One piece of evidence for common ancestry that I don’t see brought up as much is the genetic ‘mistakes’ shared within various clades. Creationists sometimes try, and fail, to address specific shared mistakes (such as the GULO pseudogene), but I don’t think many creationists are aware of the extent of this evidence and how well it supports common ancestry. Let’s go over just a few examples.
Bird evolution
Although the fossil record is replete with examples of toothed avialans (e.g., Archaeopteryx, Confuciusornis, Ichthyornis), no extant birds have true teeth. According to creationists, toothy birds are part of different ‘kinds’ than modern birds (which also fall into several different ‘kinds’), so they share no common ancestry (Garner, Wood, and Ross 2013; Brophy 2021). Under this hypothesis, there should be no evidence that organisms in the lineage of modern birds had teeth. In contrast, the common ancestry hypothesis predicts that evidence of teeth should be found in the genomes of modern birds.
The latter prediction is vindicated by genetics. As demonstrated by Harris et al. (2006), modern chickens (Gallus gallus domesticus) possess the entire genetic repertoire with which to build teeth. Chicken embryos that carry the talpid2 mutation begin to develop teeth, and not just any teeth, crocodilian teeth, also vindicating the conclusion from phylogenetics that birds are most closely related to crocodilians.
The evidence doesn’t just stop here. Not just chickens, but all modern birds, possess the genes needed to build teeth, and they all share the same eleven inactivating mutations in these genes (Meredith et al. 2014). Within modern birds (Neornithes), the different clades also share mutations in these now pseudogenized tooth genes, forming a nested hierarchy as predicted by common ancestry.
Table 1 of Meredith et al. (2014). There are eleven inactivating mutations in the tooth formation genes of all birds (Neornithes), and many others shared by all members of Palaeognathae, Neognathae, Galloanserae, and Neoaves respectively.
This evidence is conclusive against separate ancestry. Creationists who wish to dispute this and claim that different ‘kinds’ of birds were specially created by God are forced to jump to one of two conclusions:
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God created each ‘kind’ of bird with crocodilian teeth, and the genes involved in tooth development were subsequently lost in every single lineage, following the exact same eleven inactivating mutations.
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God created each ‘kind’ of bird with these pseudogenes in order to deceive us into thinking that all birds share common ancestry and used to have teeth.
Needless to say, the first option is completely implausible, and the second option is incompatible with the Bible (see Heb. 6:18 – “it is impossible for God to lie”) and would lead to radical epistemic skepticism (we can’t trust our senses if they were created by a malevolent or duplicitous deity). Creationists could also claim that these pseudogenes somehow have a necessary function, but… good luck with proving that.
Whale evolution
This one is especially interesting to me, because there are just so many pseudogenes involved in the evolution of whales. For example, whales don’t have hind limbs, but they do possess the entire genetic repertoire needed to build hind limbs (Onbe et al. 2007; Liang et al. 2022). As demonstrated by Liang et al. (2022), cetaceans all share four inactivating deletion mutations in the HLEA regulator needed to build hind limbs.
Figure 1 of Liang et al. (2022). Four inactivating deletions in the HLEA enhancer cause lack of expression of Tlx4, directly resulting in the lack of hindlimbs in cetaceans.
Likewise, the thick rubbery skin of whales is the result of gene loss. Many hair keratin genes and sebum-producing genes have been pseudogenized or entirely deleted in whales (Nery et al. 2014; Lopes-Marquez et al. 2019). Cetaceans have also lost the GSDMA, DSG4, DSC1, and TGM5, the loss of which in mice is associated with thicker epidermis, lack of hair, and increased shedding rate, all of which are characteristics of cetacean skin (Sharma et al. 2018). Other genes associated with epidermal differentiation have been lost in the cetacean lineage (Strasser et al. 2004; Holthaus et al. 2021). Whales’ eyes are adapted to water thanks to the loss of OPN1SW and OPN1LW – although there are different inactivating mutations in this gene in odontocetes and mysticetes (McGowen et al. 2014).
This is all bad enough for creationists, but there’s more. Huelsmann et al. (2019) have documented many inactivating mutations shared by all cetaceans. In terrestrial mammals, the blood coagulation system can result in thrombosis during deep diving; in cetaceans, the F12 and KLKB1 genes have been inactivated, helping them to avoid this problem. The POLM gene has also been lost, making the repair of DNA damage (caused by deep diving) more efficient. The loss of lung-expressed genes MAP3K19 and SEC14L3 aids in the collapse/reinflation of the cetacean lung during deep dives.
Adapted from Figs. 1, 2, and 3 of Huelsmann et al. (2019). (A, B) Inactivating mutations in the F12 and KLKB1 genes, shared by all cetaceans, help to prevent thrombosis during deep diving. (C, D) Inactivating mutations in the POLM gene, shared by all cetaceans, result in a more effective DNA repair mechanism adapted for deep diving. (E, F) Inactivating mutations in the MAP3K19 and SLC6A18 genes, shared by all cetaceans, result in the unique cetacean lung adapted for deep diving.
Saliva secretion, although useful in terrestrial mammals, is completely ineffective underwater; as a result, the gene SLC4A9 – the loss of which is associated with decreased saliva secretion in mice – has been inactivated in cetaceans. All of the genes involved in melatonin synthesis have also been pseudogenized in cetaceans, causing decreased time asleep and loss of the circadian rhythm, a necessary precondition for unihemispheric sleep.
Adapted from Figs. 4 and 5 of Huelsmann et al. (2019). (A, B) Inactivating mutations in the SLC4A9 gene, shared by all cetaceans, result in decreased saliva secretion. (C, D) Inactivating mutations in the AANAT, ASMT, MTNR1A, and MTNR1B genes, shared by all cetaceans, result in lack of melatonin synthesis, a necessary precondition for unihemispheric sleep.
Again, to explain this, creationists must choose one of two options: either God is malevolent and placed these genes fully functional – which would be very harmful to underwater creatures – in the genomes of cetaceans, and they were subsequently lost to the exact same inactivating mutations in all cetaceans, or he is deceptive and placed these as pseudogenes in cetacean genomes. Again, neither option is consistent with the God of the Bible, and if God is malevolent or deceptive, that means we can’t trust our senses at all.
Mammal evolution
According to universal common ancestry, mammals evolved from a more basal tetrapod ancestor, and we should expect to find evidence of this in the genome. According to special creation and separate ancestry, different mammal ‘kinds’ were created uniquely, and their genomes should reflect this. Which hypothesis is confirmed by the data? Unsurprisingly, the common ancestry hypothesis is vindicated, as all mammals share remnants of the vitellogenin gene, used to produce the egg yolk in egg-laying animals (Brawand et al. 2008).
Adapted from Figures 3 and 4 of Evograd (2019). (A) The vit1 pseudogene in humans (and other mammals) is in the exact same location in the genome as the vit1 gene in chickens. (B) There are five peaks of conserved synteny in the mammal vit1 pseudogene, spanning 7.3% of the vit1 gene of chickens (~3100 bp).
Not only is this pseudogene found in all mammals, but the same five peaks of conserved sequence (about 3100 base pairs in length) are shared by all mammals, as shown by the mVISTA analysis in the figure above. Thus, creationists must explain why remnants of this gene can be found in all mammals if mammals didn’t have egg-laying ancestors, and also why the same sequences are preserved in this (nonfunctional) pseudogene by all mammals.
YEC geneticist Jeffrey Tomkins (2015) attempted to prove the claim that this pseudogene actually has a function in mammals, but his analysis was very flawed, as shown by our very own Evograd (2019). Furthermore, even with his flawed analysis, only 150 base pairs of the ~3100bp conserved sequences can be explained. Thus, creationists are left with the same two unsatisfactory options as in the above two examples – either all mammals (including humans) were created by God with the ability to lay eggs, and we all lost that ability independently in the exact same way, or God created this pseudogene to deceive us.
Ape evolution
Here’s another example of a ‘shared mistake’ in the genomes of all apes. I just became aware of this thanks to @GutsickGibbon’s new YouTube video. All apes (Hominoidea), including humans, lack tails. According to common ancestry, apes share common ancestry with the Old World monkeys (Cercopithidae) which have tails, so there should be evidence of the loss of tails in all ape genomes. According to separate ancestry, apes form separate ‘kinds’ from tailed monkeys, so there should be no evidence that apes ever had tails.
Once again, the prediction of common ancestry is confirmed by the data. Within the TBXT gene of all ape genomes, which helps establish the vertebral column during development, a transposable element (AluY) has established itself in the sixth intron. As a result, the sixth exon is (mistakenly) excised by the spliceosome (see the figure below). Until recently, we didn’t know for sure whether this resulted in tail loss, but a study by Xia et al. (2024) demonstrated that inducing the same mutation in mice also resulted in tail loss.
Figure 1 of Xia et al. (2024). The (b) insertion of an AluY element into the TBXT gene of apes leads to the (c) excision of Exon 6 of the same gene, which is now known to result in tail loss.
To creationists: if apes don’t share common ancestry, then why do we all have the same inactivating mutation in the TBXT gene? ‘Common design’ can’t be the answer, because it would be more efficient to simply remove the sixth exon altogether, rather than inserting a transposable element that leads to an unintended splicing of the sixth exon. In fact, this mutation is known to be the cause of several rare disorders (including spina bifida), meaning that God would have to be malevolent to specially create us this way. Either God created all apes (including humans) with tails, and each ape kind subsequently lost them to the same mutation, or God is deceiving us by creating us with this transposable element in our genomes. Neither answer is satisfactory.
Human evolution
There are many pseudogenes shared by humans and other primates – after all, our genome contains about ~20,000 pseudogenes (Torrents et al. 2003), and we share 95-96% of our genome with chimpanzees. Here, though, I want to focus on one pseudogene, the GULO pseudogene, because this one has actually been disputed by some creationists. The GULO gene encodes an enzyme that produces vitamin C, but this gene is nonfunctional in many primates (Haplorrhini) including humans, along with a handful of other mammals. This is why humans can get scurvy if we don’t have enough vitamin C in our diet.
All members of Haplorrhini (including humans) share several inactivating mutations in the GULO pseudogene (see the figure below).
Figure 4 from Lachapelle and Drouin (2011). (A) Exons 2 and 3 have been lost in the human, chimp, and macaque lineages; galago represents the ancestral state with a working GULO gene. (B) The deleted region highlighted, showing the many shared mutations between human, chimp, and macaque, compared to the working GULO gene in the galago.
This should be very troubling for creationists, who claim that primates – especially humans – fall into different ‘kinds’ that share no common ancestry. For this reason, YEC geneticist Tomkins (2014) claims that this gene was originally created functional in each primate ‘kind’ and the five lost exons (1, 2, 5, 7, and 10) were lost independently in each lineage!
Setting aside the bad BLAST analysis that he does elsewhere in the paper, this claim is astounding to me. Why were the same exons lost in each lineage? And what about the identical substitutions, insertions, and deletions within the pseudogene found in human, chimp, and macaque (see the figure above)? Basically, Tomkins takes the first option of the two available options for creationists (independent losses or deceptive deity), which is so implausible as to basically be impossible.
Conclusion
The many shared ‘mistakes’ within the bird, whale, mammal, and primate lineages demonstrate virtually beyond a doubt that common ancestry holds true in these lineages. I’d love to see if any of our resident creationists (@colewd? @thoughtful?) would take a stab at explaining it, because I don’t think there is an explanation that fits their model.
Edit: Here are even more examples of shared pseudogenes from @evograd’s website.
It’s really such a shame that creationists are forced to ignore/explain away these facts, because they’re so interesting! In the case of whale evolution, it’s really cool to see that many of the unique features of cetaceans are the result of gene losses. As a theist, it amazes me how creative this process (evolution) that God used to create the diversity of life on earth is. Yet creationists are too focused on proving the minutia of the Bible from a literalistic standpoint to stop and think about the grandeur of it all.
