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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
Human Migrations

Saeed Hassanpour

Spring 2008

introduction
Introduction

Population Genetics

Co-evolution of genes with language and cultural.

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

background
Background

Genetic variation discovery: ABO blood groups (1919).

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

DNA sequencing and genotyping

definition
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

definition5
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

definition6
Definition

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

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

evolution
Evolution

Evolutionary forces:

Natural selection: Probability of survival and reproduction

Genetic drift: Change in allele frequencies entirely by chance.

evolution8
Evolution

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

Migration

genetic distance
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
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
Evolutionary History

Fst matrix analysis:

Phylogenetic tree

Based on SNP of 120 genes in 1,915 individuals

evolutionary history12
Evolutionary History

Principle components

Based on 783 microsatellites in 1,027 individuals

mitochondrial dna
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
NYR and Autosome

None-recombining part of Y chromosome.

Lower rate of the mutation

Greater length of DNA

Autosome: non-sex chromosome.

tmrca
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

tmrca16
TMRCA

Polygyny vs. Polyandry

f st matrix analysis
Fst Matrix Analysis

Oceania

America

E.Asia

C.S.Asia

Based on 650,000 SNPs in 938 individuals

Europe

Midl.East

Africa

f st matrix analysis18
Fst Matrix Analysis

Fst vs. geographic distance

Based on SNP of 120 genes in 1,915 individuals

f st matrix analysis19
Fst Matrix Analysis

(A) Europe, (B) The Middle East

Based on 650,000 SNPs in 938 individuals

genetic variance
Genetic variance

Partition molecular variance in Autosome, ChrX, Microsatellite:

Within population(WP)‏

Among-population

-within-group(AP/WG)‏

Among geographical region(AG)‏

waypoints
Waypoints

Based on 783 microsatellites in 1,027 individuals

heterozygosity
Heterozygosity

α: population in Africa.

p~ui: probability of allele u in population i

Estimate of heterozygosity in population i:

heterozygosity24
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

heterozygosity25
Heterozygosity

Considering only genetic drift

No migration between populations

n bottleneck, Nb founders at each bottleneck

Reduction in heterozygosity by factor:

1-1/(2Nb)

heterozygosity28
Heterozygosity

?

Human

Chimp

drift vs selection
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%

genes and culture
Genes and Culture

Culture transmission: Vertically and Horizontally

conclusion
Conclusion

Out of Africa theory explain the Human genetic diversity:

Genetic distance

Heterozygosity

refrences
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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