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Pérez-Aragón M, Escribano R, Rivera R, Hidalgo P. Biodiversity patterns of epipelagic copepods in the South Pacific Ocean: Strengths and limitations of current data bases. PLoS One 2024; 19:e0306440. [PMID: 38991030 PMCID: PMC11238982 DOI: 10.1371/journal.pone.0306440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/18/2024] [Indexed: 07/13/2024] Open
Abstract
Basin-scale patterns of biodiversity for zooplankton in the ocean may provide valuable insights for understanding the impact of climate change and global warming on the marine ecosystem. However, studies on this topic remain scarce or unavailable in vast regions of the world ocean, particularly in large regions where the amount and quality of available data are limited. In this study, we used a 27-year (1993-2019) database on species occurrence of planktonic copepods in the South Pacific, along with associated oceanographic variables, to examine their spatial patterns of biodiversity in the upper 200 m of the ocean. The aim of this study was to identify ecological regions and the environmental predictors explaining such patterns. It was found that hot and cold spots of diversity, and distinctive species assemblages were linked to major ocean currents and large regions over the basin, with increasing species richness over the subtropical areas on the East and West sides of the South Pacific. While applying the spatial models, we showed that the best environmental predictors for diversity and species composition were temperature, salinity, chlorophyll-a concentration, oxygen concentration, and the residual autocorrelation. Nonetheless, the observed spatial patterns and derived environmental effects were found to be strongly influenced by sampling coverage over space and time, revealing a highly under-sampled basin. Our findings provide an assessment of copepods diversity patterns and their potential drivers for the South Pacific Ocean, but they also stress the need for strengthening the data bases of planktonic organisms, as they can act as suitable indicators of ecosystem response to climate change at basin scale.
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Affiliation(s)
- Manuela Pérez-Aragón
- Doctoral Program of Oceanography, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
- Instituto Milenio de Oceanografía (IMO), Universidad de Concepción, Concepción, Chile
| | - Ruben Escribano
- Instituto Milenio de Oceanografía (IMO), Universidad de Concepción, Concepción, Chile
- Department of Oceanography, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Reinaldo Rivera
- Instituto Milenio de Oceanografía (IMO), Universidad de Concepción, Concepción, Chile
| | - Pamela Hidalgo
- Instituto Milenio de Oceanografía (IMO), Universidad de Concepción, Concepción, Chile
- Department of Oceanography, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
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2
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Svetlichny L, Rudi Strickler J, Obertegger U. Swimming and respiration in cyclopoid copepods Thermocyclops oithonoides and Oithona davisae and calanoid copepod Paracalanus parvus. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2022; 337:835-851. [PMID: 35859518 DOI: 10.1002/jez.2643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Cyclopoid and calanoid copepods differ in how they move. Cyclopoid copepods use the thoracic legs for cruise and escape swimming while most calanoid copepods use the cephalic appendages for cruise swimming and the thoracic legs for escape reactions. Apart from this gross difference, little is known on the comparative aspects of the locomotor function of copepod appendages. This study investigated the main kinematic patterns of cruise and escape swimming of two small cyclopoid copepods, Thermocyclops oithonoides and Oithona davisae, and a small calanoid copepod, Paracalanus parvus, by video filming at a frame rate of up to 1200 frames/s. During escape swimming, O. davisae and the twice as large P. parvus showed similar movement, jumping at a frequency of 150 Hz and moving at 12 cm s-1 ; however, at a lower jump frequency (∼100 Hz), the cyclopoid T. oithonoides showed an almost two times faster escape swimming than that of P. parvus which has the same body size. This higher speed can be linked to the greater role of the longer abdomen for the flopping strokes in T. oithonoides. In accordance with the Arrhenius law, the kinematic parameters of cruise and escape swimming of T. oithonoides showed temperature dependence in the range of 6.5-27°С. At a temperature of about 20°C, the respiration rate of O. davisae and P. parvus was 1.6 times higher (i.e., ∼1.5 µg O2 mg-1 h-1 ) than in T. oithonoides during normal swimming; however, in the swarming state, the respiration rate of T. oithonoides increased 3.4 times to 3.0 µg O2 mg-1 h-1 , which was nine times higher than the respiratory rate of anesthetized individuals of this species. Based on the speed and duration of locomotor acts, the cyclopoid T. oithonoides consumed about the same amount of respiratory energy as the calanoid P. parvus, but the mechanical energy required for movement in jumps mode was 1.5 times higher.
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Affiliation(s)
- Leonid Svetlichny
- Department of invertebrate Fauna and systematics, I. I. Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Johann Rudi Strickler
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
- Department of Marine science, Marine Science Institute, University of Texas at Austin, Port Aransas, Texas, USA
| | - Ulrike Obertegger
- Research Group Hydrobiology, FEM-Research and Innovation Centre, San Michele all'Adige, Italy
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3
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Bernot JP, Boxshall GA, Crandall KA. A synthesis tree of the Copepoda: integrating phylogenetic and taxonomic data reveals multiple origins of parasitism. PeerJ 2021; 9:e12034. [PMID: 34466296 PMCID: PMC8380027 DOI: 10.7717/peerj.12034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/01/2021] [Indexed: 11/20/2022] Open
Abstract
The Copepoda is a clade of pancrustaceans containing 14,485 species that are extremely varied in their morphology and lifestyle. Not only do copepods dominate marine plankton and sediment communities and make up a sizeable component of the freshwater plankton, but over 6,000 species are symbiotically associated with every major phylum of marine metazoans, mostly as parasites. Unfortunately, our understanding of copepod evolutionary relationships is relatively limited in part because of their extremely divergent morphology, sparse taxon sampling in molecular phylogenetic analyses, a reliance on only a handful of molecular markers, and little taxonomic overlap between phylogenetic studies. Here, a synthesis tree method is used to integrate published phylogenies into a more comprehensive tree of copepods by leveraging phylogenetic and taxonomic data. A literature review in this study finds fewer than 500 species of copepods have been sampled in molecular phylogenetic studies. Using the Open Tree of Life platform, those taxa that have been sampled in previous phylogenetic studies are grafted together and combined with the underlying copepod taxonomic hierarchy from the Open Tree of Life Taxonomy to make a synthesis phylogeny of all copepod species. Taxon sampling with respect to molecular phylogenetic analyses is reviewed for all orders of copepods and shows only 3% of copepod species have been sampled in phylogenetic studies. The resulting synthesis phylogeny reveals copepods have transitioned to a parasitic lifestyle on at least 14 occasions. We examine the underlying phylogenetic, taxonomic, and natural history data supporting these transitions to parasitism; review the species diversity of each parasitic clade; and identify key areas for further phylogenetic investigation.
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Affiliation(s)
- James P Bernot
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, United States of America.,Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, United States of America
| | | | - Keith A Crandall
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, United States of America.,Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, United States of America
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4
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Non-destructive genome skimming for aquatic copepods. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01129-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractCopepods are important ecologically and represent a large amount of aquatic biomass in both freshwater and marine systems. Despite this, the taxonomy of copepods and other meiofauna is not well understood, hampered by tiny sizes, cryptic taxa, intraspecific polymorphisms and total specimen destruction where DNA methods are employed. In this article we highlight these issues and propose a more up-to-date approach for dealing with them. Namely, we recommend non-destructive DNA extraction methods, coupled with high-throughput sequencing (HTS). Whilst DNA yields may be low, they should still be sufficient for HTS library preparation and DNA sequencing. At the same time morphological specimens can be preserved and the crucial link between morphology and DNA sequence is maintained. This is critical for an integrative taxonomy and a fuller understanding of biodiversity patterns as well as evolutionary processes in meiofauna.
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Hołyńska M, Wyngaard GA. Towards a phylogeny of
Cyclops
(Copepoda): (in)congruences among morphology, molecules and zoogeography. ZOOL SCR 2019. [DOI: 10.1111/zsc.12342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria Hołyńska
- Museum and Institute of Zoology Polish Academy of Sciences Warszawa Poland
| | - Grace A. Wyngaard
- Department of Biology James Madison University Harrisonburg Virginia
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6
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Unraveling the intricate biodiversity of the benthic harpacticoid genus Nannopus (Copepoda, Harpacticoida, Nannopodidae) in Korean waters. Mol Phylogenet Evol 2019; 130:366-379. [DOI: 10.1016/j.ympev.2018.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/17/2018] [Accepted: 10/03/2018] [Indexed: 11/18/2022]
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Laakmann S, Markhaseva EL, Renz J. Do molecular phylogenies unravel the relationships among the evolutionary young “Brafordian” families (Copepoda; Calanoida)? Mol Phylogenet Evol 2019; 130:330-345. [DOI: 10.1016/j.ympev.2018.10.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 10/28/2022]
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Renz J, Markhaseva EL, Laakmann S. The phylogeny of Ryocalanoidea (Copepoda, Calanoida) based on morphology and a multi-gene analysis with a description of new ryocalanoidean species. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Two new species of ryocalanoid copepods (Crustacea: Calanoida), Ryocalanus squamatus sp. nov. and Yrocalanus kurilensis sp. nov. are described together with a female of Ryocalanus infelix Tanaka, 1956, type species for the genus Ryocalanus Tanaka, 1956, from abyssal depths in the Kurile-Kamchatka trench. The new species can be assigned to the superfamily Ryocalanoidea based on the segmentation and armature of the swimming legs and the modification of the male right antennule. A new interpretation of the fusions of segments in the male right antennule of Ryocalanus shows the marked differences between the ryocalanoidean genera. The status of Ryocalanoidea within the Calanoida is discussed based on morphology and a first molecular multi-gene analysis with cytochrome oxidase subunit I, cytochrome b, nuclear ribosomal 18S and 28S rDNA and internal transcribed spacer 2. This analysis supports the close interrelationship between Ryocalanoidea and Spinocalanoidea. The monophyletic status of Ryocalanoidea could not be retrieved in the phylogenetic analysis, as specimens of Yrocalanus formed a clade within Spinocalanoidea. The inconclusive results between morphological and molecular analyses are discussed with a proposition to keep the current system until more males of taxa belonging to the Spinocalanoidea are discovered, as the male antennule plays a crucial role in the interpretation of relationships between Ryocalanoidea and Spinocalanoidea.
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Affiliation(s)
- Jasmin Renz
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg am Meer, Hamburg, Germany
| | - Elena L Markhaseva
- Laboratory of Marine Research, Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Silke Laakmann
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg am Meer, Wilhelmshaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
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9
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Ortega-Mayagoitia E, Hernández-Martínez O, Ciros-Pérez J. Phenotypic plasticity of life-history traits of a calanoid copepod in a tropical lake: Is the magnitude of thermal plasticity related to thermal variability? PLoS One 2018; 13:e0196496. [PMID: 29708999 PMCID: PMC5927456 DOI: 10.1371/journal.pone.0196496] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 04/13/2018] [Indexed: 12/15/2022] Open
Abstract
According to the Climatic Variability Hypothesis [CVH], thermal plasticity should be wider in organisms from temperate environments, but is unlikely to occur in tropical latitudes where temperature fluctuations are narrow. In copepods, food availability has been suggested as the main driver of phenotypic variability in adult size if the range of temperature change is less than 14°C. Leptodiaptomus garciai is a calanoid copepod inhabiting Lake Alchichica, a monomictic, tropical lake in Mexico that experiences regular, narrow temperature fluctuations but wide changes in phytoplankton availability. We investigated whether the seasonal fluctuations of temperature and food produce phenotypic variation in the life-history traits of this tropical species. We sampled L. garciai throughout a year and measured female size, egg size and number, and hatching success, along with temperature and phytoplankton biomass. The amplitude of the plastic responses was estimated with the Phenotypic Plasticity Index. This index was also computed for a published dataset of 84 copepod populations to look if there is a relationship between the amplitude of the phenotypic plasticity of adult size and seasonal change in temperature. The temperature annual range in Lake Alchichica was 3.2°C, whereas phytoplankton abundance varied 17-fold. A strong pattern of thermal plasticity in egg size and adult female size followed the inverse relationship with temperature commonly observed in temperate environments, although its adaptive value was not demonstrated. Egg number, relative reproductive effort and number of nauplii per female were clearly plastic to food availability, allowing organisms to increase their fitness. When comparing copepod species from different latitudes, we found that the magnitude of thermal plasticity of adult size is not related to the range of temperature variation; furthermore, thermal plasticity exists even in environments of limited temperature variation, where the response is more intense compared to temperate populations.
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Affiliation(s)
- Elizabeth Ortega-Mayagoitia
- Grupo de Investigación en Limnología Tropical, División de Investigación y Posgrado, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Edo, de México, México
- * E-mail:
| | - Osvaldo Hernández-Martínez
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Edo, de México, México
| | - Jorge Ciros-Pérez
- Grupo de Investigación en Limnología Tropical, División de Investigación y Posgrado, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Edo, de México, México
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10
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Di Capua I, Maffucci F, Pannone R, Mazzocchi MG, Biffali E, Amato A. Molecular phylogeny of Oncaeidae (Copepoda) using nuclear ribosomal internal transcribed spacer (ITS rDNA). PLoS One 2017; 12:e0175662. [PMID: 28441395 PMCID: PMC5404819 DOI: 10.1371/journal.pone.0175662] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 03/29/2017] [Indexed: 01/19/2023] Open
Abstract
Copepods belonging to the Oncaeidae family are commonly and abundantly found in marine zooplankton. In the Mediterranean Sea, forty-seven oncaeid species occur, of which eleven in the Gulf of Naples. In this Gulf, several Oncaea species were morphologically analysed and described at the end of the XIX century by W. Giesbrecht. In the same area, oncaeids are being investigated over seasonal and inter-annual scales at the long-term coastal station LTER-MC. In the present work, we identified six oncaeid species using the nuclear ribosomal internal transcribed spacers (ITS rDNA) and the mitochondrial cytochrome c oxidase subunit I (mtCOI). Phylogenetic analyses based on these two genomic regions validated the sisterhood of the genera Triconia and the Oncaea sensu stricto. ITS1 and ITS2 phylogenies produced incongruent results about the position of Oncaea curta, calling for further investigations on this species. We also characterised the ITS2 region by secondary structure predictions and found that all the sequences analysed presented the distinct eukaryotic hallmarks. A Compensatory Base Change search corroborated the close relationship between O. venusta and O. curta and between O. media and O. venusta already identified by ITS phylogenies. The present results, which stem from the integration of molecular and morphological taxonomy, represent an encouraging step towards an improved knowledge of copepod biodiversity: The two complementary approaches, when applied to long-term copepod monitoring, will also help to better understanding their genetic variations and ecological niches of co-occurring species.
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Affiliation(s)
- Iole Di Capua
- Department of Integrative Marine Ecology, StazioneZoologica Anton Dohrn, Villa Comunale Naples–Italy
| | - Fulvio Maffucci
- Department of Research Infrastructures for Marine Biological Resources, Aquarium Unit, StazioneZoologica Anton Dohrn, Villa Comunale Naples–Italy
| | - Raimondo Pannone
- Department of Research Infrastructures for Marine Biological Resources, Molecular Biology and Bioinformatics Unit, StazioneZoologica Anton Dohrn, Villa Comunale Naples–Italy
| | - Maria Grazia Mazzocchi
- Department of Integrative Marine Ecology, StazioneZoologica Anton Dohrn, Villa Comunale Naples–Italy
| | - Elio Biffali
- Department of Research Infrastructures for Marine Biological Resources, Molecular Biology and Bioinformatics Unit, StazioneZoologica Anton Dohrn, Villa Comunale Naples–Italy
| | - Alberto Amato
- Department of Integrative Marine Ecology, StazioneZoologica Anton Dohrn, Villa Comunale Naples–Italy
- * E-mail:
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11
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Ohtsuka S, Nishida S. Copepod Biodiversity in Japan: Recent Advances in Japanese Copepodology. SPECIES DIVERSITY OF ANIMALS IN JAPAN 2017. [DOI: 10.1007/978-4-431-56432-4_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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12
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Cornils A, Wend-Heckmann B, Held C. Global phylogeography of Oithona similis s.l. (Crustacea, Copepoda, Oithonidae) - A cosmopolitan plankton species or a complex of cryptic lineages? Mol Phylogenet Evol 2016; 107:473-485. [PMID: 28007567 DOI: 10.1016/j.ympev.2016.12.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 12/09/2016] [Accepted: 12/15/2016] [Indexed: 11/19/2022]
Abstract
Traditionally, many small-sized copepod species are considered to be widespread, bipolar or cosmopolitan. However, these large-scale distribution patterns need to be re-examined in view of increasing evidence of cryptic and pseudo-cryptic speciation in pelagic copepods. Here, we present a phylogeographic study of Oithona similis s.l. populations from the Arctic Ocean, the Southern Ocean and its northern boundaries, the North Atlantic and the Mediterrranean Sea. O. similis s.l. is considered as one of the most abundant species in temperate to polar oceans and acts as an important link in the trophic network between the microbial loop and higher trophic levels such as fish larvae. Two gene fragments were analysed: the mitochondrial cytochrome oxidase c subunit I (COI), and the nuclear ribosomal 28 S genetic marker. Seven distinct, geographically delimitated, mitochondrial lineages could be identified, with divergences among the lineages ranging from 8 to 24%, thus representing most likely cryptic or pseudocryptic species within O. similis s.l. Four lineages were identified within or close to the borders of the Southern Ocean, one lineage in the Arctic Ocean and two lineages in the temperate Northern hemisphere. Surprisingly the Arctic lineage was more closely related to lineages from the Southern hemisphere than to the other lineages from the Northern hemisphere, suggesting that geographic proximity is a rather poor predictor of how closely related the clades are on a genetic level.
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Affiliation(s)
- Astrid Cornils
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany.
| | - Britta Wend-Heckmann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Christoph Held
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
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13
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Predator-prey interactions in the plankton: larval fish feeding on evasive copepods. Sci Rep 2016; 6:33585. [PMID: 27658849 PMCID: PMC5034258 DOI: 10.1038/srep33585] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/31/2016] [Indexed: 11/08/2022] Open
Abstract
Capture success and prey selectivity were investigated in clownfish Amphiprion ocellaris larvae using videography. Three prey types were tested using developmental stages (nauplii, copepodites and adults) of the copepod Parvocalanus crassirostris. Predatory abilities improved rapidly between days 1 and 14 post-hatch. Initially, capture success was limited to nauplii with few attacks on larger stages. Captures of copepodites were first observed at 3 dph, and of adults at 8 dph. Consistent strikes at the larger prey were observed on the day prior to successful captures (2 dph for copepodites, 7 dph for adults). Difference in capture success between nauplii and adults at 8 dph was an order of magnitude. Differences in capture success among prey types persisted but decreased to three-fold by 14 dph. Younger A. ocellaris attacked nauplii preferentially and avoided adult prey. Strike selectivity declined with age, and no selectivity was observed after 10 dph. However, numerically 50% of the ingested prey were still nauplii at 14 dph under the experimental conditions.
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Easton EE, Thistle D. Do some deep‐sea, sediment‐dwelling species of harpacticoid copepods have 1000‐km‐scale range sizes? Mol Ecol 2016; 25:4301-18. [DOI: 10.1111/mec.13744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/19/2016] [Accepted: 06/22/2016] [Indexed: 11/29/2022]
Affiliation(s)
- E. E. Easton
- Department of Earth, Ocean and Atmospheric Science Florida State University Tallahassee FL 32306‐4320 USA
| | - D. Thistle
- Department of Earth, Ocean and Atmospheric Science Florida State University Tallahassee FL 32306‐4320 USA
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15
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Wu S, Xiong J, Yu Y. Taxonomic resolutions based on 18S rRNA genes: a case study of subclass copepoda. PLoS One 2015; 10:e0131498. [PMID: 26107258 PMCID: PMC4479608 DOI: 10.1371/journal.pone.0131498] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/01/2015] [Indexed: 01/20/2023] Open
Abstract
Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1-9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy.
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Affiliation(s)
- Shu Wu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yuhe Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- * E-mail:
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16
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Moon SY, Youn SH, Soh HY. Description of Parvocalanusleei sp. n. (Copepoda, Calanoida, Paracalanidae) in Western Korea, with comments on the taxonomic position of Paracalanusarabiensis Kesarkar & Anil, 2010. Zookeys 2015:29-47. [PMID: 25709519 PMCID: PMC4329397 DOI: 10.3897/zookeys.456.7741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 10/01/2014] [Indexed: 11/30/2022] Open
Abstract
A new species of paracalanid calanoid copepod Parvocalanusleeisp. n., is described from specimens collected in shallow waters of Western Korea. The new species is closely similar to Parvocalanusarabiensis (Kesarkar & Anil, 2010), Parvocalanuscrassirostris (F. Dahl, 1894), Parvocalanuslatus Andronov, 1972, and Parvocalanusscotti (Früchtl, 1923) in having two short terminal spines on the distal segment of the fifth leg and a similar rostrum in the female, but can be readily distinguished from its congeners by the body size, relative length of antennules, segmentation of endopod of leg 1, and pattern of ornamentation of spinules on legs 1 to 4 in the female. The taxonomic position of Parvocalanusarabiensis and the validity of the genus Parvocalanus Andronov, 1970 are also discussed.
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Affiliation(s)
- Seong Yong Moon
- Fisheries and Ocean Information Division, National Fisheries Research and Development Institute, Busan 619-705, South Korea
| | - Seok-Hyun Youn
- Fisheries and Ocean Information Division, National Fisheries Research and Development Institute, Busan 619-705, South Korea
| | - Ho Young Soh
- Faculty of Marine Technology, Chonnam National University, Yeosu 550-749, South Korea
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Zagoskin MV, Lazareva VI, Grishanin AK, Mukha DV. Phylogenetic information content of Copepoda ribosomal DNA repeat units: ITS1 and ITS2 impact. BIOMED RESEARCH INTERNATIONAL 2014; 2014:926342. [PMID: 25215300 PMCID: PMC4151598 DOI: 10.1155/2014/926342] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/08/2014] [Accepted: 07/08/2014] [Indexed: 11/17/2022]
Abstract
The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that the Mesocyclops, Thermocyclops, and Macrocyclops genera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals.
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Affiliation(s)
- Maxim V. Zagoskin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin Street. 3, Moscow 119991, Russia
| | - Valentina I. Lazareva
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia
| | - Andrey K. Grishanin
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia
- Dubna International University for Nature, Society and Man, Universitetskaya Street 19, Dubna 141980, Russia
| | - Dmitry V. Mukha
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin Street. 3, Moscow 119991, Russia
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Bradford-Grieve JM, Boxshall GA, Blanco-Bercial L. Revision of basal calanoid copepod families, with a description of a new species and genus of Pseudocyclopidae. Zool J Linn Soc 2014. [DOI: 10.1111/zoj12141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Janet M. Bradford-Grieve
- National Institute of Water and Atmospheric Research, Private Bag 14901, Kilbirnie, Wellington, 6241, New Zealand
| | - Geoffrey A. Boxshall
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Leocadio Blanco-Bercial
- Department of Marine Science, University of Connecticut, 1080 Shennecossett Road, Groton, CT, 06340, USA
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Bradford-Grieve JM, Boxshall GA, Blanco-Bercial L. Revision of basal calanoid copepod families, with a description of a new species and genus of Pseudocyclopidae. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Janet M. Bradford-Grieve
- National Institute of Water and Atmospheric Research; Private Bag 14901, Kilbirnie Wellington 6241 New Zealand
| | - Geoffrey A. Boxshall
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Leocadio Blanco-Bercial
- Department of Marine Science; University of Connecticut; 1080 Shennecossett Road Groton CT 06340 USA
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Blanco-Bercial L, Cornils A, Copley N, Bucklin A. DNA barcoding of marine copepods: assessment of analytical approaches to species identification. PLOS CURRENTS 2014; 6:ecurrents.tol.cdf8b74881f87e3b01d56b43791626d2. [PMID: 24987576 PMCID: PMC4073882 DOI: 10.1371/currents.tol.cdf8b74881f87e3b01d56b43791626d2] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
More than 2,500 species of copepods (Class Maxillopoda; Subclass Copepoda) occur in the marine planktonic environment. The exceptional morphological conservation of the group, with numerous sibling species groups, makes the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of species based on DNA sequencing of single specimens and environmental samples. Despite the recent development of diverse genetic and genomic markers, the barcode region of the mitochondrial cytochrome c oxidase subunit I (COI) gene remains a useful and - in some cases - unequaled diagnostic character for species-level identification of copepods. This study reports 800 new barcode sequences for 63 copepod species not included in any previous study and examines the reliability and resolution of diverse statistical approaches to species identification based upon a dataset of 1,381 barcode sequences for 195 copepod species. We explore the impact of missing data (i.e., species not represented in the barcode database) on the accuracy and reliability of species identifications. Among the tested approaches, the best close match analysis resulted in accurate identification of all individuals to species, with no errors (false positives), and out-performed automated tree-based or BLAST based analyses. This comparative analysis yields new understanding of the strengths and weaknesses of DNA barcoding and confirms the value of DNA barcodes for species identification of copepods, including both individual specimens and bulk samples. Continued integrative morphological-molecular taxonomic analysis is needed to produce a taxonomically-comprehensive database of barcode sequences for all species of marine copepods.
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Affiliation(s)
| | - Astrid Cornils
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhavn, Germany
| | - Nancy Copley
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Ann Bucklin
- University of Connecticut, Groton, Connecticut, USA
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Cornils A, Held C. Evidence of cryptic and pseudocryptic speciation in the Paracalanus parvus species complex (Crustacea, Copepoda, Calanoida). Front Zool 2014; 11:19. [PMID: 24581044 PMCID: PMC3948017 DOI: 10.1186/1742-9994-11-19] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/20/2014] [Indexed: 11/17/2022] Open
Abstract
Introduction Many marine planktonic crustaceans such as copepods have been considered as widespread organisms. However, the growing evidence for cryptic and pseudo-cryptic speciation has emphasized the need of re-evaluating the status of copepod species complexes in molecular and morphological studies to get a clearer picture about pelagic marine species as evolutionary units and their distributions. This study analyses the molecular diversity of the ecologically important Paracalanus parvus species complex. Its seven currently recognized species are abundant and also often dominant in marine coastal regions worldwide from temperate to tropical oceans. Results COI and Cytochrome b sequences of 160 specimens of the Paracalanus parvus complex from all oceans were obtained. Furthermore, 42 COI sequences from GenBank were added for the genetic analyses. Thirteen distinct molecular operational taxonomic units (MOTU) and two single sequences were revealed with cladistic analyses (Maximum Likelihood, Bayesian Inference), of which seven were identical with results from species delimitation methods (barcode gaps, ABDG, GMYC, Rosenberg’s P(AB)). In total, 10 to 12 putative species were detected and could be placed in three categories: (1) temperate geographically isolated, (2) warm-temperate to tropical wider spread and (3) circumglobal warm-water species. Conclusions The present study provides evidence of cryptic or pseudocryptic speciation in the Paracalanus parvus complex. One major insight is that the species Paracalanus parvus s.s. is not panmictic, but may be restricted in its distribution to the northeastern Atlantic.
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Affiliation(s)
- Astrid Cornils
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Alten Hafen 26, D-27568 Bremerhaven, Germany.
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