Population Genetics
description
Transcript of Population Genetics
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Population Genetics
Evolution depends upon mutation
to create new alleles.
Evolution occurs as a result of population
level changes in allele frequencies.
What evolutionary forces alter
allele frequencies?
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How do allele frequencies changein a population from generationto generation?
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Hardy-Weinberg Principle
(1) Allele frequencies in a population will not change, generation after generation.
(2) If allele frequencies are given by p and q, the genotype frequencies will be given by p2, 2pq, and q2.
When none of the evolutionary forces (selection, mutation, drift, migration, non-random mating) are operative:
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Allele frequencies in the gene pool:
A: 12 / 20 = 0.6a: 8 / 20 = 0.4
Alleles Combine to Yield Genotypic Frequencies
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Our mice grow-up and generate gametesfor next generations gene pool
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Allele frequency across generations: A General Single Locus, 2 Allele Model
Freq A1 = pFreq A2 = q
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Inbreeding Decreases the Frequencyof Heterozygotes
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Inbreeding can reducemean fitness by“revealing” deleteriousrecessive alleles.
Inbreeding Depression in Humans
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Inbreeding coefficient (F) = Probability that two alleles are identical by descent
AB
0.5
0.5
0.5
(0.5)4 = 0.0625
A
0.5
A
AA
AB
0.5
0.5
0.5
(0.5)4 = 0.0625
B
0.5
B
BB
0.0625 + 0.0625 = 0.125
What is F for an individual of half sib parents?
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Box 9B, Figure 1(2) Change of Genotype Frequencies by Inbreeding
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Heterozygosity inan inbred population =
Heterozygosity in arandom mating
population
Prob. not IBD
H F = HO (1 - F)
Anytime F is greater than 0, the frequency of heterozygotes islower in an inbred population than in a random mating population.
x
Heterozygosity and Inbreeding
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Box 9B, Figure 2. Change of Genotype Frequencies by Inbreeding
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9.10 Inbreeding depression in humans
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9.11 The golden lion tamarin is a small, highly endangered Brazilian monkey
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9.12 Population decline and increase in an inbred population of adders in Sweden
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Inbreeding increases egg failure in Parus major
Can organisms avoid inbreeding depression?
Mate ChoiceGenetic Incompatibility
Dispersal
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Why did fitness decreaseafter early efforts wereimplemented to conserve remnant populations?
Prairie chicken almost went extinctin the 1950’s.
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Average number of nDNA alleles per locus
Illinois Illinois Other Pops in pre-bottleneck present Midwest
5.12 3.67 5.33-5.88
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Loss of HabitatExtinction or reduced population sizes
Gene Flow - reduced / eliminated
Genetic Drift and Non-random MatingLoss of heterozygosity
Deleterious alleles increase in frequency
Inbreeding Depression -- lowered fitness
Extinction or reduced population sizes
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Measuring Genetic Variation in Natural Populations
Historical Method: Examining protein variation via electrophoresis
Modern Method: DNA sequencing and typing
TTCTTCAGGGGAGGGGGTGGAANATAAAAACAAAAACCCTACAATGTATATTCATCGCCCATAATCGGCTACTTAGACA
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More than one allele at 30-50% of all loci in a population.Such loci are called polymorphic.
LDH-B cline in Fundulus
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Most populations harbor considerable genetic diversity
Heterozygosity0.10 0.20 0.30
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Heterozygosity has a couple of interpretations:
1) Average percentage of loci that are heterozygous per individual.
or
2) Average percentage of individuals that are heterozygous per loci.
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Polymorphism
Polymorphism: when two or more alleles at a locus exist in a population at the same time.
Nucleotide diversity:
= xixjijij
Seq 1 G A G G T G C A A C 0.4Seq 2 G A G G A C C A A C 0.5Seq 3 G A G C T G G A A G 0.1
1 2 31
2 0.2
3 0.3 0.5
Freq(x)
(0.4)(0.5)(0.2) + (0.4)(0.1)(0.3) + (0.5)(0.1)(0.5) = 0.077
considers # differencesand allele frequency
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In Theory:
Under infinite-sites model: Expectation (
4Ne = frequency of heterozygotes per nucleotide site
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Nucleotide diversity is low in humans
Average nucleotide diversity per site across loci
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ATCCGGCTTTCGAK = 3 for-->ATCCGAATTTCGA
ATTCGCCTTTCGA
K= Number of segregating (variable) sites in a sample of alleles.
Polymorphism is also estimated by:
Expectation (K
In Theory:
Where a = 1 + 1/2 + 1/3 +……..1/n-1
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(75 x 2) + (24) / (102 x 2) = 85.3
75/102 + 1/2 (24/102) = 85.3
Counting alleles
or
Genotypic frequencies
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Sequencing Studies Have Revealed Enormous Genetic Diversity
CFTR Locus
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Measuring Genetic Variation in Natural Populations
Other Methods:
EST approach
AFLPs
Microsatellites
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AAAAAAAA
TTTTTTTTT
Exon3` UTR
An EST is a tiny portion of an entire gene
TTTTTTTTT
ContextualRegion
PolymorphicRegion
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Figure 4. Venn diagram of BLAST comparisons among amphibian EST projects. Values provided are numbers of reciprocal best BLAST hits (E<10-20) among quality masked A. mexicanum and A. t. tigrinum assemblies and a publicly available X. tropicalis EST assembly.
A. mex. 7909
A. t. tig. 69122296
523
X. trop.34,296
465 353
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A. mexicanum16214 bp
Unseq
UnseqUnseq
Unseq
UnseqUnseq
Unseq
12S rRNA16S rRNAND1ND2
cox 1cox 3ATP6 cox 2ATP8
ND5
cyt b
A. tigrinum15967 bp
D-loopUnseq
Unseq
12S rRNA16S rRNAND1ND2
cox1cox2ATP8ATP6cox3ND3ND4LND4
ND5cyt b
EST Projects: A quick way to obtain complete mtDNA genome sequence.
Mt DNA : 22 tRNAs, 2 rRNAs, 13 mRNAHomoplasmic, maternal transmission, evolves quicklyApproximately 1-2% sequence divergence / million years
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0
1
2
3
4
5
6
7
0 500 1000 1500 2000
EST Length (bp)
# SNPs
# SNPs per EST
A. mexicanum A. t. tigrinum
~ 5% mtDNA sequence divergence
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Microsatellites
See Figure 3.19 for pict showing gel separation of microsat alleles
Co-dominant marker typeFound in essentially all genomesEvolve at a very high rate (10-3 - 10-4 per locus per gamete per generation)
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A A T C C T A G T A T A T A
T T A G G A T C A T A T A T G T G C T T A A
5’ 3’
T T A G G A T C A T A T A T G T G C T T A A
A A T C T A T A T A C A C G A A T T 5’ 3’
TA
A GTC
Replication inserting TA
A A T C T A T A
T T A G G A T C A T A T A T G T G C T T A A
5’ 3’
TA
A GTC
Insertion during DNA replication
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A A T C C T A G T A T A T A
T T A G G A T C A T A T A T G T G C T T A A
5’ 3’
A A T C C T A G T A T A T A
T T A G A T A T G T G C T T A A
5’ 3’
GA
TAT C
Mispairing of DNAduring replication
A A T C C T A G T A T A C A C G A A T T
T T A G A T A T G T G C T T A A
5’ 3’
GA
TAT C
T A is excised
Replication of DNA
Deletion during DNA replication
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A A T C C T A G T A T A T A C A C G A A T T
T T A G G A T C A T A T A T G T G C T T A A
5’ 3’
A G
A A T C T A T A T A C A C G A A T T
T T A G G A T C A T A T A T G T G C T T A A
5’ 3’
TA
TC
Excision and repair inserts TA
G T
A A T C T A T A C A C G A A T T
T T A G G A T C A T A T T T A A
5’ 3’
TA
A GTC
AT
CG
Slipped-strand mispairing
Insertion in non-replicating DNA
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AFLP (Amplified Fragment Length Polymorphisms)
RD of DNA
Ligation of adaptorscreates PCR primerrecognition sequence
Subsequent selective PCRallows sampling of for
restrictionlength polymorphisms
E M M
Allele 1
E M
Allele 2
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AFLP Gel
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Representative Molecular Approaches Genetic/Phylogenetic Resolution vs Appropriateness
Clonality Parentage Populations Species
Restriction Fragment Analysis * * ** ***
DNA sequencing/typing overkill overkill *** ***
mt DNA na na ** ***
AFLPs * * * *
Microsatellites *** *** ** na
From Avise’s book