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Benito JB, Porter ML, Niemiller ML. Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae. BMC Genomics 2024; 25:298. [PMID: 38509489 PMCID: PMC10956265 DOI: 10.1186/s12864-024-10111-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 02/09/2024] [Indexed: 03/22/2024] Open
Abstract
Mitochondrial genomes play important roles in studying genome evolution, phylogenetic analyses, and species identification. Amphipods (Class Malacostraca, Order Amphipoda) are one of the most ecologically diverse crustacean groups occurring in a diverse array of aquatic and terrestrial environments globally, from freshwater streams and lakes to groundwater aquifers and the deep sea, but we have a limited understanding of how habitat influences the molecular evolution of mitochondrial energy metabolism. Subterranean amphipods likely experience different evolutionary pressures on energy management compared to surface-dwelling taxa that generally encounter higher levels of predation and energy resources and live in more variable environments. In this study, we compared the mitogenomes, including the 13 protein-coding genes involved in the oxidative phosphorylation (OXPHOS) pathway, of surface and subterranean amphipods to uncover potentially different molecular signals of energy metabolism between surface and subterranean environments in this diverse crustacean group. We compared base composition, codon usage, gene order rearrangement, conducted comparative mitogenomic and phylogenomic analyses, and examined evolutionary signals of 35 amphipod mitogenomes representing 13 families, with an emphasis on Crangonyctidae. Mitogenome size, AT content, GC-skew, gene order, uncommon start codons, location of putative control region (CR), length of rrnL and intergenic spacers differed between surface and subterranean amphipods. Among crangonyctid amphipods, the spring-dwelling Crangonyx forbesi exhibited a unique gene order, a long nad5 locus, longer rrnL and rrnS loci, and unconventional start codons. Evidence of directional selection was detected in several protein-encoding genes of the OXPHOS pathway in the mitogenomes of surface amphipods, while a signal of purifying selection was more prominent in subterranean species, which is consistent with the hypothesis that the mitogenome of surface-adapted species has evolved in response to a more energy demanding environment compared to subterranean amphipods. Overall, gene order, locations of non-coding regions, and base-substitution rates points to habitat as an important factor influencing the evolution of amphipod mitogenomes.
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Affiliation(s)
- Joseph B Benito
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Megan L Porter
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA.
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Premate E, Fišer C. Functional trait dataset of European groundwater Amphipoda: Niphargidae and Typhlogammaridae. Sci Data 2024; 11:188. [PMID: 38341425 PMCID: PMC10858915 DOI: 10.1038/s41597-024-03020-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Groundwater represents a vast, but mostly hidden and inaccessible ecosystem. Although often overlooked in freshwater research, groundwater organisms form a significant part of freshwater biodiversity, whereas their functions are crucial in different ecosystem processes. Knowledge on functional traits is generally lacking for most groundwater species worldwide, yet European groundwater amphipods, particularly the family Niphargidae, are an exception. They are well-researched and used as a model system in ecological and evolutionary studies. We focused on this group to assemble a first functional trait dataset dedicated to groundwater species. We gathered data for eight morphological functional traits quantified through 27 measurements for 1123 individuals which represent 180 species and 314 MOTUs. Besides functional trait data, every entry is accompanied with locality information, including habitat type, and DNA sequences if available. The structure of the dataset and data processing information provided along enable wide applicability and extension to other amphipod taxa. When coupled with phylogeny, the dataset may further enhance different aspects of groundwater research, including biodiversity patterns, community assembly processes, and trait evolution.
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Grants
- PhD grant Javna Agencija za Raziskovalno Dejavnost RS (Slovenian Research Agency)
- Program P1-0184 Javna Agencija za Raziskovalno Dejavnost RS (Slovenian Research Agency)
- J1-2464 Javna Agencija za Raziskovalno Dejavnost RS (Slovenian Research Agency)
- Biodiversa+ (grant number 101052342): co-funded by the European Commission and with the funding organizations Ministry of Universities and Research (Italy), Agencia Estatal de Investigación—Fundación Biodiversidad (Spain), Fundo Regional para a Ciência e Tecnologia (Portugal), Suomen Akatemia—Ministry of the Environment (Finland), Belgian Science Policy Office (Belgium), Agence Nationale de la Recherche (France), Deutsche Forschungsgemeinschaft e.V. –BMBF-VDI/ VDE INNOVATION + TECHNIK GMBH (Germany), Schweizerischer Nationalfonds zur Forderung der Wissenschaftlichen Forschung (Switzerland), Fonds zur Förderung der Wissenschaftlichen Forschung (Austria), Ministry of Higher Education, Science and Innovation (Slovenia) and the Executive Agency for Higher Education, Research, Development and Innovation Funding (Romania)
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Affiliation(s)
- Ester Premate
- University of Ljubljana, Biotechnical Faculty, Department of Biology, SubBioLab, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia.
| | - Cene Fišer
- University of Ljubljana, Biotechnical Faculty, Department of Biology, SubBioLab, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
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3
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Iwasa-Arai T, Siqueira SGL, Sobral-Souza T, Leite FPP, Andrade SCS. Continent-island boundary and environment-shaped evolution in the marine amphipod Ampithoe marcuzzii complex (Crustacea: Eumalacostraca: Ampithoidae). Sci Rep 2024; 14:608. [PMID: 38182880 PMCID: PMC10770051 DOI: 10.1038/s41598-023-51049-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024] Open
Abstract
Marine amphipods are crustaceans that lack a larval phase and consequently have low dispersion rates. Despite that, these crustaceans present a remarkable ability to be transported by rafting on natural floating substrata, especially macroalgae, where they find shelter, food and a mating ground. The species Ampithoe marcuzzii is widely distributed throughout the western Atlantic Ocean. Here, it was used as a model to study seascape genomics and phylogeography in invertebrates with low dispersion capacities. We anticipated that the lineages would present isolation-by-distance patterns. However, surface currents and other abiotic variables could facilitate connectivity among distant sites. Based on mitochondrial and nuclear genes, SNPs, and environmental associations, we observed the presence of a species complex within A. marcuzzii, separating mainland and insular populations. Each species showed an independent evolutionary history, with a strong latitudinal population structure and evidence of isolation-by-distance and isolation-by-environment, characterizing the 'continent' species. Historical expansion and environmental variables were observed associated with the southeastern population, and ecological niche modeling corroborated the region as a paleorefuge. Conversely, populations from 'islands' presented complicated evolutionary histories, with closer localities genetically isolated and distant localities connected. These findings indicate that insular populations with low dispersion capacity might be more susceptible to spatial connectivity by floating substrata and to changes in surface currents. In contrast, mainland populations might be more vulnerable to local climate changes due to lack of gene flow.
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Affiliation(s)
- Tammy Iwasa-Arai
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil.
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
| | - Silvana G L Siqueira
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Thadeu Sobral-Souza
- Departamento de Botânica e Ecologia, Universidade Federal do Mato Grosso, Cuiabá, Brazil
| | - Fosca P P Leite
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Degli Esposti D, Lalouette A, Gaget K, Lepeule L, Chaabi Z, Leprêtre M, Espeyte A, Delorme N, Quéau H, Garnero L, Calevro F, Chaumot A, Geffard O. Identification and organ-specific patterns of expression of two metallothioneins in the sentinel species Gammarus fossarum. Comp Biochem Physiol B Biochem Mol Biol 2024; 269:110907. [PMID: 37827361 DOI: 10.1016/j.cbpb.2023.110907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/05/2023] [Accepted: 10/08/2023] [Indexed: 10/14/2023]
Abstract
Metal pollution is a major concern for aquatic environments. Widespread contamination by various trace metal ions has been described in freshwater streams as well as their subsequent bioaccumulation, potentially leading to toxicity and trophic transfer. Metallothioneins constitute an evolutionary conserved family of low molecular weight, cysteine-rich, metal-chelating proteins, whose known physiological functions are the maintenance of the homeostasis of essential metals, the detoxification of non-essential metals, and the protection against oxidative stress and free radicals. In this study, we identified two metallothionein-coding transcripts, mt1 and mt2, in the transcriptome of the amphipod Gammarus fossarum, a sentinel species widely used to assess the quality of watersheds. For the first time, we investigated the organ-specific patterns of expression of these two mt transcripts at the individual level in the gills and the caeca of this small crustacean. In silico analysis and experimental exposures to environmentally relevant concentrations of cadmium, zinc and silver showed that G. fossarum mt1 induction is stronger after Cd exposure compared to the other tested metals. G. fossarum mt1 was more significantly induced in the caeca than in the gills of exposed organisms for any metal exposure, while G. fossarum mt2 was, at least at the individual level, more inducible in the gills than in the caeca of G. fossarum exposed to Cd and Zn. Our results provide new genetic resources that will help to improve the understanding of metal homeostasis in this sentinel species.
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Affiliation(s)
- Davide Degli Esposti
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France.
| | - Auréline Lalouette
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Karen Gaget
- INRAE, INSA Lyon, BF2I, UMR 203, Université de Lyon, 69621 Villeurbanne, France
| | - Louveline Lepeule
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Zineb Chaabi
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Maxime Leprêtre
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Anabelle Espeyte
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Nicolas Delorme
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Hervé Quéau
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Laura Garnero
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Federica Calevro
- INRAE, INSA Lyon, BF2I, UMR 203, Université de Lyon, 69621 Villeurbanne, France
| | - Arnaud Chaumot
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
| | - Olivier Geffard
- INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France
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Couton M, Studer A, Hürlemann S, Locher N, Knüsel M, Alther R, Altermatt F. Integrating citizen science and environmental DNA metabarcoding to study biodiversity of groundwater amphipods in Switzerland. Sci Rep 2023; 13:18097. [PMID: 37872363 PMCID: PMC10593815 DOI: 10.1038/s41598-023-44908-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Groundwater is the physically largest freshwater ecosystem, yet one of the least explored habitats on earth, both because of accessing difficulties and the scarcity of the organisms inhabiting it. Here, we demonstrate how a two-fold approach provides complementary information on the occurrence and diversity of groundwater amphipods. Firstly, we used a citizen science approach in collaboration with municipal water providers who sampled groundwater organisms in their spring catchment boxes over multiple weeks, followed by DNA barcoding. Secondly, we collected four 10 L water samples at each site, in one sampling event, for environmental DNA (eDNA) metabarcoding. We found that citizen science was very effective in describing the distribution and abundance of groundwater amphipods. Although the single time-point of eDNA sampling did not detect as many amphipods, it allowed the assessment of the entire groundwater community, including microorganisms. By combining both methods, we found different amphipod species co-occurring with distinct sequences from the eDNA-metabarcoding dataset, representing mainly micro-eukaryotic species. We also found a distinct correlation between the diversity of amphipods and the overall biodiversity of groundwater organisms detected by eDNA at each site. We thus suggest that these approaches can be used to get a better understanding of subterranean biodiversity.
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Affiliation(s)
- Marjorie Couton
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.
| | - Angela Studer
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Samuel Hürlemann
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Nadine Locher
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Mara Knüsel
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Roman Alther
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
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Rand DM, Nunez JCB, Williams S, Rong S, Burley JT, Neil KB, Spierer AN, McKerrow W, Johnson DS, Raynes Y, Fayton TJ, Skvir N, Ferranti DA, Zeff MG, Lyons A, Okami N, Morgan DM, Kinney K, Brown BRP, Giblin AE, Cardon ZG. Parasite manipulation of host phenotypes inferred from transcriptional analyses in a trematode-amphipod system. Mol Ecol 2023; 32:5028-5041. [PMID: 37540037 PMCID: PMC10529729 DOI: 10.1111/mec.17093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/05/2023]
Abstract
Manipulation of host phenotypes by parasites is hypothesized to be an adaptive strategy enhancing parasite transmission across hosts and generations. Characterizing the molecular mechanisms of manipulation is important to advance our understanding of host-parasite coevolution. The trematode (Levinseniella byrdi) is known to alter the colour and behaviour of its amphipod host (Orchestia grillus) presumably increasing predation of amphipods which enhances trematode transmission through its life cycle. We sampled 24 infected and 24 uninfected amphipods from a salt marsh in Massachusetts to perform differential gene expression analysis. In addition, we constructed novel genomic tools for O. grillus including a de novo genome and transcriptome. We discovered that trematode infection results in upregulation of amphipod transcripts associated with pigmentation and detection of external stimuli, and downregulation of multiple amphipod transcripts implicated in invertebrate immune responses, such as vacuolar ATPase genes. We hypothesize that suppression of immune genes and the altered expression of genes associated with coloration and behaviour may allow the trematode to persist in the amphipod and engage in further biochemical manipulation that promotes transmission. The genomic tools and transcriptomic analyses reported provide new opportunities to discover how parasites alter diverse pathways underlying host phenotypic changes in natural populations.
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Affiliation(s)
- David M Rand
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
| | - Joaquin C B Nunez
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
| | - Shawn Williams
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Stephen Rong
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
| | - John T Burley
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
| | - Kimberly B Neil
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
| | - Adam N Spierer
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
| | - Wilson McKerrow
- Division of Applied Mathematics, Brown University, Providence, Rhode Island, USA
| | - David S Johnson
- Department of Biological Sciences, Virginia Institute of Marine Science, William & Mary, Gloucester Point, Virginia, USA
| | - Yevgeniy Raynes
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
| | - Thomas J Fayton
- University of Southern Mississippi, Hattiesburg, Mississippi, USA
- Cornell University, Ithaca, New York, USA
| | - Nicholas Skvir
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - David A Ferranti
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
| | - Maya Greenhill Zeff
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
| | - Amanda Lyons
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
| | - Naima Okami
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
| | - David M Morgan
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
| | | | - Bianca R P Brown
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
| | - Anne E Giblin
- Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Zoe G Cardon
- Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
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Kabus J, Cunze S, Dombrowski A, Karaouzas I, Shumka S, Jourdan J. Uncovering the Grinnellian niche space of the cryptic species complex Gammarus roeselii. PeerJ 2023; 11:e15800. [PMID: 37551343 PMCID: PMC10404395 DOI: 10.7717/peerj.15800] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 07/05/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND The discovery of cryptic species complexes within morphologically established species comes with challenges in the classification and handling of these species. We hardly know to what extent species within a species complex differ ecologically. Such knowledge is essential to assess the vulnerability of individual genetic lineages in the face of global change. The abiotic conditions, i.e., the Grinnellian niche that a genetic lineage colonizes, provides insights into how diverse the ecological requirements of each evolutionary lineage are within a species complex. MATERIAL AND METHODS We sampled the cryptic species complex of the amphipod Gammarus roeselii from Central Germany to Greece and identified genetic lineages based on cytochrome c oxidase subunit I (COI) barcoding. At the same time, we recorded various abiotic parameters and local pollution parameters using a series of in vitro assays to then characterize the Grinnellian niches of the morphospecies (i.e., Gammarus roeselii sensu lato) as well as each genetic lineage. Local pollution can be a significant factor explaining current and future distributions in times of increasing production and release of chemicals into surface waters. RESULTS We identified five spatially structured genetic lineages in our dataset that differed to varying degrees in their Grinnellian niche. In some cases, the niches were very similar despite the geographical separation of lineages, supporting the hypothesis of niche conservatism while being allopatrically separated. In other cases, we found a small niche that was clearly different from those of other genetic lineages. CONCLUSION The variable niches and overlaps of different dimensions make the G. roeselii species complex a promising model system to further study ecological, phenotypic and functional differentiation within this species complex. In general, our results show that the Grinnellian niches of genetically distinct molecular operational taxonomic units (MOTUs) within a cryptic species complex can differ significantly between each other, calling for closer inspection of cryptic species in a conservational and biodiversity context.
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Affiliation(s)
- Jana Kabus
- Department Aquatic Ecotoxicology, Johann Wolfgang Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Sarah Cunze
- Department of Integrative Parasitology and Zoophysiology, Johann Wolfgang Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Andrea Dombrowski
- Department Aquatic Ecotoxicology, Johann Wolfgang Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Ioannis Karaouzas
- Institute of Marine Biological Resources and Inland Waters, Hellenic Centre for Marine Research, Anavyssos, Greece
| | - Spase Shumka
- Faculty of Biotechnology and Food, Agricultural University of Tirana, Tirana, Albania
| | - Jonas Jourdan
- Department Aquatic Ecotoxicology, Johann Wolfgang Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany
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Bacela-Spychalska K, Wattier R, Teixeira M, Cordaux R, Quiles A, Grabowski M, Wroblewski P, Ovcharenko M, Grabner D, Weber D, Weigand AM, Rigaud T. Widespread infection, diversification and old host associations of Nosema Microsporidia in European freshwater gammarids (Amphipoda). PLoS Pathog 2023; 19:e1011560. [PMID: 37603557 PMCID: PMC10470943 DOI: 10.1371/journal.ppat.1011560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 08/31/2023] [Accepted: 07/14/2023] [Indexed: 08/23/2023] Open
Abstract
The microsporidian genus Nosema is primarily known to infect insects of economic importance stimulating high research interest, while other hosts remain understudied. Nosema granulosis is one of the formally described Nosema species infecting amphipod crustaceans, being known to infect only two host species. Our first aim was to characterize Nosema spp. infections in different amphipod species from various European localities using the small subunit ribosomal DNA (SSU) marker. Second, we aimed to assess the phylogenetic diversity, host specificity and to explore the evolutionary history that may explain the diversity of gammarid-infecting Nosema lineages by performing a phylogenetic reconstruction based on RNA polymerase II subunit B1 (RPB1) gene sequences. For the host species Gammarus balcanicus, we also analyzed whether parasites were in excess in females to test for sex ratio distortion in relation with Nosema infection. We identified Nosema spp. in 316 individuals from nine amphipod species being widespread in Europe. The RPB1-based phylogenetic reconstruction using newly reported sequences and available data from other invertebrates identified 39 haplogroups being associated with amphipods. These haplogroups clustered into five clades (A-E) that did not form a single amphipod-infecting monophyletic group. Closely related sister clades C and D correspond to Nosema granulosis. Clades A, B and E might represent unknown Nosema species infecting amphipods. Host specificity seemed to be variable with some clades being restricted to single hosts, and some that could be found in several host species. We show that Nosema parasite richness in gammarid hosts is much higher than expected, illustrating the advantage of the use of RPB1 marker over SSU. Finally, we found no hint of sex ratio distortion in Nosema clade A infecting G. balcanicus. This study shows that Nosema spp. are abundant, widespread and diverse in European gammarids. Thus, Nosema is as diverse in aquatic as in terrestrial hosts.
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Affiliation(s)
- Karolina Bacela-Spychalska
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Remi Wattier
- Laboratoire Biogéosciences, UMR CNRS 6282, Université de Bourgogne, Dijon, France
| | - Maria Teixeira
- Laboratoire Biogéosciences, UMR CNRS 6282, Université de Bourgogne, Dijon, France
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Adrien Quiles
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
- Laboratoire Biogéosciences, UMR CNRS 6282, Université de Bourgogne, Dijon, France
| | - Michal Grabowski
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Piotr Wroblewski
- Department of Ecology and Evolution of Parasitism, Witold Stefanski Institute of Parasitology, Polish Academy of Science, Warsaw, Poland
| | - Mykola Ovcharenko
- Department of Ecology and Evolution of Parasitism, Witold Stefanski Institute of Parasitology, Polish Academy of Science, Warsaw, Poland
- Institute of Biology and Earth Sciences, Pomeranian University in Slupsk, Slupsk, Poland
| | - Daniel Grabner
- Aquatic Ecology, University of Duisburg-Essen, Essen, Germany
- Centre for Water and Environmental Research, University of Duisburg-Essen, Essen, Germany
| | - Dieter Weber
- Senckenberg Deutsches Entomologisches Institut Müncheberg, Germany
- Musée National d’Histoire Naturelle Luxembourg, Luxembourg, Luxembourg
| | | | - Thierry Rigaud
- Laboratoire Biogéosciences, UMR CNRS 6282, Université de Bourgogne, Dijon, France
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9
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Botelho MT, Militão GG, Brinkmann M, Umbuzeiro GDA. Toxicity and mutagenicity studies of 6PPD-quinone in a marine invertebrate species and bacteria. Environ Mol Mutagen 2023; 64:335-341. [PMID: 37402651 DOI: 10.1002/em.22560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/06/2023]
Abstract
N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD-quinone), an oxidation product of the tire additive, 6PPD, has been associated with high mortality of salmonids (0.1 μg/L). The objective of this study was to determine the acute toxicity using neonates and mutagenicity (micronuclei in hemolymph of exposed adults) of 6PPD-quinone in the marine amphipod Parhyale hawaiensis. Also, we studied its mutagenicity in the Salmonella/microsome assay using five strains of Salmonella with and without metabolic system (rat liver S9, 5%). 6PPD-quinone did not present acute toxicity to P. hawaiensis from 31.25 to 500 μg/L. Micronuclei frequency increased after 96 h-exposure to 6PPD-quinone (250 and 500 μg/L) when compared to the negative control. 6PPD-quinone also showed a weak mutagenic effect for TA100 only in the presence of S9. We conclude that 6PPD-quinone is mutagenic to P. hawaiensis and weakly mutagenic to bacteria. Our work provides information for future risk assessment of the presence of 6PPD-quinone in the aquatic environment.
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Affiliation(s)
| | | | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Global Institute for Water Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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10
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Dischereit A, Wangensteen OS, Præbel K, Auel H, Havermans C. Using DNA Metabarcoding to Characterize the Prey Spectrum of Two Co-Occurring Themisto Amphipods in the Rapidly Changing Atlantic-Arctic Gateway Fram Strait. Genes (Basel) 2022; 13:2035. [PMID: 36360272 PMCID: PMC9690572 DOI: 10.3390/genes13112035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 07/30/2023] Open
Abstract
The two congeneric hyperiids Themisto libellula and T. abyssorum provide an important trophic link between lower and higher trophic levels in the rapidly changing Arctic marine ecosystem. These amphipods are characterized by distinct hydrographic affinities and are hence anticipated to be impacted differently by environmental changes, with major consequences for the Arctic food web. In this study, we applied DNA metabarcoding to the stomach contents of these Themisto species, to comprehensively reveal their prey spectra at an unprecedented-high-taxonomic-resolution and assess the regional variation in their diet across the Fram Strait. Both species feed on a wide variety of prey but their diet strongly differed in the investigated summer season, showing overlap for only a few prey taxa, such as calanoid copepods. The spatially structured prey field of T. libellula clearly differentiated it from T. abyssorum, of which the diet was mainly dominated by chaetognaths. Our approach also allowed the detection of previously overlooked prey in the diet of T. libellula, such as fish species and gelatinous zooplankton. We discuss the reasons for the differences in prey spectra and which consequences these may have in the light of ongoing environmental changes.
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Affiliation(s)
- Annkathrin Dischereit
- Helmholtz Young Investigator Group ARJEL, Functional Ecology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
- BreMarE—Bremen Marine Ecology, FB2, Universität Bremen, 28334 Bremen, Germany
| | - Owen S. Wangensteen
- Faculty for Biosciences, Fisheries and Economics, Norwegian College of Fishery Science, UiT the Arctic University of Norway, 9019 Tromsø, Norway
- Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBIO), University of Barcelona, 08007 Barcelona, Spain
| | - Kim Præbel
- Faculty for Biosciences, Fisheries and Economics, Norwegian College of Fishery Science, UiT the Arctic University of Norway, 9019 Tromsø, Norway
| | - Holger Auel
- BreMarE—Bremen Marine Ecology, FB2, Universität Bremen, 28334 Bremen, Germany
| | - Charlotte Havermans
- Helmholtz Young Investigator Group ARJEL, Functional Ecology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
- BreMarE—Bremen Marine Ecology, FB2, Universität Bremen, 28334 Bremen, Germany
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11
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Major KM, Weston DP, Wellborn GA, Lydy MJ, Poynton HC. Predicting Resistance: Quantifying the Relationship between Urban Development, Agricultural Pesticide Use, and Pesticide Resistance in a Nontarget Amphipod. Environ Sci Technol 2022; 56:14649-14659. [PMID: 36201633 DOI: 10.1021/acs.est.2c04245] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Resistance alleles within the voltage-gated sodium channel (vgsc) have been correlated with pyrethroid resistance in wild populations of the nontarget amphipod, Hyalella azteca from California (CA), U.S.A. In the present study, we expand upon the relationship between land use and the evolution of pesticide resistance in H. azteca to develop a quantitative methodology to target and screen novel populations for resistance allele genotypes in a previously uninvestigated region of the U.S. (New England: NE). By incorporating urban land development and toxicity-normalized agricultural pesticide use indices into our site selection, we successfully identified three amino acid substitutions associated with pyrethroid resistance. One of the resistance mutations has been described in H. azteca from CA (L925I). We present the remaining two (vgsc I936F and I936V) as novel pyrethroid-resistance alleles in H. azteca based on previous work in insects and elevated cyfluthrin resistance in one NE population. Our results suggest that urban pesticide use is a strong driver in the evolution of resistance alleles in H. azteca. Furthermore, our method for resistance allele screening provides an applied framework for detecting ecosystem impairment on a nationwide scale that can be incorporated into ecological risk assessment decisions.
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Affiliation(s)
- Kaley M Major
- School for the Environment, University of Massachusetts Boston, Boston, Massachusetts 02125, United States
| | - Donald P Weston
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Gary A Wellborn
- Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Michael J Lydy
- Center for Fisheries, Aquaculture and Aquatic Sciences and Department of Zoology, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Helen C Poynton
- School for the Environment, University of Massachusetts Boston, Boston, Massachusetts 02125, United States
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12
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Drozdova P, Saranchina A, Madyarova E, Gurkov A, Timofeyev M. Experimental Crossing Confirms Reproductive Isolation between Cryptic Species within Eulimnogammarus verrucosus (Crustacea: Amphipoda) from Lake Baikal. Int J Mol Sci 2022; 23:ijms231810858. [PMID: 36142769 PMCID: PMC9506054 DOI: 10.3390/ijms231810858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/26/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Ancient lakes are known speciation hotspots. One of the most speciose groups in the ancient Lake Baikal are gammaroid amphipods (Crustacea: Amphipoda: Gammaroidea). There are over 350 morphological species and subspecies of amphipods in Baikal, but the extent of cryptic variation is still unclear. One of the most common species in the littoral zone of the lake, Eulimnogammarus verrucosus (Gerstfeldt, 1858), was recently found to comprise at least three (pseudo)cryptic species based on molecular data. Here, we further explored these species by analyzing their mitogenome-based phylogeny, genome sizes with flow cytometry, and their reproductive compatibility. We found divergent times of millions of years and different genome sizes in the three species (6.1, 6.9 and 8 pg), further confirming their genetic separation. Experimental crossing of the western and southern species, which are morphologically indistinguishable and have adjacent ranges, showed their separation with a post-zygotic reproductive barrier, as hybrid embryos stopped developing roughly at the onset of gastrulation. Thus, the previously applied barcoding approach effectively indicated the separate biological species within E. verrucosus. These results provide new data for investigating genome evolution and highlight the need for precise tracking of the sample origin in any studies in this morphospecies.
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Affiliation(s)
- Polina Drozdova
- Institute of Biology, Irkutsk State University, 664025 Irkutsk, Russia
- Baikal Research Centre, 664011 Irkutsk, Russia
- Correspondence: (P.D.); (M.T.)
| | | | | | - Anton Gurkov
- Institute of Biology, Irkutsk State University, 664025 Irkutsk, Russia
- Baikal Research Centre, 664011 Irkutsk, Russia
| | - Maxim Timofeyev
- Institute of Biology, Irkutsk State University, 664025 Irkutsk, Russia
- Baikal Research Centre, 664011 Irkutsk, Russia
- Correspondence: (P.D.); (M.T.)
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13
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Pinheiro MLS, Nagamachi CY, Ribas TFA, Diniz CG, O´Brien PCM, Ferguson-Smith MA, Yang F, Pieczarka JC. Chromosomal painting in Charadrius collaris Vieillot, 1818 and Vanellus chilensis Molina, 1782 and an analysis of chromosomal signatures in Charadriiformes. PLoS One 2022; 17:e0272836. [PMID: 35947613 PMCID: PMC9365183 DOI: 10.1371/journal.pone.0272836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/27/2022] [Indexed: 11/19/2022] Open
Abstract
Charadriiformes represent one of the largest orders of birds; members of this order are diverse in morphology, behavior and reproduction, making them an excellent model for studying evolution. It is accepted that the avian putative ancestral karyotype, with 2n = 80, remains conserved for about 100 million years. So far, only a few species of Charadriiformes have been studied using molecular cytogenetics. Here, we performed chromosome painting on metphase chromosomes of two species of Charadriidae, Charadrius collaris and Vanellus chilensis, with whole chromosome paint probes from Burhinus oedicnemus. Charadrius collaris has a diploid number of 76, with both sex chromosomes being submetacentric. In V. chilensi a diploid number of 78 was identified, and the Z chromosome is submetacentric. Chromosome painting suggests that chromosome conservation is a characteristic common to the family Charadriidae. The results allowed a comparative analysis between the three suborders of Charadriiformes and the order Gruiformes using chromosome rearrangements to understand phylogenetic relationships between species and karyotypic evolution. However, the comparative analysis between the Charadriiformes suborders so far has not revealed any shared rearrangements, indicating that each suborder follows an independent evolutionary path, as previously proposed. Likewise, although the orders Charadriiformes and Gruiformes are placed on sister branches, they do not share any signature chromosomal rearrangements.
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Affiliation(s)
- Melquizedec Luiz Silva Pinheiro
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Talita Fernanda Augusto Ribas
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Cristovam Guerreiro Diniz
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal do Pará, Campus de Bragança, Bragança, Pará, Brazil
| | - Patricia Caroline Mary O´Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Malcolm Andrew Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Fengtang Yang
- Cytogenetics Facility, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
- * E-mail:
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14
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Chan J, Geng D, Pan B, Zhang Q, Xu Q. Gut Microbial Divergence Between Three Hadal Amphipod Species from the Isolated Hadal Trenches. Microb Ecol 2022; 84:627-637. [PMID: 34545412 DOI: 10.1007/s00248-021-01851-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Amphipods are the dominant scavenging metazoan species in the hadal trenches at water depths below 6,000 m. The gut microbiota have been considered to be contribution to the adaptation of deep-sea organisms; however, few comparative analyses of animal gut microbiota between different isolated hadal environments have been done so far. Here, we employed high-throughput 16S rRNA sequencing to compare the gut microbial taxonomic composition and functional potential diversity of three hadal amphipod species, Hirondellea gigas, Bathycallisoma schellenbergi, and Alicella gigantea, collected from the Mariana Trench, Marceau Trench, and New Britain Trench in the Pacific Ocean, respectively. Results showed that different community compositions were detected across all the amphipod specimens based on the analyses of alpha-diversity, hierarchical cluster tree, and PCoA (principal coordinate analysis). Moreover, almost no correlation was observed between genera overrepresented in different amphipods by microbe-microbe correlations analysis, which suggested that the colonization of symbionts were host-specific. At genus level, Psychromonas was dominant in H. gigas, and Candidatus Hepatoplasma was overall dominant in A. gigantea and B. schellenbergi. Comparison of the functional potential showed that, though three hadal amphipod species shared the same predominant functional pathways, the abundances of those most shared pathways showed distinct differences across all the specimens. These findings pointed to the enrichment of particular functional pathways in the gut microbiota of the different isolated trench amphipods. Moreover, in terms of species relative abundance, alpha-diversity and beta-diversity, there was high similarity of gut microbiota between the two A. gigantea populations, which dwelled in two different localities of the same hadal trench. Altogether, this study provides an initial investigation into the gut-microbial interactions and evolution at the hadal depths within amphipod. Each of these three amphipod species would be a model taxa for future studies investigating the influence habitat difference and geography on gut-microbial communities.
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Affiliation(s)
- Jiulin Chan
- Shanghai Engineering Research Center of Hadal Science & Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
| | - Daoqiang Geng
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
| | - Binbin Pan
- Shanghai Engineering Research Center of Hadal Science & Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
| | - Qiming Zhang
- Shanghai Rainbowfish Ocean Technology Co., Ltd., Lingang New City, Shanghai, 201306, People's Republic of China
| | - Qianghua Xu
- Shanghai Engineering Research Center of Hadal Science & Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China.
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China.
- National Distant-water Fisheries Engineering Research Center, Shanghai Ocean University, Shanghai, 201306, People's Republic of China.
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15
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McAndry C, Collins M, Tills O, Spicer JI, Truebano M. Regulation of gene expression during ontogeny of physiological function in the brackishwater amphipod Gammarus chevreuxi. Mar Genomics 2022; 63:100948. [PMID: 35427917 DOI: 10.1016/j.margen.2022.100948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 10/18/2022]
Abstract
Embryonic development is a complex process involving the co-ordinated onset and integration of multiple morphological features and physiological functions. While the molecular basis of morphological development in embryos is relatively well known for traditional model species, the molecular underpinning of the development of physiological functions is not. Here, we used global gene expression profiling to investigate the transcriptional changes associated with the development of morphological and physiological function in the amphipod crustacean Gammarus chevreuxi. We compared the transcriptomes at three timepoints during the latter half of development, characterised by different stages of the development of heart form and function: 10 days post fertilisation (dpf, Early: no heart structure visible), 15 dpf (Middle: heart present but not fully functional), and 18 dpf (Late: regular heartbeat). Gene expression profiles differed markedly between developmental stages, likely representing a change in the activity of different processes throughout the latter period of G. chevreuxi embryonic development. Differentially expressed genes belonged to one of three distinct clusters based on their expression patterns across development. One of these clusters, which included key genes relating to cardiac contractile machinery and calcium handling, displayed a pattern of sequential up-regulation throughout the developmental period studied. Further analyses of these transcripts could reveal genes that may influence the onset of a regular heartbeat. We also identified morphological and physiological processes that may occur alongside heart development, such as development of digestive caeca and the cuticle. Elucidating the mechanisms underpinning morphological and physiological development of non-model organisms will support improved understanding of conserved mechanisms, addressing the current phylogenetic gap between relatively well known model species.
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Affiliation(s)
- C McAndry
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - M Collins
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - O Tills
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - J I Spicer
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - M Truebano
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK.
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16
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Walters AD, Trujillo DA, Berg DJ. Micro-endemic species of snails and amphipods show population genetic structure across very small geographic ranges. Heredity (Edinb) 2022; 128:325-337. [PMID: 35318433 PMCID: PMC9076663 DOI: 10.1038/s41437-022-00521-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 11/08/2022] Open
Abstract
Understanding variation in population genetic structure, even across small distances and for species with extremely limited ranges, is critical for conservation planning and the development of effective management strategies for imperiled species. Organisms that occupy the same geographic extent can maintain different population structures, ranging from highly diverged to panmictic. Such differences can result from differences in biological characteristics such as dispersal ability or demographic history. We used microsatellite loci to evaluate population genetic structure and variation of four desert spring invertebrates having high to low dispersal ability: the lung snail Physa acuta, two species of gilled snails (Juturnia kosteri and Pyrgulopsis roswellensis; family Hydrobiidae) and the amphipod Gammarus desperatus. The study location represents entire species ranges for the micro-endemic hydrobiids and G. desperatus, while P. acuta is ubiquitous throughout much of North America. We found little evidence of significant population genetic structure for P. acuta and J. kosteri, but much more for P. roswellensis and G. desperatus. Our results demonstrate differences in habitat preference and/or dispersal ability between the species. This information provides insight into how gene flow shapes varying population genetic structure between species across small spatial scales (<100 km2). Most importantly, our results suggest that conservation agencies should not consider these micro-endemic species to be composed of single populations, but rather, that management plans for such species should account for population genetic variation across the species' ranges.
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Affiliation(s)
| | | | - David J Berg
- Department of Biology, Miami University, Hamilton, OH, USA
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17
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Mamos T, Jażdżewski K, Čiamporová-Zaťovičová Z, Čiampor F, Grabowski M. Fuzzy species borders of glacial survivalists in the Carpathian biodiversity hotspot revealed using a multimarker approach. Sci Rep 2021; 11:21629. [PMID: 34732763 PMCID: PMC8566499 DOI: 10.1038/s41598-021-00320-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/08/2021] [Indexed: 11/21/2022] Open
Abstract
The Carpathians are one of the key biodiversity hotspots in Europe. The mountain chain uplifted during Alpine orogenesis and is characterised by a complex geological history. Its current biodiversity was highly influenced by Pleistocene glaciations. The goal of the current study was to examine the phylogenetic and demographic history of Gammarus balcanicus species complex in the Carpathians using multiple markers as well as to delimit, using an integrative approach, and describe new species hidden so far under the name G. balcanicus. Results showed that divergence of the studied lineages reaches back to the Miocene, which supports the hypothesis of their survival in multiple micro refugia. Moreover, the increase of their diversification rate in the Pleistocene suggests that glaciation was the driving force of their speciation. The climatic changes during and after the Pleistocene also played a major role in the demography of the local Carpathian lineages. Comparison of diversity patterns and phylogenetic relationships of both, the mitochondrial and nuclear markers, provide evidence of putative hybridisation and retention of ancient polymorphism (i.e., incomplete lineage sorting). The morphological examination supported the existence of two morphological types; one we describe as a G. stasiuki sp. nov. and another we redescribe as a G. tatrensis (S. Karaman, 1931).
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Affiliation(s)
- Tomasz Mamos
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland.
| | - Krzysztof Jażdżewski
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland
| | - Zuzana Čiamporová-Zaťovičová
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovakia
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Fedor Čiampor
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovakia
| | - Michał Grabowski
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland
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18
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Fung CY, Zhu KY, Major K, Poynton HC, Huff Hartz KE, Wellborn G, Lydy MJ. The contribution of detoxification pathways to pyrethroid resistance in Hyalella azteca. Environ Pollut 2021; 284:117158. [PMID: 33895574 DOI: 10.1016/j.envpol.2021.117158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/28/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Chronic exposure to pyrethroid insecticides can result in strong selective pressures on non-target species in aquatic systems and drive the evolution of resistance and population-level changes. Characterizing the underlying mechanisms of resistance is essential to better understanding the potential consequences of contaminant-driven microevolution. The current study found that multiple mechanisms enhance the overall tolerance of Hyalella azteca to the pyrethroid permethrin. In H. azteca containing mutations in the voltage-gated sodium channel (VGSC), both adaptation and acclimation played a role in mitigating the adverse effects of pyrethroid exposures. Pyrethroid resistance is primarily attributed to the heritable mutation at a single locus of the VGSC, resulting in reduced target-site sensitivity. However, additional pyrethroid tolerance was conferred through enhanced enzyme-mediated detoxification. Cytochrome P450 monooxygenases (CYP450) and general esterases (GE) significantly contributed to the detoxification of permethrin in H. azteca. Over time, VGSC mutated H. azteca retained most of their pyrethroid resistance, though there was some increased sensitivity from parent to offspring when reared in the absence of pyrethroid exposure. Permethrin median lethal concentrations (LC50s) declined from 1809 ng/L in parent (P0) individuals to 1123 ng/L in the first filial (F1) generation, and this reduction in tolerance was likely related to alterations in acclimation mechanisms, rather than changes to target-site sensitivity. Enzyme bioassays indicated decreased CYP450 and GE activity from P0 to F1, whereas the VGSC mutation was retained. The permethrin LC50s in resistant H. azteca were still two orders-of-magnitude higher than non-resistant populations indicating that the largest proportion of resistance was maintained through the inherited VGSC mutation. Thus, the noted variation in tolerance in H. azteca is likely associated with inducible traits controlling enzyme pathways. A better understanding of the mechanistic and genomic basis of acclimation is necessary to more accurately predict the ecological and evolutionary consequences of contaminant-driven change in H. azteca.
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Affiliation(s)
- Courtney Y Fung
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Department of Zoology, Southern Illinois University, Carbondale, Illinois, 62901, USA.
| | - Kun Yan Zhu
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Kaley Major
- School for the Environment, University of Massachusetts, Boston, Massachusetts, 02125, USA.
| | - Helen C Poynton
- School for the Environment, University of Massachusetts, Boston, Massachusetts, 02125, USA.
| | - Kara E Huff Hartz
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Department of Zoology, Southern Illinois University, Carbondale, Illinois, 62901, USA.
| | - Gary Wellborn
- Department of Biology, University of Oklahoma, Norman, OK, 73019, USA.
| | - Michael J Lydy
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Department of Zoology, Southern Illinois University, Carbondale, Illinois, 62901, USA.
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19
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Drozdova P, Kizenko A, Saranchina A, Gurkov A, Firulyova M, Govorukhina E, Timofeyev M. The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae). BMC Ecol Evol 2021; 21:81. [PMID: 33971810 PMCID: PMC8108468 DOI: 10.1186/s12862-021-01806-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/20/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Vision is a crucial sense for the evolutionary success of many animal groups. Here we explore the diversity of visual pigments (opsins) in the transcriptomes of amphipods (Crustacea: Amphipoda) and conclude that it is restricted to middle (MWS) and long wavelength-sensitive (LWS) opsins in the overwhelming majority of examined species. RESULTS We evidenced (i) parallel loss of MWS opsin expression in multiple species (including two independently evolved lineages from the deep and ancient Lake Baikal) and (ii) LWS opsin amplification (up to five transcripts) in both Baikal lineages. The number of LWS opsins negatively correlated with habitat depth in Baikal amphipods. Some LWS opsins in Baikal amphipods contained MWS-like substitutions, suggesting that they might have undergone spectral tuning. CONCLUSIONS This repeating two-step evolutionary scenario suggests common triggers, possibly the lack of light during the periods when Baikal was permanently covered with thick ice and its subsequent melting. Overall, this observation demonstrates the possibility of revealing climate history by following the evolutionary changes in protein families.
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Affiliation(s)
- Polina Drozdova
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
| | | | | | - Anton Gurkov
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
| | - Maria Firulyova
- Computer Technologies Department, ITMO University, St. Petersburg, Russia
| | | | - Maxim Timofeyev
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
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20
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Švara V, Krauss M, Michalski SG, Altenburger R, Brack W, Luckenbach T. Chemical Pollution Levels in a River Explain Site-Specific Sensitivities to Micropollutants within a Genetically Homogeneous Population of Freshwater Amphipods. Environ Sci Technol 2021; 55:6087-6096. [PMID: 33852288 DOI: 10.1021/acs.est.0c07839] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Anthropogenic micropollutants alter chemical and ecological conditions of freshwater ecosystems and impact aquatic species that live along the pollution gradient of a river. Species sensitivity to micropollutants depends on the site-specific exposure; however, it remains unclear to what degree this sensitivity relates to the species' genetic structure. Here, we explored the relationship between the toxic sensitivity and genetic structure of the amphipod species Gammarus pulex (Linnaeus, 1758) along an organic micropollutant gradient in the Holtemme River in central Germany. We determined the river's site-specific micropollutant patterns and analyzed the genetic structure of G. pulex using nuclear and mitochondrial genetic markers. Furthermore, we examined the exposure sensitivities and bioaccumulation of the commonly detected insecticide imidacloprid in G. pulex from different sites. Our results show that throughout the Holtemme River, G. pulex forms a well-connected and homogeneous population with no observable pollution-related differences in the genetic structure. However, G. pulex from polluted sites responded more sensitively to imidacloprid; survival times for half of the amphipods were up to 54% shorter, the percentage of immobile individuals increased up to 65%, and the modeled imidacloprid depuration rate was lower in comparison to amphipods from non-polluted sites. Altogether, these results suggest that the level of sensitivity of G. pulex amphipods to micropollutants in the river depends on the degree of pollution: amphipods may thrive in food-rich but polluted habitats; yet, their sensitivity is increased when chronically exposed to organic micropollutants.
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Affiliation(s)
- Vid Švara
- Department of Effect-Directed Analysis, Helmholtz-Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
- Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - Martin Krauss
- Department of Effect-Directed Analysis, Helmholtz-Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Stefan G Michalski
- Department of Community Ecology, Helmholtz-Centre for Environmental Research - UFZ, Theodor-Lieser-Straße 4, 06120 Halle, Germany
| | - Rolf Altenburger
- Department of Bioanalytical Ecotoxicology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
- Department of Ecosystem Analysis, Institute for Environmental Research (Biology V), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Werner Brack
- Department of Effect-Directed Analysis, Helmholtz-Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
- Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - Till Luckenbach
- Department of Bioanalytical Ecotoxicology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
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21
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Ribes-Navarro A, Navarro JC, Hontoria F, Kabeya N, Standal IB, Evjemo JO, Monroig Ó. Biosynthesis of Long-Chain Polyunsaturated Fatty Acids in Marine Gammarids: Molecular Cloning and Functional Characterisation of Three Fatty Acyl Elongases. Mar Drugs 2021; 19:226. [PMID: 33923820 PMCID: PMC8073319 DOI: 10.3390/md19040226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Long-chain (C20-24) polyunsaturated fatty acids (LC-PUFAs) are essential nutrients that are mostly produced in marine ecosystems. Previous studies suggested that gammarids have some capacity to endogenously produce LC-PUFAs. This study aimed to investigate the repertoire and functions of elongation of very long-chain fatty acid (Elovl) proteins in gammarids. Our results show that gammarids have, at least, three distinct elovl genes with putative roles in LC-PUFA biosynthesis. Phylogenetics allowed us to classify two elongases as Elovl4 and Elovl6, as they were bona fide orthologues of vertebrate Elovl4 and Elovl6. Moreover, a third elongase was named as "Elovl1/7-like" since it grouped closely to the Elovl1 and Elovl7 found in vertebrates. Molecular analysis of the deduced protein sequences indicated that the gammarid Elovl4 and Elovl1/7-like were indeed polyunsaturated fatty acid (PUFA) elongases, whereas Elovl6 had molecular features typically found in non-PUFA elongases. This was partly confirmed in the functional assays performed on the marine gammarid Echinogammarus marinus Elovl, which showed that both Elovl4 and Elovl1/7-like elongated PUFA substrates ranging from C18 to C22. E. marinus Elovl6 was only able to elongate C18 PUFA substrates, suggesting that this enzyme does not play major roles in the LC-PUFA biosynthesis of gammarids.
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Affiliation(s)
- Alberto Ribes-Navarro
- Instituto de Acuicultura de Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain; (A.R.-N.); (J.C.N.); (F.H.)
| | - Juan C. Navarro
- Instituto de Acuicultura de Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain; (A.R.-N.); (J.C.N.); (F.H.)
| | - Francisco Hontoria
- Instituto de Acuicultura de Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain; (A.R.-N.); (J.C.N.); (F.H.)
| | - Naoki Kabeya
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato, Tokyo 108-8477, Japan;
| | - Inger B. Standal
- Department of Fisheries and New Biomarine Industry, SINTEF Ocean, 7010 Trondheim, Norway; (I.B.S.); (J.O.E.)
| | - Jan O. Evjemo
- Department of Fisheries and New Biomarine Industry, SINTEF Ocean, 7010 Trondheim, Norway; (I.B.S.); (J.O.E.)
| | - Óscar Monroig
- Instituto de Acuicultura de Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain; (A.R.-N.); (J.C.N.); (F.H.)
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22
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Zapelloni F, Jurado-Rivera JA, Jaume D, Juan C, Pons J. Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea). Genes (Basel) 2021; 12:genes12020292. [PMID: 33669879 PMCID: PMC7923271 DOI: 10.3390/genes12020292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 02/02/2023] Open
Abstract
We present the sequencing and comparative analysis of 17 mitochondrial genomes of Nearctic and Neotropical amphipods of the genus Hyalella, most from the Andean Altiplano. The mitogenomes obtained comprised the usual 37 gene-set of the metazoan mitochondrial genome showing a gene rearrangement (a reverse transposition and a reversal) between the North and South American Hyalella mitogenomes. Hyalella mitochondrial genomes show the typical AT-richness and strong nucleotide bias among codon sites and strands of pancrustaceans. Protein-coding sequences are biased towards AT-rich codons, with a preference for leucine and serine amino acids. Numerous base changes (539) were found in tRNA stems, with 103 classified as fully compensatory, 253 hemi-compensatory and the remaining base mismatches and indels. Most compensatory Watson–Crick switches were AU -> GC linked in the same haplotype, whereas most hemi-compensatory changes resulted in wobble GU and a few AC pairs. These results suggest a pairing fitness increase in tRNAs after crossing low fitness valleys. Branch-site level models detected positive selection for several amino acid positions in up to eight mitochondrial genes, with atp6 and nad5 as the genes displaying more sites under selection.
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Affiliation(s)
- Francesco Zapelloni
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7,5, 07122 Palma, Spain; (F.Z.); (J.A.J.-R.); (C.J.)
| | - José A. Jurado-Rivera
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7,5, 07122 Palma, Spain; (F.Z.); (J.A.J.-R.); (C.J.)
| | - Damià Jaume
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/Miquel Marquès 21, 07190 Esporles, Spain;
| | - Carlos Juan
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7,5, 07122 Palma, Spain; (F.Z.); (J.A.J.-R.); (C.J.)
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/Miquel Marquès 21, 07190 Esporles, Spain;
| | - Joan Pons
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/Miquel Marquès 21, 07190 Esporles, Spain;
- Correspondence: ; Tel.: +34-971-173-332
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23
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Zapelloni F, Pons J, Jurado-Rivera JA, Jaume D, Juan C. Phylogenomics of the Hyalella amphipod species-flock of the Andean Altiplano. Sci Rep 2021; 11:366. [PMID: 33431936 PMCID: PMC7801522 DOI: 10.1038/s41598-020-79620-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
Species diversification in ancient lakes has enabled essential insights into evolutionary theory as they embody an evolutionary microcosm compared to continental terrestrial habitats. We have studied the high-altitude amphipods of the Andes Altiplano using mitogenomic, nuclear ribosomal and single-copy nuclear gene sequences obtained from 36 Hyalella genomic libraries, focusing on species of the Lake Titicaca and other water bodies of the Altiplano northern plateau. Results show that early Miocene South American lineages have recently (late Pliocene or early Pleistocene) diversified in the Andes with a striking morphological convergence among lineages. This pattern is consistent with the ecological opportunities (access to unoccupied resources, initial relaxed selection on ecologically-significant traits and low competition) offered by the lacustrine habitats established after the Andean uplift.
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Affiliation(s)
- Francesco Zapelloni
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7'5, 07122, Palma de Mallorca, Balearic Islands, Spain
| | - Joan Pons
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/ Miquel Marquès 21, 07190, Esporles, Balearic Islands, Spain
| | - José A Jurado-Rivera
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7'5, 07122, Palma de Mallorca, Balearic Islands, Spain
| | - Damià Jaume
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/ Miquel Marquès 21, 07190, Esporles, Balearic Islands, Spain
| | - Carlos Juan
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7'5, 07122, Palma de Mallorca, Balearic Islands, Spain.
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/ Miquel Marquès 21, 07190, Esporles, Balearic Islands, Spain.
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24
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Hupało K, Karaouzas I, Mamos T, Grabowski M. Molecular data suggest multiple origins and diversification times of freshwater gammarids on the Aegean archipelago. Sci Rep 2020; 10:19813. [PMID: 33188238 PMCID: PMC7666221 DOI: 10.1038/s41598-020-75802-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/07/2020] [Indexed: 11/09/2022] Open
Abstract
Our main aim was to investigate the diversity, origin and biogeographical affiliations of freshwater gammarids inhabiting the Aegean Islands by analysing their mtDNA and nDNA polymorphism, thereby providing the first insight into the phylogeography of the Aegean freshwater gammarid fauna. The study material was collected from Samothraki, Lesbos, Skyros, Evia, Andros, Tinos and Serifos islands as well as from mainland Greece. The DNA extracted was used for amplification of two mitochondrial (COI and 16S) and two nuclear markers (28S and EF1-alpha). The multimarker time-calibrated phylogeny supports multiple origins and different diversification times for the studied taxa. Three of the sampled insular populations most probably represent new, distinct species as supported by all the delimitation methods used in our study. Our results show that the evolution of freshwater taxa is associated with the geological history of the Aegean Basin. The biogeographic affiliations of the studied insular taxa indicate its continental origin, as well as the importance of the land fragmentation and the historical land connections of the islands. Based on the findings, we highlight the importance of studying insular freshwater biota to better understand diversification mechanisms in fresh waters as well as the origin of studied Aegean freshwater taxa.
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Affiliation(s)
- Kamil Hupało
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland.
- Aquatische Ökosystemforschung, Universität Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany.
| | - Ioannis Karaouzas
- Institute of Marine Biological Resources and Inland Waters, Hellenic Centre for Marine Research, 46.7 km Athens-Sounio Av., 19013, Anavyssos, Greece
| | - Tomasz Mamos
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Michał Grabowski
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland
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25
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Quiles A, Wattier RA, Bacela-Spychalska K, Grabowski M, Rigaud T. Dictyocoela microsporidia diversity and co-diversification with their host, a gammarid species complex (Crustacea, Amphipoda) with an old history of divergence and high endemic diversity. BMC Evol Biol 2020; 20:149. [PMID: 33176694 PMCID: PMC7659068 DOI: 10.1186/s12862-020-01719-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/04/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although the processes of co-evolution between parasites and their hosts are well known, evidence of co-speciation remains scarce. Microsporidian intracellular parasites, due to intimate relationships with their hosts and mixed mode of transmission (horizontal but also vertical, from mother to offspring), may represent an interesting biological model for investigating co-speciation. Amphipod crustaceans, especially gammarids, are regular hosts of microsporidian parasites, in particular the Dictyocoela spp., which have so far been found limited to these amphipods and are known to use a vertical mode of transmission. The amphipod genus Gammarus has a diversification history spanning the last 50-60 Mya and an extensive cryptic diversity in most of the nominal species. Here, we investigated the degree of co-diversification between Dictyocoela and Gammarus balcanicus, an amphipod with high degrees of ancient cryptic diversification and lineage endemism, by examining the genetic diversity of these parasites over the entire geographic range of the host. We hypothesised that the strong host diversification and vertical transmission of Dictyocoela would promote co-diversification. RESULTS Using the parasite SSU rDNA as a molecular marker, analyzing 2225 host specimens from 88 sites covering whole host range, we found 31 haplogroups of Dictyocoela, 30 of which were novel, belonging to four Dictyocoela species already known to infect other Gammarus spp. The relationships between Dictyocoela and gammarids is therefore ancient, with the speciation in parasites preceding those of the hosts. Each novel haplogroup was nevertheless specific to G. balcanicus, leaving the possibility for subsequent co-diversification process during host diversification. A Procrustean Approach to Co-phylogeny (PACo) analysis revealed that diversification of Dictyocoela was not random with respect to that of the host. We found high degrees of congruence between the diversification of G. balcanicus and that of Dictyocoela roeselum and D. muelleri. However, we also found some incongruences between host and Dictyocoela phylogenies, e.g. in D. duebenum, probably due to host shifts between different G. balcanicus cryptic lineages. CONCLUSION The evolutionary history of Dictyocoela and Gammarus balcanicus represents an example of an overall host-parasite co-diversification, including cases of host shifts.
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Affiliation(s)
- Adrien Quiles
- Université Bourgogne Franche-Comté, Laboratoire Biogéosciences, UMR CNRS 6282, 6 boulevard Gabriel, 21000, Dijon, France
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237, Łódź, Poland
| | - Rémi A Wattier
- Université Bourgogne Franche-Comté, Laboratoire Biogéosciences, UMR CNRS 6282, 6 boulevard Gabriel, 21000, Dijon, France
| | - Karolina Bacela-Spychalska
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237, Łódź, Poland
| | - Michal Grabowski
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237, Łódź, Poland
| | - Thierry Rigaud
- Université Bourgogne Franche-Comté, Laboratoire Biogéosciences, UMR CNRS 6282, 6 boulevard Gabriel, 21000, Dijon, France.
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26
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Park E, Poulin R. Widespread Torix Rickettsia in New Zealand amphipods and the use of blocking primers to rescue host COI sequences. Sci Rep 2020; 10:16842. [PMID: 33033309 PMCID: PMC7546637 DOI: 10.1038/s41598-020-73986-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/16/2020] [Indexed: 11/12/2022] Open
Abstract
Endosymbionts and intracellular parasites are common in arthropod hosts. As a consequence, (co)amplification of untargeted bacterial sequences has been occasionally reported as a common problem in DNA barcoding. While identifying amphipod species with universal COI primers, we unexpectedly detected rickettsial endosymbionts belonging to the Torix group. To map the distribution and diversity of Rickettsia species among amphipod hosts, we conducted a nationwide molecular screening of seven families of New Zealand freshwater amphipods. In addition to uncovering a diversity of Torix Rickettsia species across multiple amphipod populations from three different families, our research indicates that: (1) detecting Torix Rickettsia with universal primers is not uncommon, (2) obtaining 'Rickettsia COI sequences' from many host individuals is highly likely when a population is infected, and (3) obtaining 'host COI' may not be possible with a conventional PCR if an individual is infected. Because Rickettsia COI is highly conserved across diverse host taxa, we were able to design blocking primers that can be used in a wide range of host species infected with Torix Rickettsia. We propose the use of blocking primers to circumvent problems caused by unwanted amplification of Rickettsia and to obtain targeted host COI sequences for DNA barcoding, population genetics, and phylogeographic studies.
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Affiliation(s)
- Eunji Park
- Department of Zoology, University of Otago, 340 Great King Street, Dunedin, 9016, New Zealand.
| | - Robert Poulin
- Department of Zoology, University of Otago, 340 Great King Street, Dunedin, 9016, New Zealand
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27
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Burskaia V, Naumenko S, Schelkunov M, Bedulina D, Neretina T, Kondrashov A, Yampolsky L, Bazykin GA. Excessive Parallelism in Protein Evolution of Lake Baikal Amphipod Species Flock. Genome Biol Evol 2020; 12:1493-1503. [PMID: 32653919 DOI: 10.1093/gbe/evaa138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 11/12/2022] Open
Abstract
Repeated emergence of similar adaptations is often explained by parallel evolution of underlying genes. However, evidence of parallel evolution at amino acid level is limited. When the analyzed species are highly divergent, this can be due to epistatic interactions underlying the dynamic nature of the amino acid preferences: The same amino acid substitution may have different phenotypic effects on different genetic backgrounds. Distantly related species also often inhabit radically different environments, which makes the emergence of parallel adaptations less likely. Here, we hypothesize that parallel molecular adaptations are more prevalent between closely related species. We analyze the rate of parallel evolution in genome-size sets of orthologous genes in three groups of species with widely ranging levels of divergence: 46 species of the relatively recent lake Baikal amphipod radiation, a species flock of very closely related cichlids, and a set of significantly more divergent vertebrates. Strikingly, in genes of amphipods, the rate of parallel substitutions at nonsynonymous sites exceeded that at synonymous sites, suggesting rampant selection driving parallel adaptation. At sites of parallel substitutions, the intraspecies polymorphism is low, suggesting that parallelism has been driven by positive selection and is therefore adaptive. By contrast, in cichlids, the rate of nonsynonymous parallel evolution was similar to that at synonymous sites, whereas in vertebrates, this rate was lower than that at synonymous sites, indicating that in these groups of species, parallel substitutions are mainly fixed by drift.
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Affiliation(s)
- Valentina Burskaia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Moscow Oblast, Russia
| | - Sergey Naumenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Mikhail Schelkunov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Moscow Oblast, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
| | - Daria Bedulina
- Institute of Biology, Irkutsk State University, Russia
- Baikal Research Centre, Irkutsk, Russia
| | - Tatyana Neretina
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
- N.A. Pertsov White Sea Biological Station, Lomonosov Moscow State University, Primorskiy, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
| | - Alexey Kondrashov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
- Department of Ecology and Evolutionary Biology, University of Michigan
| | - Lev Yampolsky
- Department of Biological Sciences, East Tennessee State University
| | - Georgii A Bazykin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Moscow Oblast, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
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28
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Artal MC, Pereira KD, Luchessi AD, Okura VK, Henry TB, Marques-Souza H, de Aragão Umbuzeiro G. Transcriptome analysis in Parhyale hawaiensis reveal sex-specific responses to AgNP and AgCl exposure. Environ Pollut 2020; 260:113963. [PMID: 32004961 DOI: 10.1016/j.envpol.2020.113963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/09/2019] [Accepted: 01/09/2020] [Indexed: 06/10/2023]
Abstract
Analysis of the transcriptome of organisms exposed to toxicants offers new insights for ecotoxicology, but further research is needed to enhance interpretation of results and effectively incorporate them into useful environmental risk assessments. Factors that must be clarified to improve use of transcriptomics include assessment of the effect of organism sex within the context of toxicant exposure. Amphipods are well recognized as model organisms for toxicity evaluation because of their sensitivity and amenability to laboratory conditions. To investigate whether response to metals in crustaceans differs according to sex we analyzed the amphipod Parhyale hawaiensis after exposure to AgCl and Ag nanoparticles (AgNP) via contaminated food. Gene specific analysis and whole genome transcriptional profile of male and female organisms were performed by both RT-qPCR and RNA-seq. We observed that expression of transcripts of genes glutathione transferase (GST) did not differ among AgCl and AgNP treatments. Significant differences between males and females were observed after exposure to AgCl and AgNP. Males presented twice the number of differentially expressed genes in comparison to females, and more differentially expressed were observed after exposure to AgNP than AgCl treatments in both sexes. The genes that had the greatest change in expression relative to control were those genes related to peptidase and catalytic activity and chitin and carbohydrate metabolic processes. Our study is the first to demonstrate sex specific differences in the transcriptomes of amphipods upon exposure to toxicants and emphasizes the importance of considering gender in ecotoxicology.
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Affiliation(s)
- Mariana Coletty Artal
- School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, 05508-000, Brazil; School of Technology, University of Campinas, Limeira, São Paulo, 13484-332, Brazil
| | - Karina Danielle Pereira
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, São Paulo, 13484-350, Brazil; Institute of Biosciences, São Paulo State University, Rio Claro, São Paulo, 13506-900, Brazil
| | - Augusto Ducati Luchessi
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, São Paulo, 13484-350, Brazil; Institute of Biosciences, São Paulo State University, Rio Claro, São Paulo, 13506-900, Brazil
| | - Vagner Katsumi Okura
- Life Sciences Core Facility (LaCTAD), University of Campinas, Campinas, São Paulo, 13083-886, Brazil
| | - Theodore Burdick Henry
- Institute of Life and Earth Sciences, School of Energy, Geoscience, Infrastructure, and Society, Heriot-Watt University, EH14 4AS, Edinburgh, Scotland, UK; Center for Environmental Biotechnology, The University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN, 37996-1605, United States
| | - Henrique Marques-Souza
- Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo, 13083-970, Brazil.
| | - Gisela de Aragão Umbuzeiro
- School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, 05508-000, Brazil; School of Technology, University of Campinas, Limeira, São Paulo, 13484-332, Brazil.
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29
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Babin A, Motreuil S, Teixeira M, Bauer A, Rigaud T, Moreau J, Moret Y. Origin of the natural variation in the storage of dietary carotenoids in freshwater amphipod crustaceans. PLoS One 2020; 15:e0231247. [PMID: 32294101 PMCID: PMC7159244 DOI: 10.1371/journal.pone.0231247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 03/19/2020] [Indexed: 11/26/2022] Open
Abstract
Carotenoids are diverse lipophilic natural pigments which are stored in variable amounts by animals. Given the multiple biological functions of carotenoids, such variation may have strong implications in evolutionary biology. Crustaceans such as Gammarus amphipods store large amounts of these pigments and inter-population variation occurs. While differences in parasite selective pressure have been proposed to explain this variation, the contribution of other factors such as genetic differences in the gammarid ability to assimilate and/or store pigments, and the environmental availability of carotenoids cannot be dismissed. This study investigates the relative contributions of the gammarid genotype and of the environmental availability of carotenoids in the natural variability in carotenoid storage. It further explores the link of this natural variability in carotenoid storage with major crustacean immune parameters. We addressed these aspects using the cryptic diversity in the amphipod crustacean Gammarus fossarum and a diet supplementation protocol in the laboratory. Our results suggest that natural variation in G. fossarum storage of dietary carotenoids results from both the availability of the pigments in the environment and the genetically-based ability of the gammarids to assimilate and/or store them, which is associated to levels of stimulation of cellular immune defences. While our results may support the hypothesis that carotenoids storage in this crustacean may evolve in response to parasitic pressure, a better understanding of the specific roles of this large pigment storage in the crustacean physiology is needed.
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Affiliation(s)
- Aurélie Babin
- Equipe Ecologie Evolutive, UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
- * E-mail:
| | - Sébastien Motreuil
- Equipe Ecologie Evolutive, UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
| | - Maria Teixeira
- Equipe Ecologie Evolutive, UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
| | - Alexandre Bauer
- Equipe Ecologie Evolutive, UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
| | - Thierry Rigaud
- Equipe Ecologie Evolutive, UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
| | - Jérôme Moreau
- Equipe Ecologie Evolutive, UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
| | - Yannick Moret
- Equipe Ecologie Evolutive, UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
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Abstract
Crustacean amphipods are important trophic links between primary producers and higher consumers. Although most amphipods occur in or around aquatic environments, the family Talitridae is the only family found in terrestrial and semi-terrestrial habitats. The sand-hopper Trinorchestia longiramus is a talitrid species often found in the sandy beaches of South Korea. In this study, we present the first draft genome assembly and annotation of this species. We generated ~380.3 Gb of sequencing data assembled in a 0.89 Gb draft genome. Annotation analysis estimated 26,080 protein-coding genes, with 89.9% genome completeness. Comparison with other amphipods showed that T. longiramus has 327 unique orthologous gene clusters, many of which are expanded gene families responsible for cellular transport of toxic substances, homeostatic processes, and ionic and osmotic stress tolerance. This first talitrid genome will be useful for further understanding the mechanisms of adaptation in terrestrial environments, the effects of heavy metal toxicity, as well as for studies of comparative genomic variation across amphipods.
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Affiliation(s)
| | | | - Ji Yong Yoo
- National Marine Biodiversity Institute of Korea, Seocheon, 33662, South Korea
| | - Min Seop Kim
- National Marine Biodiversity Institute of Korea, Seocheon, 33662, South Korea
| | - Moon Geun Yoon
- National Marine Biodiversity Institute of Korea, Seocheon, 33662, South Korea
| | - Jeong-Hyeon Choi
- National Marine Biodiversity Institute of Korea, Seocheon, 33662, South Korea
| | - Youngik Yang
- National Marine Biodiversity Institute of Korea, Seocheon, 33662, South Korea.
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Iguchi A, Nishijima M, Yoshioka Y, Miyagi A, Miwa R, Tanaka Y, Kato S, Matsui T, Igarashi Y, Okamoto N, Suzuki A. Deep-sea amphipods around cobalt-rich ferromanganese crusts: Taxonomic diversity and selection of candidate species for connectivity analysis. PLoS One 2020; 15:e0228483. [PMID: 32027722 PMCID: PMC7004558 DOI: 10.1371/journal.pone.0228483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/16/2020] [Indexed: 11/21/2022] Open
Abstract
The aim of this study was to select a candidate deep-sea amphipod species suitable for connectivity analyses in areas around cobalt-rich ferromanganese crusts (CRCs). We applied DNA barcoding based on the mitochondrial protein-coding gene, cytochrome c oxidase subunit I (COI), to specimens collected from the Xufu Guyot (the JA06 Seamount) off southeastern Minami-Torishima Island in the North Pacific, where CRCs are distributed. We used baited traps to collect 37 specimens. Comparison of COI sequences with public reference databases (GenBank, BOLD) showed that almost all of the specimens belonged to the superfamily Lysianassoidea, which is known to be ubiquitous in deep-sea areas. In a molecular taxonomic analysis of these sequences, we detected 11 clades. One of these clades (group 9) composed of 18 sequences and was identified by DNA barcoding as a putative species belonging to Abyssorchomene, which has been reported from the New Hebrides Trench in the South Pacific. We considered this species to be a candidate for connectivity analysis and analyzed its genome by restriction site–associated DNA sequencing. The results showed that the genetic variation in this species is adequate for analyzing connectivity patterns in CRC areas in the future.
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Affiliation(s)
- Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, Nago-City, Okinawa, Japan
- * E-mail:
| | | | - Yuki Yoshioka
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, Nago-City, Okinawa, Japan
| | - Aika Miyagi
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, Nago-City, Okinawa, Japan
| | - Ryuichi Miwa
- Kaiyo Engineering Co., Ltd., Taito-ku, Tokyo, Japan
| | - Yuichiro Tanaka
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Shogo Kato
- Japan Oil, Gas and Metals National Corporation (JOGMEC), Minato-ku, Tokyo, Japan
| | - Takaaki Matsui
- Japan Oil, Gas and Metals National Corporation (JOGMEC), Minato-ku, Tokyo, Japan
| | - Yoshiaki Igarashi
- Japan Oil, Gas and Metals National Corporation (JOGMEC), Minato-ku, Tokyo, Japan
| | - Nobuyuki Okamoto
- Japan Oil, Gas and Metals National Corporation (JOGMEC), Minato-ku, Tokyo, Japan
| | - Atsushi Suzuki
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
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Gorokhova E, Martella G, Motwani NH, Tretyakova NY, Sundelin B, Motwani HV. DNA epigenetic marks are linked to embryo aberrations in amphipods. Sci Rep 2020; 10:655. [PMID: 31959811 PMCID: PMC6971077 DOI: 10.1038/s41598-020-57465-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 12/26/2019] [Indexed: 11/22/2022] Open
Abstract
Linking exposure to environmental stress factors with diseases is crucial for proposing preventive and regulatory actions. Upon exposure to anthropogenic chemicals, covalent modifications on the genome can drive developmental and reproductive disorders in wild populations, with subsequent effects on the population persistence. Hence, screening of chemical modifications on DNA can be used to provide information on the probability of such disorders in populations of concern. Using a high-resolution mass spectrometry methodology, we identified DNA nucleoside adducts in gravid females of the Baltic amphipods Monoporeia affinis, and linked the adduct profiles to the frequency of embryo malformations in the broods. Twenty-three putative nucleoside adducts were detected in the females and their embryos, and eight modifications were structurally identified using high-resolution accurate mass data. To identify which adducts were significantly associated with embryo malformations, partial least squares regression (PLSR) modelling was applied. The PLSR model yielded three adducts as the key predictors: methylation at two different positions of the DNA (5-methyl-2'-deoxycytidine and N6-methyl-2'-deoxyadenosine) representing epigenetic marks, and a structurally unidentified nucleoside adduct. These adducts predicted the elevated frequency of the malformations with a high classification accuracy (84%). To the best of our knowledge, this is the first application of DNA adductomics for identification of contaminant-induced malformations in field-collected animals. The method can be adapted for a broad range of species and evolve as a new omics tool in environmental health assessment.
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Affiliation(s)
- Elena Gorokhova
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, SE, 10691, Sweden
| | - Giulia Martella
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, SE, 10691, Sweden
| | - Nisha H Motwani
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, SE, 10691, Sweden
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Brita Sundelin
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, SE, 10691, Sweden
| | - Hitesh V Motwani
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, SE, 10691, Sweden.
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Fuller N, Smith JT, Ford AT. Impacts of ionising radiation on sperm quality, DNA integrity and post-fertilisation development in marine and freshwater crustaceans. Ecotoxicol Environ Saf 2019; 186:109764. [PMID: 31610356 DOI: 10.1016/j.ecoenv.2019.109764] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/27/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
Crustaceans have been designated as internationally important model organisms in the development of environmental radioprotection measures. Despite the known sensitivity of sperm to ionizing radiation, the impacts of chronic radiation exposure on male fertility in crustaceans have not been studied. For the first time, the present study aimed to assess the impacts of chronic radiation exposure on male fertility, sperm DNA damage and concomitant impacts on breeding in two amphipod crustaceans. Echinogammarus marinus and Gammarus pulex (male fertility only) were exposed to phosphorus-32 at dose rates of 0, 0.1, 1 and 10 mGy/d and sperm parameters, DNA damage and knock-on impacts on breeding were assessed. Sperm quality parameters and DNA damage were assessed using a fluorescent staining method and single cell gel electrophoresis respectively. Concomitant effects of male exposure to radiation on fecundity were determined by pairing phosphorus-32 exposed males to unexposed sexually mature females. In E. marinus, a statistically significant reduction of 9 and 11% in the quality of sperm was recorded at dose rates of 1 and 10 mGy/d respectively, with no significant effects recorded on sperm counts. Conversely in the freshwater G. pulex, no significant impact of radiation on sperm quantity or quality was recorded. For E. marinus, a statistically significant increase in DNA damage was recorded at doses of 10 mGy/d. Reduced fecundity and an increase in the frequency of abnormal embryos was recorded in female E. marinus breeding with males exposed to radiation. These findings suggest sperm quality may be a sensitive indicator of radiation exposure in invertebrates with potential impacts on the unexposed embryo, though unclear dose-response and differences between two closely related species necessitate further study before robust conclusions can be drawn.
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Affiliation(s)
- Neil Fuller
- Institute of Marine Sciences, School of Biological Sciences, University of Portsmouth, Ferry Road, Portsmouth, Hampshire, PO4 9LY, UK.
| | - Jim T Smith
- School of Earth & Environmental Sciences, University of Portsmouth, Burnaby Building, Burnaby Road, Portsmouth, Hampshire, PO1 3QL, UK
| | - Alex T Ford
- Institute of Marine Sciences, School of Biological Sciences, University of Portsmouth, Ferry Road, Portsmouth, Hampshire, PO4 9LY, UK.
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34
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Švara V, Norf H, Luckenbach T, Brack W, Michalski SG. Isolation and characterization of eleven novel microsatellite markers for fine-scale population genetic analyses of Gammarus pulex (Crustacea: Amphipoda). Mol Biol Rep 2019; 46:6609-6615. [PMID: 31552594 DOI: 10.1007/s11033-019-05077-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 09/13/2019] [Indexed: 11/25/2022]
Abstract
The freshwater amphipod species Gammarus pulex (Linnaeus, 1758) is widespread across Europe and Asia and is able to live in a broad range of environmental conditions. Yet, it is of great interest to which degree it is able to tolerate and adapt to the current rapid anthropogenic environmental changes affecting its habitat, such as pollution, changes in river morphology, and invasions of alien gammarid species. Microsatellite primers for genetic population studies with G. pulex have been developed but due to the existence of several genetically different lineages within the species, the application of these primers is not always successful. In order to investigate the impacts of anthropogenic environmental changes on the spatio-genetic patterns of G. pulex lineage E in streams in the Saale river catchment in Germany, we designed eleven novel polymorphic microsatellites for this lineage using a high-throughput sequencing approach. These microsatellites enabled highly specific characterization of three closely related populations. The results show genetically distinct populations reflected by both a principal coordinates analysis and an analysis of molecular variance. Several of the newly designed microsatellite primers also enabled successful cross-amplification of the respective microsatellites in specimens of G. pulex lineage C, while only two microsatellites were amplified successfully and showed polymorphisms for all of the analyzed specimens of G. fossarum Koch, 1836. The microsatellites identified here are suitable for future assessments of micro-evolutionary dynamics of G. pulex from central Germany.
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Affiliation(s)
- Vid Švara
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318, Leipzig, Germany.
- Department of Ecosystem Analysis, Institute for Environmental Research (Biology V), RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - Helge Norf
- State Office of Criminal Investigations Saxony-Anhalt, Lübecker Str. 53-63, 39124, Magdeburg, Germany
| | - Till Luckenbach
- Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Werner Brack
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318, Leipzig, Germany
- Department of Ecosystem Analysis, Institute for Environmental Research (Biology V), RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Stefan G Michalski
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Straße 4, 06120, Halle, Germany
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35
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Chan J, Pan B, Geng D, Zhang Q, Zhang S, Guo J, Xu Q. Genetic Diversity and Population Structure Analysis of Three Deep-Sea Amphipod Species from Geographically Isolated Hadal Trenches in the Pacific Ocean. Biochem Genet 2019; 58:157-170. [PMID: 31410625 DOI: 10.1007/s10528-019-09935-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 07/28/2019] [Indexed: 11/26/2022]
Abstract
Amphipods of the superfamily Lysianassoidea that inhabit the hadal zone ( > 6000 m) have large bathymetric ranges and play a key role in deep ocean ecosystems. The endemism of these amphipod species makes them a good model for investigating potent natural selection and restricted dispersal in deep ocean trenches. Here, we describe genetic diversity and intraspecific population differentiation among three amphipod species from four Pacific trenches based on a mtDNA concatenated dataset (CO Ι and 16S rRNA genes) from 150 amphipod individuals. All amphipod populations had low genetic diversity, as indicated by haplotype and nucleotide diversity values. Population geographic relationship analysis of two Alicella gigantea populations revealed no genetic differentiation between these two localities (pairwise genetic differentiation coefficient = 0.00032, gene flow = 784.58), and the major variation (99.97%) was derived from variation within the populations. Historical demographic events were investigated using Tajima's D and Fu's F neutrality tests and analysis of mismatch distribution. Consistent results provided strong evidence to support the premise that demographic expansion occurred only for the Mariana population of Hirondellea gigas, possibly within the last 2.1-3.4 million years. These findings suggest that the formation of amphipod population structure might be the result of multiple factors including high hydrostatic pressure, food distribution, trench topographic forcing and potential ecological interactions.
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Affiliation(s)
- Jiulin Chan
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
| | - Binbin Pan
- Shanghai Engineering Research Center of Hadal Science & Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Daoqiang Geng
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
| | - Qiming Zhang
- Shanghai Rainbowfish Ocean Technology Co., Ltd, Lingang New City, Shanghai, 201306, China
| | - Shun Zhang
- Shanghai Engineering Research Center of Hadal Science & Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Jian Guo
- Shanghai Engineering Research Center of Hadal Science & Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Qianghua Xu
- Shanghai Engineering Research Center of Hadal Science & Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China.
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China.
- National Distant-Water Fisheries Engineering Research Center, Shanghai Ocean University, Shanghai, 201306, China.
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Conradi M, Sánchez-Moyano JE, Galotti A, Jiménez-Gómez F, Jiménez-Melero R, Guerrero F, Parra G, Bonnail E, DelValls TÁ. CO 2 leakage simulation: Effects of the decreasing pH to the survival and reproduction of two crustacean species. Mar Pollut Bull 2019; 143:33-41. [PMID: 31789163 DOI: 10.1016/j.marpolbul.2019.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 04/04/2019] [Accepted: 04/06/2019] [Indexed: 06/10/2023]
Abstract
The effects of CO2-related acidification on two crustacean populations, the isopod Cyathura carinata and the amphipod Elasmopus rapax, were studied. Three pH levels were tested: artificial seawater without CO2 injection and two levels of reduced pH. Even though RNA:DNA ratio was reduced for both species, no statistical significant differences were found between the control and the treatments. Both species experienced a reduction in survivorship, longevity and the body length of surviving animals; although the impairment observed in E. rapax was more severe than in C. carinata. The long life span isopod and the short life span amphipod experienced a high degree of impairment in the reproduction, likely due to the reallocation of resources from reproduction to body maintenance and increasing survival by postponing the brood production. Regardless of the underlying processes and the energetic pathways, both experienced failure to reproduce, which could lead to the local extinction of these species.
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Affiliation(s)
- M Conradi
- Department of de Zoology, Faculty of Biology, University of Sevilla, Av. Reina Mercedes s/n, 41012 Sevilla, Spain
| | - J E Sánchez-Moyano
- Department of de Zoology, Faculty of Biology, University of Sevilla, Av. Reina Mercedes s/n, 41012 Sevilla, Spain
| | - A Galotti
- Department of Animal Biology, Plant Biology and Ecology, Centre of Advanced Studies in Earth Sciences, University of Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - F Jiménez-Gómez
- Department of Animal Biology, Plant Biology and Ecology, Centre of Advanced Studies in Earth Sciences, University of Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - R Jiménez-Melero
- Department of Animal Biology, Plant Biology and Ecology, Centre of Advanced Studies in Earth Sciences, University of Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - F Guerrero
- Department of Animal Biology, Plant Biology and Ecology, Centre of Advanced Studies in Earth Sciences, University of Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - G Parra
- Department of Animal Biology, Plant Biology and Ecology, Centre of Advanced Studies in Earth Sciences, University of Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - E Bonnail
- Centro de Investigaciones Costeras Universidad de Atacama (CIC-UDA), Universidad de Atacama, Copiapó, Atacama, Chile.
| | - T Á DelValls
- Department of Ecotoxicology, Santa Cecília University (UNISANTA), Santos, São Paulo, Brazil
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Li JY, Zeng C, Yan GY, He LS. Characterization of the mitochondrial genome of an ancient amphipod Halice sp. MT-2017 (Pardaliscidae) from 10,908 m in the Mariana Trench. Sci Rep 2019; 9:2610. [PMID: 30796230 PMCID: PMC6385184 DOI: 10.1038/s41598-019-38735-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 12/11/2018] [Indexed: 01/02/2023] Open
Abstract
Small amphipods (Halice sp. MT-2017) with body length <1 cm were collected from the Challenger Deep (~10,920 m below sea level). The divergence time of their lineage was approximately 109 Mya, making this group ancient compared to others under study. The mitochondrial genome of Halice sp. shared the usual gene components of metazoans, comprising 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs). The arrangement of these genes, however, differed greatly from that of other amphipods. Of the 15 genes that were rearranged with respect to the pancrustacean gene pattern, 12 genes (2 PCGs, 2 rRNAs, and 8 tRNAs) were both translocated and strand-reversed. In contrast, the mitochondrial genomes in other amphipods never show so many reordered genes, and in most instances, only tRNAs were involved in strand-reversion-coupled translocation. Other characteristics, including reversed strand nucleotide composition bias, relatively higher composition of non-polar amino acids, and lower evolutionary rate, were also identified. Interestingly, the latter two features were shared with another hadal amphipod, Hirondellea gigas, suggesting their possible associations with the adaptation to deep-sea extreme habitats. Overall, our data provided a useful resource for future studies on the evolutionary and adaptive mechanisms of hadal faunas.
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Affiliation(s)
- Jun-Yuan Li
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cong Zeng
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- Hunan Agricultural University, Changsha, Hunan, China
| | - Guo-Yong Yan
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li-Sheng He
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.
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Siegenthaler A, Wangensteen OS, Benvenuto C, Campos J, Mariani S. DNA metabarcoding unveils multiscale trophic variation in a widespread coastal opportunist. Mol Ecol 2019; 28:232-249. [PMID: 30276912 PMCID: PMC7380037 DOI: 10.1111/mec.14886] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 09/06/2018] [Accepted: 09/17/2018] [Indexed: 12/24/2022]
Abstract
A thorough understanding of ecological networks relies on comprehensive information on trophic relationships among species. Since unpicking the diet of many organisms is unattainable using traditional morphology-based approaches, the application of high-throughput sequencing methods represents a rapid and powerful way forward. Here, we assessed the application of DNA metabarcoding with nearly universal primers for the mitochondrial marker cytochrome c oxidase I in defining the trophic ecology of adult brown shrimp, Crangon crangon, in six European estuaries. The exact trophic role of this abundant and widespread coastal benthic species is somewhat controversial, while information on geographical variation remains scant. Results revealed a highly opportunistic behaviour. Shrimp stomach contents contained hundreds of taxa (>1,000 molecular operational taxonomic units), of which 291 were identified as distinct species, belonging to 35 phyla. Only twenty ascertained species had a mean relative abundance of more than 0.5%. Predominant species included other abundant coastal and estuarine taxa, including the shore crab Carcinus maenas and the amphipod Corophium volutator. Jacobs' selectivity index estimates based on DNA extracted from both shrimp stomachs and sediment samples were used to assess the shrimp's trophic niche indicating a generalist diet, dominated by crustaceans, polychaetes and fish. Spatial variation in diet composition, at regional and local scales, confirmed the highly flexible nature of this trophic opportunist. Furthermore, the detection of a prevalent, possibly endoparasitic fungus (Purpureocillium lilacinum) in the shrimp's stomach demonstrates the wide range of questions that can be addressed using metabarcoding, towards a more robust reconstruction of ecological networks.
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Affiliation(s)
- Andjin Siegenthaler
- Ecosystems and Environment Research CentreSchool of Environment and Life SciencesUniversity of SalfordSalfordUK
- Present address:
Department of Integrative BiologyUniversity of GuelphGuelphCanada
| | - Owen S. Wangensteen
- Ecosystems and Environment Research CentreSchool of Environment and Life SciencesUniversity of SalfordSalfordUK
- Present address:
Norwegian College of Fishery ScienceUiT the Arctic University of NorwayTromsøNorway
| | - Chiara Benvenuto
- Ecosystems and Environment Research CentreSchool of Environment and Life SciencesUniversity of SalfordSalfordUK
| | - Joana Campos
- CIIMARInterdisciplinary Centre of Marine and Environmental ResearchUniversity of PortoMatosinhosPortugal
| | - Stefano Mariani
- Ecosystems and Environment Research CentreSchool of Environment and Life SciencesUniversity of SalfordSalfordUK
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Østbye K, Østbye E, Lien AM, Lee LR, Lauritzen SE, Carlini DB. Morphology and life history divergence in cave and surface populations of Gammarus lacustris (L.). PLoS One 2018; 13:e0205556. [PMID: 30359400 PMCID: PMC6201897 DOI: 10.1371/journal.pone.0205556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 09/27/2018] [Indexed: 01/15/2023] Open
Abstract
Cave animals provide a unique opportunity to study contrasts in phenotype and life history in strikingly different environments when compared to surface populations, potentially related to natural selection. As such, we compared a permanent cave-living Gammarus lacustris (L.) population with two lake-resident surface populations analyzing morphology (eye- and antennal characters) and life-history (size at maturity, fecundity and egg-size). A part of the cytochrome c oxidase subunit I gene in the mitochondrion (COI) was analyzed to contrast genetic relationship of populations and was compared to sequences in GenBank to assess phylogeography and colonization scenarios. In the cave, a longer life cycle was implied, while surface populations seemed to have a shorter life cycle. Egg size, and size at maturity for both sexes, were larger in the cave than in surface populations, while fecundity was lower in the cave than in surface populations. The cave population had longer first- and second antennae with more articles, longer first- and second peduncles, and fewer ommatidia than surface populations. The cold low-productive cave environment may facilitate different phenotypic and life-history traits than in the warmer and more productive surface lake environments. The trait divergences among cave and surface populations resembles other cave-surface organism comparisons and may support a hypothesis of selection on sensory traits. The cave and Lake Ulvenvann populations grouped together with a sequence from Slovenia (comprising one genetic cluster), while Lake Lille Lauarvann grouped with a sequence from Ukraine (comprising another cluster), which are already recognized phylogenetic clusters. One evolutionary scenario is that the cave and surface populations were colonized postglacially around 9 000–10 000 years ago. We evaluate that an alternative scenario is that the cave was colonized during an interstadial during the last glaciation or earlier during the warm period before onset of the last glaciation.
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Affiliation(s)
- Kjartan Østbye
- Inland Norway University of Applied Sciences, Department of Forestry and Wildlife Management, Campus Evenstad, Koppang, Norway
- Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
- * E-mail:
| | - Eivind Østbye
- Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Laura R. Lee
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | | | - David B. Carlini
- Department of Biology, American University, Washington, D.C., United States of America
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Tempestini A, Rysgaard S, Dufresne F. Species identification and connectivity of marine amphipods in Canada's three oceans. PLoS One 2018; 13:e0197174. [PMID: 29791459 PMCID: PMC5965885 DOI: 10.1371/journal.pone.0197174] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/27/2018] [Indexed: 11/28/2022] Open
Abstract
Monitoring the distribution of marine biodiversity is a crucial step to better assess the impacts of global changes. Arctic marine fauna is dominated by amphipods in terms of abundance and biomass. These peracarids are an important marine order of crustaceans but the number of species found in the different Canadian oceans is currently unknown. Furthermore, most species are difficult to identify due to poor taxonomic descriptions and morphological convergence. The aim of this study was to assess the species diversity of marine amphipods in the three Canadian oceans using DNA barcoding. To do so, we produced a database of DNA barcodes of amphipods from the three Canadian Oceans publicly available from the BOLD website to which we added 310 new sequences from the Canadian Arctic Archipelago. We first delimited amphipod species based on barcode gap detection techniques and tree based method (bPTP) and then compared the composition of amphipods among the three oceans in order to assess the influence of past transarctic exchanges on Arctic diversity. Our analysis of 2309 sequences which represent more than 250 provisional species revealed a high connectivity between the Atlantic and Arctic Oceans. Our results also suggest that a single threshold to delimitate species is not suitable for amphipods. This study highlights the challenges involved in species delimitation and the need to obtain complete barcoding inventories in marine invertebrates.
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Affiliation(s)
- Astrid Tempestini
- Département de biologie et Québec Océan, Université du Québec à Rimouski, Rimouski, QC, Canada
- * E-mail:
| | - Søren Rysgaard
- University of Manitoba, Centre for Earth Observation Science, Winnipeg, MB, Canada
- Greenland Institute of Natural Resources, Nuuk, Greenland
- Aarhus University, Arctic Research Centre, Aarhus, Denmark
| | - France Dufresne
- Département de biologie et Centre d’étude Nordique, Université du Québec à Rimouski, Rimouski, QC, Canada
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Beermann J, Westbury MV, Hofreiter M, Hilgers L, Deister F, Neumann H, Raupach MJ. Cryptic species in a well-known habitat: applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida). Sci Rep 2018; 8:6893. [PMID: 29720606 PMCID: PMC5931980 DOI: 10.1038/s41598-018-25225-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 04/17/2018] [Indexed: 11/19/2022] Open
Abstract
Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.
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Affiliation(s)
- Jan Beermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Department of Functional Ecology, PO Box 120161, 27515, Bremerhaven, Germany.
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany.
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany.
| | - Michael V Westbury
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Michael Hofreiter
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Leon Hilgers
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Fabian Deister
- Carl von Ossietzky University Oldenburg, Institute for Biology and Environmental Sciences, PO Box 2503, 26111, Oldenburg, Germany
| | - Hermann Neumann
- Senckenberg am Meer, Department for Marine Research, Südstrand 40, 26382, Wilhelmshaven, Germany
| | - Michael J Raupach
- Carl von Ossietzky University Oldenburg, Institute for Biology and Environmental Sciences, PO Box 2503, 26111, Oldenburg, Germany
- Senckenberg am Meer, German Center of Marine Biodiversity (DZMB), Südstrand 44, 26382, Wilhelmshaven, Germany
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Gouveia D, Bonneton F, Almunia C, Armengaud J, Quéau H, Degli-Esposti D, Geffard O, Chaumot A. Identification, expression, and endocrine-disruption of three ecdysone-responsive genes in the sentinel species Gammarus fossarum. Sci Rep 2018; 8:3793. [PMID: 29491422 PMCID: PMC5830573 DOI: 10.1038/s41598-018-22235-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/14/2018] [Indexed: 11/17/2022] Open
Abstract
Taking advantage of a large transcriptomic dataset recently obtained in the sentinel crustacean amphipod Gammarus fossarum, we developed an approach based on sequence similarity and phylogenetic reconstruction to identify key players involved in the endocrine regulation of G. fossarum. Our work identified three genes of interest: the nuclear receptors RXR and E75, and the regulator broad-complex (BR). Their involvement in the regulation of molting and reproduction, along with their sensitivity to chemical contamination were experimentally assessed by studying gene expression during the female reproductive cycle, and after laboratory exposure to model endocrine disrupting compounds (EDCs): pyriproxyfen, tebufenozide and piperonyl butoxide. RXR expression suggested a role of this gene in ecdysis and post-molting processes. E75 presented two expression peaks that suggested a role in vitellogenesis, and molting. BR expression showed no variation during molting/reproductive cycle. After exposure to the three EDCs, a strong inhibition of the inter-molt E75 peak was observed with tebufenozide, and an induction of RXR after exposure to pyriproxyfen and piperonyl butoxide. These results confirm the implication of RXR and E75 in hormonal regulation of female reproductive cycles in G. fossarum and their sensitivity towards EDCs opens the possibility of using them as specific endocrine disruption biomarkers.
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Affiliation(s)
- D Gouveia
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, 5 rue de la Doua CS 20244, F-69625, Villeurbanne, France
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols sur Cèze, France
| | - F Bonneton
- IGFL, Université de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie, F-69364, Lyon, France
| | - C Almunia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols sur Cèze, France
| | - J Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols sur Cèze, France
| | - H Quéau
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, 5 rue de la Doua CS 20244, F-69625, Villeurbanne, France
| | - D Degli-Esposti
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, 5 rue de la Doua CS 20244, F-69625, Villeurbanne, France
| | - O Geffard
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, 5 rue de la Doua CS 20244, F-69625, Villeurbanne, France
| | - A Chaumot
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, 5 rue de la Doua CS 20244, F-69625, Villeurbanne, France.
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Hiki K, Nakajima F, Tobino T. Application of cDNA-AFLP to biomarker exploration in a non-model species Grandidierella japonica. Ecotoxicol Environ Saf 2017; 140:206-213. [PMID: 28260686 DOI: 10.1016/j.ecoenv.2017.02.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 06/06/2023]
Abstract
Biomarkers of exposure can be used to identify specific contaminants that are adversely affecting aquatic organisms. However, it remains prohibitively costly to investigate multiple novel biomarkers of exposure in a non-model species, despite the development of next-generation sequencing technology. In this study, we focused on the use of cDNA-amplified fragment length polymorphism (AFLP) as a cost-effective biomarker discovery tool to test whether it could identify biomarkers of exposure in the non-model amphipod species Grandidierella japonica. Loci were identified that were differentially expressed in amphipods exposed to reference chemicals (Cu, Zn, and nicotine) and to an environmental sample (road dust) at sublethal concentrations. Eight loci were shown to respond consistently to nicotine at different concentrations, but not to Cu or Zn. Some of the loci also responded to an environmental road dust sample containing nicotine. These findings suggest that loci identified using cDNA-AFLP could be used as biomarkers of nicotine exposure in environmental samples with complex matrices. Further studies with other organisms and toxicants are needed, but we have demonstrated that the use of cDNA-AFLP to identify biomarkers for ecotoxicological studies of non-model species is at least feasible.
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Affiliation(s)
- Kyoshiro Hiki
- Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Fumiyuki Nakajima
- Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tomohiro Tobino
- Environmental Science Center, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
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Beery SR, Gauthier PT, Pyle GG. Testing Local Adaptation in Five Populations of Hyalella azteca in Northern Alberta's Oil Sands Region. Arch Environ Contam Toxicol 2017; 72:189-199. [PMID: 28040852 DOI: 10.1007/s00244-016-0351-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/19/2016] [Indexed: 06/06/2023]
Abstract
Canada's oil sands hold the third largest petroleum reserves worldwide and have experienced rapid economic growth. The oil sands region provides an ideal location for studying local adaptations through reciprocal transplant (RT) because populations within the region have been historically exposed to naturally occurring bitumen. Our objectives were to (1) determine if Hyalella azteca from habitats within the oil sands region exhibited increased tolerance to constituents associated with industrial bitumen extraction compared with H. azteca from habitats outside the region; and (2) determine if any observed tolerance was attributable to local adaptation. Five populations of H. azteca were reciprocally transplanted from reclaimed and reference wetlands: four from local wetlands plus one naïve laboratory population. Survival, toxicity, and behaviour were measured before and after the RT period. Survival varied by population and site. These results show that the differences in responses among populations are likely not attributable to local adaptation and that laboratory populations of H. azteca provide ecologically relevant results when tested in the field.
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Affiliation(s)
- Steven R Beery
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Road, Thunder Bay, ON, P7B 5E1, Canada.
| | - Patrick T Gauthier
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Gregory G Pyle
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB, T1K 3M4, Canada
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Romanova EV, Aleoshin VV, Kamaltynov RM, Mikhailov KV, Logacheva MD, Sirotinina EA, Gornov AY, Anikin AS, Sherbakov DY. Evolution of mitochondrial genomes in Baikalian amphipods. BMC Genomics 2016; 17:1016. [PMID: 28105939 PMCID: PMC5249044 DOI: 10.1186/s12864-016-3357-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Amphipods (Crustacea) of Lake Baikal are a very numerous and diverse group of invertebrates generally believed to have originated by adaptive radiation. The evolutionary history and phylogenetic relationships in Baikalian amphipods still remain poorly understood. Sequencing of mitochondrial genomes is a relatively feasible way for obtaining a set of gene sequences suitable for robust phylogenetic inferences. The architecture of mitochondrial genomes also may provide additional information on the mechanisms of evolution of amphipods in Lake Baikal. RESULTS Three complete and four nearly complete mitochondrial genomes of Baikalian amphipods were obtained by high-throughput sequencing using the Illumina platform. A phylogenetic inference based on the nucleotide sequences of all mitochondrial protein coding genes revealed the Baikalian species to be a monophyletic group relative to the nearest non-Baikalian species with a completely sequenced mitochondrial genome - Gammarus duebeni. The phylogeny of Baikalian amphipods also suggests that the shallow-water species Eulimnogammarus has likely evolved from a deep-water ancestor, however many other species have to be added to the analysis to test this hypothesis. The gene order in all mitochondrial genomes of studied Baikalian amphipods differs from the pancrustacean ground pattern. Mitochondrial genomes of four species possess 23 tRNA genes, and in three genomes the extra tRNA gene copies have likely undergone remolding. Widely varying lengths of putative control regions and other intergenic spacers are typical for the mitochondrial genomes of Baikalian amphipods. CONCLUSIONS The mitochondrial genomes of Baikalian amphipods display varying organization suggesting an intense rearrangement process during their evolution. Comparison of complete mitochondrial genomes is a potent approach for studying the amphipod evolution in Lake Baikal.
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Affiliation(s)
- Elena V. Romanova
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Vladimir V. Aleoshin
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, 119991 Russian Federation
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994 Russian Federation
| | - Ravil M. Kamaltynov
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Kirill V. Mikhailov
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, 119991 Russian Federation
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994 Russian Federation
| | - Maria D. Logacheva
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, 119991 Russian Federation
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994 Russian Federation
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420012 Russian Federation
| | - Elena A. Sirotinina
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Alexander Yu. Gornov
- Institute for System Dynamics and Control Theory, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Anton S. Anikin
- Institute for System Dynamics and Control Theory, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
| | - Dmitry Yu. Sherbakov
- Laboratory of Molecular Systematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033 Russian Federation
- Faculty of Biology and Soil Studies, Irkutsk State University, Irkutsk, 664003 Russian Federation
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Leung J, Witt JDS, Norwood W, Dixon DG. Implications of Cu and Ni toxicity in two members of the Hyalella azteca cryptic species complex: Mortality, growth, and bioaccumulation parameters. Environ Toxicol Chem 2016; 35:2817-2826. [PMID: 27081924 DOI: 10.1002/etc.3457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/05/2016] [Accepted: 04/11/2016] [Indexed: 06/05/2023]
Abstract
Hyalella azteca, an amphipod crustacean, is frequently used in freshwater toxicity tests. Since the mid-1980s, numerous organizations have collected and established cultures of H. azteca originating from localities across North America. However, H. azteca is actually a large cryptic species complex whose members satisfy both the biological and the phylogenetic species concepts. Genetic analysis at the mitochondrial COI gene has revealed that only 2 clades are cultured in 17 North American laboratories; however, there are 85 genetically divergent lineages within this complex in the wild. In the present study, 2 members (clades 1 and 8) of the H. azteca species complex were identified using the mitochondrial COI gene. These 2 clades were exposed to Cu or Ni for 14 d. A saturation-based mortality model and the general growth model were used to determine mortality (lethal concentration, 25% and 50% [LC25 and LC50], lethal body concentration, 25% and 50% [LBC25 and LBC50]) and growth (inhibitory concentration, 25% [IC25, IBC25]) endpoints, respectively. A modified saturation-based model was used to estimate metal bioaccumulation parameters. Clade 8 was significantly more tolerant than clade 1, with differences in LC50s. However, the effects of the metals on growth were not significantly different between clades, even though clade 1 was significantly larger than then clade 8. Differences in Cu or Ni bioaccumulation were not observed between clades 1 and 8. The differences in Cu and Ni LC50s may have implications for risk assessments, and it is recommended that toxicity experiments should only be performed with properly identified members of the H. azteca complex to maintain consistency among laboratories. Environ Toxicol Chem 2016;35:2817-2826. © 2016 SETAC.
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Affiliation(s)
- Jessica Leung
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
| | - Jonathan D S Witt
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Warren Norwood
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - D George Dixon
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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Hoelters L, O'Grady JF, Webster SG, Wilcockson DC. Characterization, localization and temporal expression of crustacean hyperglycemic hormone (CHH) in the behaviorally rhythmic peracarid crustaceans, Eurydice pulchra (Leach) and Talitrus saltator (Montagu). Gen Comp Endocrinol 2016; 237:43-52. [PMID: 27468954 DOI: 10.1016/j.ygcen.2016.07.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 07/19/2016] [Accepted: 07/24/2016] [Indexed: 11/15/2022]
Abstract
Crustacean hyperglycemic hormone (CHH) has been extensively studied in decapod crustaceans where it is known to exert pleiotropic effects, including regulation of blood glucose levels. Hyperglycemia in decapods seems to be temporally gated to coincide with periods of activity, under circadian clock control. Here, we used gene cloning, in situ hybridization and immunohistochemistry to describe the characterization and localization of CHH in two peracarid crustaceans, Eurydice pulchra and Talitrus saltator. We also exploited the robust behavioral rhythmicity of these species to test the hypothesis that CHH mRNA expression would resonate with their circatidal (12.4h) and circadian (24h) behavioral phenotypes. We show that both species express a single CHH transcript in the cerebral ganglia, encoding peptides featuring all expected, conserved characteristics of other CHHs. E. pulchra preproCHH is an amidated 73 amino acid peptide N-terminally flanked by a short, 18 amino acid precursor related peptide (CPRP) whilst the T. saltator prohormone is also amidated but 72 amino acids in length and has a 56 residue CPRP. The localization of both was mapped by immunohistochemistry to the protocerebrum with axon tracts leading to the sinus gland and into the tritocerebrum, with striking similarities to terrestrial isopod species. We substantiated the cellular position of CHH immunoreactive cells by in situ hybridization. Although both species showed robust activity rhythms, neither exhibited rhythmic transcriptional activity indicating that CHH transcription is not likely to be under clock control. These data make a contribution to the inventory of CHHs that is currently lacking for non-decapod species.
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Affiliation(s)
- Laura Hoelters
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion SY23 3DA, UK.
| | - Joseph Francis O'Grady
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion SY23 3DA, UK.
| | - Simon George Webster
- School of Biological Sciences, Bangor University, Brambell Building, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK.
| | - David Charles Wilcockson
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion SY23 3DA, UK; School of Biological Sciences, Bangor University, Brambell Building, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK.
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Vidal-Dorsch DE, Bay SM, Moore S, Layton B, Mehinto AC, Vulpe CD, Brown-Augustine M, Loguinov A, Poynton H, Garcia-Reyero N, Perkins EJ, Escalon L, Denslow ND, Cristina CDR, Doan T, Shukradas S, Bruno J, Brown L, Van Agglen G, Jackman P, Bauer M. Ecotoxicogenomics: Microarray interlaboratory comparability. Chemosphere 2016; 144:193-200. [PMID: 26363320 DOI: 10.1016/j.chemosphere.2015.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 07/27/2015] [Accepted: 08/02/2015] [Indexed: 06/05/2023]
Abstract
Transcriptomic analysis can complement traditional ecotoxicology data by providing mechanistic insight, and by identifying sub-lethal organismal responses and contaminant classes underlying observed toxicity. Before transcriptomic information can be used in monitoring and risk assessment, it is necessary to determine its reproducibility and detect key steps impacting the reliable identification of differentially expressed genes. A custom 15K-probe microarray was used to conduct transcriptomics analyses across six laboratories with estuarine amphipods exposed to cyfluthrin-spiked or control sediments (10 days). Two sample types were generated, one consisted of total RNA extracts (Ex) from exposed and control samples (extracted by one laboratory) and the other consisted of exposed and control whole body amphipods (WB) from which each laboratory extracted RNA. Our findings indicate that gene expression microarray results are repeatable. Differentially expressed data had a higher degree of repeatability across all laboratories in samples with similar RNA quality (Ex) when compared to WB samples with more variable RNA quality. Despite such variability a subset of genes were consistently identified as differentially expressed across all laboratories and sample types. We found that the differences among the individual laboratory results can be attributed to several factors including RNA quality and technical expertise, but the overall results can be improved by following consistent protocols and with appropriate training.
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Affiliation(s)
| | - Steven M Bay
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - Shelly Moore
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - Blythe Layton
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - Alvine C Mehinto
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - Chris D Vulpe
- University of California, Berkeley, Berkeley, CA, USA
| | | | - Alex Loguinov
- University of California, Berkeley, Berkeley, CA, USA
| | | | - Natàlia Garcia-Reyero
- Mississippi State University, Starkville, MS, USA; US Army Engineer Research and Development Center, Vicksburg, MS, USA
| | - Edward J Perkins
- US Army Engineer Research and Development Center, Vicksburg, MS, USA
| | - Lynn Escalon
- US Army Engineer Research and Development Center, Vicksburg, MS, USA
| | | | - Colli-Dula R Cristina
- University of Florida, Gainesville, FL, USA; Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Mexico
| | - Tri Doan
- Agilent Technologies, Santa Clara, CA, USA
| | - Shweta Shukradas
- Agilent Technologies, Santa Clara, CA, USA; Strand Scientific Intelligence Inc., San Francisco, CA, USA
| | - Joy Bruno
- Environment Canada, North Vancouver, B.C., Canada
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Hook SE, Osborn HL, Spadaro DA, Simpson SL. Challenges for using quantitative PCR test batteries as a TIE-type approach to identify metal exposure in benthic invertebrates. Environ Sci Pollut Res Int 2015; 22:17280-17289. [PMID: 24994105 DOI: 10.1007/s11356-014-3234-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 06/18/2014] [Indexed: 06/03/2023]
Abstract
The epibenthic amphipod Melita plumulosa shows unique gene expression profiles when exposed to different contaminants. We hypothesized that specific changes in transcript abundance could be used in a battery of quantitative polymerase chain reaction (qPCR) assays as a toxicity identification evaluation (TIE)-like approach to identify the most relevant stressor in field-contaminated sediments. To test this hypothesis, seven candidate transcriptomic markers were selected, and their specificity following metal exposure was confirmed. The performance of these markers across different levels of added metals was verified. The ability of these transcripts to act as markers was tested by exposing amphipods to metal-contaminated field-collected sediments and measuring changes in transcript abundance via qPCR. For two of the three sediments tested, at least some of the transcriptomic patterns matched our predictions, suggesting that they would be effective in helping to identify metal exposure in field sediments. However, following exposure to the third sediment, transcriptomic patterns were unlike our predictions. These results suggest that the seven transcripts may be insufficient to discern individual contaminants from complex mixtures and that microarray or RNA-Seq global gene expression profiles may be more effective for TIE. Changes in transcriptomics based on laboratory exposures to single compounds should be carefully validated before the results are used to analyze mixtures.
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Affiliation(s)
- Sharon E Hook
- CSIRO Land and Water, Locked Bag 2007, Kirrawee, NSW, 2232, Australia.
| | - Hannah L Osborn
- CSIRO Land and Water, Locked Bag 2007, Kirrawee, NSW, 2232, Australia
| | - David A Spadaro
- CSIRO Land and Water, Locked Bag 2007, Kirrawee, NSW, 2232, Australia
| | - Stuart L Simpson
- CSIRO Land and Water, Locked Bag 2007, Kirrawee, NSW, 2232, Australia
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Baratti M, Cattonaro F, Di Lorenzo T, Galassi DMP, Iannilli V, Iannucci A, Jensen J, Larsen PF, Nielsen RO, Pertoldi C, Postolache D, Pujolar JM, Randi E, Ruiz-Gonzalez A, Thirstrup JP, Vendramin GG, Zalewski A. Genomic resources notes accepted 1 October 2014-30 November 2014. Mol Ecol Resour 2015; 15:458-9. [PMID: 25677171 DOI: 10.1111/1755-0998.12368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
This article documents the public availability of (i) RAD sequencing data and validated SNPs for the American mink Neovison vison and (ii) Transcriptome resources for two nonmodel freshwater crustacean species, the copepod Eucyclops serrulatus and the amphipod Echinogammarus veneris.
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