Biologists who study the evolutionary origin of animals got a bit of a surprise this month when a new study reached the opposite conclusion from a study two years ago about which organisms root the animal tree of life. Both studies originated from UC Berkeley labs.
Until 2008, most biologists thought that the simple sponge was likely at the root of the animal tree, with all animals descending from the ancient ancestor of sponges. But that year, with new animal genomes available, a genetic analysis concluded that another creature, the comb jelly, was actually the first animal. Though numerous studies over the years have split between sponges and comb jellies, in 2023 a Berkeley lab employed a totally new analysis method and came down firmly on the side of comb jellies.
Then, last week, another team of Berkeley biologists flipped it again, reporting in Science that sponges root the animal tree.
"I think we all want to know where we came from," said Nicole King, a Berkeley professor of molecular and cell biology and senior author of the new paper. The hypothesis that comb jellies evolved first - overturning years of evidence supporting the contrary - was "like finding out that the guy you thought was your dad was not your dad."
Whether sponges or comb jellies - formally called ctenophores (pronounced teen-a-fores) - are at the root of the animal tree makes a big difference to biologists who study animal evolution. In fact, biologists were hard put to explain how sponges, which lack muscles and neurons, would have evolved from ctenophore-like organisms, which likely had both. Sponges would have had to lose those characteristics, or muscles and neurons would have had to arise independently twice during the evolution of animals.
"Muscles and neurons are key animal innovations, things that make us uniquely who we are. Understanding how those features evolved reveals an important part of our history," said Berkeley postdoctoral fellow Jacob Steenwyk, first author of the new paper. "For the ctenophore-sister hypothesis, you have to evoke more complicated evolutionary scenarios, including, potentially, multiple origins of muscles and neurons. But for the sponge-sister hypothesis, it's a little bit simpler - just one innovation of muscles and neurons. Because there are cases where evolution does not inevitably lead to an increase in complexity, we have to do the research to sort this out."
Nicole King and Jacob Steenwyk/UC Berkeley
Knowing which organism is at the base of the animal tree of life also helps researchers understand how organisms are related to each other and how complex features like muscles and the nervous system evolved.
Ancient evolutionary episodes like the origin of animals are notoriously hard to reconstruct and can lead to conflicting findings, noted King, an investigator with the Howard Hughes Medical Institute (HHMI) who studies the closest living relatives of animals, the choanoflagellates. Prior to this study, she leaned toward the sponge as the earliest animal.
"We are not arguing that our study settles the debate - only the community can decide that," she said. "What we are saying is that we've found really strong evidence that favors only one hypothesis."
Referring to the two Berkeley teams, Steenwyk said that "we're both trying out new methods, because early approaches haven't resolved the controversy. That's what's exciting about these two papers: What are the new types of evidence that we can bring to this old debate? Then, given the totality of evidence, we can see where the chips lie."
New genomic methods give differing results
Steenwyk has followed the nearly two-decade back and forth between proponents of sponges and ctenophores and thought that the two main techniques used to analyze animal genomes could be combined to increase evolutionary signal and reduce noise. An expert in phylogenetics and computational biology, he originally leaned toward the ctenophore hypothesis.
Photos by Alison Yin, courtesy of HHMI
That hypothesis was bolstered in 2023, when Daniel Rokhsar, a Berkeley professor of molecular and cell biology and of physics, teamed up with Darrin Schultz and Oleg Simakov of the University of Vienna to conduct a new type of genetic analysis. They examined the physical linkage of genes on chromosomes - that is, how closeness on the genome has been inherited, a concept called synteny. They found strong support for comb jellies as the root of the animal tree.
Steenwyk and King employed their own unique analysis to tackle this question. They created a comprehensive, high-quality dataset of conserved genes from 100 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 include only those that yielded the same result with both methods, discarding genes that gave different results depending on the method used. These steps ensured the quality of their data. They also varied many different parameters to assess the stability of the findings.
A battery of statistical tests affirmed the sponge hypothesis, suggesting that these simple creatures root the animal tree of life. Specifically, 62%of the tests supported the sponge hypothesis, 38%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.
The work was funded by the Life Sciences Research Foundation and HHMI.
