The Proceedings of the Eighth International Conference on Creationism (2018)

along the branch that leads to the rest. “Using prior knowledge,” Poznik et al. (2016) chose the midpoint between A0 and A1 as the Y root. We deliberately chose to not do this. Thus, the outgroup we used (A0) was not used in any further analyses. B. Within-group variability and all other groups are fixed for either allele. This is really a special case of (A) and increases the likelihood of accurate reconstruction. For every level of branching in the tree, the probability that only one sub-branch contains the original equals the probability that the mutation happened in all other branches, which rapidly becomes vanishingly small. Thus, the more rare the variant, the more likely an accurate call. C. No within-group variability and the outgroup is variable. This is, of course, the reverse of (B). In this case, the ancestral allele is most likely the one fixed in the group, but it depends on the level of branching at which the allele is also found in other groups. Reversions are possible (frequent, in fact, at specific locations in both chromosomes). The more common the allele, and the more branches in which it is found, the more likely it is the original. In these cases, the ancestral allele is set to the “In” value. D. Within-group variability and other groups are also variable. This case requires special tests. Many such situations are due to ‘private’ mutations that occur in only one member of a specific group, and can thus be discounted. These could either be due to repeat mutations or sequencing errors, but either way the probability that the rare group allele is the ancestral allele is small. In an infinite alleles model, this should not be possible. But sequencing errors and the occasional homoplasy do create them, and they have been noted previously (Hallast et al. 2015). Second-pass tests were performed in these cases: first, within-group private mutations were removed and the samples were rerun. If the conflict was not resolved, we considered the ancestral state call for the other groups. If no more than three groups were problematic, and if all other groups unanimously called the same ancestral allele, the ancestral allele in the ambiguous cases were set to “Out” allele. For the few remaining cases, if the majority allele was identical in all groups (both the groups with no variability and the ones with variability), the ancestral allele was set to the majority allele. Poznik et al. (2016) mentioned that pooling sequences into sub- trees first (essentially our method) is computationally more efficient and creates a method less prone to difficulties due to homoplasy. It also leads to simple ancestral state reconstruction. Further, our methods allowed for sorting and visual examination of the data at multiple stages. This allowed for double-checking and validation of multiple conclusions we drew from the analyses that would not have been possible using an off-the-shelf phylogeny package. All Carter et al. ◀ Y Chromosome Noah and mitochondrial Eve ▶ 2018 ICC 136 Figure 3. An unrooted neighbor-joining phylogenetic tree of the Y chromosomes from the Simons Genome Diversity Project. Unlike 1000 Genomes, which sampled heavily from specific populations, SGDP attempted to sample from a much wider range of peoples. The result is a tree that better represents total worldwide Y chromosome diversity. Noah and/or Shem, Ham, and Japheth would be located near the center of the starburst. The scale bar represents approximately 700 mutations.