hybridsim: AFLP simulator with selection

In fbalao/AFLPsim: Hybrid Simulation and Genome Scan for Dominant Markers

Description

This function simulates AFLP profiles (or other dominant markers) of parentals and several hybrid classes (F1 and backcrosses on both parentals). In addition, selection on several markers can be simulated for the hybrid progeny.

Usage

hybridsim(Nmarker, Na, Nb, Nf1, Nbxa = Nf1, Nbxb = Nf1, Nf2 = Nf1,
 type = "selection", hybrid = "all", Nsel = Nmarker * 0.1, S = 0, apa = 0.5, apb = 0.5)

Arguments

Nmarker	The number of AFLP loci to simulate.
Na	number of AFLP profiles for Parental A.
Nb	number of AFLP profiles for Parental B.
Nf1	number of AFLP profiles for F1.
Nbxa	number of AFLP profiles for BxA.
Nbxb	number of AFLP profiles for BxB.
Nf2	number of AFLP profiles for F2.
type	type of simulation: 'neutral' or 'selection'.
hybrid	hybrid classes to simulate. By default 'all'. Also 'F1', 'BxA', 'BxB' or 'F2'.
Nsel	number of loci under selection.
S	Selection coefficient (see Details)
apa	value for parameter 1 of the beta distribution
apb	value for parameter 2 of the beta distribution

Details

Simulate dominant markers (AFLP, RFLP...). Parental allele frequencies are calculated following a beta distribution (Wright 1931). F1, F2, Backcrosses to parental A (BxA) and Backcrosses to parental b (BxB) can be simulated with and without selection. The selection coefficient S is a integer value from -1 to ∞.This coefficient is 0 when there is no selection (similar to type = "neutral") and it varies following negative and positive directional selection (negative and positive values, respectively).

Value

Object hybridsim with:

PA	AFLP profile parental population A
PB	AFLP profile parental population A
F1	AFLP profile F1 hybrid population
F2	AFLP profile F2 hybrid population
BxA	AFLP profile Backcrosses to parental population A
BxB	AFLP profile Backcrosses to parental population B
Nsel	Loci under selection. NA under neutral selection
S	Selection Coefficient

Author(s)

F. Balao [e-mail], J.L. García-Castaño

References

Balao, F. and García-Castaño, J.L. AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations. Plant Methods 10:40

Balao, F., Casimiro-Soriguer, R., García-Castaño, J.L., Terrab, A., Talavera, S. 2013. Big thistle eats the little thistle: Non-neutral unidirectional introgression endangers the conservation of Onopordum hinojense. New Phytologist, in press.

Wright, S. 1931. Evolution in Mendelian Populations. Genetics 16: 97-159.

See Also

hybridize

Examples

hybrids<-hybridsim(Nmarker=100, Na=30, Nb=30, Nf1=30, type="selection", S=10, Nsel=25, hybrid="F1")

fbalao/AFLPsim documentation built on May 16, 2019, 11:09 a.m.