Cryptic species complex
||This article may be too technical for most readers to understand. (May 2010)|
The species in a cryptic complex are typically very close relatives, or sibling species, and in many cases cannot be easily distinguished by molecular phylogenetic studies. If lineage sorting has not yet been completed, members of a cryptic species complex widely share plesiomorphic haplotypes, while individual species might not have evolved distinctive autapomorphic mutations yet. But usually, individual species within the complex can be separated by analysing data from multiple sources, such as by comparing polytene chromosomes, DNA sequence analyses, bioacoustics and thorough life history studies.
They may be parapatric, are frequently sympatric, and are sometimes allopatric. Cryptic species complexes are not the same as populations undergoing speciation: they typically represent a situation where speciation has already broken the gene flow between populations, but where evolution has not progressed to a point where easily recognizable adaptations have taken place.
Cryptic species that do not form a complex may be somewhat more distantly related and simply represent lineages that have been so successful as to require little evolutionary change, possibly coupled with parallel evolution. A famous example are the Eurasian and Short-toed Treecreepers, perhaps the first cryptic species to be recognized as such (by Christian Ludwig Brehm in 1820). Other ornithologists refused to accept that more than one species was involved until Brehm presented his bioacoustic studies, which left no room for doubt. The European Treecreeper has since been found to be a very close relative of the Himalayan Hodgson's Treecreeper, while the Short-toed Treecreeper is probably the sister species of the North American Brown Creeper. Cryptic species are also common in certain families of insects such as Chironomidae. 
A related concept is the superspecies. This is a clade of at least two more or less distinctive species with approximately parapatric distributions. Not all cryptic species complexes are superspecies, and vice versa, but many are.
- Algerian Barb (several species suspected)
- Anopheles gambiae (A significant carrier of the malaria pathogen, with at least 7 species known)
- Audubon's Shearwater (several species suspected)
- Asian glass catfishes (several cases known, most notoriously K. minor)
- Brachionus plicatilis complex (at least 14 species)
- Common Bush-tanager (several species suspected)
- Golden/Mangrove/Yellow Warblers (at least two species suspected)
- Flax Tortrix complex (more than 5 species)
- Grey-cheeked Thrush and Bicknell's Thrush
- Leopard frogs
- Mouse lemurs (16 species)
- Killer Whale (possible)
- "Placidochromis" (over 30 species described in 2004)
- Pogonomyrmex barbatus and P. rugosus (at least six lineages within the two morphospecies)
- Red-legged frogs
- Rhacophorus flying frogs (several cases suspected)
- Scalloped hammerhead shark (two species suspected)
- Scytalopus tapaculos
- Two-barred Flasher (suspected)
- Trichoplax adhaerens (multiple species suspected)
- White-tailed Eagle and Bald Eagle
- Armillaria mellea (turned out to include 10+ species)
Consequences for biological studies 
It has been suggested that cryptic species complexes are very common in the marine environment. Although this suggestion antedated the detailed analysis of many systems using DNA sequence data, it has been proven correct. The increased use of DNA sequence in the investigation of organismal diversity (also called Phylogeography and DNA barcoding) has led to the discovery of a great many cryptic species complexes in all habitats. In the marine bryozoan Celleporella hyalina, detailed morphological analyses and mating compatibility tests between the isolates identified by DNA sequence analysis were used to confirm that these groups consisted of more than 10 ecologically distinct species that had been diverging for many million years.
Evidence from the identification of cryptic species has led some[who?] to conclude that current estimates of global species richness are too low. For example, mitochondrial DNA research published in January 2008 suggests that there are at least 11 genetically distinct populations of giraffes. Similar methods also found that the Amazonian frog Eleutherodactylus ockendeni is actually at least 3 different species that diverged over 5 million years ago.
See also 
- >Int Panis L, Kiknadze I, Bervoets L, Aimanova A (1994). "Karyological identification of some species of the genus Chironomus Meigen, 1803 from Belgium". Bull. Annls Soc. R. Belge Ent. 130: 135–142.
- >Кикнадзе ИИ, Михайлова П, Истомина АГ, Голыгина ВВ, Инт Панис Л, Крастанов Б (2006). "Хромосомный полиморфизм и дивергенция популяций у Chironomus nuditarsis Keyl (Diptera, Chironomidae)". Tsitologia 48: 595–609.
- Knowlton, N (1993). "Sibling Species in the Sea". Annual Review of Ecology and Systematics 24 (1): 189–216. doi:10.1146/annurev.es.24.110193.001201. ISSN 0066-4162.
- Knowlton, N (2000-02). "Molecular genetic analyses of species boundaries in the sea". Hydrobiologia 420 (1): 73–90. doi:10.1023/A:1003933603879. ISSN 0018-8158.
- Gómez, Africa; Peter J Wright, David H Lunt, Juan M Cancino, Gary R Carvalho, Roger N Hughes (2007-01-22). "Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon". Proceedings. Biological Sciences / the Royal Society 274 (1607): 199–207. doi:10.1098/rspb.2006.3718. ISSN 0962-8452. PMC 1685843. PMID 17035167.
- "Giraffes And Frogs Provide More Evidence Of New Species Hidden In Plain Sight". Science Daily. 01 2008.
- Brown, David; Rick Brenneman, Klaus-Peter Koepfli, John Pollinger, Borja Mila, Nicholas Georgiadis, Edward Louis, Gregory Grether, David Jacobs, Robert Wayne (2007). "Extensive population genetic structure in the giraffe". BMC Biology 5: 57. doi:10.1186/1741-7007-5-57. ISSN 1741-7007. PMC 2254591. PMID 18154651.
- Elmer, Kathryn; Jose Davila, Stephen Lougheed (2007). "Cryptic diversity and deep divergence in an upper Amazonian leaflitter frog, Eleutherodactylus ockendeni". BMC Evolutionary Biology 7: 247. doi:10.1186/1471-2148-7-247. ISSN 1471-2148. PMC 2254618. PMID 18154647.
- Shellee Morehead, Jon Seger, Don Feener and Brian Brown, A cryptic species complex in the ant parasitoid Apocephalus paraponerae (Diptera: Phoridae)