A Strange New Paternal Lineage

[Update: Waking up this morning I find that the ICR article this was based on has vanished (it may still return at a later date). I have a zotero capture if anyone wants a full copy of it.] [Update #2: It is indeed back now, and I’ve added a TL;DR summary at the bottom.]

In mammals (including humans) most DNA gets mixed together as it gets passed on from generation to generation: chromosomes come in pairs, one from the mother and the other from the father; but when sperm and eggs are produced these chromosomes swap segments, and the chromosome that ends up in a given sperm or egg is entirely random. There are two exceptions to this rule. Mitochondrial DNA (mtDNA) can only be inherited from the mother – though both sexes have it – while the “Y chromosome” is only passed down from father to son.

This property makes these two varieties of DNA extremely useful in tracing ancestry, as distinct lineages can be found and compared. When these lineages are traced backwards they can only merge, never split, and thus will eventually converge to a point. The human mitochondrial genome has famously been traced back to “Mitochondrial Eve,” who lived between somewhere 140 and 240 thousand years ago, probably in Africa. “Y-chromosomal Adam” (which doesn’t roll off the tongue quite as well) meanwhile is only dated to around 60 to 140 thousand years before the present, but lived on the same continent.

This ability to determine ancestry has more mundane uses as well. Due to the slave trade, African-Americans generally know next to nothing about their ancestors prior to their captivity – “African” is an incredibly broad group, with greater diversity than all other continents combined, and slaves were taken from all across Africa. One African-American from South Carolina, in the United States, had his Y chromosome analysed to find out where his ancestors came from. When placed on the tree used to calculate the age of Y-chromosomal Adam it was found that this chromosome diverged from the rest around 338 thousand years ago (237–581 thousand is their 95% confidence interval), pushing back “Adam” at least a hundred thousand years. Searching through the databases of Y chromosome sequence that have been created, 11 Mbo people from Cameroon were found to be relatively closely related to the African American, meaning that he’s not alone in his strange paternal parentage .(N.B.: his genome as a whole is unlikely to be all that unusual, just his paternal line.) The paper in which this is detailed is called “An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree” (pdf), published in early March in the American Journal of Human Genetics.

For today’s article Jeff Tomkins claims that “Modern Y-Chromosome Variation Surpasses Archaic Humans.” What he means is that this new find means that the variation in human Y chromosome sequence is so broad as to encompass Neanderthals and Denisovans, our nearest known relatives, which would allow him to claim that those two groups were “fully human” and (somehow) dismiss evolution. It’s not entirely clear where he gets this idea from, however.

So far as I can tell the data for Neanderthal and Denisovan Y chromosome sequence is a little sketchy. I haven’t managed to find any studies that attempt to directly answer the question of how long ago their Y chromosomes diverged, which is unfortunate as that would be the most useful piece of information here. This new paper doesn’t mention the issue at all, but what it does say is that the ~338 thousand year date is earlier than the fossil date for the earliest “anatomically modern humans” (AMHs), which may be where he’s getting confused. Tomkins incessantly claims that Denisovans and Neanderthals were “fully human,” but in terms of fossils at least they are not counted as “anatomically modern” which is reserved for those which show all the traits of living humans. But just because the 338 split took place before the oldest known AMHs doesn’t automatically mean that it’s older than the split between the lineage of modern humans and the Neanderthals/Denisovans, but that seems to be what Tomkins has assumed.

The Wikipedia article on Neanderthals, for some context, currently claims from fossil evidence that “The first humans with proto-Neanderthal traits are believed to have existed in Europe as early as 600,000–350,000 years ago.” Studies on whole Denisovan and Neanderthal genomes show that they are more closely related to each other than to modern humans, and that all modern human lineages are more closely related to each other than to either. In other words even if this study really did show that the human Y chromosome variation was so large as to include that of Denisovans and Neanderthals it would be in contradiction with all our other evidence to the contrary.

Tomkins goes on to claim:

Not surprisingly, this new discovery confirms the conclusions and predictions first proposed by researchers when the entire Neandertal genome draft sequence was published in 2010. In this report, the authors state, “Neandertals are expected to be more closely related to some present-day humans than they are to each other.” The new Y-chromosome study now fully confirms this hypothesis made by evolutionists themselves.

This is from the 2010 Draft Sequence of the Neandertal Genome. Not only is this not true (as we just saw) it’s also a bit of a quote mine. The full paragraph actually says: (Tomkins quote bolded.)

A challenge in detecting signals of gene flow between Neandertals and modern human ancestors is that the two groups share common ancestors within the last 500,000 years, which is no deeper than the nuclear DNA sequence variation within present-day humans. Thus, even if no gene flow occurred, in many segments of the genome, Neandertals are expected to be more closely related to some present-day humans than they are to each other. However, if Neandertals are, on average across many independent regions of the genome, more closely related to present-day humans in certain parts of the world than in others, this would strongly suggest that Neandertals exchanged parts of their genome with the ancestors of these groups.

The “more closely related to some present-day humans than they are to each other” part is not in terms of the genome when considered as a whole, but just parts of it. But this paragraph also claims that “the two groups [Neanderthals and modern humans] share common ancestors within the last 500,000 years, which is no deeper than the nuclear DNA sequence variation within present-day humans.” I have to question whether or not this is true, but I don’t think that it changes much either way.

Another Y-chromosome study of great importance in the human-origins debate is the recent report of extreme differences between the human and chimpanzee MSY (male determining) regions [MSY actually means “male specific region.”]. The MSY region contains most of the genes in the Y-chromosome. In this report, approximately 50% of the DNA sequence did not even match between chimps and humans. Humans also had twice as many genes as chimps in the MSY region. In fact, the evolutionary authors of the study shockingly note that given “6 million years of separation, the difference in MSY gene content in chimpanzee and human is more comparable to the difference in autosomal gene content in chicken and human, at 310 million years of separation.”

Tomkins mistakenly says in his footnotes that this paper – Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content (pdf) – was published in 2013 (it was really published in early 2010, making it hardly “recent” given this fast-moving field). The quote does check out, however – here’s a blog post on the subject for more information. The changes are impressive, but are most likely due to gene loss in chimpanzees and the creation of new, repetitive sequences. The conclusion that we should draw from the differences seen between the comparisons of Y and normal chromosomes is not that there really is “310 million years of separation,” but that the Y chromosome isn’t following the same rules.

Tomkins adds:

Confirming this stunning human-chimp Y-chromosome data is another recent research report in which the analysis of all chimpanzee chromosomes showed only a 70% DNA similarity on average to human.

This is, of course, his own research, which I really need to get back to looking at. If we were to assume that it was accurate, however, we would have to throw out all the other non-Tomkins numbers we’ve looked at above. Tomkins arrived at his conclusions by rubbishing many of the assumptions made by other researchers (complaints which may or may not be valid), so his figure cannot be compared with any others. His number is also entirely useless on it’s own: it may be true that chimps and humans are only 70% (and not 96%) similar, but Tomkins cannot have his cake and eat it too by leaving the traditional “99%” similarity between living humans unchallenged. He must calculate the similarities between animals he concedes are related for comparison before he can claim that his 70% is too great of a gap to bridge.

Finally, Tomkins concludes that:

• Modern humans, Neandertals, and Denisovans are all part of the same human “created kind.”
• Chimpanzees are simply a type of ape, created distinctly and uniquely as their own “kind.”

And says:

These findings fully confirm the Bible which states in the book of Genesis that all living things were created with distinct genetic boundaries “after their kind.” The Bible also clearly tells us that, concerning mankind’s genetics, God “hath made of one blood all nations of men for to dwell on all the face of the earth” (Acts 17:26).

Kind of a round about way to come to that conclusion, I have to say.

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TL;DR

Tomkins makes a number of different claims here:

• He says that genetic study of Denisovans and Neanderthals have shown them to be “fully human,” but does not elaborate. While if members of either group existed today they would have to be called “human,” their genetics have shown that they form their own group, closely related to living humans. There is the potential for great ambiguity in what “human” actually means in this context giving that we have both living and extinct varieties to consider.
• The main claim is that the new discovery means that human Y chromosome diversity is so broad as to encompass Neanderthals and Denisovans as well. While it’s true that the chromosome found is different enough from that of other living humans that it would have had to have diverged prior to the appearance of the first fossils of “anatomically modern” humans (those that look like living humans, but not Neanderthals or Denisovans), this does not automatically mean that it predates the split between living humans and Neanderthals/Denisovans. It is not clear whether Tomkins has any evidence beyond this for his claim, but it seems unlikely.
• The Y chromosome of humans and chimps are indeed very different, but this is likely more to do with large-scale gene loss and the loss and gain of repetitive regions than anything that would be more difficult to modify via evolution.
• Finally, for a much better look at the “70%” claim, go and read Adam Benton’s recent post on it.