Chromosomes are the physical carriers of genetic information in the form of genes, which are found lined up along each chromosome. Although chromosomes are crucial in the functioning of complex life, the way in which they initially formed in the earliest cells and the details of their changes over evolutionary time have not been studied.
More than 20 years after the start of the Human Genome Project, however, scientists now have access to technologies that can reveal the complete genetic sequence of entire chromosomes and this enables them to conduct analyses of how chromosomes have changed.
A recent study led by Daniel Rokhsar, a professor of biological sciences at the University of California, Berkeley, has tracked changes in chromosomes in order to make sense of the ways in which genes are arranged on the chromosomes of different groups of animals.
Although it has long been known that certain genes stick together – they always occur next to each other on a chromosome – these clumps of genes appear on different chromosomes and in various chromosomal locations in different types of animals. The question is: how did they get there?
In order to follow the evolution of chromosomes in early groups of animals, Rokhsar and colleagues from the University of Vienna and UC Berkeley identified 29 groups of linked genes that they termed ancestral linkage groups, or elements, that were present in most animal lineages. These elements have been remarkably conserved in all animal groups over the past 600 million years of evolutionary history, indicating a strong selective pressure to keep them from changing.
Using the groups of linked genes as markers, the researchers worked out how the chromosomes changed in early animals, including bilaterians (animals with bilateral symmetry), cnidarians (such as jellyfish and hydras), and sponges. They found that, while the chromosomal elements remained constant in terms of which genes they contained, they got shuffled around between chromosomes. Each element consisted of the same linked genes, but their location on the chromosomes could change. This means that geneticists can describe the chromosomes of a species by designating which elements are in which chromosomes.
“So now, for example, we can break down each human chromosome into its elements using algebraic notation. Then we deduce what happened to these primordial elements in different species and genera such as corals, mollusks, birds and many others, and what new chromosomes these elements had assembled into,” explains molecular biologist Oleg Simakov from the University of Vienna.
Elements move to a new chromosome by means of genetic mistakes during cell division, such as chromosome breakages, translocations, insertions and fusions. The researchers also found that, once an element had changed location to a different chromosome, this new arrangement was passed on to all subsequent descendants in that animal lineage. Every descendent species would inherit the new arrangement. This implies that the arrangement of chromosomal elements can be used as a map of the evolutionary relationships between species.
“Such events are irreversible in evolution and every group of animals – from corals to humans – has such unique combinations that will forever distinguish the descendants of these groups and set these groups apart from others,” Simakov said.
Another consequence of the findings of this study is that researchers can now predict the arrangement of elements on the chromosomes of species for which genome sequencing has yet to be conducted.
“One of my favorite aspects of our study is that we make predictions about what to expect in genomes that are yet to be sequenced,” Rokhsar wrote in an email to Quanta. For example, his team discovered that diverse invertebrates classified as spiralians all share four specific element patterns that imply the fusion of chromosomes has occurred in their common ancestor. “It follows that ALL spiralians should show these [same] patterns,” Rokhsar wrote.
He added, “You don’t get to make those kinds of grand pronouncements about evolutionary history very often.”
The findings of the study, published in the journal Science Advances, also show that certain single-celled animals contain some of the 29 highly conserved elements in their genomes. These organisms are the closest relatives of multicellular animals and this discovery sheds light on how chromosomes were formed in the very earliest ancestors of current animal lineages. “These ancient linkage units provide a framework for understanding gene and genome evolution in animals,” the scientists noted in their paper.
The reasons why ancestral linked genes have been so highly conserved over time, and the evolutionary significance of moving elements to new chromosomal positions have yet to be investigated.