Lositan A selection detection workbench based on a Fst outlier method Tiago Antao Liverpool School of Tropical Medicine
The question <ul><li>Detect loci under selection </li></ul><ul><li>Why? </li></ul><ul><ul><li>To do some analysis that req...
A solution <ul><li>An Fst-outlier method (Beaumont and Nichols 1996) where an area (Fst and heterozygosity) where neutral ...
The method - I <ul><li>A coalescent simulation </li></ul><ul><ul><li>Neutral </li></ul></ul><ul><ul><li>Island model </li>...
The method - II
What you need to supply? <ul><li>How many populations you have </li></ul><ul><li>How many populations exist </li></ul><ul>...
Lositan <ul><li>Doubles as... </li></ul><ul><ul><li>Easy to use interface compared to the original implementation </li></u...
Sorting a few issues <ul><li>The neutral Fst of your data is not easy to compute </li></ul><ul><ul><li>In the initial data...
Limitations <ul><li>No support for the dominant variation </li></ul><ul><li>Thousands of markers and thousands of individu...
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Lositan

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The Lositan selection detection workbench

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Lositan

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

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