simPedDFC: Double first cousin pedigree construction

In matthewwolak/nadiv: (Non)Additive Genetic Relatedness Matrices

Double first cousin pedigree construction

Description

Simulates a pedigree for the “double first cousin” mating design (Fairbairn and Roff 2006).

Usage

simPedDFC(F, gpn = 4, fsn = 4, s = 2, fws = 2, prefix = NULL)

Arguments

F	Number of blocks for the design
gpn	Number of grandparent pairs in the 0/GP generation (must be >= 2). Equals the number of full-sib families in the 1/P generation.
fsn	Number of offspring in each full-sib family of the 1/P and 2/F1 generations (must be an even number >= 4).
s	Number of sires per full-sib family in the 1/P generation (must be >=2)
fws	Number of 1/P generation families with sires. Together, with s, sets up how cousins and double first cousins are produced
prefix	Optional prefix to add to every identity

Details

This is an adaption to a half-sib breeding design which also produces first cousins and double first cousins. Double first cousins are produced by mating two brothers to two sisters (the offspring of the resulting two families are double first cousins with one another). This is described in Fairbairn and Roff (2006) as being particularly effective for separating autosomal additive genetic variance from sex chromosomal additive genetic variance. It is also amenable to estimating dominance variance, however, it still has difficulty separating dominance variance from common maternal environmental variance (Meyer 2008).

For a given unit of the design (F total), 2*gpn 0-generation (grandparental or GP) individuals are created and paired to make gpn full-sib families. Then the first fws families are each allocated s males/sires and s*(fws-1) females/dams in the 1/P generation. The remaining (gpn-fws) families (only when: gpn > fws) are assigned s*fws females/dams. If fsn > (s*fws), the remaining 1/P generation individuals in each full-sib family (fsn - (s*fws)) are allocated to each family with equal numbers of females and males (this allows for more individuals to be phenotyped in the 1/P generation than are used to produce the 2/F1 generation). The 2/F1 generation is then assigned, based on the mating design in Fairbairn and Roff (2006) - essentially each sire (of the s per full-sib family in the 1/P generation) is mated to a female from each of the other gpn-1 full-sib families to produce fsn offspring (with equal numbers of females and males).

Value

A data.frame with columns corresponding to: id, dam, sire, and sex. Sex is M for males and F for females.

Author(s)

[e-mail]

References

Fairbairn, D.J. and D.A. Roff. 2006. The quantitative genetics of sexual dimorphism: assessing the importance of sex-linkage. Heredity 97:319-328.

Meyer, K. 2008. Likelihood calculations to evaluate experimental designs to estimate genetic variances. Heredity 101:212-221.

See Also

simPedHS, warcolak

Examples

  DFC1 <- simPedDFC(F = 1, gpn = 2, fsn = 4, s = 2, fws = 2)

matthewwolak/nadiv documentation built on July 7, 2023, 1:24 p.m.