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

Prolonged period can increase the fixation rate ofbeneficial function-altering mutations

• Reduction in genetic diversity

The selected allele rises to fixation, bringingwith it closely linked variants

• High-frequency derived alleles

In a selective sweep, derived alleles linked to the beneficial allele can hitchhike to high frequency

Time

Kelley, J.(2007)

Signatures of selection

• Differences between populations

Positive selection may change the frequency ofan allele in one population but not in another

• Long haplotypes

Selected allele may rise in prevalence rapidlyenough that recombination does not break downthe association with alleles at nearby loci.

Methods for detect microevolution selection

Based on high frequency derived alleles

Tajima’s D statistical test

Detect - Positive - Balancing

Based on long haplotypes

Extended haplotype homozygosis (EHH). statistical test

TI

MET

IM

E

Frequency spectrum

Linkage disequilibrium

Vitti, J.(2013)

Detect - Partial or

incomplete selective sweep

- Balancing

Methods for detect microevolution selection T

IM

E

Wright’s fixation index (Fst)

Population differentiation

Composite methods

Detect:- Positive - Negative

Allele frequencies

Combine the results of one or a

few tests for many variants

Combine the results of many tests at a

single site

Fst

IHS (kind of LD)

XP-EHH

Vitti, J.(2013)

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

Gene under selectionLCT

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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