What did Dinosaur DNA look like?

22 May 2018
Posted by Becky O'Connor.

What did the DNA of a dinosaur look like?

This is a question that my team and I at the University of Kent have been studying for some time. To decipher what is ostensibly more than a 66 million year old mystery, we've been comparing the genomes of the descendants of dinosaurs - species like birds and turtles - to figure out how the overall genome structure - meaning the chromosomes - of our favourite dinosaur species, like the Velociraptor or Tyrannosaurus, might have appeared.

We started with the likely genome structure of an ancestor that both birds and turtles would have shared and then the traced the chromosome changes that would have happened to a reptile over the evolutionary time between the "dinosaur dynasty" and the present day. The most striking thing we found was that, although the positions of some of the genes have been shuffled about within each of the chromosomes, there's no sign of genes jumping between chromosomes. So a gene on, let's say, chromosome 1 doesn't later jump ship and land up later on chromosome 12.

The Dinosaur Family Tree

But before we look into this further, let's consider what we mean by "dinosaurs". This iconic group of animals first appeared on Earth around 240 million years ago. For the next 170 million years afterwards, these creatures dominated the planet. Mammals, like us, did exist but only in low numbers and most of them were very small and nocturnal, probably because anything any larger quickly became a dinosaur's lunch.

The dinosaurs were so successful they managed to side-step a series major extinction events that happened during their reign. That is, until a city-sized asteroid fragment measuring 10-15 kilometres across slammed into the Earth 66 million years ago and caused such a catastrophic shift in the climate that almost all of them were wiped out. Only their smaller relatives - the birds - and more ancient species like crocodiles lived to tell the genetic tale.

Apart from birds, lizards and turtles are also closely related to dinosaurs, and they all shared a common ancestor about 275 million years ago and 255 million years ago respectively. It is the dinosaurs, however, that are the lineage that led directly to modern birds. In fact, while dinosaurs are widely considered to have gone extinct, the reality is that they are alive and well as their descendants the birds....meaning that your average pigeon, parrot, ostrich or chicken is in fact a living dinosaur. There Is plenty of evidence to support this: both dinosaurs and birds share features such as egg-laying, feathers/proto-feathers, brooding behaviour and have similar skeletons with bones that contain air sacs. But, until now we had no idea whether their genomes would look the same too.

What is a genome, and what are chromosomes?

A genome is the entire complement of DNA in each of the cells in an organism's body. The genome includes all of the genes and therefore contains the genetic instructions that make that organism grow, develop and function. The DNA itself is contained within the nuclei of cells where it is divided up into coiled chunks called chromosomes that each contain up to a few thousand genes. Packaging up the DNA like this ensures that cells can duplicate their genes correctly when they make copies of themselves to allow cells to divide. Remarkably, this pattern of coiling is identical in virtually every cell division and remains consistent from individual to individual within the same species. These species-specific chromosomes can be visualised as a ‘karyotype’ which is essentially a map of the genome.

The picture below shows a female human karyotype with 23 pairs of chromosomes.

From an evolutionary perspective, karyotypes are really interesting given that the overall structure is unique to each species.  In fact, the number and shape of the karyotype can vary enormously between species, for example, some deer have only 6 chromosomes while some rats have 102 chromosomes.

What do bird chromosomes look like?
Birds have really unusual genomes in that almost all species of bird have the same overall structure, made up of around 10 pairs of large chromosomes (called macrochromosomes) and around 30 pairs of tiny microchromosomes, all of which are about the same size as each other and impossible to tell apart as you can see in the picture below. In this case, these chromosomes are from a canary.

What is also unusual about birds is that these tiny chromosomes contain almost half of the animal's genes, even though they only make up a quarter of the genome. In most other species, the genes are more evenly distributed across the chromosomes. There are many theories as to why birds' chromosomes are organised this way, and some scientists argue that this structure probably helps with the high energy requirements of flight. Birds are also unusual in that there are so many different types, with over 10,000 species: some are as tiny as a hummingbird and some are huge, like an ostrich; between these two extremes is a huge variety of different shapes and sizes. Having so many chromosomes might also help to generate this enormous species diversity.

Can we find chromosomes in a dinosaur fossil?
Unfortunately not! The only way to make chromosome preparations is by using living tissue or a blood sample. And even if DNA could be extracted from dinosaur bones, which we don't think it can (at least at the moment), it wouldn’t give us the right material to make chromosomes. The only method currently available to understand dinosaur genomes is therefore through looking at the genomes of their closest relatives, which is what we've done in our study.

So what did we discover?
First, by using a computer to compare the sequence of DNA letters in the genomes of multiple bird and reptile species, we've been able to produce a best guess at what the genome structure would have looked like in the last ancestor share by all of these species millions of years ago. Then, based on that ancestor's genome structure, we were able to work out the most likely pattern of chromosome rearrangements that would have led from this ancestor to their living relatives. From this information we could then work out how genes must have been rearranged through evolution in a dinosaur.

What we found was actually quite surprising: very little change had occurred between the chromosomes in the species we considered. That is, the overall chromosome structure has stayed the same. Also surprising was that relatively little change had occurred in the way the genes are organised within the chromosomes themselves. Together, these two results suggest that there must have been some kind of advantage to keeping this unusual bird-style genome structure.

How do turtles fit in?
Turtles shared an ancestor with modern birds about 255 million years ago, so any similarities in their genomes must have also been present in this ancestor. In fact, turtles are one of the very few species that have similar looking chromosomes to birds. Until now though, the tools required to compare their chromosomes were not available. In our study, we added fluorescent labels, called "DNA probes", to the chromosomes of birds and turtles so that we could locate the stretches of DNA that match in the two species. What we found was an extraordinary degree of genome stability – in this case we found multiple examples of whole chromosomes that had stayed unchanged in not only in all of the bird species tested but also in turtles too. The picture below shows an example of one of these regions lit up in the genome of (a) a chicken and (b) a turtle, demonstrating how this chromosome has not changed between species over more than a quarter of a billion years. The results demonstrate that if these chromosomes are the same in modern birds and the turtles, then they must have been the same in the ancestor and in their descendants along the way which of course includes the dinosaurs. Given that this also means that these chromosomes have remained unchanged over a period of nearly 260 million years of evolution, there must be some selective advantage to keeping these tiny chromosomes intact.

(a) Chicken chromosomes with chicken microchromosome fluorescent DNA probes:

(b) Turtle chromosomes with chicken microchromosome fluorescent DNA probes

So if scientists can identify dinosaur DNA, does this mean Jurassic Park could really happen?
I'm afraid not! The idea of extracting DNA from mosquitoes in amber and then creating new dinosaurs from that DNA is very much science fiction! But what our results do reveal are new insights into how birds and other species have evolved, illustrating that their genome structure had much older origins than we previously appreciated. In fact, for many years scientists believed that this bird-style genome had evolved as a mechanism to support flight. Our results suggest otherwise, because flight only appeared around 130 million years ago.

In summary, our results suggest that the genome structures of dinosaurs was remarkably similar to that of modern birds with an overall pattern of a few large chromosomes and multiple gene-rich tiny chromosomes. Genomic stability over such an astonishing length of time would suggest that this unique genome is one of the key features that underpins the extraordinary diversity and success of dinosaurs both living and extinct.

Publication details:

Reconstruction of genome organization in the diapsid common ancestor permits tracing of chromosome evolution in avian and non-avian dinosaurs is published in Nature Communications
doi: 10.1038/s41467-018-04267-9

Authors: Rebecca E. O’Connor1, Michael N. Romanov1, Lucas G. Kiazim1, Paul M. Barrett2, Marta Farré3, Joana Damas3, Malcolm Ferguson-Smith4, Nicole Valenzuela5, Denis M. Larkin3*, Darren K. Griffin1*.

1 School of Biosciences, University of Kent, Canterbury, Kent CT5 7NJ, UK
2 Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
3 Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
4 Department of Veterinary Medicine, Cambridge University, Cambridge CB3 0ES, UK
5 Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Iowa 50011, USA

*Joint last authors

Becky O'connor agreed to write this article after she met with the Naked Scientists at a workshop they were running recently for the Genetics Society to help scientists to develop enhanced skills in science communication.

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