A Flock of Genomes Reveals the Toothy Ancestry of Birds

A tidal wave of genomic information seems to wash up on shore each year.   In 2014, an especially large wave – in those days long ago! – came ashore in the form of 45 entire genome sequences of birds.   The relevance of these genomes and their hundreds of billions of letters of code representing all the major groups of birds were discussed in a series of scientific papers in the journal Science.  Prior to 2014 only three bird genomes had been completed which were the chicken, turkey and finch.

To give you some perspective on the sheer magnitude of this data set, in 2000 the first genome of a mammal was reported.  That genome was the human genome and it took 10 years and over a billion dollars to complete.  The chicken genome took years to finish and cost millions of dollars.  In 2014 nearly every day a genome of an organism was published and the pace of sequencing has only accelerated since them.  Many of these genomes are much larger and more complex than the human genome.  DNA sequencers have become so fast and sophisticated that they can now read the entire genetic code of an organism in a few days and in some cases a single day. The challenge is no longer obtaining DNA sequences but rather processing the terabytes of data that a single DNA sequencing machine can produce in a few hours.

When produced my first DNA sequences as a graduate student I was thrilled to be able to generate a portion of a single gene for a few organisms in a few weeks.  Even in 2000 when I set up my independent lab I never dreamed it would be possible to sequence whole genomes in a matter of hours.  Today, billions of nucleotides–the ATCGs of the code–can be obtained for a few thousand dollars.

What can be learned from a flock of 45 bird genomes? 

The published papers in Science (see references) report on the genome structure, relationships among birds.  They also delve into comparisons of specific genes that are involved in unique bird characters such as bird songs, feathers, and teeth.

Photograph of Sulcavis geeorum skull, a fossil bird from the Early Cretaceous (120 million-years-ago) of Liaoning Province, China with scale bar in millimeters. Credit: Stephanie Abramowicz Read more at: http://phys.org/news/2013-01-fossil-bird-teeth-specialized-tough.html#jCp

Photograph of Sulcavis geeorum skull, a fossil bird from the Early Cretaceous (120 million-years-ago) of Liaoning Province, China with scale bar in millimeters. Credit: Stephanie Abramowicz
Read more at: http://phys.org/news/2013-01-fossil-bird-teeth-specialized-tough.html#jCp

Teeth?  But, birds lack true teeth don’t they?  It is true, no modern bird has true teeth, but nonetheless there is an entire paper devoted to looking at the genetics of teeth in modern  birds.  Birds do not produce enamel or dentin, the hard materials that make up teeth in mammals and some reptiles.   However, we can readily observe that there are very ancient bird fossils from the time of the dinosaurs that clearly had true teeth.   From that we can infer that although no birds have teeth today their ancestors did.

Until recently it might be possible to object to this inference of ancestral connections by claiming that although fossil birds had teeth that there is no connection between those fossil birds and toothless birds today.  Some creationists might counter that God could have created toothed birds as separate kinds of birds but then all of them perished in a global flood and only non-toothed birds survived to become the birds that we have today.

Bird genomes reveal the toothy history of all birds

The case of a toothed ancestry of all living birds got a big boost from the bird genome sequencing project.  Our ability to peer into the genomes of any organism on earth is rapidly becoming a reality.  In those genomes we find the history of species written in their DNA.  This history is not too dissimilar to reading the fossil record to reconstruct that past.   Genes that were used in the past by a species are frequently found discarded in the genome where they decay over time.  But that genomic decay process takes a long time and so when we read the genome we not only read all the genes that are actively doing things today to make a bird a bird we are also reading all of its code that it has used in the past but are no longer using.

This process of discovery of discarded genes would be similar to looking at the hard drive of a 10-year-old computer.  After a few years you start to use new programs and others go into disuse. Even when your “erase” a program you really only erase the information about where the files are and allow that space to be written over again with new code. Many files from those old programs are still there but you have no way of using them because they are just broken pieces.

So what do these new genomes reveal about teeth and birds? 

They reveal what we already knew from a few genomes but now we know from all major groups of birds:  All birds contain the genes for making true teeth in their genomes!

From many studies of mammalian teeth we know there are at least six genes involved in constructing the dentin and enamel of teeth.  All six of those genes are found in modern birds.

But if they have all these genes for making teeth why don’t they have teeth?  It is very simple, although they all have the genes, those genes all have serious errors in their code or in some cases large pieces of the genes are missing.   These are programs for making enamel and dentin that are not used by the birds because they are too messed up to work.

With 48 entire genomes of birds scientists now have the data to show that the main gene responsible for enamel has the same function-losing mutation in every bird. This is very strong evidence that the ancestral genome, and by extension the ancestral bird, that gave rise to all modern birds experienced this mutation and then passed that same problematic gene on to all its descendants.  Without the ability to produce enamel the other genes for tooth formation were not needed. Without any natural selection to maintain the integrity of those gene sequences, they have accumulated hundreds of mutations rendering all of these genes non-functional in all birds.

So the genetic evidence strongly supports what was already inferred from the fossil record – that ancestral birds were able to produce teeth but then lost that ability before the diversified into the species that we see today.   Birds aren’t the only animals that have tooth-making genes but don’t use them. Turtles, anteaters, and baleen whales also do not have teeth but, like birds, they also have broken versions of teeth-making genes.

Addendum:  Implications for young earth creationist’ view of the origin of birds

Let’s explore briefly some of the implications of these genomes on the view of young earth creationists (YECs) view of origins.  YECs don’t accept common descent of all birds from a common ancestor much less from an ancient theropod dinosaur.  They accept that birds have speciated within biblical “kinds” or “baramins.”  These are groups of species, generally at the taxonomic level of a family that have a common ancestor but these ancestors were specially created separately from one another very recently.  For example, all penguins may be a kind and thus God may have created one penguin species originally that was preserved on Noah’s ark and then diversified (ie. evolved) into all of the species of penguins that exist today and are in the fossil record.  For more see my article on bird diversity on the ark:  10 Invoking Super-Speed Evolution: How to Squeeze 10,000 Bird Species on Noah’s Ark.

If chicken, eagles, penguins, ostriches, finches, etc.. are each members of separately created bird kinds then each was created with their special attributes as we see them today.  None of these bird groups have teeth but they all possess broken genes for making teeth.

Why then do all these bird groups have genomes with genes for making teeth in them?   I don’t think that any YEC would a priori predict that these birds would have genes for making teeth.   Such a prediction is made from the assumption of common ancestry.  Sometimes creationists appeal to common design for similarities between organisms they believe don’t share a common ancestor.  Most often this claim is made in reference to why humans and chimpanzees share so many features and have DNA sequences that are so similar.

Bird beaks are very diverse. They are adapted for many different tasks.

Bird beaks are very diverse. They are adapted for many different tasks yet none retain or use true teeth despite the genetic “roots” to do so.

Does common design explain these toothy gene in birds?  No! Common design might have some appeal when their common design makes sense but why would God need to make birds with broken genes for making teeth.  Aren’t birds “perfectly” designed for this world with beaks?   Common design of non-functional parts makes no sense.  Our “design intuition,” which intelligent design advocates such as Douglas Axe espouse, doesn’t tell us that modern birds with no teeth should all have broken genes for making teeth.  This is not common sense for the creationists. However, it is very much common sense from an evolutionary biology perspective.

There is one other possibility.  A YEC could appeal to the fossil record and say since there were some birds that had teeth maybe all birds were created with teeth.  Maybe birds lost their teeth because of Adam’s sin. Maybe beaks are the result of a degraded and less-perfect world.  I think this is a bit silly. Beaks are amazing and clearly are adapted to serve birds amazingly well.   How could a YEC possibly want to say that God didn’t create beaks but only gave them the ability to make beaks later because he knew they would lose their ability to make teeth.

Birds aren’t the only example of these problems for creationists.   See these blog articles by two other biologists,  Birds, turtles and other toothless vertebrates have remnants of tooth genes,  and Pseudogenes testify to the evolutionary ancestry of animals each of which also discuss the loss of teeth at a broader scale showing that other groups of mammals that don’t have teeth also have the genes in their genomes.

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Featured image by: Julie McMahon / University of Illinois

Reference:

Merideth et al.  Evidence for a single loss of mineralized teeth in the common avian ancestor

Science 12 December 2014: 346 (6215), 1254390 [DOI:10.1126/science.1254390]  Abstract,

Full Text (PDF), Supplementary Materials

Abstract:  Edentulism, the absence of teeth, has evolved convergently among vertebrates, including birds, turtles, and several lineages of mammals. Instead of teeth, modern birds (Neornithes) use a horny beak (rhamphotheca) and a muscular gizzard to acquire and process food. We performed comparative genomic analyses representing lineages of nearly all extant bird orders and recovered shared, inactivating mutations within genes expressed in both the enamel and dentin of teeth of other vertebrate species, indicating that the common ancestor of modern birds lacked mineralized teeth. We estimate that tooth loss, or at least the loss of enamel caps that provide the outer layer of mineralized teeth, occurred about 116 million years ago.

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This article is an updated and revised version of an article that was first published in 2014.

Comments

  1. Great post, is it just a coicidence that you published this a couple of weeks after my blog post that touched on this subject, or did I perhaps inspire you to write about this?
    I’ll have to update my original post with a link to this post and Meredith et al. 2014. Unfortunately when I was writing my blog post I was kind of rushing it so didn’t have time to do a more complete search of the literature that would have no doubt uncovered it, so I had to rely on Meredith et al. 2009 and 2013 instead.

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    • I honestly can’t remember for sure. Your 2014 post was from Nov 8 while the original version of this post was from December of 2014. However, I remember reading the Science article and writing this post. I think I wasn’t aware of your blog at that point and so we independently wrote about nearly the same thing making the same point. I think I would have referred to your post if I had know about it earlier. BTW, I just told my genomics class about your “third eye” paper as an example of searching genomes for ancient genes.

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      • I think you might have confused me with Christopher Emerling! But if you originally wrote this post at the end of 2014 I obviously couldn’t have influenced it as I wrote mine in January 2018. I’m glad you linked to Christopher’s blog through, I wasn’t aware of it before and I’ve been binge-reading it over the last couple of days.

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        • Ah, yes, I did get you confused. I did read your post just recently. My post on the birds was written in 2014 and I was looking at some of my older posts for something to update an publish since I have been so busy with other things and can’t write new stuff. Your post was great. Maybe I was subconsciously influenced to revise this one because it reminded of what a great story psuedogenes are. I’ve just added a link to your article to the blog post. BTW, I’ve been anxiously awaiting your reviews of the next two chapters of Jeanson’s book. JD

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          • Thanks! I know, it really bugs me that I haven’t been able to finish off Jeanson’s book yet. I was able to publish the blog posts on the first 2/3rds of the book in unusually quick succession because I had a fairly light workload, but since November I’ve much busier working on my thesis and teaching. I don’t have the mental energy to trawl through Jeanson’s claims about an entirely different field of biology at the moment!
            It helps that there wasn’t really much of substance in those first chapters of Jeanson’s book too. When tackling the final ones I want to make sure I do them justice by being as thorough as possible.

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  2. I think this is where AiG steps in and says, “In a biblical worldview, we would not expect to find the genetic material responsible for producing teeth in birds.”

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    • I think that is what they would have said 20 years ago not knowing that there would fossil birds with teeth found and now the genes for making teeth in modern birds. That should be their prediction but since they know their prediction isn’t confirmed they will modify their prediction to be something like, all birds have a common design in the creators mind and thus used comment genetic elements. That really doesn’t help understand seemingly wasted genetic pieces though they could just pull out the catch-all “we just don’t know what those genes are doing today and someday we will find out that what appears to be tooth genes are doing some other function” This their generic response to most pseudogenes.

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      • I’ve heard the “It’s not a broken gene for X; it’s a functioning gene for something we’ll discover later” claim before. But how do we identify them as broken versions of existing genes to begin with? Is it that their locations and sequences are so similar to the functioning versions that calling them pseudogenes is the most reasonable explanation? Are there genes that might be pseudogenes but are so damaged/degraded that we can’t make a solid inference?

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        • Hi Mel, essentially yes: with pseudogenes like these (unitary pseudogenes) they are in the same location as the functional genes and have relatively high similarity to the functional genes in other species. In this case, they used a crocodilian for reference (what we believe to be the closest living relatives to birds) and found quite a bit of similarity despite the fact that they were pretty trashed. Furthermore, when you estimate their evolutionary history using molecular phylogenetic methods (basically using sequence similarity and assuming models of mutation) they come out exactly where you’d expect them to based on their inferred evolutionary history. For instance, I don’t think Meredith et al. did this, but what we’d expect that the bird tooth pseudogenes would come out closest to crocodilians, just like functional genes do.

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  3. You sent me back to Stephen J Gould’s Hen’s teeth and horse’s toes, in which the correct bit of chick epithelium persuaded mouse mesenchyme to produce dentine.

    Liked by 1 person

  4. Thayne Stacey says:

    I’m curious if bird ancestry can be mapped by tracing the specific ways these genes are corrupted. Is that something that is studied?

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  5. Another Matt says:

    I think you’ve anticipated almost all of the YEC responses, and they could almost hold together according to a just-so story:

    Toothy birds were another kind that simply died out. They were similar enough to birds that we would expect to see similar genomes according to similar design. These “broken tooth genes” you speak of could be explained one of two main ways: 1) parts of them could have been necessary in order to keep the genome coherent in some way we don’t know yet, or they could function in some other way besides tooth production. 2) Since we know that genomes can only lose information over time due to mutation [at least, according to YEC lore], it’s likely that all the individual baramins of birds had teeth before the Flood but didn’t need them afterward; so bird teeth disappeared in every bird kind as a result of mutations that didn’t reduce fitness.

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    • Not that you’re advocating for YECs but nonetheless…

      If they countered with point #2, it raises the question of why some (all?) of the tooth genes in birds belonging to different baramins have identical mutations. For instance, basically all birds that have had the ENAM (enamelin) gene examined have an eight base pair and 13 base pair deletion in the exact same location, both of which are incredibly rare. This would seem to run counter to the YEC claim that convergent evolution should be expected to be exceedingly rare.

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  6. Could the creationist respond by saying the broken genes are in-built design for future diversification? That is, rather than having it be from the past, could they claim its part of God’s design for the bird “kinds” to have teeth in the future?

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    • Ooohh. I like it. I should have thought of that since I’ve written about the YEC pre-loaded genetics for the future before. Yeah, the birds we have today are still adapting and in the future each “kind” will need teeth. Todd Wood proposed that looking for evidence of hidden genetic traits would be evidence for creation. It seems he need not have to look very far:-)

      Liked by 2 people

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  1. […] 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 […]

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