CEng 713 Evolutionary Computation, Lecture Notes

Principles of Principles of Genetics, A BRIEF Genetics, A BRIEF

INTRODUCTIONINTRODUCTION

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

p2+2pq + q2 = 1● Mendelian population with diploid organisms,

p=1-q

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 nucleotidebases in double helixstructure.

● 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 theRNA sequence to ribosome

● rRNA, ribosomal RNA, forms complexes called ribosomes withprotein

●

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.