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Guy-Haim T, Kolodny O, Frumkin A, Achituv Y, Velasquez X, Morov AR. Shedding light on the Ophel biome: the trans-Tethyan phylogeography of the sulfide shrimp Tethysbaena (Peracarida: Thermosbaenacea) in the Levant. PeerJ 2023; 11:e16690. [PMID: 38144178 PMCID: PMC10748474 DOI: 10.7717/peerj.16690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/27/2023] [Indexed: 12/26/2023] Open
Abstract
Background Tethysbaena are small peracarid crustaceans inhabiting extreme environments such as subterranean lakes and thermal springs, represented by endemic species found around the ancient Tethys, including the Mediterranean, Arabian Sea, Mid-East Atlantic, and the Caribbean Sea. Two Tethysbaena species are known from the Levant: T. relicta, found along the Dead Sea-Jordan Rift Valley, and T. ophelicola, found in the Ayyalon cave complex in the Israeli coastal plain, both belonging to the same species-group based on morphological cladistics. Along the biospeleological research of the Levantine subterranean fauna, three biogeographic hypotheses determining their origins were proposed: (1) Pliocenic transgression, (2) Mid-late Miocenic transgression, and (3) The Ophel Paradigm, according to which these are inhabitants of a chemosynthetic biome as old as the Cambrian. Methods Tethysbaena specimens of the two Levantine species were collected from subterranean groundwaters. We used the mitochondrial cytochrome c oxidase subunit I (COI) gene and the nuclear ribosomal 28S (28S rRNA) gene to establish the phylogeny of the Levantine Tethysbaena species, and applied a molecular clock approach for inferring their divergence times. Results Contrary to the morphological cladistic-based classification, we found that T. relicta shares an ancestor with Tethysbaena species from Oman and the Dominican Republic, whereas the circum-Mediterranean species (including T. ophelicola) share another ancestor. The mean age of the node linking T. relicta from the Dead Sea-Jordan Rift Valley and Tethysbaena from Oman was 20.13 MYA. The mean estimate for the divergence of T. ophelicola from the Mediterranean Tethysbaena clade dated to 9.46 MYA. Conclusions Our results indicate a two-stage colonization of Tethysbaena in the Levant: a late Oligocene transgression, through a marine gulf extending from the Arabian Sea, leading to the colonization of T. relicta in the Dead Sea-Jordan Rift Valley, whereas T. ophelicola, originating from the Mesogean ancestor, inhabited anchialine caves in the coastal plain of Israel during the Mid-Miocene.
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Affiliation(s)
- Tamar Guy-Haim
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Oren Kolodny
- Department of Ecology, Evolution, and Behavior, Institute for Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amos Frumkin
- Institute of Earth Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yair Achituv
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Ximena Velasquez
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Arseniy R. Morov
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
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Premate E, Kepic T, Fišer C. Is the relationship between body length and body mass consistent across habitats? A case study on Niphargus (Crustacea: Amphipoda). ZOOLOGY 2023; 161:126120. [PMID: 37696118 DOI: 10.1016/j.zool.2023.126120] [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: 12/13/2022] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/13/2023]
Abstract
Body size is one of the main characteristics of any organism and influences various aspects of individual's biology. In animal ecology, it represents a key functional trait that can be quantified using different measures and is often used as a proxy for different organismal functions. The way we quantify body size is critical in any study using this measure alone or to scale other organismal traits. It is especially important in groups that act as model systems across different fields of biological research. One of such groups are amphipods, which are at focus in many ecological studies where appropriate quantification of body size is needed. Here, we explored the relationship between body length and body mass in the largest freshwater amphipod genus Niphargus, and evaluated whether the two measures lead to different conclusions in a putative ecological study of species coexistence. We selected 16 species inhabiting two different subterranean habitats, cave lakes and cave streams. The relationship between log-transformed body mass and body length was linear in all species, but body mass increased steeper among species from cave lakes than from cave streams, reflecting the stouter body shape of the former. In the simulated ecological study, the comparisons of the two measures showed that they may yield different results: in 10 % of cases, body length detected differences between species when body mass did not and vice versa (13 %). Usage of body length or body mass can thus lead to different conclusions. We recommend avoiding direct transformations between body length and body mass in ecological studies. Whenever needed, such transformations should be done with caution using habitat-specific body mass - body length ratios.
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Affiliation(s)
- Ester Premate
- University of Ljubljana, Biotechnical Faculty, Department of Biology, SubBio Lab, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
| | - Tinkara Kepic
- University of Ljubljana, Biotechnical Faculty, Department of Biology, SubBio Lab, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Cene Fišer
- University of Ljubljana, Biotechnical Faculty, Department of Biology, SubBio Lab, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
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3
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Groundwater Amphipods of the Hyporheic Interstitial: A Case Study from Luxembourg and The Greater Region. DIVERSITY 2023. [DOI: 10.3390/d15030411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Hyporheic interstitials are ecologically dynamic and often neglected aquatic environments. In this study, groundwater amphipods (Niphargidae, Pseudoniphargidae and Crangonyctidae) were sampled in hyporheic interstitials throughout Luxembourg and The Greater Region and specimens were analyzed by DNA barcoding. Sites characterized by gravel or coarse sand and high flow velocities of incoming water were the most species- and specimen-rich. A total of 11 species were detected, of which the Niphargus aquilex lineage EF of the N. aquilex cryptic species complex and juveniles of N. schellenbergi dominated the data set, but an unknown lineage of the N. aquilex-complex was also found. Some regions appeared to be devoid of groundwater amphipods. We hypothesize that underlying sandstone formations resulting in low sediment porosity may prevent physical colonization, but also that historical water pollution may have a long-lasting effect, either through the persistence of contaminants in the sediment or low recolonization rates of affected populations. In summary, our approach expanded regional species inventories, confirmed known occurrences, and validated previously questionable or historical morphology-based detections. In addition, the collection of absence data provided valuable insights into local extinctions. Finally, DNA-based distribution data are needed to gather information on the ecological affinities of groundwater amphipods to understudied hyporheic interstitial environments.
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Not the Last Piece of the Puzzle: Niphargus Phylogeny in Hungary. DIVERSITY 2023. [DOI: 10.3390/d15020223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The Palaearctic genus Niphargus is a promising model system to understand subterranean fauna genesis in Europe. The Pannonian Plain (mainly covered by Hungary) in Central Europe, once being the area of the Paratethys, is a key area for Niphargus diversification. However, our knowledge on Hungarian species of Niphargus is primarily based on sporadic taxonomical works from the pre-molecular era. Here, we studied 14 localities, covering the eight valid Hungarian species of Niphargus and including nine previously unstudied populations. Based on sequences of three gene fragments, we reconstructed their phylogeny using maximum likelihood and Bayesian approaches. We found that not all Hungarian species of Niphargus are closely related, and even species sampled at the same localities can belong to different clades. Some Hungarian species form monophyletic clades, while others are nested in various non-Hungarian lineages. The new populations are all genetically distinct from the known species. Our results suggest that the Hungarian Niphargus fauna has originated from seven unrelated clades and its diversity is underestimated due to unknown populations and cryptic species. The detection of genetically distinct species of Niphargus from non-carbonate regions calls for further research efforts. The high diversity and the number of putative new species in the N. tatrensis clade warrants further, high-resolution phylogenetic studies.
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Hancock ZB, Ogawa H, Light JE, Wicksten MK. Origin and evolution of the Haustoriidae (Amphipoda): a eulogy for the Haustoriidira. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Abstract
Haustoriid amphipods have received little recent attention and their systematics and phylogenetics are largely unresolved. Some efforts have been made at classifying the family within the broader Amphipoda, but there is persistent incongruence in its placement among different authors and techniques. Furthermore, there exists no phylogenetic hypothesis of intrafamilial relationships. In this work, we evaluate the competing hypotheses on the phylogenetic position of the Haustoriidae within Amphipoda by examining new and previously published sequences of nearly 100 species across 38 families. We find strong support for the Haustoriidae as basal gammarids, and that other families placed within the parvorder ‘Haustoriidira’ are spread across Amphipoda. The radiation began during the Eocene and may have been driven in North America by the rapid filling of a coastal niche opened by the Chesapeake Bay impact crater. Unlike previous work, we find that the Pacific-endemic genus Eohaustorius is the most basal haustoriid, and that it separated from the rest of the family ~31 Mya. Finally, we provide taxonomic recommendations for relationships within Haustoriidae, including the elevation of a new genus, Cryptohaustorius gen. nov.. We conclude by recommending that the ‘Haustoriidira’ be abandoned.
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Affiliation(s)
- Zachary B Hancock
- Department of Biology, Texas A&M University, Butler Hall, 3258, 525 Lubbock St, College Station, TX, USA
- Ecology and Evolutionary Biology Interdisciplinary Program, Texas A&M University, College Station, TX, USA
| | - Hiroshi Ogawa
- Association for Protection of Marine Communities, 69 Jodoji-shimobanbacho, Sakyo, Kyoto, Japan
| | - Jessica E Light
- Ecology and Evolutionary Biology Interdisciplinary Program, Texas A&M University, College Station, TX, USA
- Department of Ecology and Conservation Biology, Texas A&M University, Building #1537–534 John Kimbrough Blvd, College Station, TX, USA
| | - Mary K Wicksten
- Department of Biology, Texas A&M University, Butler Hall, 3258, 525 Lubbock St, College Station, TX, USA
- Ecology and Evolutionary Biology Interdisciplinary Program, Texas A&M University, College Station, TX, USA
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Borko Š, Trontelj P, Seehausen O, Moškrič A, Fišer C. A subterranean adaptive radiation of amphipods in Europe. Nat Commun 2021; 12:3688. [PMID: 34140494 PMCID: PMC8211712 DOI: 10.1038/s41467-021-24023-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 06/01/2021] [Indexed: 02/05/2023] Open
Abstract
Adaptive radiations are bursts of evolutionary species diversification that have contributed to much of the species diversity on Earth. An exception is modern Europe, where descendants of ancient adaptive radiations went extinct, and extant adaptive radiations are small, recent and narrowly confined. However, not all legacy of old radiations has been lost. Subterranean environments, which are dark and food-deprived, yet buffered from climate change, have preserved ancient lineages. Here we provide evidence of an entirely subterranean adaptive radiation of the amphipod genus Niphargus, counting hundreds of species. Our modelling of lineage diversification and evolution of morphological and ecological traits using a time-calibrated multilocus phylogeny suggests a major adaptive radiation, comprised of multiple subordinate adaptive radiations. Their spatio-temporal origin coincides with the uplift of carbonate massifs in South-Eastern Europe 15 million years ago. Emerging subterranean environments likely provided unoccupied, predator-free space, constituting ecological opportunity, a key trigger of adaptive radiation. This discovery sheds new light on the biodiversity of Europe.
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Affiliation(s)
- Špela Borko
- SubBio Lab, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Peter Trontelj
- SubBio Lab, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Ajda Moškrič
- SubBio Lab, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Agricultural institute of Slovenia, Ljubljana, Slovenia
| | - Cene Fišer
- SubBio Lab, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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7
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Marin I, Palatov D. Cryptic refugee on the northern slope of the Greater Caucasian Ridge: Discovery of niphargus (Crustacea: Amphipoda: Niphargidae) in the North Ossetia–Alania, North Caucasus, separated from its relatives in the late Miocene. ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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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: 0.8] [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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9
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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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10
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Patoka J, Prabowo RE, Petrtýl M, Reynolds JD, Kuříková P, Zámečníková-Wanma BPD, Kalous L. Marine hitchhikers: a preliminary study on invertebrates unintentionally transported via the international pet trade. NEOBIOTA 2020. [DOI: 10.3897/neobiota.61.57682] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The pet trade in aquatic organisms is a significant source of non-indigenous species introductions. In comparison with ornamental animals, unintentionally transported invertebrate assemblages are easily overlooked by traders and keepers. Moreover, hitchhiking species detection and identification is difficult even for experts. The densities of “hitchhikers” in aquaria may be relatively higher than those in the wild. These phenomena are known in freshwater aquaria but poorly studied in marine ones. We found 17 species of non-ornamental marine invertebrates in one of the leading importers of aquarium species in the Czech Republic in November 2017. The set comprised six gastropods, two bivalves, three cnidarians, two echinoderms, two crustaceans, and two polychaete worms. In one case, a symbiont was also detected, associated with the host “hitchhiker”. No “live rocks” are traded by the surveyed wholesaler. Thus, the found animals were not imported together with this item as larvae or eggs. Contrary to the transport of targeted ornamental species, it is clear that transport of “hitchhikers” is occurring despite standard legislative regulations and should be brought to the attention of conservationists, wildlife managers, policymakers and other stakeholders.
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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: 34] [Impact Index Per Article: 6.8] [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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Stoch F, Christian E, Flot JF. Molecular taxonomy, phylogeny and biogeography of the Niphargus tatrensis species complex (Amphipoda, Niphargidae) in Austria. ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-020-00462-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Zamanpoore M, Bakhshi Y, Sadeghi S, Malek-Hosseini MJ. Niphargus keeleri n. sp., a new cave Amphipod (Arthropoda: Crustacea) from the Zagros Mountains, Iran. J NAT HIST 2020. [DOI: 10.1080/00222933.2019.1704456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Mehrdad Zamanpoore
- Department of Hydrobiology and Fisheries, Agricultural Research, Education, and Extension Organization, AREEO, Shiraz, Iran
| | - Yaser Bakhshi
- Department of Biology, Faculty of Sciences, Shiraz University, Shiraz, Iran
| | - Saber Sadeghi
- Department of Biology, Faculty of Sciences, Shiraz University, Shiraz, Iran
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Copilaş-Ciocianu D, Borko Š, Fišer C. The late blooming amphipods: Global change promoted post-Jurassic ecological radiation despite Palaeozoic origin. Mol Phylogenet Evol 2020; 143:106664. [DOI: 10.1016/j.ympev.2019.106664] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/19/2019] [Accepted: 10/24/2019] [Indexed: 01/04/2023]
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Borko Š, Collette M, Brad T, Zakšek V, Flot JF, Vaxevanopoulos M, Sarbu SM, Fišer C. Amphipods in a Greek cave with sulphidic and non-sulphidic water: phylogenetically clustered and ecologically divergent. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1670273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Špela Borko
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, SI-1000, Slovenia
| | - Martin Collette
- Evolutionary Biology & Ecology, Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, Brussels, B-1050, Belgium
| | - Traian Brad
- ‘Emil Racoviţă’ Institute of Speleology, Strada Clinicilor 5, Cluj-Napoca, 400006, Romania
| | - Valerija Zakšek
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, SI-1000, Slovenia
| | - Jean-François Flot
- Evolutionary Biology & Ecology, Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, Brussels, B-1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels – (IB)2, Brussels, Belgium
| | | | - Serban M. Sarbu
- Department of Biological Sciences, California State University, Chico, Holt Hall 205, Chico, CA, 95929-515, USA
- ‘Emil Racoviţă’ Institute of Speleology, Calea 13 Septembrie 13, Bucharest, 050711, Romania
| | - Cene Fišer
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, SI-1000, Slovenia
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16
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Marin I, Palatov D. A new species of the genusNiphargus(Crustacea: Amphipoda: Niphargidae) from the south-western part of the North Caucasus. ZOOLOGY IN THE MIDDLE EAST 2019. [DOI: 10.1080/09397140.2019.1663907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ivan Marin
- A. N. Severtzov Institute of Ecology and Evolution, Moscow, Russia
- Biological Department, Altai State University, Barnaul, Russia
| | - Dmitry Palatov
- Biological Department, Moscow State University, Moscow, Russia
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Moškrič A, Verovnik R. Five nuclear protein-coding markers for establishing a robust phylogenetic framework of niphargid crustaceans (Niphargidae: Amphipoda) and new molecular sequence data. Data Brief 2019; 25:104134. [PMID: 31297423 PMCID: PMC6598839 DOI: 10.1016/j.dib.2019.104134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/27/2019] [Accepted: 06/03/2019] [Indexed: 11/03/2022] Open
Abstract
The data presented here includes selection of 5 successfully amplified protein-coding markers for inferring phylogenetic relationships of the family of amphipod crustaceans Niphargidae. These markers have been efficiently amplified from niphargid samples for the first time and present the framework for robust phylogenetic assessment of the family Niphargidae. They are useful for phylogenetic purposes among other amphipod genera as well. In detail, the data consists of two parts: 1. Information regarding markers, specific oligonucleotide primer pairs and conditions for PCR reaction that enables successful amplification of specific nucleotide fragments. Two pairs of novel oligonucleotide primers were constructed which enable partial sequence amplification of two housekeeping genes: arginine kinase (ArgKin) and glyceraldehyde phosphate dehydrogenase (GAPDH), respectively. Additionally, 3 existing combinations of oligonucleotide primer pairs for protein-coding loci for glutamyl-prolyl tRNA synthetase (EPRS), opsin (OP) and phosphoenolpyruvate carboxykinase (PEPCK) were proven to be suitable to amplify specific nucleotide fragments from selected amphipod specimens; 2. Information on novel nucleotide sequences from amphipod taxa of the family Niphagidae and related outgroup taxa. Unilocus phylogenetic trees were constructed using Bayesian analysis and show relationships among selected taxa. Altogether 299 new nucleotide sequences from 92 specimens of the family Niphargidae and related outgroup amphipod taxa are deposited in GenBank (NCBI) repository and available for further use in phylogenetic analyses.
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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: 1.6] [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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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: 37.6] [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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Is subterranean lifestyle reversible? Independent and recent large-scale dispersal into surface waters by two species of the groundwater amphipod genus Niphargus. Mol Phylogenet Evol 2018; 119:37-49. [DOI: 10.1016/j.ympev.2017.10.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/23/2017] [Accepted: 10/27/2017] [Indexed: 12/18/2022]
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22
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Esmaeili-Rineh S, Mohammad-Niakan A, Akmali V. Niphargus sarii sp. n., a new subterranean niphargid (Crustacea: Amphipoda) from Iran based on molecular and morphological characters. ACTA ZOOL ACAD SCI H 2018. [DOI: 10.17109/azh.64.2.113.2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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23
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Completion of molecular taxonomy: description of four amphipod species (Crustacea: Amphipoda: Niphargidae) from Iran and release of database for morphological taxonomy. ZOOL ANZ 2017. [DOI: 10.1016/j.jcz.2017.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Delić T, Trontelj P, Rendoš M, Fišer C. The importance of naming cryptic species and the conservation of endemic subterranean amphipods. Sci Rep 2017; 7:3391. [PMID: 28611400 PMCID: PMC5469755 DOI: 10.1038/s41598-017-02938-z] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/20/2017] [Indexed: 11/15/2022] Open
Abstract
Molecular taxonomy often uncovers cryptic species, reminding us that taxonomic incompleteness is even more severe than previous thought. The importance of cryptic species for conservation is poorly understood. Although some cryptic species may be seriously threatened or otherwise important, they are rarely included in conservation programs as most of them remain undescribed. We analysed the importance of cryptic species in conservation by scrutinizing the South European cryptic complex of the subterranean amphipod Niphargus stygius sensu lato. Using uni- and multilocus delineation methods we show that it consists of 15 parapatric and sympatric species, which we describe using molecular diagnoses. The new species are not mere “taxonomic inflation” as they originate from several distinct branches within the genus and coexist with no evidence of lineage sharing. They are as evolutionarily distinct as average nominal species of the same genus. Ignoring these cryptic species will underestimate the number of subterranean endemics in Slovenia by 12 and in Croatia by four species, although alpha diversity of single caves remains unchanged. The new taxonomy renders national Red Lists largely obsolete, as they list mostly large-ranged species but omit critically endangered single-site endemics. Formal naming of cryptic species is critical for them to be included in conservation policies and faunal listings.
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Affiliation(s)
- Teo Delić
- SubBio lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, 1000, Slovenia
| | - Peter Trontelj
- SubBio lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, 1000, Slovenia
| | - Michal Rendoš
- State Nature Conservancy, Slovak Caves Administration, Hodžova 11, 031 01, Liptovský, Mikuláš, Slovakia
| | - Cene Fišer
- SubBio lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, 1000, Slovenia.
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Delić T, Švara V, Coleman CO, Trontelj P, Fišer C. The giant cryptic amphipod species of the subterranean genusNiphargus(Crustacea, Amphipoda). ZOOL SCR 2017. [DOI: 10.1111/zsc.12252] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Teo Delić
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
| | - Vid Švara
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
| | | | - Peter Trontelj
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
| | - Cene Fišer
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
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Copilaș-Ciocianu D, Fišer C, Borza P, Balázs G, Angyal D, Petrusek A. Low intraspecific genetic divergence and weak niche differentiation despite wide ranges and extensive sympatry in two epigean Niphargus species (Crustacea: Amphipoda). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlw031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Esmaeili-Rineh S, Mirghaffari SA, Sharifi M. The description of a new species of Niphargus from Iran based on morphological and molecular data. SUBTERRANEAN BIOLOGY 2017. [DOI: 10.3897/subtbiol.22.11286] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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28
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Bruce NL, Brix S, Balfour N, Kihara TC, Weigand AM, Mehterian S, Iliffe TM. A new genus for Cirolana troglexuma Botosaneanu & Iliffe, 1997, an anchialine cave dwelling cirolanid isopod (Crustacea, Isopoda, Cirolanidae) from the Bahamas. SUBTERRANEAN BIOLOGY 2017. [DOI: 10.3897/subtbiol.21.11181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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FiŠer C, Konec M, Alther R, Švara V, Altermatt F. Taxonomic, phylogenetic and ecological diversity of Niphargus (Amphipoda: Crustacea) in the Hölloch cave system (Switzerland). SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1249112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Cene FiŠer
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Marjeta Konec
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 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
| | - Vid Švara
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - 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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Drastic underestimation of amphipod biodiversity in the endangered Irano-Anatolian and Caucasus biodiversity hotspots. Sci Rep 2016; 6:22507. [PMID: 26928527 PMCID: PMC4772388 DOI: 10.1038/srep22507] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/16/2016] [Indexed: 11/17/2022] Open
Abstract
Biodiversity hotspots are centers of biological diversity and particularly threatened by anthropogenic activities. Their true magnitude of species diversity and endemism, however, is still largely unknown as species diversity is traditionally assessed using morphological descriptions only, thereby ignoring cryptic species. This directly limits evidence-based monitoring and management strategies. Here we used molecular species delimitation methods to quantify cryptic diversity of the montane amphipods in the Irano-Anatolian and Caucasus biodiversity hotspots. Amphipods are ecosystem engineers in rivers and lakes. Species diversity was assessed by analysing two genetic markers (mitochondrial COI and nuclear 28S rDNA), compared with morphological assignments. Our results unambiguously demonstrate that species diversity and endemism is dramatically underestimated, with 42 genetically identified freshwater species in only five reported morphospecies. Over 90% of the newly recovered species cluster inside Gammarus komareki and G. lacustris; 69% of the recovered species comprise narrow range endemics. Amphipod biodiversity is drastically underestimated for the studied regions. Thus, the risk of biodiversity loss is significantly greater than currently inferred as most endangered species remain unrecognized and/or are only found locally. Integrative application of genetic assessments in monitoring programs will help to understand the true magnitude of biodiversity and accurately evaluate its threat status.
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Delić T, Trontelj P, Zakšek V, Fišer C. Biotic and abiotic determinants of appendage length evolution in a cave amphipod. J Zool (1987) 2016. [DOI: 10.1111/jzo.12318] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- T. Delić
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
| | - P. Trontelj
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
- Museum für Naturkunde; Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin; Berlin Germany
| | - V. Zakšek
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
| | - C. Fišer
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
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