POPULATION GENETICS studies the genetic. It includes the study of forces that induce evolution (the

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1 POPULATION GENETICS

2 POPULATION GENETICS studies the genetic composition of populations and how it changes with time. It includes the study of forces that induce evolution (the change of the genetic constitution) of populations through time: genetic drift, mutation, gene flow and selection.

3 R. A. Fisher J. B. S. Haldane S. Wright...they had said everything of truly fundamental importance about the theory of genetic change in populations and it is due mainly to man s infinite capacity to make more and more out of less and less, that the rest of us are not currently among the unemployed. R. C. Lewontin (1963)

4 IMPORTANT CONCEPTS IN POPULATION GENETICS Genome Autosomes Gene family Gene X and Y chromosomes Pseudogenes Locus mtdna Exons Allelel cpdna Introns Genotype Promotors Homozygote Linkage disequilibrium Flanking regions Heterozygote Independency Haploid Recombination Diploid Haplotype Polyploid

5 IMPORTANT CONCEPTS IN STATISTICS Deterministic and stochastic models Parameters Monte Carlo Simulations Sample Estimates Randomness Mean Variance Standard deviation Arithmetic mean Harmonic mean Binomial Distribution Multinomial Distribution Poisson Distribution Null hypothesis Type I and II errors

6 STRUCTURE OF GENOMES

7 STRUCTURE AND INHERITENCE The structure and inheritance of genomes described here will be biased towards the most common pattern in mammals. One must be aware that there is variation across organisms and that t patterns of diversity it also depend d on this. For example: - Ploidy; - Sex determination; - Cytoplasmic compartments of inheritance; -Etc.

8 OVERVIEW OF THE GENOME

9 DNA FIGURE - 4 nucleotides The succession of the nucleotides in a DNA molecule is The succession of the nucleotides in a DNA molecule is a DNA SEQUENCE (e.g. AGCTATTTCCAGGA).

10 CHROMOSOMES

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13 GENES Most of the DNA present in a genome has no specific p g p function, but some segments contain the instructions for the synthesis of proteins (or sometimes RNA): GENES.

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16 NONCODING DNA About 98.5% of the DNA does not contain coding sequences: - Single copy DNA (e.g. most of the introns); R titi l t ( t d t - Repetitive elements (e.g. tandem repeats; interspersed elements).

17 INHERITANCE OF GENETIC ELEMENTS

18 INHERITANCE OF GENOMIC REGIONS

19 INHERITANCE OF GENOMIC REGIONS

20 CONCEPTS

21 GENETIC VARIATION

22 MUTATION -Istheultimate source of genetic variation. - It refers to any change that produces a new allele; - Only mutations that occur in the germ-line are passed to the next generation; - Types of mutation: - Inversions and translocations; - Duplications, insertions, deletions; - Substitutions. - It covers a broad spectrum, from the substitution of single nucleotide in the genome to changes in chromosome number.

23 MUTATION

24 BASE SUBSTITUTIONS -Is the simplest difference between homologous DNA sequences. - Are cause by i) misincorporation of nucleotides during replication or ii) chemical or physical mutagenesis. - The originated polymorphisms are called Single Nucleotide Polymorphisms SNPs (where single base insertions or deletions are also included).

25 BASE SUBSTITUTIONS -Transition vs. transversion: - Synonymous vs. non-synonymous.

26 SNPs WITHIN GENES

27 VARIABLE NUMBER OF TANDEM REPEATS

28 MICROSATELLITES (STRs)

29 OTHER MUTATIONS - Transposable element insertions: -LINEs - SINEs - Structural mutations: L i i d l ti d li ti l ht - Large inversions, deletions, duplications, lenght variations

30 RECOMBINATION - Reciprocal transfer of genetic information.

31 GENE CONVERSION - Nonreciprocal transfer of genetic information.

32 DETECTING GENETIC VARIATION

33 CLASSICAL-BALANCE VIEWS OF GENOME STRUCTURE

34 PROTEIN ELECTROPHORESIS

35 PROTEIN ELECTROPHORESIS

36 PROTEIN ELECTROPHORESIS

37 PROTEIN ISOELECTIC FOCUSING

38 PROTEIN ISOELECTIC FOCUSING

39 POLIMERASE CHAIN REACTION (PCR)

40 VARIABLE NUMBER OF TANDEM REPEATS

41 RESTRICTION FRAGMENT LENGHT POLYMORPHISM

42 RFLP s

43 OTHER SNPs GENOTYPING PROCEDURES

44 SEQUENCING

45 SEQUENCING

46 HIGH THROUGHPUT SEQUENCING 454 Illumina

47 ALLELIC VS. SEQUENCE DATA

48 QUANTITATIVE TRAIT LOCI Corn seeds University of Illinois 1896-present)

49 Gasterosteus aculeatus

50 QUANTITATIVE TRAIT LOCI