Although our population pairs do share ancestry, this is no guarantee that they are currently segregating the same causative alleles.
Several scenarios were considered, including scenarios with six hypothetical recessive alleles and 12 recessive alleles that are currently segregating in the US Holstein population.
We retrieved natural variation of human individuals from the Hapmap Genome project [28] to identify amino acid altering single nucleotide polymorphisms (SNPs) in NAD metabolic enzymes that are currently segregating in the human population at high frequencies (> 20%, Table 3).
Any mutations that are currently segregating in the population necessarily must have occurred at the position of the mutation at some point in the local genealogy, i.e. it must have happened on an edge of a local genealogy [ 11].
The strong dependence on motif and initial length implies that the average genome mutation rate depends on the relative frequency of the various motif types and on the distribution of allele sizes currently segregating in the population.
The Galileo transposon was discovered in Drosophila buzzatii, where it has caused three large chromosomal inversions, which are currently segregating naturally in the population (Cáceres et al., 1999; Casals et al., 2003; Delprat et al., 2009).
Computer simulation was used to compare four systems of mating applied to scenarios including hypothetical recessive alleles, as well as 12 recessive alleles that are currently segregating in the US Holstein population.
Twelve recessive loci that currently segregate in the US Holstein population were used to determine how the modified Pryce method performed in a commercial livestock population: bovine leukocyte adhesion deficiency (BLAD), brachyspina, CVM, DUMPS, HH1 HH5, horned, mulefoot, and red coat color.
Moreover, the presence of inversion 3f in the Santa Catalina Island population suggests that the flies that colonized this island came from Baja California populations, where this inversion is currently segregating, and not from the Mojave Desert, where this inversion is not present (Delprat et al. 2014).
