A recent1 review paper proposed a controversial claimthat 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 Thalers 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 justifiedso much so that I will summarize their arguments by liberally quoting from their paper.
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 organisms 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 12 mtDNA differences in each individuals 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 arent 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 34 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.
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 barcodessmall 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 ) 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 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 hypothesissome 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.
Though Stoeckle and Thaler dont perform this step, lets 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. Ive already mentioned that my own experience with mtDNA matches theirsbarcodes are a useful first approximation and should be treated as such. Yet this first approximation has revealed a consistent patternlow numbers of mtDNA differences within species and higher numbers of mtDNA differences between species.
Furthermore, since Stoeckle and Thaler explore the origin of individual speciesrather than the origin of whole classification groups, like mammalstheir 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 kindsnot one that explores changes from one kind into another. In other words, for Stoeckle and Thalers particular question, evolutionists and creationists agree on the question of common ancestry.
Nevertheless, they differ sharply on the question of timewhen 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 4,5006,000 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 Thalers 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 elements14 about 6,000 years ago.
Lets 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 Darwins ideas are well on their way to being replaced.
As this article was going to press, the theistic evolutionary organization BioLogos posted a critique of Stoeckle and Thalers 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?
Lets 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 Thalers 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 didnt 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 authors intent is invisible unless the author clearly states it, Duffs suggested methodology to justify his strong critique is a creative way to tackle a scientific controversy.
After examining Stoeckle and Thalers intent to Duffs satisfaction, Duffs journalism gets more questionable. Weve 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 Thalers 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 theory17 [emphasis theirs]. In case the intent of their statement wasnt 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.18 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 weve just observed, the conclusion about the timing of the origin of species is implied. Furthermore, Thaler makes the conclusion explicit in the press releasethe 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 specieswe all likely originated by similar processes and most animal species are likely young19. [emphasis added]
How did Biologos miss this?
Duff advances a second argument in his critique of the implications of Stoeckle and Thalers 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? Ive 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 (geneticsmtDNA) gives a clear answer?
Ive also documented that the process of speciation involves several stepsat 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. Weve already documented the fact that our evolutionary opponents dont 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 Thalers 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.
See more here:
Hundreds of Thousands of Species in a Few Thousand Years?
- 11-minute video on human genetics can make people more accepting of others, reveals new study - Hindustan Times - February 24th, 2025
- Advancing Cancer Genetic Testing to Improve Prevention and Patient Treatment - The Scientist - February 24th, 2025
- Environmental factors, lifestyle choices have greater impact on health than genes, study finds - ABC News - February 24th, 2025
- Study finds lifestyle, environment have greater impact on lifespan than genetics - CBS Boston - February 24th, 2025
- Safeguard repressor locks hepatocyte identity and blocks liver cancer - Nature.com - February 24th, 2025
- Mass spectrometry-based mapping of plasma protein QTLs in children and adolescents - Nature.com - February 24th, 2025
- The Avestagenome Project and TIGS Sign Strategic Alliance to Advance Research in Rare Genetic Disorders - The Tribune India - February 24th, 2025
- Researchers make breakthrough discovery after studying genetics of trees: 'There is a need for proactive conservation' - MSN - February 24th, 2025
- iPSCs and iPSC-derived cells as a model of human genetic and epigenetic variation - Nature.com - February 24th, 2025
- Beyond genetics: The biggest factors that influence health and aging - Earth.com - February 24th, 2025
- Genetic diversity and dietary adaptations of the Central Plains Han Chinese population in East Asia - Nature.com - February 24th, 2025
- How a uniquely human genetic tweak changed the voices of mice - NPR - February 24th, 2025
- Genetic evidence identifies a causal relationship between EBV infection and multiple myeloma risk - Nature.com - February 24th, 2025
- Genetic markers of early response to lurasidone in acute schizophrenia - Nature.com - February 24th, 2025
- Bupa to offer first genetic test for disease prediction in UK - The Times - February 24th, 2025
- Advancing Therapeutic Knowledge of Genetic Influence in ALS: Matthew B. Harms, MD - Neurology Live - February 24th, 2025
- Association of dietary carbohydrate ratio, caloric restriction, and genetic factors with breast cancer risk in a cohort study - Nature.com - February 24th, 2025
- Evaluation of polygenic scores for hypertrophic cardiomyopathy in the general population and across clinical settings - Nature.com - February 24th, 2025
- Familiar autism-linked genes emerge from first analysis of Latin American cohort - The Transmitter: Neuroscience News and Perspectives - February 24th, 2025
- Almost 90% of people would agree to genetic testing to tailor medication use, survey finds - Medical Xpress - February 24th, 2025
- Largest Genetic Study of Bipolar Disorder Identifies 298 Regions of the Genome That Increase Risk for the Condition - Mount Sinai - January 27th, 2025
- Study Sheds Light On The Origin Of Earth Lifes Genetic Code - Astrobiology News - January 27th, 2025
- Largest study on the genetics of bipolar disorder to date gives new insights into the underlying biology - Medical Xpress - January 27th, 2025
- Genetic Swiss Army Knife: New Tool For Gene Editing And Therapy - Forbes - January 27th, 2025
- Uhm Ji-won says the power of genetics is undeniable with Hyun Bin and Son Ye-jin's son - - January 27th, 2025
- Integrative proteogenomic analysis identifies COL6A3-derived endotrophin as a mediator of the effect of obesity on coronary artery disease -... - January 27th, 2025
- Genetic analysis reveals the genetic diversity and zoonotic potential of Streptococcus dysgalactiae isolates from sheep - Nature.com - January 27th, 2025
- Eight psychiatric disorders share the same genetic causes, study says - Medical Xpress - January 27th, 2025
- Exploring genetic associations and drug targets for mitochondrial proteins and schizophrenia risk - Nature.com - January 27th, 2025
- Predictive Genetic Testing and Consumer Genomics Market - GlobeNewswire - January 27th, 2025
- Evolution without sex: How mites have survived for millions of years - EurekAlert - January 27th, 2025
- Our Understanding of Rules that Produce Lifes Genetic Code May Require a Revision - DISCOVER Magazine - January 27th, 2025
- Personalized therapy for rare genetic diseases: Patient-derived organoids offer new hope - Medical Xpress - January 27th, 2025
- The One Thing That's More Important for Longevity Than Your Genes - Parade Magazine - January 27th, 2025
- Complete recombination map of the human genome created - Medical Xpress - January 27th, 2025
- Evidence of genetic determination of annual movement strategies in medium-sized raptors - Nature.com - January 27th, 2025
- Genetic study of Alaska red king crabs suggests species is more diverse and resilient to climate change - Global Seafood Alliance - January 27th, 2025
- Smartwatches reveal insights into psychiatric illnesses and genetic links - Medical Xpress - January 27th, 2025
- Unlocking the Blueprint of Human Life With a Revolutionary DNA Map - SciTechDaily - January 27th, 2025
- Largest Genetic Study of Bipolar Disorder Identifies Nearly 300 Risk-Associated Genome Regions - Inside Precision Medicine - January 27th, 2025
- Genetic Discrimination Is Coming for Us All - The Atlantic - November 16th, 2024
- Family connection: Genetics of suicide - WNEM - November 16th, 2024
- Study links heart shape to genetic risk of cardiovascular diseases - News-Medical.Net - November 16th, 2024
- Genetic architecture of cerebrospinal fluid and brain metabolite levels and the genetic colocalization of metabolites with human traits - Nature.com - November 16th, 2024
- Genetic connectivity of wolverines in western North America - Nature.com - November 16th, 2024
- Toward GDPR compliance with the Helmholtz Munich genotype imputation server - Nature.com - November 16th, 2024
- Leveraging genetic variations for more effective cancer therapies - News-Medical.Net - November 16th, 2024
- Bringing precision to the murky debate on fish oil - University of Arizona News - November 16th, 2024
- International experts gathered in Tashkent to tackle rare disease for Uzbekistan - EurekAlert - November 16th, 2024
- Mercys Story: Living life with 22q, a genetic condition - WECT - November 16th, 2024
- Cold case with ties to Houghton County solved through genetic genealogy after 65 years - WLUC - November 16th, 2024
- 23andMe customer? Here's what to know about the privacy of your genetic data. - CBS News - November 16th, 2024
- Single-cell RNA analysis finds possible genetic drivers of bone cancer - Illumina - November 16th, 2024
- Multi-trait association analysis reveals shared genetic loci between Alzheimers disease and cardiovascular traits - Nature.com - November 16th, 2024
- With 23andMe Struck by Layoffs, Can You Delete Genetic Data? Here's What We Know - CNET - November 16th, 2024
- Genetic testing firm 23andMe cuts 40% of its workforce amid financial struggles - The Guardian - November 16th, 2024
- Genetic study solves the mystery of 'selfish' B chromosomes in rye - Phys.org - November 16th, 2024
- Genetic changes linked to testicular cancer offer fresh insights into the disease - Medical Xpress - November 16th, 2024
- Eating less and genetics help you to live longer, but which factor carries the most weight? - Surinenglish.com - November 16th, 2024
- We must use genetic technologies now to avert the coming food crisis - New Scientist - November 16th, 2024
- NHS England to screen 100,000 babies for more than 200 genetic conditions - The Guardian - October 6th, 2024
- Largest-ever genetic study of epilepsy finds possible therapeutic targets - Medical Xpress - October 6th, 2024
- 23andMe is on the brink. What happens to all its DNA data? - NPR - October 6th, 2024
- The mountains where Neanderthals forever changed human genetics - Big Think - October 6th, 2024
- Gene Activity in Depression Linked to Immune System and Inflammation - Neuroscience News - October 6th, 2024
- Integrative multi-omics analysis reveals genetic and heterotic contributions to male fertility and yield in potato - Nature.com - October 6th, 2024
- Genetic and non-genetic HLA disruption is widespread in lung and breast tumors - Nature.com - October 6th, 2024
- Aneuploidy as a driver of human cancer - Nature.com - October 6th, 2024
- Myriad Genetics and Ultima Genomics to Explore the UG - GlobeNewswire - October 6th, 2024
- Biallelic and monoallelic variants in EFEMP1 can cause a severe and distinct subtype of heritable connective tissue disorder - Nature.com - October 6th, 2024
- Genetic and clinical correlates of two neuroanatomical AI dimensions in the Alzheimers disease continuum - Nature.com - October 6th, 2024
- Cracking the Genetic Code on Facial Features - DISCOVER Magazine - October 6th, 2024
- Ancestry vs. 23andMe: How to Pick the Best DNA Testing Kit for You - CNET - October 6th, 2024
- The Mercedes-AMG C63 is bold, but beholden to its genetics - Newsweek - October 6th, 2024
- The Austin Chronic: Texas A&Ms Hemp Breeding Program Adds Drought-Resistant Genetics to the National Collection - Austin Chronicle - October 6th, 2024
- Genetics and AI Help Patients with Early Detection of Breast Cancer Risk - Adventist Review - October 6th, 2024
- 23andMe Is Sinking Fast. Can the Company Survive? - WIRED - October 6th, 2024
- Genetic variations in remote UK regions linked to higher disease risk - Medical Xpress - October 6th, 2024
- Comprehensive mapping of genetic activity brings hope to patients with chronic pain - Medical Xpress - October 6th, 2024
- Genetics - Definition, History and Impact | Biology Dictionary - June 2nd, 2024