Relatedness analysis

Analyses of population structure are generally biased when closely-related individuals such as full-siblings are included in the analyses [59]. To identify full-sibling relationships among our samples, we calculated Loiselle’s k [60] using the program SPAGeDi [61]. First and second-degree kin relations can be ascertained with confidence using large SNP datasets [33, 41, 62–64], wherein individuals with pairwise k > 0.1875 are full-siblings, and those with 0.1875 > k > 0.09375 are half-siblings, if each pair is assigned the most likely kinship category [65]. We sampled one individual from each putative full-sibling group with the smallest percentage of missing data, leaving 116 individuals for analysis of genetic structure.

We were also interested in observing related pairs at different sampling sites. Larval Ae. aegypti full-siblings have been caught in traps up to 1.3 km apart [33], well above the active dispersal range of Ae. albopictus [11, 34–37]. As the minimum distance between sites in this study was more than double this distance, movement at these scales would most likely also be human-mediated. To avoid incorrectly identifying the relationship of closely-related pairs we used the program ML-Relate [66] to perform specific hypothesis tests of relationship. For each pair we ran one test that estimated the relationship assuming that the kinship category assigned using k was more likely than the next most likely kinship category, followed by tests that assumed that the kinship category assigned using k was less likely to be correct. Thus, for pairs with k > 0.1875, tests would determine whether the pair were full-siblings or half-siblings, while for pairs with 0.1875 > k > 0.09375 tests would help determine whether the pair were full-siblings, half-siblings or unrelated. Tests were run using 10,000,000 simulations of random genotype pairs for each.