SelectedLoci

• 1 Files specific to mode w
  • fitness of SNPs (--fitness)
    • absolute fitness [w]
      • sex specific absolute fitness [w]
    • selection coefficient [s]
      • sex specific selection coefficient [s]
  • epistatic effects of SNPs (--epistasis)
• 2 Files specific to mode qt and qff
  • effect sizes of SNPs (--effect-size)
    • sex specific effect sizes of SNPs (--effect-size)

1 Files specific to mode w

fitness of SNPs (--fitness)

The fitness of selected SNPs may be provided in two distinct ways.
The first line of the file is used to distinguish between these options.

absolute fitness [w]

Allows providing the absolute fitness (w) of all three genotypes (aa, aA, AA) for an arbitrary number of SNPs.
The first line in the file must be [w] (identification of the file format).

The fitness effects of a SNP are specified at a single line. Columns are tab separated.
Every entry has the following form:

chr    pos    a/A     waa    waA    wAA

• chr: chromosome of the SNP
• pos: position of the SNP
• a/A: the two alleles at the SNP in the form a/A (the first character is the a-allele and the second character the A-allele)
• waa: absolute fitness of genotype aa
• waA: absolute fitness of genotype aA
• wAA: absolute fitness of genotype AA

Note an arbitrary number of SNPs may be provided per file
Note For haploids only the fitness of the homozygous genotypes is considered where wa=waa and wA=wAA
Note Hemizygous sex chromosomes are treated like haploids (see note above); hence the fitness of wa=waa and of wA=WAA (the heterozygous effects are thus ignored)

Following an example:

[w]
X        3929069    C/A       0.8    1.0    1.2
X       3929070     A/C      1.1    1.0     0.9
3R      23302904      G/C      1.0    0.8     0.9
2L      11543234      T/C      1.0    1.0     0.8

sex specific absolute fitness [w]

It is also possible to provide sex specific estimates of absolute fitness. This simply requires adding more columns so that we have three entries for males, females and hermaphrodites

chr    pos    a/A     waa_m    waA_m    wAA_m   waa_f    waA_f    wAA_f   waa_h    waA_h    wAA_h

• chr: chromosome of the SNP
• pos: position of the SNP
• a/A: the two alleles at the SNP in the form a/A (the first character is the a-allele and the second character the A-allele)
• waa_m, waA_m, wAA_m fitness of the three genotypes for males
• waa_f, waA_f, wAA_f fitness of the three genotypes for females
• waa_h, waA_h, wAA_h fitness of the three genotypes for hermaphrodites

Note it is possible to mix sex specific estimates with not-sex specific estimates within a single file
Note for clonal evolution we do not recommend to provide sex specific effect sizes; in case they are provided the effect size of the hermaphrodites will be used;

selection coefficient [s]

Allows to provide the selection coefficient (s) and the heterozygous effect (h); From these to parameters the fitness of all three genotypes (aa, aA, AA) can be computed.
The first line in the file must be [s] (identification of the file format).

The selection coefficients for SNP are specified at a single line. Columns are tab separated.
Every entry has the following form:

chr    pos    a/A     s    h

• chr: chromosome of the SNP
• pos: position of the SNP
• a/A: the two alleles at the SNP in the form a/A (the first character is the a-allele and the second character the A-allele)
• s: selection coefficient; Note s may also be negative!
• h: heterozygous effect

Based on s and h the fitness of the three genotypes will be computed

• waa=1
• waA=1+sh
• wAA=1+s

Following an example:

[s]
X        3929069    C/A       0.2    0.5
X       3929070     A/C       0.3    0.5
3R      23302904      G/C     -0.2    0.8
2L      11543234      T/C      1.0    1.0

Note an arbitrary number of SNPs may be provided per file
Note For haploids only the fitness of the homozygous genotypes is considered where wa=waa and wA=wAA
Note Hemizygous sex chromosomes are treated like haploids (see note above); hence the fitness of wa=waa and of wA=WAA (the heterozygous effects are thus ignored)

sex specific selection coefficient [s]

It is also possible to provide sex specific estimates of selection coefficients. This simply requires adding more columns so that we have two entries for males, females and hermaphrodites

chr    pos    a/A     s_m    h_m     s_f    h_f     s_h    h_h

• chr: chromosome of the SNP
• pos: position of the SNP
• a/A: the two alleles at the SNP in the form a/A (the first character is the a-allele and the second character the A-allele)
• s_m, h_m: selection coefficient and heterozygous effect for males
• s_f, h_f: selection coefficient and heterozygous effect for females
• s_h, h_h: selection coefficient and heterozygous effect for hermaphrodites

Note it is possible to mix sex specific estimates with not-sex specific estimates within a single file
Note for clonal evolution we do not recommend to provide sex specific effect sizes; in case they are provided the effect size of the hermaphrodites will be used;

epistatic effects of SNPs (--epistasis)

Allows providing epistatic interactions between pairs of SNPs. The fitness of the nine possible allelic combinations must be provided. Specification of every epistatic interaction requires three rows. The columns are tab-separated.

A single epistatic interaction has the following form:

chr1    pos1    a/A 
chr2    pos2    b/B      
waabb   waabB    waaBB    waAbb    waAbB    waABB    wAAbb    wAAbB    wAABB

• chr1 chromosome of the first SNP
• pos1 position of the first SNP
• the two alleles of the first SNP in the form a/A (the first is a the second A)
• chr2 chromosome of the second SNP
• pos2 position of the second SNP
• the two alleles of the second SNP in the form b/B (the first is a the second A)
• waabb fitness of the genotype aa at the first SNP and bb at the second
• ....
• wAABB fitness of the genotype AA at the first SNP and BB at the second

Note the genotypes Aa and aA are identical (same applies for Bb and bB)
Note the epistasis file may contain an arbitrary number of entries
Note for simulations of haploids or for hemizygous sex chromosome the genotype a will be treated as aa; similarly A will be treated as AA; thus it is not necessary to provide a separate table of epistatic effects for haploids or hemizygous sex chromosomes

Following an example:

1        3929069    C/A      
3R      23302904      G/C      
0.9   0.8   0.9   1.0   0.9    0.8    0.9    1.0    1.1
2L        1000  T/A      
4      1022001      T/C      
0.0   0.0   0.9   1.0   0.9    0.8    1.2    1.0    1.1

2 Files specific to mode qt and qff

effect sizes of SNPs (--effect-size)

Provide the effect sizes of the SNPs contributing to a quantitative trait. Every SNP

Following an example:

X       3929069         C/A       1.1    0
3R      23302904        A/T       0.6    0.5

• col1: chromosome
• col2: position
• col3: the two alleles at the SNP in the form b/B; Homozygous bb will have the genotypic value a and homozygous BB will have the value -a; Heterozygotes will have the genotypic value d
• col4: a additive effect size
• col5: d heterozygous effect size)

Note an arbitrary number of loci may be provided.
Note For haploids only the effect size of the homozygous genotypes is considered; the genotypeb will have the effect size of bb; and similarly the genotypeB will have the effect size of BB
Note Hemizygous sex chromosomes are treated like haploids (see note above)

sex specific effect sizes of SNPs (--effect-size)

It is possible to provide sex specific effect sizes of additive SNPs. It is only necessary to add more columns such that we obtain estimates of effect sizes for males, females, and hermaphrodites.

chr    pos    b/B     a_m    d_m     a_f    d_f     a_h    d_h

• chr: chromosome of the SNP
• pos: position of the SNP
  b/B the two alleles at the SNP in the form b/B; Homozygous bb will have the genotypic value a and homozygous BB will have the value -a; Heterozygotes will have the genotypic value d*
• a_m, d_m additive effect size and heterozygous effect size for males
• a_f, d_f additive effect size and heterozygous effect size for females
• a_h, d_h additive effect size and heterozygous effect size for hermaphrodites