Cryptic Species

Cryptic species are groups of organisms that are morphologically indistinguishable from one another but are genetically distinct enough to be considered separate species. These species pose significant challenges for taxonomists and ecologists because traditional methods of species identification, which often rely on visible physical traits, fail to distinguish them. Instead, cryptic species can only be reliably identified through genetic, biochemical, or sometimes behavioral analyses. The concept of cryptic species emphasizes the complexity of biodiversity and the need for molecular tools in modern taxonomy. An example of cryptic species is found in the Bocourt’s terrapin (Mauremys rivulata), a freshwater turtle found in the Mediterranean. Initially, these turtles were thought to be a single species, but genetic studies have revealed that they are a complex of several cryptic species, each with distinct genetic profiles but nearly identical appearances. Another well-known case involves the African elephant, where what was once thought to be a single species has been identified as two distinct species, the African bush elephant (Loxodonta africana) and the African forest elephant (Loxodonta cyclotis), through DNA analysis.

The terms “cryptic species,” “sibling species,” and “sister species” are often used in discussions of species differentiation and speciation but have distinct meanings:

1. Cryptic Species: As described, these are species that appear identical or nearly identical in morphology but are genetically distinct and reproductively isolated. Cryptic species are often discovered through molecular techniques rather than traditional morphological examination.
2. Sibling Species: Sibling species are a type of cryptic species; they are two or more species that are morphologically similar but genetically distinct. The term “sibling” implies that these species are closely related and may have recently diverged in evolutionary terms. Sibling species are often sympatric (living in the same geographic area) and may occupy slightly different ecological niches or exhibit subtle differences in behavior or physiology.
3. Sister Species: Sister species are the closest relatives to each other on the evolutionary tree, meaning they share a most recent common ancestor not shared with any other species. While sister species can be morphologically distinct or similar, they are defined primarily by their phylogenetic relationship rather than their appearance. Sister species can result from recent speciation events or represent lineages that diverged longer ago but have maintained a close evolutionary relationship.

Using Molecular Tools to Understand Cryptic Species

DNA barcoding has emerged as a pivotal technique for species identification. This method relies on sequencing a standardized region of the genome, typically the mitochondrial cytochrome c oxidase I (COI) gene in animals, to produce a unique genetic identifier or “barcode” for each species. These barcodes can then be compared to a comprehensive reference library to confirm species identity. The utility of DNA barcoding extends to delineating cryptic species by uncovering genetic disparities between organisms that appear identical. For example, in the butterfly genus Astraptes, what was once thought to be a single species was revealed to be at least ten cryptic species using DNA barcoding. Additionally, this technique aids in discovering new species by identifying barcodes that do not match any known sequences in the database, indicating potentially unrecorded biodiversity.

Metabarcoding extends the principles of DNA barcoding to analyze entire biological communities from environmental samples such as soil, water, or feces. This method extracts DNA from these bulk samples and identifies multiple species simultaneously by comparing the sequences to a reference database. Metabarcoding is particularly effective for delineating cryptic species within complex ecosystems where traditional survey methods may miss less conspicuous or elusive organisms. Moreover, this approach can signal the presence of new species by revealing sequences that are absent in current reference databases, particularly in ecosystems that are difficult to sample or are less studied, like deep-sea or dense rainforest habitats.

Environmental DNA (eDNA) barcoding represents another leap in non-invasive species detection. By extracting DNA directly from environmental matrices such as water or sediment, eDNA barcoding captures the genetic signatures of organisms present in the ecosystem without the need for direct observation or specimen collection. This technique is invaluable for monitoring elusive or rare cryptic species and has proven especially powerful in aquatic environments. For instance, eDNA sampling has successfully identified different salmonid species in rivers, uncovering distribution patterns that are not easily observed through conventional methods. Furthermore, eDNA barcoding can lead to the discovery of new species by capturing genetic material from a range of organisms, including previously unknown microbial, fish, and amphibian species.