Question 1. The initial analysis of genetic variation for both species in this study identified and corrected for any cases of loci that were significantly different from HWE or that showed significant linkage disequilibrium. Given that we know HWE is always violated in real populations and that loci are often linked, why did the authors want to avoid using loci that showed deviations from HWE or that were in linkage disequilibrium?
Question 2. Based on the microsatellite genetic data (= nuclear loci that evolve quickly, hence reflecting “contemporary” genetics per the paper’s terminology), the island racoon species showed genetic evidence of both recent and older bottleneck events, but the coati species did not. Also, the effective population size was much lower for the racoon (Ne = 21.3) vs the coati (Ne = 127.3) island populations. When looking at the cytb haplotype data (= mitochondrial and more slowly evolving, thus showing “historical” genetics per the paper’s terminology), was the same pattern recovered, or did the authors find something different?
Question 3. For the racoon species, every metric indicates very low genetic diversity on the island. This was not the case for the coati island population, as several metrics showed much higher levels of diversity. However, the authors conclude that both species are at risk of extinction due to low genetic diversity. Describe at least one analysis from this study that highlights reduced genetic diversity in the island versus mainland coati populations.