These pseudogenes are, to anyone who understands them, some of the best evidence, not only for evolution but also against any notion of intelligent design, as I explain in my book, Unintelligent Design: Refuting the Intelligent Design Hoax.
To add to this embarrassment, three scientists led by Christopher A. Emerling of the Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA and the Institut des Sciences de l’Évolution de Montpellier (ISEM), Université de Montpellier, Montpellier, France published an open access paper in Science Advances in May 2018, in which they reported finding that mammals have remnants of one or more of five gene for digesting the chitin exoskeleton of insects, even those mammals which never eat insects, such as rhinoceroses, tigers, elephants and donkeys.
These pseudogenes are thought to be remnants of the time when the stem mammals were small, insectivores living at the time when dinosaurs were the dominant carnivores and herbivores and the early mammals were small, probably nocturnal to avoid the diurnal dinosaurs, shrew like insectivores with sharp pointed teeth, much like those of shrews and hedgehogs today.
As Christopher Emerling in his blog, Evolution For Skeptics, explains:
Palaeontologists have long noted how mammal fossils seem to change dramatically in form from one era to the next. In fact, few things in the fossil record seem to contrast more than the mammals that lived alongside the dinosaurs and those that survived after most dinosaurs went extinct some 66 million years ago.In an example of how the Theory of Evolution can make predictions which prove to be correct, Dr. Emerling and his colleagues reasoned that if the evolutionary pattern implied in the fossil record, that all extant mammals had this small, Mesozoic insectivore as their common ancestor, there should be genetic evidence of an insectivorous diet in the form of remnants (pseudogenes).
One of the most obvious changes is that the Mesozoic (dinosaur era) mammals were generally very small and had teeth with sharp, pointed ends, both of which are characteristic of modern insect-eating mammals. Post-Mesozoic mammals, however, attained much larger body sizes and had teeth that were clearly used for grinding up plant material or slicing meat.
Why did mammals change? The typical thought among scientists is that when dinosaurs were the dominant land animals, they occupied nearly all of the herbivore and carnivore niches, restricting mammals to insect-eating and therefore small body sizes. Then when these dinosaurs went extinct, mammals were able to evolve and adapt to occupy these newly vacant ‘jobs’ within their respective ecosystems.
Together, this implies that all modern herbivores and carnivores, ranging from rhinos and cows to tigers and dolphins, descended from tiny, insect-eating ancestors. At some point, these ancestors began foregoing their insect prey in favor of plants and/or meat, and their bodies changed in form and function along with these newfound diets. To help you imagine the scope of what this means, picture the small insectivorous Mesozoic mammal below (top left), being the greatest of grandmothers to the herbivorous mammals in the images alongside it.
Early insectivorous mammal (top, left).
All the other mammals have inherited the genes for digesting insects, yet none of them do.
And that is exactly what they found. They went looking for the gene encoding an enzyme called acidic mammalian chitinase (CHIA), which is produced in the stomach and other digestive organs and can break down the chitin-rich exoskeletons of insects. They found that there are five of these genes and that all five are common to placental mammals.
Fig. 1 Placental mammal CHIA gene tree, simplified from fig. S3.
Closed circles indicate functional CHIAs, and open circles indicate pseudogenic CHIAs and/or CHIAs lacking a chitinolytic and/or chitin-binding domain. Colored branches correspond to a subset of placental mammal clades: green, Cetartiodactyla; orange, Carnivora; pink, Perissodactyla; red, Xenarthra; purple, Afrotheria; brown, Scandentia; cyan, Strepsirrhini; blue, Anthropoidea; yellow, Dermoptera. Silhouettes and licenses here and throughout are from phylopic.org.
Closed circles indicate functional CHIAs, and open circles indicate pseudogenic CHIAs and/or CHIAs lacking a chitinolytic and/or chitin-binding domain. Colored branches correspond to a subset of placental mammal clades: green, Cetartiodactyla; orange, Carnivora; pink, Perissodactyla; red, Xenarthra; purple, Afrotheria; brown, Scandentia; cyan, Strepsirrhini; blue, Anthropoidea; yellow, Dermoptera. Silhouettes and licenses here and throughout are from phylopic.org.
Fig. 3 Examples of CHIA shared inactivating mutations.
AS Dr. Emerling puts it:
What’s more is that many of these mammals that are thought to be related, based on DNA and anatomical similarity, share the exact same mutations in some or all of the chitinase genes. For example, horses and rhinos look quite different from one another, yet have been considered by anatomists, paleontologists and geneticists to be related for over a century and a half. They are both herbivores, which implies their diet was inherited from a common ancestor, and indeed the earliest fossils that resemble them had teeth and jaws that appeared to be particularly good at eating plants. Such adaptations would have rendered insect-digesting genes relatively useless. Indeed, horses and rhinos have pseudogene remnants for four of the five chitinases, and they share at least one disabling mutation in each gene, suggesting they inherited defunct copies from a plant-eating ancestor.Dr Emerling then throws out this question to Creationists, which, judging by the comments on his blog, none have yet managed to answer:Humans also possess three chitinase pseudogenes, alongside a single functional chitinase gene. Two of the pseudogenes share the same inactivating mutations with monkeys and apes, and a third shares a mutation only with apes. Interestingly, many of the earliest primate fossils appear to have been insect-eaters, but as monkeys and apes appeared, plants, as well as meats, became more important for their diets, so insect-digesting genes were likely less useful.
Together, these data suggest that in our very own genomes, we retain ‘molecular fossils’, that hearken back to a time when our distant ancestors were not the top of the food chain, but rather scurried along amidst dinosaurs, eating insects.
Questions for CreationistsMore technical details of the research are in the published paper in Science Advances:
Why would the Creator design humans, rhinos, tigers and other mammals that never or almost never eat insects with remnants of insect-digesting genes? Is it just a coincidence that the earliest mammal fossils, found alongside dinosaurs, appear to have been insect eaters, and modern herbivores and carnivores have remnants of insect-digesting genes? For those that believe that all animals were plant-eaters in the Garden of Eden, why do so many herbivores have remnants of insect-eating genes? If mammals were created in the last 10,000–6,000 years, how could they evolve from insect-eaters to herbivores and carnivores so quickly, modifying their teeth, jaws, intestinal tracts, etc. to be optimized for their new diets?
AbstractI wonder if any Creationists will ever pluck up the courage to deal with Dr. Emerling's question!
The end-Cretaceous extinction led to a massive faunal turnover, with placental mammals radiating in the wake of nonavian dinosaurs. Fossils indicate that Cretaceous stem placentals were generally insectivorous, whereas their earliest Cenozoic descendants occupied a variety of dietary niches. It is hypothesized that this dietary radiation resulted from the opening of niche space, following the extinction of dinosaurian carnivores and herbivores. We provide the first genomic evidence for the occurrence and timing of this dietary radiation in placental mammals. By comparing the genomes of 107 placental mammals, we robustly infer that chitinase genes (CHIAs), encoding enzymes capable of digesting insect exoskeletal chitin, were present as five functional copies in the ancestor of all placental mammals, and the number of functional CHIAs in the genomes of extant species positively correlates with the percentage of invertebrates in their diets. The diverse repertoire of CHIAs in early placental mammals corroborates fossil evidence of insectivory in Cretaceous eutherians, with descendant lineages repeatedly losing CHIAs beginning at the Cretaceous/Paleogene (K/Pg) boundary as they radiated into noninsectivorous niches. Furthermore, the timing of gene loss suggests that interordinal diversification of placental mammals in the Cretaceous predates the dietary radiation in the early Cenozoic, helping to reconcile a long-standing debate between molecular timetrees and the fossil record. Our results demonstrate that placental mammal genomes, including humans, retain a molecular record of the post-K/Pg placental adaptive radiation in the form of numerous chitinase pseudogenes.
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