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New Study Raises More Questions about Evolution

Contrary to the claims made by many scientists, evolution is a theory in crisis. A recent study published in PLoS Biology highlights just one of the many problems that confront evolutionary biologists.

A team of collaborators from The Institute of Genomic Research, The J. Craig Venter Institute, and the Institute of Molecular and Cell Biology in Singapore just sequenced the elephant shark genome and compared it with the human genome and those of other fish.1 This comparison raises uncomfortable questions for the evolutionary paradigm.

Scientists glean valuable insight into the makeup of the human genome by comparing it with the genomes of other organisms. Comparisons of the human genome with vertebrate genomes, for example, have led to the discovery of several hundred novel genes and regulatory sequences.

Researchers find the elephant shark genome interesting for several reasons. First is its relatively small size. This makes the elephant shark’s genetic material amenable to rapid sequencing by techniques like shotgun sequencing. Second is the relationship of the elephant shark to other vertebrates. As a cartilaginous fish, the elephant shark is one of the vertebrates most distantly related to humans. This makes it an important reference when the human genome is compared to those of other vertebrates.

From an evolutionary standpoint, jawed vertebrates (Gnathostomes) consist of two lineages: the bony fish (Osteichthyes) and the cartilaginous fish (Chondrichthyes). The cartilaginous fish, in turn, consist of two groups: 1) the elasmobranchs (sharks, rays, and skates); and 2) the holocephalians (chimaeras, which include elephant sharks). The bony fish also bifurcate into two groups: 1) the ray-finned fishes, and 2) the lobe-finned fishes. Included in the lobe-finned fish grouping are tetrapods, land-based vertebrates that include humans.

Based on these evolutionary relationships, biologists expect that the human genome will have much more in common with the genomes of ray-finned fish than to the genomes of cartilaginous fish. The study published in PLoS Biology, however, tells a different story. It turns out that even though the elephant shark is much more distantly related to humans than the teleost fish (a subgroup of ray-finned fish) its genome bears a much greater similarity to the human genome. For example, there are a greater number of conserved DNA sequences and more extensive synteny (gene order along the length of the chromosomes) between humans and elephant sharks, than between humans and teleost fishes. According to the evolutionary paradigm, DNA sequences should increasingly differ and synteny should progressively dissipate as organisms diverge from one another. In other words, the opposite results should have been obtained by these researchers—if evolution explains life’s history.

How do the researchers account for these unexpected results? They speculate that the human and elephant shark genomes mutate at a much slower rate than do the genomes of teleost fish. In other words, after the ray-finned and lobe-finned fish diverged, the genomes of the ray-finned fish must have undergone much more extensive genetic change and rearrangement than did the genomes of lobe-finned fish (including tetrapods) and cartilaginous fish.

On the surface this explanation seems reasonable—until the timescales and the extent of these evolutionary changes are considered. The first cartilaginous fish appear in the fossil record 450 million years ago. According to the evolutionary model, bony and cartilaginous fish diverge from one another about 410 million years ago, and ray-finned and lobe-finned fish diverge from one another about 390 million years ago. Both teleost fish and tetrapods first appear in the fossil record about 385 million years ago.

According to evolutionary models, changes in gene sequences, duplication, deletion, and rearrangement of genetic material are the creative forces behind evolutionary change. It’s troubling to think that the teleost fish have undergone such extensive changes to their genomes with relatively little morphological and physiological change while in the same time period (385 million years) tetrapods have undergone incredible morphological and physiological change (moving from the water to the land, followed by the transformation from amphibians to reptiles, from reptiles to mammals, and from shrew-like creatures to modern humans) with relatively limited genetic change compared to cartilaginous fish.

The attempt to account for the surprising similarity between the human and elephant shark genomes from an evolutionary perspective raises as many questions as the straightforward rendering of the results of the comparative analysis. This discovery and other discoveries like it are the reason why a growing number of scientists, including those at RTB, express skepticism about biological evolution and the increasingly muddled explanations it provides for life’s history and diversity.



1 Byrappa Venkatesh et al., “Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome,” PLoS Biology 5 no. 4 (2007): e101.