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Choi BS, Kim DH, Kim MS, Park JC, Lee YH, Kim HJ, Jeong CB, Hagiwara A, Souissi S, Lee JS. The genome of the European estuarine calanoid copepod Eurytemora affinis: Potential use in molecular ecotoxicology. MARINE POLLUTION BULLETIN 2021; 166:112190. [PMID: 33711609 DOI: 10.1016/j.marpolbul.2021.112190] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/02/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
In this study, we sequenced and assembled the genome of a European estuarine calanoid copepod using Oxford Nanopore PromethION and Illumina HiSeq 2500 platforms. The length of the assembled genome was 776.1 Mb with N50 = 474.9 kb (BUSCO 85.9%), and the genome consisted of 2473 contigs. A total of 18,014 genes were annotated and orthologous gene clusters were analyzed in comparison to other copepods. In addition, genome-wide identification of cytochrome P450s, glutathione S-transferases, and ATP-binding cassette transporters in E. affinis was performed to determine gene repertoire of these detoxification-related gene families. Results revealed the presence of species-specific gene inventories, indicating that these gene families have evolved through species-specific gene loss/expansion processes, possibly due to adaptation to different environmental stressors. Our study provides a new inventory of the European estuarine calanoid copepod E. affinis genome with emphasis on phase I, II, and III detoxification systems.
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Affiliation(s)
| | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jun Chul Park
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Young Hwan Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Hee-Jin Kim
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki 852-8521, Japan
| | - Chang-Bum Jeong
- Department of Marine Science, College of Nature Science, Incheon National University, Incheon 22012, South Korea
| | - Atsushi Hagiwara
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki 852-8521, Japan; Organization for Marine Science and Technology, Nagasaki University, Nagasaki 852-8521, Japan
| | - Sami Souissi
- Université de Lille, CNRS, Université du Littoral Côte d'Opale, UMR 8187 LOG, Laboratoire d'Océanologie et de Géosciences, Station marine de Wimereux, F-59000 Lille, France
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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Karlsson K, Winder M. Adaptation potential of the copepod Eurytemora affinis to a future warmer Baltic Sea. Ecol Evol 2020; 10:5135-5151. [PMID: 32551088 PMCID: PMC7297749 DOI: 10.1002/ece3.6267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/25/2020] [Accepted: 03/20/2020] [Indexed: 11/11/2022] Open
Abstract
To predict effects of global change on zooplankton populations, it is important to understand how present species adapt to temperature and how they respond to stressors interacting with temperature. Here, we ask if the calanoid copepod Eurytemora affinis from the Baltic Sea can adapt to future climate warming. Populations were sampled at sites with different temperatures. Full sibling families were reared in the laboratory and used in two common garden experiments (a) populations crossed over three temperature treatments 12, 17, and 22.5°C and (b) populations crossed over temperature in interaction with salinity and algae of different food quality. Genetic correlations of the full siblings' development time were not different from zero between 12°C and the two higher temperatures 17 and 22.5°C, but positively correlated between 17 and 22.5°C. Hence, a population at 12°C is unlikely to adapt to warmer temperature, while a population at ≥17°C can adapt to an even higher temperature, that is, 22.5°C. In agreement with the genetic correlations, the population from the warmest site of origin had comparably shorter development time at high temperature than the populations from colder sites, that is, a cogradient variation. The population with the shortest development time at 22.5°C had in comparison lower survival on low quality food, illustrating a cost of short development time. Our results suggest that populations from warmer environments can at present indirectly adapt to a future warmer Baltic Sea, whereas populations from colder areas show reduced adaptation potential to high temperatures, simply because they experience an environment that is too cold.
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Affiliation(s)
- Konrad Karlsson
- Department of Arctic BiologyUniversity Centre in SvalbardSvalbardNorway
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
| | - Monika Winder
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
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Sługocki Ł, Rymaszewska A, Kirczuk L. Insights into the morphology and molecular characterisation of glacial relict Eurytemoralacustris (Poppe, 1887) (Crustacea, Copepoda, Calanoida, Temoridae). Zookeys 2019; 864:15-33. [PMID: 31346308 PMCID: PMC6646299 DOI: 10.3897/zookeys.864.34259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/13/2019] [Indexed: 11/12/2022] Open
Abstract
Eurytemoralacustris (Poppe, 1887) is a stenothermic glacial relict whose narrow environmental requirements make it an indicator species for good ecological conditions. The primary threats to this species are eutrophication and global warming. Many authors have described E.lacustris in taxonomic keys; however, its morphological description is unsatisfactory. Therefore, in this study, we aimed to review morphological characteristics of E.lacustris that were previously undescribed in the literature and to provide the molecular characteristics based on the two conservative mitochondrial genes: cytochrome c oxidase I (COI) and cytochrome b (cytb). The new record of E.lacustris indicates that it is a more widespread species than previously hypothesized. Width-to-length ratio of the last female endopod segment of legs indicates variation among the widely distributed species of the genus in Europe (i.e., E.lacustris, E.velox (Lilljeborg, 1853), and E.affinis (Poppe, 1880)). We also found variability of number of setae on the second segment of male endopod. Furthermore, our analysis confirms the occurrence of species in different than exclusively freshwater habitats.
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Affiliation(s)
- Łukasz Sługocki
- University of Szczecin, Faculty of Biology, Szczecin, PolandUniversity of SzczecinSzczecinPoland
- University of Szczecin, Center of Molecular Biology and Biotechnology, Szczecin, PolandUniversity of SzczecinSzczecinPoland
| | - Anna Rymaszewska
- University of Szczecin, Faculty of Biology, Szczecin, PolandUniversity of SzczecinSzczecinPoland
| | - Lucyna Kirczuk
- University of Szczecin, Faculty of Biology, Szczecin, PolandUniversity of SzczecinSzczecinPoland
- University of Szczecin, Center of Molecular Biology and Biotechnology, Szczecin, PolandUniversity of SzczecinSzczecinPoland
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Sukhikh NM, Castric V, Polyakova NV, Souissi S, Alekseev VR. Isolated populations of Eurytemora americana Williams (Crustacea, Copepoda) in the White Sea rock pools—postglacial relicts or anthropogenic invasions? RUSSIAN JOURNAL OF BIOLOGICAL INVASIONS 2016. [DOI: 10.1134/s2075111716040093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Vasquez AA, Hudson PL, Fujimoto M, Keeler K, Armenio PM, Ram JL. Eurytemora carolleeae in the Laurentian Great Lakes revealed by phylogenetic and morphological analysis. JOURNAL OF GREAT LAKES RESEARCH 2016; 42:802-811. [PMID: 27713595 PMCID: PMC5047287 DOI: 10.1016/j.jglr.2016.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In the Laurentian Great Lakes, specimens of Eurytemora have been reported as E. affinis since its invasion in the late 1950s. During an intensive collection of aquatic invertebrates for morphological and molecular identification in Western Lake Erie in 2012-2013, several specimens of Eurytemora were collected. Analysis of these specimens identified them as the recently described species E. carolleeae Alekseev and Souissi 2011. This result led us to assess E. carolleeae's identifying features, geographic distribution and historical presence in the Laurentian Great Lakes in view of its recent description in 2011. Cytochrome oxidase I (COI) DNA sequences of Eurytemora specimens were identified as closer (2 - 4% different) to recently described E. carolleeae than to most Eurytemora affinis sequences (14% different). Eurytemora from other areas of the Great Lakes and from North American rivers as far west as South Dakota (Missouri River) and east to Delaware (Christina River) also keyed to E. carolleeae. Morphological analysis of archival specimens from 1962 and from all the Great Lakes were identified as E. carolleeae. Additionally, Eurytemora drawings in previous publications from studies in the Holarctic region were reassessed to determine if these specimens were E. carolleeae. Additional morphological characters that may distinguish the North American E. carolleeae from other taxa are also described. We conclude that E. carolleeae is the correct name for the species of Eurytemora that has inhabited the Great Lakes since its invasion, as established by both morphological and COI sequence comparisons to reference keys and sequence databases in present and archival specimens.
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Affiliation(s)
- Adrian A. Vasquez
- Department of Physiology, Wayne State University School of Medicine, 5374 Scott Hall, 540 E. Canfield St., Detroit, MI, 48201, USA
| | - Patrick L. Hudson
- US Geological Survey, Great Lakes Science Center, 1451 Green Road, Ann Arbor, MI 48105, USA
| | - Masanori Fujimoto
- Department of Physiology, Wayne State University School of Medicine, 5374 Scott Hall, 540 E. Canfield St., Detroit, MI, 48201, USA
| | - Kevin Keeler
- US Geological Survey, Great Lakes Science Center, 1451 Green Road, Ann Arbor, MI 48105, USA
| | - Patricia M. Armenio
- US Geological Survey, Great Lakes Science Center, 1451 Green Road, Ann Arbor, MI 48105, USA
| | - Jeffrey L. Ram
- Department of Physiology, Wayne State University School of Medicine, 5374 Scott Hall, 540 E. Canfield St., Detroit, MI, 48201, USA
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DNA Barcoding of Metazoan Zooplankton Copepods from South Korea. PLoS One 2016; 11:e0157307. [PMID: 27383475 PMCID: PMC4934703 DOI: 10.1371/journal.pone.0157307] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 05/30/2016] [Indexed: 12/03/2022] Open
Abstract
Copepods, small aquatic crustaceans, are the most abundant metazoan zooplankton and outnumber every other group of multicellular animals on earth. In spite of ecological and biological importance in aquatic environment, their morphological plasticity, originated from their various lifestyles and their incomparable capacity to adapt to a variety of environments, has made the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of cryptic or sibling species based on DNA sequence data. We examined sequence variation of a partial mitochondrial cytochrome C oxidase I gene (COI) from 133 copepod individuals collected from the Korean Peninsula, in order to identify and discriminate 94 copepod species covering six copepod orders of Calanoida, Cyclopoida, Harpacticoida, Monstrilloida, Poecilostomatoida and Siphonostomatoida. The results showed that there exists a clear gap with ca. 20 fold difference between the averages of within-specific sequence divergence (2.42%) and that of between-specific sequence divergence (42.79%) in COI, suggesting the plausible utility of this gene in delimitating copepod species. The results showed, with the COI barcoding data among 94 copepod species, that a copepod species could be distinguished from the others very clearly, only with four exceptions as followings: Mesocyclops dissimilis–Mesocyclops pehpeiensis (0.26% K2P distance in percent) and Oithona davisae–Oithona similis (1.1%) in Cyclopoida, Ostrincola japonica–Pseudomyicola spinosus (1.5%) in Poecilostomatoida, and Hatschekia japonica–Caligus quadratus (5.2%) in Siphonostomatoida. Thus, it strongly indicated that COI may be a useful tool in identifying various copepod species and make an initial progress toward the construction of a comprehensive DNA barcode database for copepods inhabiting the Korean Peninsula.
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Sukhikh N, Souissi A, Souissi S, Winkler G, Castric V, Holl AC, Alekseev V. Genetic and morphological heterogeneity among populations of Eurytemora affinis (Crustacea: Copepoda: Temoridae) in European waters. C R Biol 2016; 339:197-206. [PMID: 27156447 DOI: 10.1016/j.crvi.2016.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/28/2016] [Indexed: 11/29/2022]
Abstract
Our understanding of the systematics of the Eurytemora affinis complex developed at a fast pace over the last decades. Formerly considered as a complex of cryptic species, it is now believed to include three valid species: E. affinis, Eurytemora carolleeae, and Eurytemora caspica. American and European representatives have been studied in detail with respect to fine-scale geographic distribution, levels of genetic subdivision, evolutionary and demographic histories. Morphological components have been less explored. In this study, an analysis of the phylogeny and morphology of E. affinis was done, with a special focus on European populations. A total of 447 individuals of E. affinis from Europe were analyzed with genetic tools and 170 individuals according to morphological criteria. Common and new morphological and genetic features were analyzed. For this, we used ML and Bayesian methods to analyze the bar coding mt-DNA gene cytochrome c oxidase I subunit. Both genetic and morphological analyses showed high heterogeneities among the E. affinis populations from Europe. As a result, three local populations of E. affinis in Western Europe, including the European part of Russia, were established. Their genetic and morphological heterogeneity corresponded to the subspecies level.
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Affiliation(s)
| | - Anissa Souissi
- Université de Lille, CNRS, ULCO, UMR 8187, Laboratoire d'océanologie et de géosciences (LOG), 62930 Wimereux, France
| | - Sami Souissi
- Université de Lille, CNRS, ULCO, UMR 8187, Laboratoire d'océanologie et de géosciences (LOG), 62930 Wimereux, France
| | - Gesche Winkler
- Institut des sciences de la mer de Rimouski, Québec-Océan, Université du Québec à Rimouski, 310, allée des Ursulines, Rimouski, QC G5L 3A1, Canada
| | - Vincent Castric
- Université Lille-1 (Sciences et Technologies), UMR CNRS 8016, UFR de biologie, 59655 Villeneuve-d'Ascq cedex, France
| | - Anne-Catherine Holl
- Université Lille-1 (Sciences et Technologies), UMR CNRS 8016, UFR de biologie, 59655 Villeneuve-d'Ascq cedex, France
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Sukhikh N, Alekseev V. Genetic and morphological heterogeneity within Eucyclops serrulatus(Fischer, 1851) (Crustacea: Copepoda: Cyclopidae). J NAT HIST 2015. [DOI: 10.1080/00222933.2015.1056267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Lajus D, Sukhikh N, Alekseev V. Cryptic or pseudocryptic: can morphological methods inform copepod taxonomy? An analysis of publications and a case study of the Eurytemora affinis species complex. Ecol Evol 2015; 5:2374-85. [PMID: 26120427 PMCID: PMC4475370 DOI: 10.1002/ece3.1521] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/23/2015] [Indexed: 11/07/2022] Open
Abstract
Interest in cryptic species has increased significantly with current progress in genetic methods. The large number of cryptic species suggests that the resolution of traditional morphological techniques may be insufficient for taxonomical research. However, some species now considered to be cryptic may, in fact, be designated pseudocryptic after close morphological examination. Thus the “cryptic or pseudocryptic” dilemma speaks to the resolution of morphological analysis and its utility for identifying species. We address this dilemma first by systematically reviewing data published from 1980 to 2013 on cryptic species of Copepoda and then by performing an in-depth morphological study of the former Eurytemora affinis complex of cryptic species. Analyzing the published data showed that, in 5 of 24 revisions eligible for systematic review, cryptic species assignment was based solely on the genetic variation of forms without detailed morphological analysis to confirm the assignment. Therefore, some newly described cryptic species might be designated pseudocryptic under more detailed morphological analysis as happened with Eurytemora affinis complex. Recent genetic analyses of the complex found high levels of heterogeneity without morphological differences; it is argued to be cryptic. However, next detailed morphological analyses allowed to describe a number of valid species. Our study, using deep statistical analyses usually not applied for new species describing, of this species complex confirmed considerable differences between former cryptic species. In particular, fluctuating asymmetry (FA), the random variation of left and right structures, was significantly different between forms and provided independent information about their status. Our work showed that multivariate statistical approaches, such as principal component analysis, can be powerful techniques for the morphological discrimination of cryptic taxons. Despite increasing cryptic species designations, morphological techniques have great potential in determining copepod taxonomy.
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Affiliation(s)
- Dmitry Lajus
- Saint-Petersburg State University Saint-Petersburg, Russia
| | - Natalia Sukhikh
- Zoological Institute of Russian Academy of Sciences Saint-Petersburg, Russia
| | - Victor Alekseev
- Zoological Institute of Russian Academy of Sciences Saint-Petersburg, Russia
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Gutiérrez-Aguirre MA, Cervantes-Martínez A, Elías-Gutiérrez M. An example of how barcodes can clarify cryptic species: the case of the calanoid copepod Mastigodiaptomus albuquerquensis (Herrick). PLoS One 2014; 9:e85019. [PMID: 24465470 PMCID: PMC3897401 DOI: 10.1371/journal.pone.0085019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 11/18/2013] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The freshwater calanoid Mastigodiaptomus is a genus with high richness in the Americas and is composed of nine species, seven recorded in Mexico and four that are apparently endemic to small areas. Mastigodiaptomus albuquerquensis is a common, widely distributed species ranging from the southern USA to Central America. This species can be easily identified by a notable butterfly-like sclerotization on the basis of the right fifth leg of males. Nevertheless, morphological differences observed among populations throughout this species distributional range have led to the description of several related species or subspecies, such as M. albuquerquensis patzcuarensis from Lake Pátzcuaro in the Central Plateau of Mexico. METHODS Genetic results based on barcodes, morphology based on scanning electron and light microscopy images, and morphometric analyses were used to describe cryptic species within the M. albuquerquensis complex. RESULTS The morphological analyses coincided partially with the genetic markers, suggesting the existence of at least two sibling species: M. albuquerquensis s. str. and M. patzcuarensis. A third species was genetically separated but was morphologically indistinguishable from the M. patzcuarensis group. CONCLUSIONS Hidden diversity has been a major problem in establishing real patterns of species distribution and genetic acquisition from megadiverse hotspots such as Mexico, where the Nearctic and the Neotropical regions of the Americas meet. Barcodes can help taxonomists to reveal and formally name these new species. Here, we describe two of three potential species highlighted by the use of barcodes: M. albuquerquensis s. str. in the northern semi-desert and M. patzcuarensis on the Central Plateau at more than 2000 m above sea level.
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Individual-based model of the phenology of egg-bearing copepods: Application to Eurytemora affinis from the Seine estuary, France. Ecol Modell 2013. [DOI: 10.1016/j.ecolmodel.2013.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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