/******************************* ** Global parameters ** *******************************/ title = "test Soay admixture"; nrep = 1; //Number of replicates h2 = 0.2; //Heritability qtlh2 = 0.0; //QTL heritability phvar = 1.0; //Phenotypic variance /******************************* ** Historical population ** *******************************/ begin_hp; hg_size = 1000 [0] //Size of the historical generations 1000 [1000]; nmlhg = 500; //Number of males in the last generation end_hp; /******************************* ** Populations ** *******************************/ begin_pop = "RedMaasai"; begin_founder; male [n = 100, pop = "hp"]; female [n = 100, pop = "hp"]; end_founder; ls = 1; //Litter size pmp = 0.5 /fix; //Proportion of male progeny (default 0.5) ng = 1000; //Number of generations md = rnd; //Mating design (default rnd, random mating) sr = 0.2 0.25 [1] //Replacement ratio for sires 0.2 0.0 [10]; dr = 0.2 0.25 [1] //Replacement ratio for dams 0.2 0.0 [10]; begin_popoutput; stat; genotype /gen 1000; end_popoutput; end_pop; begin_pop = "European"; begin_founder; male [n = 300, pop = "hp"]; female [n = 300, pop = "hp"]; end_founder; ls = 1; //Litter size pmp = 0.5 /fix; //Proportion of male progeny ng = 300; //Number of generations md = rnd; //Mating design sr = 0.2 0.25 [1] //Replacement ratio for sires 0.2 0.0 [10]; dr = 0.2 0.25 [1] //Replacement ratio for dams 0.2 0.0 [10]; begin_popoutput; stat; end_popoutput; end_pop; begin_pop = "SBF"; begin_founder; male [n = 100, pop = "European", gen = 300]; female [n = 100, pop = "European", gen = 300]; end_founder; ls = 1; //Litter size pmp = 0.5 /fix; //Proportion of male progeny ng = 700; //Number of generations md = rnd; //Mating design sr = 0.2 0.25 [1] //Replacement ratio for sires 0.2 0.0 [10]; dr = 0.2 0.25 [1] //Replacement ratio for dams 0.2 0.0 [10]; begin_popoutput; stat; genotype /gen 700; end_popoutput; end_pop; begin_pop = "DF"; begin_founder; male [n = 100, pop = "European", gen = 300]; female [n = 100, pop = "European", gen = 300]; end_founder; ls = 1; //Litter size pmp = 0.5 /fix; //Proportion of male progeny ng = 700; //Number of generations md = rnd; //Mating design sr = 0.2 0.25 [1] //Replacement ratio for sires 0.2 0.0 [10]; dr = 0.2 0.25 [1] //Replacement ratio for dams 0.2 0.0 [10]; begin_popoutput; stat; end_popoutput; end_pop; begin_pop = "BOR"; begin_founder; male [n = 50, pop = "DF", gen = 675]; male [n = 50, pop = "SBF", gen = 675]; female [n = 50, pop = "DF", gen = 675]; female [n = 50, pop = "SBF", gen = 675]; end_founder; ls = 1; //Litter size pmp = 0.5 /fix; //Proportion of male progeny ng = 25; //Number of generations md = rnd; //Mating design sr = 0.2 0.25 [1] //Replacement ratio for sires 0.2 0.0 [10]; dr = 0.2 0.25 [1] //Replacement ratio for dams 0.2 0.0 [10]; begin_popoutput; stat; genotype /gen 25; end_popoutput; end_pop; begin_pop = "SOA_noadm"; begin_founder; male [n = 100, pop = "European", gen = 300]; female [n = 100, pop = "European", gen = 300]; end_founder; ls = 1; //Litter size pmp = 0.5 /fix; //Proportion of male progeny ng = 700; //Number of generations md = rnd; //Mating design sr = 0.2 0.25 [1] //Replacement ratio for sires 0.2 0.0 [10]; dr = 0.2 0.25 [1] //Replacement ratio for dams 0.2 0.0 [10]; begin_popoutput; stat; genotype /gen 700; end_popoutput; end_pop; begin_pop = "SOA_adm"; begin_founder; male [n = 10, pop = "DF", gen = 668]; male [n = 90, pop = "SOA_noadm", gen = 668]; female [n = 10, pop = "DF", gen = 668]; female [n = 90, pop = "SOA_noadm", gen = 668]; end_founder; ls = 1; //Litter size pmp = 0.5 /fix; //Proportion of male progeny ng = 32; //Number of generations md = rnd; //Mating design sr = 0.2 0.25 [1] //Replacement ratio for sires 0.2 0.0 [10]; dr = 0.2 0.25 [1] //Replacement ratio for dams 0.2 0.0 [10]; begin_popoutput; stat; genotype /gen 32; end_popoutput; end_pop; /******************************* ** Genome ** *******************************/ begin_genome; begin_chr = 26; chrlen = 115; //Chromosome length nmloci = 1923; //Number of markers mpos = rnd; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 0; //Number of QTL qpos = rnd; //QTL positions nqa = rnd 2 3 4; //Number of QTL alleles qaf = eql; //QTL allele frequencies qae = rndg 0.4; //QTL allele effects end_chr; end_genome; /******************************* ** Output options ** *******************************/ begin_output; linkage_map; end_output;