Pressrelease: Machine learning measures the pulse of diversity in the fossil record


New study applies powerful machine learning methods to visualise the entire fossil record of the last 600 million years.

Fossil records
Credit: Jennifer Hoyal Cuthill

Patterns of diversity seen in the fossil record pulse dynamically around an equilibrium of 19 million years. This is one of the principle findings of a new scientific paper published in Nature by an international team of scientists from the University of Essex UK, Uppsala University, the Tokyo Institute of Technology,  and the companies Good AI and Cross Compass.

It has been known for almost two hundred years that the fossil record shows dramatic changes in diversity through time, with major radiations creating more species, and mass extinctions that kill them off, such as the meteorite at the end of the Cretaceous some 66 million years ago that wiped out the dinosaurs. It has also often been thought that there should be a link between these two sorts of events – after a mass extinction, a similarly-sized radiation of species should take place to fill up newly-emptied ecological roles.

This study applies powerful machine learning methods to visualise the entire fossil record of the last 600 million years in order to understand the relationship between these sorts of events. Using archived age distributions of over 100 000 fossil species, the machine learning method represents each of these species in a virtual space that best represents their relative ages. This provides a human-readable visualisation of the overlaps of fossil species in time, which helped the researchers to see the impacts of major events in evolutionary history.

The study looked at both occurrences of fossil species over time and co-existence of different species at the same time. Occurrences tell us about the length of time species tend to exist for and how normal species lifespans are disrupted by major evolutionary events like mass extinctions. Co-occurrences also tell us about whether these species were likely to meet each other.

For example, the probability of co-occurrence between species like ours living today and species from the Cretaceous, like Tyrannosaurus rex is close to zero. ‘T. rex was born too soon for us to have a chance to meet it’, said lead author Dr Jennifer Hoyal Cuthill.

The study then showed that the top 30 extinction or radiation events in evolutionary history markedly disrupted the structure of the fossil record. The most extreme extinction event was the end-Permian mass extinction 252 million years ago, which was so severe it is called the ‘great dying’. The most extreme radiation measured was the Cambrian explosion of diversity, 541 million years ago when many groups of animals first appear in the fossil record.

When the scale and timing of these top 30 events was compared, the researchers found that extinction and radiation of similar sizes generally occurred at different times. An exception to this rule was the extremely severe end-Permian mass extinction, which was followed by two major radiations. This general decoupling of extinction and radiation in time differs from the traditional expectation that major radiations should generally follow immediately after major extinctions had cleared the way. Instead, the most significant evolutionary radiations were observed at times when life exploited brand new ecological opportunities, such as in the Cambrian explosion or the Carboniferous diversification of life on land.

The researchers then used the distances between species in the machine-learnt space, alongside more traditional statistics, to measure the time scale of evolutionary disruptions. To do this they developed a new measure called the decay-clock count. The decay-clock looks back in time from any given point, to see when the species present at that particular time first appeared. The decay-clock is reset when fewer than 10% of species in question are present, in a process called evolutionary decay.

The decay-clock counts that were measured for each point in evolutionary history showed that, as expected, major extinction events, such as the big five mass extinctions, rapidly erased prior connections to the past by simultaneously removing large proportions of existing species. More surprisingly, the study also showed that evolutionary radiations, in which many species simultaneously appeared, could also lead to rapid evolutionary decay. This is because large number of newly evolved species can swamp those that existed previously causing rapid changes in the evolutionary community, or biota.

Professor Graham Budd
"One of the most interesting things our observations show is that after mass extinctions such as the one that killed off the dinosaurs, life doesn’t just evolve to fill up the emptied ecological space", says Graham Budd, one of the researchers behind teh new study. 

What about the present day? The Quaternary period, which began two and a half million years ago has experienced repeated climate upheavals including dramatic alternations of glacial and interglacial times, and many extinctions have taken place including examples such as the cave bear. This means that the present day extinction crisis is eroding biodiversity that is already disrupted, and will thus take even longer (from at least 8 million years) to recover to the long term average. Dr Hoyal Cuthill comments that  ‘each extinction that happens on our watch erases a species, which may have existed for millions of years up to now, further increasing our current decay-clock debt’.

Link to the pressrelease (In Swedish).

News from the Department of Earth Sciences

Last modified: 2022-09-30