In the world of phylogenetics, there's team sponge and team comb jelly.
Which creature roots the animal tree of life — the simple sponge or the more complex comb jelly — has stirred fierce debate among phylogeneticists, researchers who study evolutionary history.
Scientists long assumed the muscle-less and neuron-less sponges gave rise to more complex organisms, including humans. But genomic analyses in 2008 comparing hundreds of genes from many different animals and their relatives delivered a surprising result: comb jellies (i.e. ctenophores) — which have muscles and neurons — may have been the first animals.
Knowing which animal is at the base of the tree of life helps researchers understand how organisms are related to each other and how complex features like the nervous system evolved. The comb jelly findings, which suggested that sophisticated systems developed and were later lost in sponges but retained in all other animals, were a shock to biologists.
Subsequent research bounced back and forth between the two hypotheses, dividing scientists into distinct camps. Then, in 2023, a new type of genetic analysis examining the physical linkage of genes on chromosomes found strong support for the comb jellies as the root of the animal tree.
"I think we all want to know where we came from," says HHMI Investigator Nicole King, whose lab at the University of California, Berkeley studies animal origins. The hypothesis that comb jellies evolved first was "like finding out that the guy you thought was your dad was not your dad."
Contributing to the Debate About the First Animal
Mapping organisms onto the tree of life is necessary for King's research, which compares living organisms within a phylogenetic framework to understand how animals originated.
While King favored the sponge hypothesis, she was happy to watch the debate play out from the sidelines.
"While I use phylogenies, I haven't been a card-carrying phylogeneticist for a long time and it was never my area of specialty," King says. "This was not a debate I wanted to get into."
Then Jacob Steenwyk joined the King Lab as a postdoctoral researcher. Steenwyk is an expert in phylogenetics and computational biology — and previously leaned toward the ctenophore hypothesis.
"Jacob came in hypothesizing that the ctenophore sister idea was correct, while I hypothesized that the sponge sister idea was correct, and so we thought, why not? Let's go for it," King says. "We wanted a more accurate idea of how all these organisms are related to each other and I thought that, with Jacob's talents, we might have a chance to make a meaningful contribution to this debate."
A New Way to Map the Tree of Life
Steenwyk and King implemented a new approach that unifies historically disparate methods to better separate signal from noise.
The team created a comprehensive, high-quality dataset of conserved genes from a variety of different organisms. Then, they analyzed these genes using their integrative approach, which generated results supporting either the ctenophore hypothesis or the sponge hypothesis. From these results, the researchers narrowed down the genes in their dataset to only include genes that yielded the same result with both methods, discarding genes that gave different results depending on the method used. They also varied many different parameters to assess the stability of the findings. These steps further ensured the quality of their data.
The team then conducted a series of statistical tests to determine whether there was significant support for one hypothesis over the other, or if the results were inconclusive.
Statistical tests affirmed the sponge hypothesis, suggesting that the simple creatures root the animal tree of life. Specifically, 62 percent of the tests supported the sponge hypothesis, 38 percent of the tests were inconclusive, and there was no support for the ctenophore hypothesis.
"I think the way we've done this analysis lends very strong support for the hypothesis that sponges evolved first, which is consistent with studies based on morphology. But I still think there's room for investigating this question further. I hope that everyone interested will jump in, and together we'll keep hammering on this," King says.
"We are not arguing that our study settles the debate – only the community can decide that. What we are saying is that we've found really strong evidence that favors only one hypothesis."
