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0:03
Next, we'll talk about
the program GLOBETROTTER,
which similarly can
identify and date admixture
assuming a pulse model.
As can a more efficient,
recently released program
called fastGLOBETROTTER.
0:15
I'll describe the intuition of
this approach briefly
on this slide.
These programs use
a technique called
chromosome painting that
takes in individuals
genetic variation data,
such as h_4 here,
at a five SNP sequence
and compares it to those
from a set of
surrogate populations
represented here by
different colors,
h_1, h_2 and h_3.
Here, h_4 matches the
first two SNPs to h_1.
The last three you
see can match h_2.
We color or paint h_4
to show this matching.
GLOBETROTTER and
fastGLOBETROTTER
use the program CHROMOPAINTER
to do this painting.
According to this, it looks
like h_4 is a mixture
of the populations
represented by h_1 and h_2,
with one block of
SNPs inherited from
the blue population
and the other block from
the red population.
The programs then measure
how the correlation
amongst these blocks decays with
genetic distance
between the blocks.
The decay should follow an
exponential distribution
with rate equal to when
the admixture occurred.
This is quite similar to the
approach of ALDER/MALDER.
But in contrast, these programs
incorporate haplotype
information in the way that they
consider blocks of
contiguous SNPs,
rather than analyzing
each SNP independently.
This can increase power
in certain situations.
1:29
Running GLOBETROTTER,
with fastGLOBETROTTER run
in a nearly identical way,
requires three steps.
First, another
program that I had
previously mentioned,
CHROMOPAINTER,
which is described in
Lausanne et al. 2012,
has to be run twice.
The first time it is run to
paint sampled individuals
from surrogate populations
against each other.
The second time is to paint
sampled individuals in the
admixed target population
against the surrogates.
We then run GLOBETROTTER
or fastGLOBETROTTER
using the combined results
from steps 1 and 2.
To run this,
first extract the files
in both of these programs
and compile them using their
provided instructions.
