Computing power and data from the human genome project have allowed Trinity College researchers to support an old theory about how animals withbackbones may have arisen, writes Dick Ahlstrom
Research groups at Trinity College Dublin and Iowa State University have independently confirmed a 30-year-old theory about how animals with backbones may have evolved. Both groups point to a sudden unprecedented increase in genetic complexity, in turn leading to a new family of animal species.
Susumu Ohno developed the theory in a 1970 book, Evolution by Gene Duplication, but his ideas lay idle and unproven. He suggested that the greater complexity of animals with backbones occurred because of a dramatic doubling of the number of genes in their genetic code through a process called polyploidy.
Polyploidy is a process where a genetic mistake, either during cell division or when male and female sex cells fuse, causes a doubling of the genome of a species. Instead of a creature having the same number of chromosomes and genes as its parents, the amount of genetic material doubles up, encouraging the emergence of completely new organisms.
Polyploidy is nothing new in the plant kingdom and it is also known in fish, but was unknown in animals with spines or chordates. Polyploidy gave rise to a new fish species, the salmon, as recently as 10 million years ago. About 70 per cent of flowering plants and 95 per cent of ferns underwent polyploidy.
Now the Trinity and Iowa groups demonstrate at least one major event of polyploidy in chordates, an occurrence that may have allowed the greater complexity of backboned animals to arise. Their separate research findings are published in the current issue of Nature Genetics.
Work at Trinity started three years ago with funding from the Health Research Board. Science Foundation Ireland funding then came on stream about a year ago.
Ohno knew that polyploidy was at work in the fish DNA, explains Prof Ken Wolfe, assistant professor of genetics at Trinity's Department of Genetics. "He could see these early polyploid events in the fish genome," he says and theorised something similar was at work in chordates. "It was an unprovable theory", however, and remained so until the human genome project laid bare the contents of the entire human genetic code.
His lab was involved in the genome project and sequenced elements of our DNA. "We have now used the human DNA sequence to test \ theory," says Prof Wolfe. "We have come in and said yes it looks like he was right."
The confirmation comes as a result of bioinformatics, the business of using computers to analyse the billions of steps in human DNA. The computers can scan for duplicate fragments, "just pieces, maybe a few million base pairs long that match others on different chromosomes", explains Prof Wolfe.
The assumption was that if polyploidy occurred, then it happened hundreds of millions of years ago, before the chordate group emerged. It could have arisen in a single organism or the merger of two to form one with double the number of genes, says Prof Wolfe.
His team, which included Aoife McLysaght and Karsten Hokamp, set up the kinds of matches to search for. The computers churned through the mass of data for six hours before returning a positive verdict. The team found matching fragments well separated on different chromosomes, the longest including 29 genes and 40 million base pairs. The researchers found many duplicated DNA sequences. "We have about 100 of them and they occupy about half the genome."
They also assessed when this might have occurred and suggest what is likely to have been a once-off "point event" happened between 350 million and 650 million years ago. To put this timing in perspective, the divergence that separated humans and fish on the evolutionary tree occurred about 420 million years ago and the human/mouse divide is estimated at 100 million years ago.
"We can't really say what triggered it, just that it happened," says Prof Wolfe. "One of the interesting questions is what are the functions of these genes. The big advantage of duplicating genes is one of the genes can sit there as a back-up and can change."
If the size of the chordate genome doubled, all the existing genes would have had a working match. That would have allowed the extra gene to specialise over time, and become something different from the original without harming the organism. This would have added to the range and function of the proteins being produced by these genes.
"One of the next things we want to do is look at the mouse genome," says Wolfe. The team will try to confirm polyploidy in its genome and this may enable them to refine a timing for the genetic doubling event. They will also see whether they can confirm another Ohno theory, that polyploidy happened twice in chordate history.