The Speciation Enigma

The Presumed Evolutionary & Fossil Record Trees Are Strikingly Divergent

If observations or experiments produce "strikingly divergent results" from what a scientific model predicts, what does that tell us about the viability of the model? A new study on speciation and extinction rates suggests that the widely accepted naturalistic scenario for life's development may be less sturdy than the community of biologists has resoundingly affirmed.

Standard Model Predictions

A fundamental tenet of all naturalistic models for the history of Earth's life is that natural changes in the genome of living things will be responsible for the observed changes in their physical body structures (morphology) over time. Consequently, evolutionary trees, or phylogenies of the presumed past history of life have been constructed from the genomic patterns observed in today's life-forms. A key component for building these phylogenetic trees is a set of assumptions about the rate of naturally occurring changes (mutations) in those genomes. Evolutionary biologists refer to the rates at which genomes change as molecular clocks.

If researchers assume that strictly natural processes are responsible for the changes observed throughout life's history, then their phylogenetic trees should match both the morphological changes and the timing of those changes as observed in the fossil record—the paleontological trees. However, evidence, both old and new, shows significant mismatches between phylogenetic and paleontological trees—and not just in the case of one or a few life-forms. In an open-access paper published in Nature Communications,a team of four computational biologists and biochemists led by Daniele Silvestro and Rachel Warnock acknowledge this discrepancy:¹

The fossil record and molecular phylogenies of living species can provide independent estimates of speciation and extinction rates, but often produce strikingly divergent results.²

Divergence Is Real & Striking

Because biologists use over a dozen different definitions of species, the members of the Silvestro-Warnock team clarify, in their paper, what they mean by the term. They define a species as "an identifiable taxonomic unit (a lineage) that can persist through time, give rise to other species, and become extinct."³

The team begins by affirming that since "extant [still existing] and fossil species are samples of the same underlying diversification [variation-yielding] process,"⁴ a strictly natural diversification process would predict that in all cases, the phylogenetic (presumed evolutionary) trees should match the paleontological (fossil record) trees. However, evolutionary biologists must now acknowledge the reality of frequent and striking differences between phylogenetic and paleontological trees.

The Silvestro-Warnock team cited a recent study of currently existing terrestrial Carnivora.⁵ There, the mean species longevity, based on fossil evidence, is an estimated 2.0 million years, contrasted with the estimated 9.8 million years derived from phylogenetics (or, calculated natural changes in the genomes). The team also cited a study demonstrating inconsistencies between phylogenies and fossils for primates.⁶ They noted that, at least for mammals, the occurrence of congruence is actually rare.⁷

Speciation rates derived from phylogenetics consistently exceed those derived from the fossil record, while calculated extinction rates are consistently lower than speciation rates. Perhaps the best studied example of the problem comes from research on cetaceans (whales, dolphins, and porpoises). The Silvestro-Warnock team cited these unexpected research findings:

Phylogenetic estimates of diversification rates among cetaceans suggest speciation has exceeded extinction over the past 12 Myr [million years]^[8] implying diversity has increased towards the recent. In contrast, analyses of the cetacean fossil record indicate extinction has exceeded speciation over this same interval, and that the diversity of cetaceans was in fact much higher [in the past] than it is today.⁹

In other words, the naturalistic evolutionary model based on standard phylogenetics predicts that the introduction of new species will exceed extinctions, but the fossil record shows that the reverse has occurred.

The research team made no comment on another of its observations: discrepancies between phylogenetics and the fossil record appear to increase with the complexity and adult body size of the genus. It seems worth noting that this correlation would, in fact, fit the predictions of a model that allows for the involvement of an intentional Creator.¹⁰

Silvestro, Warnock, and their collaborators do point out that other researchers have attempted to explain the discrepancies, suggesting that perhaps they result from underestimates of the statistical and systematic errors in the research methodology. However, the reported discrepancies appear much too large to fit this proposed explanation.¹¹

An Attempted Reconciliation

The Silvestro-Warnock team suggested that many of the discrepancies between phylogenetics and the fossil record are due to sensitivities to different speciation modes. They identify three distinct modes of speciation that can leave behind fossil evidence without impacting the calculated phylogenetic trees:

1. Budding: a speciation event that gives rise to one new species while the ancestral species persists.

2. Bifurcation: a speciation event that gives rise to two new species that replace the ancestral species, which then becomes extinct.

3. Anagenesis: evolutionary changes along a lineage that result in the origination of one new species and the extinction of the ancestral species.

They also point out that extinction without replacement is a frequent occurrence. In other words, many species become extinct without leaving any descendants. The fossil record includes extant and extinct species, whereas phylogenetic trees typically include only extant species.

Silvestro, Warnock, and their team propose a model that unifies the three modes of speciation and extinction in a single "birth-to-death chronospecies" process, or BDC. Yet their model suggests that phylogenetic and paleontological speciation and extinction rate estimates will be equal only if all speciation has occurred through the first of their three listed modes of speciation. They write:

[E]ven in an ideal scenario with fully sampled and errorless data sets, speciation and extinction rates can be equal across phylogenetic and stratigraphic inferences only if all speciation events have occurred through budding [the first speciation mode in their list] and no speciation has occurred through bifurcation or anagenesis [the second and third speciation modes in their list].¹² (emphasis added)

Also, according to their BDC model, phylogenetic analysis indicating an extinction rate equal to zero does not necessarily imply that extinction did not occur.

More Problems

The team's BDC model establishes that, relative to the fossil record, phylogenetics always underestimates extinction rates. The fossil record, which remains largely incomplete, also underestimates actual extinction rates. Much higher extinction rates, however, pose a serious challenge to all strictly naturalistic models for Earth's life—for the obvious reason that higher extinction rates require higher speciation rates to explain the increasing diversity of life observed in the fossil record.

This requirement of higher speciation rates proves all the more problematic for a naturalistic scenario describing the emergence of Earth's most advanced species. For mammals, birds, and advanced plants, the observed extinction rates far exceed the observed speciation rates during the era of human history. According to Genesis 2, God ceased from his work of creating new life-forms once he made humanity; since then (the seventh day), he has allowed natural processes to continue operating.

An example of the naturalist's problem is that the number of existing mammal species at the time of humanity's origin was a little more than 8,000, while today the number is only about 4,000. Of those remaining 4,000, not even one is a new species that did not exist at the time of humanity's origin.

A Reasonable Reconciliation

Thus, the Silvestro-Warnock BDC model exposes a fundamental limitation of naturalistic explanations for the history of Earth's life. Given that all naturalistic models require more than one speciation mode, and given that the only way to reconcile phylogenetics and paleontology is to posit just one speciation mode, it would appear that something other than strictly natural processes must have been involved in the speciation process.

To salvage a reconciliation between phylogenetics and paleontology, some evolutionary biologists will insist that some unknown natural process must exist. However, it seems highly unlikely that a natural process of sufficient magnitude to achieve this grand-scale reconciliation remains undiscovered.

On the other hand, a worldview perspective based on biblical revelation is open to the idea that a supernatural, personal Creator intervened at various times throughout life's history to replace life-forms driven to extinction by environmental changes. This possibility fully reconciles the observed "discrepancy," and it brings to mind a verse from Psalm 104, the most comprehensive of the creation psalms:

How many are your works, Lord! In wisdom you made them all; the earth is full of your creatures. (104:24)

Notes:
1. Daniele Silvestro et al., "Closing the gap between palaeontological and neonotological speciation and extinction rate estimates," Nature Communications 9 (Dec. 7, 2018): id. 5237, doi:10.1038/s41467-018-07622-y.
2. Ibid., note 1.
3. Ibid., note 1.
4. Ibid., note 1.
5. Oskar Hagen et al., "Estimating Age-Dependent Extinction: Contrasting Evidence from Fossils and Phylogenies," Systematic Biology 67, no. 3 (May 2018): 458–474, doi:10.1093/sysbio/syx082.
6. James P. Herrera, "Primate diversification inferred from phylogenies and fossils," Evolution 71, no. 12 (December 2017): 2845–2857, doi:10.1111/evo.13366.
7. Juan L. Cantalapiedra et al., "Congruent Phylogenetic and Fossil Signatures of Mammalian Diversification Dynamics Driven by Tertiary Abiotic Change," Evolution 69, no. 11 (November 2015): 2941–2953, doi:10.1111/evo.12787.
8. Daniel L. Rabosky, "Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees," PLoS ONE 9, no. 2 (Feb. 26, 2014): id. E89543, doi:10.1371/journal.pone.0089543.
9. Charles R. Marshall, "Five paleobiological laws needed to understand the evolution of the living biota," Nature Ecology and Evolution 1 (May 23, 2017): id. 0165, doi:10.1038/s41559-017-0165; Lee Hsiang Liow, Tiago B. Quental, and Charles R. Marshall, "When Can Decreasing Diversification Rates Be Detected with Molecular Phylogenies and the Fossil Record?", Systematic Biology 59, no. 6 (December 2010): 646–659, doi:10.1093/sysbio/syq052; Catalina Pimiento et al., "The pliocene marine megafauna extinction and its impact on functional diversity," Nature Ecology and Evolution 1 (June 26, 2017): 1100–1106, doi:10.1038/s41559-017-0223-6.
10. Hugh Ross, More Than a Theory: Revealing a Testable Model for Creation (Baker, 2009), 149–179.
11. Silvestro et al., "Closing the Gap," note 1.
12. Silvestro et al., note 1.