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Which came first, the bird or the smaller genome?

Which came first, the bird or the smaller genome?

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Published by Steve Matheson

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Categories:Types, Research, Science
Published by: Steve Matheson on May 25, 2011
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06/11/2011

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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 metaphorsused to explain genes and genomes ( blueprint,  book of life, Rosetta Stone) can give one the impression that everything in a genome is useful or functional. But genomes are, in fact, packed with debris. Many genomes contain huge collections ofossil 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 over1 million copies of a single type of mobile genetic element, the Alu transposon. Together, the varioustypes of mobile genetic elements comprisenearly 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 mostcompelling 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 ingenome sizeamong 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, thechicken genome has been fully sequencedand 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 inadvance? In other words, we can propose at least two alternative scenarios:1) flight drove the genome change, by favoring small genomes, or2) 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 therelevant ancestors of birds are dinosaurs; in fact, today's birds are considered to be flying
1
 
dinosaurs. The recent description of protein sequences from
.
boneprovided strongconfirmation 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 fascinatingstudies. 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 tohave larger cells. This relationship was first described in red blood cells, but Organ et al. show thatit holds quite well in bone cells as well. Using bones from living species, they created a statisticalmodel 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-extinctanimals, and were able to estimate the genome size of dozens of extinct species, including 31dinosaur species and several extinct bird species. Their results are remarkable: small genomes arefound in the entire lineage (with one interesting exception,
Oviraptor 
) that gave rise to birds, allthe way back to thetheropod dinosaursthat are the typical reference point in the dinosaur-to-birdstory. Here's how the authors put it: "Except for
Oviraptor 
, all of the inferred genome sizes forextinct theropods fall within the narrow range of genome sizes for living birds." Even if you don'thave access to
 Nature
, you can have a look at the cool family tree in Figure 2, which shows small genomes 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 someinteresting questions about the interplay of physiological function (e.g., energy consumptionassociated with flight) and genome structure. Certainly scenario #1 above is not favored by thesefindings: 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, remainsunclear and even mildly controversial. Organ et al. acknowledge that the two characteristics did notarise together, but after reference to the larger genomes in flightless birds, they conclude theirpaper by noting that "the two may be functionally related, perhaps at a physiological level." Andthey postulate that small genome sizes may have been favored by warm-bloodedness and itsassociated energetic demands. But aminireview of the paper raises several criticisms of thesehypotheses, and it is clear that the evolutionary forces acting on genome size are complex and yetpoorly 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. Followingare some aspects of the story that create interesting questions for creationists and/or designadvocates.Consider the results presented in Figure 2. Outside of common ancestry, how are we to account forthese 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. haveconclusively uncoupled genome size and flight. Of course those of us who see the universe as acreation 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 methat "design" does not serve a significant
explanatory
role here. On the contrary, I maintain thatthe work of Organ et al. demonstrates the following: in dinosaur lineages, the best way to predictgenome size in an extinct species is to know the
ancestry
of the species. Common design aspects
2

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