Evolution Basics: Genomes as Ancient Texts, Part 2

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June 14, 2013 Tags: Genetics

Today's entry was written by Dennis Venema. Please note the views expressed here are those of the author, not necessarily of The BioLogos Foundation. You can read more about what we believe here.

Evolution Basics: Genomes as Ancient Texts, Part 2

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 examine the DNA sequences of several fruit fly species to test the hypothesis that they arose through speciation events.

In yesterday’s post, we discussed some features of what we would expect when comparing genomes between similar species, if indeed those species descended from a common ancestral population. Returning to our “book” analogy for genomes, we made the point that the first thing to look for would be overall structure of two genomes proposed to be descended from a common ancestral genome: are the “chapters,” “paragraphs,” etc., in the same order? Do they use the same “sentences”? and so on. In other words, do the genomes of any existing species look like they are slightly modified copies of each other?

The answer to this question from modern comparative genomics is an emphatic yes. What we see when we compare genomes of species that we suspect to be relatives is very much that they do indeed look like copies of each other. In some cases, the match between two genomes can be in excess of 95%, DNA monomer for DNA monomer, for the bulk of the two genomes. Not only do they have the same genes, but they have them in the same order on their chromosomes, with each chromosome in the two species having a match in the other species. Imagine finding a book that was 95% identical to another manuscript, with chapters, paragraphs and sentences all in the same order, with only small differences between them – that is the sort of impression one gets when comparing genomes between some species.

One group that has been analyzed in some detail are various species of fruit flies (in the genus Drosophila (pronounced “Dro-SOF-i-la”). Scientists have now determined the complete genome sequences for twelve Drosophila species and compared them with one another. Some species have nearly identical genomes, exactly as one would predict if they were once the same species with a common genome. While it’s not possible to show large amounts of DNA sequence here, let’s examine a small fragment of one “sentence” (i.e. gene) in three species of fruit flies (Drosophila yakuba, Drosophila simulans, and Drosophila sechellia) – all known to be distinct fly species:

The first impression one gets when looking over the sequences is that they are nearly identical. This is not unusual for these three species – indeed, this pattern applies to every gene they have (and they all have the same genes). The second thing one notices, however, is that there are rare differences – in this small snippet, two of the species (D. simulans and D. sechellia) have an “a” in the fourth position of this gene, where D. yakuba has a “t”.

Think back to the analogy that we used yesterday – that of book printings and typos shared between them. These sequences in these three species are very much like the hypothetical printings in our analogy, and we can make sense of the pattern we observe in much the same way:

(Now, astute readers will also note that the other possibility is that the “a” at the fourth position is the original text, that the “t” is the typo, and that a (t to a) mutation happened once on the lineage leading to D. yakuba. If you’re wondering about this option, well done. The trick to deciding what the original text is to look at as many copies as possible  - and in this case, when we look at a wide number of additional Drosophila species, we see an “t” in the fourth position in most other species, and an “a” only in D. simulans and D. sechellia. This means the most parsimonious choice is that the “t” is the original, and the “a” is a mutation).

While this is only a small example, it illustrates what scientists observe when comparing the genomes of species they suspect to be relatives based on other criteria (such as morphology). What they see is precisely what one would expect if indeed speciation events had occurred to produce the species in question: nearly identical genomes, with small changes shared between some species.

Identity beyond what’s necessary for function at the DNA level

A further observation that supports the hypothesis that these sequences are copies of an ancestral sequence is that the level of identity (matching of sequence) between them is greater than it needs to be, even when the function of the gene is considered. Let’s return to the gene fragment that we were just examining. This sequence, as the start of a gene, codes for a protein with the same function in all three species. (If you need a refresher on how genes are made up into DNA monomers that are eventually translated into a sequence of amino acid monomers, you can refer to two prior posts in this series, here and here.) In these species this protein has the following sequence for the first eight monomers (amino acids):

As you can see, the second amino acid is different between the two sequences, but the other amino acids are identical. What is important for our purposes here is to note that that there are many, many ways to write this “sentence” and arrive at the same meaning (sequence of amino acids). This is possible because for most amino acids, there are several DNA monomer combinations (of three nucleotides) that produce the same amino acid when translated. For example, the sequence in D. yakuba could also be written as follows (among many other options):

This sequence is quite different from what we see in the other two species:

In this case, only 14 of the 27 DNA monomers match – an identity of only about 52%). What we observe between these species, however, is that 26 out of the 27 monomers match (over 96% identity). In other words, it would be possible for these two genes to be much less identical at the DNA level, and still have the same amino acid sequences that we observe in the two species. Yet, what we see when we compare the two genes, is that they match at the DNA level much more than they need to in order to have the same amino acid sequence. A simple explanation is that the two sequences match because they are copied from the same original sequence.

Identity beyond what’s necessary for function at the amino acid level

A second observation that supports the hypothesis that the D. yakuba, D. simulans and D. sechellia gene sequences are in fact copies follows from examining other fly species that are less closely related to these three. All Drosophila species examined to date have this gene, but in more distant relatives the sequence can be somewhat different. For example, this gene in D. mojavensis has the following DNA sequence:

Again, some of the sequence remains identical in all four species (supporting the hypothesis that this sequence is also a copy, but with more changes), but now we see greater differences. Despite these differences, however, the D. mojavensis version of the gene is perfectly functional and does the exact same job as the gene in the other three more closely related species.

So, these observations indicate that there is no biological need for nearly identical genes at the amino acid level, or even at the DNA level, in different species. Numerous amino acid sequences, and even numerous DNA sequences, are equally capable of performing the same function. Yet, what we see time and again (across whole genomes!) are nearly identical genes, with a few (often shared) differences – exactly what speciation events would be expected to produce.

What about “common design”?

One question I am frequently asked when presenting this sort of data is that of “common design” as an alternative explanation. In other words, could these sorts of patterns be explained as separately created species that do not share ancestry, but rather were designed (created) to have the same (or similar) genes because those genes need to have the same (or similar) functions?

We have already seen the basic problems with this line of argument – that genes (and entire genomes) of similar species match much more than they need to – and that the differences we see in closely related species are arranged in exactly the pattern one would predict if speciation events had produced them.

Just flies

Of course, most Christians don’t lose sleep over the possibility that numerous fruit fly species arose over time through multiple speciation events. As we have mentioned previously, even most Young Earth Creationists accept speciation events such as these. What is more contentious, of course, is the question of whether the pattern of shared ancestry extends to our own species. In the next post in this series, we’ll examine this question by comparing the human genome to the genomes of our proposed nearest living relatives – the great apes. 


Dennis Venema is Fellow of Biology for The BioLogos Foundation and associate professor of biology at Trinity Western University in Langley, British Columbia. His research is focused on the genetics of pattern formation and signalling.

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Allen Last - #81067

June 14th 2013

Having looked at this throughotu my professional life from Biochemist to physician, speciation and evolution woudl appear to be true.  It does not, to my eye, necessarily prove or even suggest that all of life as in the creation sprang from nothing or nonliving matter, nor does this process necessarily account for all of the diversity of life on Earth.  While speciation by natural selection appears to be one way that diversity of life can occur, it really fails to prove that it is the only way.  It is certainly possible that God created numerous living creatures fully formed, but built into them the ability to adapt through the generations to changing environments.  In fact that ability to slowly change is an ingenious design, rather than an amazingly unlikely unintended consequence of DNA.  From those numerous designed creatures multiple others or variations on themes could have occurred through evolution. 

Perhaps I am missing something theological, scientific or philosophical that woudl refute these contentions.  Any thoughts?

Lou Jost - #81070

June 14th 2013

Yes, it is logically possible that many forms were specially created and then diversified. However, the patterns described by Dennis in this post extend even to very distantly related animals. The patterns get gradually weaker with phylogenetic distance; there are no abrupt massive rearrangements when crossing generic or familial boundaries (eg cats vs dogs, or hippos vs whales). Also, the fossil record rules out your hypothesis and confirms the story told by the genes.

Allen Last - #81075

June 14th 2013

That may be true.  Last time I looked, which is granted some time ago, the fossil record was still not very complete with significant gaps.  Have these been closed now?

Also, and I really am not married to the idea of multiple forms and then diversified, simply exploring the possibility, is it not reasonable or possible for God to have used similar DNA patterns and sequences between animals since they work for similar purposes?

Lou Jost - #81079

June 15th 2013

There will always be gaps in the fossil record, but most are small. There are a few big ones—pterosaurs for example seem to come out of nowhere. And the transition from soft to hard fossils in the Cambrian is rather sudden. The trend has definitely been a slow filling of even these gaps, though. Don’t forget how spotty the fossil record is. Many species are known only from a single incomplete specimen. One can use the number of species known from single specimens to calculate the completeness of the fossil record, and it proves to be very incomplete.

About your last point, read Dennis’ two posts on this again. He answered your question very nicely in multiple ways.

beaglelady - #81092

June 15th 2013

Lou is correct. Remember that fossilization is a rare event, the exception rather than the rule.   The animal or plant must be buried quickly for fossilization to occur.    

Lou Jost - #81097

June 15th 2013

And then we still have to find it millions of years later!! Very few spots are able to be sampled for fossils, so our geographic and habitat coverage is very poor.

Rainforests are especially under-represented because of poor conditions for making fossils. And that is where most of  the earth’s species live today.

beaglelady - #81098

June 15th 2013

And funding for the whole operation must be secured before fossil hunting can begin.  The fossils are often brought out in chunks of rock, wrapped in plaster, and then taken to some museum.  Only then can the preparator (a specialist) start on extracting the fossil—if you’re lucky, as  that takes a LONG time and more funds.  I think a lot of museums have bones  still wrapped in plaster sitting around awaiting preparation.    

And paleontologists have to be present at fossil digs to supervise the operation—otherwise you could get fraud. (That’s why a lot of them look like sun-burned cowboys.)   Paleontologists need permission from foreign governments to go on digs in their lands.  And if the country is at war it could be too dangerous to work there anyway.    


glsi - #81109

June 16th 2013

Of course fossilization is a rare event and their aquistion and preparation is expensive.  Notwithstanding, they’re found all the time and when the funds are raised to properly extract and study them more often than not they turn out to be yet another duplicate individual of a species previously discovered.  That’s the real reason so many are sitting around in boxes in museums.  If somebody thinks they have a real evolutionary score I’m sure Templeton would pitch in a pile of dough to have them studied.  But nobody wants to pony up for the same old thing.  When new species are discovered they are  found fully-formed and appear suddenly in the fossil record.  If Darwinism were true you would see continuums showing slow, gradual change but this is not the case.  That is the central prediction of Darwinism, but it’s turned out to be false.

beaglelady - #81110

June 16th 2013

Not true.  Some species are known only by a single specimen.   But some fossils are so abundant that people can dig their own, e.g. at Lake Florissant in Colorado. 

I think that lack of resources could be a reason for  fossils awaiting extraction by preparators.   

It’s extremely valuable to have multiple specimens of  a species when only a few have been found.  Even when a species is well-represented in the fossil record another museum might want to have one. 

We do see gradualism in the fossil record.  Consider the fossil record of horses.

btw,  What does it mean to be fully-formed?  As opposed to what?  Partially formed?   


glsi - #81124

June 16th 2013

I’m not clear what you’re saying is not true.  I agree fossils are very abundant.  That’s why you need to see thousands of examples of gradualism if Darwinism is true.

Fully-formed means you’re not finding slightly modified versions of things in the process of gradual change.  You don’t find a giraffe with half a neck for example.  You don’t find the predessor to the playpus as a platypus without its duckbill for example.   

The proposed mechanism of Darwinism is mutation/selection.  That would be gene to new, modified gene slowly, slowly being selected for and showing up in the fossil record.  Indeed, very slow and very gradual.  This is not at all what shows up in real life.  Although puncuated equilibrium has been proposed as a solution for this problem, no neoDarwinian mechanism has ever been able to account for the sudden jumps.

Are you saying the fossil record of horse species are direct descendants of each other?  I don’t think they are.  Which means the horse fossils don’t show gradualism either.

beaglelady - #81125

June 16th 2013

You don’t find a giraffe with half a neck for example.  

Yes, you do find giraffe ancestors with shorter necks.   

See this video Inside Nature’s Giants: Giraffe

That would be gene to new, modified gene slowly, slowly being selected for and showing up in the fossil record.

Don’t know what you are talking about. Transitional species are abundant.  We find whale ancestors that have both baleen AND teeth.  And vestigial hind limbs. Sometimes they don’t even stick out of the body.  See this video: 

Inside Nature’s Giants: Sperm Whale

Are you saying the fossil record of horse species are direct descendants of each other?  I don’t think they are.

No Some branches died out.   There used to be multiple species living at the same time in North America.  But they all descended from ancestral species.  

PNG - #81132

June 16th 2013

Funny you should mention the toothed whale to baleen transition - I found this ref. the other day. Haven’t been to the library yet to get the paper, but it sounds interesting. The whole dolphin genome should be published soon, and there should be more interesting stuff in it.

Morphological and molecular evidence for a stepwise evolutionary transition from teeth to baleen in mysticete whales. http://www.ncbi.nlm.nih.gov/pubmed/18266181/

The origin of baleen in mysticete whales represents a major transition in the phylogenetic history of Cetacea. This key specialization, a keratinous sieve that enables filter-feeding, permitted exploitation of a new ecological niche and heralded the evolution of modern baleen-bearing whales, the largest animals on Earth. To date, all formally described mysticete fossils conform to two types: toothed species from Oligocene-age rocks (approximately 24 to 34 million years old) and toothless species that presumably utilized baleen to feed (Recent to approximately 30 million years old). Here, we show that several Oligocene toothed mysticetes have nutrient foramina and associated sulci on the lateral portions of their palates, homologous structures in extant mysticetes house vessels that nourish baleen. The simultaneous occurrence of teeth and nutrient foramina implies that both teeth and baleen were present in these early mysticetes. Phylogenetic analyses of a supermatrix that includes extinct taxa and new data for 11 nuclear genes consistently resolve relationships at the base of Mysticeti. The combined data set of 27,340 characters supports a stepwise transition from a toothed ancestor, to a mosaic intermediate with both teeth and baleen, to modern baleen whales that lack an adult dentition but retain developmental and genetic evidence of their ancestral toothed heritage. Comparative sequence data for ENAM (enamelin) and AMBN (ameloblastin) indicate that enamel-specific loci are present in Mysticeti but have degraded to pseudogenes in this group. The dramatic transformation in mysticete feeding anatomy documents an apparently rare, stepwise mode of evolution in which a composite phenotype bridged the gap between primitive and derived morphologies; a combination of fossil and molecular evidence provides a multifaceted record of this macroevolutionary pattern.

beaglelady - #81135

June 16th 2013

I mentioned it because I went to the most marvelous whale exhibition at the AMNH.   It was developed and presented by the Museum of New Zealand Te Papa Tongarewa and has been traveling throughout the U.S. and Canada.  LOTS of great fossils and 2 articulated skeletons of modern whales. (Just imagine schlepping that around!) The AMNH even displayed some of its own rare fossils that they rarely show to the public,  such as Andrewsarchus mongoliensis. 

Lou Jost - #81151

June 17th 2013

Sounds truly wonderful!

glsi - #81126

June 16th 2013

That video isn’t even about fossil giraffes.  The ancient species claimed to be ancestors of the giraffe are gigantic leaps and take a great deal of imagination or faith to be believable.  Nowhere near gradualism.

The whales are make more of a case, but why always the whales?  Where’s all the other thousands upon thousands of needed cases?  And like the horses are these whales direct descendants of each other?  If not, why can’t one sole example of a gradual contiuum be exhibited?

beaglelady - #81136

June 16th 2013

It does explain about the evolution of giraffes and shows ancestors.  But if they aren’t related, does God get tired of existing species, wipe them out, make new ones,  and turn them loose?

We don’t talk only about whales here.


btw, evolution doesn’t work like a ladder.  

glsi - #81142

June 16th 2013

The part “explaining” giraffe evolution was computer animated.  Nice artwork and special effects.  I liked Shrek better though. 

beaglelady - #81144

June 17th 2013

Sketches and animations are meant to show what the animals looked like.

Lou Jost - #81130

June 16th 2013

Remember the DNA shows common descent, and the spotty geographic coverage of fossil locations and changing climates means a given site will usually not be continuously sampling a species as it changes.

What is the alternative explanation of the pattern? God continuously creates new species every millenium?

glsi - #81134

June 16th 2013

For the moment I’ll have to grant you that the DNA evidence looks like common descent.  Not being able to study it myself, I’m trusting Venema and the many other authorities who say so.  They might also be mistaken since its a new and complex science.

Even so, I think there’s something wrong with Darwinism or whatever you choose to call it.  I think there’s something missing.  Although I’m Christian, I’m not talking about a religious objection.

 I can’t answer your questions and I don’t think anyone really knows.  It may actually be that God creates new species every millenium.  That should not be a shock.  I think most all chemists and rational people know that nothing in chemistry provides for random chemicals coming together and forming the first life.  It took a miracle by a designer to do it so why should that be the last miracle of design to occur?

Yes, I’ve read you’re an atheist, but these are my convictions.

beaglelady - #81137

June 16th 2013

 It may actually be that God creates new species every millenium.

So where are the new ones from 2000?

glsi - #81138

June 16th 2013

Ask Lou.  Doesn’t he keep finding the orchids?

beaglelady - #81140

June 16th 2013

That doesn’t mean they began in 2000.  

glsi - #81141

June 16th 2013

I really don’t think God gives a hoot about our calendar.

beaglelady - #81147

June 17th 2013

Well, he can’t be impressed by our month and day names, that’s for sure.   e.g. Wednesday = Odin’s Day.  

Lou Jost - #81145

June 17th 2013

Yes, I do keep finding new ones, but mainly when I go to areas that have never been explored. We do DNA analysis on them and we find the kinds of clues about descent that Dennis talks about here. Even without the DNA it is usually easy to see which species are their nearest relatives. The DNA almost always confirms this.

We can also roughly date the divergence from ancestral species. The highest speciation rate is in my 30 new Teagueia species, where the number of species has been  doubling every few hundred thousand years. This is a  very fast rate for a group of flowering plants.

As a taxonomist I have to classify and name my plants, and this is where one quickly discovers that species, genera, and even families often have blurry edges. This is what we would expect from evolution.

The biogeography of orchids also gives good evidence from common descent, independent of the genetic evidence. Dennis wrote about the evidence from biogeography in one of his first posts of this series.

The distribution of orchids can help you understand why there are gaps in the fossill record. My Teagueia species all grow in a tiny area not more than 100km long and 20 km wide.  Suppose some day they spread to the rest of the Andes. The chances of some future paleontologist doing a fossil dig right here are remote (and conditions for fossilization are terrible so even if someone did dig here, they probably wouldn’t find anything). But in a future fossil dig anywhere else in the Andes, my orchids would seem to appear suddenly, since they originated here, not there. This is what we expect of most species.

Furthermore, climate changes a lot over a few million years, so species ranges expand and shrink and shift. No one spot is likely to have a continuous record of the evolutionary history of a given species. Instead we should see a series of snapshots at any single site, and this is what we do see.

glsi - #81155

June 17th 2013

You have an awesome job.  In Christianity we’re not supposed to covet but it’s difficult.

Lou Jost - #81165

June 18th 2013

Thanks!!! I don’t think of it as work….

melanogaster - #81146

June 17th 2013

For the moment I’ll have to grant you that the DNA evidence looks like common descent.  Not being able to study it myself,”

Why not, gisi? It’s all available to you if you have the courage to look for yourself.

glsi - #81156

June 17th 2013

Well, I really don’t think it’s courage, but more to do with three and a half billion letters of a new language I don’t understand.  But thanks for the encouragement.

beaglelady - #81166

June 18th 2013

Would you be interested in a free opportunity to learn more?

melanogaster - #81179

June 19th 2013

No one is suggesting that you study all the evidence, just a representative sample. But I think you know that.

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