Download Detection of the footprint of natural selection in the genome

Detection of the footprint
of natural selection in the
genome
Lorena Blanco Fernández
A brief history of natural selection
• Darwin began formulating his theory
of natural selection in the late 1860
•
Wallace help Darwin in his studies
• The descent of species from common
ancestors were well accepted
• Natural selection took a harder time
to be accept
Kinds of selection
Signatures of selection
• High proportion of function altering mutations
Time
Prolonged period can increase the fixation rate of
beneficial function-altering mutations
• Reduction in genetic diversity
The selected allele rises to fixation, bringing
with it closely linked variants
• High-frequency derived alleles
In a selective sweep, derived alleles linked to the
beneficial allele can hitchhike to high frequency
Kelley, J.(2007)
Signatures of selection
• Differences between populations
Positive selection may change the frequency of
an allele in one population but not in another
• Long haplotypes
Selected allele may rise in prevalence rapidly
enough that recombination does not break down
the association with alleles at nearby loci.
Methods for detect microevolution selection
Linkage
disequilibrium
Frequency
spectrum
Detect
- Positive
- Balancing
Extended haplotype
homozygosis (EHH).
statistical test
Detect
- Partial or
incomplete
selective sweep
- Balancing
Vitti, J.(2013)
I M E
T
Tajima’s D statistical test
Based on long haplotypes
T
I M E
Based on high frequency
derived alleles
Methods for detect microevolution selection
Population
differentiation
Allele frequencies
I M E
Wright’s fixation
index (Fst)
Composite methods
Combine the
results of one or a
few tests for
many variants
Combine the results
of many tests at a
single site
T
Fst
Detect:
- Positive
- Negative
Vitti, J.(2013)
XP-EHH
IHS (kind
of LD)
Gene under selection
LCT
Traces of selection
• High Fst values for the 99 flanking DNA sites on LCT locus.
• REHH was estimated to be extremely high
• Selective sweep acting since 2000-20000 years ago
Kelley, J.(2007)
Bibliography
• Vitti, J. J., Grossman, S. R., & Sabeti, P. C. (2013). Detecting natural selection in genomic data. Annual Review of Genetics, 47, 97–120.
http://doi.org/10.1146/annurev-genet-111212-133526
• Kelley, J. L., & Swanson, W. J. (2008). Positive selection in the human genome: from genome scans to biological significance. Annual Review of
Genomics and Human Genetics, 9, 143–160. http://doi.org/10.1146/annurev.genom.9.081307.164411
• Ridley, M. (2004). Evolution. Evolution. http://doi.org/10.1007/978-3-0348-6133-5
• Sabeti, P. C., Schaffner, S. F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., … Lander, E. S. (2006). Positive natural selection in the human lineage.
Science (New York, N.Y.), 312(5780), 1614–1620. http://doi.org/10.1126/science.1124309
• Oleksyk, T. K., Smith, M. W., & O’Brien, S. J. (2010). Genome-wide scans for footprints of natural selection. Philosophical Transactions of the Royal
Society of London. Series B, Biological Sciences, 365(1537), 185–205. http://doi.org/10.1098/rstb.2009.0219
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