Caves as Nature's Evolutionary Laboratories
Deep beneath the surface, in a world of perpetual night, scientists are discovering secrets about evolution that could rewrite our understanding of life itself.
Recent discoveries from the Nullarbor Plain in Australia reveal a world-first: a cave-adapted wasp, eyeless and long-legged, frozen in time alongside thousands of other "mummified" invertebrates. For Dr. Jess Marsh and her team, this remarkable find represents more than just a new species—it provides "a unique glimpse into the biodiversity of the Nullarbor caves" and an extraordinary example of evolution in extreme environments1 .
These discoveries, along with many others, are why caves have become one of science's most powerful model systems for understanding fundamental ecological and evolutionary principles.
The first known cave-adapted wasp discovered in Nullarbor caves, showing no functional eyes and elongated appendages1 .
Yale researchers developed a "mutational clock" using vision-related genes to date cave colonization events.
Fifty years after the groundbreaking work of Poulson and White, who in 1969 proposed caves as natural laboratories, scientists are fully realizing their vision. These secluded underground environments offer what surface systems cannot: controlled conditions with minimal human disturbance, stable climates, and simple food webs that allow researchers to study ecological processes in their purest form2 .
This allows scientists to observe how different species arrive at similar evolutionary solutions independently, a phenomenon known as convergent evolution3 .
As Stefano Mammola emphasized in his 2019 review, caves have expanded beyond their original role to become "eco-evolutionary laboratories" for studying community ecology, trophic webs, conservation biology, and climate change impacts2 3 .
Controlled environments with minimal human disturbance
Similar solutions to darkness evolve independently
Study community ecology and climate impacts
The recent discovery of a highly cave-adapted wasp in the Nullarbor caves stunned researchers. This wasp represents the only known example worldwide to show physical adaptations for life in complete darkness, with no functional eyes, greatly elongated legs and antennae, and extremely reduced wings1 .
"What the cave contains is thousands of such invertebrates," described Dr. Marsh. "Some, bizarrely, had died mid-way through climbing the cave walls—caught frozen in time."1 The pristine, dry cave environment had preserved these specimens so perfectly that researchers cannot yet determine their age—they could be dozens, hundreds, or even many thousands of years old1 .
Meanwhile, Yale researchers studying amblyopsid cavefishes have developed a revolutionary method for dating cave ecosystems. By analyzing genetic mutations in vision-related genes across different cavefish species, they created a "mutational clock" that estimates when each species began losing their eyesight.
Their findings, published in August 2025, revealed that different cavefish species colonized caves independently, with the Ozark cavefish beginning its visual degeneration up to 11.3 million years ago—far beyond the dating range of traditional geological methods. According to graduate researcher Chase Brownstein, "Determining the ages of cave-adapted fish lineages allows us to infer the minimum age of the caves they inhabit because the fishes wouldn't have started losing their eyes while living in broad daylight."
Ozark cavefish begin visual degeneration based on molecular clock analysis
Poulson and White propose caves as natural laboratories2
Air sampling in Spanish gypsum caves reveals microbial diversity5
Discovery of eyeless wasp in Nullarbor caves and development of mutational clock for cavefish1
Until recently, studying cave microorganisms relied heavily on culture-based methods that captured only a fraction of the true diversity, as most bacteria cannot be grown in laboratory conditions. A 2025 study of Covadura and C3 caves in Spain's Gypsum Karst set out to overcome this limitation by comparing traditional culturing with modern genetic sequencing5 .
The research team conducted a meticulous comparative analysis:
Researchers first established baseline conditions by measuring temperature, relative humidity, and concentrations of CO₂ and CH₄ at multiple locations within each cave5 .
Using two different air samplers simultaneously, the team collected 18 air samples from both inside and outside the caves on October 4-5, 20235 .
Each sample was analyzed using both methods—traditional culturing with high-volume SAS samplers and next-generation sequencing (NGS) of 16S rRNA genes5 .
| Location | Distance from Entrance | Temperature (°C) | Relative Humidity (%) | CO₂ (ppm) |
|---|---|---|---|---|
| C3 Entrance | 0 m | 19.5 | 78 | 420 |
| C3 Deep | 150 m | 14.6 | 92 | 620 |
| Covadura Upper Level | 90 m | 15.2 | 85 | 580 |
| Covadura Deep Gallery | 200 m | 13.8 | 95 | 710 |
| External Air | N/A | 22.3 | 65 | 410 |
The findings demonstrated a staggering disparity between the two methods. Culture-based approaches identified only 24 bacterial genera, predominantly Gram-positive spore-forming bacteria from the phyla Bacillota and Actinomycetota5 .
In dramatic contrast, NGS revealed 749 bacterial genera—including numerous Gram-negative and rare airborne bacteria completely missed by traditional methods5 . The NGS results showed that airborne communities more closely resembled those found in cave biofilms and sediments than the cultured isolates, suggesting that a significant portion of cave aerobiomes originates from within the cave itself5 .
| Method | Genera Detected | Dominant Groups |
|---|---|---|
| Culture-Based (SAS) | 24 | Bacillota, Actinomycetota |
| Next-Generation Sequencing (NGS) | 749 | Diverse Gram-negative bacteria |
Culture-based methods captured only 3% of the bacterial diversity revealed by genetic sequencing5 .
Most significantly, by combining microbial data with gas tracer measurements, researchers could identify distinct zones within the caves with different ventilation patterns and degrees of isolation, each maintaining a unique airborne microbial community5 .
Contemporary cave science requires an interdisciplinary arsenal that blends traditional field equipment with cutting-edge technology.
| Tool or Technique | Primary Function | Research Application |
|---|---|---|
| Next-Generation Sequencing (NGS) | Characterizes uncultivable microorganisms | Revealed 749 bacterial genera in gypsum caves versus 24 with culturing5 |
| Portable CRDS Analyzer | Measures CO₂, CH₄ concentrations and isotopic signatures | Identified cave zones with different ventilation patterns5 |
| High-Volume Air Samplers (SAS) | Collects airborne microorganisms for culturing | Traditional aerobiological studies; provides living isolates5 |
| Genomic Sequencing Platforms | Sequences entire genomes of cave-adapted species | Revealed eye degeneration mutations in cavefish over 11 million years |
| Microclimate Monitoring Stations | Tracks temperature, humidity, air pressure | Correlates environmental factors with species distribution5 |
Reveals evolutionary history and adaptation mechanisms
Captures microbial diversity in cave atmospheres
Tracks microclimatic conditions in real-time
As research progresses, caves continue to offer insights that extend far beyond their rocky confines. The genetic discoveries in cavefish not only help date ancient cave systems but may also "shed light on human eye diseases," according to Yale's Professor Thomas Near. Similarly, the microbial communities in caves represent an untapped resource for biotechnology, with potential applications from medicine to industry5 .
However, this research faces a race against time. Many cave species, like the newly discovered Nullarbor spider that may exist in only a single cave, are "at very high risk of extinction"1 .
The discovery of fox scat and a dead fox in the spider's cave highlights the vulnerability of these isolated ecosystems to human disturbance and invasive species1 .
With "thousands of caves on the Nullarbor" and elsewhere still awaiting scientific surveys, the coming years will likely yield even more extraordinary discoveries1 .
As Dr. Marsh reflected on her challenging journey more than 1.5 kilometers into the Nullarbor caves: "There is an otherworldly beauty inside the caves... I would repeat it in a second."1
Fifty years after Poulson and White recognized the potential of caves as biological models, we are just beginning to appreciate the profound answers waiting to be found in the dark.
Acknowledgments: This article is based on the scientific work of researchers at the University of Adelaide, Yale University, and numerous other institutions worldwide who brave the darkness to expand our understanding of life's diversity and evolution.