AFLPsim (version 0.4-2)

hybridsim: AFLP simulator with selection

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

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

encoding

latin1

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 $\infty$.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).

References

Balao, F. and Garc�a-Casta�o, 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., Garc�a-Casta�o, 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")