Genomic clues to the origin of the vertebrates

An international team including scientists from Oxford, Spain and France reports how more complex and specialised gene regulation was pivotal in the origin of the vertebrates. The work, published in Nature, compares genomic, epigenomic and gene expression data between several animals, including a small fish-like relative, amphioxus. 

The vertebrates, or animals with backbones, are the animal group to which humans belong, along with other mammals, birds, reptiles, amphibians and fish. Vertebrates have complex brains and large bodies and have colonised virtually all of the planet’s ecosystems. Over 20 years ago, research conducted in Professor Peter Holland’s laboratory in the Department of Zoology at University of Oxford showed that many new genes arose in the evolution of vertebrates, but it was unclear how the extra genes contributed to the evolutionary rise of vertebrates.

In the new study, Peter Holland and his Oxford colleague Ferdinand Marletaz collaborated with experts in gene regulation from the Spanish National Research Council (Seville), Centre for Genomic Regulation (Barcelona)and National Centre for Scientific Research (CNRS, France), to ask how gene regulation – the switching on and off of genes – differs between vertebrates and a close non-vertebrate relative, amphioxus. The work, published by the prestigious scientific journal Nature, examines genomes, plus ‘epigenomic’ and gene expression data, revealing functional changes associated with the evolution of higher complexity in the vertebrates.

Choosing amphioxus was key to this work”, explains Holland, “because of its evolutionary position. Amphioxus are beautiful marine animals that look like very small fish, but they are not true fish – they are close relatives of vertebrates without some of the complexities and without the extra genes. 

Héctor Escriva (CNRS, Banyuls sur Mer, France) adds “Amphioxus can serve as a reference in evolutionary comparisons to understand our lineage”.

“We found two key differences between vertebrates and invertebrates”, explains Manuel Irimia of the Centre for Genomic Regulation (Barcelona)and one of the joint leads for the work. “First of all, we observed that generally speaking our gene regulation is much more complex than that of the invertebrates. The second difference is that we have copies of genes that originally performed only very general functions, but which in the vertebrates went on to specialise in much more specific functions, particularly in the brain”.

“Our study gives an overview of the genome’s different regulatory layers and a detailed description of the vertebrates’ unique genomic regulation characteristics”, states José Luis Gómez-Skarmeta, one of joint leads of the work from the Centro Andaluz de Biología del Desarrollo (CSIC – Universidad Pablo de Olavide).  

The research also included participation from other researchers in the UK, France, Australia, the Czech Republic, Netherlands, Japan, China, Portugal, Italy, Taiwan, Norway and the United States, and was funded by the European Research Council and national agencies in each country.