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

for nearly every haplogroup founder there were modern individuals with sequences who were technically outside of his descendent haplogroup(s), yet were actually closer to the founder than many of his living descendants. After replacing the divergence values by rank order, a stronger picture emerges (Fig. 6). For example, in the evolutionary model, “Ancestor A1” is the ancestor of every man in this study. Yet the three sequences in haplogroup A1 were ranked much higher (i.e., closer) to Ancestor A1 than expected. Since there were so fewA1 sequences available, we might discount this observation were it not for further examples. A similar pattern is seen among the sequences in haplogroup B. With the exception of the individuals belonging to haplogroup A, evolutionists believe “Ancestor B” is the ancestor of everyone in this study. Yet, the B individuals were also ranked much higher than expected. And even though the ancestors of haplogroups C and D/E are only four SNVs apart, the sequences in the two groups rank very differently, with the C sequences consistently ranking lower (i.e., further away) than the D/E sequences (some of which are African). Clearly, mutational divergence rates might not be constant in all lineages. Because of this, we used Tukey’s Multiple Comparisons of Means to calculate family-wise 95% confidence intervals for all pair-wise divergence differences among the sequences within each major haplogroup of chrY and chrM (Figs. 7 and 8). Under evolutionary assumptions, all pairs should be equally diverged from their common ancestor. Instead, what is seen is that many family pairs have different degrees of divergence (i.e., there were many statistically significant differences among the group pairs). For example, members of Y chromosome haplogroups A1 and B were significantly less diverged (i.e., picked up fewer mutations in the same amount of time) from Ancestor A1 than members of the other haplogroups. At the same time, haplogroup C was significantly more diverged from Ancestor C than the other descendant haplogroups. The differences between the other groups were smaller, but N/O was significantly more diverged and Q/R was significantly less diverged from Ancestor A1 than all others. Regardless of which common ancestor is used for comparison, we get differential divergence rates among the descendant sequence groups. Among the mitochondrial haplogroups, the one group that stands out is haplogroup L3, which is significantly closer to the L0 ancestor than all other groups except L4/6. Why did the members of this haplogroup accumulate less mutations in the same amount of evolutionary time? The situation is even more profound if Eve is placed at the L3/M root. Patterns like this exist at all scales. Haplogroup H/V/R displays shorter branch lengths than the related groups F and U/K (see Fig. 1), for example, but they were lumped into the macrohaplogroup R for these calculations. The distances (in standard deviations) of all sequences to their haplogroup founder for chrY and chrM are shown as a histogram in Figs. 9 and 10, respectively. Here we see that some sequences are simply more diverged than expected. As we showed above, this is not due to a high false-positive error rate or missing data. As can be seen in the scatter in Figs. 1 and 2, the ‘clock’ does not tick at the same rate in the family lines of every individual. Another way to assess the spectrum of accumulating mutations is by generating a histogram of the number of private mutations, meaning mutations that only appear in a single Y chromosome sequence in the database (Fig. 11). While the status of a private mutation is very much dependent on how closely related other sequences are, this can still give us a rough guess of the allele frequency distribution. Parallel to this, the minor allele frequency plot of Fig. 12 shows that nearly all variants are rare. This is very similar to the mitochondrial data we presented in Carter et al. (2008). The majority of variants between 0.04 and 0.50 are due to structured sampling. That is, if a variant appears along a branch that leads to a major haplogroup, it will appear in all members of that haplogroup. Thus, the three A1 sequences contribute many of the alleles in the <0.01 category and the Q/R individuals contribute many of the 116 alleles in the 0.30–<0.31 category. 8. Improved resolution of polytomies and near-polytomies: A polytomy is a point in a phylogeny where more than two branches arise simultaneously. Under most scenarios, all branches are expected to resolve to dichotomies. Since most new mutations are lost to drift over time, the rise of even a single new branch is uncommon. Thus, it should be exceedingly rare for an individual Carter et al. ◀ Y Chromosome Noah and mitochondrial Eve ▶ 2018 ICC 139 Figure 5. The average distance from each chrY haplogroup ancestor to the members of that haplogroup. Error bars are +1 SD. Figure 6. The average rank of the sequences within each chrY haplogroup to their haplogroup ancestor. Error bars are +1 SD. The red bars indicate the expected average rank based on the number of sequences descended from each ancestor, assuming the evolutionary order. Under the molecular clock hypothesis, if all individuals in this database descend from the ancestral A1 node, the A1 sequences should be randomly distributed among the divergence measurements and have an average rank distribution of approximately 615. Instead, the A1 sequences are among the closest sequences. The same is true for the haplogroup B sequences (after excluding A1). After excluding A1 and B, sequences from haplogroup C are more diverged than expected, even if we lumped them with the closely- related haplogroup D/E sequences. The rest follow independent trends.