Paper: Recent mitochondrial DNA barcoding results bode well for the recent origin of species

A recent¹ review paper proposed a controversial claim—that the vast majority of animal species arose contemporary with modern humans. Not surprisingly, this claim was met with backlash from the evolutionary community. On what basis did the authors make this wide-reaching claim? Is their assertion true? Furthermore, what ramifications do their data have for the creationist explanation of the origin of species from the originally created min or “kinds”?

The main focus of Stoeckle and Thaler’s paper is genetics. Specifically, they focus on a subset of DNA in human and animal cells, termed mitochondrial DNA (mtDNA). Their analysis of mtDNA is clear, straightforward, and carefully justified—so much so that I will summarize their arguments by liberally quoting from their paper.

DNA Barcoding

About 15 years ago, “DNA barcoding was first proposed as a tool for practical taxonomy.”² Taxonomy is the field of science concerned with the classification of life, and scientists thought that taking small subsets of DNA would aid in identifying and classifying species. “The particular mitochondrial sequence that has become the most widely used” is “the 648 base pair (bp) [think of base pairs as DNA letters] segment of the gene [a subsection of DNA sequence] encoding mitochondrial cytochrome c oxidase subunit I (COI).”³

With a subset of a subset of DNA, “Skeptics of COI barcoding raised a number of objections about its power and/or generality as a single simple metric applicable to the entire animal kingdom, including: the small fraction of the genome (about 5% of the mitochondrial genome and less than one millionth of the total organism’s genome [total DNA in an organism]) might not be sensitive or representative.”⁴

A simple example from humans illustrates this concern. For instance, on average any two humans differ at 0.2%–0.5% of their mtDNA base pairs. Theoretically, if all mtDNA differences are evenly distributed around the human mtDNA genome, you would expect 1–2 mtDNA differences in each individual’s 648 bp COI barcode. With numbers this low, one generation of an extra mutation or two in the COI barcode sequence might throw a real classification pattern (i.e., one based on comparisons of hundreds of anatomical and physiological features) into confusion.

However, since the early days of DNA barcoding, such objections have been mostly mollified. I can attest to this from my own experience in handling thousands of mtDNA sequences. As a representative of the mtDNA diversity among species and individuals, a subset of mtDNA sequence is a good first approximation. Though subsets aren’t always perfect representations of the whole sequence, they are good initial data points.

Furthermore, over several decades of mtDNA barcoding, scientists have discovered a specific clustering pattern among mtDNA barcodes from individuals across diverse species: “a general observation is that barcode clusters correspond best to species in well-studied animal groups, where taxonomists have mostly decided and agreed upon what species are. Thus there is good support in several major phyla, including Chordata [e.g., vertebrates and a handful of other species], Arthropoda [e.g., insects, arachnids, and crustaceans], Mollusca [e.g., shellfish, octopi], Echinodermata [e.g., starfish]. We note that these phyla are estimated to contain about 3⁄4 of named animal species.”⁵

This fact has two major ramifications: “First, the cluster structure of the animal world found in COI barcode analysis is independent of any definition(s) of species. Second, domain experts’ judgments of species tend to agree with barcode clusters and many apparent deviations turn out to be ‘exceptions that prove the rule.’”⁶ In other words, the initial fears of those skeptical of DNA barcoding have not been met. Instead, barcoding has been very successful.

Barcoding and the Origin of Species

In light of these successes, the authors acknowledge the unexpected implications for explanations for the origin of species: “At its origin DNA barcoding made no claim of contributing to evolutionary theory,”⁷ yet “the pattern of DNA barcode variance is the central fact of animal life that needs to be explained by evolutionary theory.”⁸

Expanding our scope beyond the narrow evolutionary focus of the authors, we can generalize their statement: These mtDNA barcode patterns need to be explained by any model purporting to account for the origin of species.

The barcode patterns take a very specific form: “the clustering structure of COI barcodes—small variance within species and often but not always sequence gaps among nearest neighbor species” is “the primary fact that a model of evolution and speciation must explain.” Furthermore, “the average pairwise difference among individuals (APD; equivalent to population genetics parameter π) within animal species is between 0.0% and 0.5%. The most data are available for modern humans, who have an APD of 0.1% calculated in the same way as for other animals.”⁹

Stoeckle and Thaler recognize the sweeping potential in these patterns: “The agreement of barcodes and domain experts implies that explaining the origin of the pattern of DNA barcodes would be in large part explaining the origin of species. Understanding the mechanism by which the near-universal pattern of DNA barcodes comes about would be tantamount to understanding the mechanism of speciation.”¹⁰

In their evolutionary model, Stoeckle and Thaler invoke two hypotheses to account for the barcode cluster patterns: “Either 1) COI barcode clusters represent species-specific adaptations, OR 2) extant populations have recently passed through diversity-reducing regimes whose consequences for sequence diversity are indistinguishable from clonal bottlenecks.”¹¹

Their conclusion? “Modern human mitochondria and Y chromosome [another subset of DNA, but inherited paternally] originated from conditions that imposed a single sequence on these genetic elements between 100,000 and 200,000 years ago.”₁₂ In other words, to account for human CO barcode patterns, they favor the second hypothesis—some sort of population dynamic (contraction) that reduced the genetic diversity of the population.

Stoeckle and Thaler then extrapolate their conclusions to controversial heights. To justify their extrapolation, they caution that “one should not as a first impulse seek a complex and multifaceted explanation for one of the clearest, most data rich and general facts in all of evolution.” Then they draw a parallel: “The simple hypothesis is that the same explanation offered for the sequence variation found among modern humans applies equally to the modern populations of essentially all other animal species. Namely that the extant population, no matter what its current size or similarity to fossils of any age, has expanded from mitochondrial uniformity within the past 200,000 years.”¹³ In other words, based on mtDNA barcodes, Stoeckle and Thaler claim that the vast majority of species have originated contemporary with modern humans.

Recent Origin for 100k Species?

Though Stoeckle and Thaler don’t perform this step, let’s revisit their data and take their results to the next logical conclusion. We can do this because creationists have no problems with the observations that Stoeckle and Thaler describe. I’ve already mentioned that my own experience with mtDNA matches theirs—barcodes are a useful first approximation and should be treated as such. Yet this first approximation has revealed a consistent pattern—low numbers of mtDNA differences within species and higher numbers of mtDNA differences between species.

Furthermore, since Stoeckle and Thaler explore the origin of individual species—rather than the origin of whole classification groups, like mammals—their reasoning applies almost seamlessly to the creationist explanation for the origin of species. Their claim that species arose recently is one that focuses on species within kinds—not one that explores changes from one kind into another. In other words, for Stoeckle and Thaler’s particular question, evolutionists and creationists agree on the question of common ancestry.

Nevertheless, they differ sharply on the question of time—when these individual species arose. Unlike Stoeckle and Thaler, creationists invoke not two, but three potential explanations for low numbers of mtDNA sequence differences within species: (1) species-specific adaptations; (2) changing population sizes or past bottlenecks (see especially the discussion of American bison (Bison bison) mtDNA and African buffalo (Syncerus caffer) mtDNA in this paper; (3) time— recent origin (e.g., within the last 4,500–6,000 years).

We now have two decades’ worth of direct measurements of the rate at which human mtDNA mutates, and it matches exactly the 6,000-year timescale and rejects the evolutionary timescale (see “Genetics Confirms the Recent, Supernatural Creation of Adam and Eve” and references therein). Thus, taking Stoeckle and Thaler’s results to their logical conclusion, we can revise their statement to “Modern human [mitochondrial DNA] originated from conditions that imposed a single sequence on these genetic elements” about 6,000 years ago.

Let’s now re-extrapolate these results to other species. “The simple hypothesis is that the same explanation offered for the sequence variation found among modern humans applies equally to the modern populations of essentially all other animal species. Namely that the extant population, no matter what its current size or similarity to fossils of any age, has expanded from mitochondrial uniformity within the past” 6,000 years.

We can refine this conclusion even more, with more spectacular implications for the creationist model: In the last two decades, the mtDNA mutation rate in a handful of invertebrate species has also been directly measured, and these rates¹⁴ are around 10 times higher (or more!) than the human mtDNA mutation rate (again, see this article and references therein). This would imply that multiple species within a genus (or perhaps even a family) have originated within the last 6,000 years.

In other words, these broad mtDNA barcode results suggest that, in general, the predictions¹⁵ I made for mtDNA mutation rates in diverse species are likely to be fulfilled. This is good evidence that Darwin’s ideas are well on their way to being replaced.

Note Added in Proof: Have Evolutionists Found a Flaw in This Study?

As this article was going to press, the theistic evolutionary organization BioLogos posted a critique of Stoeckle and Thaler’s paper. More specifically, BioLogos posted a critique of creationist responses to Stoeckle and Thaler. BioLogos took strong exception to the type of thesis that I advanced above. For example, consider the following quote from BioLogos: “Did Stoeckel [sic] and Thaler conclude that “90% of animal species appeared at same time as humans”? The answer is No” [emphasis theirs].

Did I miss a key element of the Stoeckle and Thaler paper?

Let’s take a look at the BioLogos article, which was written by PhD biologist and professor Joel Duff. Duff clearly desired to minimize the implications of Stoeckle and Thaler’s paper. For example, Duff characterized the journal in which it was published as “a low-profile Italian journal.” He also downplayed the impact, saying that the “extended press release didn’t generate much reaction inside or outside of the scientific community.” More strongly, Duff denounced claims like the one I made above as “mischaracterization of the original research.” He said it was an “incorrect claim that most species originated about the same time.”

Why?

To support his assertion, Duff proposed an examination of “the original intent of the authors of this paper.” Since an author’s intent is invisible unless the author clearly states it, Duff’s suggested methodology to justify his strong critique is a creative way to tackle a scientific controversy.

After examining Stoeckle and Thaler’s intent to Duff’s satisfaction, Duff’s journalism gets more questionable. We’ve already examined his emphatic assertion: “Did Stoeckel [sic] and Thaler conclude that ‘90% of animal species appeared at same time as humans’? The answer is No.” Duff justifies his forceful condemnation with a quote from Stoeckle and Thaler’s paper: “the extant population, no matter what its current size or similarity to fossils of any age, has expanded from mitochondrial uniformity within the past 200,000 years.”¹⁶ In light of this quote, Duff concludes, “In other words, the genetic diversity observed in mitochondrial genomes of most species alive today can be attributed to the accumulation of mutations from an ancestral genome within the past 200,000 years,” and Duff asserts that “the authors never claim that most ‘species’ came into existence within the past 200,000 years.”

For a critique that began with a proposal to examine intent, Duff seems to have missed the actual intent of the authors. The title of their paper is, “Why should mitochondria define species?” After discussing and justifying at length the observation that mtDNA differences do, in fact, delineate species, the authors then make a startling statement: “The pattern of DNA barcode variance is the central fact of animal life that needs to be explained by evolutionary theory”¹⁷ [emphasis theirs]. In case the intent of their statement wasn’t transparent, the authors make it explicit: “The agreement of barcodes and domain experts implies that explaining the origin of the pattern of DNA barcodes would be in large part explaining the origin of species. Understanding the mechanism by which the near-universal pattern of DNA barcodes comes about would be tantamount to understanding the mechanism of speciation.” They then spend the next chunk of their paper discussing what mtDNA barcodes imply about the mechanism of speciation. Clearly, Stoeckle and Thaler are concerned with much more than just “the accumulation of mutations from an ancestral genome within the past 200,000 years.” Instead, they have a strong focus on the origin of species.

But did “the authors never claim that most ‘species’ came into existence within the past 200,000 years”? In one sense, if we split hairs, Duff is technically correct: In their paper, Stoeckle and Thaler never say so explicitly. Yet as we’ve just observed, the conclusion about the timing of the origin of species is implied. Furthermore, Thaler makes the conclusion explicit in the press release—the very one that Duff cited:

Our paper strengthens the argument that the low variation in the mitochondrial DNA of modern humans also explains the similar low variation found in over 90% of living animal species—we all likely originated by similar processes and most animal species are likely young¹⁸. [emphasis added]

How did Biologos miss this?

Duff advances a second argument in his critique of the implications of Stoeckle and Thaler’s paper. He says that the mtDNA results “at best, [tell] us the minimum age of the species. It tells us little to nothing about the maximum age of a species” [emphasis his]. For the maximum age, Duff thinks the fossil record is essential. Furthermore, he states that “an examination of the mitochondrial genome of any species will only tell us when the common ancestor of all modern members of this species existed, which will almost invariably occur after the evolutionary origin of the species.”

But how does Duff know that this is true? I’ve already documented that fossils do not directly record genealogical relationships; only DNA does. Why would Duff defer the genealogical question of ancestry (a.k.a. the question of the origin of species) to an indirect field of science (paleontology) when a direct field (genetics—mtDNA) gives a clear answer?

I’ve also documented that the process of speciation involves several steps—at a minimum, (1) the formation of one or more distinct individuals, (2) the multiplication of these distinct individuals into a population, and (3) the isolation of this distinct population from the parent species. How does Duff know that the supposed ancestors (recorded by fossils) of modern species were isolated enough from the other populations alive at the time to be called a new species? Duff is trying to win a scientific argument, not by data and by experimentation, but by assertion. This is not a scientific way to resolve the controversy.

BioLogos’ response is sad, if not ironic. We’ve already documented the fact that our evolutionary opponents don’t read our literature (Duff included , despite BioLogos’ professed commitment to “dialogue with those who hold other views); yet they call us liars. Sometimes I wonder if they carefully read even the evolutionary literature. Either way, BioLogos’ main critique (of the implications of Stoeckle and Thaler’s paper) amounts to misrepresentation and speculation— even approaching outright denial. If this is the best that the evolutionary community can do, then perhaps my scientific conclusions (above) are even stronger than they first appear.