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Kisekelwa T, Snoeks J, Decru E, Schedel FBD, Isumbisho M, Vreven E. A mismatch between morphological and molecular data in lineages of Enteromius (Cypriniformes: Cyprinidae) from the Lowa basin (East Democratic Republic of the Congo: DRC) with the description of a new species. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2135630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Tchalondawa Kisekelwa
- Centre of Research in Biodiversity, Ecology, Evolution and Conservation (CRBEC), DRC
- Département de Biologie-Chimie, Unité d’Enseignement et de Recherche en Hydrobiologie Appliquée, Institut Supérieur Pédagogique (ISP) of Bukavu, Bukavu, 854, DRC
- 3Vertebrates section, Ichthyology, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, Tervuren, 3080, Belgium
- Biology Department, Fish Diversity and Conservation, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
| | - Jos Snoeks
- 3Vertebrates section, Ichthyology, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, Tervuren, 3080, Belgium
- Biology Department, Fish Diversity and Conservation, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
| | - Eva Decru
- 3Vertebrates section, Ichthyology, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, Tervuren, 3080, Belgium
- Biology Department, Fish Diversity and Conservation, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
| | - Frederic B. D. Schedel
- Zoological Institute, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, Großhaderner Straße 2, Planegg-Martinsried, 82152, Germany
| | - Mwapu Isumbisho
- Département de Biologie-Chimie, Unité d’Enseignement et de Recherche en Hydrobiologie Appliquée, Institut Supérieur Pédagogique (ISP) of Bukavu, Bukavu, 854, DRC
| | - Emmanuel Vreven
- 3Vertebrates section, Ichthyology, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, Tervuren, 3080, Belgium
- Biology Department, Fish Diversity and Conservation, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
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van den Berg-Stein S, Hahn HJ, Thielsch A, Schwenk K. Diversity and dispersal of aquatic invertebrate species from surface and groundwater: Development and application of microsatellite markers for the detection of hydrological exchange processes. WATER RESEARCH 2022; 210:117956. [PMID: 35032894 DOI: 10.1016/j.watres.2021.117956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Groundwater is one of our most important resources, however groundwater ecosystems are among the most understudied habitats of the planet earth. Studies on groundwater organisms are hampered by the difficult accessibility of species, the lack of morphological differentiation and the limitation for laboratory cultures. One important approach to overcome these shortcomings is to provide sensitive genetic methods to unravel patterns of biodiversity, population structure and gene flow in natural populations. In this study we present five sets of microsatellite markers developed for the isopods Asellus aquaticus and Proasellus slavus, the cyclopoides Paracyclops fimbriatus and Acanthocyclops sensitivus and the harpacticoide Bryocamptus echinatus (Crustacea). Two of these species were subjected to detailed population genetic analyses: We studied 501 specimens of Asellus aquaticus from four different regions in Northern Germany using nine microsatellite markers and 70 specimens of Bryocamptus echinatus using nine microsatellite markers from three different sampling sites in South-Western Germany. Our results show that genetic diversity is high (A. aquaticus: 10 to 20 and B. echinatus: 4 to 18 alleles per locus) among populations of aquatic invertebrates, populations are highly differentiated (FST > 0.2) and genetic differentiation was associated with geographic patterns. Applications of molecular genetic methods and their use for the detection of hydrological exchange processes relevant for drinking water suppliers are demonstrated and discussed.
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Affiliation(s)
- Susanne van den Berg-Stein
- Molecular Ecology, Institute for Environmental Sciences (iES), University of Koblenz-Landau, Campus Landau, Fortstraße 7, Landau/Pfalz 76829, Germany; Institute for Groundwater Ecology IGÖ GmbH, University of Koblenz-Landau, Campus Landau, Fortstraße 7, Landau/Pfalz 76829, Germany.
| | - Hans Jürgen Hahn
- Molecular Ecology, Institute for Environmental Sciences (iES), University of Koblenz-Landau, Campus Landau, Fortstraße 7, Landau/Pfalz 76829, Germany; Institute for Groundwater Ecology IGÖ GmbH, University of Koblenz-Landau, Campus Landau, Fortstraße 7, Landau/Pfalz 76829, Germany
| | - Anne Thielsch
- Molecular Ecology, Institute for Environmental Sciences (iES), University of Koblenz-Landau, Campus Landau, Fortstraße 7, Landau/Pfalz 76829, Germany
| | - Klaus Schwenk
- Molecular Ecology, Institute for Environmental Sciences (iES), University of Koblenz-Landau, Campus Landau, Fortstraße 7, Landau/Pfalz 76829, Germany
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A new species rises from beneath Florida: molecular phylogenetic analyses reveal cryptic diversity among the metapopulation of Crangonyx hobbsi Shoemaker, 1941 (Amphipoda: Crangonyctidae). ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-020-00433-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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4
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Dumnicka E, Galas J, Najberek K, Urban J. The influence of Pleistocene glaciations on the distribution of obligate aquatic subterranean invertebrate fauna in Poland. ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2020.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ecophysiological and life-history adaptations of Gammarus balcanicus (Schäferna, 1922) in a sinking-cave stream from Western Carpathians (Romania). ZOOLOGY 2020; 139:125754. [PMID: 32088526 DOI: 10.1016/j.zool.2020.125754] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 12/12/2019] [Accepted: 01/27/2020] [Indexed: 11/21/2022]
Abstract
Freshwater gammarids are known to colonise occasionally sinking-cave streams, providing contrasting morphological, life-history and ecophysiological adaptations compared to their surface conspecifics. In this study, a subterranean and a surface population of the species Gammarus balcanicus was surveyed for one year in a sinking-cave stream from the Western Carpathians (Romania). The results showed that the cave-dwelling population comprised individuals that were significantly larger compared to their surface conspecifics, had larger body-size at sexual maturity and that the females produced fewer, but larger eggs, compared to the population situated outside the cave. The trophic position and the omnivory were significantly higher for the cave-dwelling compared to surface population and the elemental imbalance for C:P molar ratios lower, but similar for C:N. However, the subterranean population did not present troglomorphic characters or longer lifespan as known for other cave-surface paired crustaceans. This, together with the rather extensive hydrological connection of the habitats, suggests active gene-flow between populations and similar response to seasonality for body-size distributions, indicating that the observed ecophysiological and life-history differences are rather the consequence of phenotypic plasticity than the result of genetic adaptation.
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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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Saccò M, Blyth A, Bateman PW, Hua Q, Mazumder D, White N, Humphreys WF, Laini A, Griebler C, Grice K. New light in the dark - a proposed multidisciplinary framework for studying functional ecology of groundwater fauna. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 662:963-977. [PMID: 30795483 DOI: 10.1016/j.scitotenv.2019.01.296] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/12/2019] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
Groundwaters provide the vast majority of unfrozen freshwater resources on the planet, but our knowledge of subsurface ecosystems is surprisingly limited. Stygofauna, or stygobionts -subterranean obligate aquatic animals - provide ecosystem services such as grazing biofilms and maintaining water quality, but we know little about how their ecosystems function. The cryptic nature of groundwaters, together with the high degree of local endemism and stygofaunal site-specific adaptations, represent major obstacles for the field. To overcome these challenges, and integrate biodiversity and ecosystem function, requires a holistic design drawing on classical ecology, taxonomy, molecular ecology and geochemistry. This study presents an approach based on the integration of existing concepts in groundwater ecology with three more novel scientific techniques: compound specific stable isotope analysis (CSIA) of amino acids, radiocarbon analysis (14C) and DNA analyses of environmental samples, stygofauna and gut contents. The combination of these techniques allows elucidation of aspects of ecosystem function that are often obscured in small invertebrates and cryptic systems. Carbon (δ13C) and nitrogen (δ15N) CSIA provides a linkage between biogeochemical patterns and ecological dynamics. It allows the identification of stygofaunal food web structures and energy flows based on the metabolic pathway of specific amino groups. Concurrently, 14C provides complementary data on the carbon recycling and incorporation within the stygobiotic trophic webs. Changes in groundwater environmental conditions (e.g. aquifer recharge), and subsequent community adaptations, can be pinpointed via the measurementof the radiocarbon fingerprint of water, sediment and specimens. DNA analyses are a rapidly expanding approach in ecology. eDNA is mainly employed as a biomonitoring tool, while metabarcoding of individuals and/or gut contents provides insight into diet regimes. In all cases, the application of the approaches in combination provides more powerful data than any one alone. By combining quantitative (CSIA and 14C) and qualitative (eDNA and DNA metabarcoding) approaches via Bayesian Mixing Models (BMM), linkages can be made between community composition, energy and nutrient sources in the system, and trophic function. This suggested multidisciplinary design will contribute to a more thorough comprehension of the biogeochemical and ecological patterns within these undervalued but essential ecosystems.
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Affiliation(s)
- Mattia Saccò
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, 6102, WA, Australia.
| | - Alison Blyth
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, 6102, WA, Australia
| | - Philip W Bateman
- School of Molecular and Life Sciences, Curtin University, Perth, 6102, WA, Australia
| | - Quan Hua
- Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Debashish Mazumder
- Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Nicole White
- School of Molecular and Life Sciences, Curtin University, Perth, 6102, WA, Australia
| | - William F Humphreys
- Collections and Research Centre, Western Australian Museum, Welshpool, WA 6986, Australia; School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Alex Laini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale G.P. Usberti 33/A, 43124 Parma, Italy
| | - Christian Griebler
- Helmholtz Center Munich, Institute of Groundwater Ecology, Neuherberg, Germany; University of Vienna, Dept of Limnology and Bio-Oceanography, Vienna, Austria
| | - Kliti Grice
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, 6102, WA, Australia
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Pârvulescu L, Pérez‐Moreno JL, Panaiotu C, Drăguț L, Schrimpf A, Popovici I, Zaharia C, Weiperth A, Gál B, Schubart CD, Bracken‐Grissom H. A journey on plate tectonics sheds light on European crayfish phylogeography. Ecol Evol 2019; 9:1957-1971. [PMID: 30847085 PMCID: PMC6392496 DOI: 10.1002/ece3.4888] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 12/08/2018] [Accepted: 12/14/2018] [Indexed: 12/03/2022] Open
Abstract
Crayfish can be used as model organisms in phylogeographic and divergence time studies if reliable calibrations are available. This study presents a comprehensive investigation into the phylogeography of the European stone crayfish (Austropotamobius torrentium) and includes samples from previously unstudied sites. Two mitochondrial markers were used to reveal evolutionary relationships among haplogroups throughout the species' distributional range and to estimate the divergence time by employing both substitution rates and geological calibration methods. Our haplotype network reconstruction and phylogenetic analyses revealed the existence of a previously unknown haplogroup distributed in Romania's Apuseni Mountains. This haplogroup is closely related to others that are endemic in the Dinarides, despite their vast geographical separation (~600 km). The separation is best explained by the well-dated tectonic displacement of the Tisza-Dacia microplate, which started in the Miocene (~16 Ma) and possibly carried part of the A. torrentium population to the current location of the Apuseni Mountains. This population may thus have been isolated from the Dinarides for a period of ca. 11 m.y. by marine and lacustrine phases of the Pannonian Basin. The inclusion of this geological event as a calibration point in divergence time analyses challenges currently accepted crayfish evolutionary time frames for the region, constraining the evolution of this area's crayfish to a much earlier date. We discuss why molecular clock calibrations previously employed to date European crayfish species divergences should therefore be reconsidered.
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Affiliation(s)
- Lucian Pârvulescu
- Department of Biology‐Chemistry, Faculty of Chemistry, Biology, GeographyWest University of TimisoaraTimisoaraRomania
| | - Jorge L. Pérez‐Moreno
- Department of BiologyFlorida International University – Biscayne Bay CampusNorth MiamiFlorida
| | - Cristian Panaiotu
- Paleomagnetic Laboratory, Faculty of PhysicsUniversity of BucharestMagureleRomania
| | - Lucian Drăguț
- Department of Geography, Faculty of Chemistry, Biology, GeographyWest University of TimisoaraTimisoaraRomania
| | - Anne Schrimpf
- Institute for Environmental SciencesUniversity Koblenz‐LandauLandauGermany
| | - Ioana‐Diana Popovici
- Department of Biology‐Chemistry, Faculty of Chemistry, Biology, GeographyWest University of TimisoaraTimisoaraRomania
- Institute for Environmental SciencesUniversity Koblenz‐LandauLandauGermany
| | - Claudia Zaharia
- Department of Mathematics, Faculty of Mathematics and Computer ScienceWest University of TimisoaraTimisoaraRomania
| | - András Weiperth
- MTA Centre for Ecological Research, Danube Research InstituteBudapestHungary
| | - Blanka Gál
- MTA Centre for Ecological Research, Danube Research InstituteBudapestHungary
- Doctoral School of Environmental SciencesEötvös Loránd UniversityBudapestHungary
| | - Christoph D. Schubart
- Department of Zoology and Evolutionary BiologyUniversity of RegensburgRegensburgGermany
| | - Heather Bracken‐Grissom
- Department of BiologyFlorida International University – Biscayne Bay CampusNorth MiamiFlorida
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Zagmajster M, Malard F, Eme D, Culver DC. Subterranean Biodiversity Patterns from Global to Regional Scales. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/978-3-319-98852-8_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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10
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Yasser AG, Sheldon F, Hughes JM. Spatial distributions and environmental relationships of two species complexes of freshwater atyid shrimps. Ecosphere 2018. [DOI: 10.1002/ecs2.2388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- A. Gh. Yasser
- Australian Rivers Institute; Griffith University; 170 Kessels Road Nathan Queensland 4111 Australia
| | - F. Sheldon
- Australian Rivers Institute; Griffith University; 170 Kessels Road Nathan Queensland 4111 Australia
| | - J. M. Hughes
- Australian Rivers Institute; Griffith University; 170 Kessels Road Nathan Queensland 4111 Australia
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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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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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Espíndola A, Ruffley M, Smith ML, Carstens BC, Tank DC, Sullivan J. Identifying cryptic diversity with predictive phylogeography. Proc Biol Sci 2017; 283:rspb.2016.1529. [PMID: 27798300 DOI: 10.1098/rspb.2016.1529] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/27/2016] [Indexed: 01/14/2023] Open
Abstract
Identifying units of biological diversity is a major goal of organismal biology. An increasing literature has focused on the importance of cryptic diversity, defined as the presence of deeply diverged lineages within a single species. While most discoveries of cryptic lineages proceed on a taxon-by-taxon basis, rapid assessments of biodiversity are needed to inform conservation policy and decision-making. Here, we introduce a predictive framework for phylogeography that allows rapidly identifying cryptic diversity. Our approach proceeds by collecting environmental, taxonomic and genetic data from codistributed taxa with known phylogeographic histories. We define these taxa as a reference set, and categorize them as either harbouring or lacking cryptic diversity. We then build a random forest classifier that allows us to predict which other taxa endemic to the same biome are likely to contain cryptic diversity. We apply this framework to data from two sets of disjunct ecosystems known to harbour taxa with cryptic diversity: the mesic temperate forests of the Pacific Northwest of North America and the arid lands of Southwestern North America. The predictive approach presented here is accurate, with prediction accuracies placed between 65% and 98.79% depending of the ecosystem. This seems to indicate that our method can be successfully used to address ecosystem-level questions about cryptic diversity. Further, our application for the prediction of the cryptic/non-cryptic nature of unknown species is easily applicable and provides results that agree with recent discoveries from those systems. Our results demonstrate that the transition of phylogeography from a descriptive to a predictive discipline is possible and effective.
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Affiliation(s)
- Anahí Espíndola
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA .,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
| | - Megan Ruffley
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA.,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
| | - Megan L Smith
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA.,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA.,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
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Niemiller ML, Porter ML, Keany J, Gilbert H, Fong DW, Culver DC, Hobson CS, Kendall KD, Davis MA, Taylor SJ. Evaluation of eDNA for groundwater invertebrate detection and monitoring: a case study with endangered Stygobromus (Amphipoda: Crangonyctidae). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0785-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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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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20
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Raschmanová N, Žurovcová M, Kováč Ľ, Paučulová L, Šustr V, Jarošová A, Chundelová D. The cold-adapted population ofFolsomia manolachei(Hexapoda, Collembola) from a glaciated karst doline of Central Europe: evidence for a cryptic species? J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12150] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Natália Raschmanová
- Institute of Biology and Ecology; Faculty of Science; P. J. Šafárik University; Košice Slovakia
| | - Martina Žurovcová
- Institute of Entomology; Biology Centre AS CR v. v. i.; České Budějovice Czech Republic
- Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Ľubomír Kováč
- Institute of Biology and Ecology; Faculty of Science; P. J. Šafárik University; Košice Slovakia
| | - Lenka Paučulová
- Institute of Biology and Ecology; Faculty of Science; P. J. Šafárik University; Košice Slovakia
| | - Vladimír Šustr
- Institute of Soil Biology; Biology Centre AS CR v. v. i.; České Budějovice Czech Republic
| | - Andrea Jarošová
- Institute of Entomology; Biology Centre AS CR v. v. i.; České Budějovice Czech Republic
- Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Daniela Chundelová
- Institute of Entomology; Biology Centre AS CR v. v. i.; České Budějovice Czech Republic
- Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
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21
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Mráz P, Ronikier M. Biogeography of the Carpathians: evolutionary and spatial facets of biodiversity. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12918] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Patrik Mráz
- Herbarium and Department of Botany; Charles University; Benátská 2 12801 Prague Czech Republic
| | - Michał Ronikier
- W. Szafer Institute of Botany; Polish Academy of Sciences; Lubicz 46 31-512 Kraków Poland
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22
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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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23
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Fišer Ž, Novak L, Luštrik R, Fišer C. Light triggers habitat choice of eyeless subterranean but not of eyed surface amphipods. Naturwissenschaften 2016; 103:7. [PMID: 26757929 DOI: 10.1007/s00114-015-1329-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 12/04/2015] [Accepted: 12/19/2015] [Indexed: 10/22/2022]
Abstract
Boundaries of species distributions are the result of colonization-extinction processes. Survival on the boundary depends on how well individuals discriminate optimal from suboptimal habitat patches. Such behaviour is called habitat choice and was only rarely applied to macroecology, although it links species ecological niche and species distribution. Surface and subterranean aquatic species are spatially strongly segregated, even in the absence of physical barriers. We explored whether a behavioural response to light functions as a habitat choice mechanism that could explain species turnover between surface and subterranean aquatic ecosystems. In a controlled laboratory experiment, we studied the behavioural response to light of ten pairs of surface and subterranean amphipods that permanently co-occur in springs. Surface species showed a weak photophobic, photoneutral, and in one case, photophilic response, whereas all subterranean species showed a strong photophobic response. Eyeless subterranean but not eyed surface amphipods appear to orient themselves with light cues. On a local scale, this difference possibly diminishes harmful interactions between the co-occurring amphipods, whereas on a regional scale, photophobia could explain limited dispersal and a high degree of endemism observed among subterranean species.
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Affiliation(s)
- Žiga Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, Slovenia.
| | - Luka Novak
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, Slovenia.
| | - Roman Luštrik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, Slovenia.
| | - Cene Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, Slovenia.
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24
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Dénes AL, Kolcsár LP, Török E, Keresztes L. Phylogeography of the micro-endemicPedicia staryigroup (Insecta: Diptera): evidence of relict biodiversity in the Carpathians. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12667] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Avar-Lehel Dénes
- Hungarian Department of Biology and Ecology; Faculty of Biology and Geology; Babeș-Bolyai University; Clinicilor 5-7 400006 Cluj-Napoca Romania
- Interdisciplinary Research Institute on Bio-Nano-Sciences of Babeş-Bolyai University; Treboniu Laurian 42 400271 Cluj-Napoca Romania
| | - Levente-Péter Kolcsár
- Hungarian Department of Biology and Ecology; Faculty of Biology and Geology; Babeș-Bolyai University; Clinicilor 5-7 400006 Cluj-Napoca Romania
| | - Edina Török
- Hungarian Department of Biology and Ecology; Faculty of Biology and Geology; Babeș-Bolyai University; Clinicilor 5-7 400006 Cluj-Napoca Romania
- Romanian Academy, Institute of Biology; Splaiul Independenţei 296 060031 Bucureşti Romania
| | - Lujza Keresztes
- Hungarian Department of Biology and Ecology; Faculty of Biology and Geology; Babeș-Bolyai University; Clinicilor 5-7 400006 Cluj-Napoca Romania
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25
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Morphologically Cryptic Amphipod Species Are "Ecological Clones" at Regional but Not at Local Scale: A Case Study of Four Niphargus Species. PLoS One 2015; 10:e0134384. [PMID: 26226375 PMCID: PMC4520478 DOI: 10.1371/journal.pone.0134384] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/08/2015] [Indexed: 11/19/2022] Open
Abstract
Recent studies indicate that morphologically cryptic species may be ecologically more different than would be predicted from their morphological similarity and phylogenetic relatedness. However, in biodiversity research it often remains unclear whether cryptic species should be treated as ecologically equivalent, or whether detected differences have ecological significance. In this study, we assessed the ecological equivalence of four morphologically cryptic species of the amphipod genus Niphargus. All species live in a small, isolated area on the Istrian Peninsula in the NW Balkans. The distributional ranges of the species are partially overlapping and all species are living in springs. We reconstructed their ecological niches using morphological traits related to feeding, bioclimatic niche envelope and species’ preference for epi-hypogean habitats. The ecological meaning of differences in niches was evaluated using distributional data and co-occurrence frequencies. We show that the species comprise two pairs of sister species. All species differ from each other and the degree of differentiation is not related to phylogenetic relatedness. Moreover, low co-occurrence frequencies in sympatric zones imply present or past interspecific competition. This pattern suggests that species are not differentiated enough to reduce interspecific competition, nor ecologically equivalent to co-exist via neutral dynamics. We tentatively conclude that the question of ecological equivalence relates to the scale of the study: at a fine scale, species’ differences may influence dynamics in a local community, whereas at the regional level these species likely play roughly similar ecological roles.
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26
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Esmaeili-Rineh S, Sari A, Delić T, Moškrič A, Fišer C. Molecular phylogeny of the subterranean genusNiphargus(Crustacea: Amphipoda) in the Middle East: a comparison with European Niphargids. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12296] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Somayeh Esmaeili-Rineh
- Department of Biology, Faculty of Science; Razi University of Kermanshah; Kermanshah Iran
| | - Alireza Sari
- Department of Animal Biology; School of Biology and Centre of Excellence in Phylogeny of Living Organisms; University of Tehran; Tehran Iran
| | - Teo Delić
- Department of Biology; Biotechnical Faculty, University of Ljubljana; Jamnikarjeva 101 SI-1000 Ljubljana Slovenia
| | - Ajda Moškrič
- Department of Biology; Biotechnical Faculty, University of Ljubljana; Jamnikarjeva 101 SI-1000 Ljubljana Slovenia
| | - Cene Fišer
- Department of Biology; Biotechnical Faculty, University of Ljubljana; Jamnikarjeva 101 SI-1000 Ljubljana Slovenia
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27
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Angyal D, Balázs G, Zakšek V, Krízsik V, Fišer C. Redescription of two subterranean amphipods Niphargusmolnari Méhely, 1927 and Niphargusgebhardti Schellenberg, 1934 (Amphipoda, Niphargidae) and their phylogenetic position. Zookeys 2015; 509:53-85. [PMID: 26175603 PMCID: PMC4493343 DOI: 10.3897/zookeys.509.9820] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/09/2015] [Indexed: 11/15/2022] Open
Abstract
A detailed redescription of two endemic, cave-dwelling niphargid species of the Hungarian Mecsek Mts., Niphargusmolnari Méhely, 1927 and Niphargusgebhardti Schellenberg, 1934 is given based on newly collected material. Morphology was studied under light microscopy and with scanning electon microscopy. Morphological descriptions are complemented with mitochondrial cytochrome c oxidase subunit I (COI) sequences as barcodes for both species and with notes on their ecology. Using three independent molecular markers we showed that Niphargusgebhardti belongs to the clade distributed between Central and Eastern Europe, whereas phylogenetic relationship of Niphargusmolnari to the rest of Niphargus species is not clear. The two species from the Mecsek Mts. are phylogenetically not closely related. Both species need to be treated as vulnerable according to IUCN Red List of Threatened Species.
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Affiliation(s)
- Dorottya Angyal
- Department of Zoology, Hungarian Natural History Museum, Baross u. 13, 1088 Budapest, Hungary
- Doctoral School of Animal-and Agricultural Environmental Sciences, Department of Animal Sciences and Animal Husbandry, Georgikon Faculty, University of Pannonia, Deák Ferenc u. 16, 8360 Keszthely, Hungary
| | - Gergely Balázs
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Valerija Zakšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Virág Krízsik
- Laboratory of Molecular Taxonomy, Hungarian Natural History Museum, Ludovika tér 2, 1083 Budapest, Hungary
| | - Cene Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
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28
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Phylogeny and biogeography of three new species of Niphargus (Crustacea: Amphipoda) from Greece. ZOOL ANZ 2015. [DOI: 10.1016/j.jcz.2015.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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