CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Molecular Evolution Course #27615 Anders Gorm Pedersen Molecular Evolution Group Center for Biological Sequence.

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Presentation transcript:

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Molecular Evolution Course #27615 Anders Gorm Pedersen Molecular Evolution Group Center for Biological Sequence Analysis Technical University of Denmark (DTU)

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Neutral Theory of Molecular Evolution Evolution is a two-step process: 1.Mutation (random) 2.Selection (non-random) Detrimental mutation =>negative selection =>Mutation not seen Beneficial mutation =>positive selection =>Mutation seen

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Selectionist Views of What Drives Molecular Evolution Majority of all mutations are detrimental and not seenMajority of all mutations are detrimental and not seen Most observed mutations have adaptive valueMost observed mutations have adaptive value Classical school:Classical school: –Single predominant version of gene (“wild type”) present in population –Natural selection rapidly fixates new, advantageous mutations Balance school:Balance school: –Appreciable amount of polymorphism in gene pool –Polymorphism maintained actively by natural selection (e.g., sickle cell anemia)

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Neutralist Views of What Drives Molecular Evolution Electrophoretic studies in 1960’s showed much higher polymorphism than anticipated by either classical or balance school selectionistsElectrophoretic studies in 1960’s showed much higher polymorphism than anticipated by either classical or balance school selectionists Kimura and others proposed the “Neutral Theory of Molecular Evolution”.Kimura and others proposed the “Neutral Theory of Molecular Evolution”. Detrimental mutation => negative selection => Mutation not seen Neutral mutation => no selection => Mutation may be seen (genetic drift) Beneficial mutation => positive selection => Mutation seen

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Difference Between Selectionist and Neutralist Views of Evolution Selectionist view: Most observed mutations represent functional innovation Neutralist view: Most observed mutations represent conservative changes, changes in unimportant regions

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS All Agree that Adaptations are Caused by Natural Selection

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS All Agree that Adaptations are Caused by Natural Selection

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS All Agree that Adaptations are Caused by Natural Selection

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS All Agree that Adaptations are Caused by Natural Selection

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS All Agree that Adaptations are Caused by Natural Selection

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS The molecular clock

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Genetic drift Gen. 1

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Genetic drift Gen. 1

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Genetic drift Gen. 1

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Genetic drift Gen. 1

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Genetic drift Gen. 1 Gen. 2

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Genetic drift Gen. 1 Gen. 2

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Genetic drift Gen. 1 Gen. 2

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Genetic drift Gen. 1 Gen. 2 Gen. 3

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Genetic drift Gen. 1 Gen. 2 Gen. 3

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Genetic drift Gen. 1 Gen. 2 Gen. 3

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Genetic drift Gen. 1 Gen. 2 Gen. 3 Gen. 4

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Genetic drift Alleles will eventually reach a frequency of 0 or 1 Genetic diversity decreases Effect is more strongly felt in small populations

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Time to fixation and time between fixations

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Drift and mutation

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Genetic Drift: The bottleneck effect “Alleles” in original population “Alleles” remaining after bottleneck

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS CheetahBottleneck effect

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Northern Elephant Seal Reduced to 20 individuals in 1896 Now 30,000 individuals, with no detectable genetic diversity Bottleneck Effect

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Genetic Drift: 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.

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Scorpaenidae Lionfish Pterois volitans Founder Effect New Atlantic population, maybe from only 10 individuals

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Exercise: Genetic drift simulation Starting point: population with N individuals, fraction p has genotype A, fraction (1-p) has genotype aStarting point: population with N individuals, fraction p has genotype A, fraction (1-p) has genotype a All individuals produce 200 offspring of same genotype as parent. (offspring also has fraction p genotype A)All individuals produce 200 offspring of same genotype as parent. (offspring also has fraction p genotype A) Survival rate = 1/200 => Constant population size NSurvival rate = 1/200 => Constant population size N Death strikes randomly: each generation N random individuals surviveDeath strikes randomly: each generation N random individuals survive Investigate drift of allele A frequency:.Investigate drift of allele A frequency:. –Find proportion of populations where A is fixed (p=0.4; N=20, N=80) –Find average time to fixation of A (p=0.4, N=10, 20,...130)