human migrations saeed hassanpour spring 2008. introduction population genetics co-evolution of...
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Introduction
• Population Genetics
Co-evolution of genes with language and cultural.
• Human evolution: genetics, history, statistics, physical/social anthropology, archaeology, demography, linguistic,...
Background
• Genetic variation discovery: ABO blood groups (1919).
Biochemical methods(e.g. PCR): stain, radioactive, fluorescent markers visualization.
• DNA sequencing and genotyping
Definition• Allele: Different forms of a gene.• Genotype: The specific allele in an
individual.• Phenotype: The expression of a
genotype.
Allele
Genotype
Phenotype
Homozygote
Homozygote
Heterozygote
Definition• Microsatellite: Short consecutive repeats:
• Single nucleotide polymorphism (SNP): Variation in a single nucleotide of a genome between two individuals.
AC ACAC ACACACACAC
Definition• Linkage disequilibrium (LD): Correlation
between alleles at two different position.
• Haplotype: Combination of alleles at multiple linked loci which are transmitted together.
Evolution• Evolutionary forces:
- Natural selection: Probability of survival and reproduction
Genetic drift: Change in allele frequencies entirely by chance.
Evolution
- Mutation: Change in nucleotide sequence of genes caused by copying error or exposure to radiation, chemical substance, viruses,...
Migration
Genetic Distance
Fixation Index (Fst): Measure of population differentiation.
• ΠBetween(ΠWithin): Average number of pairwise difference between two individuals sampled from different (the same) population.
ΠBetween
ΠWithin
Natural selection
• Find Genes which are candidates to have been under selection:
Very low and very high Fst distance.
Compare expected and observed values of Fst.
Evolutionary History
Fst matrix analysis:
- Phylogenetic tree
Based on SNP of 120 genes in
1,915 individuals
Mitochondrial DNA• Mitochondrial DNA (mtDNA):
In mitochondria (out of nucleus)
• transmitted along only female lineages.
• No recombination.
High mutation rate:
• Abundance of polymorphic
Difficult genealogy reconstruction
NYR and Autosome
• None-recombining part of Y chromosome.
- Lower rate of the mutation
- Greater length of DNA
Autosome: non-sex chromosome.
TMRCA• Time of the fist major separation in
evolutionary tree between african and non-african.
Bayesian analysis and maximum-likelihood methods:
• Using mtDNA: TMRCA≈230,000
• Using NRY: TMRCA≈100,000
Fst Matrix Analysis
Oceania
America
E.Asia
C.S.Asia
Europe
Midl.East
Africa
Based on 650,000
SNPs in 938 individuals
Genetic variance
• Partition molecular variance in Autosome, ChrX, Microsatellite:
Within population(WP)
• Among-population
-within-group(AP/WG)
• Among geographical region(AG)
Heterozygosity
• α: population in Africa.
p~ui: probability of allele u in population i
Estimate of heterozygosity in population i:
Heterozygosity
• Expansion of modern human from a single center.
• Each migration is a sampling from the original population. (Serial Founder)
KNb
K K
1 2 n
Nb
Heterozygosity
• Considering only genetic drift
No migration between populations
• n bottleneck, Nb founders at each bottleneck
Reduction in heterozygosity by factor:
1-1/(2Nb)
Drift vs. Selection
• Since regression explain 76%-78% of observed genetics variation
Lower bound on genetic drift effect: 76%-78%
• Upper bound on Selection effect: 22%-24%
Conclusion
• Out of Africa theory explain the Human genetic diversity:
Genetic distance
• Heterozygosity
Refrences
• The application of molecular genetic approaches to the study of human evolution, Cavalli-Sforza & Feldman, 2003
Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa, Ramachandran et al., 2005
• Worldwide Human Relationships Inferred from Genome from Genome-Wide Patterns of Variation, Jun Li et all., 2008
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