Previous genomic analyses "flip-flopped" between whether sponges or comb jellies are our deepest ancestors.
However, new research led by the researchers at the University of Bristol in the UK identified the cause of this "flip-flop" effect, and revealed that sponges are the most ancient lineage.
They analysed all key genomic datasets released between 2015 and 2017.
"The fact is, hypotheses about whether sponges or comb jellies came first suggest entirely different evolutionary histories for key animal organ systems like the nervous and the digestive systems," said Davide Pisani, from the University of Bristol
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For the study published in the journal Current Biology, scientists used cutting edge statistical techniques to test whether the evolutionary models routinely used in phylogenetics can adequately describe the genomic datasets used to study early animal evolution.
They found that, for the same dataset, models that can better describe the data favour sponges at the root of the animal tree, while models that drastically fail to describe the data favour the comb jellies.
"Evidence for comb jellies as the earliest branching animal lineage first emerged in 2008, a decade ago, in the first, large-scale, phylogenomic analysis of the animal phyla," he said.
"We have now better analytical tools and data and this study seriously challenges the accepted status quo," he added.