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# Lositan

## by tiago on Sep 04, 2009

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The Lositan selection detection workbench

The Lositan selection detection workbench

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## LositanPresentation Transcript

• Lositan A selection detection workbench based on a Fst outlier method Tiago Antao Liverpool School of Tropical Medicine
• The question
• Detect loci under selection
• Why?
• To do some analysis that require neutral loci (i.e., you have to remove loci under selection). Most of the analysis presented here require this
• You actually want to know loci under selection
• Put your own reason here...
As per Gordon's presentation...
• A solution
• An Fst-outlier method (Beaumont and Nichols 1996) where an area (Fst and heterozygosity) where neutral markers are supposed to fall is calculated.
• It is up to you to decide if you trust this method (especially in the context of your datasets)!
• The method - I
• A coalescent simulation
• Neutral
• Island model
• A bunch of loci (many thousands)
• You get an area where neutral markers are supposed to fall...
• The method - II
• What you need to supply?
• How many populations you have
• How many populations exist
• The mutation model
• The neutral Fst from your data
• Migration for the island model is calculated from the Fst
• Lositan
• Doubles as...
• Easy to use interface compared to the original implementation
• Fdist is command-line, prone to errors
• Fdist has its own data file format
• Sorts out a few practical problems with deviations from theory
• We will get back to this
Lets give it a try...
• Sorting a few issues
• The neutral Fst of your data is not easy to compute
• In the initial dataset candidate selected loci are used to calculate the neutral Fst
• Lositan removes them when computing “neutral” Fst
• The Fst formula:
• is only valid for infinite populations and the infinite alleles model
• This means that fdist might fail to simulate your Fst
• Lositan forces the correct Fst
Lets correct it...
• Limitations
• No support for the dominant variation
• Thousands of markers and thousands of individuals not supported
• Strict Genepop parsing (not a limitation)