Tuesday, 9 July 2013

Dating the Eukaryotes

Over 3.5 billion years ago in the boiling, acidic oceans of the Archaean Earth, something incredible occurred. Organic molecules began to accrete, resulting in a torrent of reactions which led to the creation of the ancestor of all life on the planet, a cell known as LUCA (Last Universal Common Ancestor). Over hundreds of millions of years, through countless rounds of cell division, the kingdoms of bacteria and archaea evolved. Life took hold on the planet.

At this stage, however, all life was simple. Bacteria and archaea are part of a larger group of organisms known as the prokaryotes (Greek for 'before the nucleus), a name which references the fact that such creatures lack any membrane bound structures (organelles) within their cells. The rest of life on Earth, such as animals and plants, are complex animals or eukaryotes to give them their proper name. The question therefore is how cells made the jump from simple to complex entities?

In the 1960s, the American microbiologist Lynn Margulis, proposed a radical new theory: that a prokaryotic cell engulfed a smaller cell. Yet instead of being digested, it formed a symbiotic relationship with its captor and eventually lost its independent nature, becoming an organelle. The resulting hybrid of cells was the first eukaryote on the planet.

Mitochondria, structures within cells which may have evolved from bacteria
At first this theory was met with scepticism. Today it is the orthodox explanation for the origin of complex cells. Once the theory was established amongst evolutionary biologists, it was a case of identifying when the event occurred in Earth history.

Based on the limited fossils we have from the Precambrian super-eon, alongside rather more exacting geochemical evidence, suggests the origin of chloroplasts, the photosynthetic structures found in plants and algae evolved 2.7 billion years ago and the energy-generating structures of animal cells, the mitochondrion, 2.1 billion years ago.

These dates seemed to fit in nicely with the image of how our planet developed since life first appeared. Yet a study conducted by researchers from the University of California, Berkeley, is set to overturn existing theories about eukaryote evolution and how it impacted the Earth. The main problem with studying events this far back in time is that fossil evidence is almost non-existent. As a result, we have to use other means to infer what happened and when.

'When you are talking about these really ancient events, scientists have estimated numbers that are all over the board,' said graduate student Patrick Shih. 'We came up with a novel way of decreasing the uncertainty and increasing our confidence in dating these events.' In order to get a more accurate view of what happened when, Shih and his colleague Nicholas Matzke, examined directly the product of the symbiotic event, the mitochondria and chloroplasts of eukaryotic cells and even more importantly, the fragments of DNA contained within them.

'These genes, such as ATP synthase, a gene critical to the synthesis of the energy molecule ATP, were present in our single-celled ancestors and present now, and are really, really conserved,' said Matzke. 'These go back to the last common ancestor of all living things, so it helps us constrain the tree of life.' Since mitochondrial, chloroplast and nuclear genes do not evolve at exactly the same rate, the researchers used what are known as Bayesian statistics to estimate the rate of variation in order to backtrack to the moment when bacteria joined forces to form eukaryotes.

The dates they came up with were incredible. According to Matzke and Shih, the cellular mitochondrion is barely 1.2 billion years old, almost a billion years younger than evolutionary biologists had proposed. Even more surprising, the chloroplast is apparently even younger, just 900 million years old, almost 2 billion years from the previous proposed date.

The methods used by the researchers are far more accurate than previous studies with an uncertainty rate of between 14 and 26%. Assuming the maximum level of uncertainty, chloroplasts are only 1.134 billion years old, still a far shot away from the 2.7 billion from previous studies. While it is wonderful to have solid dates for such an important evolutionary event, it throws all our theories off kilter.

Our original image of the progression of the planet and its life made a lot of sense backed up by multiple lines of evidence. Photosynthetic cyanobacteria evolved early on in Earth history, producing oxygen which made the atmosphere toxic to many species of microorganism. Soon, forming a symbiotic relationship with another cell became a viable method of survival in a newly harsh world. This led to the creation of the first eukaryotic cells with chloroplasts 2.7 billion years ago.

These new photosynthetic creatures, alongside the cyanobacteria, increased the oxygen levels in the atmosphere to such an extent that other, aerobically-respiring bacteria, were able to form a viable symbiotic relationship to form the first eukaryotic cells with mitochondria 2.1 billion years ago. The equal and opposite metabolic processes of prokaryotes and eukaryotes led to the geochemical stagnation of the Earth during a time known as the boring billion which ran from 1.8 to just 800 million years ago.

As photosynthetic prokaryotes and eukaryotes removed carbon dioxide from the atmosphere during the boring billion, the planet's protective layer of greenhouse gases was depleted, causing the Earth to cool to such an extent that it was plunged into an ice age 1 billion years ago. This ice age, known as Snowball Earth, spelled the end of the boring billion, allowing eukaryotes to evolve, giving rise to the first animals around 600 million years ago. The events were laid out in a neat progression.

Now we have the boring billion, Snowball Earth and the origins of eukaryotes layered on top of each other in one great mess. While we have definitive dates for when complex cells evolved, they have changed our understanding of the planet's evolutionary history. It will be a while before we can unpick this puzzle.