Rosa Rubicondior: Refuting Creationism - How Deep-Sea Species Evolved

A field of deep-sea mussels (Bathymodiolus sp.) on the Atlantic margin seafloor near a cold methane seep.

Image: Deepwater Canyons 2013 -
Pathways to the Abyss, NOAA-OER/BOEM/USGS.

Into the deep: scientists find two paths | News | Physical Sciences Division | The University of Chicago

A recent paper in Proceedings of the Royal Society B should ring alarm bells for any creationist with the courage and personal integrity to risk reading it. It reports on the findings of a team of three researchers led by scientists at the University of Chicago and including Stewart M. Edie, of the National Museum of Natural History, Smithsonian Institution, Washington DC, that species adapted to deep-sea living evolved to survive in that difficult environment by two different evolutionary pathways.

The first problem for creationists here is that there is no doubt expressed anywhere in the paper that the explanation requires anything other than the Theory of Evolution. There is no sign — as with every other biomedical paper published so far this year — that evolutionary theory is proving inadequate and that biologists are turning instead to creationism, with its unevidenced magic entities and mysteries posing as answers to scientific questions. That narrative exists only in the imagination of creationists.

The second problem arises from the arrogant creationist belief that all living organisms were created especially for humans. If that were so, why ‘design’ some of them to live in the inaccessible depths of the oceans, where for much of human history their existence was entirely unknown? This question has been posed many times in these blog posts, yet not a single creationist has managed to produce anything more convincing than an appeal to ‘mysterious ways’.

The research team set out to understand how organisms living on the abyssal plain — where temperatures hover just a few degrees above freezing, pressures are immense enough to crush all but the most robust submersibles, sunlight never penetrates, and food is scarce — managed to adapt to such extreme conditions. Clearly, they had to undergo substantial evolutionary change, which is probably why relatively few lineages have made the transition, including certain bivalve molluscs such as mussels, oysters, scallops and clams.

The scientists examined the lineages of two groups of bivalves that successfully inhabit the deep sea. They found that one group, already adapted to harsh conditions, moved into the deep-sea environment and adjusted to those conditions without diversifying greatly. A second group, by contrast, radiated into a swarm of new species from a single ancestral lineage.

Life on the Abyssal Plain.
The abyssal plain is one of the largest habitats on Earth, covering vast areas of ocean floor at depths between roughly 3,000 and 6,000 metres. It is a world defined by extremes.

Environmental Conditions

Perpetual darkness – Sunlight does not penetrate beyond about 1,000 metres. Photosynthesis is impossible at abyssal depths.
Near-freezing temperatures – Typically 1–4°C.
Immense pressure – At 4,000 metres, pressure exceeds 400 atmospheres — more than 400 times surface pressure.
Low energy availability – Most food arrives as “marine snow”: a slow rain of organic debris from surface waters.
Geological dynamism – In some regions, hydrothermal vents and cold seeps create chemically rich oases that support specialised communities.

How Life Survives

Because photosynthesis cannot occur, abyssal ecosystems depend on two main energy sources:

Detrital input from above – Organic particles sinking from surface waters.
Chemosynthesis – Microbes use chemical energy (for example from hydrogen sulphide or methane) to fix carbon, forming the base of vent and seep food webs.
Geothermal energy - around geothermal vents.

Many abyssal animals show distinctive adaptations:

Slow metabolism and long lifespans.
Pressure-stable proteins and cell membranes.
Reduced or absent eyes.
Enhanced sensory structures for detecting scarce food.
Symbiotic bacteria in some bivalves, enabling them to exploit chemical energy sources.

Evolutionary Significance

The abyss is not a static museum of ancient life. Geological evidence shows that deep-sea conditions have changed over time with shifts in ocean circulation, oxygen levels and climate. Lineages have repeatedly:

Invaded the deep sea from shallower environments.
Diversified after colonisation.
Gone extinct when conditions changed.

The deep ocean therefore provides a natural laboratory for studying evolutionary innovation under extreme constraints — precisely the kind of gradual, adaptive change predicted by evolutionary theory.

Details of the team’s research are given in a UChicago news item by Maureen Searcy.

Into the deep: scientists find two paths
UChicago paleontologists investigate how life entered and adapted to the deep sea.
The deep sea is a dark, cold place. It’s just a few degrees above freezing, subject to immense pressure, and beyond the reach of the sunlight needed for photosynthesis. It is an inhospitable habitat for most forms of marine life, which primarily rely on microscopic plants. The life that does survive in such a hostile place must find a different way to thrive.

To help understand how certain species adapted to deep-sea living, scientists can look at when their ancestors moved into those harsh depths and whether they were already fit for such conditions.

A new study led by scientists at the University of Chicago examined the lineages of two groups of bivalves—marine invertebrates that include clams, oysters, mussels, and scallops—that successfully inhabit the deep sea. They found that some lineages already well-suited to the harsh environment moved into that habitat in a sporadic way without diversifying much once they were there. For other lineages, a single species made its way down and, having adapted to conditions there, split into a swarm of new species.

The deep sea is the biggest habitat on the planet, but very few lineages have actually managed to penetrate that environment. You might imagine one key to fit that lock, but we found that there are different ways of getting through.

Professor David Jablonski, co-author
Department of the Geophysical Sciences
University of Chicago
Chicago, IL, USA.

Tracing adaptations

Two of the best-sampled groups of bivalves include mussels and a type of marine clam called hatchet shells. These ancient families include hundreds of species found all over the world in deep and shallow water.

Jablonski’s team used these lineages as case studies to trace how and when these organisms became suited to different environments, including adaptations that allow them to live deep under water.

There is a wealth of publicly available information on these lineages, including molecular data, such as genetic and protein sequences. This material can be used to build a phylogeny, or an evolutionary family tree that helps infer the relationship between related organisms.

The team then integrated multiple datasets including molecular data, depth ranges, geographical distribution, and fossil records.

From there, we conducted statistical analyses to test for patterns among these lineages. For example, are shallow-water species that are closely related to deep-sea lineages more likely to live in colder temperatures? That might have prepared them to enter the deep sea.

Dr. Ava Ghezelayagh, first author
Department of the Geophysical Sciences
University of Chicago
Chicago, IL, USA.

These analyses helped the team trace which lineages failed to make it to the deep sea, which ones got there but died out, and which ones made the leap and established residence.

‘Dribs and drabs’ versus a breakthrough

Most bivalves feed on phytoplankton, which rely on sunlight—a diet incompatible with the deep sea. Certain lineages of hatchet shells and mussels are successful in the deep sea because they have both developed a symbiotic relationship with bacteria that derive energy from sulfur, methane, and other chemicals released by hydrothermal vents and cold seeps at the bottom of the ocean. These bacteria live in the bivalves’ gills and share their energy with their hosts.

The results of the study show that these bivalve lineages managed to acquire this ability in different ways,

...and that seems to have affected how they invaded and then exploited the deep-sea environment. Clearly there’s more than one path into the deep sea.

Dr Stewart M. Edie, co-author
Department of Paleobiology
National Museum of Natural History
Smithsonian Institution
Washington, DC, USA.

The hatchet shells set up their partnership with the bacteria in shallow water very early on, with evidence dating back to the early Paleozoic, more than 450 million years ago. For 300 million years, they seemed content to remain in the shallows, cooperating with their symbiotic bacteria.

[Then in the mid-Mesozoic,] they began invading the deep-sea in dribs and drabs. [Because of their relationship to the bacteria,] they were ‘preadapted’ for the deep-sea, and so—we think—just opportunistically slid an occasional species into the deep when the chance arose, but they almost never diversified down there.

Professor David Jablonski.

The team calls this a “piecemeal model” of entry to the deep sea.

Mussels, on the other hand, followed an “in-situ diversification model.” About 60 million years ago, one lineage of mussels acquired the same partnership with bacteria for their nutrition, allowing it to break into the deep-sea habitat. That one entry diversified into at least 70 species.

Of course, there are nuances and complications, and when we look across all bivalve lineages, we find some that fall somewhere in between, but the idea that lineages can trickle into the deep sea and not do much or can send one branch down there with a key adaptation and explode provides a new framework to guide future study of the evolution and biodiversity in this really harsh, strange environment.

Professor David Jablonski.

3D evolutionary tree

3D scans for a deep-sea mytilid (left) and lucinid.
Image: Smithsonian Institution.

Studies like this depend on the completeness of the evolutionary family tree. While hatchet shells, mussels, and other bivalve families are well-sampled, there are still gaps in the molecular DNA data.

Bivalves aren’t a sexy group. There’s not a lot of people sequencing them, other than the ones that are important for the food industry.

Dr. Ava Ghezelayagh.

A related but separate project that Ghezelayagh and Edie are working on is creating a more comprehensive phylogeny using machine learning.

To build an evolutionary family tree, scientists can use molecular data, like their genetic sequence, or morphology, the form and structure of their bodies. Ghezelayagh and Edie are working on a hybrid bivalve phylogeny by marrying these two types of data.

Jablonski’s team has 3D micro-CT scanned images of 90% of living bivalve genera, which can show physical traits such as shell shape and texture, muscle attachments, and details of how the hinge fits the two shells together. Morphological data from fossils can also be integrated into the hybrid evolutionary tree. But gathering such data is a slow and painstaking effort, requiring someone to go through each taxon one by one. Machine learning can speed up the process considerably.

We can include living and extinct taxa, which you normally can't do in a molecular tree. This project allows for a level of completeness that’s never been attained. Then we can ask some really great new questions.

Dr. Ava Ghezelayagh.

Publication:
Ava Ghezelayagh, Stewart M. Edie, David Jablonski;
Alternative pathways into the deep sea: patterns in Bivalvia. Proc Biol Sci 1 February 2026; 293 (2064): 20252002. https://doi.org/10.1098/rspb.2025.2002

Abstract
Relatively few clades have colonized the deep sea. Here, we analyse evolutionary pathways into this harsh environment, as a continuum defined by two potential endmembers—a ‘piecemeal model’, with exclusively deep-sea species (deep-sea endemics herein) derived from multiple, independent entries and an ‘in situ diversification model’ with one entry followed by species proliferation. We focus first on two ancient, distantly related subclades in Class Bivalvia, Mytilidae and Lucinidae, each with hundreds of species occurring globally from the intertidal to abyssal plains. Placing bathymetric ranges into newly inferred molecular phylogenies, we find that the deep-sea endemics within Lucinidae derive in piecemeal fashion, estimating up to 16 phylogenetically isolated entries and perhaps one modest in situ diversification. Mytilidae entered the deep sea just four times, with most endemics stemming from the prolific in situ diversification of Bathymodiolinae. We suggest that the contrasting phylogenetic patterns of entry and proliferation in these clades may be determined by differences in ancestral adult feeding modes. Across Bivalvia, we find that under half of extant families have deep-sea endemics, with the piecemeal model occurring more frequently. Taken together with other clades, we suggest that evolutionary pathways to deep-sea endemicity are more often shaped by multiple, independent events than by in situ diversification.

Phylogenetic distributions of minimum bathymetries for Mytilidae (A) and Lucinidae (B). Cladograms are based on the phylogenies shown in the electronic supplementary material, figures S1 and S2.

Ava Ghezelayagh, Stewart M. Edie, David Jablonski;
Alternative pathways into the deep sea: patterns in Bivalvia. Proc Biol Sci 1 February 2026; 293 (2064): 20252002. https://doi.org/10.1098/rspb.2025.2002

Copyright: © 2026 The authors.
Published by The Royal Society. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

What this study shows, yet again, is that life does not require special pleading or supernatural tinkering to explain its distribution in even the most hostile corners of the planet. The deep sea is not an afterthought of creation, nor a decorative flourish in a human-centred drama. It is an environment with physical constraints, limited energy, and severe selective pressures — and organisms that colonise it do so in ways that reflect their evolutionary history. Some lineages arrive pre-adapted and change little; others radiate into a diversity of forms once ecological opportunity presents itself. Both outcomes are exactly what evolutionary theory predicts.

Far from revealing inadequacy in the theory, research of this kind demonstrates its explanatory power. It accounts for why closely related groups can follow different trajectories under similar environmental pressures, why some diversify explosively while others remain relatively conservative, and why the deep ocean contains a patchwork of lineages with distinct evolutionary backstories.

For creationism, however, this poses a persistent problem. A model based on separate acts of design offers no predictive framework for why one lineage should diversify dramatically while another does not, or why repeated invasions of extreme environments should occur at all. Evolution, by contrast, treats the abyss not as a mystery requiring mystical explanation, but as another arena in which variation, selection and historical contingency shape the living world.

Even in the lightless depths four kilometres beneath the waves, the same natural processes apply. And once again, the evidence points not to design, but to descent with modification.

Advertisement

Amazon