1
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de Souza PE, Souza-Silva M, Ferreira RL. The ticking clock in the dark: Review of biological rhythms in cave invertebrates. Chronobiol Int 2024; 41:738-756. [PMID: 38722073 DOI: 10.1080/07420528.2024.2348010] [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: 01/07/2024] [Accepted: 04/19/2024] [Indexed: 05/22/2024]
Abstract
Circadian clocks, internal mechanisms that generate 24-hour rhythms, play a crucial role in coordinating biological events with day-night cycles. In light-deprived environments such as caves, species, particularly isolated obligatory troglobites, may exhibit evolutionary adaptations in biological rhythms due to light exposure. To explore rhythm expression in these settings, we conducted a comprehensive literature review on invertebrate chronobiology in global subterranean ecosystems, analyzing 44 selected studies out of over 480 identified as of September 2023. These studies revealed significant taxonomic diversity, primarily among terrestrial species like Coleoptera, with research concentrated in the United States, Italy, France, Australia, and Brazil, and a notable gap in African records. Troglobite species displayed a higher incidence of aperiodic behavior, while troglophiles showed a robust association with rhythm expression. Locomotor activity was the most studied aspect (>60%). However, approximately 4% of studies lacked information on periodicity or rhythm asynchrony, and limited research under constant light conditions hindered definitive conclusions. This review underscores the need to expand chronobiological research globally, encompassing diverse geographical regions and taxa, to deepen our understanding of biological rhythms in subterranean species. Such insights are crucial for preserving the resilience of subsurface ecosystems facing threats like climate change and habitat loss.
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Affiliation(s)
| | - Marconi Souza-Silva
- Department of Ecology and Conservation, Federal University of Lavras, Lavras, Brazil
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2
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Hlebec D, Podnar M, Kučinić M, Harms D. Molecular analyses of pseudoscorpions in a subterranean biodiversity hotspot reveal cryptic diversity and microendemism. Sci Rep 2023; 13:430. [PMID: 36624298 PMCID: PMC9829860 DOI: 10.1038/s41598-022-26298-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/13/2022] [Indexed: 01/11/2023] Open
Abstract
Nested within the Mediterranean biodiversity hotspot, the Dinaric Karst of the western Balkans is one of the world's most heterogeneous subterranean ecosystems and renowned for its highly diverse and mostly endemic fauna. The evolutionary processes leading to both endemism and diversity remain insufficiently understood, and large-scale analyses on taxa that are abundant in both subterranean and surface habitats remain infrequent. Here, we provide the first comprehensive molecular study on Croatian pseudoscorpions, a lineage of arachnids that is common and diverse in both habitats. Phylogenetic reconstructions using 499 COI sequences derived from 128 morphospecies collected across the Dinaric Karst show that: (i) occurrence in karstic microhabitats boosters speciation and endemism in the most diverse genera Chthonius C.L. Koch, 1843 (37 morphospecies) and Neobisium Chamberlin, 1930 (34 morphospecies), (ii) evidence for ongoing diversification is found in many species and species complexes through low optimal thresholds (OTs) and species delineation analyses, and (iii) landscape features, such as mountain ranges, correlate with patterns of genetic diversity in the diverse genus Neobisium. We present two synonymies: Protoneobisium Ćurčić, 1988 = Neobisium, syn. nov., and Archaeoroncus Ćurčić and Rađa, 2012 = Roncus L. Koch, 1873, syn. nov. Overall, our study suggests that karstic microhabitats promote diversification in soil- and cave-dwelling arthropods at all taxonomic levels, but also provide important refugia for invertebrates in past and present periods of environmental change.
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Affiliation(s)
- Dora Hlebec
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia. .,Section of Arachnology, Department of Invertebrates, Museum of Nature Hamburg - Zoology, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany. .,Croatian Biospeleological Society, Zagreb, Croatia.
| | - Martina Podnar
- grid.452330.30000 0001 2230 9365Croatian Natural History Museum, Zagreb, Croatia
| | - Mladen Kučinić
- grid.4808.40000 0001 0657 4636Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Danilo Harms
- grid.517093.90000 0005 0294 9006Section of Arachnology, Department of Invertebrates, Museum of Nature Hamburg - Zoology, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany
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3
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Borko Š, Altermatt F, Zagmajster M, Fišer C. A hotspot of groundwater amphipod diversity on a crossroad of evolutionary radiations. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Špela Borko
- SubBio Lab Department of Biology Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
| | - Florian Altermatt
- Department of Aquatic Ecology EawagSwiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich Switzerland
| | - Maja Zagmajster
- SubBio Lab Department of Biology Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
| | - Cene Fišer
- SubBio Lab Department of Biology Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
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4
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Martinsson S, Malmberg K, Bakken T, Korshunova T, Martynov A, Lundin K. Species delimitation and phylogeny of
Doto
(Nudibranchia: Dotidae) from the Northeast Atlantic, with a discussion on food specialization. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Svante Martinsson
- Systematics and Biodiversity Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
| | | | - Torkild Bakken
- NTNU University Museum Norwegian University of Science and Technology Trondheim Norway
| | | | | | - Kennet Lundin
- Gothenburg Natural History Museum Gothenburg Sweden
- Gothenburg Global Biodiversity Centre University of Gothenburg Gothenburg Sweden
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5
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Jażdżewska AM, Tandberg AHS, Horton T, Brix S. Global gap-analysis of amphipod barcode library. PeerJ 2021; 9:e12352. [PMID: 34760373 PMCID: PMC8572522 DOI: 10.7717/peerj.12352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/29/2021] [Indexed: 12/02/2022] Open
Abstract
In the age of global climate change and biodiversity loss there is an urgent need to provide effective and robust tools for diversity monitoring. One of the promising techniques for species identification is the use of DNA barcoding, that in Metazoa utilizes the so called 'gold-standard' gene of cytochrome c oxidase (COI). However, the success of this method relies on the existence of trustworthy barcode libraries of the species. The Barcode of Life Data System (BOLD) aims to provide barcodes for all existing organisms, and is complemented by the Barcode Index Number (BIN) system serving as a tool for potential species recognition. Here we provide an analysis of all public COI sequences available in BOLD of the diverse and ubiquitous crustacean order Amphipoda, to identify the barcode library gaps and provide recommendations for future barcoding studies. Our gap analysis of 25,702 records has shown that although 3,835 BINs (indicating putative species) were recognised by BOLD, only 10% of known amphipod species are represented by barcodes. We have identified almost equal contribution of both records (sequences) and BINs associated with freshwater and with marine realms. Three quarters of records have a complete species-level identification provided, while BINs have just 50%. Large disproportions between identification levels of BINs coming from freshwaters and the marine environment were observed, with three quarters of the former possessing a species name, and less than 40% for the latter. Moreover, the majority of BINs are represented by a very low number of sequences rendering them unreliable according to the quality control system. The geographical coverage is poor with vast areas of Africa, South America and the open ocean acting as "white gaps". Several, of the most species rich and highly abundant families of Amphipoda (e.g., Phoxocephalidae, Ampeliscidae, Caprellidae), have very poor representation in the BOLD barcode library. As a result of our study we recommend stronger effort in identification of already recognised BINs, prioritising the studies of families that are known to be important and abundant components of particular communities, and targeted sampling programs for taxa coming from geographical regions with the least knowledge.
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Affiliation(s)
- Anna Maria Jażdżewska
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | | | - Tammy Horton
- National Oceanography Centre, Southampton, United Kingdom
| | - Saskia Brix
- Department for Marine Biodiversity Research (DZMB), Senckenberg am Meer, Hamburg, Germany
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6
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Sympatric and independently evolving lineages in the Thoropa miliaris - T. taophora species complex (Anura: Cycloramphidae). Mol Phylogenet Evol 2021; 166:107220. [PMID: 34481948 DOI: 10.1016/j.ympev.2021.107220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 04/28/2021] [Accepted: 06/01/2021] [Indexed: 11/20/2022]
Abstract
Species delimitation can be challenging and affected by subjectivity. Sibling lineages that occur in sympatry constitute good candidates for species delimitation regardless of the adopted species concept. The Thoropa miliaris + T. taophora species complex exhibits high genetic diversity distributed in several lineages that occur sympatrically in the southeastern Atlantic Forest of Brazil. We used 414 loci obtained by anchored hybrid enrichment to characterize genetic variation in the Thoropa miliaris species group (T. saxatilis, T megatympanum, T. miliaris, and T. taophora), combining assignment analyses with traditional and coalescent phylogeny reconstruction. We also investigated evolutionary independence in co-occurring lineages by estimating gene flow, and validated lineages under the multispecies coalescent. We recovered most previously described lineages as unique populations in assignment analyses; exceptions include two lineages within T. miliaris that are further substructured, and the merging of all T. taophora lineages. We found very low probabilities of gene flow between sympatric lineages, suggesting independent evolution. Species tree inferences and species delimitation yielded resolved relationships and indicate that all lineages constitute putative species that diverged during the Pliocene and Pleistocene, later than previously estimated.
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7
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Bargrizaneh Z, Fišer C, Esmaeili-Rineh S. Groundwater amphipods of the genus Niphargus Schiødte, 1834 in Boyer-Ahmad region (Iran) with description of two new species. ZOOSYSTEMA 2021. [DOI: 10.5252/zoosystema2021v43a7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Zeinab Bargrizaneh
- Department of Biology, Faculty of Science, Razi University, Baghabrisham 6714967346, Kermanshah (Iran)
| | - Cene Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, PO Box 2995, SI-1001 Ljubljana (Slovenia)
| | - Somayeh Esmaeili-Rineh
- Department of Biology, Faculty of Science, Razi University, Baghabrisham 6714967346, Kermanshah (Iran)
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8
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First insight into cryptic diversity of a Caucasian subterranean amphipod of the genus Niphargus (Crustacea: Amphipoda: Niphargidae). ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2020.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Walters AD, Cannizzaro AG, Trujillo DA, Berg DJ. Addressing the Linnean shortfall in a cryptic species complex. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Biodiversity is being lost at an alarming rate, but the rate of this loss is likely to be underestimated as a result of a deficit in taxonomic knowledge (i.e. the Linnean shortfall). This knowledge gap is more extensive for morphologically indistinct taxa. The advancement of molecular techniques and delimitation methods has facilitated the identification of such cryptic species, but a majority of these taxa remain undescribed. To investigate the effects of taxonomic uncertainty on understanding of biodiversity, we applied the general lineage concept of species to an amphipod species complex, the Gammaruslacustris lineage that occupies springs of the northern Chihuahuan Desert, which is emerging in contemporary times. We investigated species boundaries using a validation-based approach and examined genetic structure of the lineage using a suite of microsatellite markers to identify independently evolving metapopulations. Our results show that each spring contains a genetically distinct population that is geographically isolated from other springs, suggesting evolutionary independence and status as separate species. Additionally, we observed subtle interspecific morphological variation among the putative species. We used multiple lines of evidence to formally describe four new species (Gammarus langi sp. nov., G. percalacustris sp. nov., G. colei sp. nov. and G. malpaisensis sp. nov.) endemic to the northern Chihuahuan Desert. Cryptic speciation is likely to be high in other aquatic taxa within these ecosystems, and across arid landscapes throughout North America and elsewhere, suggesting that the magnitude of the Linnean shortfall is currently underestimated in desert springs worldwide.
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Affiliation(s)
| | | | | | - David J Berg
- Department of Biology, Miami University, Hamilton, OH USA
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10
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Wattier R, Mamos T, Copilaş-Ciocianu D, Jelić M, Ollivier A, Chaumot A, Danger M, Felten V, Piscart C, Žganec K, Rewicz T, Wysocka A, Rigaud T, Grabowski M. Continental-scale patterns of hyper-cryptic diversity within the freshwater model taxon Gammarus fossarum (Crustacea, Amphipoda). Sci Rep 2020; 10:16536. [PMID: 33024224 PMCID: PMC7538970 DOI: 10.1038/s41598-020-73739-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022] Open
Abstract
Traditional morphological diagnoses of taxonomic status remain widely used while an increasing number of studies show that one morphospecies might hide cryptic diversity, i.e. lineages with unexpectedly high molecular divergence. This hidden diversity can reach even tens of lineages, i.e. hyper cryptic diversity. Even well-studied model-organisms may exhibit overlooked cryptic diversity. Such is the case of the freshwater crustacean amphipod model taxon Gammarus fossarum. It is extensively used in both applied and basic types of research, including biodiversity assessments, ecotoxicology and evolutionary ecology. Based on COI barcodes of 4926 individuals from 498 sampling sites in 19 European countries, the present paper shows (1) hyper cryptic diversity, ranging from 84 to 152 Molecular Operational Taxonomic Units, (2) ancient diversification starting already 26 Mya in the Oligocene, and (3) high level of lineage syntopy. Even if hyper cryptic diversity was already documented in G. fossarum, the present study increases its extent fourfold, providing a first continental-scale insight into its geographical distribution and establishes several diversification hotspots, notably south-eastern and central Europe. The challenges of recording hyper cryptic diversity in the future are also discussed.
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Affiliation(s)
- Remi Wattier
- UMR CNRS 6282 Biogéosciences, Université Bourgogne Franche Comté, Dijon, France.
| | - Tomasz Mamos
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Lodz, Poland.,Zoological Institute, University of Basel, Basel, Switzerland
| | - Denis Copilaş-Ciocianu
- Institute of Ecology, Nature Research Centre, Vilnius Nature Research Centre, Institute of Ecology, Vilnius, Lithuania
| | - Mišel Jelić
- Department of Natural Sciences, Varaždin City Museum, Varaždin, Croatia
| | - Anthony Ollivier
- UMR CNRS 6282 Biogéosciences, Université Bourgogne Franche Comté, Dijon, France
| | - Arnaud Chaumot
- Laboratoire d'écotoxicologie, INRAE, UR RiverLy, Villeurbanne, France
| | - Michael Danger
- UMR CNRS 73602 LIEC, Université de Lorraine, Metz, France
| | - Vincent Felten
- UMR CNRS 73602 LIEC, Université de Lorraine, Metz, France
| | | | - Krešimir Žganec
- Department of Teacher Education Studies in Gospić, University of Zadar, Gospić, Croatia
| | - Tomasz Rewicz
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Lodz, Poland.,University of Guelph, Centre for Biodiversity Genomics, Guelph, ON, Canada
| | - Anna Wysocka
- Department of Genetics and Biosystematics, University of Gdansk, Gdansk, Poland
| | - Thierry Rigaud
- UMR CNRS 6282 Biogéosciences, Université Bourgogne Franche Comté, Dijon, France
| | - Michał Grabowski
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Lodz, Poland.
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11
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Lukić M, Delić T, Pavlek M, Deharveng L, Zagmajster M. Distribution pattern and radiation of the European subterranean genusVerhoeffiella(Collembola, Entomobryidae). ZOOL SCR 2019. [DOI: 10.1111/zsc.12392] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Marko Lukić
- Croatian Biospeleological Society Zagreb Croatia
- SubBioLab Department of Biology Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
- Ruđer Bošković Institute Zagreb Croatia
| | - Teo Delić
- SubBioLab Department of Biology Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
| | - Martina Pavlek
- Croatian Biospeleological Society Zagreb Croatia
- Ruđer Bošković Institute Zagreb Croatia
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute Universitat de Barcelona Barcelona Spain
| | - Louis Deharveng
- Institut de Systématique, Evolution, Biodiversité ISYEB ‐ UMR 7205 ‐ CNRS MNHN, UPMC, EPHE, Museum national d'Histoire naturelle Sorbonne Universités Paris France
| | - Maja Zagmajster
- SubBioLab Department of Biology Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
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12
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Bedek J, Taiti S, Bilandžija H, Ristori E, Baratti M. Molecular and taxonomic analyses in troglobiotic Alpioniscus (Illyrionethes) species from the Dinaric Karst (Isopoda: Trichoniscidae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Species richness of terrestrial isopods is high in caves of the Dinaric Karst, which hosts ~10% of the world’s nominal oniscidean troglobionts. The most widespread taxon is the southern European genus Alpioniscus, which consists of two subgenera: Alpioniscus s.s. and Illyrionethes. Before this study, 14 nominal troglobiotic Illyrionethes taxa were recorded from the Dinaric Karst. Our molecular analyses using two mitochnodrial DNA (16S rRNA and COI) fragments and a nuclear gene (H3) fragment on all known Dinaric taxa identified three distinct lineages: strasseri-, heroldi- and magnus-lineage. Our results confirmed the validity of most nominal species. The exceptions are Alpioniscus balthasari, which consists of two different species including Alpioniscus iapodicus, and Alpioniscus heroldi, which is paraphyletic with respect to Alpioniscus bosniensis. The strasseri-lineage was highly supported by all phylogenetic methods used; therefore, we performed a detailed morphological analysis to distinguish and characterize the species of this group. New morphological characters, such as body part ratios, are proposed for future species identification. In addition, we redescribe three known species (Alpioniscus strasseri, Alpioniscus christiani and Alpioniscus balthasari) and describe two new ones (Alpioniscus hirci sp. nov. and Alpioniscus velebiticus sp. nov.). As a result, 15 nominal species of Illyrionethes are currently known from the Dinaric Karst.
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Affiliation(s)
- Jana Bedek
- Croatian Biospeleological Society, Zagreb, Croatia
| | - Stefano Taiti
- Istituto di Ricerca sugli Ecosistemi Terrestri, CNR, Sesto Fiorentino (Florence), Italy
- Museo di Storia Naturale dell’Università di Firenze, Sezione di Zoologia ‘La Specola’, Florence, Italy
| | - Helena Bilandžija
- Croatian Biospeleological Society, Zagreb, Croatia
- Ruđer Bošković Institute, Zagreb, Croatia
| | - Emma Ristori
- Institute of Biosciences and Bioresources IBBR, CNR, Sesto Fiorentino (Florence), Italy
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Mariella Baratti
- Institute of Biosciences and Bioresources IBBR, CNR, Sesto Fiorentino (Florence), Italy
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13
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García‐Rodríguez FJ, Chollet‐Villalpando JG, Martínez‐Guevara A, De La Cruz‐Agüero J. Supporting the existence of two isolated evolutionary lineages of
Gerres
(Perciformes: Gerreidae) in America. ZOOL SCR 2019. [DOI: 10.1111/zsc.12352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Francisco J. García‐Rodríguez
- Instituto Politécnico Nacional‐Centro Interdisciplinario de Ciencias Marinas, Departamento de Pesquerías y Biología Marina Colección Ictiológica La Paz B.C.S. México
| | - Jorge G. Chollet‐Villalpando
- Instituto Politécnico Nacional‐Centro Interdisciplinario de Ciencias Marinas, Departamento de Pesquerías y Biología Marina Colección Ictiológica La Paz B.C.S. México
| | - Adriana Martínez‐Guevara
- Instituto Politécnico Nacional‐Centro Interdisciplinario de Ciencias Marinas, Departamento de Pesquerías y Biología Marina Colección Ictiológica La Paz B.C.S. México
| | - José De La Cruz‐Agüero
- Instituto Politécnico Nacional‐Centro Interdisciplinario de Ciencias Marinas, Departamento de Pesquerías y Biología Marina Colección Ictiológica La Paz B.C.S. México
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14
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Copilaș‐Ciocianu D, Zimța A, Petrusek A. Integrative taxonomy reveals a newGammarusspecies (Crustacea, Amphipoda) surviving in a previously unknown southeast European glacial refugium. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12248] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Denis Copilaș‐Ciocianu
- Department of Ecology Faculty of Science Charles University Prague Czechia
- Laboratory of Evolutionary Ecology of Hydrobionts Nature Research Centre Vilnius Lithuania
| | - Alina‐Andreea Zimța
- Department of Ecology Faculty of Science Charles University Prague Czechia
- Department of Biology–Chemistry Faculty of Chemistry, Biology, Geography West University of Timişoara Timişoara Romania
| | - Adam Petrusek
- Department of Ecology Faculty of Science Charles University Prague Czechia
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15
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Stokkan M, Jurado-Rivera JA, Oromí P, Juan C, Jaume D, Pons J. Species delimitation and mitogenome phylogenetics in the subterranean genus Pseudoniphargus (Crustacea: Amphipoda). Mol Phylogenet Evol 2018; 127:988-999. [PMID: 30004011 DOI: 10.1016/j.ympev.2018.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/28/2018] [Accepted: 07/04/2018] [Indexed: 11/29/2022]
Abstract
The amphi-Atlantic distributions exhibited by many thalassoid stygobiont (obligate subterranean) crustaceans have been explained by fragmentation by plate tectonics of ancestral shallow water marine populations. The amphipod stygobiont genus Pseudoniphargus is distributed across the Mediterranean region but also in the North Atlantic archipelagos of Bermuda, Azores, Madeira and the Canaries. We used species delimitation methods and mitogenome phylogenetic analyses to clarify the species diversity and evolutionary relationships within the genus and timing their diversification. Analyses included samples from the Iberian Peninsula, northern Morocco, the Balearic, Canarian, Azores and Madeira archipelagoes plus Bermuda. In most instances, morphological and molecular-based species delimitation analyses yielded consistent results. Notwithstanding, in a few cases either incipient speciation with no involvement of detectable morphological divergence or species crypticism were the most plausible explanations for the disagreement found between morphological and molecular species delimitations. Phylogenetic analyses based on a robust calibrated mitochondrial tree suggested that Pseudoniphargus lineages have a younger age than for other thalassoid amphipods displaying a disjunct distribution embracing both sides of the Atlantic Ocean. A major split within the family was estimated to occur at the Paleocene, when a lineage from Northern Iberian Peninsula diverged from the rest of pseudoniphargids. Species diversification in the peri-Mediterranean area was deduced to occur in early Miocene to Tortonian times, while in the Atlantic islands it started in the Pliocene. Our results show that the current distribution pattern of Pseudoniphargus resulted from a complex admix of relatively ancient vicariance events and several episodes of long- distance dispersal.
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Affiliation(s)
- Morten Stokkan
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/ Miquel Marquès 21, Esporles, 07190 Balearic Islands, Spain
| | - José A Jurado-Rivera
- Dept. of Biology, Universitat de les Illes Balears, Ctra. Valldemossa km 7'5, Palma 07122, Balearic Islands, Spain
| | - Pedro Oromí
- Dept. of Animal Biology, Edaphology and Geology, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez, s/n. Campus de Anchieta, Ap. correos 456, La Laguna 38200, Tenerife, Spain
| | - Carlos Juan
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/ Miquel Marquès 21, Esporles, 07190 Balearic Islands, Spain; Dept. of Biology, Universitat de les Illes Balears, Ctra. Valldemossa km 7'5, Palma 07122, Balearic Islands, Spain
| | - Damià Jaume
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/ Miquel Marquès 21, Esporles, 07190 Balearic Islands, Spain
| | - Joan Pons
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/ Miquel Marquès 21, Esporles, 07190 Balearic Islands, Spain.
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Fišer C, Alther R, Zakšek V, Borko Š, Fuchs A, Altermatt F. Translating Niphargus barcodes from Switzerland into taxonomy with a description of two new species (Amphipoda, Niphargidae). Zookeys 2018; 760:113-141. [PMID: 29872366 PMCID: PMC5986823 DOI: 10.3897/zookeys.760.24978] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 04/24/2018] [Indexed: 01/21/2023] Open
Abstract
The amphipod genus Niphargus (Amphipoda: Niphargidae Bousfield, 1977) is the most species-rich genus of freshwater amphipods in the World. Species of this genus, which live almost exclusively in subterranean water, offer an interesting model system for basic and applied biodiversity science. Their use, however, is often limited due to the hitherto unresolved taxonomy within the whole genus. As a comprehensive taxonomic revision of the currently >425 Niphargus species is too demanding, it has been suggested that the taxonomy of the genus could be advanced in smaller steps, by reviewing regional faunas, that would eventually integrate into a global revision. In this study, we provide such a revision of Niphargus in Switzerland. First, we molecularly delimited, morphologically diagnosed, and formally described two new species, namely Niphargus luchoffmannisp. n. and Niphargus tonywhittenisp. n. Second, we updated and revised a checklist of Niphargus in Switzerland with new findings, and prepared a list of reference sequences for routine molecular identification, available at BOLD and GenBank. All available specimens of 22 known species from the area were morphologically examined, and their morphological variation was compiled in a data file of DEscription Language for TAxonomy, which can be used for automated generation of dichotomous or interactive keys. The data file is freely available at the World Amphipoda Database. Together, the checklist, the library of reference sequences, the DELTA file, but also a list of hitherto unresolved aspects are an important step towards a complete revision of the genus within a well-defined and biogeographically interesting area in Central Europe.
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Affiliation(s)
- Cene Fišer
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Roman Alther
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Valerija Zakšek
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Špela Borko
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Andreas Fuchs
- Institut für Grundwasserökologie IGÖ GmbH an der Universität Koblenz-Landau, Campus Landau Fortstraße 7, D-76829 Landau, Germany
| | - Florian Altermatt
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
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Zimmermann BL, Crivellaro MS, Hauschild CB, Bartholomei-Santos ML, Crandall KA, Pérez-Losada M, Giri F, Collins P, Santos S. Phylogeography reveals unexpectedly low genetic diversity in a widely distributed species: the case of the freshwater crab Aegla platensis (Decapoda: Anomura). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/blx166] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Bianca L Zimmermann
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Marcelo S Crivellaro
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Caroline B Hauschild
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Marlise L Bartholomei-Santos
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Keith A Crandall
- Computational Biology Institute, George Washington University, Ashburn, VA, USA
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Marcos Pérez-Losada
- Computational Biology Institute, George Washington University, Ashburn, VA, USA
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Vairão, Portugal
| | - Federico Giri
- Laboratorio de Macrocrustáceos, Instituto Nacional de Limnología, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Pablo Collins
- Laboratorio de Macrocrustáceos, Instituto Nacional de Limnología, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Sandro Santos
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
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Fišer C, Robinson CT, Malard F. Cryptic species as a window into the paradigm shift of the species concept. Mol Ecol 2018; 27:613-635. [DOI: 10.1111/mec.14486] [Citation(s) in RCA: 263] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Cene Fišer
- SubBio Lab; Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
| | - Christopher T. Robinson
- Department of Aquatic Ecology; Eawag; Dübendorf Switzerland
- Institute of Integrative Biology; ETH Zürich; Zürich Switzerland
| | - Florian Malard
- Université Lyon; Université Claude Bernard Lyon 1; CNRS; ENTPE; UMR5023 LEHNA Villeurbanne France
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