number of individuals) !! 17! Population Genetics What is Hardy-Weinberg Equilibrium? If there are two alleles, A1 and A2 !! And they have frequencies !! f(A1) = p and f(A2) = q !! And certain conditions are met (more later) !! Then, the frequency of the genotypes will be: f(A1A1) = p2; f(A1A2) = 2pq; f(A2A2) = q2 !! Why? !! Population Genetics What is Hardy-Weinberg Equilibrium? Let’s say ! !! p = f(A1) = 0.6 and !! q = f(A2) = 0.4 !! 18! Population Genetics Violations of HWE - Selection !! Hardy-Weinberg tells us ! !! What happens to allele frequencies if H-W conditions apply !! !! Nothing What the genotypic frequencies will be if H-W conditions apply Population Genetics Violations of HWE !! Evolutionary agents !! !! Can change allele frequencies E.g. !! !! !! !! Mutation Migration Drift Selection 19! General selection !! What part of ! don’t you understand? General selection !! What part of ! do you understand? 20!