3 Waves Of Evolutionary İnnovation Shaped Diversity Of Vertebrates

Over the past 530 million years, the vertebrate lineage branched out from a primitive jawless fish wriggling through Cambrian seas to encompass all the diverse forms of fish, birds, reptiles, amphibians, and mammals. Now researchers combing through the DNA sequences of vertebrate genomes have identified three distinct periods of evolutionary innovation that accompanied this remarkable diversification. The study, led by scientists at the University of California, Santa Cruz, and published this week in Science, focused on regulatory elements that orchestrate the activity of genes. They found three broad categories of evolutionary innovations in gene regulation that increased in frequency during different periods in vertebrate evolution. The first period, for example, was dominated by regulatory innovations affecting genes involved in embryonic development. These changes occurred during the period leading up to about 300 million years ago, when mammals split off from birds and reptiles.

"So many new body plans evolved during this time, it makes sense that the strongest signal in our analysis is for changes affecting genes involved in the development of the body plan and the complex regulation of other genes," said David Haussler, a distinguished professor of biomolecular engineering in the Baskin School of Engineering at UC Santa Cruz and corresponding author of the paper. First author Craig Lowe worked on the study as a graduate student in Haussler's group at UCSC and is now a postdoctoral researcher at Stanford University.

Many previous studies have shown that important evolutionary changes in animals have resulted from the gain, loss, or modification of gene regulatory elements, rather than from the evolution of new protein-coding genes. "Most of the changes that have happened during vertebrate evolution, as animals acquired new body plans and features like feathers and hair, were not the result of new genes but of new regulatory elements that turn genes on and off in different patterns," Haussler said.

The new study identified millions of these regulatory innovations by using computational methods to look for DNA sequences that are still the same in species that have evolved separately over long periods of time. These sequences have presumably been conserved by natural selection because they serve an important function, so most mutations that change them would be harmful to the organism. Conserved sequences outside of known genes are likely to be gene regulatory elements. By comparing the genomes of species whose evolutionary lineages diverged at different times in the past, researchers can see when in evolutionary history a particular conserved sequence first appeared.