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 Which came first, the bird or the smaller genome?

 by Stephen F. MathesonOriginally published on Quintessence of Dust, August 2007.

It’s easy to think of a genome as a collection of genes, perhaps because so many of the metaphors

used to explain genes and genomes ( blueprint,  book of life, Rosetta Stone) can give one theimpression that everything in a genome is useful or functional. But genomes are, in fact, packed

 with debris. Many genomes contain huge collections of fossil genes: genes that have beeninactivated by mutation but were never discarded, sort of like the old cheap nonfunctional VCRs inmy basement. And many genomes contain even more massive collections of another kind of fossil-like DNA: mobile elements, or their remnants. The human genome, for example, contains over 1million copies of a single type of mobile genetic element, the Alu transposon. Together, the varioustypes of mobile genetic elements comprise nearly half of the human genome.

Think about that. Almost half of the human genome is made up of known mobile elements, piecesof DNA that can move around, either within a genome or between genomes with the help of a virus.This extraordinary fact – and many of the specifics surrounding it – constitutes one of the most

compelling sources of evidence in favor of common descent, the kind of data for which only common ancestry provides a complete (or even reasonable) explanation. I’ll come back to this topicregularly.

Now it turns out, not surprisingly, that differences in genome size among types of organisms aredetermined primarily by the numbers of these mobile elements, and not by the number of genes. Infact, there is wild variation in genome size among types of organisms, and the variation has little todo with the numbers of genes expressed by those organisms. Consider birds, the subject of a 2007report in Nature (“Origin of avian genome size and structure in non-avian dinosaurs,” Organ et al.,8 March 2007).

Birds have remarkably small genomes, averaging 1/2 to 1/3 of the size of typical mammalian

genomes. (The chicken genome, for example, is less than half the size of the mouse genome.) Why might this be? In other words, how might we explain this difference? The authors point to twoimportant ideas. First, the chicken genome has been fully sequenced and analyzed, and it containsfar less of the debris mentioned above. It seems that the processes that create (or multiply) mobilegenetic elements are significantly less active in birds than in mammals and other vertebrates.Second, small genome size is intriguingly correlated with flight. Bats, compared to other mammals,have small genomes, and flightless birds, compared to other birds, have larger genomes. This hasled to the proposal that small genome size might offer a selective advantage to flying animals, by reducing the energy cost associated with hauling all that debris around. So, it seems that a smallergenome is advantageous for flying vertebrates, and that genome size can be reduced by restrainingthe production of mobile genetic elements. And this raises several interesting questions, includingthis one: did the reduction in genome size accompany the origin of bird flight, or did it happen in

advance? In other words, we can propose at least two alternative scenarios:

1) flight drove the genome change, by favoring small genomes, or

2) the genome change happened first, and helped to get flight off the ground.

How can we even hope to distinguish between these possible explanations? We would need,

somehow, to look at the genomes of the ancestors of birds. And all evidence indicates that the

relevant ancestors of birds are dinosaurs; in fact, today's birds are considered to be flying

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dinosaurs. The recent description of protein sequences from T . rex bone provided strong

confirmation of the birds-from-dinosaurs hypothesis, but no DNA was recovered from the samples,

and no information about genome structure can be inferred from those otherwise fascinating

studies. If only, a la Jurassic Park, we could get some dino DNA...

Enter Organ et al. with a wonderfully creative idea. It turns out that, in organisms alive today, cellsize is strongly correlated with genome size. In other words, organisms with large genomes tend to

have larger cells. This relationship was first described in red blood cells, but Organ et al. show that

it holds quite well in bone cells as well. Using bones from living species, they created a statistical

model that enabled them to infer genome size by looking at the size of bone cells. Then they 

combined their model with measurements of bone cell size from fossilized bones of long-extinct

animals, and were able to estimate the genome size of dozens of extinct species, including 31

dinosaur species and several extinct bird species. Their results are remarkable: small genomes are

found in the entire lineage (with one interesting exception, Oviraptor ) that gave rise to birds, all

the way back to the theropod dinosaurs that are the typical reference point in the dinosaur-to-bird

story. Here's how the authors put it: "Except for Oviraptor , all of the inferred genome sizes for

extinct theropods fall within the narrow range of genome sizes for living birds." Even if you don't

have access to Nature, you can have a look at the cool family tree in Figure 2, which shows smallgenomes in red and larger ones in blue. It's a compelling image.

The results suggest that small genomes arose long before dinosaurs took to the air, and raise some

interesting questions about the interplay of physiological function (e.g., energy consumption

associated with flight) and genome structure. Certainly scenario #1 above is not favored by these

findings: flight apparently arose in organisms that already had much smaller genomes than many 

of their earthbound cousins. The relationship between flight and small genome size, then, remains

unclear and even mildly controversial. Organ et al. acknowledge that the two characteristics did not

arise together, but after reference to the larger genomes in flightless birds, they conclude their

paper by noting that "the two may be functionally related, perhaps at a physiological level." And

they postulate that small genome sizes may have been favored by warm-bloodedness and itsassociated energetic demands. But a minireview of the paper raises several criticisms of these

hypotheses, and it is clear that the evolutionary forces acting on genome size are complex and yet

poorly understood.

Notwithstanding the unanswered questions regarding genome evolution, this paper is the kind of 

scientific article that should be carefully considered by those who deny common descent. Following

are some aspects of the story that create interesting questions for creationists and/or design

advocates.

Consider the results presented in Figure 2. Outside of common ancestry, how are we to account for

these data? The strong correlation between flight and small genome size in living organisms mightlook like some kind of "design" to someone who favors that sort of thinking, but Organ et al. have

conclusively uncoupled genome size and flight. Of course those of us who see the universe as a

creation will be happy to marvel at the advantages presented by small genomes to flying organisms,

and perhaps we'll all think of these wonders as evidence of brilliant "design." But it seems to me

that "design" does not serve a significant explanatory role here. On the contrary, I maintain that

the work of Organ et al. demonstrates the following: in dinosaur lineages, the best way to predict

genome size in an extinct species is to know the ancestry of the species. Common design aspects

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don't help. Common descent explains the pattern.

 And yet, I think it gets much worse than that for anti-evolution thinkers. I regularly see certain old-

earth creationists (e.g. the folks at Reasons To Believe) and design proponents (e.g. William

Dembski) arguing that "junk DNA" (which includes, but is not limited to, the 45% of the human

genome composed of mobile elements and their debris) is not "junk" but can have importantfunctions. (The arguments of these critics are flawed in several ways, which I'll detail some other

time.) While it's true that mobile elements have contributed to the formation of new genes from

time to time, and are thought to be significant sculptors of genomic evolution, it's also true that

mobile elements are indiscriminate in their jumping, and their continued hopping about is a

documented cause of harmful mutation. Here, though, is a significant quandary for a design

advocate considering a bird genome: if these mobile elements have important functions in the

organism, then how is it that birds can get by with 1/4 as many of them as, say, squirrels? Why, if 

these elements have important functions in the organism, do bats seem to need far fewer of them

than, say, rats? (The genome of the big brown bat is 40% the size of the genome of the aardvark.

Hello!) It seems to me that these facts are best understood when one considers the possibility that

most of this DNA is essentially parasitic, and that some types of organisms have benefited by 

restraining its spread. A "design" perspective with regard to genome size is just not helpful, and if that perspective insists on excluding common ancestry, then it's worse than worthless.

Article(s) discussed in this post:

Organ, C.L., Shedlock, A.M., Meade, A., Pagel, M. and Edwards, S.V. (2007) Origin of 

avian genome size and structure in non-avian dinosaurs. Nature 446:180-184. 

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