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Evolution Basics: Genomes as Ancient Texts, Part 4

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June 28, 2013 Tags: Genetics
Evolution Basics: Genomes as Ancient Texts, Part 4

Today's entry was written by Dennis Venema. You can read more about what we believe here.

Note: This series of posts is intended as a basic introduction to the science of evolution for non-specialists. You can see the introduction to this series here. In this post we compare gene sequences between humans and other mammals to test the hypothesis that they are modified copies derived from an ancestral genome.

In yesterday’s post, we saw that at a large scale of organization, the human genome has the features it should have if indeed we share ancestry with other great apes. Continuing with our “book” analogy, we now turn to comparing these texts at a finer level of detail – that of sentences and words.

Comparing genomes at the “sentence” level

In a previous post, we compared the DNA sequences of a gene found in a number of species of Drosophila. Such comparisons are also possible using DNA sequences from mammals (including humans and other primates), and the pattern they produce is by now familiar:

As we saw for the Drosophila sequences, this gene is nearly identical across a number of species. Specifically, the human sequence and the sequences of three other primates (chimpanzees, gorillas and orangutans) differ by only a handful of DNA monomers (at the most, 4 of the 90 are different). Also, as we have seen before, there is no biological need for these sequences to be this identical – in fact, even for this small region of this gene, there are over 53 million (!) different ways to code for the exact same amino acid sequence. Most of those sequences are much more different from the human sequence than the nearly identical sequences we observe in other primates. To carry the point further, there is also no particular biological need for this gene to have the exact amino acid sequence we see shared among primates. In other organisms (such as dogs and wolves) a slightly different sequence performs the same task equally well.

Of course it is not possible to show DNA alignments of large swaths of DNA sequence in this format. This small gene segment, however, is representative of genes (and even whole genomes) among primates. A detailed comparison of all gene sequences between humans and chimpanzees, for example, reveals that they are 99.4% identical across 1.85 x 107 (18 million) DNA monomers. Note that regions of the genome that code for genes are a tiny minority of genome sequences - humans and chimpanzees have over 3.0 x 109 (3 billion) DNA monomers in their genomes. Of these 3 billion monomers, 2.7 billion of them align with each other with only a 1.23% difference between them.

In short, when comparing DNA sequences between humans and other primates, we see exactly the pattern we would predict based on shared ancestry – a pattern consistent with slight modifications to an ancestral genome.

Looking for typos

In a previous post in this series, we discussed how DNA replication is a highly accurate process, but not a perfect one. These two features of DNA replication mean that mutations can occur to genes when they are copied, and that future copies made from a mutated template will faithfully pass that mutation on (at least, until a second mutation occurs at the same location to change things once again). What this means is that gene sequences can persist in genomes for a long time after they are mutated to a non-functional sequence if there is not a selective disadvantage for losing the function in question. (If a mutation does result in a disadvantage, then natural selection will tend to remove it from its population, as we have discussed previously.)

One such example involves a gene that codes for an enzyme (L-gulonolactone oxidase, or “GULO”) that is required the synthesis of vitamin C in mammals. Most mammals make their own vitamin C from other compounds in their diet, and the GULO gene is necessary for the last step in the process that converts a vitamin C precursor to the final product. As we have seen for other genes, the sequence for this gene is conserved between mammals – it has a nearly identical sequence that is maintained through natural selection. For example, a portion of this gene in cows, dogs and rats has the following sequence (with differences from the cow sequence outlined in black):

In all three of these species, this gene is functional, and all three can make their own vitamin C without obtaining it directly from their diet.

Humans, of course, cannot make their own vitamin C – we get scurvy if we do not obtain vitamin C from our diet. This atypical situation (for a mammal) is shared by other great apes, and for the same reason. Though these species have some of the DNA sequence for the GULO gene, it has numerous mutations in it that render the gene unable to make a functional enzyme product. The same region of the GULO gene shown in the above figure has the following sequences in humans, chimpanzees and orangutans (now with differences from the human sequence outlined in black):

Homo sapiensHuman
Pan troglodytesChimpanzee
Pongo pygmaeusOrangutan
Bos taurusCow
Canis lupusDog/Wolf
Rattus norvegicusRat
Functional GULO sequences from cow, dog, and rat compared to nonfunctional sequences in several primates. A portion of exon 12 is shown. Differences from the human sequence are shown in black. Primates share a single nucleotide deletion (highlighted in yellow) in common in this region.

Once again we notice that the primate sequences are nearly identical to one another. One new feature to note here, however, is that these three copies of the GULO gene are non-functional in part because they have a deletion mutation – the removal of one DNA monomer (highlighted in yellow in the primate sequences). This deletion mutation is identical in all three species, providing evidence that it is a “shared typo” copied from a prior text – or, in biological terms, a deletion mutation that happened once in the common ancestor of humans, chimpanzees and orangutans, and was then inherited by all three species. Dogs, cows and rats, however, branched off of the lineage leading to primates before this deletion event occurred:

The loss of GULO function does not seem to have been a selective disadvantage for primates at the time – likely because they had a diet rich in vitamin C. Indeed, even for humans, this loss is not a serious problem unless one finds oneself without a source of vitamin C for a prolonged period of time.

The nose knows

As interesting as the GULO example is (and it is an example I have discussed in more detail [http://biologos.org/blog/a-tale-of-three-creationists-part-3] in another context) it is but one of many examples of shared, identical mutations found in the human genome and other primate genomes. One study that examined shared primate mutations in detail investigated mutations in genes devoted to the sense of smell. These genes, called olfactory receptors, are proteins found on the membrane of cells in the nasal epithelium in mammals. Olfactory receptors do their job by binding on to compounds in the air, changing shape in the process, and signaling that change in shape to the nervous system in what we perceive as the sense of smell. The combined action of numerous olfactory receptors acting in concert is what gives any given smell its distinctive features. Mammals dedicate a disproportionate amount of their genome to olfactory receptor genes, most likely because such genes are so useful for finding food, finding mates, and in general perceiving one’s environment. Despite their usefulness, these genes can also be mutated and lost – and indeed, the human genome shows that our species has lost several due to mutation. As for the GULO gene, however, these defective olfactory gene sequences persist in recognizable form. What is more important for our purposes, however, is the pattern these mutated genes form when compared to other primate genomes. As we first introduced with our copied book analogy, we expect to find some typos that are shared between texts, and other typos that are unique to one edition. For defective olfactory genes, we observe precisely these two categories – shared mutations, and unique mutations:

As you can see from the diagram above, humans share the most identical olfactory gene mutations with chimpanzees, fewer with gorillas, and fewer still with orangutans. Of the 12 mutations that are identical between humans and chimpanzees, 9 are also identical with gorillas, and 6 with orangutans. These shared mutations and the pattern we find them in are easily explained through shared ancestry, as indicated in red on the diagram above. The mutations unique to a given species are also easily explained as arising after populations separate (in blue).

It’s also important to note what we do not see when comparing these mutations between primates. We do not observe identical mutations between humans and gorillas, for example, unless we always see the exact same mutation in chimpanzees. This makes perfect sense if the common ancestral population of humans and gorillas is also the common ancestral population of humans, gorillas and chimpanzees. Likewise, if we observe identical mutations shared between humans and orangutans, we can predict with confidence that we will observe these exact mutations in gorillas and chimpanzees – and in fact we do. This pattern of shared mutations is precisely what one would predict if in fact it was produced by shared ancestry – with nothing out of place.

Multiple lines of evidence, one conclusion

In the next post in this series, we’ll circle back and discuss how the multiple lines of genomics evidence for human evolution that we’ve examined cohere into a mutually supportive pattern. 

Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.

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marklynn.buchanan - #81513

July 1st 2013

Thanks Dennis for such a clear article.

A couple of questions:

How many pseudogenes do humans share with the great apes? Or the related question ‘How many ERVs do humans share with the great apes?’

Is is possible to quantify the chances of the same mutation in the same gene in two or more different populations to produce the same pseudogene?

If there are answers to the above it would be relatively easy to quantify the overall probability that humans did not have a common ancestor with the great apes. It’s obvious that the probability is very low but it would be nice to have a relatively accurate number.

PNG - #81632

July 4th 2013

There are over a million orthologous Alu element insertions in human and chimp genomes. Getting an Alu element into the corresponding site in both genomes is at least a million to one shot. So, ignoring all the other orthologous insertions (L1s, ERVs, etc.), corresponding pseudogenes and the like, 1,000,000 to the 1,000,000th power. How many impossible things can you believe before breakfast?

Eddie - #81737

July 6th 2013

Glad to hear that you acknowledge the near-demonstrative power of probablistic arguments, PNG.  The next time Dembski or others from the ID side use arguments much like the one you’ve just used, I’ll be sure to call on you to come to their defense.  

PNG - #81742

July 6th 2013

All probablistic arguments require assumptions, including the one above. The assumptions I made above fit with what is known about transposition of the specific elements. Dembski’s arguments assume things that we don’t really know, and may not ever know. And, no, I don’t really want to argue about it.

Eddie - #81748

July 6th 2013

Neither do I.  Didn’t you see my smiley face?    :-)

I was just ribbing you, PNG.  I can’t bring myself to antagonize a scientist who likes Epic poetry.  

PNG - #81743

July 6th 2013

I should add that it is interesting to me that, preoccupied as he is with arguments based on calculating very long odds, Dembski rejects the argument above (implicitly) and denies common descent. It seems that he accepts probablistic arguments only when they fit his ideology.

Eddie - #81749

July 6th 2013

I’m not doing to respond for Dembski, because I don’t know what he’d say.  I’d rather see Dembski go head-to-head with his critics, than pretend that I can stand in for him.

As I’ve said before, I wish that BioLogos would host actual debates between ID and TE people, so that these mathematical and scientific details could be thrashed out in person.

I don’t like this culture-war practice of one-sided op-eds being posted on one side’s blog, and equally one-sided op-eds being posted on the others side’s blog.

Oh, I know BioLogos printed Dembski’s thoughts on religion (as part of its Southern Baptist series), but it hasn’t given Dembski a chance to respond here at length on the frequent TE criticisms of his scientific arguments.  Nor has it given Behe a chance, or Wells.  It did give Meyer a slight opportunity, long ago, to respond to Ayala, but only grudgingly, as the then-President’s rather schoolteacherly admonitory comments made clear.  And the vast majority of attacks on Meyer here have not been accompanied by a Meyer rebuttal column.  

ID-TE debates—I don’t mean arguments between commenters on blogs, I mean formal debates between leading figures, with set scientific topics that both sides can research for (Cambrian explosion, origin of life, capability of neo-Darwinian mechanisms, nature of biological information, etc.)—delivered in back-and-forth columns, or on stage, would be helpful.  But the TE side frequently seems to shy away from them.  Francis Collins refused on principle to debate ID people, even when he was not NIH head; at the Vibrant Dance of Science and Faith Conference, the TE team backed out of the scheduled debate there; and at the Wheaton conference, one or more members of the TE team (though the identity of the person(s) has never been established) vetoed the idea of recording the proceedings, which prevents the rest of the Christian and scientific world from watching those debates and rendering a judgment whose side seemed stronger.

There is the odd exception, of course.  Steve Matheson once debated some ID folks, but he was paired with Arthur Hunt, an atheist.  And Lamoureux did the same, but paired with Ruse, an agnostic or atheist.  Ken Miller, too, was often paired with unbelievers such as Eugenie Scott in his anti-ID stage and video appearances.  It’s almost as if the TEs in those cases were “leaning” a bit on the atheists for support, as if they didn’t think they could carry the scientific argument very well without atheist help.  But whatever the motive was, it would be nice to have a debate entirely between Christian scientists, ID on one side, TE on the other, without the atheist factor to cloud the issues.

But will this ever happen?  I was hoping the new management of BioLogos, free perhaps from some of the historical and emotional “baggage” of the past, might initiate something along these lines.  I even suggested it in response to the new President’s opening message.  But so far, it’s business as usual:  columns on genetics to educate the fundamentalists, reprinted columns celebrating the magical creative powers of randomness (with no more engagement between columnists and readers than when the columns were printed the first time), criticisms of ID and creationism, etc.  I don’t see any fundamental change in direction accompanying the new management.  Steady as she goes.  

I of course like Ted Davis’s columns, but they are sui generis on this site—columns designed purely to inform the reader of intellectual options, not to persuade the reader that one side is right and the other wrong.  The new management is to be congratulated for continuing Ted’s series, but still, I don’t see any serious outreach by the new management to the ID community.  Offers of content-oriented debates where TEs would treat ID proponents as scientific peers—that would be genuine outreach.

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