An Arctic comb jelly (Mertensia ovum). Kevin Raskoff

Just a couple of genes are responsible for some of the longest running and most contentious arguments in evolutionary biology, a new study has shown.

The study, led by Antonis Rokas of Vanderbilt University in Tennessee, US, analysed hundreds of thousands of genes sequenced from target organisms to try to resolve heredity issues that up until now have seemed intractable.

Among other ongoing debates, Rokas and colleagues set out to determine whether marine sponges or ocean predators known as comb jellies represented the oldest branch of the animal family tree.

For the best part of a century, sponges were held to be the earliest form of animal life, based primarily on the observed simplicity of their structures. In recent decades, however, genetic sequencing has thrown up the comb jellies – or ctenophores – as an arguably better candidate.

And thus the argument has raged. A 2008 genetic study favoured the jellies. Earlier this year, another study opted for the sponges.

For Rokas’s team, the object of the analysis was not only to try to resolve the matter but also to understand how the controversy arose in the first place. After all, in 95 per cent of cases genetic sequencing answers questions of evolutionary precedence without ambiguity.

To do so, the researchers dug into the fine detail of genes shared across the species groups under investigation.

“The trick is to examine the gene sequences from different organisms to figure out who they identify as their closest relatives,” explains Rokas.

“When you look at a particular gene in an organism, let’s call it A, we ask if it is most closely related to its counterpart in organism B? Or to its counterpart in organism C? And by how much?”

By applying this method, the team determined that comb jellies had more genes than sponges that supported the theory that they diverged first.

The scientists also succeeded in resolving another long-running evolutionary question, concerning whether crocodiles are more closely related to birds or turtles. The results suggested that 74 per cent of shared genes between the three groups indicate that crocs and birds are “sisters”, while crocs and turtles are “cousins”.

Phylogenetic data creates these occasional controversies, the researchers discovered, because a handful of “strongly opinionated” genes sometimes confound the statistical analyses employed to produce results.

By correcting for the influence of these genes, Rokas and colleagues hope that future conflicts can be resolved quickly.

“We believe that our approach can help resolve many of these long-standing controversies and raise the game of phylogenetic reconstruction to a new level,” Rokas says.

The team’s study is published in Nature Ecology and Evolution.