Example of population genomic
analysis
Using the chromopainter software
package
What is genomic data?
• Genomic data consists of genetic markers called SNPs.
• Single Nucleotide Polymorphisms (SNPs) are single bases within the
genome of an organism that show variation within a sample of
individuals.
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E.g. AGCTCCCGTAACG
AGCTCCGGTAACG
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• Due to recent advances in sequencing technology, hundreds of
thousands of SNP markers, scattered across the genome, can be
identified and genotyped relatively easily.
• The volume of data within such large datasets provides additional
power for inferring population structure.
The chromopainter package
• Designed specifically for the analysis of large
SNP datasets.
• Some applications:
– Identifying patterns of genetic structure.
– Identifying genetic clusters within the dataset, as
well as the relationships between clusters.
– Identifying cases of admixture.
Advantage of the chromopainter
approach
• Shown to have high sensitivity for detecting
subtle, fine-scale population structure.
Chromopainter has the advantage of
using linkage information
• If a reference genome is available for the study organism, it
is possible to know the position of each of the genotyped
SNPs.
E.g. AGCTCCCGTAACG
AGCTCCGGTAACG
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• This provides additional information that can be used in
Chromopainter to improve the accuracy of inferences.
The Linkage model
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• In the absence of recombination,
entire chromosomes are inherited as
single genetic blocks.
• Recombination breaks up ancestral
relationships between regions of the
chromosome.
• The likelihood of a recombination event between two SNPs
increases with the physical distance between them, so SNPs
that are further apart are more likely to be inherited
independently.
Chromopainter output
• The main output is a coancestry matrix
heatmap, which enables the visualisation of
shared ancestry between pairs of individuals.
Here is an example coancestry
matrix – each row and column
represents an individual, and the
colour of each square represents
the level of shared ancestry for
that pair of individuals.
Chromopainter output
• Aggregated coancestry matrix and
reconstructed evolutionary relationships.
– The aggregated coancestry matrix illustrates the
aggregated shared ancestry between genetic
clusters.
An example aggregated coancestry
matrix illustrating the shared ancestry
between clusters. A tree illustrating the
evolutionary relationships between
inferred clusters is also displayed.
A brief example
• The nematode species
Pristionchus pacificus
was sampled from
multiple locations on
two Indian Ocean
islands: Mauritius and
La Réunion.
SNP analysis with Chromopainter
• Distribution of the
genetic clusters correlates
with that of climatic zones
across La Réunion island.
•These results all
supported previous
inferences using
STRUCTURE and other
analyses, but added
further detail on fine-scale
population structure.
Thanks!
• For anyone interested, the web address for
chromopainter:
www.paintmychromosomes.org