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popsim-consortium / stdpopsim

A library of standard population genetic models
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References for BGS models #391

Open ckyriazis opened 4 years ago

ckyriazis commented 4 years ago

Here are some DFE inference papers to get the BGS modeling conversation started. Please feel free to add any that I have missed!

Keightley & Eyre Walker 2007 (humans and drosophila) https://www.genetics.org/content/177/4/2251

Boyko 2008 (humans) https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000083

Torgerson 2009 (non coding loci in humans) https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000592

Tataru 2017 (chimps) https://www.genetics.org/content/207/3/1103.abstract

Kim 2017 (humans) https://www.genetics.org/content/206/1/345.abstract

Huber 2017 (humans, mice, flies) https://www.pnas.org/content/114/17/4465

Booker & Keightley 2018 (mice) https://academic.oup.com/mbe/article/35/12/2971/5123518

Zhen 2018 (humans, mice, flies) https://www.biorxiv.org/content/10.1101/427583v1

grahamgower commented 4 years ago

So the main things this needs are an exon model and a distribution of fitness effects? Is there anything else this requires?

The DFE should be straightforward to add into the slim engine. Is it expected that we'll use exon positions from a given species annotation, or have a parameterized exon model (i.e. generate exon positions from a distribution)? The former will require a framework in stdpopsim for importing and using annotations.

dschride commented 4 years ago

I think we would eventually want the flexibility to take an annotation that has more than one sequence type (e.g. CDS vs. UTR vs. intron, etc, rather than just exon vs non-exon). Then each sequence type (GenomicElementType in SLiM) could have its own DFE (or mixture of DFEs, or MutationTypes in SLiM).