In my role at BioLogos, I frequently explore the diverse and extensive evidence for common ancestry – the evolutionary idea that species we see in the present day share common ancestors in the past. One such line of evidence is the presence of mutated genes that no longer perform their original function. These sorts of sequences, called pseudogenes, are widespread. Moreover, for many of these defective genes, we share identical mutations with other species – most often with chimpanzees, then with gorillas, then with orang-utans, and so on. The pattern of these shared mutations forms what is known as a nested hierarchy. Shared mutations in pseudogenes that form nested hierarchies are an excellent way to determine how species are related to one another. For example, prior to genome sequencing that provided these data, there were a few scientists that maintained that gorillas were a closer relative to humans than chimpanzees. They based their argument on anatomical evidence, though their views were very much a minority view. Genome sequencing helped resolve this question, in part by examining shared mutations in pseudogenes.
The nose knew
An example that illustrates this well is olfactory receptor pseudogenes. Olfactory receptors are proteins present on nasal surfaces (the olfactory epithelium) that bind on to chemicals in the air we breathe, change their shape in response to that binding, and then use their changed shape to transmit signals to our nervous system that we perceive as smell. Humans, chimpanzees, and gorillas have lost the function of many olfactory receptor genes, and we share many identical mutations in common with these other apes. If humans are more closely related to chimpanzees, this means that we share a longer common ancestral lineage with them than we do with gorillas. If we are more closely related to gorillas, the converse is true. These two hypotheses predict one of two patterns for olfactory receptor pseudogenes. If we are closer relatives to chimpanzees, we should observe some mutations in olfactory receptor pseudogenes that we share with chimpanzees but not with gorillas. Conversely, if we are more closely related to gorillas, we should see some mutations that are shared between humans and gorillas but not with chimpanzees:
When we examine genome sequencing data, we see many identical mutations shared by all three species, but more importantly some mutations shared between humans and chimpanzees that gorillas do not have. This evidence (which also happens to line up with all other genome sequence evidence) shows us that chimpanzees are our closest relatives.
You’ve come a long way, baby
While it’s not too surprising to see olfactory receptor pseudogenes in mammals, pseudogene sequences can persist for a very long time in a lineage – long enough that their presence can become incongruous with the lifestyle of the organism that harbors them. One example that I have discussed several times in the past is the curious case of vitellogenin pseudogenes in placental mammals. Vitellogenins are large proteins used by egg-laying organisms to provide a store of nutrition to their embryos in egg yolk. Since vitellogenins are so large, they are a good source of amino acids when digested (proteins are made of amino acids linked together). Many of the amino acids in vitellogenins have sugars attached to them as well, so they also serve as a source of carbohydrates. The three-dimensional shape of vitellogenin proteins also acts as a carrier for lipids. As such, vitellogenins can be synthesized in the mother and transferred to the yolk as a ready-made supply of amino acids, sugars, and lipids for the developing embryo.
Placental mammals, on the other hand, use a different strategy for nourishing their embryos during development: the placenta. This connection between the mother and embryo allows for nutrient transfer right up until birth. As such, there is no need for vitellogenins, or storing up a supply in the egg yolk for the embryo to use. Evolutionary biology predicts that placental mammals descend from egg-laying ancestors, however – and one good line of evidence in support of that hypothesis (among many) is that placental mammals, humans included, have the remains of vitellogenin gene sequences in their genomes.
Looking for Answers
Not surprisingly, this evidence is problematic for those holding an anti-evolutionary perspective. Back in 2012, I surveyed the websites of anti-evolutionary groups to examine how they handled this evidence – but came up empty-handed. Though young-earth groups (such as the Institute for Creation Research and Answers in Genesis), old-earth groups (such as Reasons to Believe), and supporters of Intelligent Design (such as the Discovery Institute) all had articles discussing pseudogene evidence in general, as well as the particular case of the GULO pseudogene that makes humans and other apes dependent on dietary vitamin C, none specifically dealt with vitellogenin pseudogenes in particular:
Interestingly, this situation has now changed. Though the Discovery Institute and Reasons to Believe remain silent on the topic, a paper has now been published by young-earth creationist (YEC) researcher Jeffery Tomkins that claims to debunk the vitellogenin pseudogene story. The paper is published in Answers Research Journal (a journal owned and operated by Answers in Genesis), though Tomkins works for ICR. In a blog post entitled “Evolutionists Lay an Egg: Vitellogenin Pseudogene Debunked.” Tomkins introduces his work on the ICR website as follows (where he abbreviates vitellogenin as “vtg”):
One study claimed to have found genetic evidence of an ancient vtg gene in the human genome. Because the actual data for this discovery were questionable, the evolutionary community in general did not actively popularize the alleged finding. However, BioLogos, a religious group of evolutionary scientists and liberal Christian theologians, has been promoting the so-called egg-laying pseudogene discovery as evidence of evolution. Because this type of propaganda is targeted to the Christian community, the claim should be more thoroughly investigated.
Tomkins goes on to claim that he has overturned the evidence that the human genome has a vitellogenin pseudogene, claiming rather that it is part of a functional gene. As such, he claims the evidence shows that the “so-called egg-laying pseudogene” is not evidence for evolution, and that BioLogos is in error in presenting it as such. Since I am the primary BioLogos author who uses this example, and since I am committed to representing scientific evidence as accurately as possible for the BioLogos community, I was naturally interested in Tomkins’ claims. Do I have vitellogenin on my face, as it were?
In a nutshell, I do not think the case Tomkins makes stands up to scrutiny – but explaining why will require some effort. As we undertake a careful analysis of his work, we will also have opportunity to delve more fully into the science related to how placental reproduction came to be within our lineage – an area of biology that is fascinating in its own right.
In the next post in this series, we’ll start by examining the vitellogenin sequences found in the human genome, and begin to discuss the lines of evidence that support their evolutionary history.