Our paper will report an analysis of the history of the human Y chromosome. Thousands of full-length Y chromosome sequences from multiple world populations have recently become available for the first time. This data gives us an unprecedented opportunity to look backwards into human history. The Y chromosome is ideal for such analysis because it combines direct paternal inheritance with no recombination along most of its length. Any newly arising mutation that first appears in any male child will be directly inherited by every descendant of that male. This means that every branch on a phylogenetic tree of the Y chromosome reveals a historical individual, who lived at a specific time, and who is the founder (patriarch) of a unique lineage.
We use a technique called ancestral reconstruction to calculate the sequences of the major haplogroup and macrohaplogroup founders. We then compare the Y chromosome sequence of each founder to their descendants, and also to the other founders. We report three basic findings.
First, we report the sequence of each founder patriarch. We will show that three of the earliest patriarchs were very closely related. It is clear that most human male lineages trace back to just a few men who were separated by a surprisingly few number of mutations. This is remarkably consistent with the biblical account of how all males were derived from three brothers (Shem, Ham, and Japheth).
Second, we report that different lineages appear to have mutated at a different rates, suggesting that the molecular clock is not reliable. This directly contradicts one of the major assumptions behind the out-of-Africa hypothesis.
Third, we approximate the sequence of the common ancestor of the three primary patriarchs. It is possible this common ancestor is the Biblical Noah, sitting at the center of our Y chromosome phylogenetic tree. The sequence of this person, in turn, may represent a reasonable approximation of Adam’s Y chromosomal sequence. Lastly, we will attempt to put a time interval between Noah/Adam and his living descendants using published y-chromosome mutation rates, while allowing for divergent mutation rates among various lineages.