AFLPsim (version 0.4-2)

hybridize: AFLP simulator with selection from parental data

Description

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

Usage

hybridize(pa,pb,Nf1, Nbxa = Nf1, Nbxb = Nf1, Nf2 = Nf1, type = "selection",
 hybrid = "all", Nsel = Nmarker * 0.1, S = 0)

Arguments

pa

AFLP profile of Parental A. A data.frame or matrix.

pb

AFLP profile of Parental B. A data.frame or matrix.

Nf1

number of AFLP profiles for F1.

Nbxa

number of AFLP profiles for BxA.

Nbxb

number of AFLP profiles for BxA.

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)

Value

• Object hybridsim with:
• PA
  Parental A AFLP profile
• PB
  Parental B AFLP profile
• F1
  F1 hybrid AFLP profile
• F2
  F2 hybrid AFLP profile
• BxA
  Backcross to Parental A AFLP profile
• BxB
  Backcross to Parental B AFLP profile
• Nsel
  Loci under selection (default, under neutral selection)
• S
  Selection coefficient

encoding

latin1

Details

simulates F1, F2, Backcross to Parental A (BxA) and Backcross to Parental B (BxB) with and without selection. Parental profiles must be included (individuals in rows and markers in columns). he 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

hybridsim

Examples

## AFLP profile Species A
SpeciesA<-read.table(system.file("/files/SpeciesA.txt",package="AFLPsim"),header=TRUE, row.names=1)


## AFLP profile Species B
SpeciesB<-read.table(system.file("/files/SpeciesB.txt",package="AFLPsim"),header=TRUE, row.names=1)

## simulate F1 hybrids
F1hybrids<-hybridize(pa=SpeciesA,pb=SpeciesB, Nf1=30, type="neutral", hybrid="F1")