Hundreds of Thousands of Species in a Few Thousand Years?

Sugar sprinkle 100's and 1000's

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

by by Dr. Nathaniel T. Jeanson

A recent 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.” 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).”

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.”

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.”

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.’” 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,” yet “the pattern of DNA barcode variance is the central fact of animal life that needs to be explained by evolutionary theory.”

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.”

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.”

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.”

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.” 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.” In other words, based on mtDNA barcodes, Stoeckle and Thaler claim that the vast majority of species have originated contemporary with modern humans…

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