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README.md

Bayesian Estimator of Selfing (BES)

BES is a software package for estimating self-fertilization (selfing) rates and other mating system parameters from genotype data. BES estimates parameters in a Bayesian framework using Markov chain Monte Carlo (MCMC).

BES contains a generic model for estimating selfing rates and mutation rates independent of a mating system. BES also contains models of

  • pure hermaphroditism
  • androdioecy (hermaphrodites + males)
  • gynodioecy (hermaphrodites + females)

Additional non-genetic information, such as field observations of the number of females or males, is required for to estimate mating system parameters.

See the paper and figures.

A more robust estimator

BES version 0.1.3 has been changed to be more robust by estimating the loss-of-heterozygosity (f) that is not due to selfing as well as the selfing rate (s or s*). You can disable this by setting f to 0. However, without allowing for an extra source of loss-of-heterozygosity, the estimates of the selfing rate can be too high, since they assume that selfing is the only source of decreased heterozygosity.

The model of non-selfing inbreeding assumes that two alleles from the first two outbred ancestors of a selfed individual have probability f of being identical, and probability (1-f) of being drawn independently from the gene pool. No mechanism is specified for this inbreeding coefficient. It is simply assumed to result from some genealogical process that happens effectively instantaneously on the time-scale of a coalescent event. Thus the f parameter is the probability that an allele from an individual I1 and an individual I2 are IBD conditional on I1 and I2 having a viable offspring.

With enough loci, it is easy to separate the loss of heterozygosity that comes from selfing versus loss of heterozygosity that comes from other sources. This is because selfing affects different individuals in different ways, having no effect on non-selfed individuals and a large effect on individuals with many generations of selfing. Other sources of inbreeding cause a loss of heterozygosity in all individuals alike.

Install

  1. Install the MCMC program BAli-Phy version 3.5.0 or higher.

    See the full documentation or the quick install documentation.

  2. Install the BES package for bali-phy:

    bali-phy --version
    bali-phy-pkg install BES
    bali-phy-pkg packages
    
  3. Install the BES example scripts:

    git clone https://github.com/bredelings/BayesianEstimatorSelfing.git
    

For further instructions in installation and usage, see the README.pdf

Overview

BES is run as a Unix command line program. It is not a GUI program; instead you must run it in a terminal. Therefore, you might want to keep a Unix Tutorial or Unix cheat sheet handy while you work.

BES runs on Linux, Mac OS X, and Windows. BES is distributed as an extension package for the BAli-Phy inference framework. You might therefore wish to refer to the BAli-Phy Documentation as well.

BES contains a number of modules that correspond to different mating system models. Each model allows estimating a different set of parameters. The generic model and the pure hermaphrodite model without inbreeding depression can be run without modification to estimate the selfing rate and locus-specific mutation rates.

However, the gynodioecious model and the androdiecious model require additional information besides the genetic data, such as (for example) field observations on the fraction of hermaphrodites. Therefore, the user must edit these modules to add this information before attempting to run these models. This manual describes how to add information, but is not a substitute for understanding something about the structure of the model.

Usage

  1. To try a test run, do
cd BayesianEstimatorSelfing
bali-phy -m Generic.hs -l tsv --test --- Examples/outfile.001.70.001.phase1
bali-phy -m Generic.hs -l tsv        --- Examples/outfile.001.70.001.phase1

The script Generic.hs is a template can be modified if you wish to adjust the priors.

  1. If you want to use a FastPhase of Phase2-formatted input file, you can use the Generic2.hs template:
bali-phy -m Generic2.hs -l tsv --test --- Examples/test.fastphase
bali-phy -m Generic2.hs -l tsv --test --- Examples/test.phase2
  1. If you leave off the -l tsv then logging will be done in JSON format.

Installing the development version of BES

Note: You should probably just run bali-phy-pkg install BES instead of doing this!

To install the unreleased development version of BES from github:

git clone https://github.com/bredelings/BayesianEstimatorSelfing.git
cd BayesianEstimatorSelfing
./make_package
bali-phy-pkg install-archive BES_<version>.tar.gz

This will probably require the latest (unreleased) version of bali-phy from github as well.

Contact

You can send questions to the mailing list [https://groups.google.com/forum/#!forum/bayesian-estimator-selfing]. If you don't join the group first, your question will be held until I have a chance to check that it is not spam.

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A Bayesian method for estimating self-fertilization rates and other mating system parameters

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