Pseudogenes Testify to the Evolutionary History of Animals

Pseudogenes Testify to the Evolutionary History of Animals

I’ve written about pseudogenes before on this blog, but I focused on their application to dating species divergence times and their implications for common ancestry amongst those species. This time I’m going to focus on their ability to inform us about the phenotypes of an animal’s evolutionary ancestors.

The principle is simple, and I’ll illustrate it using a well-known example of a pseudogene: GULOP. In most mammals, this gene functions in the biosynthesis of vitamin C, but in humans (and other dry-nosed primates) this gene is a pseudogene which has lost this function, hence we need to consume foods containing vitamin C like citrus fruits in order to prevent diseases like scurvy which result from vitamin C deficiency. So, putting aside any implications for common descent for a moment, the simple fact that we humans have a broken gene for vitamin C synthesis in our genome indicates that at some point in the past, humans (or the ancestors of humans) were capable of producing their own vitamin C.

This fact alone doesn’t seem to pose much of a problem for creationists. They can just say “sure, the original humans could produce their own vitamin C, now we can’t because of “devolution” since the fall”, or something similar. For the purposes of this blog post I’ll accept that answer, and not go into the details about how shared GULO pseudogenes provides a clear signature of common descent with the other haplorhini, but if you’re interested you can read about that here.

In this blog post I’ll document a couple of examples of pseudogenes that creationists won’t want to accept quite as readily, because they testify to an evolutionary history of macroevolutionary changes that creationists deny.

Olfactory Receptors in Whales

Olfaction (smelling) is an important sensory mechanism for survival. It allows animals to sniff out prey, for example. Olfaction works by the animal having a wide repertoire of olfactory receptors in their noses (or similar organs) – each receptor can detect a specific set of molecules and send a signal via olfactory neurons to be interpreted as smells by the brain. A higher number of distinct receptors leads to the ability to discriminate between more smells. Mammals have particularly extensive sets of olfactory receptor genes in their genomes, often numbering in the hundreds or even more than 1000 genes. In fact, olfactory receptors make up the single largest gene superfamily in mammal genomes. These numbers include the pseudogenised olfactory receptors though. For example approximately 20% of the 1300 olfactory receptor genes in mice are pseudogenes, no longer producing their proteins.

It was quickly hypothesised that the proportion of olfactory pseudogenes in a mammalian genome would correlate with the overall olfactory ability and anatomical complexity of the olfactory apparatus of the species, and this trend was found to be real, perhaps unsurprisingly. So, a bunch of mammals might have been able to smell better in the past, what’s the big deal?

Well, whales are mammals, and it’s clear from the fossil record and molecular phylogenies that whales (and other cetaceans) evolved from terrestrial mammals. Creationists, on the other hand, almost unanimously believe that whales are their own “created kind”, and so did not have any terrestrial ancestors.

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Figure 1 | Phylogenetic relationships of extant and extinct cetaceans. Fossil lineages are dashed, and extinct genera are marked by crosses. Major character transitions and/or acquisitions are listed to the right. For character mappings that are ambiguous, a range of nodes is given. Taken from McGowen et al. (2014).

Importantly, these olfactory receptors primarily function to detect airborne odours, an ability that isn’t particularly useful to most whales – not while they’re underwater anyway. Because of this, it’s unsurprising that mysticetes (baleen whales) have reduced olfactory apparatus, and odontocetes (toothed whales) lack it altogether.

Based on this information we can make predictions of what to expect in the whale genomes when it comes to olfactory receptors for both the evolutionary model and the creation model. Since creationism dictates that whales were originally created in their marine environments without the need to detect airborne smells, a creation model would surely predict that whales were not created with a significant number of olfactory receptor genes, and that of those that they were created with, most of them would still be functional in some way.

On the other hand, the evolutionary model dictates that the ancestors of whales were terrestrial mammals which would have had a need to detect airborne odours, and that this ability was lost in whales once they evolved to be adapted to a marine lifestyle. Therefore we could predict that there would be a higher proportion of olfactory receptor pseudogenes in whales than in terrestrial mammals that still require olfaction. Generating predictions like this is essential for a scientific theory, and successful predictions constitute powerful evidence in support of the theory.

Consistent with the evolutionary prediction, several studies examining the olfactory receptor genes in whales have found that much higher proportions of pseudogenes are found, from 74%-100% in odontocetes, and from 29%-54% in mysticetes (McGowen et al., 2014). The latter number might not seem that high, but remember that mysticetes are the clade of whales that do seem to have retained some olfactory structures and in turn likely retain some amount of olfactory sense (corroborated by anecdotal behavioural observations). Odontocetes, on the other hand, have lost the olfactory bulb altogether.

This data bears out the correlation between olfactory ability and proportion of olfactory receptor pseudogenes predicted by the evolutionary model. This kind of trend also holds for other classes of genes involved in olfaction. During the transition from land to water, the whale lineage (primarily the odontocetes) gradually lost the unnecessary ability to detect airborne odours in large part through pseudogenisation.

To put it as simply as possible: the ancient ancestors of whales clearly had large numbers of functional genes involved in airborne odour detection, indicting that these ancestors were terrestrial mammals.

As an added bonus, the mutations found in these whale pseudogenes accumulate neutrally (since the sequence is already non-functional), and as such possess a pretty clear signal of the relatedness of these whales that phylogeneticists can use to robustly reconstruct/confirm the whale phylogeny (McGowen et al., 2008).

This story also relates to us humans, as approximately half of all human olfactory receptor genes are pseudogenes as well, and this is thought to be the result of us coming to rely more on our trichromatic (3-colour) vision for foraging etc than our sense of smell. This is supported by the fact that primates with trichromatic vision tend to have higher number of olfactory pseudogenes than other primates with dichromatic (2-colour) vision (Gilad et al., 2004).

This example of olfactory genes, while relating to a morphological structure (olfactory organs) and environment, is really about a molecular phenotype, but what about morphological phenotypes? Can they be inferred from the pseudogenes littering the genomes of extant animals? Remarkably, the answer is yes, and the implications for testing evolutionary hypotheses about common ancestry should be immediately apparent. Based on the morphology and inferred phylogenies of animals in the fossil record, we can make predictions about what pseudogenes might be found in certain genomes, and vice versa.

Genes for Teeth in Birds, Turtles, and Toothless Mammals

Enamel is found primarily in the teeth of a diverse range of vertebrate animal species. Instead of getting into the details of the early history of enamel and it’s functions in fish, I’ll skip all the way to tetrapods. It goes without saying that overwhelming evidence shows that enamel was present in the teeth of the last common ancestor of mammals, birds+reptiles, and amphibians. That’s the long-standing evolutionary model that can be put to the test.

Of course, not all extant tetrapods have enamel on their teeth – some of them don’t have any teeth at all! This leads to the conclusion that during evolutionary history, enamel-covered teeth must have been lost in certain lineages. Therefore, as before, we can make some predictions about finding pseudogenes that used to function in the production of enamel-covered teeth in these species.

toothless.png

With regards to placental mammals, Meredith et al. (2009) say:

Most placental mammals have teeth with enamel, but there are also edentulous (toothless) mammals (pangolins, baleen whales, anteaters) and mammals with enamelless teeth (sloths, armadillos, pygmy and dwarf sperm whales, aardvark). Among edentulous mammals, there is evidence for aborted tooth bud development in mysticetes [15], pangolins [16],[17], and anteaters [17]. Rudimentary teeth are best developed in mysticetes, but enamel is not deposited and the tooth buds are degraded and resorbed prior to parturition (reviewed in reference [15]).

So before we even go looking for teeth pseudogenes, we have evidence from developmental biology indicating that these species begin to develop teeth as embryos, but that this process is aborted, providing more excellent evidence that these toothless mammals descended from toothed ancestors. I could write an entire blog post on these kinds of developmental atavisms (and maybe I will in the future, although I think other sources have already covered the subject quite well), but for now, back to pseudogenes.

Further examples outside of Mammalia include birds and turtles, which have lost the teeth from their reptilian ancestors in favour of beaks and beak-like structures respectively. While creationists might not flinch at the idea of anteaters being originally created with teeth and losing them secondarily, I suspect they would feel a little differently about birds originally having teeth as this would go some way to corroborate the dinosaurian ancestry of birds which creationists can’t possibly allow.

I’ll let Meredith et al. (2009) describe their results themselves:

Given this ancestry, we predicted that mammalian species without teeth or with teeth that lack enamel would have copies of the gene that codes for the enamelin protein, but that the enamelin gene in these species would contain mutations that render it a nonfunctional pseudogene. To test this hypothesis, we sequenced most of the protein-coding region of the enamelin gene in all groups of placental mammals that lack teeth or have enamelless teeth. In every case, we discovered mutations in the enamelin gene that disrupt the proper reading frame that codes for the enamelin protein. Our results link evolutionary change at the molecular level to morphological change in the fossil record and also provide evidence for the enormous predictive power of Charles Darwin’s theory of descent with modification.

A few years after they published this paper focusing on placental mammals, Dr. Robert Meredith and his colleagues went looking for the same enamelin (ENAM) gene, as well as 2 others involved in the development of enamel-covered teeth, ameloblastin (AMBN) and amelogenin (AMEL) in the genomes of birds and turtles (and placental mammals again): Meredith et al., (2013).

As expected, they recovered pseudogenised versions of 1 or all of these genes in the genomes of the species of birds and turtles they examined. They were even able to identify the precise inactivating mutations and map them onto a phylogeny to show the likely order of inactivating mutations (Figure 2).

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Figure 2 | Phylogeny with inferred inactivating mutations of enamel matrix protein genes. A species tree of the mammals, turtles, and birds examined in the study, as well as some extinct taxa in their inferred positions. Fossil lineages are dashed, and extinct genera are marked by crosses. White nodes represent toothlessness, grey nodes represent the presence of teeth without enamel, black nodes represent the presence of teeth with enamel. The presence of a particular inactivating mutation in a branch is represented by the vertical bars (pink = ENAM [E], blue = AMBN [B], green = AMEL [A]). Taken from Meredith et al. (2013).
Quoting their conclusion:

Edentulism [lack of teeth – RM] has evolved independently in multiple lineages of living amniotes including turtles, birds, echidnas, baleen whales, anteaters, and pangolins. There are also mammals with enamelless teeth including pygmy sperm whale, narwhal, sloths, armadillos, and aardvarks. In every case these edentulous or enamelless forms have descended from ancestors with enamel-capped teeth. Thus, amniote diversity provides a natural laboratory for testing hypotheses of tooth-specific gene function [3]. Moreover, this laboratory includes multiple, replicated experiments. AMBN, AMEL, and ENAM have all been postulated to have tooth-specific or even enamel-specific gene functions [11, 12, 13, 14, 15, 16, 17], although pleiotropic functions have been suggested for AMBN[9, 48, 60, 61] and AMEL[62, 63]. The widespread occurrence of EMP pseudogenes in turtles, birds, and several mammalian lineages (Table 1) provides compelling evidence that the only unique, non-redundant function of these genes in amniotes is in enamel formation: functional copies of these genes have not been retained by natural selection when enamel production was abrogated independently in distantly related lineages. By contrast, representative sequences from amniotes with enamel-capped teeth retain intact coding sequences for AMBN[1, 48]; also see Additional file 11, AMEL[3, 48, 64], and ENAM[1, 2, 18, 37, 65].

The evolution of tooth loss in multiple amniote lineages also provides a model system for integrating the fossil record, phylogenetics, and genomics. This system allows for reciprocal hypothesis testing and provides a multifaceted, synthetic view on macroevolutionary transitions in testudines, birds, and edentulous/enamelless mammals [1, 2]. The fossil record and phylogenetics combine to predict the occurrence of molecular fossils of tooth-specific genes in the genomes of edentulous and enamelless amniotes, and molecular fossils have been discovered in all lineages that have been investigated.

I couldn’t have put it better myself. Clear evidence that birds, turtles, and toothless mammals evolved from ancestors with enamel-covered teeth, matching the prediction based on the fossil record and phylogenetics.

Update 1: The day after I published this blog post, the genome assemblies of the (toothless) Chinese and Malayan Pangolins were published in Genome Research (Choo et al., 2018), whereupon the pseudogenised copies of ENAM, AMEL, and AMBN were identified. Previously, only the ENAM gene was known to be pseudogenised in pangolins (Meredith et al. 2009).

Update 2: Joel Duff has written a post over on his blog describing the findings of a paper Meredith and colleagues published in 2014 about the pervasiveness of teeth-related pseudogenes in birds (Meredith et al., 2014). Both the paper and blog post are well worth checking out.

Update 3: Another great paper on this subject was published by Springer et al. (2019). The authors studied 165 placental mammal species, including 19 species that lack enamel-covered teeth or lack teeth altogether, and found that they all possessed pseudogenised versions of the ODAM gene, a gene known to be involved in tooth development. The introduction to the paper is replete with references to more research like this involving other (pseudo)genes.

 

Comments and queries are welcome.

-RM

7 thoughts on “Pseudogenes Testify to the Evolutionary History of Animals

  1. I’m getting a request for my password when I log in to your latest (14 Sep) post. I didn’t know I had a password for you, and my WordPress password doesn’t work.

    Btw, your choices, but is Jeanson really worth all that time and effort when you couuld be writing admirable and inforative posts, such as this one, about far worthier subjects?

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    1. Today’s post is a draft. I’ve sent it to some people to review it and iron out any kinks before releasing the finished version. I wrote it in wordpress so the best way to keep the formatting intact was to publish it here as a protected article, and I gave the reviewers the password.

      Don’t worry, as soon as I’m done with Jeanson I’ll get back to more interesting subjects. I didn’t anticipate quite how much time I’d spend on Jeanson’s book here when I started out, but now that I’m most of the way through, I want to finish it strongly. I do feel there is value in responding thoroughly to the technical arguments made by the “big names” in creationism/ID.

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      1. Understood. The problem always is to keep things in control; a rebuttal can end up longer than the item being rebutted, especially if it’s very sciency. (Ofc sciency =/= scientific). I don’t know if you’ve checked out commetns on Amazon – a depressing read

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  2. i have an interesting argument that show why nature was designed: what if we will see a self replicating robot ( lets say even with dna) on a far planet? do we need to conclude design or a natural process in this case? remember that according to evolution if its made from organic components and have a self replicating system we need to conclude a natural process because it has living traits. but we know that even a self replicating robot is evidence for design. therefore a penguin for instance need design too.

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