Phylogeography

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PhylogeographyDemography

• Adam Eyre-Walker

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Phylogeography

• The geographical distribution of organisms from a
  phylogenetic/evolutionary perspective.

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Phylogeography
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Phylogeography
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Phylogeography
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Phylogeography
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Phylogeography
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Human mitochondrial DNA
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Problem I - mutation
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Problem I - mutation
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Problem I - mutation
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Problem I - mutation
A
B
C
D
Haplogroup
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Haplotypes haplogroups
Haplotype 1 C T G A A T G C C A A T Haplotype
1 C T G A A T G C C A A T Haplotype 2 C T T
A A T G C C A T T Haplotype 3 C T G A A T A C C
A A T Haplotype 4 C T G C A T A C C G A
T Haplotype 3 C T G A A T A C C A A T
Haplo- group X
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Nomenclature - mtDNA

• Africa - L haplogroup
• Non-Africans - M and N haplogroups
• Sub-groups M C, D, E, G M
• N A, B, F, H, I, J, K, R,
  T, U V

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Nomenclature - Y chromosome

• NRY non-recombining Y
• Haplogroups A to R
• Africa - A B
• Africa and non-africa - all others

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Haplotypes haplogroups
Haplotype 1 C T G A A T G C C A A T Haplotype
1 C T G A A T G C C A A T Haplotype 2 C T T
A A T G C C A T T Haplotype 3 C T G A A T A C C
A A T Haplotype 4 C T G C A T A C C G A
T Haplotype 3 C T G A A T A C C A A T
Haplo- group X
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Haplotypes haplogroups
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Example - Andaman Islands
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Example - Andaman Islands

• Inhabited by aboriginal people
• Short stature
• Dark skin
• Little contact with outsiders
• Come from
• Africa?
• Asia?

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Two studies

• Thangaraj et al.
• Typed mtDNA Y-chromosome in Andaman islanders
• Endicott et al.
• Sequenced mtDNA from Victorian bone collections

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Y-chromosome
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mtDNA
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Problem II - loss of variation
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Problem II - loss of variation
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Problem II - loss of variation
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Problem II - loss of variation
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Solution

• Use multiple loci

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Demography

• Study of population size

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Allele frequency distribution
Human1 C T G A A T G C C A A T G T C G Human2
C T G A A T G C C A A T G T C G Human3 C T T A
A T G C C A T T G T C G Human4 C T G A A T A C
C A T T G C C G Human5 C T G C A T A C C G A T
G C C G Human6 C T G A A T A C C A A T G T C G
1
2
3
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expansion
1
2
3
1
2
3
contraction
1
2
3
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Contraction - bottleneck
Human1 C T G A A T G C C A A T G T C G Human2
C T G A A T G C C A A T G T C G Human3 C T T A
A T G C C A T T G T C G Human4 C T G A A T A C
C A T T G C C G Human5 C T G C A T A C C G A T
G C C G Human6 C T G A A T A C C A A T G T C G
1
2
3
1
2
3
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Demographic model
Parameters No start popn size Nint popn after
bottleneck Nrec final popn size T time back to
bottleneck fint Nint / No frec Nrec / No T
Nrec
No
Population size
Nint
T
Time
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Simulate data
fint 1 frec 1 T 0
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Simulate data
fint 0.1 frec 1 T 0.1
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A more complex model
N1
N2
m1
m2
No
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Further reading

• Jobling Human evolutionary genetics Chapters 6
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