gl.sim.cross {dartR.base}

Generates random crosses between fathers and mothers

Description

Generates random crosses between fathers (in one genlight object) and mothers (in a second genlight object) then randomly selects a specified number of offspring to retain.

Usage

gl.sim.crosses(
  fathers,
  mothers,
  broodsize = 10,
  sexratio = 0.5,
  n = 1000,
  error.check = TRUE,
  compliance.check = TRUE,
  verbose = NULL
)

Arguments

fathers

Genlight object of potential fathers [required].

mothers

Genlight object of potential mothers simulated [required].

broodsize

Number of offspring per mother [required].

sexratio

Sex ratio of simulated offspring [default 0.5].

n

Number of offspring to retain [default 1000 or mothers*broodsize whichever is the lesser]

error.check

If TRUE, will perform error checks on the provided parameters [default TRUE]

compliance.check

If TRUE, will perform a compliance check on the resultant genlight object before returning it [default TRUE]

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default NULL, unless specified using gl.set.verbosity]

Details

This script is to be used in conjunction with gl.subsample.ind() applied initially to a base genlight object containing initial male and female genotypes. The workflow is to

(a) Select the males from the base genlight object using gl.keep.pop() with pop.list="male" and the as.pop parameter set to sex. (b) Select the females from the base genlight object using gl.keep.pop() with pop.list="female" and the as.pop parameter set to sex. (c) Subsample a cohort of males for breeding and a cohort of females for breeding using gl.subsample.ind() and the replace parameter as follows:

To enforce monogamy – generate the fathers and mothers from the base genlight object using gl.subsample.ind() with replace=FALSE. To admit polygyny – generate the fathers from the base genlight object using gl.subsample.ind() with replace=FALSE and the mothers from the base genlight object using gl.subsample.ind() with replace=TRUE. To admit polyandry – generate the fathers from the base genlight object using gl.subsample.ind() with replace=TRUE and the mothers from the base genlight object using gl.subsample.ind() with replace=FALSE. To admit promiscuity – generate the fathers and mothers from the base genlight object using gl.subsample.ind() with replace=TRUE.

These are simple scenarios that leave the number of maternal mates per father (polygyny) and the number of paternal mates per mother (polyandry) to chance, depending on the random selection of males and females with replacement from the base genlight object.

(d) Cross the males with the females using gl.sim.crosses() retaining a subset of offspring at random.

So the input for this function is a genlight object with a sample of male individuals (fathers) selected from a larger set at random with or without replacement; a similar sample of female individuals in a second genlight object (mothers); specified broodsize; and desired offspring sex ratio.

Set check.error to FALSE if using this script in simulations

Value

A genlight object with n offspring of both sexes.

Author(s)

Custodian: Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)