More Incurred Cost

I recently tried to show you a pattern that speaks to foresight.  Specifically, one way to infer foresight is if we detect a) a past cost that is b) linked to a future benefit.  Given the growing list of evidence that the last common ancestor of all eukaryotes  had as many or more introns than current metazoans*, we are now in a position to infer a past cost if many/most of the lineages that evolved from this state showed a net loss of introns (costly enough to be removed by selection) and a future benefit if introns play a significant role in multicellular development and/or physiology.

We have seen a hint of future benefit through the manner in which alternative splicing may play a key role in the emergence tissues and organs.  This, and other possibilities, need more exploration.

We have also seen a hint of past cost, where the evolution of chromalveolates was dominated by intron loss.    Well, it turns out that another lineage appears to show the same pattern.

Let’s pull out our eukaryotic tree again:

While the chromalveolates were the lower left pink panel, let’s now look at the upper right yellow panel – the excavates.  This time, let’s use the following paper:

Slamovits CH, Keeling PJ. 2006. A high density of ancient spliceosomal introns in oxymonad excavates. BMC Evol Biol. 6:34.

I mentioned earlier that trypanosomes, a member of the kinetoplastids, have very few introns.  The authors mention two other lineages:

However, despite the accumulation of a considerable quantity of molecular data from both Giardia and Trichomonas, as well as the identification of proteins involving splicing in Trichomonas [6], evidence for introns in their genomes remained intriguingly elusive. Indeed, only recently were introns finally characterized in these organisms [7-9], and remain extremely rare. Only three introns have been found in G. intestinalis among thousands of known genes [8,9] and forty-one introns were identified in the T. vaginalis genome after exhaustive searches [7].

Giardia belong to the group called diplomonads, while Trichomonas belong to the Trichomonads. When these lineages converge with the kinetoplastids, we are at the base of the excavates and thus might assume the last common ancestor of excavates had very few introns.

But the researchers went and surveyed a set of genes from a protist known as Streblomastix strix. This little guy would represent the oxymonads on the tree. And they found:

We find that Streblomastix genes contain an unexpectedly high intron density of about 1.1 introns per gene. Moreover, over 50% of these are at positions shared between a broad spectrum of eukaryotes, suggesting theyare very ancient introns, potentially present in the last common ancestor of eukaryotes.

So they conclude:

The present sampling of protein-coding gene sequences from Streblomastix suggests that oxymonad genomes contain a relatively large number of canonical splicesomal introns, many of which are at ancient conserved positions. This is in contrast to the better studied excavate genomes such as those of kinetoplastids, Giardia and Trichomonas where canonical spliceosomal introns are either rare or have been co-opted in specific ways, such as the spliced leaders in euglenozoa. The fact that many Streblomastix introns are ancient shows that the genome of the ancestor of these organisms, and indeed probably all extant eukaryotes, contained many introns and that the intron poor state found in Giardia and Trichomonas is more likely independently derived.

So it would seem the theme of intron loss we saw in the lower left pink panel in the eukaryotic tree also occurred in the upper right yellow panel.  As far as the unicellular cell plan goes, it looks more and more as if introns have been too costly.

*The situation can only become more interesting when we begin to ponder how it is that the ancestral eukaryote came to exist with so many introns.


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