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Human Migrations Saeed Hassanpour Spring 2008 Introduction Population Genetics Co-evolution of genes with language and cultural. Human evolution: genetics, history, statistics, physical/social anthropology, archaeology, demography, linguistic,... Background

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Human migrations l.jpg
Human Migrations

Saeed Hassanpour

Spring 2008


Introduction l.jpg
Introduction

Population Genetics

Co-evolution of genes with language and cultural.

Human evolution: genetics, history, statistics, physical/social anthropology, archaeology, demography, linguistic,...


Background l.jpg
Background

Genetic variation discovery: ABO blood groups (1919).

Biochemical methods(e.g. PCR): stain, radioactive, fluorescent markers visualization.

DNA sequencing and genotyping


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Definition

Allele: Different forms of a gene.

Genotype: The specific allele in an individual.

Phenotype: The expression of a genotype.

Allele

Homozygote

Phenotype

Heterozygote

Genotype

Homozygote


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Definition

Microsatellite: Short consecutive repeats:

Single nucleotide polymorphism (SNP): Variation in a single nucleotide of a genome between two individuals.

AC

AC

AC

AC

AC

AC

AC

AC


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Definition

Linkage disequilibrium (LD): Correlation between alleles at two different position.

Haplotype: Combination of alleles at multiple linked loci which are transmitted together.


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Evolution

Evolutionary forces:

Natural selection: Probability of survival and reproduction

Genetic drift: Change in allele frequencies entirely by chance.


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Evolution

Mutation: Change in nucleotide sequence of genes caused by copying error or exposure to radiation, chemical substance, viruses,...

Migration


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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


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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.


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Evolutionary History

Fst matrix analysis:

Phylogenetic tree

Based on SNP of 120 genes in 1,915 individuals


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Evolutionary History

Principle components

Based on 783 microsatellites in 1,027 individuals


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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


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NYR and Autosome

None-recombining part of Y chromosome.

Lower rate of the mutation

Greater length of DNA

Autosome: non-sex chromosome.


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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


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TMRCA

Polygyny vs. Polyandry


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Fst Matrix Analysis

Oceania

America

E.Asia

C.S.Asia

Based on 650,000 SNPs in 938 individuals

Europe

Midl.East

Africa


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Fst Matrix Analysis

Fst vs. geographic distance

Based on SNP of 120 genes in 1,915 individuals


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Fst Matrix Analysis

(A) Europe, (B) The Middle East

Based on 650,000 SNPs in 938 individuals


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Genetic variance

Partition molecular variance in Autosome, ChrX, Microsatellite:

Within population(WP)‏

Among-population

-within-group(AP/WG)‏

Among geographical region(AG)‏



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Waypoints

Based on 783 microsatellites in 1,027 individuals


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Heterozygosity

α: population in Africa.

p~ui: probability of allele u in population i

Estimate of heterozygosity in population i:


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Heterozygosity

Expansion of modern human from a single center.

Each migration is a sampling from the original population. (Serial Founder)‏

K

K

K

Nb

Nb

1

2

n


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Heterozygosity

Considering only genetic drift

No migration between populations

n bottleneck, Nb founders at each bottleneck

Reduction in heterozygosity by factor:

1-1/(2Nb)




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Heterozygosity

?

Human

Chimp


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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%


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Genes and Culture

Culture transmission: Vertically and Horizontally


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Conclusion

Out of Africa theory explain the Human genetic diversity:

Genetic distance

Heterozygosity


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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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