Feature Article - May 2018
by Do-While Jones

Ancestry From DNA

Can DNA be used to trace our evolutionary history?

Three recent headlines caught our attention and started us thinking about DNA analysis: “Reconstructing the genetic history of late Neanderthals;” 1 “African DNA hints at mystery hominin species;” 2 and “Use and Abuse of ancient DNA.” 3 The first of these three articles is the most important—but we might not have noticed it if not for the other two articles appearing at nearly the same time.

Politics

The third article, about the use of DNA data, was primarily political.

Simplistic readings of culture history have encouraged people with political agendas to falsely draw clear boundaries between the behaviour and the claimed territory of some ancient (and not-so-ancient) populations — and to infer similarities with their claimed modern equivalents. … They became notorious following their use by the Nazi party to legitimize its territorial goals and beliefs about the racial superiority of German-speaking peoples. 4

The editors of Nature were concerned that dubious DNA analysis might be used to advance a political agenda. We are concerned because dubious DNA analysis certainly is used to advance an evolutionary agenda, which is both political and religious.

Speculation

The New Scientist article about DNA hinting at a mystery species is an excellent example of dubious DNA analysis.

It appears the ancestors of modern Yoruba interbred with members of a distinct population, but it’s not clear what this “ghost lineage” was. It might have been a group of Homo sapiens that remained isolated from the rest of the population for thousands of years, or it may have been another hominin species altogether. 5

The notion of a “ghost lineage” is not really scientific—and, they say, “it may have been another hominin species altogether.”

The study is a reminder that our species did not emerge from a single founding population, says Thomas. Instead, there were many populations scattered across Africa, many of which remained isolated and evolved on their own for thousands of years before coming back together with their neighbours. 6

No, the study is really a reminder that people can get papers that are nothing more than foolish speculation published in New Scientist.

Neanderthal Ancestry

That brings us to the first article, which says:

Analyses of the first Neanderthal genomes have provided evidence of gene flow from Neanderthals into modern humans between 50,000 and 60,000 years ago (ka), resulting in around 2% of Neanderthal DNA in the genomes of non-Africans today. Additionally, genetic analyses of an approximately 39,000–42,000-year-old modern human from Romania (Oase 1) showed that interbreeding between Neanderthals and modern humans also happened in Europe at a later point in time. However, little is known about the diversity of late Neanderthal populations across Europe and western Asia shortly before their disappearance, or about their relationship to the population that admixed with early modern humans. To date, only a handful of Neanderthal remains have been identified with a sufficiently high content of endogenous DNA and low enough levels of microbial and human DNA contamination to allow analysis of larger parts of their genomes, limiting our ability to study their genetic history. 7

Given all the weasel words at the end of the previous paragraph, how much confidence can one have in the conclusion in the first part of that paragraph? “Little is known.” There is only a “handful” of remains that (they think) aren’t contaminated with modern DNA. They weren’t kidding when they said their ability to study the genetic history was limited.

We estimated the population split times between each of the low-coverage Neanderthal genomes and the two high-coverage Neanderthal genomes by determining the fraction of sites at which each of the low-coverage Neanderthal genomes shares a derived allele that occurs in the heterozygote state in one of the high-quality genomes (F(A|B) statistics). This fraction was then used to estimate the population split times for each pair of Neanderthals using previous inferences of how Neanderthal population sizes changed over time. Owing to the uncertainties in the mutation rate and generation times, we caution that although the times presented are likely to accurately reflect the relative ages of the population split times, the absolute estimates in years are approximate. 8

They used just the fraction of the DNA that they think shared a derived allele for their estimates. What if they had used a different fraction?

After estimating the time when modern humans split from Neanderthals (who really existed), they estimate (with 95% confidence) when modern humans split from the mythical Denisovans (who probably never even existed).

The estimates of the population split times from the common ancestors shared with the Denisovan and with modern humans are around 400 ka (95% confidence interval, 367–484 ka) and about 530 ka (95% confidence interval, 503–565 ka; Extended Data Table 4 and Supplementary Information 8), respectively, consistent with previous estimates using the Altai and Vindija 33.19 Neanderthal genomes. 9

We’ve told you about the mythical Denisovans in previous newsletters,10 11 12 so we won’t repeat that discussion here.

As always, more money is needed to solve the problem.

We caution that given the small number of analysed Neanderthals we cannot exclude that such gene flow occurred. … Further work is necessary to determine whether this was the case. 13

In the METHODS section, they explained which parts of the DNA molecule they compared, and how they rearranged the data from the samples to make the comparisons. Of course, they would have gotten different results if they had used different parts of the DNA molecule for their comparison.

How do we know this? We know this from Lezlie’s DNA.

Lezlie’s DNA

According to the AncestryDNA website,

Growing up, Lezlie had always encountered curiosity about her ethnicity from people she'd meet. “I probably got the question 3 to 4 times a week if I was Asian or Moroccan or something else,” she shared. So she jumped at the opportunity to find out through AncestryDNA.

And it turns out, Lezlie's DNA results did include African, European, and Asian. “It was great because it helped confirm what I knew in my gut… with a little surprise.” 14

Where’s the Chimp?

The little surprise is that Lezlie is 0% chimpanzee. Evolutionists love to tell us that human DNA is 96% to 98% identical to chimpanzee DNA, which they claim is convincing proof that men and chimpanzees had a close common ancestor. If that is true, the pie chart should show Lezlie is 98% chimpanzee. And the other 2% should be the Neanderthal DNA that Hajdinjak claimed is in non-Africans today!

As we have shown in previous newsletters, 15 16 one must compare the “right” parts of the DNA molecule to get the desired result.

The AncestryDNA test uses microarray-based autosomal DNA testing, which surveys a person's entire genome at over 700,000 locations, all with a simple saliva sample. 17

What is a “Location?”

The human genome consists of more than three billion base pairs divided into 46 chromosomes. Each chromosome contains lots of genes. We know, “lots” isn’t very specific—but we don’t really know how many genes there are, and we aren’t alone in our ignorance.

The meeting coincided with the publication of three reports in the June issue of Nature Genetics, each describing a different approach to calculating the number of human genes; the estimates ranged from 28,000 to 120,000. 18

So, each of the 700,000 locations must be smaller than a single gene. Since AncestryDNA is trying to impress potential customers with the largest number possible, a location is probably just a base pair (but it could be an arbitrarily small gene fragment). If so, then they are analyzing just 0.02% of the DNA molecule.

They warn us,

The AncestryDNA test may predict if you are at least partly Native American, which includes some tribes that are indigenous to North America, including the U.S., Canada and Mexico. The results do not currently provide a specific tribal affiliation. (Please note that your AncestryDNA ethnicity results cannot be used as a substitute for legal documentation.) 19

If their DNA analysis is accurate, shouldn’t it be more reliable than legal documentation?

Why Does it Matter?

Let’s summarize our main point and explain why we think it is important.

The computed numerical value depends upon how the data is processed. That is, it depends upon what parts of the DNA are chosen to be compared. Presumably, the parts are chosen because they are assumed to be the most diagnostic—but how do they know which parts are most diagnostic? Is it because analysis of those particular parts gives the most “reasonable” result? And, is the result judged to be “reasonable” because it confirms expectations?

AncestryDNA decided to compare certain locations to determine ethnic ancestry. We believe they had good reasons for making the choices they did, and that they believe they made the correct choices. We aren’t saying that they made bad (or dishonest) choices; but we are saying that any other geneticists might have had other equally good reasons for making other choices which could have produced significantly different results.

The fact is, even with an abundance of uncontaminated genetic material to work with, ancestry determination from DNA analysis is questionable. Therefore, ancestral connections between modern humans, Neanderthals, and Denisovans based on fragmentary DNA material (some of which has had thousands of years to degrade) is worthless.

In the same way, the fictional ancestral connection between humans and apes is based on partial comparisons of human and ape DNA. In fact, in a previous article 20 we extensively quoted the peer-reviewed research published in a respected scientific journal which said they were only able to find 1% of the ape and human genomes that were similar enough to compare (after some rearrangement) and concluded that the 1% they were able to compare was 98% identical.

Why Ancestry Matters

Why does it matter if Lezlie is 35% British and 2% Asian and not 35% Asian and 2% British? Lezlie said she just wanted to know so that she could answer the rude questions she gets 3 to 4 times a week. Why do people ask her insensitive racial questions? Ethnicity shouldn’t matter—but unfortunately it does matter in America because of racial politics.

One well-known example involves a certain (white) American politician who earned the nickname Pocahontas (or Faux-cahontas) because she falsely claimed to have Native American ancestry in order to get an unfair advantage over other applicants for a teaching job.

Non-whites are given special treatment in America because some politicians believe that non-whites can’t compete with whites on a level playing field, and have passed race-based laws to make it easier for people of allegedly inferior races to succeed. And, as we saw at the beginning of this essay, ancestry also has an impact upon territorial claims in the Middle East, and possibly other places. Politics largely determines “scientific” conclusions.

In the same way, “reconstruction of the genetic history of late Neanderthals” matters because it advances a political agenda.

The New Scientist study we quoted at the beginning of this essay claimed that our species did not emerge from a single founding population. It attempts to preserve the idea that humans evolved from apes while debunking the traditional evolutionary notion that Africans have not evolved as much as Europeans have. It is more politically correct to believe that all the different human races evolved independently from apes, so no one race is superior.

Nobody would care about ancestry or evolution if not for racist or political reasons.

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Footnotes:

1 Hajdinjak, et al., Nature, 29 March 2018, “Reconstructing the genetic history of late Neanderthals”, pages 652–656, https://www.nature.com/articles/nature26151
2 New Scientist, 7 April, “African DNA hints at mystery hominin species.”, page 9, https://www.newscientist.com/article/2165308-dna-from-another-mystery-human-ancestor-lingers-in-some-people/
3 Nature, 28 March 2018, “On the use and abuse of ancient DNA”, page 559, https://www.nature.com/articles/d41586-018-03857-3
4 ibid.
5 New Scientist, 7 April, “African DNA hints at mystery hominin species.”, page 9, https://www.newscientist.com/article/2165308-dna-from-another-mystery-human-ancestor-lingers-in-some-people/
6 ibid.
7 Hajdinjak, et al., Nature, 29 March 2018, “Reconstructing the genetic history of late Neanderthals”, pages 652–656, https://www.nature.com/articles/nature26151
8 ibid.
9 ibid.
10 Disclosure, July 2011, “Ancestor Arguments”, http://scienceagainstevolution.info/v15i10f.htm
11 Disclosure, July 2013, “Denisovans”, http://www.scienceagainstevolution.info/v17i10n.htm
12 Disclosure, January 2014, “DNA Stunner”, http://www.scienceagainstevolution.info/v18i4n.htm
13 Hajdinjak, et al., Nature, 29 March 2018, “Reconstructing the genetic history of late Neanderthals”, pages 652–656, https://www.nature.com/articles/nature26151
14 https://www.ancestry.com/dna/
15 Disclosure, January 2003, “98% Chimp”, http://scienceagainstevolution.info/v7i4f.htm
16 Disclosure, October 2005, “Chimps Are Like Us”, http://scienceagainstevolution.info/v10i1f.htm
17 https://www.ancestry.com/dna/
18 Bijal P. Trivedi, Genome News Network, 26 May 2000, “How many human genes?”, http://www.genomenewsnetwork.org/articles/05_00/how_many_genes.shtml
19 https://www.ancestry.com/dna/
20 Disclosure, January 2003, “98% Chimp”, http://scienceagainstevolution.info/v7i4f.htm