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

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

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

Crossing over (recombination)

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.4/39

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

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

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

One female ancestor? of what? When? Where?

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.8/39

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

“Scientists find Eve”

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.10/39

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

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

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

One generation of a (small) population

Time

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.14/39

... and its parent generation

Time

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.15/39

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

Coalescent genealogy for one gene

Time

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.17/39

Coalescent genealogy for one gene

Time

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.18/39

Coalescent genealogy for one gene

Time

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.19/39

Coalescent genealogy for one gene

Time

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.20/39

Coalescent genealogy for one gene

Time

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.21/39

Coalescent genealogy for one gene

Time

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.22/39

Coalescent genealogy for one gene

Time

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.23/39

Coalescent genealogy for one gene

Time

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.24/39

Coalescent genealogy for one gene

Time

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.25/39

Coalescent genealogy for one gene

Time

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.26/39

Coalescent genealogy for one gene

Time

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.27/39

Untangling the crossed lines ...

Time

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.28/39

Genealogy of a sample of 3 copies

Time

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.29/39

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

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

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

An accurate analogy: Bugs In A Box

... hyperactive ...

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.33/39

An accurate analogy: Bugs In A Box

... indiscriminate ...

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.34/39

An accurate analogy: Bugs In A Box

... voracious ...

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.35/39

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

An accurate analogy: Bugs In A Box

... and insatiable.

Mitochondrial Eve and Y-chromosome Adam: Who do your genes come from? – p.37/39

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

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