# Demonstrate isofemales

# Creation of isofemale lines

The package GenomeAdmixR was designed to simulate the generation of iso-female lines, and simulate genomic changes during, and after, formation of iso-female lines. Furthermore, it allows for simulation of effects after crossing individuals from iso-female lines.

    library(GenomeAdmixR)
    library(ggplot2)
    packageVersion("GenomeAdmixR")

    ## [1] '2.1.12'

We will analyze whether we can genetically tell apart two populations, where one population was founded by crossing two isofemale lines that were created from the same source population, and the other population was founded by crossing two isofemale lines created from different source populations.

First, we generate two source populations using and then increase the founder labels in the second population to ensure that both populations do not share founder labels.

    pops <-
      simulate_admixture(
            module = ancestry_module(),
            migration = migration_settings(migration_rate = 0,
                                             population_size = c(100, 100),
                                             initial_frequencies =
                                     list(c(1, 1, 1, 1, 0, 0, 0, 0),
                                          c(0, 0, 0, 0, 1, 1, 1, 1))),
         total_runtime = 1000)

    ## Warning in check_initial_frequencies(initial_frequencies): starting frequencies were normalized to 1
    ## Warning in check_initial_frequencies(initial_frequencies): starting frequencies were normalized to 1

    pop_1 <- pops$population_1
    pop_2 <- pops$population_2

To ensure that our two wild populations are not inbred, we estimate the average Linkage Disequilibrium (LD) for both populations using the function calculate_LD. In the absence of inbreeding, we expect the average LD to be low or zero.

    mean(calculate_ld(pop = pop_1,
                      sampled_individuals = 10,
                      markers = 30)$ld_matrix,
         na.rm = TRUE)

    ## [1] 0

    mean(calculate_ld(pop = pop_2,
                      sampled_individuals = 10,
                      markers = 30)$ld_matrix,
         na.rm = TRUE)

    ## [1] 0

Now we can start to generate isofemale lines from both populations, using .

    iso_females_pop_1 <- create_iso_female(
                              module = ancestry_module(input_population = pop_1),
                                           n = 2,
                                           inbreeding_pop_size = 100)
    iso_females_pop_2 <- create_iso_female(
                              module = ancestry_module(input_population = pop_2),
                                           n = 2,
                                           inbreeding_pop_size = 100)

Using the function we then create three populations, two where the isofemales are drawn from the same source population, and one where we mix the two, e.g. 1x1, 1x2 and 2x2, where isofemales 1 and 2 indicate isofemales from source populations 1 and 2 respectively.

    pop_1_1 <- simulate_admixture(
                   module = ancestry_module(input_population = iso_females_pop_1),
                                  pop_size = 1000,
                                  total_runtime = 1000)

    pop_1_2 <- simulate_admixture(
                        module = ancestry_module(input_population =
                                                   list(iso_females_pop_1[[1]],
                                                        iso_females_pop_2[[1]])),
                                   pop_size = 1000,
                                   total_runtime = 1000)

    pop_2_2 <- simulate_admixture(
                    module = ancestry_module(input_population = iso_females_pop_2),
                                  pop_size = 1000,
                                  total_runtime = 1000)

Then, using the function we calculate all pairwise FST values. Here, we expect to find the highest FST for the 1x2 comparison.

    f1 <- calculate_fst(pop_1_1, pop_1_2,
                        sampled_individuals = 10, number_of_markers = 100)
    # this one should be highest
    f2 <- calculate_fst(pop_1_1, pop_2_2,
                        sampled_individuals = 10, number_of_markers = 100)
    f3 <- calculate_fst(pop_1_2, pop_2_2,
                        sampled_individuals = 10, number_of_markers = 100)
    f1

    ## [1] 0.3901849

    f2

    ## [1] 0.3362761

    f3

    ## [1] 0.3303208

Which confirms our hypothesis and demonstrates how combining isofemale lines from different source populations generates a population with maximal genetic diversity.