Table 1. Open in new tab Parameters used...

Parameter

Symbol

Typical value

Explanation

Population size

500

The current number of adults in the population

Carrying capacity

500

The number of adults is randomly culled to this number before reproduction (but after selection) each generation

Female fecundity

Number of offspring produced per female

Migration rate

0.016

The proportion of juveniles in a population that originated from the other population

Sample size

100

The size of the simulated sample of adults used for genotyping per population

Number of linkage groups

n_L

The number of linkage groups (chromosomes) onto which the marker loci and QTL are placed

Recombination rate per linkage group

0.25

The expected number of recombination events per linkage group per meiosis during the production of gametes

Number of QTL per linkage group

n_q1, n_q2, n_qP

The number of QTL per linkage group. The QTL fall into 3 categories: those affecting trait 1 (n_q1), those affecting trait 2 (n_q2), and those that are pleiotropic (n_qP).

Number of marker loci per linkage group

n_m

2000

The number of neutral marker loci (e.g., single nucleotide polymorphisms) per linkage group

Marker mutation rate

μ_m

0.0002

The probability per allele per meiosis of a mutation at a marker locus

QTL mutation rate

μ_q

0.0002

The probability per allele per meiosis of a mutation at a QTL

Mutational variances

α₁₁, α₂₂

0.2

The variance of the Gaussian distribution (with mean 0) from which new allelic effects are drawn for the 2 traits when a mutation occurs. This allelic effect is added to an allele’s existing effect.

Mutational covariance

α₁₂

The covariance of a bivariate normal distribution (with means 0) from which allelic effects are drawn when a mutation occurs at a pleiotropic locus

Environmental variance

σ_{E n v}^{2}

The variance of the normal distribution, with mean 0, from which environmental effects are drawn. These effects are added to an individual’s breeding value to determine the phenotype.

Variance in epistatic parameters

σ_{ε}^{2}

0, 1.6

The variance of the normal distribution, with mean 0, from which epistatic parameters are drawn. Larger values result in epistatic parameters with larger absolute effects on average.

Trait optima

θ₁, θ₂

4, −4

The position of the optimum for each trait. Each population has a value of θ₁ (the trait 1 optimum) and θ₂ (the trait 2 optimum), and these values can differ between populations.

Elements of the ω-matrix

ω₁₁, ω₂₂, ω₁₂

49, 49, 0

The ω-matrix specifies the steepness and orientation of the individual selection surface. Lower values result in stronger selection (toward the optimum), and ω₁₂ determines the strength of correlational selection.

Parameter

Symbol

Typical value

Explanation

Population size

500

The current number of adults in the population

Carrying capacity

500

The number of adults is randomly culled to this number before reproduction (but after selection) each generation

Female fecundity

Number of offspring produced per female

Migration rate

0.016

The proportion of juveniles in a population that originated from the other population

Sample size

100

The size of the simulated sample of adults used for genotyping per population

Number of linkage groups

n_L

The number of linkage groups (chromosomes) onto which the marker loci and QTL are placed

Recombination rate per linkage group

0.25

The expected number of recombination events per linkage group per meiosis during the production of gametes

Number of QTL per linkage group

n_q1, n_q2, n_qP

The number of QTL per linkage group. The QTL fall into 3 categories: those affecting trait 1 (n_q1), those affecting trait 2 (n_q2), and those that are pleiotropic (n_qP).

Number of marker loci per linkage group

n_m

2000

The number of neutral marker loci (e.g., single nucleotide polymorphisms) per linkage group

Marker mutation rate

μ_m

0.0002

The probability per allele per meiosis of a mutation at a marker locus

QTL mutation rate

μ_q

0.0002

The probability per allele per meiosis of a mutation at a QTL

Mutational variances

α₁₁, α₂₂

0.2

Mutational covariance

α₁₂

The covariance of a bivariate normal distribution (with means 0) from which allelic effects are drawn when a mutation occurs at a pleiotropic locus

Environmental variance

σ_{E n v}^{2}

The variance of the normal distribution, with mean 0, from which environmental effects are drawn. These effects are added to an individual’s breeding value to determine the phenotype.

Variance in epistatic parameters

σ_{ε}^{2}

0, 1.6

The variance of the normal distribution, with mean 0, from which epistatic parameters are drawn. Larger values result in epistatic parameters with larger absolute effects on average.

Trait optima

θ₁, θ₂

4, −4

The position of the optimum for each trait. Each population has a value of θ₁ (the trait 1 optimum) and θ₂ (the trait 2 optimum), and these values can differ between populations.

Elements of the ω-matrix

ω₁₁, ω₂₂, ω₁₂

49, 49, 0

Table 1.

Open in new tab

Parameters used in the model and their values in the core parameter set

Parameter	Symbol	Typical value	Explanation
Population size	N	500	The current number of adults in the population
Carrying capacity	K	500	The number of adults is randomly culled to this number before reproduction (but after selection) each generation
Female fecundity	2B	4	Number of offspring produced per female
Migration rate	m	0.016	The proportion of juveniles in a population that originated from the other population
Sample size	S	100	The size of the simulated sample of adults used for genotyping per population
Number of linkage groups	n_L	4	The number of linkage groups (chromosomes) onto which the marker loci and QTL are placed
Recombination rate per linkage group	R	0.25	The expected number of recombination events per linkage group per meiosis during the production of gametes
Number of QTL per linkage group	n_q1, n_q2, n_qP	1	The number of QTL per linkage group. The QTL fall into 3 categories: those affecting trait 1 (n_q1), those affecting trait 2 (n_q2), and those that are pleiotropic (n_qP).
Number of marker loci per linkage group	n_m	2000	The number of neutral marker loci (e.g., single nucleotide polymorphisms) per linkage group
Marker mutation rate	μ_m	0.0002	The probability per allele per meiosis of a mutation at a marker locus
QTL mutation rate	μ_q	0.0002	The probability per allele per meiosis of a mutation at a QTL
Mutational variances	α₁₁, α₂₂	0.2	The variance of the Gaussian distribution (with mean 0) from which new allelic effects are drawn for the 2 traits when a mutation occurs. This allelic effect is added to an allele’s existing effect.
Mutational covariance	α₁₂	0	The covariance of a bivariate normal distribution (with means 0) from which allelic effects are drawn when a mutation occurs at a pleiotropic locus
Environmental variance	$σ_{E n v}^{2}$	1	The variance of the normal distribution, with mean 0, from which environmental effects are drawn. These effects are added to an individual’s breeding value to determine the phenotype.
Variance in epistatic parameters	$σ_{ε}^{2}$	0, 1.6	The variance of the normal distribution, with mean 0, from which epistatic parameters are drawn. Larger values result in epistatic parameters with larger absolute effects on average.
Trait optima	θ₁, θ₂	4, −4	The position of the optimum for each trait. Each population has a value of θ₁ (the trait 1 optimum) and θ₂ (the trait 2 optimum), and these values can differ between populations.
Elements of the ω-matrix	ω₁₁, ω₂₂, ω₁₂	49, 49, 0	The ω-matrix specifies the steepness and orientation of the individual selection surface. Lower values result in stronger selection (toward the optimum), and ω₁₂ determines the strength of correlational selection.

Parameter	Symbol	Typical value	Explanation
Population size	N	500	The current number of adults in the population
Carrying capacity	K	500	The number of adults is randomly culled to this number before reproduction (but after selection) each generation
Female fecundity	2B	4	Number of offspring produced per female
Migration rate	m	0.016	The proportion of juveniles in a population that originated from the other population
Sample size	S	100	The size of the simulated sample of adults used for genotyping per population
Number of linkage groups	n_L	4	The number of linkage groups (chromosomes) onto which the marker loci and QTL are placed
Recombination rate per linkage group	R	0.25	The expected number of recombination events per linkage group per meiosis during the production of gametes
Number of QTL per linkage group	n_q1, n_q2, n_qP	1	The number of QTL per linkage group. The QTL fall into 3 categories: those affecting trait 1 (n_q1), those affecting trait 2 (n_q2), and those that are pleiotropic (n_qP).
Number of marker loci per linkage group	n_m	2000	The number of neutral marker loci (e.g., single nucleotide polymorphisms) per linkage group
Marker mutation rate	μ_m	0.0002	The probability per allele per meiosis of a mutation at a marker locus
QTL mutation rate	μ_q	0.0002	The probability per allele per meiosis of a mutation at a QTL
Mutational variances	α₁₁, α₂₂	0.2	The variance of the Gaussian distribution (with mean 0) from which new allelic effects are drawn for the 2 traits when a mutation occurs. This allelic effect is added to an allele’s existing effect.
Mutational covariance	α₁₂	0	The covariance of a bivariate normal distribution (with means 0) from which allelic effects are drawn when a mutation occurs at a pleiotropic locus
Environmental variance	$σ_{E n v}^{2}$	1	The variance of the normal distribution, with mean 0, from which environmental effects are drawn. These effects are added to an individual’s breeding value to determine the phenotype.
Variance in epistatic parameters	$σ_{ε}^{2}$	0, 1.6	The variance of the normal distribution, with mean 0, from which epistatic parameters are drawn. Larger values result in epistatic parameters with larger absolute effects on average.
Trait optima	θ₁, θ₂	4, −4	The position of the optimum for each trait. Each population has a value of θ₁ (the trait 1 optimum) and θ₂ (the trait 2 optimum), and these values can differ between populations.
Elements of the ω-matrix	ω₁₁, ω₂₂, ω₁₂	49, 49, 0	The ω-matrix specifies the steepness and orientation of the individual selection surface. Lower values result in stronger selection (toward the optimum), and ω₁₂ determines the strength of correlational selection.

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