In this series, we explore the genetic evidence that indicates humans became a separate species as a substantial population, rather than descending uniquely from an ancestral pair.
In the last two posts in this series (here and here), we have been exploring the anti-evolutionary arguments of Dr. Vern Poythress in his brief book Did Adam Exist? – specifically, his arguments alleging that that the human and chimpanzee genomes are only 70% identical. As we have seen, this line of argumentation is intended to call human – chimpanzee common ancestry into question, in part because shared ancestry is used in some methods of estimating the ancestral population size of our lineage. Since Poythress intends to argue that human ancestral population genetics cannot establish that humans descend from a population, rather than a pair, attempting to undermine confidence in common ancestry is part of the overall thrust of the book.
As we have seen, the argument in Did Adam Exist? for ~70% identity is as follows (pp. 7-8):
“If the comparison focuses only on substitutions within aligned protein-coding regions, the match is 99 percent. Indels constitute roughly a 3 percent difference in addition to the 1 percent for substitutions, leading to the figure of 96 percent offered by the NIH… But we have only begun. The 96 percent figure deals only with DNA regions for which an alignment or partially matching sequence can be found. It turns out that not all the regions of human DNA align with chimp DNA. A technical article in 2002 reported that 28 percent of the total DNA had to be excluded because of alignment problems, and that “for 7% of the chimpanzee sequences, no region with similarity could be detected in the human genome.”
Even when there is alignment, the alignment with other primate DNA may be closer than the alignment with chimp DNA: “For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions.” The study in question analyzed similarities with orangutan, gorilla, and rhesus monkey, and found cases where human DNA aligns better with one of them than with chimpanzees.
We have already dealt with the first section of the argument, and showed that the 2002 paper Poythress cites cannot bear the weight of his claims for it. Accordingly, we now turn to the second section of the argument – but as we shall see, it too fails to establish what Poythress claims for it.
The main thrust of the argument here seems to be that if a sizeable portion of our genome more closely matches a species other than chimpanzee, then a sizeable portion of our genome is not all that similar to the chimpanzee genome. This is an incorrect assumption, but it will take some effort to understand why.
Perhaps the best way to appreciate how this works is to look at actual DNA sequences. Shown below is a section of 90 bases of DNA from the human, chimpanzee and gorilla genomes:
There are a few things to notice here. First, all three sequences are highly identical to each other, with only a few differences. Second, the human and gorilla sequences are the closest match to each other, with only one difference present. Third, the human and chimpanzee sequences have three differences. This pattern is representative for the sequence nearby as well, outside of what can be shown in a small figure. For a stretch of DNA in this area of the genome, the human and gorilla versions match more closely (98.5% identical) than do the human and chimpanzee versions (98.2% identical). As such, this genome region is part of the 23% of our genome that does not find its closest match in chimpanzees, but rather in gorillas.
The problem for Poythress’s argument should be immediately apparent. The fact that 23% of our genome matches the gorilla genome more closely does not imply that this very same DNA does not also match the chimpanzee genome with very high identity. In fact, this portion of our genome is highly identical to chimpanzees – it’s just that it’s slightly more identical to gorillas. The issue is that the human, chimpanzee and gorilla genomes are all highly identical to each other – but that for some portions of our genome, we are just a tiny bit more identical to gorillas than to chimps.
This observation, of course, raises the question of how this pattern arises between these three genomes. The answer, as it happens, is something we have already discussed in this series: incomplete lineage sorting. Since humans, chimpanzees, and gorillas are all descendants of a common ancestral population, we expect this phenomenon to occur, since not every DNA variant in the original population (i.e the one ancestral to all three descendant species) will sort down to all three modern-day species:
So, what Poythress sees as a problem for common ancestry does not, in fact, support his claim that large swaths of the human genome are dissimilar to the chimpanzee genome. Perhaps the confusion arose from failing to understand just how similar the genomes of humans, gorillas, and chimpanzees are – and that more closely matching gorillas is not at all an indication of dissimilarity with chimpanzees. The pattern produced by incomplete lineage sorting is (ironically enough) predicted by common ancestry – shared ancestry between three species. So, far from being a problem for common ancestry, this pattern is genome-wide evidence for common ancestry.
Having dealt with the human – chimpanzee identity issue, Poythress then shifts his focus to population genetics. His intent is to argue that the evidence we have discussed in this series is unable to conclusively assert that our species descends from a population, rather than a pair. As we will see in the next post in this series, however, this claim is similarly bereft of scientific support.