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Fjelde MO, Timdal E, Haugan R, Bendiksby M. Paraphyly and cryptic diversity unveils unexpected challenges in the "naked lichens" (Calvitimela, Lecanoromycetes, Ascomycota). Mol Phylogenet Evol 2024; 190:107944. [PMID: 37844854 DOI: 10.1016/j.ympev.2023.107944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 09/28/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
Molecular phylogenetics has revolutionized the taxonomy of crustose lichens and revealed an extensive amount of cryptic diversity. Resolving the relationships between genera in the crustose lichen family Tephromelataceae has proven difficult and the taxon limits within the genus Calvitimela are only partly understood. In this study, we tested the monophyly of Calvitimela and investigated phylogenetic relationships at different taxonomic levels using an integrative taxonomic approach. We performed a global sampling of all species currently assigned to Calvitimela and conducted additional sampling of C. melaleuca sensu lato across Norway. We included 108 specimens and produced more than 300 sequences from five different loci (ITS, LSU, MCM7, mtSSU, TEF1-α). We inferred phylogenetic relationships and estimated divergence times in Calvitimela. Moreover, we analyzed chemical and morphological characters to test their diagnostic values in the genus. Our molecular phylogenetic results show evolutionarily old and deeply divergent lineages in Calvitimela. The morphological characters are overlapping between divergent subgenera within this genus. Chemical characters, however, are largely informative at the level of subgenera, but are often homoplastic at the species level. The subgenus Calvitimela is found to include four distinct genetic lineages. Detailed morphological examinations of C. melaleuca s. lat. reveal differences between taxa previously assumed to be morphologically cryptic. Furthermore, young evolutionary ages and signs of gene tree discordance indicate a recent divergence and possibly incomplete lineage sorting in the subgenus Calvitimela. Phylogenetic analysis and morphological observations revealed that C. austrochilensis and C. uniseptata are extraneous to Calvitimela (Tephromelataceae). We also found molecular evidence supporting C. septentrionalis being sister to C. cuprea. In the subgenus Severidea, one new grouping is recovered as a highly supported sister to C. aglaea. Lastly, two fertile specimens were found to be phylogenetically nested within the sorediate species C. cuprea. We discuss the need for an updated classification of Calvitimela and the evolution of cryptic species. Through generic circumscription and species delimitation we propose a practical taxonomy of Calvitimela.
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Affiliation(s)
- Markus Osaland Fjelde
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, NO-0318 Oslo, Norway; Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, NO-0316, Norway.
| | - Einar Timdal
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, NO-0318 Oslo, Norway
| | - Reidar Haugan
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, NO-0318 Oslo, Norway
| | - Mika Bendiksby
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, NO-0318 Oslo, Norway; NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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Bachmann L, Beermann J, Brey T, de Boer HJ, Dannheim J, Edvardsen B, Ericson PGP, Holston KC, Johansson VA, Kloss P, Konijnenberg R, Osborn KJ, Pappalardo P, Pehlke H, Piepenburg D, Struck TH, Sundberg P, Markussen SS, Teschke K, Vanhove MPM. The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022. ZOOL SCR 2023. [DOI: 10.1111/zsc.12593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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Holzhausen A, Nowak P, Ballot A, Becker R, Gebert J, Gregor T, Karol KG, Lambert E, Pérez W, Raabe U, Schneider SC, Stewart N, van de Weyer K, Wilde V, Schubert H. Plastid DNA sequences and oospore characters of some European taxa of Tolypella section Tolypella (Characeae) identify five clusters, including one new cryptic Tolypella taxon from Sardinia, but they do not coincide with current morphological descriptions. FRONTIERS IN PLANT SCIENCE 2023; 14:1096181. [PMID: 36938048 PMCID: PMC10014841 DOI: 10.3389/fpls.2023.1096181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
In Europe, the genus Tolypella (Characeae) comprises four to eight Tolypella taxa in sections Rothia and Tolypella that have been distinguished by vegetative morphology and gametangial characters such as antheridial size and oospore wall ornamentation. However, morphological differentiation is difficult in some cases due to overlapping and variable vegetative features, which in many cases are difficult to observe clearly. To clarify the taxonomic status of the five European taxa of Tolypella in section Tolypella, sequence data of the plastid genes atpB, rbcL and psbC for Tolypella glomerata (Desv.) Leonh., Tolypella hispanica Allen, Tolypella nidifica (O.F. Müll.) A. Braun, Tolypella normaniana (Nordst.) Nordst. and Tolypella salina Cor. were combined with data on oospore morphology, including oospore wall ornamentation. Gene sequence data identified five distinct clusters, but they were not consistent with the morphologically identified five taxa. T. glomerata consisted of some of the samples morphologically identified as T. glomerata and seven samples of T. normaniana, while the remaining T. glomerata samples clustered with specimens of unclear affiliation (Tolypella sp.). We identified two clusters of T. hispanica within the European material: cluster T. hispanica I consisted of samples from various locations, whereas the second cluster (T. hispanica II) consisted of samples of T. hispanica from Sardinia Island. The remaining cluster consisted of all the specimens that had been determined as T. salina or T. nidifica in addition to two specimens of T. normaniana. Oospore morphology was most clearly distinguishable for T. glomerata. Oospore characteristics for all other taxa were not as informative but showed some geographical and/or environmentally influenced differences, especially for T. nidifica and T. salina. Our results suggest the need to further check the different taxonomy of Tolypella sect. Tolypella in which specimens normally identified as T. glomerata might be two different taxa, T. glomerata and an unidentified taxon; T. nidifica and T. salina are not separate taxa; T. normaniana is a diminutive variant of two different Tolypella taxa; and T. hispanica comprises two different taxa, one from the Mediterranean island Sardinia.
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Affiliation(s)
- Anja Holzhausen
- Institute of Biological Sciences, Aquatic Ecology, University Rostock, Rostock, Germany
- Department of Biology, Plant Cell Biology, University Marburg, Marburg, Germany
| | - Petra Nowak
- Institute of Biological Sciences, Aquatic Ecology, University Rostock, Rostock, Germany
| | | | | | - Jasmina Gebert
- Institute of Biological Sciences, Aquatic Ecology, University Rostock, Rostock, Germany
| | - Thomas Gregor
- Senckenberg Forschungsinstitut und Naturmuseum, Botanik und Molekulare Evolutionsforschung, Frankfurt am Main, Germany
| | - Kenneth G. Karol
- Program for Molecular Systematics Studies, The New York Botanical Garden, Bronx, NY, United States
| | - Elisabeth Lambert
- Département de Biologie Environnement, Faculté des Sciences, Université Catholique de l’Ouest, Angers, France
| | - William Pérez
- Program for Molecular Systematics Studies, The New York Botanical Garden, Bronx, NY, United States
| | - Uwe Raabe
- Independent Researcher, Marl, Germany
| | | | - Nick Stewart
- Independent Researcher, Glastonbury, United Kingdom
| | | | - Volker Wilde
- Paläontologie und Historische Geologie, Paläobotanik, Senkenberg Forschungsinstitut und Naturmuseum, Frankfurt am Main, Germany
| | - Hendrik Schubert
- Institute of Biological Sciences, Aquatic Ecology, University Rostock, Rostock, Germany
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Lienhard A, Krisper G. Hidden biodiversity in microarthropods (Acari, Oribatida, Eremaeoidea, Caleremaeus). Sci Rep 2021; 11:23123. [PMID: 34848782 PMCID: PMC8632897 DOI: 10.1038/s41598-021-02602-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/17/2021] [Indexed: 11/22/2022] Open
Abstract
A challenge for taxonomists all over the world and across all taxonomic groups is recognizing and delimiting species, and cryptic species are even more challenging. However, an accurate identification is fundamental for all biological studies from ecology to conversation biology. We used a multidisciplinary approach including genetics as well as morphological and ecological data to assess if an easily recognizable, widely distributed and euryoecious mite taxon represents one and the same species. According to phylogenetic (based on mitochondrial and nuclear genes) and species delimitation analyses, five distinct putative species were detected and supported by high genetic distances. These genetic lineages correlate well with ecological data, and each species could be associated to its own (micro)habitat. Subsequently, slight morphological differences were found and provide additional evidence that five different species occur in Central and Southern Europe. The minuteness and the characteristic habitus of Caleremaeus monilipes tempted to neglect potential higher species diversity. This problem might concern several other "well-known" euryoecious microarthropods. Five new species of the genus Caleremaeus are described, namely Caleremaeus mentobellus sp. nov., C. lignophilus sp. nov., C. alpinus sp. nov., C. elevatus sp. nov., and C. hispanicus sp. nov. Additionally, a morphological evaluation of C. monilipes is presented.
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Affiliation(s)
- Andrea Lienhard
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria.
| | - Günther Krisper
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria.
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A taxonomist's nightmare - Cryptic diversity in Caribbean intertidal arthropods (Arachnida, Acari, Oribatida). Mol Phylogenet Evol 2021; 163:107240. [PMID: 34197900 DOI: 10.1016/j.ympev.2021.107240] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 12/28/2022]
Abstract
There has been a long controversy about what defines a species and how to delimitate them which resulted in the existence of more than two dozen different species concepts. Recent research on so-called "cryptic species" heated up this debate as some scientists argue that these cryptic species are only a result of incompatible species concepts. While this may be true, we should keep in mind that all concepts are nothing more than human constructs and that the phenomenon of high phenotypic similarity despite reproductive isolation is real. To investigate and understand this phenomenon it is important to classify and name cryptic species as it allows to communicate them with other fields of science that use Linnaean binomials. To provide a common framework for the description of cryptic species, we propose a possible protocol of how to formally name and describe these taxa in practice. The most important point of this protocol is to explain which species concept was used to delimitate the cryptic taxon. As a model, we present the case of the allegedly widespread Caribbean intertidal mite Thalassozetes barbara, which in fact consists of seven phenotypically very similar but genetically distinct species. All species are island or short-range endemics with poor dispersal abilities that have evolved in geographic isolation. Stabilizing selection caused by the extreme conditions of the intertidal environment is suggested to be responsible for the morphological stasis of this cryptic species complex.
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Marchán DF, Fernández R, Domínguez J, Díaz Cosín DJ, Novo M. Genome-informed integrative taxonomic description of three cryptic species in the earthworm genus Carpetania (Oligochaeta, Hormogastridae). SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1730474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Daniel Fernández Marchán
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Vigo, E-36310, Spain
| | - Rosa Fernández
- Institute of Evolutionary Biology (CSIC-Universitat, Pompeu Fabra), Passeig Marítim de la Barceloneta 37-,49, Barcelona, 08003, Spain
| | - Jorge Domínguez
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Vigo, E-36310, Spain
| | - Darío J. Díaz Cosín
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Marta Novo
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
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Cerca J, Meyer C, Purschke G, Struck TH. Delimitation of cryptic species drastically reduces the geographical ranges of marine interstitial ghost-worms (Stygocapitella; Annelida, Sedentaria). Mol Phylogenet Evol 2020; 143:106663. [DOI: 10.1016/j.ympev.2019.106663] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 10/25/2022]
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Pfingstl T, Baumann J, Lienhard A. The Caribbean enigma: the presence of unusual cryptic diversity in intertidal mites (Arachnida, Acari, Oribatida). ORG DIVERS EVOL 2019; 19:609-623. [PMID: 31885493 PMCID: PMC6913133 DOI: 10.1007/s13127-019-00416-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 08/22/2019] [Indexed: 01/25/2023]
Abstract
The definition, as well as the existence of cryptic species, is still a subject of controversial debates. Some scientists claim that cryptic diversity is a real phenomenon that should be extensively studied while others argue that cryptic species do not exist as they are nothing more than an incompatibility of species concepts. We investigated the enigmatic case of two widely distributed Caribbean intertidal oribatid mites, Carinozetes bermudensis and Carinozetes mangrovi, consisting of five distinct genetic lineages. Morphological features allowing to clearly distinguish between these lineages are absent, and despite certain congruence with genetic data, comprehensive morphometric analyses also do not show clear separation. Species delimitation analyses based on COI sequence data, on the other hand, suggest five distinct genetic species. Despite the lack of diagnostic characters for these suggested species, the lineages can be classified at least into two morphological groups, the bermudensis and the mangrovi group which can only be distinguished by the arrangement of cuticular ventral carinae. Specimens within a group show nearly identical phenotypes, impeding morphological identification and hence rendering the found diversity cryptic. Stabilizing selection caused by the extreme conditions of the intertidal environment is suggested to be responsible for the found morphological stasis. The genetic lineages show more or less clear geographic patterns; in C. mangrovi, there is a northern, an Antillean, and a Pacific lineage, whereas in C. bermudensis, there is a Bermudian and a Caribbean lineage. In a few places, e.g., the Bahamas and Panama, distributions may overlap. Neither the found biogeographic pattern nor the observed ecological needs could explain the reason for the genetic diversification of Caribbean Carinozetes.
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Affiliation(s)
- Tobias Pfingstl
- Institute of Biology, Department for Biodiversity and Evolution, University of Graz, Universitaetsplatz 2, 8010 Graz, Austria
| | - Julia Baumann
- Institute of Biology, Department for Biodiversity and Evolution, University of Graz, Universitaetsplatz 2, 8010 Graz, Austria
| | - Andrea Lienhard
- Institute of Biology, Department for Biodiversity and Evolution, University of Graz, Universitaetsplatz 2, 8010 Graz, Austria
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Multilevel fine-scale diversity challenges the 'cryptic species' concept. Sci Rep 2019; 9:6732. [PMID: 31043629 PMCID: PMC6494890 DOI: 10.1038/s41598-019-42297-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 03/29/2019] [Indexed: 01/08/2023] Open
Abstract
‘Cryptic’ species are an emerging biological problem that is broadly discussed in the present study. Recently, a cryptic species definition was suggested for those species which manifest low morphological, but considerable genetic, disparity. As a case study we present unique material from a charismatic group of nudibranch molluscs of the genus Trinchesia from European waters to reveal three new species and demonstrate that they show a dual nature: on one hand, they can be considered a ‘cryptic’ species complex due to their overall similarity, but on the other hand, stable morphological differences as well as molecular differences are demonstrated for every species in that complex. Thus, this species complex can equally be named ‘cryptic’, ‘pseudocryptic’ or ‘non-cryptic’. We also present evidence for an extremely rapid speciation rate in this species complex and link the species problem with epigenetics. Available metazoan-wide data, which are broadly discussed in the present study, show the unsuitability of a ‘cryptic’ species concept because the degree of crypticity represents a continuum when a finer multilevel morphological and molecular scale is applied to uncover more narrowly defined species making the ‘cryptic’ addition to ‘species’ redundant. Morphological and molecular methods should be applied in concordance to form a fine-scale multilevel taxonomic framework, and not necessarily implying only an a posteriori transformation of exclusively molecular-based ‘cryptic’ species into morphologically-defined ‘pseudocryptic’ ones. Implications of the present study have importance for many fields, including conservation biology and fine-scale biodiversity assessments.
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Bannikova A, Lebedev V, Dubrovskaya A, Solovyeva E, Moskalenko V, Kryštufek B, Hutterer R, Bykova E, Zhumabekova B, Rogovin K, Shenbrot G. Genetic evidence for several cryptic species within theScarturus elaterspecies complex (Rodentia: Dipodoidea): when cryptic species are really cryptic. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Anna Bannikova
- Lomonosov Moscow State University, Vorobievy Gory, Moscow, Russia
| | | | - Anna Dubrovskaya
- Lomonosov Moscow State University, Vorobievy Gory, Moscow, Russia
| | | | | | | | - Rainer Hutterer
- Das Zoologische Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Elena Bykova
- Institute of Zoology Tashkent, Uzbekistan Academy of Science, Uzbekistan
| | | | - Konstantin Rogovin
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Georgy Shenbrot
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
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