Invisible biodiversity: When one species turns out to be many

The Chinese giant salamander was long considered a single species. The animal, which can grow to nearly two meters in length, is one of the largest amphibians on Earth and was regarded as the same species throughout China under the name Andrias davidianus.

But genetic analyses brought a surprise to light in 2018: behind the seemingly uniform animal lay several evolutionarily distinct lineages that had developed over millions of years in different river systems. Some of them have since been described as separate species. In addition to A. davidianus, these include Andrias sligoi from southern China, A. cheni from river systems in the Huangshan Mountains, and A. jiangxiensis from Jiangxi Province.

The problem: when the animals were still considered a single species, they were bred en masse on farms, transported between regions, and released back into the wild. This led to the mixing of populations that had evolved independently of one another for four to ten million years. In the worst case, distinct species could disappear before their existence is even recognized.

The giant salamander is thus a striking example of so-called cryptic species—literally “hidden species.” These are species that are nearly indistinguishable in outward appearance but form genetically distinct evolutionary lineages. Yet the giant salamander is not an isolated case. In fact, many biologists now suspect that such hidden species occur far more frequently in nature than long assumed.

How widespread cryptic species actually are was investigated by evolutionary biologist Yinpeng Zhang and his colleague John J. Wiens in an analysis of genetic studies on vertebrates. Their results suggest that the diversity of vertebrates may have been significantly underestimated. Extrapolated to all vertebrates, this could mean that there are considerably more species than previously assumed—possibly even nearly twice as many.

What Are Cryptic Species?

Since the early days of zoology, species have been distinguished primarily by their external appearance: body structure, size, coloration, or anatomical details. This approach was successful for centuries but also has its limitations.

Some species look almost identical on the outside yet are genetically clearly separated from one another. Such hidden species are called cryptic species. They form distinct evolutionary lineages, even though they are nearly indistinguishable in appearance and may even still be able to interbreed. Such lineages often remain undiscovered for long periods. Only genetic analyses make this “invisible” biodiversity visible.

The study: 373 investigations, more than 1,000 species

To estimate how widespread cryptic species actually are among vertebrates, Zhang and Wiens evaluated a large number of previously published studies on molecular species delimitation. Between January and July 2024, they systematically searched Google Scholar for studies that used genetic data to distinguish between species.

Studies from all major vertebrate groups were included: ray-finned fishes (Actinopterygii), cartilaginous fishes (Chondrichthyes), amphibians, reptiles such as snakes, lizards, turtles, and crocodilians, birds, and mammals.

In total, 373 studies met the criteria of the analysis. Together, they encompassed 1,041 morphologically defined species—that is, species originally described based on external characteristics.

For each study, the authors calculated a simple yet informative measure: the ratio between genetically identified lineages and the originally morphologically defined species. A value above 1 means that genetic analyses identify additional, previously unrecognized lineages—that is, potential cryptic species. A value below 1, on the other hand, suggests that several presumed species are genetically barely distinguishable and may belong to a single species.

The analysis also took into account different types of genetic data. Some studies were based exclusively on mitochondrial DNA (mtDNA), others on nuclear DNA (nucDNA), or on a combination of both. This comparison is particularly relevant because there has been an ongoing debate in taxonomy for years about whether mtDNA analyses systematically overestimate the number of species. By directly comparing the data types, Zhang and Wiens were also able to investigate this question.

The most striking result: A universal pattern

The most striking result of the study is not a particularly high or low number in any specific animal group, but rather the remarkable uniformity of the results.

For the five most species-rich vertebrate groups—ray-finned fishes, amphibians, reptiles, birds, and mammals—the average ratio between genetically identified lineages and morphologically described species in analyses using nuclear DNA ranged between approximately 1.8 and 2.1. In other words: behind a morphologically defined vertebrate species, there are on average about two genetically distinguishable lineages.

Remarkably, this ratio barely differs across all major vertebrate groups. Statistical analyses showed that the differences between groups are not significant. Cryptic species are thus apparently not a special case of individual animal groups but a widespread feature of vertebrate diversity—possibly even a fundamental component of evolutionary processes.

Why do cryptic species arise so frequently?

Why this pattern is so consistent remains an open question. Zhang and Wiens suspect that the major differences between animal groups—such as the ability to fly, warm-bloodedness, or aquatic lifestyles—are not the decisive factors. More important may be factors that operate at the level of individual species or populations, such as the size of the geographic range, geographic isolation, population structure, or climatic changes.

Many cryptic species likely arise when populations are spatially separated from one another over long periods. If they continue to evolve under similar environmental conditions, their external appearance can remain remarkably stable while increasingly large differences accumulate in their genomes.

Far more species than assumed

Taken at face value, the actual number of vertebrate species could be significantly higher than previously assumed. If many morphologically defined species actually consist of two or more evolutionarily distinct lineages, a portion of biodiversity has simply remained invisible.

John Wiens had already found similar results for insects as early as 2023: there, an average of about three genetic lineages were identified per morphologically described species. Together, these studies suggest that cryptic species are not a rare curiosity but a fundamental pattern of biodiversity.

mtDNA or nucDNA? A long-standing debate

For decades, biologists have debated whether mitochondrial DNA (mtDNA) can be reliably used to delimit species. The reason for this controversy lies in the properties of this genetic material: mtDNA is relatively easy to sequence technically and was therefore long the most important basis for genetic species studies. At the same time, however, it represents only a single genetic marker and is inherited exclusively through the maternal line.

Critics therefore fear that mtDNA could provide a distorted picture of species diversity—for example, when hybridization or other evolutionary processes skew the genetic signals.

The analysis by Zhang and Wiens now provides a particularly comprehensive look at this question. For many vertebrate groups, the authors were able to compare studies that used either only mitochondrial DNA, only nuclear DNA (nucDNA), or both data types.

The result: analyses based on mtDNA do on average identify somewhat more potential cryptic species than studies using nuclear DNA. While the ratio of genetically identified lineages to morphologically described species for nuclear data was mostly around two, mtDNA analyses yielded values of about 2.5. The difference is thus present but considerably smaller than often assumed. In most vertebrate groups, it was not statistically significant; only in ray-finned fishes was there a clear difference.

The authors therefore conclude: nuclear data are indeed considered more robust because they encompass many independent genetic markers. However, mitochondrial DNA frequently already provides a reliable initial estimate of hidden species diversity.

Especially at a time when many species are disappearing before they have even been described, mtDNA can therefore be a valuable screening tool—provided its results are later verified through more comprehensive genetic analyses.

The consequences for conservation

The potential consequences of these results for conservation are substantial. If several evolutionarily distinct lineages are hiding behind many morphologically described species, a portion of biological diversity may remain invisible in conservation programs.

This is because conservation measures are usually based on formally described species. They form the fundamental unit for Red Lists, conservation laws, and international agreements. However, if several distinct species are classified under a single name, endangered lineages can go unnoticed.

The example of the Chinese giant salamander illustrates this problem clearly. It was long considered a single, widespread species (Andrias davidianus). Genetic analyses, however, revealed several deeply divergent lineages that had evolved over millions of years in different river systems. Some of these lineages have since been described as separate species.

As a result, the actual range of each individual species shrinks dramatically. What previously appeared to be a relatively widespread species turns out to be several locally restricted and critically endangered species, each considerably more vulnerable to habitat loss, overexploitation, or disease.

There is an additional problem: many cryptic species are genetically identified but never officially described as new species. In the literature evaluated by Zhang and Wiens, only about 2 to 14% of the identified cryptic lineages were actually formally described taxonomically. The majority remain nameless and therefore cannot be included in conservation lists or management plans.

The authors see this as one of the greatest challenges for biodiversity research: without targeted genetic investigations and subsequent taxonomic work, a portion of species diversity could disappear before it has even been scientifically documented.

Consequences for evolutionary research and fossil interpretation

The study also has implications for our understanding of evolutionary history. Fossils can by their nature only be distinguished by morphological characteristics—precisely those features where cryptic species are particularly difficult to detect. If living species on average contain more genetic diversity than their morphology suggests, the biodiversity of past ages may also have been systematically underestimated.

This affects, among other things, estimates of species richness, speciation rates, and extinction events over the course of Earth’s history. If a portion of actual species diversity remains invisible in the fossil record, the evolutionary patterns derived from it can be distorted.

Phylogenetic analyses of living species can also be affected. If cryptic lineages are not accounted for in diversification analyses, the picture of evolutionary dynamics can change considerably. In an earlier study of several freshwater fish clades, for example: without accounting for cryptic species, the data suggested a declining speciation rate over time—but with them, a largely constant rate of diversification.

Such results illustrate that cryptic species are not merely a taxonomic detail. They can change our understanding of how species originate, how biodiversity is distributed, and how life on Earth has evolved over time.

More species than thought

The study by Zhang and Wiens shows how much biodiversity may have remained hidden until now. Behind many known species, there may be several evolutionarily distinct lineages that are nearly indistinguishable in appearance.

For conservation, this has far-reaching consequences. If cryptic species remain undiscovered, locally restricted and highly endangered lineages can stay hidden under the name of a seemingly widespread species. Conservation measures could then unintentionally overlook a portion of actual diversity.

At the same time, the discovery of cryptic species also changes our picture of evolution. It shows that a portion of biodiversity only becomes visible through genetic analyses. The biodiversity of Earth is therefore likely richer and more complex than classical, purely morphological taxonomy long suggested. A portion of this diversity is still hidden—and waiting to be discovered.

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Sources

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• Li, X., & Wiens, J. J. (2023). Estimating Global Biodiversity: The Role of Cryptic Insect Species, Systematic Biology, Volume 72, Issue 2, March 2023, 391–403, https://doi.org/10.1093/sysbio/syac069
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• Zhang, Y. & Wiens, J. J. (2026). Cryptic species are widespread across vertebrates. Proceedings of the Royal Society B, 293, 20252377. https://doi.org/10.1098/rspb.2025.2377