Lecture 2: Roots of Molecular Ecology - Origins, Evolution and Genetic Forces, Study notes of Biology

Download Lecture 2: Roots of Molecular Ecology - Origins, Evolution and Genetic Forces and more Study notes Biology in PDF only on Docsity! Lecture 2: Roots of Molecular Ecology August 23, 2006 Plan for Today The quiz (eek!) Historical backdrop for molecular ecology Preview and background for the readings Origins of Molecular Ecology Systematics: classification of organisms into hierarchical groups First molecular systematics study (1867) by Church: phylogeny of the African Turaco based on Turacin Ecology grew out of systematics in part: common roots Genetic Roots Significance of pus in molecular ecology? 1869: first DNA extraction (nuclein) 1900: Mendel's experiments 'rediscovered': surge of interest in genetics Cell biology thriving 1903: Sutton- Mendel's "factors" are chromosomes, that contain 'loci' (genes) Mendel Terminology Chromosome: structural unit of genetic material, containing DNA and protein Homologous: genetic material that pairs during meiosis in diploid cells Diploid: two sets of homologous chromosomes (one from each parent) Haploid: one set of chromosomes Locus: position on a chromosome Allele: different forms of the same locus What Controls Genetic Diversity of Populations? 4 major evolutionary forces Diversity Mutation + Drift - Selection +/- Migration + Only mutation can increase species diversity!!! Modes of selection on single genes • Directional – One extreme genotype has the highest fitness (purifying selection) • Overdominance – An intermediate genotype has the highest fitness (balancing selection) • Underdominance – The two extreme genotypes have the highest fitness (diversifying selection) 0 0.2 0.4 0.6 0.8 1 AA Aa aa sAA < sAa < saa or saa < sAa < sAA 0 0.2 0.4 0.6 0.8 1 AA Aa aa 0 0.2 0.4 0.6 0.8 1 AA Aa aa sAa < saa & sAA sAa > saa & sAA w w w Fisherian View Fisher's fundamental theorem: The rate of change in fitness of a population is proportional to the genetic variation present Ultimate outcome of strong directional selection is no genetic variation Most selection is directional 0.0 1.0 2.0 3.0 4.0 x 0.00 0.10 0.20 0.30 0.40 0.50 pr ob ab ili ty o f i m pr ov m en t Genetic Drift, part A: The bottleneck effect “Alleles” in original population “Alleles” remaining after bottleneck Cheetah www.petsdoc.com/pics/funpages/ wildlifephotos/cheetah.jpg Bottleneck effect Genetic Drift, Part B: The founder effect • Change in allele frequencies when a new population arises from only a few individuals e.g., only a few fish are introduced into a lake e.g., only a few birds make it to an island Genetics vs Environment Many advances made in evolutionary theory based on morphology Problem was variation could be exaggerated Only variable 'loci' scored Phenotype vs Genotype Var(phenotype) = Var(genotype + Var(environment) Heritability: Var(genotype) / Var(phenotype) Phenotypic plasticity: organisms with the same genotype have different phenotypes under different conditions Solution: control environmental variance by raising organisms in common environment Genecology Study of intraspecific variation and genetic composition relative to the environment Introduced by Turesson in 1922: coined 'ecotype'-a locally adapted population within a species Stanford group: Jens Clausen (cytology and genetics) William Hiesey (physiology) David Keck (botany/taxonomy) The Studies of Clausen, Keck, and Hiesey Clausen, Jens; Keck, David D.; Hiesey, William M. 1948. Experimental studies on the nature of species. III: Environmental responses of climatic races of Achillea. Publication 581; Washington, D.C.: Carnegie Institution of Washington. Achillea lanulosa exhibits clinal variation in natural populations across the elevational gradient in the Sierra Nevada Achillea lanulosa - wooly yarrow Most Mutations are Neutral Very small proportion of DNA codes for proteins, so little basis for selection Populus Genome 75% noncoding 15% introns 10% exons Degenerate Genetic Code TAB The Genetic Code (RNA to Amino Acids)” First Position (5’ end) Second Position Cc A Tyr Tyr Stop Stop Stop Trp His Arg His Arg, Leu Arg Leu (Met)* Arg, Ile r Ser Ile Ser lle Lys Arg Met (start) ) Arg Val 5 Gly Val ‘ Gly Val Ala Gly Val (Met)* Ala Glu Gly *AUG is the most common initiator codon; GUG usually codes for valine, and CUG for leucine, but, rarely, these codons can also code for methionine to initiate a protein chain. Third Position (3' end) Role of Molecular Markers Reveal hidden variation in unbiased fashion Direct comparison of mutation rates in different genomic locations and in response to different perturbations Direct assessment of neutral theory