1. Evolutionary genetics Charles Darwin

2. Darwin’s theory of evolution through natural selection 1.Principle of variation Among individuals within any population, there is variation in morphology, physiology and behavior 2.Principle of heredity Offspring resemble their parents more than they resemble unrelated individuals 3.Principle of selection Some forms are more successful at surviving and reproducing than other forms in a given environment Natural selection The process of differential survival and reproduction of individual variants already existing in the group

3. - The Darwin explanation of evolution apply to two different aspects of the history of life ; Phyletic evolution, Diversification Change in the shell size and curvature in the bivalve Mollusc Gryphaea during its Phyletic evolution in the early Jurassic (No net increase in species diversity) - Successive change of form & function that occurs in a single continuous line of descent time Phyletic evolution Diversification An ancestral species  gives rise to a variety of diverse species through repeated diversification ( Net increase in species diversity ) - Many different contemporaneous species having quite different forms and living in different ways A variety of bivalve mollusc shell forms that have appeared in the past 300 millions years of evolution Species not only must be changing, but must give rise to new and different species in the course of evolution Heritable variation within populations  heritable differences between population in time & space

4. A synthesis of forces: variation and divergence of population The effects on gene frequency of various forces of evolution The blue arrows ; a tendency toward increased variations within the population The red arrows ; a tendency toward decreased variation In evolution, the various forces of breeding structure, mutation and selection are all acting simultaneously in populations * Forces that increase or maintain variation within population ( mutation or migration ) * Forces that make each population homozygous ( random drift or inbreeding ) Prevent the differentiation of populations from each other Cause different populations to diverge

5. Divergence of the Galapagos finches from ancestral colonizers from the South American mainland A synthesis of forces: variation and divergence of population (1) Founder effect The loss of genetic variation when a new colony is formed by a very small number of individuals from a larger population (2) Directional selection pushes a population toward homozygosity if mutation occurs and is advantageous, a new homozygous state is created depends on the environment and on chance events The thirteen species of finches found in the Galapagos Islands

6. The Balance between Inbreeding and New Variation Distribution of gene frequencies among island populations after various numbers of generations of isolation, where the number of generations that have passed (t) is given in multiples of the population size (N). All populations start at q (and p) = 0.5 As the number of generations passed increases, the populations begin to diverge from the 0.5 frequency (due to sampling error). As some populations go to q = 1.0, approximately the same number will go to p = 1.0 The distribution of allele frequencies found in the populations spreads symmetrically. When the allelic frequency in a population reaches 1.0, the allele is the only one left in the population, and it becomes fixed. The other allele is lost. Populations in which an allele has become either fixed or lost, the process of random genetic drift stops in that population. Without further input (mutation), the populations that have allelic frequencies of 1.0 or 0 for either allele will maintain those allelic frequencies constantly. ; Founder effect

7. Actual variation available for natural selection ; a balance between the introduction of new variation ( migration or mutation) and its loss through local inbreeding if m 1 or u 1 a population will retain its heterozygosity > > NN Human populations have a higher migration rate

8. ; Two different genotypes can lead to equally adaptive phenotypes for a given environmental challenge ex) increase of wing size ( number / size ) - Adaptive peaks : A high point (perhaps one of several) on an adaptive landscape; selection tends to drive the genotype composition of the population toward a combination corresponding to an adaptive peak.adaptive landscapegenotypepopulation - Adaptive landscape (or Adaptive surface) The surface plotted in a three-dimensional graph; with all possible combinations of allele frequencies for different loci plotted in the plane; and mean fitness for each combination plotted in the third dimension.allele frequencieslocifitness - The existence of multiple peaks some of differences between species are the result of history and not of environmental differences - Which peak the population will ascend? the initial genetic composition drives the population to a local maximum of w Multiple adaptive peaks

9. Exploration of adaptive peaks - Without random drift, both populations would have moved toward aB/aB as a result of selection alone - Selection and random drift can interact to produce different changes in gene frequency in an adaptive landscape - natural selection, multiple adaptive peak, random fixation of less fit alleles  evolution Adaptation failed 1) Random drift is so great 2) intensity of selection is insufficient random drift may improve adaptation Pathway IPathway II

10. Exploration of adaptive peaks mutation  which kind ? which time order?  evolution

11. Heritability of Variation The scutellar bristles of the adult Drosophila - phenotypic variation  genotypic differences (  evolution) - all variable traits are heritable (X) ex) behavior trait - canalized character ; substantial genetic variation + no morphological variation stressful environment or severe mutation  morphological variation

12. Population : 1 to 3 (African), 4 to 7 (American indian), 8 to 13 (Asian), 14 to 15 (Australian aborigine), 16 to 20 (European) Observed variation within and between population neighboring points do not correspond to geographical races Each point represents the allelic composition of a population - Relative amounts of variation within and between populations vary from to species to species, depending on history and environments - Different human populations show rather similar frequencies for polymorphic genes ex) the ABO blood group : i, I A, I B

13. Process of speciation - Species ; a group of organisms that can exchange genes among themselves but are genetically unable to exchange genes in nature with other groups - Speciation ; common ancestors  new species 1. single mutation  complete mating incompatibility between carrier of that mutation and original species  very rare 2. biologically isolated populations by mechanical barrier (geographical)  diverge by mutation, selection, and genetic drift (no migration)  new species (usual pathway : allopatric speciation) - Biological isolating mechanism 1. Prezyogotic isolating mechanism prevent the formation of viable zygotes a. Lack of mating opportunity : ecological, temporal isolation b. Lack of mating compatibility : behavioral, mechanical, gametic isolation 2. Postzyogotic isolating mechanism prevent hybrids from passing on their genes Hybrid inviability, hybrid sterility, hybrid breakdown

14. Genetics of species isolation Testis size in backcross hybrids between Drosophilla pseudoobscura (1) and D. persimilies (2). - closely related species (incomplete hybrid sterility and hybrid breakdown) ex) Drosophila - cross of 1 & 2 species  F1 male sterile, F1 female fertile - an X chromosome from one species (1) + complete diploid set of autosomes from other species (2)  testis are at a minimum

15. Origin of new genes Frequency distribution of haploid chromosome numbers in dicotyledonous plants An individual containing more than two sets of genes and chromosomes.geneschromosomes 1. Polyploidy * New functions - continuous transformations of shape - qualitative novelty (change of the level of genes)

16. Origin of new genes 2. Duplication Developmental changes in the synthesis of the alpha-like and beta like globins The occurrence of a second copy of a particular sequence of DNA  no functional change or a complete qualitative divergence in function ex) human beta-globin Chromosomal distribution of the genes for the alpha family of globins and the beta family of globins in humans.

17. Reconstruction of the diversification of the beta globin gene family in the evolution of the vertebrate

18. 2. Duplication  a complete qualitative divergence in function Origin of new genes Structural homology of the gene for hen lysozyme and mammalian  -lactalbumin. - Exons and introns are indicated by dark green bars and light green bars, respectively - Nucleotide sequences at the beginning and end of each intron are indicated, and the numbers refer to the nucleotide lengths of each segment.

19. 3. Imported DNA Repeatedly in evolution, Extra DNA has been imported into the genome from outside sources by mechanisms other than normal sexual reproduction - Mitochondria and chloroplasts (symbionts) transfer much of their genome to the nuclei of their eukaryotic hosts 1) Cellular organelles - Important evidence for the extracellular origin of mitochondria ; their genetic code 2) Horizontal transfer ; transposable elements - transposition can act as an source of selectable variation - retrotransposition Origin of new genes

20. Relation of Genetic to Functional Changes - No regular relation genetic to functional changes ex) lysozyme in eukaryotes, carboxyesterase of blow fly - The order in which mutations occur in the evolution of the molecule may be critical

21. Rate of molecular evolution which states that there is a positive linear relationship between time since two species diverged and amount of genetic divergence (e.g., DNA sequence difference) between those species. Molecular clock (  ) Mutation rate to neutral alleles :  intrinsic neucleotide mutation rate: M The propotion all mutations that are neutral: f  = M Xf - Mutations of DNA 1) deleterious 2) increase fitness 3) neutral mutation - effective neutral mutation rate of neutral replacement = 2N  X 1/2N = 

22. Rate of molecular evolution Number of amino acid substitutions in the evolution of the vertebrates as a function of time since divergence - Different proteins will have different clock rates  different sensitivity of a protein’s function to amino acid changes

23. Rate of molecular evolution - Detection of a adaptive evolution of a protein