cubeAlleleSail: Inheritance Cube: 3-Piece Allele Sail

In MGDrivE: Mosquito Gene Drive Explorer

Inheritance Cube: 3-Piece Allele Sail

Description

A generalized implementation of the Allele Sail (\Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41467-024-50992-9")}) idea.

Usage

cubeAlleleSail(
  cMM = 0,
  crMM = 0,
  cPM = 0,
  crPM = 0,
  cMF = 0,
  crMF = 0,
  cPF = 0,
  crPF = 0,
  dMW = 0,
  dMrW = 0,
  dPW = 0,
  dPrW = 0,
  crF12 = 0.5,
  crM12 = 0.5,
  crF23 = 0.5,
  crM23 = 0.5,
  eta = NULL,
  phi = NULL,
  omega = NULL,
  xiF = NULL,
  xiM = NULL,
  s = NULL
)

Arguments

cMM	Cutting efficacy of maternally-inherited Cas9 in males
crMM	Resistance rate of maternally-inherited Cas9 in males
cPM	Cutting efficacy of paternally-inherited Cas9 in males
crPM	Resistance rate of paternally-inherited Cas9 in males
cMF	Cutting efficacy of maternally-inherited Cas9 in females
crMF	Resistance rate of maternally-inherited Cas9 in females
cPF	Cutting efficacy of paternally-inherited Cas9 in females
crPF	Resistance rate of paternally-inherited Cas9 in females
dMW	Female deposition cutting rate, maternal Cas9
dMrW	Female deposition functional resistance rate, maternal Cas9
dPW	Female deposition (HH) cutting rate, paternal Cas9
dPrW	Female deposition (HH) functional resistance rate, paternal Cas9
crF12	Female crossover rate between loci 1 and 2, 0 is completely linked, 0.5 is unlinked, 1.0 is complete divergence
crM12	Male crossover rate between loci 1 and 2, 0 is completely linked, 0.5 is unlinked, 1.0 is complete divergence
crF23	Female crossover rate between loci 2 and 3, 0 is completely linked, 0.5 is unlinked, 1.0 is complete divergence
crM23	Male crossover rate between loci 2 and 3, 0 is completely linked, 0.5 is unlinked, 1.0 is complete divergence
eta	Genotype-specific mating fitness
phi	Genotype-specific sex ratio at emergence
omega	Genotype-specific multiplicative modifier of adult mortality
xiF	Genotype-specific female pupatory success
xiM	Genotype-specific male pupatory success
s	Genotype-specific fractional reduction(increase) in fertility

Details

This is an autosomal, 3-locus system. The first locus contains the Cas9 allele, the second locus carries the gRNA, and the third locus is the target. All loci can be linked/unlinked to the locus before it (so, 1 to 2 or 2 to 3). Cas9 efficacy due to provenance (mother vs father) is included.

This construct is very similar to our 2-locus Cleave and Rescue design for Oberhofer et. al.(\Sexpr[results=rd]{tools:::Rd_expr_doi("10.1101/2020.07.09.196253")}).

This construct has 3 alleles at the first locus, 2 alleles at the second locus, and 3 alleles at the third locus.

• Locus 1

  • W: Wild-type

  • P: Paternal Cas9

  • M: Maternal Cas9

• Locus 2

  • W: Wild-type

  • G: gRNAs

• Locus 3

  • W: Wild-type

  • R: Resistant 1

  • B: Resistant 2

Female deposition is implemented incorrectly. Right now, it is performed on male alleles prior to zygote formation - it should happen post-zygote formation. Since this construct doesn't have HDR, this should be fine.

Value

Named list containing the inheritance cube, transition matrix, genotypes, wild-type allele, and all genotype-specific parameters.

MGDrivE documentation built on Sept. 9, 2025, 5:42 p.m.