RecombinationRate
1 Recombination rate (--recombination-rate)
MimicrEE2 allows providing the recombination rate in three different ways. The lambda value of a Poisson distribution, the fraction of recombined gametes or the centi-Morgan per megabase may be provided. The recombination rate has to be provided for windows. The first line of the recombination rate file is used to distinguish between the options. All columns should be tab-delimited.
Note it is not allowed to provide a recombination rate for simulations of clonal evolution; an error message will be shown
2 Lambda-value of a Poisson distribution
[lambda] 2L:4500..4600 0.02 2L:4600..4700 0.0115 2L:4700..4800 0.01 2L:4800..4900 0.01
- col1: the position of the recombination window in the form: chromosome:start..end
- col2: the lambda value of a Poisson distribution. This lambda will be used to generate a Poisson distributed random number, i.e. the number of crossovers in the given window
Note in the above example the recombination windows are not overlapping; the actual start position used by MimicrEE2 is 'start+1' (eg 4501 for 4500), while the end position is used as provided by the user.
3 Recombination fraction
[rf] 2L:4500..4600 0.00094 2L:4600..4700 0.00088 2L:4700..4800 0.00258 2L:4800..4900 0.00480
- col1: the position of the recombination window in the form: chromosome:start..end
- col2: the recombination fraction for the window, i.e the probability that markers at the boundaries of the window will recombine; must be smaller than 0.5; MimicrEE2 is translating the rf into the lambda-value of a Poisson distribution using Haldane's map function (1919), thus double, triple, etc crossovers may occur in windows, especially in windows with a rf close to 0.5).
Note If your species has no recombination in males (e.g. Drosophila) you should provide half the recombination fraction of females.
4 CentiMorgan per Mb
[cM/Mb] 2L:4500..4600 4.2 2L:4600..4700 10.0 2L:4700..4800 12.1 2L:4800..4900 13.2
- col1: the position of the recombination window in the form: chromosome:start..end
- col2: the recombination rate in centi-Morgan per megabase for the window. Must be smaller than 50. MimicrEE2 translates this value into the lambda-value of a Poisson distribution using Haldane's map function (1919).
5 Sex specific recombination rate
MimicrEE2 allows providing different recombination rates for males, females and hermaphrodites. This could be achieved by simply adding two more columns to the recombination file. Sex specific recombination rates are supported for all three input formats of the recombination rate ([cM/Mb], [rf] and [lambda]). Following an example using centiMorgan per megabase:
[cM/Mb] 2L:4500..4600 4.2 0.0 1.0 2L:4600..4700 10.0 0.3 10.0 2L:4700..4800 12.1 0.6 12.1 2L:4800..4900 13.2 0.5 3.0
- col1: the position of the recombination window in the form: chromosome:start..end
- col2: recombination rate for males
- col3: recombination rate for females
- col3: recombination rate for hermaphrodites
Note if only two columns are provided an identical recombination rate will be used for all three sexes
Note sex specific entries (4 columns) and non-sex specific entries (2 columns) may be mixed within a single file; Hence sex specific recombination may easily be provided just for some chromosomes or chromosomal regions.
6 Recombination rate for haploid organism
For simulations of haploids a recombination rate may be provided. Haploids will transiently form a diploid zygote where recombination may take place. It is not possible to assign a sex to the transient diploid stage. MimicrEE2 will thus always use the recombination rate of hermaphrodites for haploid organisms.
The following two examples of recombination files are equivalent for haploid simulations:
[cM/Mb] 2L:4500..4600 1.0 2L:4600..4700 10.0 2L:4700..4800 12.1 2L:4800..4900 3.0
[cM/Mb] 2L:4500..4600 0.0 0.0 1.0 2L:4600..4700 0.0 0.0 10.0 2L:4700..4800 0.0 0.0 12.1 2L:4800..4900 0.0 0.0 3.0
