28 July 2010. Joe Felsenstein Evening At The Genomeevolution.gs.washington.edu/atthegenome.pdffrom...
Transcript of 28 July 2010. Joe Felsenstein Evening At The Genomeevolution.gs.washington.edu/atthegenome.pdffrom...
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Mitochondrial Eve and Y-chromosome Adam: Who doyour genes come from?
28 July 2010.
Joe Felsenstein
Evening At The Genome
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.1/39
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Evolutionary trees from molecular sequences
from Amrine-Madsen, H. et al., 2003, Molecular Phylogenetics and Evolution
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.2/39
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My ancestor?
Joe
Eleanor Jake
Helen Will Sheimdel Lev
Cornelia John Maud William Itzhak Jacob
1850s
1880s
1910s
1942
747
about 44 more generations
bornCharles the Great
(Charlemagne)
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.3/39
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Crossing over (recombination)
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.4/39
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Did someone at General Motors take a biology course?
The GMC Hybrid logo.
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.5/39
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Chromosome 1, back up one lineage
now
−1
−2
−3
−4
−5
−6 (none)
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.6/39
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The “mitochondrial Eve” study in 1987
Rebecca Cann, Mark Stoneking, and the late Allan Wilson. In 1987 theymade a molecular tree of mitochondria from humans.
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.7/39
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One female ancestor? of what? When? Where?
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.8/39
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The “Out Of Africa” hypothesis
Africa
Europe Asia
(vertical scale is not time or evolutionary change)
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.9/39
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“Scientists find Eve”
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.10/39
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Who was where when Out Of Africa happened?
Africa Asia Europe
100k
now
H. neanderthalis
H. heidelbergensis
H. sapiens
H. erectusH. ergaster
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.11/39
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The Y chromosome
A genealogical tree of Y chromosome types, recent version, “growing”downwards. Geographical origin of the populations is color-coded alongthe bottom.
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.12/39
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What about all the other parts of the genome?
Part of the genome bases protein genesHuman mitochondrion 16,569 13Human Y chromosome 60,000,000 45All other human chromosomes 3,300,000,000 20,000 - 25,000
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.13/39
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One generation of a (small) population
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.14/39
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... and its parent generation
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.15/39
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Where do the copies of the genes come from?
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.16/39
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Coalescent genealogy for one gene
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.17/39
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Coalescent genealogy for one gene
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.18/39
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Coalescent genealogy for one gene
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.19/39
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Coalescent genealogy for one gene
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.20/39
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Coalescent genealogy for one gene
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.21/39
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Coalescent genealogy for one gene
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.22/39
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Coalescent genealogy for one gene
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.23/39
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Coalescent genealogy for one gene
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.24/39
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Coalescent genealogy for one gene
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.25/39
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Coalescent genealogy for one gene
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.26/39
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Coalescent genealogy for one gene
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.27/39
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Untangling the crossed lines ...
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.28/39
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Genealogy of a sample of 3 copies
Time
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.29/39
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J. F. C. Kingman’s (1982) “coalescent”
Go back a random length of time, drawn from an exponentialdistribution with mean 4N/(k(k − 1))
Join a random pair of lineages
Reduce k by 1.
If k = 1 then stop
Otherwise go up to first step.
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.30/39
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An accurate analogy: Bugs In A Box
There is a box ...
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.31/39
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An accurate analogy: Bugs In A Box
with bugs that are ...
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.32/39
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An accurate analogy: Bugs In A Box
... hyperactive ...
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.33/39
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An accurate analogy: Bugs In A Box
... indiscriminate ...
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.34/39
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An accurate analogy: Bugs In A Box
... voracious ...
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.35/39
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An accurate analogy: Bugs In A Box
... (eats other bug) ...
Gulp!
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.36/39
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An accurate analogy: Bugs In A Box
... and insatiable.
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.37/39
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A typical locus showing SNP variation
(From Debbie Nickerson’s SeattleSNPs project). Single-nucleotidepolymorphisms (SNPs) at the Matrix Metalloproteinase 3 locus.
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.38/39
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Members of our labCurrent members
Mary Kuhner
Jon YamatoElizabeth Walkup
Bob GiansiracusaJim McGillBrendan O’Fallon
Recent members, sadly departed
Lucian SmithChul Joo Kang
Eric Rynes
Ian Robertson
Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.39/39