February 2, 2005 | David F. Coppedge

Genes Evolving Downward

Those assuming the evolution of eukaryotic genomes has progressed upward in complexity may find the following abstract from PNAS1 startling:

We use the pattern of intron conservation in 684 groups of orthologs from seven fully sequenced eukaryotic genomes to provide maximum likelihood estimates of the number of introns present in the same orthologs in various eukaryotic ancestors.  We find: (i) intron density in the plant-animal ancestor was high, perhaps two-thirds that of humans and three times that of Drosophila; and (ii) intron density in the ancestral bilateran was also high, equaling that of humans and four times that of Drosophila.  We further find that modern introns are generally very old, with two-thirds of modern bilateran introns dating to the ancestral bilateran and two-fifths of modern plant, animal, and fungus introns dating to the plant-animal ancestor.  Intron losses outnumber gains over a large range of eukaryotic lineages.  These results show that early eukaryotic gene structures were very complex, and that simplification, not embellishment, has dominated subsequent evolution. (Emphasis added in all quotes.)

In their paper, Harvard biologists Scott Roy and Walter Gilbert used the maximum-likelihood phylogenetic method instead of maximum parsimony, and feel it provided a better ancestral tree.  In fact, they used the same data as other scientists who used parsimony, and got very different results.  They are emphatic about their conclusions:

These results push back the origin of very introndense genome structures over a billion years to the plant-animal split.  Indeed, ancestors at the divergences between major eukaryotic kingdoms as well as the ancestral bilateran appear to have harbored nearly as many introns as the most intron-dense modern organisms.  This is a sharp repudiation of the common assumption that intron-riddled gene structures arose only recently.
    In addition, our analysis shows that the majority of introns are themselves very old.  Two-thirds of bilateran introns were present in the bilateran ancestor; 40% of opisthokont introns were present in the opisthokont ancestor; and 40% of plant, animal, and fungal introns were present in the plant�animal ancestor.  This is quite different from what is commonly assumed and surprising in light of relatively fast rates of intron turnover observed in nematodes and flies.

This bias toward intron loss instead of gain appears to be a general trend among eukaryotes, they conclude.  What does this mean?  The only way to rescue an evolution toward “improvement” with these results is to suggest that introns are bad, like parasites, and that over time, eukaryotes got better at ridding themselves of them.  They reject that and other notions, assuming instead that “It seems much more likely that different selection or mutation regimes for introns along different lineages are driving the observed instances of gene streamlining.”  Although intron function and evolution is still largely unknown, they leave only an admission of ignorance of what their results mean – only that geneticists had better re-examine their assumptions:

These results contradict the assumption that genome complexity has increased through evolution.  Instead, species have repeatedly abandoned complex gene structures for simpler ones, questioning the purpose and value of intricate gene structures.  These results suggest a reconsideration of the genomics of eukaryotic emergence.

1Scott W. Roy and Walter Gilbert, “Complex early genes,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0408355101, published online before print February 1, 2005.

Introns and the complex molecular machines that process them (spliceosomes – see 09/12/2002 and 09/17/2004 entries) are still mysterious, but does anyone see a neat picture of evolution here?  Why would some introns be ultra-conserved (see 05/27/2004 entry), and others be removed?  Evolutionary theory is not helping explain introns or spliceosomes, and may be missing entirely the picture of what is going on.  Why not approach the data from the perspective of intelligent design and entropy?  The complexity was apparently present from the start.  Where did it come from?  The notions of ancestry in this picture are fictional.  The assumed trees are filled with gaps.  What seems apparent is devolution, not evolution.
    Some have suggested that introns provide opportunities to expand the genetic code through alternative splicing, so that more information can be gleaned out of a compact code.  Others have pointed to robustness and repair as possible functions.  Let a new generation of geneticists approach this problem without fogged-up Darwinian glasses on.  They certainly cannot see things any worse than the Darwin Party has done so far.

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