Simple Sponges or Complex Jellies? Why Ctenophores Remain as Metazoa's Most Likely Ancestor

Introduction: The Phylogenomic Pendulum - Ctenophores to Porifera

In the grand library of life on Earth, the very first chapter of the animal kingdom has remained stubbornly illegible. For over a century, biologists have debated which lineage represents the "sister group" to all other animals—the first branch to split from our common ancestor. This is not merely a question of taxonomic bookkeeping; it is a fundamental inquiry into the origins of complexity itself. Did the first animals possess muscles, nerves, and a gut? Or were they simple, sedentary filter-feeders, devoid of tissues and organs?

The debate has traditionally pitted two candidates against one another: the morphologically simple sponges (Phylum Porifera) and the complex, gelatinous comb jellies (Phylum Ctenophora). For decades, the "Sponge-Sister" hypothesis held sway, aligning with a gradualist view of evolution where complexity accrues slowly over distinct epochs. However, the advent of high-throughput genomic sequencing in the 21st century threw this narrative into disarray, with increasing evidence suggesting the "Ctenophore-Sister" hypothesis—a scenario that implies complex traits like neurons evolved twice or were lost in sponges.

In late 2025, a landmark study published in the journal Science appeared to resolve this conflict once and for all. Authored by Jacob L. Steenwyk and Nicole King, the paper titled "Integrative phylogenomics positions sponges at the root of the animal tree" promised a unification of conflicting methodologies.¹ Using a novel approach termed "integrative phylogenomics," the authors reported overwhelming statistical support for sponges as the earliest branching animal lineage, seemingly ending the "Ctenophore wars".²

Yet, the certainty provided by this study was short-lived. In a dramatic turn of events that underscores the rigor and vulnerability of modern data science, the paper was retracted less than three months after publication.⁴ Independent researchers, utilizing open-source code and data, identified critical analytical errors that, when corrected, completely reversed the study's conclusions.⁵

This report provides a comprehensive examination of this scientific episode. We will explore the deep biological stakes of the sponge-versus-ctenophore debate, dissect the innovative yet flawed methodology of the 2025 study, and analyze the forensic statistics that led to its retraction. Beyond the specific taxonomic question, this case serves as a profound case study for undergraduate researchers on the dangers of "black box" bioinformatics, the necessity of open science, and the relentless, self-correcting machinery of the scientific method.

Part I: The Biological Stakes of the Deepest Branch

To understand why a statistical error in a phylogenomic pipeline matters, one must first appreciate the organisms at the center of the controversy. The distinction between a sponge and a comb jelly is not just a difference in shape; it represents two fundamentally different architectures of life. The placement of these groups at the base of the animal tree dictates our understanding of how the defining features of animal life—nervous systems, muscles, and digestive tracts—came to be.

The Case for Sponges (Porifera) and the Gradualist Narrative

Sponges are the archetype of simplicity. They are sessile, meaning they are fixed in one place, attaching themselves to the sea floor. They lack true tissues, organs, a mouth, or a gut. Instead, their bodies are organized as a system of water canals. Specialized cells called choanocytes, or collar cells, use whip-like flagella to generate a current, drawing water through pores (ostia) to filter out bacteria and organic particles.⁶

From an evolutionary perspective, the "Sponge-Sister" hypothesis is intuitively satisfying. It suggests a linear progression of complexity.

• The Ancestor: The last common ancestor of all animals (the Urmetazoan) was likely a colonial organism similar to modern choanoflagellates—single-celled protists that form colonies and bear a striking resemblance to sponge choanocytes.⁷

• The Trajectory: If sponges branched off first, the story of animal evolution is one of accumulation. The lineage started with simple multicellularity (sponges), then invented tissues and radial symmetry (cnidarians like jellyfish), and finally developed bilaterian symmetry and centralization (worms, insects, vertebrates).

• Implications for Systems: Under this view, the nervous system and muscles are unique innovations that occurred once, after the sponge lineage had already diverged. This supports the idea that complex structures differ in kind, not just degree, from the simple precursors found in proto-animals.

For decades, morphology—the study of form—supported this view. Sponges simply looked like the transition between a colony of cells and a true animal. They have no neurons to fire and no muscles to contract. They represent the "grade" of organization one would expect at the very dawn of multicellularity.

The Case for Comb Jellies (Ctenophora) and the Complexity Paradox

Ctenophores, or comb jellies, challenge the gradualist narrative. Though they are gelatinous and superficially resemble jellyfish, they are evolutionarily distinct. They are active predators that swim through the world's oceans using rows of iridescent cilia—the "combs" from which they take their name.

Unlike sponges, ctenophores are complex.

• Anatomy: They possess a "through-gut" with a distinct mouth and anal pores, allowing for unidirectional digestion—a feature once thought to be exclusive to Bilateria (the group including humans).⁸

• Nervous System: They have a decentralized "nerve net" that coordinates swimming, feeding, and light production (bioluminescence). They possess an apical organ, a sensor that detects gravity and controls balance.⁹

• Muscles: They possess smooth muscle cells used to maintain body integrity and manipulate shape.

The "Ctenophore-Sister" hypothesis—the idea that these complex animals branched off before the simple sponges—introduces a paradox. If the first branch of the animal tree contained organisms with nerves and muscles, then the evolutionary history of these traits becomes incredibly complicated.

• Scenario A (Loss): The common ancestor of all animals was complex, possessing a nervous system and muscles. Sponges, which branched off later, subsequently lost these traits, reverting to a simpler, sessile lifestyle. This would imply that the simplicity of the sponge is a derived adaptation, not a primitive state.²

• Scenario B (Convergence): The common ancestor was simple. Ctenophores evolved their nervous systems and muscles independently from the rest of the animal kingdom. This would mean that the "neuron"—the very cell type allowing you to read this sentence—is not a singular evolutionary invention but a functional solution that nature discovered twice, using different genetic blueprints.⁹

The Stalemate of the Early 21st Century

Prior to the 2025 Steenwyk and King study, the field of evolutionary biology was effectively deadlocked.

• Morphological Data: Favored sponges. The visible simplicity of sponges made them the logical stepping stone from protists.¹⁰

• Early Phylogenomics (2008-2015): The first massive genetic studies favored ctenophores. In 2008, a study led by Casey Dunn shocked the community by placing ctenophores at the base. However, critics argued this was an artifact.⁵

• Long Branch Attraction (LBA): The primary criticism against the Ctenophore-Sister hypothesis was a statistical phenomenon known as Long Branch Attraction. Ctenophores have genomes that evolve very rapidly. When phylogenetic algorithms analyze rapidly evolving lineages, they can mistake the high number of random mutations for shared history, artificially grouping distinct lineages together or pulling them toward the "root" of the tree. For over a decade, researchers argued back and forth: was the ctenophore signal real, or was it just LBA masquerading as history?.⁶

In 2023, a study by Schultz et al. published in Nature introduced a new line of evidence called "synteny"—the order of genes on chromosomes—which strongly supported ctenophores.¹² However, the conflict between sequence-based methods (analyzing DNA letters) remained unresolved. It was into this fractured landscape that Steenwyk and King stepped, proposing a method to heal the divide.

Part II: The Promise of Integrative Phylogenomics

The central innovation of the Steenwyk and King paper was a methodology designed to bypass the limitations of previous studies. They recognized that the debate had become a war of algorithms, with different software and mathematical models yielding contradictory results. To resolve this, they proposed Integrative Phylogenomics, a framework intended to unify the two dominant approaches in the field: Concatenation and Coalescence.

The Two Pillars of Phylogenetics

To understand their approach, one must understand the tools of the trade. When biologists reconstruct evolutionary trees from DNA data, they generally use one of two strategies:

1. Concatenation (The Supermatrix):

2. Concept: Researchers take individual genes (Gene A, Gene B, Gene C...) from all species, align them, and stitch them together into one massive super-gene, often millions of DNA letters long.

3. Logic: By pooling all the data, the true evolutionary signal should emerge through sheer statistical power, drowning out the noise of individual genes.

4. weakness: This method assumes all genes share the exact same evolutionary history. In reality, due to a phenomenon called Incomplete Lineage Sorting (ILS), different genes can trace different paths through the species tree, especially when speciation events happen in rapid succession.¹³

5. Coalescence (The Gene Tree Summary):

6. Concept: Researchers build a separate evolutionary tree for each individual gene. If they have 1,000 genes, they build 1,000 small trees. They then use summary software (like ASTRAL) to find the species tree that best explains the distribution of these gene trees.

7. Logic: This method explicitly accounts for the variation in gene histories caused by ILS.

8. Weakness: It relies heavily on the accuracy of the individual gene trees. If the individual genes are short or lack sufficient signal, the resulting gene trees will be "noisy," and the summary will be unreliable.¹³

The "Integrative" Solution

Steenwyk and King argued that the Sponge-Ctenophore conflict persisted because some genes favored one method while others favored the other. Their solution was to identify and isolate only the "consistent" genes—those that told the same story regardless of which method was used.¹

The workflow described in the paper was rigorous and computationally intensive:

1. Data Collection: They assembled a massive dataset of 869 genes from 100 species, covering sponges, ctenophores, cnidarians, bilaterians, and outgroups (non-animals).⁵

2. Dual Scoring: For every single gene, they calculated two scores:

3. A Concatenation Score (using Log-Likelihood) to see if the gene preferred the Sponge-Sister or Ctenophore-Sister tree when analyzed as sequence data.

4. A Coalescence Score (using Quartet Support) to see if the gene's internal branching pattern supported Sponges or Ctenophores.³

5. Filtration: They kept only the genes that were "consistent." If a gene supported Sponges in concatenation and Coalescence, it was retained. If it supported Ctenophores in both, it was retained. If it conflicted (e.g., supported Sponges in one method but Ctenophores in the other), it was discarded as unreliable noise.

The Findings: A Landslide Victory for Sponges

The results published in November 2025 were staggering. The authors reported that they had subjected their new matrices and 10 previously published datasets to 785 different topology tests.

• 490 tests showed statistically significant support for the Sponge-Sister hypothesis.

• 0 tests supported the Ctenophore-Sister hypothesis.

• The remaining 295 tests were inconclusive.¹

The paper concluded that the "Ctenophore signal" seen in previous years was largely driven by inconsistent genes—noise that had now been successfully filtered out. The authors wrote, "These results provide compelling evidence for the sponge-sister hypothesis and suggest that integrative phylogenomics provides a robust and powerful approach for disentangling branches in the tree of life".¹

The scientific community reacted with relief and excitement. The study seemed to validate the classical, morphological view of evolution. It suggested that we did not need to rewrite the textbooks on the origin of neurons; the simple sponge was indeed our earliest cousin.

Part III: The Anatomy of Error

The certainty offered by the Steenwyk and King paper evaporated in a matter of weeks. The catalyst for this reversal was not a new discovery in the field or a fresh fossil find, but a rigorous re-analysis of the paper's own data by a team of critics.

Casey Dunn, a professor at Yale University, along with colleagues Xiaofan Zhou, Jingxuan Chen, and others, downloaded the data provided by Steenwyk and King. They attempted to reproduce the "integrative" scoring pipeline. What they found was a series of methodological flaws so severe that they rendered the original conclusions invalid. The critique, published initially as a GitHub repository (sk25) and later as an eLetter to Science, dissected the analysis step by step.⁵

The errors identified by the Dunn team were not simple typos; they were fundamental misunderstandings of how phylogenetic software processes data. These errors generated false confidence, creating a mirage of support for sponges where none existed.

Error 1: The Likelihood Artifact (The Concatenation Flaw)

The first red flag that alerted the Dunn team was the magnitude of the support scores reported in the paper. In phylogenetics, researchers compare two trees by calculating their "Log-Likelihood" (ln(L)). The difference between two trees ( Δln(L)) indicates how much better one tree fits the data than the other. Typically, for a single gene, this difference is small—often in the single digits or low double digits.

Steenwyk and King reported Δln(L) values in the thousands.¹⁴ Such numbers are astronomically high for single-gene analyses and immediately signaled that something was mathematically amiss.

The Technical Failure:

To calculate these scores, the authors used the software IQ-TREE. They intended to ask the software: "What is the likelihood of this gene fitting a Sponge-Sister tree versus a Ctenophore-Sister tree?"

• The Mistake: Instead of providing fully resolved trees (where every branch is defined), the authors provided "constraint trees." A constraint tree is a rough outline—it might say "Sponges are one group, and everything else is another group," but it leaves the relationships within those groups undefined (a state known as a polytomy).

• The Consequence: When IQ-TREE was asked to calculate the likelihood of a constraint tree without optimizing the internal branches first (a specific misuse of the -z command line argument), it returned meaningless values. The software was effectively penalizing the trees for having undefined branches, resulting in the massive, thousands-point differences.⁵

The Correction:

When the Dunn team fixed the code to first infer the best fully resolved tree under each hypothesis and then calculate the likelihood, the massive support scores vanished. The Δln(L) values returned to the normal range of -10 to +10. More importantly, for the vast majority of genes, the direction of support flipped. The signal that supposedly favored sponges was a computational artifact of analyzing unresolved trees.

Error 2: The Quartet Bias (The Coalescence Flaw)

The second pillar of the "Integrative" method—the Coalescence Score—was equally flawed. This metric relied on analyzing "quartets," or subsets of four species. The logic is that by looking at all possible combinations of four species, one can deduce the overall tree structure.

The Technical Failure:

The authors defined a "match" for the Sponge-Sister hypothesis in a way that was heavily biased by their sampling strategy.

1. Imbalanced Sampling: The dataset contained a large number of sponges (29 species) but a relatively small number of ctenophores (13 species).¹⁴

2. Collapsed Nodes: To score the quartets, the authors used reference trees where they "collapsed" large groups of animals into single nodes. For the Sponge-Sister reference tree, they grouped "Ctenophores + Cnidarians + Bilaterians" into one single blob.

3. The Spurious Signal: Because of this collapsing, any quartet that contained two sponges and two non-sponges was automatically scored as supporting the Sponge-Sister hypothesis, regardless of the actual evolutionary relationship shown by the gene.

4. Analogy: Imagine trying to determine if Team A is better than Team B. You decide to count "fan support." However, your counting method automatically counts every person wearing a red hat as a supporter of Team A. If you hold the rally in a city where everyone wears red hats, Team A wins 100% of the time, even if those people actually prefer Team B.

The sheer number of sponges in the dataset meant there were millions of these uninformative quartets. They swamped the calculation, creating a statistical illusion that the genes supported sponges.⁵

Error 3: The Ghost Genes

Perhaps the most damning error identified by the Dunn team was the inclusion of genes that contained no relevant information whatsoever. To determine if Sponges or Ctenophores are the "sister" to all other animals, a gene must contain sequences from four distinct groups:

1. Sponges

2. Ctenophores

3. Other Animals (Cnidarians/Bilaterians)

4. Outgroups (Non-animals like Choanoflagellates to "root" the tree).

If a gene is missing the Ctenophores, it obviously cannot tell you where Ctenophores belong. If a gene is missing the Outgroup, you cannot tell which direction time flows (you cannot root the tree).

The Discovery: The Dunn analysis revealed that 56 of the 869 genes in the dataset were missing either Ctenophores, Outgroups, or both. These genes were mathematically incapable of resolving the debate. Yet, in the Steenwyk and King analysis, 45 of these uninformative genes were scored as "Consistent Support for Sponge-Sister".⁵

This was the "smoking gun." It proved that the scoring pipeline was not measuring evolutionary signal; it was measuring the structural bias of the dataset. The pipeline was so biased that it could find support for sponges in genes that didn't even have ctenophore data to compare against.

Part IV: The Retraction and the Reversal

The accumulation of these errors—likelihood artifacts, quartet bias, and the inclusion of uninformative genes—led to a complete collapse of the study's conclusions. It was not merely a case of the support becoming weaker; the support evaporated and re-condensed around the opposing hypothesis.

The Corrected Analysis

When the Dunn team corrected the code, filtered out the "ghost" genes, and re-ran the "Integrative Phylogenomics" pipeline on the original dataset (the "92.5 matrix"), the picture changed dramatically.

• Original Claim: 82 genes consistent for Sponge-Sister; 6 genes consistent for Ctenophore-Sister.

• Corrected Reality: 174 genes consistent for Sponge-Sister; 370 genes consistent for Ctenophore-Sister.⁵

Once the artifacts were removed, the "consistent" genes—those that showed the same signal in both concatenation and coalescence—overwhelmingly favored the Ctenophore-Sister hypothesis. The very method designed by Steenwyk and King to prove the sponge hypothesis had, when properly executed, proven the opposite.

The Response from the Authors

In a field often marred by defensiveness and ego, the response from Jacob Steenwyk and Nicole King was a model of scientific integrity. Upon receiving the critique and the code from the Dunn team, they did not double down or attempt to obfuscate. They reviewed the findings, acknowledged the errors, and took immediate action.

On January 9, 2026, the authors requested the retraction of their paper. In their statement, they wrote:

"We unwittingly included errors in our analysis pipeline that artifactually influenced the results... In the interest of maintaining the integrity of the scientific record, we have requested that the editors of Science retract our study".¹⁴

The retraction was officially published in February 2026.⁴ The speed of this correction—from publication in November to retraction in February—was made possible by the "Open Science" practices employed by both teams. Because Steenwyk and King had publicly shared their data matrices, and because the Dunn team publicly shared their analysis code on GitHub, the community was able to audit the science in real-time.

Part V: Synteny and the "Third Way"

The retraction of the Steenwyk and King paper has done more than just remove an erroneous result from the record; it has clarified the landscape of the debate. With the "Sponge-Sister" phylogenomic evidence now discredited, the field is seeing a convergence of evidence around the Ctenophore-Sister hypothesis.

Crucially, the corrected sequence data from the Steenwyk study now aligns with a completely different type of genomic evidence: Synteny.

Beyond Sequence: The Order of Genes

Most phylogenomic studies, including the retracted one, look at the sequence of DNA letters (A, C, T, G) within genes. However, over millions of years, these sequences can become saturated with mutations, making it hard to see ancient relationships (the "Long Branch Attraction" problem mentioned earlier).

In 2023, a study by Darrin Schultz and colleagues published in Nature took a different approach. They looked at Synteny, or the order of genes on chromosomes. Chromosomes are like libraries; genes are the books. Over time, evolution shuffles the books. However, certain "linkages"—groups of genes sitting next to each other—are incredibly ancient and resistant to change.¹²

The Synteny Findings:

Schultz et al. found that Ctenophores and Sponges both share ancient gene linkages with non-animals (the outgroups). However, Ctenophores possess a specific pattern of chromosomal fusions that places them as the earliest branch. Sponges, Cnidarians, and Bilaterians all share a distinct set of chromosomal rearrangements that Ctenophores lack.

• The Implication: This shared pattern in Sponges and other animals (excluding Ctenophores) is a "derived" trait. It implies that Sponges and the rest of us share a common ancestor after the Ctenophore lineage had already split off.¹²

Synteny is considered a "Rare Genomic Change" (RGC). Unlike a single letter mutation in DNA, which can easily happen back and forth (A turns to T, then back to A), moving a block of genes is a major structural event that is unlikely to happen identically twice by chance. Therefore, synteny is often viewed as a more robust marker of deep evolutionary history than sequence data.

The fact that the corrected Steenwyk and King data (sequence-based) now agrees with the Schultz et al. data (synteny-based) provides a powerful "consilience" of evidence. Two independent methods, looking at different aspects of the genome, now both point to Ctenophores as the sister to all other animals.

Part VI: Implications for the Future of Biology

The collapse of the Sponge-Sister hypothesis in this high-profile case leaves biologists grappling with the profound implications of the Ctenophore-Sister reality. If comb jellies are indeed the earliest branch, we must rethink the evolution of complexity.

The Independent Evolution of Neurons

The most provocative implication concerns the nervous system. Ctenophores have neurons. Sponges do not. Cnidarians (jellyfish) and Bilaterians (us) have neurons.

If the tree looks like this: (Ctenophores (Sponges (Cnidarians + Bilaterians))), then we have two choices:

1. Massive Loss: The ancestor of all animals had a nervous system. Sponges (and another simple group, the Placozoans) lost it entirely. While possible, this requires assuming that a highly advantageous trait like a nervous system was discarded by multiple lineages.

2. Convergent Evolution: The ancestor was simple. Ctenophores evolved a nervous system. Then, independently, the lineage leading to Cnidarians and Bilaterians evolved a nervous system.

Evidence is mounting for the second scenario—Convergence. Ctenophore neurons are weird. They use different neurotransmitters than our neurons (they lack dopamine and serotonin signaling in the same way we use them). Their "synapses" (connections between neurons) have different structural proteins.⁹ This suggests that nature "invented" the neuron twice. It implies that the nervous system is not a singular miracle of evolution, but a functional engineering solution that life can arrive at through different pathways.

The Pipeline Problem in Bioinformatics

For the undergraduate researcher, the Steenwyk and King retraction serves as a cautionary tale about the tools of modern science. We live in an era of "Black Box" biology. It is easy to download a dataset, feed it into a pipeline script (like the one used in the 2025 study), and accept the output as truth.

The error in the Steenwyk paper—calculating likelihoods on unoptimized constraint trees—was a technical nuance, a misuse of a specific software parameter. Yet, it generated numbers that "looked" scientific but were meaningless.

This episode reinforces the need for:

• Sanity Checks: If a result looks too good to be true (like a likelihood difference of 5,000 when 10 is normal), it probably is.

• Visualizing Data: Had the authors looked at the trees or the distribution of quartets visually, the bias might have been obvious.

• Understanding the Math: You cannot treat phylogenetic software as a magic wand. You must understand what the algorithm is actually calculating.

Conclusion: Science as a Verb

The retraction of DOI 10.1126/science.adw9456 is not a failure of science; it is a triumph of the scientific process. In many human endeavors, errors are buried or defended. In science, they are exposed and corrected.

In November 2025, the community was presented with a hypothesis backed by massive data. By February 2026, that hypothesis had been dismantled, not by authority or dogma, but by code and calculation. The "Sponge-Sister" hypothesis, which stood for over a century as the textbook explanation of animal origins, has likely faced its final defeat.

We are left with a new view of our own history—one that is stranger and more complex than we imagined. The animal kingdom did not begin with a simple, passive filter-feeder that slowly learned to move and think. It began with a bifurcation: one path led to the sponges and their quiet, stationary simplicity. The other path led to the ctenophores—ghostly, glowing predators patrolling the ancient oceans—and eventually, through a long and winding road of innovation, to us.

The tree of life has been pruned, and while the branch we thought was the root has been moved, the tree itself stands stronger, its shape refined by the relentless friction of evidence and debate. For now, Ctenophores remain as the basal path that metazoans (animals) traveled through in evolutionary history.

Data Summary Tables

Table 1: Comparison of Methodological Frameworks

Feature	Concatenation (Supermatrix)	Coalescence (Gene Trees)	Integrative Phylogenomics (Proposed)
Unit of Analysis	Combined sequence of all genes	Individual gene trees	Genes consistent across both methods
Assumption	All genes share one history	Genes have different histories (ILS)	Inconsistent genes are "noise"
Strength	High statistical power	Models gene history variation	Removes conflicting signal
Weakness in 2025 Paper	Error: Likelihood calculated on unresolved trees	Error: Biased quartet scoring due to collapsing nodes	Result: Filtered out the true signal

Table 2: The Reversal of Fortune (Comparison of Results)

Metric	Original 2025 Paper (Flawed)	Corrected Analysis (Dunn et al.)
Support for Sponge-Sister	490 Tests	174 Genes
Support for Ctenophore-Sister	0 Tests	370 Genes
Likelihood Difference (Δln(L))	Thousands (Artifact)	< 10 (Typical)
Conclusion	"Compelling Evidence for Sponges"	"Strong Support for Ctenophores"

Table 3: Biological Implications of the Root

Hypothesis	Sponge-Sister	Ctenophore-Sister
Evolution of Neurons	Evolved once (single origin)	Evolved twice (convergence) OR lost in sponges
Evolution of Muscles	Evolved once	Evolved twice OR lost in sponges
Ancestral Complexity	Simple (sponge-like)	Complex (ctenophore-like) or Mosaic
Current Status	Discredited by retraction & synteny	Supported by corrected phylogenomics & synteny

(Note: This report synthesizes information from the retracted Science article ¹, the retraction notice ⁴, the critique by Dunn et al. ⁵, and supporting literature on synteny and ctenophore biology.⁹)

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