Supergroups in Search of Their Roots

The early stages of eukaryotic evolution are proving hard to reconstruct.

There is normal evolution, and then there are great evolutionary transitions. Not to say that the latter don't obey the principles of normal evolution, but they go by so fast, and render so many transitional forms obsolete along the way, that there is little record left of what happened. Among those great transitions are the origin of life itself, the origin of humans, and the origin of eukaryotes. We are slowly piecing together human evolution, from the exceedingly rare fossils of intermediate forms and branch off-shoots. But looking at the current world, we are the lone hominin, having displaced or killed off all competitors and predecessors to stand alone atop the lineage of primates, and over the biosphere generally. Human evolution didn't violate any natural laws, but it seems to have operated under uniquely directional selection, especially for intelligence and social sophistication, which led to a sort of arms race of rapid evolution that laid the groundwork for an exponential rate in the invention of technologies and collective social forms over the last million years.

Similarly, it is clear that however the origin of life started out, it was a very humble affair, with each innovation quickly displacing its progenitors, just as the early cell phones came out in quick succession, until a technological plateau was reached from which further development was / is less obvious. While the origin and success of eukaryotes did not erase the prokaryotic kingdoms from which they sprang, it does seem to have erased the early stages of its own development, to the point that those stages are very hard to reconstruct, especially given the revolutionary and multifarious nature of their innovations.

Eukaryotes differ from prokaryotes in possessing: nuclei and a nuclear membrane with specialized pores; mitochondria descended from a separate bacterial ancestor (and photosynthetic plastids descended from yet other bacterial ancestors in some cases); sex and meiosis; greater size by several orders of magnitude; phagocytosis by amoeboid cells; internal membrane organelles like golgi, peroxisomes, lysosomes, endocytic and exocytic vesicles; cyclins that run the cell cycle; microtubules that participate in the cell cycle, cytoskeleton, and cilia; cilia, as distinct from flagella; an active actin-based cytoskeleton, with novel motor proteins; a greatly elaborated transcriptional apparatus with modular enhancers and novel classes of transcription regulators; histones; mRNA splicing and introns; nucleolus and small nucleolar RNAs; telomeres on linear chromosomes; a significant increment in the size of both ribosomal subunits. Indeed, the closer one looks at the molecular landscape, the more differences accumulate. This was quite simply a quantum leap in cellular organization, which happened sometime between 1.8 and 3 billion years ago. Indeed, eukaryotes are not just the McMansions of the microbial world, but the Downton Abbeys- with dutiful servants and complex and luxurious internal economies that prokaryotic cells couldn't conceive of.

Major lineages of eukaryotes are traced back to their origins in a molecular-based phylogeny. Animals (and fungi!) are in the Opisthokonta, plants in the Chloroplastida. So many groups connect right to the "root" of this tree that there is little way to figure out which came first. Also, the dashed lines indicate uncertainty about those orderings/rootings as well, which leaves a great deal of early eukaryotic evolution obscure. Some abbreviations / links are- CRuMs: collodictyonids (syn. diphylleids) + rigifilida + mantamonas; excavates, hemimastigophora, haptista, TSAR:  telonemids, stramenopiles, alveolates, and rhizaria.

A recent paper recounts the current phylogenetic state of affairs, and a variety of other papers over the last decade delve into the many questions surrounding eukaryotic origins. While molecular phylogenies have improved tremendously with the advent of faster, whole-genome sequencing and the continued collection of obscure single-celled eukaryotes, (aka protists), the latest phylogeny, as shown above, remains inconclusive. The deepest root is both uncertain with regard to its bacterial progenitor, and to which current eukaryotes bear the closest relation. There are occasional fossil kelps, algae, and other biochemical traces back to 2.0 to 2.7 billion years, (though some do not put the origin earlier than 1.8 billion years) but these have not been able to shed any light on the order of events either.

Nevertheless, the field can agree on a few ideas. One is that the assimilation of mitochondria (whether willing or unwilling) is perhaps the dominant event in the sequence. That doesn't mean it was necessarily the first event, but means that it created a variety of conditions that led to a cascade of other consequences and features. The energy mitochondria provided enabled large cell sizes and the accumulation of a whole new household full of junk, like lipids in several new membrane compartments. The genome that they contributed brought in thousands of new genes, including introns. 

Secondly, the loss of cell walls and the adoption of amoeboid carnivory is likely one of the first events in the evolutionary sequence. Shedding the obligatory cell wall that all bacteria have necessitates a cytoskeleton of some kind, and it is also conducive to the engulfment of the proto-mitochondrion. For while complicated co-symbiotic metabolic arguments have been devised to explain why these two cells may have engaged in a long-term mutual relationship long before their ultimate consumation, the most convenient hypothesis for assimilation remains the simplest- that one engulfed the other, in a meal that lasted well over a billion years.

Thirdly, the question of what the progenitor cell was has been refined somewhat. One of the most intriguing findings of the last half-century of biology was the discovery of archaebacteria (also called archaea)- a whole new kingdom of bacteria characterized by their tendency to occupy extreme habitats, their clear separation from bacteria by chemical and genetic criteria, and also their close relationship to eukaryotes, especially what is presumed to be the original host genome. Many proposals have been made, (including that archaea are the original cell, preceding other bacteria), but the best one currently is that archaea split from the rest of bacteria rather late, after which eukaryotes split off from archaea, thus making the latter two sister groups. This explains the many common traits they share, while allowing significant divergence, plus the incorporation of many bacterial features into eukaryotes, either through the original lineage, or by later transfer from the proto-mitochondrion. So here at last is one lineage that survived out of the gradual development of eukaryotes- the archaea, though one wouldn't guess it from looking at them. It took analysis at the molecular level to even know that archaea existed, let alone that they are the last extant eukaryotic sister group.

A comically overstuffed figure from an argument for the late development of archaebacteria out of pre-existing bacteria (prokaryotes), with subsequent split and diversification of eukaryotes out of a proto-archaeal lineage. Many key molecular and physiological characters are mentioned.

Lastly, surveying the various outlying protist lineages for clues about which might hearken back to primitive eukaryotic forms, one research group suggests that the collodictyonids might fit the bill. Being an ancient lineage means that it is lonesome, without a large family of evolutionary development to show diversification and change. It also means that in molecular terms, it is highly distinct, branching deeply from all other groups. Whether that all means that it resembles an ancient / early form of the eukaryotic cell, or went its own way on a unique evolutionary trajectory, is difficult to say. For each trait, (including sequence traits), a phylogenetic analysis is done to figure out whether it is differential- shared with some other lineages but not all- whether those without the trait lost it at some later point, or whether it was gained by a sub-group. After analyzing enough such traits, one can make a statement about the overall picture, and thus the "ancient-ness", of an organism.

Is anything special about collodictyon? Not really. It is predatory, and has four flagella and a feeding groove, which functions as a sort of mouth. It can make pseudopods, has normal microtubule organizing centers for its flagella, and generally all the accoutrements of a eukaryotic cell. It lacks nothing, and thus may be an early branching eukaryote, but is not in any way a transitional form.

An unassuming protist (collodictyon) as possible representative of early eukaryotes. Its cilia are numbered.

At this point, we are left still peering darkly into the past, though obscure living protists and their molecular fossils, trying to figure out what happened when they split from the bacteria and archaea. A tremendous amount happened, but little record survives of the path along the way. That tends to be characteristic of the most momentous evolutionary events, which cause internal and external cataclysms, (including the opening of whole new lifestyles to exploit), that necessitate a rapid dynamic of further adaptation before their descendents achieve a stable and successful state sufficient to ride out the ensuing billion or more years ... before we come on the scene with the ability and interest to contemplate what went before.

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