Universal Genetic code table. Lecture Goals 1.Gene duplication – concerted evolution 2.Neutral...

Universal Genetic code table

Lecture Goals

1. Gene duplication – concerted evolution

2. Neutral theory and clocks

3. Epigenetics

2

Mitosis and meiosis

Meiosis: Metaphase I

Homologous Recombination

Homologous Recombination

DNA replication: repairs accidents at replication fork

Repairs double strand DNA (dsDNA) breaks

Occurs at meiosis (cross-overs)

Occurs at other times between highly similar sequences

Recombination -- Holliday Junction

Proposed by Dr. Holliday (Holliday R. 1964. A mechanisms for gene conversion in fungi.

Genet. Res. 5:282-304)

Holliday structures

ds-stranded breaks not uncommon

Meiosis

Created by topoisomerase-like enzymes

Mitosis

Radiation

Mutagens (e.g. chemicals)

Stalled replication forks

Specialized endonucleases (eg site-specific HO endonuclease in switching of yeast matting type (MAT) genes)

Gene Conversion

A special type of homologous recombination: Non-reciprocal transfer of genetic material from ‘donor’to ‘acceptor’

Initiated by double strand DNA (dsDNA) breaks

Outcome: portion of ‘donor’ sequence copied to ‘acceptor’and original ‘donor’ copy unchanged

donor acceptor

geneconversion

Gene Conversion is not uncommon

Yeast mating type switch (MAT) genes

Human repetitive sequence elements (Alu and LINE-1 sequences)*

Human gene families (e.g. MHC alleles, Rh blood group antigens, olfactory receptor genes)

Chicken B cells Ig gene diversification

Pathogen clonal antigenic variation (e.g. African Trypanosomes and Babesia bovis)

* Chen et al. 2007 Gene conversion: mechanisms, evolution and human disease Nature Reviews Genetics. 8: 762-775.

Lecture Goals

1. Gene duplication – concerted evolution

2. Neutral theory and clocks

3. Epigenetics

14

Neutral theory

• Proposed to explain considerable levels of molecular variation in populations

• Majority of mutations are effectively neutral and therefore subject to drift.

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Terms to own

Genetic drift: Changes in the allele frequencies due to effects of chance on sampling between generations

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Genetic drift

•Cause of drift: sampling error in finite population

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Genetic Drift

• Drift simulations• More drift simulations

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Practice this!

Genetic drift: more important in smaller populations

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Terms to own

Genetic drift: Changes in the allele frequencies due to effects of chance on sampling between generations

Effective population size: “the number of breeding individuals in an idealized population that would show the same amount of dispersion of allele frequences under random genetic drift as the population under consideration” (Sewall Wright)

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Effective population sizeEstimate of long term ‘relevant’ size of population.

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Effective population size

• A population that has experienced a bottleneck will have a lower effective population size than a population of the same census size that has been stable.

• This is because alleles are lost due to genetic drift so it is as if you have fewer individuals following bottleneck as compared to idealized population.

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Cheetahs23

Cheetahs: small Ne

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Cheetahs: small Ne

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Cheetahs: small Ne = skin graft26

Cheetahs: inbreeding depression

• Very low heterozygosity• 70% abnormal sperm and low sperm counts• Very high mortality to disease:

– 1982, Wildlife Safari in Oregon, 60 cheetahs– Coronavirus (e.g., SARS, common cold) killed 60%

(vs. 10% mortality in humans from SARS)

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Motoo Kimura

1968 “Evolutionary Rate at the Molecular Level,” Nature 217: 624-626.

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Neutral theory

• Let neutral mutation rate be µ (= new mutant copies of a gene per generation)

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Neutral theory

• Let neutral mutation rate be µ (= new mutant copies of a gene per generation)

• How many mutations in a population?

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Neutral theory

• Let neutral mutation rate be µ (= new mutant copies of a gene per generation)

• In a diploid population of size 2Ne, there will be 2Neµ new

mutations at a gene per generation

• What is probability of fixation? Loss?

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Neutral theory

• Let neutral mutation rate be µ (= new mutant copies of a gene per generation)

• In a diploid population of size Ne, there will be 2Neµ new mutations at a gene per generation

• Since these mutations are neutral, the probability of eventual fixation of any one mutation is 1/2Ne, and probability of loss is 1 - (1/2Ne)

Most new neutral mutations will be lost by drift within a few generations, but occasionally a new mutation will increase infrequency and replace previously existing alleles

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Random Walk: how long will it take for a “happy” man to fall of ledge?

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Time to fixation34

Neutral theory

Average number of allelic fixations per generation

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Neutral theory

Average number of allelic fixations per generation is equal to the number of new mutations per generation x the probability that any one mutation eventually becomes fixed

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Neutral theory

Average number of allelic fixations per generation is equal to the number of new mutations per generation x the probability that any one mutation eventually becomes fixed

# new mutations per generation =

37

Neutral theory

Average number of allelic fixations per generation is equal to the number of new mutations per generation x the probability that any one mutation eventually becomes fixed

# new mutations per generation = 2Neµ

prob. fixation of a new mutation =

38

Neutral theory

Average number of allelic fixations per generation is equal to the number of new mutations per generation x the probability that any one mutation eventually becomes fixed

# new mutations per generation = 2Neµ

prob. fixation of a new mutation = 1/2Ne

39

Neutral theory

Average number of allelic fixations per generation is equal to the number of new mutations per generation x the probability that any one mutation eventually becomes fixed

# new mutations per generation = 2Neµ

prob. fixation of a new mutation = 1/2Ne

So, average # fixations per generation =

40

Neutral theory

Average number of allelic fixations per generation is equal to the number of new mutations per generation x the probability that any one mutation eventually becomes fixed

# new mutations per generation = 2Neµ

prob. fixation of a new mutation = 1/2Ne

So, average # fixations per generation = µ

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Neutral theory

Average # allelic fixations per generation = µ

Average time between fixations =

42

Neutral theory

Average # allelic fixations per generation = µ

Average time between fixations = 1/µ

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Neutral theory

Average # allelic fixations per generation = µ

Average time between fixations = 1/µ

This is the molecular clock!

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• Your thoughts: neutral theory

Lecture Goals

1. Gene duplication – concerted evolution

2. Neutral theory and clocks

3. Epigenetics

46

47

Epigenetics• Epigenetics – quick history and definition• The Epigenome• Examples of Non-Mendelian inheritance

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Epigenetics: a brief history • Epigenesis: organisms develop through

transitions from egg to adult

• Preformationism:

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Epigenetics: brief history

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Epigenetics: brief history • Epigenesis: organisms develop through

transitions from egg to adult

• Preformationism: organisms are fully-formed throughout life cycle

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Epigenetics: brief history • Epigenesis: organisms develop through

transitions from egg to adult

• Preformationism: organisms are fully-formed throughout life cycle

• Epigenetics originally defined by Waddinton 1942: “branch of biology which studies the causal interactions between genes and their products which bring the phenotype into being”

52Epigenetics: Waddington

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Epigenetics – a term to struggle with• Epigenetics is the study of heritable changes in gene

expression that occur without a change in DNA sequence

• Epigenetics describes phenomena underlying many examples of non-Mendelian inheritance

• ‘Epigenetics has always been all the weird and wonderful things that cannot be explained by genetics’ - Denise Barlow, Vienna Austria (discovered first imprinted gene)

54Epigenetics

Certainly NOT the exception:

1. Maternal Effects

2. Imprinting

3. Other Epigenetic Phenomena

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Maternal Effect

A. E. Boycott (1920s)– First study of maternal effect– Water snail, Limnea peregra

• Shell and internal organs either right- or left-handed

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Maternal Effect

A. E. Boycott (1920s)– Began with two different true-breeding strains

• One dextral, one sinistral

– Dextral ♀ x sinistral ♂ dextral offspring– Reciprocal cross sinistral offspring– Contradict a Mendelian pattern of inheritance

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Maternal Effect

A. E. Boycott (1920s); Alfred Sturtevant (1923)– Sturtevant proposed that Boycott’s results could be

explained by a maternal effect gene• Dextral (D) is dominant to sinistral (d)• Phenotype of offspring is determined by genotype of

mother

Other Epigenetic PhenomenaMorphological evidence: Spirotrichea

Morphological evidence: Spirotrichea

Other Epigenetic Phenomena

Other Epigenetic Phenomena

• Trans-generational inheritance in Arabidopsis• Paramutation in mice

61Transgenerational memory - Arabidopsis

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Transgenerational memory - Arabidopsis

63Arabidopsis: homologous recombination

64Transgenerational memory - Arabidopsis

65Homologous recombination

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Mouse phenotype: kit

Kit null mutant (heterozygotes)

• Kit is a tyrosine kinase gene

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68Kit mutant

69Kit null mutant (heterozygotes)

70Kit mutant

71Kit* (paramutated) = decrease polyA Kit RNA

72Kit knockout = increase aberrant Kit RNA

73Kit RNA microinjection: offspring!

Kit Summary

• Paramutation: Kit allele transforms phenotype of offspring (white tipped tail and feet)

• Associated with build up of aberrant RNAs that are specifically packaged in sperm

• Injection of these RNAs also causes phenotype

Challenges central dogma!

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• Your thoughts: epigenetics