Where multiple paternity was detected clearly, the program GERUD [38] was used to estimate the minimum number of males and to infer the most possible genotypes of males.
However, for rare variants, most of these possible genotype groups will not be seen because of low MAF, and, instead, we observe only M + 1 patterns, denoted P0, P1, …, P M, where P 0 represents a pattern of common homozygotes only.
Results from sequence analyses showed that most pair wise associations among X, 2L and 3L markers were present in the overall sample: 7 of 9 possible genotype associations between X and 2L, all possible associations between X and 3L, and 8 of 9 possible associations between 2L and 3L (Table S2).
All possible genotype combinations were observed in the control and dead mosquitoes, whereas only three genotypes were recorded in surviving mosquitoes, most of which were either double heterozygotes (L1014F/L1014S) or homozygotes for the "West African" kdr mutation (L1014F/L1014F).
This would put most possible attackers off.
If there are no epistatic incompatibilities among beneficial mutations, and if there is only one most fit genotype out of all possible genotypes, parallel evolution is likely to occur [22], [23].
In most applications SNPs are diallelic, resulting in three possible genotypes.
The probability P(s i = 1) thus depends on the genotype of animal i, denoted g i. Posit a set of n possible genotypes ranked by increasing susceptibility: G1 corresponds to the most resistant genotype, while G n corresponds to the most susceptible one.
Both strategies, selecting the most likely genotype and selecting the posterior distribution of all possible genotypes, have demonstrated the capacity to improve power in follow-up association analysis [5], [6], [16].
