BioC16 lecture 1-4 notes.doc

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Biological Sciences
Mark Fitzpatrick

Lecture1 Individuals do not evolve populations evolve Evolution -Mutation -Genetic drift -Migration -Natural selection Only natural selection leads to Adaptation Modern evolutionary genetics Early – macroscale 1960s – microscale Complex traits -Quantitative traits -Numerical value Modern revelation -Some genes with a very large effects -Many with very small additive effects Reverse transcription is possible Primary transcript has no promoter –> mature transcript only exons –> proteins Coding DNA Exon's code for proteins, tRNA, rRNA Non-coding DNA Intron's, pseudogens, repetitive DNA Purines include: A, G transition | C for G transversion Pyrimidines include: C, T transition. | T for A transversion Lecture2 Transition– going from purine to purine or pyrimidine to pyrimidine. Transversion– going from purine to pyrimidine or pyrimidine to purine. -Transversions are much more difficult to do than transitions - PURe As Gold -> purines = adenine and guanine Measuring genetic variation - What is evolutionarygenetics? Interface between ecology, evolution, and genetics – Understand the process of evolution by considering differences in gene frequencies and genotype frequency within a population. -So evolutionary genetics is also population genetics Populationgenetics: the study of naturally occurring differences between organisms. -Differences are genetic variation Three hierarchical levels: I) within populations II) between populations of species III) between different species Phenotype with the underlying gene Phenotype gene unknown Phenotype and gene both known – Evolutionary processes are primarily occurring within population. Populations evolve through changes in allele frequencies. Most, if not all concepts in this course are important, only in the context of populations, not individuals. – Genetic variation – Allele frequency – Gene flow – Drift – Natural selection – Heritability – Genetic correlation Figure2.1– B equals populations. A represents everything including the populations and is called the meta-population. We can also consider A as the population and B would be considered as subpopulations , demes, or local populations. Figure2.2– Whitlock in 1992 – fungus beetle – allele frequencies decrease as population size increases Genetic variation Withinapopulation: – there is more than one allele at a given locus – Segregating variation – polymorphic (many types) means that there is variation – some loci are fixed - homozygous for the same allele What makes an allele different? – E.g.: change/remove intron, change in nucleotide, etc. Betweenpopulations: – this is called genetic differentiation – each population could be fixed for different alleles Goalsofpopulationgenetics: 1. Explain the origin and maintenance of genetic variation 2. Explain the patterns and organization of this variation (why some populations have more variation than others) 3. Understand the mechanisms that cause changes in allele frequencies Four agents of evolution: -drift, mutation, gene flow, and natural selection. Genetic markers – Determine which alleles are present – useful for many questions – mating systems - how inbreed is the population? – gene flow and population structure –> migration – determine paternity and heritability (h2) – generate genetic maps to identify genes underlying complex traits – conservation genetics Types of genetic markers – Visibly discrete polymorphisms – few distinct morphs – robust to environmental variation – e.g.: Marine isopod –> paracercius sculptor (Shuster and Wads) - sponge – within holes of a sponge there were different types of isopods (crustaceans) for males but only one type of female - Alpha males – territorial and very successful meeting – beta males – female mimic not a threat to alpha male because he looks like a female – gamma males – sneaker male - sneaks both males alpha and Beta Molecular markers – Electrophoresis – protein, DNA, or RNA – Many modern methods – vary – protein allozyme's (first molecular markers) – RFLP – RAPDs – AFLPs – VNTRs – SSCP – what is the source Of these molecular markers? Mutation Mutation – Mutation is the ultimate source of genetic variation. Somatic Germline – E.g.: tumor, non-heritable (in the absence – heritable of genetic predisposition of underlying trait) – in the cells that produce gametes. –– mutation is past to daughter cells but not sexually produced offspring. Point mutations Chromosomal – single bases – change in segment of DNA – loss, gain, or substitution – – Loss, duplication, or All mutations rearrangement. are changes in it types sequences Terms to know – silent – missense – nonsense – frameshift – insertion/deletion (Indel) – duplication – inversion – translocation Protein allozyme's – 1960s – Richard Lee wanted at Harvard (Gould and Wilson) – Electrophoresis: smaller things are more faster severe found lower down (see figure 2.3) – Allozyme = different enzymes Figure 2.4: – homozygous both bands on top of each other appears as one - slow/slow – heterozygous because bands shown as two separate bands - fast/slow F(aster) = smaller S(lower) = larger How variable are proteins? Polymorphisms Mammals – 15% Birds – 22% Insects – 33% Plants – 25% Advantage of allozyme's – cheap, markers, and are codominant (both homozygotes and heterozygotes are expressed) Disadvantage of allozyme's – reveals only small amount of variation – many DNA polymorphisms don't result in change in allozyme – some amino acid changes don't affect mobility on gel RFLP–restrictionfragmentlengthpolymorphism – enzymes cut DNA at specific sequences (nonrandom) – sites are often palindromes - reads the same backwards and forwards – e.g.: ALU I EcoRI 5' AGCT 3' 5' GAATTC 3' 3' TCGA 5' 3' CTTAAG 5' –usually done at 37°C –Two individuals both exposed to ALU I and EcoRI – so if we run on gel electrophoresis then individual one will be slower because it is larger – for individual one we see a band at 9 and for individual two we see a band at 4 and 5 – The polymorphism could be very variable so you don't know if the
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