Gene-Tree Conflicts Make a Case for Creation

Earth’s life history shows the rapid introduction of complex life-forms, followed by mass extinctions, followed again by novel life-forms. Which model for life’s history better explains such events: evolution or creation?

In scientific research, conflicts between different data sets and sets of measurements, or between observations and theoretical explanations for the observations typically are strong indications that the scientific model undergirding the measurements, observations, and theoretical explanations is either incorrect or in need of major revision. Nearly two years ago, I wrote an article, New Speciation Model Challenges Evolution, Supports Creation, in which I showed that major mismatches exist between phylogenetic trees (evolutionary history based on genetics) and paleontological trees (what the fossil record shows). These inconsistencies present a major challenge to deistic and nontheistic evolution models for the history of Earth’s life and, alternately, strong evidence for a biblical creation interpretation.

Now, a team of three computational evolutionary biologists has written a paper examining the biological significance of the many examples of phylogenetic conflicts and rapid morphological (having to do with form, structure) innovations that biologists and paleontologists have observed in the history of Earth’s life.1 Specifically, they demonstrated that “instances of high gene-tree conflict (discordance in phylogenetic signal across genes) in mammals, birds, and several major plant clades correspond to rate increases in morphological innovation.”2

Branching Tree Model for the History of Earth’s Life
The reigning paradigm in evolutionary biology is that all life on Earth is descended by strictly natural means from the last universal common ancestor (LUCA), the first microbe that appeared about 3.8 billion years ago. In this scenario, life naturally evolved into more complex and diverse organisms through natural selection, mutations, and gene exchange. This model for life’s history predicts that changes in the genomes of organisms will give rise to changes in the body structures or morphologies of organisms.

Based on the reigning paradigm, evolutionary biologists trace the history of Earth’s life through phylogenetic and paleontological trees. A phylogenetic tree is where evolutionary biologists construct a branching history of life through molecular differences and presumed changes in the genomes of different species (see figure). A paleontological tree is where evolutionary biologists construct a branching history of the morphological features of species based on the fossil record.

Figure: An Evolutionary Tree Depicting an Hypothesized Portion of Earth’s Life History

Gene Tree Conflict
Gene-tree conflict refers to instances in which evolutionary biologists observe discord between the phylogenetic and paleontological trees that they construct. In their paper, the three computational evolutionary biologists evaluated the degree of gene-tree conflict for six clades spanning vertebrates and plants. (In evolutionary biology a clade is defined as a group of species that share sufficient morphological features to presume that all the species in the group are descended from a common ancestor.) They found that the greatest and most dramatic instances of gene-tree conflict corresponded with extremely high rates of morphological innovation. They also pointed out that these instances occur episodically throughout the history of Earth’s life.

The team concluded that the repeated correspondences between exceptionally high gene-tree conflicts and extraordinarily high phenotypic (morphological) innovation rates imply that both must result from the same causal processes. They then pointed out that during epochs of very high gene-tree conflict, complex population processes are frequently observed. During such epochs, paleontologists infer that population levels of individual species must be undergoing extremely rapid growth or extremely rapid collapse.

Causal Processes
Without giving any specifics or explanations, the three evolutionary biologists assert that population-level processes must be driving the major evolutionary transitions where they observe high gene-tree conflict. They conclude their paper with the suggestion that closer examination of episodes of high gene-tree conflict “may yield improved connections between micro- and macroevolution and increase our understanding of the processes that shape the origin of major lineages across the Tree of Life.”3

Episodes of dramatic instances of gene-tree conflict accompanied by extremely high rates of morphological innovation correspond to mass speciation events in the fossil record. These mass speciation events follow—within a relatively brief time period—every mass extinction event. The evolutionary biologists are correct that these events are characterized by complex population processes. Real-time field observations reveal that, without human intervention, rapid population collapse within a species leads to the extinction of that species. Likewise, without human intervention, very rapid population growth, with rare exceptions, results in species extinction. The latter arises as a consequence of overconsumption of food and nutrients.

Complex population processes do provide adequate explanations for extinctions and mass extinction events. They can also explain the increasing population and habitat spread of newly appearing species. They even, on occasion, can explain how one species can divide into two, where eventually members of one of the two refrain from mating with members of the other. However, it is a stretch, to say the least, to claim that complex population processes can explain the origin of a new phylum, class, or order.

The fossil record shows that mass speciation events, such as the Avalon and Cambrian explosions, are characterized by the sudden appearance of at least 6 and 30 new phyla, respectively.4 In the case of the Cambrian explosion, the sudden appearance of new phyla may have included as many as 100, with several of these new phyla being vertebrates.5 Furthermore, the fossil record shows that “there are no indications that the evolutionary activity at the family level was driving the origination of higher-level taxa.”6 In fact, “the diversification of phyla occurs before that of classes, classes before that of orders, and orders before that of families”7 (emphasis added). These observations and the suddenness of the appearance of new phyla are not what population-level processes would predict.

Scientific Observation Points to Creation
The fossil record observations described above are exactly consistent, however, with the actions of a super-intelligent, supernatural Mind. That intelligent Being appears intent on compensating for the Sun’s increasing brightness while ensuring Earth is packed with as much diverse life as physically possible. At the origin of Earth’s life, Earth’s atmosphere contained 6,000–7,000 parts per million of carbon dioxide and 20–50 parts per million of methane.8 Both are powerful greenhouse gases that kept Earth’s surface warm enough for life in spite of the Sun being about 20–25% dimmer than it is today.9

At the start of the industrial revolution (circa 1750 AD), just 275 parts per million of carbon dioxide and 0.7 parts per million of methane remained. The Mind created life in just-right forms, at just-right times, and at just-right abundance and diversity levels and replaced those life-forms via mass extinction events followed quickly by mass speciation events. The new life-forms removed the just-right extra amounts of carbon dioxide and methane from the atmosphere to perfectly compensate for the brightening Sun. My point is that without an intelligent Mind there is no possibility of perfectly compensating for the increasing brightness of the Sun so that life can be continuously sustained on Earth throughout the past 3.8 billion years. That Being is endowed with the power to supernaturally create and remove physical life-forms of his choosing and design and one who knows with precision the future physics of the Sun, Earth, and Moon. No naturalistic process or set of processes is able to guarantee that Earth always possesses the just-right life.

We find a hint of that supernatural Being’s work in the Bible, which indicates that God employs mass extinction and mass speciation events so as to ensure that at the moment God creates humans, Earth is endowed with a maximal level and diversity of life. One example is found in Psalm 104:29–30:

“When you hide your face, they are terrified; when you take away their breath, they die and return to the dust. When you send your Spirit, they are created, and you renew the face of the ground. “


  1. Caroline Parins-Fukuchi, Gregory W. Stull, and Stephen A. Smith, “Phylogenomic Conflict Coincides with Rapid Morphological Innovation,” Proceedings of the National Academy of Sciences USA 118, no. 19 (May 11, 2021): e2023058118, doi:10.1073/pnas.2023058118.
  2. Parins-Fukuchi, Stull, and Smith, “Phylogenomic Conflict,” 1.
  3. Parins-Fukuchi, Stull, and Smith.
  4. Guy M. Narbonne, “The Ediacara Biota: Neoproterozoic Origin of Animals and Their Ecosystems,” Annual Review of Earth and Planetary Sciences 33 (May 2005): 421–442, doi:10.1146/annurev.earth.33.092203.122519; Graham E. Budd, “The Cambrian Fossil Record and the Origin of the Phyla,” Integrative and Comparative Biology 43, no. 1 (February 2003): 157–165, doi:10.1093/icb/43.1.157; Simon Conway Morris, “The Cambrian ‘Explosion’ of Metazoans and Molecular Biology: Would Darwin Be Satisfied?International Journal of Developmental Biology 47, nos. 7–8 (February 2003): 505–515.
  5. Roger Lewin, “A Lopsided Look at Evolution,” Science 241, no. 4863 (July 15, 1988): 291–293, doi:10.1126/science.241.4863.291.
  6. Douglas H. Erwin, James W. Valentine, and J. John Sepkoski, Jr., “A Comparative Study of Diversification Events: The Early Paleozoic Versus the Mesozoic,” Evolution 41, no. 6 (November 1987): 1183, doi:10.1111/j.1558-5646.1997.tb02459.x.
  7. Erwin, Valentine, and Sepkoski, Jr., “A Comparative Study.”
  8. Minik T. Rosing et al., “No Climate Paradox under the Faint Early Sun,” Nature 464 (April 1, 2010): 744–747, doi:10.1038/nature08955.
  9. Hugh Ross, Improbable Planet (Grand Rapids, MI: Baker Books, 2016): 143–159.