Journal articles: 'Cryptic species'

1

Dudgeon, Steve, Janet E. Kübler, John A. West, Mitsunobu Kamiya, and Stacy A. Krueger-Hadfield. "Asexuality and the cryptic species problem." Perspectives in Phycology 4, no. 1 (May 1, 2017): 47–59. http://dx.doi.org/10.1127/pip/2017/0070.

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Zhang, Da-Yong, Kui Lin, and Ilkka Hanski. "Coexistence of cryptic species." Ecology Letters 7, no. 3 (February 9, 2004): 165–69. http://dx.doi.org/10.1111/j.1461-0248.2004.00569.x.

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Shivas, Roger G., and Lei Cai. "Cryptic fungal species unmasked." Microbiology Australia 33, no. 1 (2012): 36. http://dx.doi.org/10.1071/ma12036.

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The word cryptic is derived from the Greek adjective krupt�s which means hidden. Morphologically indistinguishable species that have been revealed by molecular phylogenetic methods, and 37ultimately only recognised by their DNA sequences, are referred to as cryptic species. The importance of cryptic species for plant pathologists is that they may have significant differences in the severity of diseases they cause, host range and geographic distribution. It is these differences that are of concern to many biosecurity agencies, particularly in Australia.

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Cruse, Michael, Robin Telerant, Thomas Gallagher, Thomas Lee, and John W. Taylor. "Cryptic species inStachybotrys chartarum." Mycologia 94, no. 5 (September 2002): 814–22. http://dx.doi.org/10.1080/15572536.2003.11833175.

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Bannikova, Anna, Vladimir Lebedev, Anna Dubrovskaya, Evgenia Solovyeva, Viktoria Moskalenko, Boris Kryštufek, Rainer Hutterer, et al. "Genetic evidence for several cryptic species within theScarturus elaterspecies complex (Rodentia: Dipodoidea): when cryptic species are really cryptic." Biological Journal of the Linnean Society 126, no. 1 (December 3, 2018): 16–39. http://dx.doi.org/10.1093/biolinnean/bly154.

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Pérez-Ponce de León, Gerardo, and Robert Poulin. "Taxonomic distribution of cryptic diversity among metazoans: not so homogeneous after all." Biology Letters 12, no. 8 (August 2016): 20160371. http://dx.doi.org/10.1098/rsbl.2016.0371.

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Cryptic diversity plagues estimates of biodiversity, conservation efforts and attempts to control diseases and invasive species. Here, we re-visit a decade-old assessment of whether or not cryptic species are homogeneously reported among higher metazoan taxa. We compiled information from an extensive survey of the literature to recover all reports of cryptic species among metazoans. After correcting for currently known species richness and research effort per taxon, we find that cryptic species are over-reported in some taxa and under-reported in others. Although several taxa showing either a lack or an excess of reported cryptic species were poorly studied invertebrate groups, we found that cryptic species were over-reported in amphibians, reptiles and crustaceans, all relatively well-studied groups. The observed heterogeneity in the distribution of reported cryptic species may reflect taxon-specific properties affecting either the propensity for cryptic species to be formed or their likelihood of being detected by conventional taxonomy. Either way, the implications of cryptic diversity may not apply equally across all taxonomic groups.

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Lombard, Natasha, Margaretha Marianne Le Roux, and Ben-Erik van Wyk. "Electronic identification keys for species with cryptic morphological characters: a feasibility study using some Thesium species." PhytoKeys 172 (February 16, 2021): 97–119. http://dx.doi.org/10.3897/phytokeys.172.53484.

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The popularity of electronic identification keys for species identification has increased with the rapid technological advancements of the 21st century. Although electronic identification keys have several advantages over conventional textual identification keys and work well for charismatic species with large and clear morphological characters, they appear to be less feasible and less effective for species with cryptic morphology (i.e. small, obscure, variable characters and/or complicated structures associated with terminology that is difficult to interpret). This is largely due to the difficulty in presenting and illustrating cryptic morphological characters unambiguously. When taking into account that enigmatic species with cryptic morphology are often taxonomically problematic and therefore likely exacerbate the taxonomic impediment, it is clear that species groups with cryptic morphology (and all the disciplines dependent on their correct identification) could greatly benefit from a user-friendly identification tool, which clearly illustrates cryptic characters. To this end, the aim of this study was to investigate and develop best practices for the unambiguous presentation of cryptic morphological characters using a pilot interactive photographic identification key for the taxonomically difficult plant genus Thesium (Santalaceae), as well as to determine its feasibility. The project consisted of three stages: (1) software platform selection, (2) key construction and (3) key evaluation. The proposed identification key was produced with Xper3 software and can be accessed at http://www.xper3.fr/xper3GeneratedFiles/publish/identification/1330098581747548637/mkey.html. Methodologies relating to amongst others, character selection and delineation, visual and textual descriptions, key construction, character coding and key evaluation are discussed in detail. Seventeen best practices identified during this study are subsequently suggested for future electronic key compilation of species with cryptic morphology. This study indicates that electronic identification keys can be feasible and effective aids for the identification of species with cryptic morphological characters when the suggested best practices are followed.

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Schlick-Steiner, Birgit C., Bernhard Seifert, Christian Stauffer, Erhard Christian, Ross H. Crozier, and Florian M. Steiner. "Without morphology, cryptic species stay in taxonomic crypsis following discovery." Trends in Ecology & Evolution 22, no. 8 (August 2007): 391–92. http://dx.doi.org/10.1016/j.tree.2007.05.004.

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Cruse, Michael, Robin Telerant, Thomas Gallagher, Thomas Lee, and John W. Taylor. "Cryptic Species in Stachybotrys chartarum." Mycologia 94, no. 5 (September 2002): 814. http://dx.doi.org/10.2307/3761696.

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10

Hayashibara, T., and K. Shimoike. "Cryptic species of Acropora digitifera." Coral Reefs 21, no. 2 (July 2002): 224–25. http://dx.doi.org/10.1007/s00338-002-0229-6.

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11

Kikuchi, David W., and David W. Pfennig. "High-model abundance may permit the gradual evolution of Batesian mimicry: an experimental test." Proceedings of the Royal Society B: Biological Sciences 277, no. 1684 (December 2, 2009): 1041–48. http://dx.doi.org/10.1098/rspb.2009.2000.

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In Batesian mimicry, a harmless species (the ‘mimic’) resembles a dangerous species (the ‘model’) and is thus protected from predators. It is often assumed that the mimetic phenotype evolves from a cryptic phenotype, but it is unclear how a population can transition through intermediate phenotypes; such intermediates may receive neither the benefits of crypsis nor mimicry. Here, we ask if selection against intermediates weakens with increasing model abundance. We also ask if mimicry has evolved from cryptic phenotypes in a mimetic clade. We first present an ancestral character-state reconstruction showing that mimicry of a coral snake ( Micrurus fulvius ) by the scarlet kingsnake ( Lampropeltis elapsoides ) evolved from a cryptic phenotype. We then evaluate predation rates on intermediate phenotypes relative to cryptic and mimetic phenotypes under conditions of both high- and low-model abundances. Our results indicate that where coral snakes are rare, intermediate phenotypes are attacked more often than cryptic and mimetic phenotypes, indicating the presence of an adaptive valley. However, where coral snakes are abundant, intermediate phenotypes are not attacked more frequently, resulting in an adaptive landscape without a valley. Thus, high-model abundance may facilitate the evolution of Batesian mimicry.

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12

Zhao, Qing, Hufang Zhang, and Jiufeng Wei. "Climatic niche comparison across a cryptic species complex." PeerJ 7 (May 31, 2019): e7042. http://dx.doi.org/10.7717/peerj.7042.

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According to current molecular evidence, the Chionaspis pinifoliae heterophyllae species complex has been recognized as 10 cryptic species. In this study, we construct potential distribution maps for seven cryptic species based on climatic variables. This was done to assess the main environmental factors that have contributed to the distribution map and test the degree of niche overlap across the seven cryptic species. We used MaxEnt to build the climatic niche models under climatic variables. For these models, the similarities and differences of the niches across the cryptic species were estimated. By comparing the potential distribution model of each cryptic species, our results suggested parapatric, sympatric and allopatry populations for this cryptic species complex. Our results showed high variability in niche overlap, and more often niche conservatism than niche divergence. The current species delimitation of the Chionaspis pinifoliae heterophyllae complex by molecular information and the hypothesis that the niche overlap in the sympatric population is higher than that of the allopatry population were supported based on the findings. This study will provide baseline data and a distribution range to facilitate the further control of these insects and formulate quarantine measures.

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13

Imbert, Sébastien, Anne Cécile Normand, Frédéric Gabriel, Sophie Cassaing, Christine Bonnal, Damien Costa, Laurence Lachaud, et al. "Multi-centric evaluation of the online MSI platform for the identification of cryptic and rare species of Aspergillus by MALDI-TOF." Medical Mycology 57, no. 8 (January 25, 2019): 962–68. http://dx.doi.org/10.1093/mmy/myz004.

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Abstract The taxonomy of Aspergillus species has recently been revolutionized with the introduction of cryptic species and section concepts. However, their species-level identification in routine laboratories remains a challenge. The aim of this study was to prospectively assess the identification accuracy of cryptic species of Aspergillus in various laboratories using the mass spectrometry identification (MSI) platform, an independent and freely accessible online mass spectrometry database. Over a 12-month period, when a select set of MSI users identified cryptic species, they were contacted and requested to send the isolates to our laboratory for sequence-based identification. Sequence and MSI identification results were then compared. During the study period, 5108 Aspergillus isolates were identified using MSI including 1477 (28.9%) cryptic species. A total of 245 isolates that corresponded to 56 cryptic species and 13 sections were randomly selected for DNA sequencing confirmation. Agreement between the two methods was 99.6% at the section level and 66.1% at the species level. However, almost all discrepancies (72/83, 86.7%) were misidentifications between closely related cryptic species belonging to the same section. Fifty-one isolates from noncryptic species were also identified, thus yielding 100% and 92.2% agreement at the section and species level, respectively. Although the MSI fungus database is a reliable tool to identify Aspergillus at the section level, the database still requires adjustment to correctly identify rare or cryptic species at the species level. Nevertheless, the application properly differentiated between cryptic and sensu stricto species in the same section, thus alerting on possible specific isolate characteristics.

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Chacón, Isidro, Daniel Janzen, Winnie Hallwachs, James Sullivan, and Mehrdad Hajibabaei. "Cryptic species within cryptic moths: new species of Dunama Schaus (Notodontidae, Nystaleinae) in Costa Rica." ZooKeys 264 (February 6, 2013): 11–45. http://dx.doi.org/10.3897/zookeys.264.4440.

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15

Moraes, Simeão S., Ygor Montebello, Mariana A. Stanton, Lydia Fumiko Yamaguchi, Massuo J. Kato, and André V. L. Freitas. "Description of three new species of Geometridae (Lepidoptera) using species delimitation in an integrative taxonomy approach for a cryptic species complex." PeerJ 9 (May 18, 2021): e11304. http://dx.doi.org/10.7717/peerj.11304.

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The genus Eois Hübner (Geometridae: Larentiinae) comprises 254 valid species, 217 of which were described from the Neotropics and 31 of those having their type locality in Brazil. Since this species rich genus has never been revised, and may potentially include many cryptic undescribed species, Eois embodies a problematic taxonomic scenario. The actual diversity of Eois is greatly underestimated and the Brazilian fauna is poorly known, both because of inadequate sampling and because of the potential existence of cryptic species "hidden" within some nominal taxa. In this study we investigated the diversity within a cryptic species complexes associated to the E. pallidicosta and E. odatis clades. We describe three new species Eois oya Moraes & Montebello sp. nov., Eois ewa Moraes & Stanton sp. nov., and Eois oxum Moraes & Freitas sp. nov., in an integrative taxonomy approach, using morphology, host plant use and species delimitation tools.

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16

Saha, Atal, Lorenz Hauser, Rasmus Hedeholm, Benjamin Planque, Svein-Erik Fevolden, Jesper Boje, and Torild Johansen. "Cryptic Sebastes norvegicus species in Greenland waters revealed by microsatellites." ICES Journal of Marine Science 74, no. 8 (April 28, 2017): 2148–58. http://dx.doi.org/10.1093/icesjms/fsx039.

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Abstract Identification of cryptic species can have profound implications in fishery management, conservation and biodiversity contexts. In the North Atlantic, the genus Sebastes is currently represented by four species, although additional cryptic species have been assumed. The connectivity of the gene-pools within the genus in Greenland waters, in particular, remains largely unexplored. Using a panel of 13 microsatellite markers for 720 fish, we explored the species complex of Sebastes norvegicus in Greenland waters. Genetic analyses provided evidence for three cryptic species in samples that were morphologically identified as S. norvegicus. They were termed S. norvegicus-A, S. norvegicus-B, and S. norvegicus-giants. A few phenotypic features exist to identify adult S. norvegicus giants, but no characteristics have been identified for the two other cryptic species. The proposed cryptic species should be recognized in the management regime to ensure sustainable exploitation and conservation of Sebastes species in Greenland waters.

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17

BRAY, RODNEY A., and THOMAS H. CRIBB. "Are cryptic species a problem for parasitological biological tagging for stock identification of aquatic organisms?" Parasitology 142, no. 1 (February 25, 2014): 125–33. http://dx.doi.org/10.1017/s0031182014000092.

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SUMMARYThe effective use of biological tags in stock assessment relies on the reliable identification of the parasites concerned. This may be compromised if cryptic species are not recognized. Here we review what is known about cryptic species in aquatic hosts and its potential importance in this respect. Although strictly cryptic species may be considered as species which can be distinguished only by molecular data, we accept the far looser but more practical definition of species that cannot be readily distinguished morphologically. Cryptic species appear to have been identified most frequently as occurring in separate host species; this is heartening in that this has no significant impact on tagging studies. But cryptic species have occasionally been identified in single hosts sympatrically and are relatively common in geographically distinct populations of the same host species. Ignorance of both kinds of occurrences has the capacity to undermine the reliability of tagging analysis. We review in detail what is known of intra- and interspecific genetic variation over geographical ranges in the trematodes, based on recent molecular studies. Although the existence of cryptic species and evidence of intraspecific variability may appear daunting, we suspect that these complexities will add, and indeed have already added, to the sophistication of the information that can be derived from tagging studies.

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18

Fenchel, T. "Cosmopolitan microbes and their cryptic species." Aquatic Microbial Ecology 41 (2005): 49–54. http://dx.doi.org/10.3354/ame041049.

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19

Wilke, Thomas, Jasmin Renz, Torsten Hauffe, Diana Delicado, and Janna Peters. "Proteomic Fingerprinting Discriminates Cryptic Gastropod Species." Malacologia 63, no. 1 (September 10, 2020): 131. http://dx.doi.org/10.4002/040.063.0113.

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20

Crespo, Ana, and H. Thorsten Lumbsch. "Cryptic species in lichen-forming fungi." IMA Fungus 1, no. 2 (November 23, 2010): 167–70. http://dx.doi.org/10.5598/imafungus.2010.01.02.09.

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21

Palomares-Rius, Juan E., Carolina Cantalapiedra-Navarrete, and Pablo Castillo. "Cryptic species in plant-parasitic nematodes." Nematology 16, no. 10 (2014): 1105–18. http://dx.doi.org/10.1163/15685411-00002831.

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This paper summarises the current knowledge concerning cryptic species of plant-parasitic nematode and briefly reviews the different methods available for their detection and characterisation. Cryptic species represent an important component of biodiversity, such speciation being common among plant-parasitic nematodes and occurring in diverse groups with different life history traits, including the spiral, virus vector, root-lesion and false root-knot nematodes. Cryptic species are important for a number of reasons, including food security, quarantine, non-chemical management technologies and species conservation, and should not be ignored. The magnitude of the phenomenon is largely unknown, but the available data on plant-parasitic nematodes demonstrate that reliance on morphology alone for species delimitation seriously underestimates the total number of taxa. Future research should focus on appropriately designed case studies using combined approaches, including large-scale, whole sample analyses by next-generation sequencing or proteomics in order to be able to answer the many questions that still remain.

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Puillandre, N., C. Cruaud, and Yu I. Kantor. "Cryptic species in Gemmuloborsonia (Gastropoda: Conoidea)." Journal of Molluscan Studies 76, no. 1 (August 25, 2009): 11–23. http://dx.doi.org/10.1093/mollus/eyp042.

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23

Lee, Michael S. Y., and Paul M. Oliver. "Count cryptic species in biodiversity tally." Nature 534, no. 7609 (June 2016): 621. http://dx.doi.org/10.1038/534621a.

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DENNIS, ALICE B., and MICHAEL E. HELLBERG. "Ecological partitioning among parapatric cryptic species." Molecular Ecology 19, no. 15 (July 8, 2010): 3206–25. http://dx.doi.org/10.1111/j.1365-294x.2010.04689.x.

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Alekseev, V., and N. Sukhikh. "Copepod cryptic species as aquatic invaders." Limnology and Freshwater Biology, no. 5 (2022): 1645–55. http://dx.doi.org/10.31951/2658-3518-2022-a-5-1645.

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Abstract. The dispersal of aquatic organisms has especially increased since the 19th century, mainly due to the introduction of metal ships with ballast compartments or with birds. Along with easily visible aquatic organisms, there are invasions of less noticeable aquatic organisms, like copepods, which can mainly be recognized by experts. A special group is made up of cryptic species for which morphological identification is inaccessible or very difficult. This review is devoted to the identification, description and analysis of the dispersal routes of three copepod cryptic species complexes into waterbodies. Using molecular-genetic methods, Eurytemora carolleeae introduction were revealed in 2007. After describing this invader as a new species, its distribution was also studied using morphology. The invasions of Acanthocyclops americanus and Eurytemora caspica were mainly studied using morphological methods since the species have already been described; however, molecular-genetic methods were also used to confirm their distinctions from local forms. The real distribution of the former cosmopolitan species Eucyclops serrulatus was studied using a multidisciplinary approach that combined molecular-genetic, cross-hybridization and morphological methods. Judging by the distribution of local E. serrulatus sensu stricto populations in coastal waterbodies of most continents, this species can apparently serve as a good marker of the species dispersal processes with ships. The three possible scenarios resulting from cryptic species introductions and their interaction with local fauna were competitive displacement (A. americanus), competitive coexistence (E. carrolleeae) and independent development without competition (E. serrulatus). The role of cryptic species invasion in aquatic biodiversity modification is discussed.

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Masuyama, Shigeo. "Cryptic species in the fern Ceratopteris thalictroides (Parkeriaceae). III. Referential diagnostic characters of three cryptic species." Journal of Plant Research 121, no. 3 (April 18, 2008): 279–86. http://dx.doi.org/10.1007/s10265-008-0159-7.

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27

Poulin, Robert. "Uneven distribution of cryptic diversity among higher taxa of parasitic worms." Biology Letters 7, no. 2 (September 22, 2010): 241–44. http://dx.doi.org/10.1098/rsbl.2010.0640.

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Cryptic species cause problems for estimates of biodiversity. In the case of parasites, cryptic species also plague efforts to detect potential zoonotic diseases or invasive pathogens. It is crucial to determine whether the likelihood of finding cryptic species differs among higher parasite taxa, to better calibrate estimates of diversity and monitor diseases. Using published reports of cryptic species of helminth parasites identified using molecular tools, I show that the number of species found is strongly related to the number of parasite individuals sequenced, weakly influenced by the number of host species from which parasites were obtained, and unaffected by the genetic markers used. After correction for these factors, more cryptic species of trematodes are found than in other helminth taxa. Although several features distinguish trematodes from other helminths, it is probable that our inability to discriminate among sibling species of trematodes results from their lack of structures serving as species-specific morphological markers. The available data suggest that current estimates of helminth diversity may need to be doubled (tripled for trematodes) to better reflect extant diversity.

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Asenjo, Angélico, Marcus Paulo Alves de Oliveira, Renato R. M. Oliveira, Eder Soares Pires, Marcely Valois, Guilherme Oliveira, and Santelmo Vasconcelos. "The complete mitochondrial genome and description of a new cryptic Brazilian species of Metopiellus Raffray (Coleoptera: Staphylinidae: Pselaphinae)." PeerJ 11 (July 27, 2023): e15697. http://dx.doi.org/10.7717/peerj.15697.

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Metopiellus Raffray, 1908 is a genus of South American rove beetles typically found in tropical humid forests. Here we describe a new cryptic species from Eastern Amazon, in northern Brazil, Metopiellus crypticus Asenjo sp. nov., and its major morphologic diagnostic features, which were photographed and illustrated. In addition, we bring the complete mitochondrial genome sequence of M. crypticus sp. nov., and its position within the phylogenetic context of the family, including previously available mitogenomes of Staphylinidae species.

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NADLER, STEVEN A., and GERARDO PÉREZ-PONCE DE LEÓN. "Integrating molecular and morphological approaches for characterizing parasite cryptic species: implications for parasitology." Parasitology 138, no. 13 (February 1, 2011): 1688–709. http://dx.doi.org/10.1017/s003118201000168x.

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SUMMARYHerein we review theoretical and methodological considerations important for finding and delimiting cryptic species of parasites (species that are difficult to recognize using traditional systematic methods). Applications of molecular data in empirical investigations of cryptic species are discussed from an historical perspective, and we evaluate advantages and disadvantages of approaches that have been used to date. Developments concerning the theory and practice of species delimitation are emphasized because theory is critical to interpretation of data. The advantages and disadvantages of different molecular methodologies, including the number and kind of loci, are discussed relative to tree-based approaches for detecting and delimiting cryptic species. We conclude by discussing some implications that cryptic species have for research programmes in parasitology, emphasizing that careful attention to the theory and operational practices involved in finding, delimiting, and describing new species (including cryptic species) is essential, not only for fully characterizing parasite biodiversity and broader aspects of comparative biology such as systematics, evolution, ecology and biogeography, but to applied research efforts that strive to improve development and understanding of epidemiology, diagnostics, control and potential eradication of parasitic diseases.

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Brasier, Madeleine J., Helena Wiklund, Lenka Neal, Rachel Jeffreys, Katrin Linse, Henry Ruhl, and Adrian G. Glover. "DNA barcoding uncovers cryptic diversity in 50% of deep-sea Antarctic polychaetes." Royal Society Open Science 3, no. 11 (November 2016): 160432. http://dx.doi.org/10.1098/rsos.160432.

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The Antarctic marine environment is a diverse ecosystem currently experiencing some of the fastest rates of climatic change. The documentation and management of these changes requires accurate estimates of species diversity. Recently, there has been an increased recognition of the abundance and importance of cryptic species, i.e. those that are morphologically identical but genetically distinct. This article presents the largest genetic investigation into the prevalence of cryptic polychaete species within the deep Antarctic benthos to date. We uncover cryptic diversity in 50% of the 15 morphospecies targeted through the comparison of mitochondrial DNA sequences, as well as 10 previously overlooked morphospecies, increasing the total species richness in the sample by 233%. Our ability to describe universal rules for the detection of cryptic species within polychaetes, or normalization to expected number of species based on genetic data is prevented by taxon-specific differences in phylogenetic outputs and genetic variation between and within potential cryptic species. These data provide the foundation for biogeographic and functional analysis that will provide insight into the drivers of species diversity and its role in ecosystem function.

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Bulan, Jakaphan, Sinchai Maneekat, Giuseppe C. Zuccarello, and Narongrit Muangmai. "Phylogeographic patterns in cryptic <italic>Bostrychia tenella</italic> species (Rhodomelaceae, Rhodophyta) across the Thai-Malay Peninsula." Algae 37, no. 2 (June 15, 2022): 123–33. http://dx.doi.org/10.4490/algae.2022.37.6.4.

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Genetic diversity and distribution patterns of marine macroalgae are increasingly being documented in Southeast Asia. These studies show that there can be significant levels of genetic diversity and isolation between populations on either side of the Thai-Malay Peninsula. Bostrychia tenellla is a common filamentous red seaweed in the region and the entity is represented by at least two cryptic species. Despite being highly diverse and widespread, genetic variation and population structure of this species complex remains understudied, especially around the Thai-Malay Peninsula. We analyzed genetic diversity and inferred the phylogeographic pattern of specimens identified as B. tenella using the plastid RuBisCo spacer from samples from the Andaman Sea and the Gulf of Thailand. Our genetic analysis confirmed the occurrence of the two cryptic B. tenella species (B and C) along both coasts. Cryptic species B was more common in the area and displayed higher genetic diversity than species C. Historical demographic analyses indicated a stable population for species B, but more recent population expansion for species C. Our analyses also revealed that both cryptic species from the Andaman Sea possessed higher genetic diversity than those of the Gulf of Thailand. We also detected moderate to high levels of gene flow and weak phylogeographic structure of cryptic species B between the two coasts. In contrast, phylogeographic analysis showed genetic differences between populations of both cryptic species within the Andaman Sea. Overall, these results suggest that cryptic B. tenella species around Thai-Malay Peninsula may have undergone different demography histories, and their patterns of genetic diversity and phylogeography were likely caused by geological history and regional sea surface current circulation in the area.

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Lombard, L., M. Sandoval-Denis, S. C. Lamprecht, and P. W. Crous. "Epitypification of Fusarium oxysporum – clearing the taxonomic chaos." Persoonia - Molecular Phylogeny and Evolution of Fungi 43, no. 1 (December 31, 2019): 1–47. http://dx.doi.org/10.3767/persoonia.2019.43.01.

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Fusarium oxysporum is the most economically important and commonly encountered species of Fusarium. This soil-borne fungus is known to harbour both pathogenic (plant, animal and human) and non-pathogenic strains. However, in its current concept F. oxysporum is a species complex consisting of numerous cryptic species. Identification and naming these cryptic species is complicated by multiple subspecific classification systems and the lack of living ex-type material to serve as basic reference point for phylogenetic inference. Therefore, to advance and stabilise the taxonomic position of F. oxysporum as a species and allow naming of the multiple cryptic species recognised in this species complex, an epitype is designated for F. oxysporum. Using multi-locus phylogenetic inference and subtle morphological differences with the newly established epitype of F. oxysporum as reference point, 15 cryptic taxa are resolved in this study and described as species.

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Korshunova, Tatiana, and Alexander Martynov. "The Phyloperiodic Approach Removes the “Cryptic Species” and Puts forward Multilevel Organismal Diversity." Diversity 16, no. 4 (April 6, 2024): 220. http://dx.doi.org/10.3390/d16040220.

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The notion of the “cryptic species” has recently become an important agenda in biodiversity research. In this study, we show, by applying a periodic-like morphological and molecular framework to the nudibranch genus Cadlina from the world’s least explored locations in the Kuril Islands in the northwestern Pacific, including a description of six new species, that the term “cryptic species” should be removed from biodiversity research terminology. We explicitly show that different species of this complex have various degrees of molecular phylogenetic distances and morphological distinctness, revealing a truly multilevel system of fine-scale differences and similarities. Therefore, to designate any of these species as “cryptic” or “non-cryptic” would be completely arbitrary, non-operational, and generally meaningless. By this, we finally strongly propose to remove the notion of “crypticity” and the term “cryptic species” (in the sense of an “indistinguishable species”) from the arsenal of modern biology, including phylogeny and taxonomy. The importance of fine-scale species differentiation in the multilevel framework is shown for addressing conservation and global warming challenges. Six new species are named after scientists who have not always received the honours they deserve, including two women who did not receive their respective Nobel Prizes.

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Wawrzyniak, Rafał, Wiesław Wasiak, Beata Jasiewicz, Alina Bączkiewicz, and Katarzyna Buczkowska. "Chemical Fingerprinting of Cryptic Species and Genetic Lineages of Aneura pinguis (L.) Dumort. (Marchantiophyta, Metzgeriidae)." Molecules 26, no. 4 (February 22, 2021): 1180. http://dx.doi.org/10.3390/molecules26041180.

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Aneura pinguis (L.) Dumort. is a representative of the simple thalloid liverworts, one of the three main types of liverwort gametophytes. According to classical taxonomy, A. pinguis represents one morphologically variable species; however, genetic data reveal that this species is a complex consisting of 10 cryptic species (named by letters from A to J), of which four are further subdivided into two or three evolutionary lineages. The objective of this work was to develop an efficient method for the characterisation of plant material using marker compounds. The volatile chemical constituents of cryptic species within the liverwort A. pinguis were analysed by GC-MS. The compounds were isolated from plant material using the HS-SPME technique. Of the 66 compounds examined, 40 were identified. Of these 40 compounds, nine were selected for use as marker compounds of individual cryptic species of A. pinguis. A guide was then developed that clarified how these markers could be used for the rapid identification of the genetic lineages of A. pinguis. Multivariate statistical analyses (principal component and cluster analysis) revealed that the chemical compounds in A. pinguis made it possible to distinguish individual cryptic species (including genetic lineages), with the exception of cryptic species G and H. The classification of samples based on the volatile compounds by cluster analysis reflected phylogenetic relationships between cryptic species and genetic lineages of A. pinguis revealed based on molecular data.

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Andrimida, Anthon, and Rudi Hermawan. "Assessing cryptic marine fauna diversity as underwater macrophotography (UMP) objects in Sempu Strait, Indonesia." E3S Web of Conferences 153 (2020): 01001. http://dx.doi.org/10.1051/e3sconf/202015301001.

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Cryptic marine fauna refers to organisms that live inside habitats that hidden from direct exposure to their outer environment. Its cryptic nature made these animals rarely observed, and hence understudied. Whereas, they are very popular among experienced divers alike as underwater macrophotography objects. The aim of this study is to assess the diversity of cryptic marine fauna on the proximity of coral reef area at Sempu Strait to bring up its underwater macrophotography tourism potential. While the definition of cryptic marine fauna itself could include any major group of marine organisms, we limit the extent of our study only into the four most popular animal groups in underwater macrophotography which are: fishes, sea slugs, arthropods, and flatworms. We conducted underwater surveys using roving diver technique spanning from October 2017 to June 2019 at eleven dive sites of Sempu Strait and yielded 84 species that consists of 45 species of sea slug, 29 Species of fish, 8 species of arthropods, and 2 species of flatworms. The overall fauna diversity shows that Sempu Strait has high diversity of sea slug and cryptic fishes, while the site-specific diversity shows that Stumbut dive site has the highest marine cryptic fauna diversity.

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Eda, M., T. Yamasaki, H. Izumi, N. Tomita, S. Konno, M. Konno, H. Murakami, and F. Sato. "Cryptic species in a Vulnerable seabird: shorttailed albatross consists of two species." Endangered Species Research 43 (November 19, 2020): 375–86. http://dx.doi.org/10.3354/esr01078.

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The occurrence of cryptic species within a threatened taxon is rare, but where they do occur, understanding species boundaries is essential for planning an effective conservation strategy. The short-tailed albatross Phoebastria albatrus is a Vulnerable seabird that mainly breeds on Torishima and the Senkaku Islands in the western North Pacific. Although it has been tacitly regarded as a single management unit with 2 breeding sites, the species is known to comprise 2 genetically separated populations (Senkaku-type and Torishima-type). However, morphological examination of birds from both populations has not been conducted owing to the difficulty in accessing the Senkaku Islands. In this study, we examined the morphological differences between immigrants from the Senkaku Islands to Torishima (Senkaku-type) and native birds on Torishima (Torishima-type) and found significant differences in morphological characteristics between the 2 bird types. In general, Torishima-type birds were larger than Senkaku-type birds, whereas Senkaku-type birds had relatively longer beaks. Based on the morphological differences found in this study as well as genetic and ecological differences revealed in previous studies, we believe that Senkaku- and Torishima-type birds should be classified as different cryptic species. To the best of our knowledge, this is the first case of cryptic species being identified in a threatened avian species.

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SRINIVASULU, BHARGAVI, and ADITYA SRINIVASULU. "A new species of the Miniopterus australis species complex (Chiroptera: Miniopteridae) from the Western Ghats, India." Zootaxa 5296, no. 2 (May 26, 2023): 233–49. http://dx.doi.org/10.11646/zootaxa.5296.2.5.

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The genus Miniopterus is highly diverse in cryptic species. Based on integrated approaches of morphometrics, echolocation call analysis, and molecular phylogenetics, we present evidence of a hitherto undescribed species, Srini’s Bent-winged bat Miniopterus srinii sp. nov.. The new species, found in the Western Ghats of southern Karnataka, India, closely resembles the Small Bent-winged bat Miniopterus pusillus, found elsewhere in Karnataka, Kerala, and Tamil Nadu, India. Although it shows external similarity with Miniopterus pusillus sensu stricto from the Nicobar Islands, the new species is relatively larger and distinct in craniodental measurements and echolocation call parameters, despite slight overlaps. Importantly, Miniopterus srinii exhibits morphological convergence with Miniopterus pusillus as despite similarities in morphologies, there is a significant genetic distance of 10.84 ± 0.22%. The new cryptic species shares distribution with Miniopterus phillipsi and Miniopterus pusillus in the Western Ghats, further highlighting the need to study both the genus’ cryptic diversity, and the region’s conservation importance.

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Darwell, C. T., and J. M. Cook. "Cryptic diversity in a fig wasp community-morphologically differentiated species are sympatric but cryptic species are parapatric." Molecular Ecology 26, no. 3 (February 2017): 937–50. http://dx.doi.org/10.1111/mec.13985.

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Niwa, Kyosuke, Norio Kikuchi, Mi Sook Hwang, Han-Gu Choi, and Yusho Aruga. "Cryptic species in thePyropia yezoensiscomplex (Bangiales, Rhodophyta): Sympatric occurrence of two cryptic species even on same rocks." Phycological Research 62, no. 1 (September 4, 2013): 36–43. http://dx.doi.org/10.1111/pre.12035.

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M Américo, Fernanda, Lumena P Machado Siqueira, Gilda Maria B Del Negro, Viviane M Favero Gimenes, Mario Roberto S Trindade, Adriana L Motta, Roseli Santos de Freitas, et al. "Evaluating VITEK MS for the identification of clinically relevant Aspergillus species." Medical Mycology 58, no. 3 (June 17, 2019): 322–27. http://dx.doi.org/10.1093/mmy/myz066.

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Abstract Aspergillus spp. identification has become more relevant in clinical practice since azole-resistant cryptic species have been related to invasive fungal infections. Conventional morphologic identification is not able to discriminate Aspergillus species, and DNA sequencing is not feasible for clinical laboratories. MALDI-TOF mass spectrometry is an emergent technology that has been explored to provide fast and accurate identification of microorganisms, including clinically relevant moulds. However, only a few studies have explored the platform VITEK MS for the identification of Aspergillus species. Hence, we provided additional data regarding the performance of the VITEK MS system for the identification of Aspergillus species, including azole-resistant ones. We also improved the RUO system by adding additional spectral profiles from well-identified Aspergillus strains belonging to different noncryptic and cryptic species. The IVD library correctly identified 91.6% of the organisms at genus and section level, and 84.7% at species level, including the azole-resistant Aspergillus lentulus and Aspergillus calidoustus. The organisms belonging to Aspergillus cryptic species had only 31.2% of correct species identification. The RUO library plus our in-house SuperSpectra correctly identified 100% of the organisms at genus and section level and 91.6% at species level. Among organisms belonging to Aspergillus cryptic species, 68.7% had correct species identification. Some closely related Aspergillus cryptic species showed similar spectral profiles and were difficult to be differentiated.

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Wang, Rui, Clement K. M. Tsui, and Chongjuan You. "Cryptic Species Diversity and Phylogenetic Relationship in the Rust Genus Chrysomyxa from China." Journal of Fungi 8, no. 1 (January 15, 2022): 83. http://dx.doi.org/10.3390/jof8010083.

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Chrysomyxa rusts are fungal pathogens widely distributed in the Northern hemisphere, causing spruce needle and cone rust diseases, and they are responsible for significant economic losses in China. Taxonomic delimitation and precise species identification are difficult within this genus because some characters often overlap in several species. Adequate species delimitation, enhanced by the use of DNA-based methodologies, will help to establish well-supported species boundaries and enable the identification of cryptic species. Here, we explore the cryptic species diversity in the rust genus Chrysomyxa from China. Species delimitation analyses are conducted using a distance-based method (ABGD) and three tree-based methods (GMYC, bPTP, and mPTP) based on combined LSU and ITS sequences of over 60 specimens. Although there is some incongruence among species delimitation methods, two new species and three putative cryptic species are identified. The key to 20 Chrysomyxa species distributed in China is presented. These results suggest that a significant level of undiscovered cryptic diversity is likely to be found in Chrysomyxa from China. Future studies should consider multiple analytical methods when dealing with multi-locus datasets.

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Gill, B. A., B. C. Kondratieff, K. L. Casner, A. C. Encalada, A. S. Flecker, D. G. Gannon, C. K. Ghalambor, et al. "Cryptic species diversity reveals biogeographic support for the ‘mountain passes are higher in the tropics’ hypothesis." Proceedings of the Royal Society B: Biological Sciences 283, no. 1832 (June 15, 2016): 20160553. http://dx.doi.org/10.1098/rspb.2016.0553.

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The ‘mountain passes are higher in the tropics’ (MPHT) hypothesis posits that reduced climate variability at low latitudes should select for narrower thermal tolerances, lower dispersal and smaller elevational ranges compared with higher latitudes. These latitudinal differences could increase species richness at low latitudes, but that increase may be largely cryptic, because physiological and dispersal traits isolating populations might not correspond to morphological differences. Yet previous tests of the MPHT hypothesis have not addressed cryptic diversity. We use integrative taxonomy, combining morphology (6136 specimens) and DNA barcoding (1832 specimens) to compare the species richness, cryptic diversity and elevational ranges of mayflies (Ephemeroptera) in the Rocky Mountains (Colorado; approx. 40°N) and the Andes (Ecuador; approx. 0°). We find higher species richness and smaller elevational ranges in Ecuador than Colorado, but only after quantifying and accounting for cryptic diversity. The opposite pattern is found when comparing diversity based on morphology alone, underscoring the importance of uncovering cryptic species to understand global biodiversity patterns.

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Funk, W. Chris, Marcel Caminer, and Santiago R. Ron. "High levels of cryptic species diversity uncovered in Amazonian frogs." Proceedings of the Royal Society B: Biological Sciences 279, no. 1734 (November 30, 2011): 1806–14. http://dx.doi.org/10.1098/rspb.2011.1653.

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One of the greatest challenges for biodiversity conservation is the poor understanding of species diversity. Molecular methods have dramatically improved our ability to uncover cryptic species, but the magnitude of cryptic diversity remains unknown, particularly in diverse tropical regions such as the Amazon Basin. Uncovering cryptic diversity in amphibians is particularly pressing because amphibians are going extinct globally at an alarming rate. Here, we use an integrative analysis of two independent Amazonian frog clades, Engystomops toadlets and Hypsiboas treefrogs, to test whether species richness is underestimated and, if so, by how much. We sampled intensively in six countries with a focus in Ecuador ( Engystomops : 252 individuals from 36 localities; Hypsiboas : 208 individuals from 65 localities) and combined mitochondrial DNA, nuclear DNA, morphological, and bioacoustic data to detect cryptic species. We found that in both clades, species richness was severely underestimated, with more undescribed species than described species. In Engystomops , the two currently recognized species are actually five to seven species (a 150–250% increase in species richness); in Hypsiboas , two recognized species represent six to nine species (a 200–350% increase). Our results suggest that Amazonian frog biodiversity is much more severely underestimated than previously thought.

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Paraskevopoulou, Sofia, Ralph Tiedemann, and Guntram Weithoff. "Differential response to heat stress among evolutionary lineages of an aquatic invertebrate species complex." Biology Letters 14, no. 11 (November 2018): 20180498. http://dx.doi.org/10.1098/rsbl.2018.0498.

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Under global warming scenarios, rising temperatures can constitute heat stress to which species may respond differentially. Within a described species, knowledge on cryptic diversity is of further relevance, as different lineages/cryptic species may respond differentially to environmental change. The Brachionus calyciflorus species complex (Rotifera), which was recently described using integrative taxonomy, is an essential component of aquatic ecosystems. Here, we tested the hypothesis that these (formerly cryptic) species differ in their heat tolerance. We assigned 47 clones with nuclear ITS1 (nuITS1) and mitochondrial COI (mtCOI) markers to evolutionary lineages, now named B. calyciflorus sensu stricto (s.s.) and B. fernandoi . We selected 15 representative clones and assessed their heat tolerance as a bi-dimensional phenotypic trait affected by both the intensity and duration of heat stress. We found two distinct groups, with B. calyciflorus s.s. clones having higher heat tolerance than the novel species B. fernandoi . This apparent temperature specialization among former cryptic species underscores the necessity of a sound species delimitation and assignment, when organismal responses to environmental changes are investigated.

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SUKHIKH, N., and V. ALEKSEEV. "TWO LIFE STRATEGIES IN COPEPOD CRYPTIC SPECIES: COEXISTENCE AND DISPLACEMENT." Russian Journal of Biological Invasions 16, no. 3 (September 6, 2023): 196–99. http://dx.doi.org/10.35885/1996-1499-16-3-196-199.

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Among invasive species there is a special group so named cryptic species for which morphological identification is very difficult. This review is devoted to analysis of the dispersal routes of two copepod cryptic species complexes into aquatic ecosystems. Eurytemora carolleeae introduction was revealed in 2007 with bar-code. The species was described as a new taxon; its distribution was also studied using morphology. Biological invasions of two other Copepod species Acanthocyclops americanus and Eurytemora caspica were mainly studied using morphological methods since the species have already been described. At the same time, to confirm their distinctions from local forms, molecular genetic tools were also used. Two scenarios resulting from cryptic species’ invasions and their competitions with native species were the partly ( E. carrolleeae ) or full displacement ( A. americanus ). Example: the invasion of Eurytemora carolleeae into the Baltic Sea and the Atlantic coast of Europe. When assessing the possible negative impact of invasive species on competitors, the most attention should be paid to predator species. Identification of cryptic species significantly complicates the situation with the assessment of bioinvasion and needs the use of molecular methods.

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NAUER, FABIO, D. WILSON FRESHWATER, DANIELLE C. HATT, ALAIN DURAN, MARIANA C. OLIVEIRA, JUSTIN E. CAMPBELL, MUTUE T. FUJII, and LIGIA COLLADO-VIDES. "Diversity of Hypnea (Rhodophyta) in South Florida, with description of H. spiniformis sp. nov." Phytotaxa 635, no. 1 (January 22, 2024): 43–58. http://dx.doi.org/10.11646/phytotaxa.635.1.2.

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The genus Hypnea is well known to be rich in cryptic species, with many new species being recognized recently based on molecular data. Therefore, we used mitochondrial (COI-5P) and plastid (rbcL) molecular markers, in addition to aspects of morphology, to investigate the diversity of Hypnea on the coast of South Florida. Molecular divergences and phylogenetic inferences indicated that four species were present: H. caraibica and H. cryptica, both new occurrences on the Florida coast; H. musciformis, already previously reported and H. spiniformis sp. nov. described in this work. Our data reinforce the importance of studies with an integrative taxonomy approach to delimit species and correctly identify them.

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Santamaria, Carlos A., Joanna K. Bluemel, Nancy Bunbury, and Melinda Curran. "Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods." PeerJ 5 (October 6, 2017): e3894. http://dx.doi.org/10.7717/peerj.3894.

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Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently.

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Roy, Barbara A., Detlev R. Vogler, Thomas D. Bruns, and Timothy M. Szaro. "Cryptic Species in the Puccinia monoica Complex." Mycologia 90, no. 5 (September 1998): 846. http://dx.doi.org/10.2307/3761326.

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Schultheis, Lisa M. "Morphologically Cryptic Species Within Downingia yina (Campanulaceae)." Madroño 57, no. 1 (January 2010): 20–41. http://dx.doi.org/10.3120/0024-9637-57.1.20.

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Lowry, M., and B. O. Schlumpberger. "Lobivia minutiflora: a cryptic species finally recognised." Bradleya 31, no. 31 (August 31, 2013): 89–95. http://dx.doi.org/10.25223/brad.n31.2013.a11.

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Journal articles on the topic 'Cryptic species'

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