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CEng 713 Evolutionary Computation, Lecture Notes Principles of Genetics, A BRIEF INTRODUCTION Darwin's Theory of Evolution ● ● ● ● The common descent of all organisms from a single ancestor. The manifestation of novel traits in a lineage. The mechanisms that cause some traits to persist while others perish. Forces of evolution: – Survival of the fittest – Recombination,mutation – Gene flow – Genetic drift Population Genetics ● ● Investigates genetic variation among individuals withing groups (populations, gene pools) Investigates the genetic basis for evoluitionary change and seeks to understand how patterns vary geographically and through time. ● How genetic diversity affected by evolution? – Mutation + – Selection -/+ – Genetic drift - – Migration +/- – Non-random mating - ● ● Hardy-Weinberg assumptions: – population is infinetely large – mating is random – no natural selection – no mutation – no migration Hardy-Weinberg law: – If assumptions are met, population will be in genetic equililibrium 2 2 Genetic Drift ● ● ● ● Random increase or decrease in the trait frequencies in the gene pool of a population. Sampling affect. Each population is a sample of its parent population. For small populations, sampling errors will be significant. An allele can be fixed (p=1) or go extinct (p=0) Gene Flow ● Gene flow/migration: movements of genes from one population to the other – Introduce and spreads unique allelles to new population – Allele frequencies of populations change Natural Selection and Adaptation ● ● ● Natural selection and adaptation Ecological selection: organisms which survive and reproduce increase the frequency of their genes in the gene pool wrt. organisms who cannot survive Sexual selection: organisms which are more attractive to the opposite sex because of their features reproduce more and thus increase the frequency of those features in the gene pool ● ● ● ● Purifying selection: eliminates the deterious mutations Positive selection: increase frequency of beneficial mutations Balancing selection: maintain the variance of population – heterozygous forms are more fit than the homozygous forms – frequency dependent selection: rare variants have high fitnes or sexual attractivity. Baldwinian evolution: culturial species that are able the learn can change the environment to introduce new selection forces. Speciation ● ● ● Creation of two or more species from one. Allopatric speciation: geographical isolation. Habitat fragmentation, migration. Sympatric speciation: same habitat. Adaptive Landscape ● ● ● ● genetic compositions with mean fitness is high gets a higher position in the landscape. Selection move population to high fitness (probably a local maxima) Drift may move the population to lower position in the landscape. Interaction of species, parasites, symbiotic life, migration, climate conditions,... Fitness definition is complicated. Chromosome ● ● ● ● DNA: nucleic acid that contains the genetic instructions specifying the biological development of all cellular forms of life Chromosome: macromolecule package of DNA. A sequence of nucleotide bases in double helix structure. Human genetic information: ~3,000,000,000 bases, 32,000 genes in 46 chromosomes. Structure of the DNA ● Double helix model ● Nucleotides, 4 bases: ● – Adenine – Thymin (only in DNA) – Cytosine – Guanine – Uracil (only in RNA) Purpose: Protein synthesis Gene Structure ● ● ● ● Sequence of 3 nucleotide bases form a codon. Each codon defines an amino acid. Each gene defines the information for synthesis of a protein. Introns: non-coding segments. they are not realized in the phenotype. Exons: coding segments ● ● ● ● ● enhancer and promoter codons facilate RNA alignment with the gene. genes may overlap. Introns in one gene can be exon in the other. Several genes can affect a phenotypical characteristic. existence of a gene can affect the activityof the other (ephistasis) A more complicated picture. Transcription and Translation ● ● ● ● Transcription of data in a gene into mRNA, messenger RNA. tRNA, transfer RNA, transports the RNA sequence to ribosome rRNA, ribosomal RNA, forms complexes called ribosomes with protein Reproduction ● During the Meiosis, two chromosomes are crossovered. Crossover ● During crossover, offspring gets half of its genome from either parents. Mutation ● ● ● ● Error during the crossover of two DNA sequences. Some portion of DNA can be deleted, inserted, inverted during the copying. There is a repair mechanism however not all of the sequences can be repaired. So genes can have: – point mutation – frameshift – transposition – inversion Glossary ● ● ● ● ● ● Allele: An alternative form of a gene that occurs at a specified chromosomal position (locus) Codon: A group of thre nucleotide bases within the DNA that encodes a single amino acid or start and stop information for the transcription process. Crossover: A process of information exchange of genetic material that occurs between adjacent chromatids during meiosis. Deme: An independent subpopulation. Diploid: In diploid organisms, each body cell carries two sets of chromosomes; each chromosome exists in two homolohous forms, one of which is phenotypically realized. DNA: Deoxyribonucleic acid, a double-stranded macromolecule of hlical structure determining building plan of an organism. ● ● ● ● ● Exon: A region of codons within a gene that is expressed for the phenotype of an organism. Intron: A region of codons within a gene that do not bear genetic information that is expressed for the phenotype of an organism. Gamete: A haploid germ cell that fuses with another in fertilization to form a zygote. Gene: A unit of codons on the DNA that encodes the synthesis for a protein. Genome: The total genetic information of an organism. ● ● ● ● ● ● ● Genotype: The sum of inherited characters maintained within the entire reproducing population. Phenotype: The behavioiral expression of the genotype in a specific environment. Locus:A particular location on a chromosome. Meiosis: The process of cell division in diploid organisms through which germ cells (gametes) are created. Mitosis: The process by which a cell separates its duplicated genome into two identical halves. Niche: Adapatatoin of species occurs with respect to any major kind of environment, the adaptive zone of this species. Polygeny: The combined influence of several genes on a single phenotypical characteristics. ● RNA: Ribonucleic acid. The transcription process in the cell nbucleus generates a copy of the nucleitode sequence on the coding strand of the DNA.