Archive for September 21st, 2015

The tree of life should be a garden. With bushes.

21 September, 2015

Biologists like to talk of and depict, “the” tree of life. This is shown here as in most places, with a bacterial and an archaeal bifurcation coming off a LUCA base, and then another bifurcation of archaea into modern archaea and eukaryotes.

Of course, there are also the anastomoses: an early intracellular colonisation of a eukaryote ancestor by a bacterium, which gave rise to mitochondria, and then another later event, where a cyanobacterium became chloroplasts in the ancestor of green plants and algae.

What is not generally appreciated is that the latter occurred more than once – with different photosynthetic bacteria providing distinctly different types of chloroplasts in the various lineages of algae, The situation then becomes more complicated, with minor and more complex anastomoses among eukarya, with unicellular eukaryotic algae becoming intracellular symbionts and then complex organelles – with evidence in some cases that this happened more than once, as evidenced by multiple layers of membranes surrounding chloroplasts in photosynthetic organisms whose closest relatives are non-photosynthetic.

Thus,”the” Tree of Life already has some internal interconnections that make parts of it more a reticulated network than a bifurcating tree – but this complication pales into insignificance when one takes into account the fact that “the” Tree does not take into account the wildly bushy garden of shrubs that would be viruses.

Seriously: despite repeated urging by folk like me, the multitude of Tree designers have consistently ignored the majority of organisms on this planet. Indeed, in a comment in a recent Twitter exchange on a new Tree, answering my comment that it took no notice of viruses, @phylogenomics: wrote “it does say tree of “Life” not tree of weird parasites of still unknown origin ….”

So I just HAD to reply ” …that happen to be life forms in good standing. In everyone B-) And [which] outnumber everything else.”

A good-natured exchange followed, which prompted the writing of this post – because, really, the Tree of Life SHOULD be a Garden of Life, with one tree and a collection of distinct bushes, some pretty big, representing different virus lineages. The biggest bushes would probably be the so-called megaviruses, and collections of viruses dignified by being grouped into taxonomic Orders, such as the tailed phages in the order Caudovirales and the ssRNA(-) viruses grouped as Mononegavirales.

And of course, some components of those bushes meet up with some of the roots of the tree – in the form of specific genes like DNA polymerases, which may well have a common origin with cellular genes.

Some of those bushes also inerconnect underground, like some of the reverse transcriptase-dependent viruses which have nothing else in common; the RNA viruses which share RNA-dependent RNA pol enzymes, but with other components from different origins – the okapi-like viruses, as they were termed by Rob Goldbach.

Some bushes in fact parasitise the tree, just like parasitic plants grow on other plants: the polydnaviruses of wasps, for example, are effectively genome components, and are used by their hosts to aid in parasitising their target hosts.

So, a garden – and one that it would be challenging to portray.

Which I would like to leave up to someone with far more artistic ability than me B-)