Amphioxus research sheds light on the origin of vertebrates

A special issue containing a number of articles in aspects of amphioxus genetics research, authored by leading international scientists, has just been published in International Journal of Biological Sciences.

The discovery in the 1980’s that animals as diverse as flies and mouse shared a toolkit of basic developmental genes helped to unite biologists, leading to the creation of the new discipline of evolutionary developmental biology that tries to explain the evolutionary change by means of changes in developmental genes and gene networks. One of the important questions in this new discipline is how vertebrates originate from their closest invertebrate relatives. For this, scientists have been using amphioxus, regarded as the closest invertebrate relative to the vertebrates, as the model system to study evolutionary genetics of vertebrates.

“Since human beings have often wondered about their own origins, it is not surprising that there have been many studies aimed at understanding the evolutionary history of chordates (i.e. the origin of chordates and the diversification of vertebrates) “, wrote Marlétaz et al, scientists at CNRS, France and University of California San Diego, USA.

We human are Chordates, a group of animals that include ascidians, amphioxus, and all vertebrates (fishes, amphibians, reptiles, and mammals among others).

Amphioxus possess a vertebrate-like body plan, with nothocord, hollow dorsal nerve cord, segmented muscle blocks, perforated pharyngeal region and post anal tail. Since its first developmental genetics recorded in about 1992, it is clear that amphioxus represents the best preduplicative stand-in of the vertebrate genome. Very recently, the position of cephalochordates as the closest invertebrate relative of vertebrates has been challenged, and phylogenomic data suggest that amphioxus may in fact be the earlier chordate, or even lower deuterostomes. In this special issue and the following issue of Int J Biol Sci, leading research groups give insights into the genome organization, developmental biology, neurobiology and anatomy of amphioxus, to understand the genetic mechanisms that underlie evolutionary change in Chordates. Amphioxus, at the genomic and morphological level, is an example of a “living fossil”, invaluable to illuminate the origin of Chordates in the tree of life, after some 500 M years.

The Guest Editor of the special issue, Dr. Jordi Garcia-Fernàndez, a prominent researcher of amphioxus genetics and professor of University of Barcelona, said: “It has been predicted that sequencing the amphioxus genome will give the answer on whether vertebrates are or not octaploids in origin. Well, the genome is finished (Joint Genome Institute), and in the process of annotation, so most probably 2006 will give the answer to the 2R hypothesis -two rounds of genome duplications at the origins of vertebrates, a question mark left after the sequencing of the human genome in 2000- for the origin of vertebrates. Just to remind, the amphioxus genome showed the more prototypical and single chordate Hox cluster in 1994, and also was the place where to discover the ParaHox cluster in 1998, that changed the views on the origin and evolution of the Hox genes.

“Amphioxus research is giving interesting inputs into the evolution of the nervous system, and into the origin of neural vertebrate innovations (MHB-midbrain-hindbrain boundary, neural crests, etc). This is in the reviews and hypothesis papers by Lacalli, Wada. Satoh. Langeland, Candiani, Benito Gutierrez, in this and the forthcoming special issues. In other words, amphioxus may hold the answer in the path that from a gently filter-feeding animal, the furious vertebrate predators arose, by means of the complications of the neural system.

“In 2006 the position of amphioxus in the evolutionary tree is changing, giving it even a more basal position within chordates, as seen in the paper by Vienne and Pontarotti in the special issue. The ’smell’ that the genome is on its way is seen also in the 4 papers of Permanyer, Osborne, Holland and Jimenez in the special issue dealing with genome stuff (transposon, cis-regulatory analyses, etc).

“And finally, amphioxus seems entering into the experimental era, by the first trials of gene manipulation. This was not done before because the most difficult thing with amphioxus is to get embryos. Now, it seems that the spawning of the animals, hence the obtaining of ’on demand’ embryos is starting to be possible. I do hope to see the first ’fluorescent animal’ in the very near future”, said Garcia-Fernandez.

Highlights of papers include Osborne et al of University of Oxford and University of Reading reporting five novel Miniature Inverted-repeat Transposable Elements (MITEs) identified by an analysis of amphioxus DNA sequence. The estimated high copy numbers of these elements implies that MITEs are probably the most abundant type of mobile element in amphioxus, and are thus likely to have been of fundamental importance in shaping the evolution of the amphioxus genome. Vienne and Pontarotti reported the analysis of 82 protein families presenting homologs between urochordata and other deuterostomes, and showed that the urochordates are the sister groups of the vertebrate and that gene loss played a major role in structuring the Ciona genome.

These special issues have authors from leading Research Organizations and Universities of USA, England, Canada, France, Italy, Spain, and Japan.

International Journal of Biological Sciences publishes peer-reviewed scientific papers of significance in all areas of biological sciences. Abstracts are indexed in PubMed and full texts of articles are freely available in the journal web site http://www.biolsci.org as well as PubMed Central http://www.pubmedcentral.nih.gov, the U.S. National Institutes of Health (NIH) digital archive of biomedical journal literature.