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Kulagin DN, Lunina AA, Simakova UV, Vedenin AA, Vereshchaka AL. Revision of the 'Acanthephyra purpurea' species complex (Crustacea: Decapoda), with an emphasis on species diversification in the Atlantic. Mol Phylogenet Evol 2024; 195:108070. [PMID: 38574781 DOI: 10.1016/j.ympev.2024.108070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/14/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
We inventoried all nine species of the 'Acanthephyra purpurea' complex, one of the most abundant and cosmopolitan group of mesopelagic shrimps. We used 119 specimens at hand and genetic data for 124 specimens from GenBank and BOLD. Phylogenetic analysis of four genes (COI, 16S, NaK, and enolase) showed that the 'Acanthephyra purpurea' complex is polyphyletic and encompasses two species groups, 'A. purpurea' (mostly Atlantic) and 'A. smithi' (Indo-West Pacific). The 'A. purpurea' species group consists of two major molecular clades A. pelagica and A. kingsleyi - A. purpurea - A. quadrispinosa. Molecular data suggest that hitherto accepted species A. acanthitelsonis, A. pelagica, and A. sica should be considered as synonyms. The Atlantic is inhabited by at least two cryptic genetic lineages of A. pelagica and A. quadrispinosa. Morphological analyses of qualitative and quantitative (900 measurements) characters resulted in a tabular key to species and in a finding of four evolutionary traits. Atlantic species showed various scenarios of diversification visible on mitochondrial gene level, nuclear gene level, and morphological level. We recorded and discussed similar phylogeographic trends in diversification and in distribution of genetic lineages within two different clades: A. pelagica and A. kingsleyi - A. purpurea - A. quadrispinosa.
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Affiliation(s)
- Dmitry N Kulagin
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia
| | - Anastasiia A Lunina
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia
| | - Ulyana V Simakova
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia
| | | | - Alexander L Vereshchaka
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia.
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2
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Matthews SA, Blanco‐Bercial L. Divergent patterns of zooplankton connectivity in the epipelagic and mesopelagic zones of the eastern North Pacific. Ecol Evol 2023; 13:e10664. [PMID: 37933324 PMCID: PMC10625861 DOI: 10.1002/ece3.10664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/11/2023] [Accepted: 10/13/2023] [Indexed: 11/08/2023] Open
Abstract
Due to historical under-sampling of the deep ocean, the distributional ranges of mesopelagic zooplankton are not well documented, leading to uncertainty about the mechanisms that shape midwater zooplankton community composition. Using a combination of DNA metabarcoding (18S-V4 and mtCOI) and trait-based analysis, we characterized zooplankton diversity and community composition in the upper 1000 m of the northeast Pacific Ocean. We tested whether the North Pacific Transition Zone is a biogeographic boundary region for mesopelagic zooplankton. We also tested whether zooplankton taxa occupying different vertical habitats and exhibiting different ecological traits differed in the ranges of temperature, Chl-a, and dissolved oxygen conditions inhabited. The depth of the maximum taxonomic richness deepened with increasing latitude in the North Pacific. Community similarity in the mesopelagic zone also increased in comparison with the epipelagic zone, and no evidence was found for a biogeographic boundary between previously delineated mesopelagic biogeochemical provinces. Epipelagic zooplankton exhibited broader temperature and Chl-a ranges than mesopelagic taxa. Within the epipelagic, taxa with broader temperature and Chl-a ranges also had broader distributional ranges. However, mesopelagic taxa were distributed across wider dissolved oxygen ranges, and within the mesopelagic, only oxygen ranges covaried with distributional ranges. Environmental and distributional ranges also varied among traits, both for epipelagic taxa and mesopelagic taxa. The strongest differences in both environmental and distributional ranges were observed for taxa with or without diel vertical migration behavior. Our results suggest that species traits can influence the differential effects of physical dispersal and environmental selection in shaping biogeographic distributions.
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Affiliation(s)
- Stephanie A. Matthews
- California Current Ecosystem Long‐Term Ecological Research Site, Integrative Oceanography Division, Scripps Institution of OceanographyUniversity of California San DiegoLa JollaCaliforniaUSA
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3
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Laso-Jadart R, O'Malley M, Sykulski AM, Ambroise C, Madoui MA. Holistic view of the seascape dynamics and environment impact on macro-scale genetic connectivity of marine plankton populations. BMC Ecol Evol 2023; 23:46. [PMID: 37658324 PMCID: PMC10472650 DOI: 10.1186/s12862-023-02160-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Plankton seascape genomics studies have revealed different trends from large-scale weak differentiation to microscale structures. Previous studies have underlined the influence of the environment and seascape on species differentiation and adaptation. However, these studies have generally focused on a few single species, sparse molecular markers, or local scales. Here, we investigated the genomic differentiation of plankton at the macro-scale in a holistic approach using Tara Oceans metagenomic data together with a reference-free computational method. RESULTS We reconstructed the FST-based genomic differentiation of 113 marine planktonic taxa occurring in the North and South Atlantic Oceans, Southern Ocean, and Mediterranean Sea. These taxa belong to various taxonomic clades spanning Metazoa, Chromista, Chlorophyta, Bacteria, and viruses. Globally, population genetic connectivity was significantly higher within oceanic basins and lower in bacteria and unicellular eukaryotes than in zooplankton. Using mixed linear models, we tested six abiotic factors influencing connectivity, including Lagrangian travel time, as proxies of oceanic current effects. We found that oceanic currents were the main population genetic connectivity drivers, together with temperature and salinity. Finally, we classified the 113 taxa into parameter-driven groups and showed that plankton taxa belonging to the same taxonomic rank such as phylum, class or order presented genomic differentiation driven by different environmental factors. CONCLUSION Our results validate the isolation-by-current hypothesis for a non-negligible proportion of taxa and highlight the role of other physicochemical parameters in large-scale plankton genetic connectivity. The reference-free approach used in this study offers a new systematic framework to analyse the population genomics of non-model and undocumented marine organisms from a large-scale and holistic point of view.
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Affiliation(s)
- Romuald Laso-Jadart
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 3 rue Michel-Ange, Paris, France
| | - Michael O'Malley
- STOR-i Centre for Doctoral Training/Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
| | - Adam M Sykulski
- STOR-i Centre for Doctoral Training/Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
| | | | - Mohammed-Amin Madoui
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 3 rue Michel-Ange, Paris, France.
- Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-Aux-Roses, France.
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, 21000, Dijon, France.
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4
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Wang L, Deng Z, Blair D, Hu W, Yin M. Phylogeography and genetic diversity of the Scapholeberis kingii species complex (Cladocera: Daphniidae) in China. Mol Phylogenet Evol 2023; 181:107725. [PMID: 36736845 DOI: 10.1016/j.ympev.2023.107725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023]
Abstract
There is increasing interest in the diversity and phylogeography of aquatic invertebrate zooplankton in the Eastern Palearctic, yet this topic remains largely unexplored in China. Here, we investigated the lineage diversity and phylogeography of an important cladoceran taxon, the Scapholeberis kingii (Cladocera: Daphniidae) species complex, members of which live in the surface layers of freshwater ecosystems. We identified only the S. smirnovi morphospecies from this species complex in 29 of 491 Chinese water bodies examined. Its phylogenetic position was verified using both a mitochondrial (mitochondrial cytochrome c oxidase subunit I; COI) and a nuclear marker (the nuclear large subunit ribosomal RNA gene; 28S). Pronounced geographical separation among three S. smirnovi mitochondrial lineages was observed in China: only a single lineage (Lineage A) was present in the Eastern Plain, whereas Lineages B and C were restricted to the Inner Mongolia-Xinjiang Plateau and the Qinghai-Tibetan Plateau respectively. This deep mtDNA divergence and the substantial genetic differentiation among S. smirnovi populations from different regions is likely a result of the rapid uplift of the Qinghai-Tibetan Plateau and associated ecological changes. This study contributes to an understanding of the genetic diversity of the S. kingii complex, a key component of neustonic zooplankton.
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Affiliation(s)
- Lugege Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Zhixiong Deng
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - David Blair
- College of Science and Engineering, James Cook University, Townsville, Qld 4811, Australia
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China; Department of Microbiology and Bioengineering, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China.
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Johnston NM, Murphy EJ, Atkinson A, Constable AJ, Cotté C, Cox M, Daly KL, Driscoll R, Flores H, Halfter S, Henschke N, Hill SL, Höfer J, Hunt BPV, Kawaguchi S, Lindsay D, Liszka C, Loeb V, Manno C, Meyer B, Pakhomov EA, Pinkerton MH, Reiss CS, Richerson K, Jr. WOS, Steinberg DK, Swadling KM, Tarling GA, Thorpe SE, Veytia D, Ward P, Weldrick CK, Yang G. Status, Change, and Futures of Zooplankton in the Southern Ocean. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.624692] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In the Southern Ocean, several zooplankton taxonomic groups, euphausiids, copepods, salps and pteropods, are notable because of their biomass and abundance and their roles in maintaining food webs and ecosystem structure and function, including the provision of globally important ecosystem services. These groups are consumers of microbes, primary and secondary producers, and are prey for fishes, cephalopods, seabirds, and marine mammals. In providing the link between microbes, primary production, and higher trophic levels these taxa influence energy flows, biological production and biomass, biogeochemical cycles, carbon flux and food web interactions thereby modulating the structure and functioning of ecosystems. Additionally, Antarctic krill (Euphausia superba) and various fish species are harvested by international fisheries. Global and local drivers of change are expected to affect the dynamics of key zooplankton species, which may have potentially profound and wide-ranging implications for Southern Ocean ecosystems and the services they provide. Here we assess the current understanding of the dominant metazoan zooplankton within the Southern Ocean, including Antarctic krill and other key euphausiid, copepod, salp and pteropod species. We provide a systematic overview of observed and potential future responses of these taxa to a changing Southern Ocean and the functional relationships by which drivers may impact them. To support future ecosystem assessments and conservation and management strategies, we also identify priorities for Southern Ocean zooplankton research.
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Sugier K, Laso-Jadart R, Vacherie B, Käfer J, Bertrand L, Labadie K, Martins N, Orvain C, Petit E, Wincker P, Jamet JL, Alberti A, Madoui MA. Male Differentiation in the Marine Copepod Oithona nana Reveals the Development of a New Nervous Ganglion and Lin12-Notch-Repeat Protein-Associated Proteolysis. BIOLOGY 2021; 10:biology10070657. [PMID: 34356512 PMCID: PMC8301441 DOI: 10.3390/biology10070657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/30/2021] [Accepted: 07/08/2021] [Indexed: 11/23/2022]
Abstract
Simple Summary Copepods are tiny crustaceans and the most abundant animals on Earth; they also play a crucial role in the marine food chain. Among copepods, Oithona is one of most ecologically successful and is known for its differential behavior between males and females. The males adopt the strategy “live fast, die young”: they are constantly in motion to search for females, more vulnerable to predators, feed less, and have a higher mortality rate. In our study, we found the presence of a new male-specific ganglion in Oithona nana probably involved in female cues sensing. We also demonstrate the potential role of new Lin-12 Notch Repeat proteins in the development of this ganglion by interacting with proteins involved in the development of the nervous system. Thanks to our findings, we propose that the “live fast, die young” strategy of the O. nana males is optimized by the explosion of these Lin-12 Notch Repeat proteins in the male proteome involved in the development of the male-specific olfactory ganglion to increase female cue sensing and mating. Abstract Copepods are among the most numerous animals, and they play an essential role in the marine trophic web and biogeochemical cycles. The genus Oithona is described as having the highest density of copepods. The Oithona male paradox describes the activity states of males, which are obliged to alternate between immobile and mobile phases for ambush feeding and mate searching, respectively, while the female is less mobile and feeds less. To characterize the molecular basis of this sexual dimorphism, we combined immunofluorescence, genomics, transcriptomics, and protein–protein interaction approaches and revealed the presence of a male-specific nervous ganglion. Transcriptomic analysis showed male-specific enrichment for nervous system development-related transcripts. Twenty-seven Lin12-Notch Repeat domain-containing protein coding genes (LDPGs) of the 75 LDPGs identified in the genome were specifically expressed in males. Furthermore, some LDPGs coded for proteins with predicted proteolytic activity, and proteases-associated transcripts showed a male-specific enrichment. Using yeast double–hybrid assays, we constructed a protein–protein interaction network involving two LDPs with proteases, extracellular matrix proteins, and neurogenesis-related proteins. We also hypothesized possible roles of the LDPGs in the development of the lateral ganglia through helping in extracellular matrix lysis, neurites growth guidance, and synapses genesis.
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Affiliation(s)
- Kevin Sugier
- Génomique Métabolique, Genoscope, Institut François Jacob, Univ Evry, Université Paris-Saclay, 91000 Evry, France; (K.S.); (R.L.-J.); (L.B.); (N.M.); (C.O.); (P.W.); (A.A.)
| | - Romuald Laso-Jadart
- Génomique Métabolique, Genoscope, Institut François Jacob, Univ Evry, Université Paris-Saclay, 91000 Evry, France; (K.S.); (R.L.-J.); (L.B.); (N.M.); (C.O.); (P.W.); (A.A.)
| | - Benoît Vacherie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, 91000 Evry, France; (B.V.); (K.L.); (E.P.)
| | - Jos Käfer
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université Lyon 1, Université de Lyon, 69622 Villeurbanne, France;
| | - Laurie Bertrand
- Génomique Métabolique, Genoscope, Institut François Jacob, Univ Evry, Université Paris-Saclay, 91000 Evry, France; (K.S.); (R.L.-J.); (L.B.); (N.M.); (C.O.); (P.W.); (A.A.)
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, 91000 Evry, France; (B.V.); (K.L.); (E.P.)
| | - Nathalie Martins
- Génomique Métabolique, Genoscope, Institut François Jacob, Univ Evry, Université Paris-Saclay, 91000 Evry, France; (K.S.); (R.L.-J.); (L.B.); (N.M.); (C.O.); (P.W.); (A.A.)
| | - Céline Orvain
- Génomique Métabolique, Genoscope, Institut François Jacob, Univ Evry, Université Paris-Saclay, 91000 Evry, France; (K.S.); (R.L.-J.); (L.B.); (N.M.); (C.O.); (P.W.); (A.A.)
| | - Emmanuelle Petit
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, 91000 Evry, France; (B.V.); (K.L.); (E.P.)
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, Univ Evry, Université Paris-Saclay, 91000 Evry, France; (K.S.); (R.L.-J.); (L.B.); (N.M.); (C.O.); (P.W.); (A.A.)
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, 91000 Evry, France; (B.V.); (K.L.); (E.P.)
| | - Jean-Louis Jamet
- Mediterranean Institute of Oceanography, Université de Toulon, Aix-Marseille Université, CEDEX 9, 83041 Toulon, France;
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, Univ Evry, Université Paris-Saclay, 91000 Evry, France; (K.S.); (R.L.-J.); (L.B.); (N.M.); (C.O.); (P.W.); (A.A.)
| | - Mohammed-Amin Madoui
- Génomique Métabolique, Genoscope, Institut François Jacob, Univ Evry, Université Paris-Saclay, 91000 Evry, France; (K.S.); (R.L.-J.); (L.B.); (N.M.); (C.O.); (P.W.); (A.A.)
- Correspondence:
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Phenological responses of the Arctic, ubiquitous, and boreal copepod species to long-term changes in the annual seasonality of the water temperature in the White Sea. Polar Biol 2021. [DOI: 10.1007/s00300-021-02851-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Mendes CB, Norenburg JL, Andrade SCS. Species delimitation integrative approach reveals three new species in the Nemertopsis bivittata complex. INVERTEBR SYST 2021. [DOI: 10.1071/is20048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The presence of cryptic species is fairly frequent in many invertebrate groups and even more so among invertebrates with simple morphology, such as nemerteans. Consequently, the use of molecular methods for species delimitation has become a needed tool to complement morphological analyses to better recognise such species. Nemertopsis bivittata is one example of species with subtle morphological variation, but ample geographic distribution, being a good candidate for a species complex study. Here we applied two mitochondrial genes, and 2903 single nucleotide polymorphism (SNP) variants in addition to morphological characters to investigate the presence of cryptic species among specimens previously identified as N. bivittata along the Brazilian Coast. To do so, specimens were collected at 15 different sites in the north-east, south-east and southern regions. Three new species of Nemertopsis are described based on morphological and molecular analyses: Nemertopsis caete sp. nov., Nemertopsis pamelaroeae sp. nov. and Nemertopsis berthalutzae sp. nov. The species N. pamelaroeae and N. berthalutzae present broad distributions from north-east to south-east; N. caete, however, is restricted to the north-east coast. This is the first study to use this combined approach in nemerteans and shows the advantages of integrating genomic markers with classical taxonomy, and applying objective approaches to delimiting species as independently evolving entities.
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Laakmann S, Blanco-Bercial L, Cornils A. The crossover from microscopy to genes in marine diversity: from species to assemblages in marine pelagic copepods. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190446. [PMID: 33131432 PMCID: PMC7662206 DOI: 10.1098/rstb.2019.0446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
An accurate identification of species and communities is a prerequisite for analysing and recording biodiversity and community shifts. In the context of marine biodiversity conservation and management, this review outlines past, present and forward-looking perspectives on identifying and recording planktonic diversity by illustrating the transition from traditional species identification based on morphological diagnostic characters to full molecular genetic identification of marine assemblages. In this process, the article presents the methodological advancements by discussing progress and critical aspects of the crossover from traditional to novel and future molecular genetic identifications and it outlines the advantages of integrative approaches using the strengths of both morphological and molecular techniques to identify species and assemblages. We demonstrate this process of identifying and recording marine biodiversity on pelagic copepods as model taxon. Copepods are known for their high taxonomic and ecological diversity and comprise a huge variety of behaviours, forms and life histories, making them a highly interesting and well-studied group in terms of biodiversity and ecosystem functioning. Furthermore, their short life cycles and rapid responses to changing environments make them good indicators and core research components for ecosystem health and status in the light of environmental change. This article is part of the theme issue 'Integrative research perspectives on marine conservation'.
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Affiliation(s)
- Silke Laakmann
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstrasse 231, 26129 Oldenburg, Germany.,Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | | | - Astrid Cornils
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
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Barth-Jensen C, Koski M, Varpe Ø, Glad P, Wangensteen OS, Præbel K, Svensen C. Temperature-dependent egg production and egg hatching rates of small egg-carrying and broadcast-spawning copepods Oithona similis, Microsetella norvegica and Microcalanus pusillus. JOURNAL OF PLANKTON RESEARCH 2020; 42:564-580. [PMID: 32939156 PMCID: PMC7484935 DOI: 10.1093/plankt/fbaa039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 07/31/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Reproductive rates of copepods are temperature-dependent, but poorly known for small copepods at low temperatures, hindering the predictions of population dynamics and secondary production in high-latitude ecosystems. We investigated egg hatching rates, hatching success and egg production of the small copepods Oithona similis and Microsetella norvegica (sac spawners) and Microcalanus pusillus (broadcast spawner) between March and August. Incubations were performed at ecologically relevant temperatures between 1.3 and 13.2°C, and egg production rates were calculated. All egg hatching rates were positively correlated to temperature, although with large species-specific differences. At the lowest temperatures, M. pusillus eggs hatched within 4 days, whereas the eggs from sac spawners took 3-8 weeks to hatch. The egg hatching success was ≤25% for M. pusillus, >75% for O. similis and variable for M. norvegica. The maximum weight-specific egg production rate (μg C μg-1 C d-1) of M. pusillus was higher (0.22) than O. similis (0.12) and M. norvegica (0.06). M. norvegica reproduction peaked at 6-8°C, the prevailing in situ temperatures during its reproductive period. The difference in reproductive rates indicates species-specific thermal plasticity for the three copepods, which could have implications for present and future population dynamics of the species in arctic fjords.
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Affiliation(s)
| | - Marja Koski
- NATIONAL INSTITUTE FOR AQUATIC RESOURCES, TECHNICAL UNIVERSITY OF DENMARK, LYNGBY, DENMARK
| | - Øystein Varpe
- NORWEGIAN INSTITUTE FOR NATURE RESEARCH, BERGEN, NORWAY
- DEPARTMENT OF BIOLOGICAL SCIENCES, UNIVERSITY OF BERGEN, BERGEN, NORWAY
| | - Peter Glad
- FACULTY OF BIOSCIENCES, FISHERIES AND ECONOMICS, UIT THE ARCTIC UNIVERSITY OF NORWAY, TROMSø, NORWAY
| | - Owen S Wangensteen
- FACULTY OF BIOSCIENCES, FISHERIES AND ECONOMICS, UIT THE ARCTIC UNIVERSITY OF NORWAY, TROMSø, NORWAY
| | - Kim Præbel
- FACULTY OF BIOSCIENCES, FISHERIES AND ECONOMICS, UIT THE ARCTIC UNIVERSITY OF NORWAY, TROMSø, NORWAY
| | - Camilla Svensen
- FACULTY OF BIOSCIENCES, FISHERIES AND ECONOMICS, UIT THE ARCTIC UNIVERSITY OF NORWAY, TROMSø, NORWAY
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11
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Laso‐Jadart R, Sugier K, Petit E, Labadie K, Peterlongo P, Ambroise C, Wincker P, Jamet J, Madoui M. Investigating population-scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866). Ecol Evol 2020; 10:8894-8905. [PMID: 32884665 PMCID: PMC7452778 DOI: 10.1002/ece3.6588] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/04/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022] Open
Abstract
Acclimation allowed by variation in gene or allele expression in natural populations is increasingly understood as a decisive mechanism, as much as adaptation, for species evolution. However, for small eukaryotic organisms, as species from zooplankton, classical methods face numerous challenges. Here, we propose the concept of allelic differential expression at the population-scale (psADE) to investigate the variation in allele expression in natural populations. We developed a novel approach to detect psADE based on metagenomic and metatranscriptomic data from environmental samples. This approach was applied on the widespread marine copepod, Oithona similis, by combining samples collected during the Tara Oceans expedition (2009-2013) and de novo transcriptome assemblies. Among a total of 25,768 single nucleotide variants (SNVs) of O. similis, 572 (2.2%) were affected by psADE in at least one population (FDR < 0.05). The distribution of SNVs under psADE in different populations is significantly shaped by population genomic differentiation (Pearson r = 0.87, p = 5.6 × 10-30), supporting a partial genetic control of psADE. Moreover, a significant amount of SNVs (0.6%) were under both selection and psADE (p < .05), supporting the hypothesis that natural selection and psADE tends to impact common loci. Population-scale allelic differential expression offers new insights into the gene regulation control in populations and its link with natural selection.
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Affiliation(s)
- Romuald Laso‐Jadart
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
- Research Federation for the study of Global Ocean Systems Ecology and EvolutionFR2022/Tara Oceans GO‐SEEParisFrance
| | - Kevin Sugier
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
| | - Emmanuelle Petit
- CEA, GenoscopeInstitut de Biologie François JacobUniversité Paris‐SaclayEvryFrance
| | - Karine Labadie
- CEA, GenoscopeInstitut de Biologie François JacobUniversité Paris‐SaclayEvryFrance
| | | | | | - Patrick Wincker
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
- Research Federation for the study of Global Ocean Systems Ecology and EvolutionFR2022/Tara Oceans GO‐SEEParisFrance
| | - Jean‐Louis Jamet
- Mediterranean Institute of Oceanology (MIO)AMU‐UTLN UM110CNRS UMR7294, IRDUMR235Equipe Ecologie Marine et Biodiversité (EMBIO)Université de ToulonToulon Cedex 9France
| | - Mohammed‐Amin Madoui
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
- Research Federation for the study of Global Ocean Systems Ecology and EvolutionFR2022/Tara Oceans GO‐SEEParisFrance
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12
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Ni Y, Ebido CC, Odii EC, Wang J, Orakwelu CH, Abonyi FC, Ngene CI, Okoro JO, Ubachukwu PO, Hu W, Yin M. Phylogeography and genetic diversity of the copepod family Cyclopidae (Crustacea: Cyclopoida) from freshwater ecosystems of Southeast Nigeria. BMC Evol Biol 2020; 20:45. [PMID: 32316908 PMCID: PMC7171763 DOI: 10.1186/s12862-020-01608-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Background Copepods are key components of aquatic ecosystems and can help regulate the global carbon cycle. Much attention has been paid to the species diversity of copepods worldwide, but the phylogeography and genetic diversity of copepods in Nigeria is unexplored. Results Using a mitochondrial cytochrome c oxidase subunit I marker, we preformed phylogenetic and phylogeographic analyses for Cyclopidae copepods in Southeast Nigeria. A high species diversity of Cyclopidae in Nigeria: 5 species of Tropocyclops, 5 species of Mesocyclops and 2 species of Thermocyclops from Cyclopidae were identified in 15 populations. Moreover, we detected 18 unique haplotypes, which fell into two distinct clades. Pairwise genetic distances (uncorrected p-distances) among the species of Cyclopidae ranged from 0.05 to 0.257. Several species co-existed in the same lake, and some haplotypes were shared among different geographic populations, suggesting a dispersal of Cyclopidae in our sampling region. Finally, we found that the population genetic diversity for each species of Cyclopidae was low in Nigeria. Conclusions Our findings explored the species diversity and distribution of copepods within the family Cyclopidae for 15 Nigerian freshwater ecosystems: a high species diversity of Cyclopidae copepods was detected over a small geographic sampling range. Results from this study contribute to a better understanding of copepod diversity of Nigerian freshwater ecosystems.
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Affiliation(s)
- Yijun Ni
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Chike Chukwuenyem Ebido
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Elijah Chibueze Odii
- Department of Zoology and Environmental Biology, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | - Jinhui Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Chinemerem Hodges Orakwelu
- Department of Zoology and Environmental Biology, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | - Francis Chukwuemeka Abonyi
- Department of Zoology and Environmental Biology, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | - Chinedu Innocent Ngene
- Department of Zoology and Environmental Biology, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | - Joseph Onyekwere Okoro
- Department of Zoology and Environmental Biology, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | - Patience Obiageli Ubachukwu
- Department of Zoology and Environmental Biology, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China.
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13
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Wall-Palmer D, Hegmann M, Goetze E, Peijnenburg KT. Resolving species boundaries in the Atlanta brunnea species group (Gastropoda, Pterotracheoidea). Zookeys 2019; 899:59-84. [PMID: 31871402 PMCID: PMC6923281 DOI: 10.3897/zookeys.899.38892] [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: 08/07/2019] [Accepted: 10/29/2019] [Indexed: 12/22/2022] Open
Abstract
Atlantid heteropods are a family of holoplanktonic marine gastropods that occur primarily in tropical and subtropical latitudes. Atlantids bear a delicate aragonitic shell (<14 mm) and live in the upper ocean, where ocean acidification and ocean warming have a pronounced effect. Therefore, atlantids are likely to be sensitive to these ocean changes. However, we lack sufficiently detailed information on atlantid taxonomy and biogeography, which is needed to gain a deeper understanding of the consequences of a changing ocean. To date, atlantid taxonomy has mainly relied on morphometrics and shell ornamentation, but recent molecular work has highlighted hidden diversity. This study uses an integrated approach in a global analysis of biogeography, variation in shell morphology and molecular phylogenies based on three genes (CO1, 28S and 18S) to resolve the species boundaries within the Atlanta brunnea group. Results identify a new species, Atlanta vanderspoeli, from the Equatorial and South Pacific Ocean, and suggest that individuals of A. brunnea living in the Atlantic Ocean are an incipient species. Our results provide an important advance in atlantid taxonomy and will enable identification of these species in future studies of living and fossil plankton.
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Affiliation(s)
- Deborah Wall-Palmer
- Marine Biodiversity Group, Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
| | - Mona Hegmann
- Marine Biodiversity Group, Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
- Institute for Biosciences, University of Rostock, Albert Einstein Straβe 3, 18059 Rostock, GermanyUniversity of RostockRostockGermany
| | - Erica Goetze
- Department of Oceanography, University of Hawaii at Manoa, 1000 Pope Road, Honolulu, Hawaii, 96822, USAUniversity of Hawaii at ManoaHawaiiUnited States of America
| | - Katja T.C.A. Peijnenburg
- Marine Biodiversity Group, Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P. O. Box 942480 1090 GE Amsterdam, The NetherlandsUniversity of AmsterdamAmsterdamNetherlands
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14
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Han CC, Hsu KC, Fang LS, Cheng IM, Lin HD. Geographical and temporal origins of Neocaridina species (Decapoda: Caridea: Atyidae) in Taiwan. BMC Genet 2019; 20:86. [PMID: 31752677 PMCID: PMC6868699 DOI: 10.1186/s12863-019-0788-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 10/31/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The freshwater species on Taiwan Island have been documented to have originated from mainland China and the Japanese islands from multiple events and by multiple colonization routes. Moreover, the sequences from the mitochondrial DNA cytochrome c oxidase subunit I (COI) have been used for DNA barcoding to identify the species. This study used the COI sequences to identify Neocaridina species in Taiwan and to examine their geographical and temporal origins. RESULTS In total, 479 specimens were collected from 35 localities, which covered almost all rivers in Taiwan. In addition, some sequences were downloaded from GenBank. The maximum likelihood (ML) tree displayed that all sequences were sorted into 13 taxa (clades), and all sequences in Taiwan were sorted into four clades. The Bayesian skyline plots revealed that these four Neocaridina species have declined recently in Taiwan. CONCLUSIONS All results support that (1) there are four Neocaridina species in Taiwan, which are N. davidi, N. saccam, N. ketagalan and an undescribed Neocaridina species (N. sp.); (2) these four species colonized Taiwan Island in four colonization events; (3) N. sp. colonized Taiwan first; (4) after the island reached its shape, N. ketagalan and N. saccam colonized Taiwan from the Japanese islands and mainland China, respectively; (5) N. davidi colonized northern Taiwan last; and (6) the cyclic glacial and landform changes in East Asia shaped the colonization events and population structures of the Neocaridina species.
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Affiliation(s)
- Chiao-Chuan Han
- National Museum of Marine Biology and Aquarium, Pingtung, 944 Taiwan
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, 944 Taiwan
| | - Kui-Ching Hsu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088 China
| | - Lee-Shing Fang
- Center for Environmental Toxin and Emerging-Contaminant Research,Cheng Shiu University, Kaohsiung, 83347 Taiwan
- Department of Leisure and Sport Management, Cheng Shiu University, Kaohsiung, 83347 Taiwan
| | - I-Ming Cheng
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 80424 Taiwan
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, 701 Taiwan
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15
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Ni Y, Ma X, Hu W, Blair D, Yin M. New lineages and old species: Lineage diversity and regional distribution of Moina (Crustacea: Cladocera) in China. Mol Phylogenet Evol 2019; 134:87-98. [PMID: 30753887 DOI: 10.1016/j.ympev.2019.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 10/27/2022]
Abstract
The distribution and genetic diversity of freshwater zooplankton is understudied in the Eastern Palearctic. Here, we explored the lineage diversity and regional distribution of the genus Moina in China. Members of this genus are often keystone components of freshwater ecosystems and have been frequently subjected to toxicological and physiological studies. Four species of Moina were identified, based on morphology, in 50 of 113 Chinese water bodies examined, and their phylogenetic position was analyzed using both a mitochondrial (mitochondrial cytochrome c oxidase subunit I; COI) and a nuclear marker (the nuclear internal transcribed spacer; ITS-1). Both molecular markers identified four clades corresponding broadly to the morphological species. Mitochondrial DNA analysis showed the presence of four species complexes with eleven lineages across China, five of which were new. However, some lineages (and even individual haplotypes) were widespread in Eurasia, suggesting an ability to disperse over long distances. In contrast, a few lineages exhibited restricted distributions. The nuclear phylogeny also recognized four species of Moina within China and seven very distinct clades. Interestingly, one specimen possessing Moina cf. micrura mtDNA had ITS-1 alleles of the M. cf. brachiata clade. This discordance between mtDNA and nuclear ITS-1 phylogenies is indicative of interspecific introgression and hybridization. Additionally, our COI phylogeny showed apparent paraphyly in two Moina species groups, suggesting introgression of their mitochondrial genomes. Our data shows the regional distribution/diversity of the Moina species complex in a Eurasian context.
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Affiliation(s)
- Yijun Ni
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Xiaolin Ma
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - David Blair
- College of Marine and Environmental Sciences, James Cook University, Townsville, Qld 4811, Australia
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China.
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16
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Pfaller JB, Payton AC, Bjorndal KA, Bolten AB, McDaniel SF. Hitchhiking the high seas: Global genomics of rafting crabs. Ecol Evol 2019; 9:957-974. [PMID: 30805133 PMCID: PMC6374717 DOI: 10.1002/ece3.4694] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 12/04/2022] Open
Abstract
Population differentiation and diversification depend in large part on the ability and propensity of organisms to successfully disperse. However, our understanding of these processes in organisms with high dispersal ability is biased by the limited genetic resolution offered by traditional genotypic markers. Many neustonic animals disperse not only as pelagic larvae, but also as juveniles and adults while drifting or rafting at the surface of the open ocean. In theory, the heightened dispersal ability of these animals should limit opportunities for species diversification and population differentiation. To test these predictions, we used next-generation sequencing of genomewide restriction-site-associated DNA tags (RADseq) and traditional mitochondrial DNA sequencing, to investigate the species-level relationships and global population structure of Planes crabs collected from oceanic flotsam and sea turtles. Our results indicate that species diversity in this clade is low-likely three closely related species-with no evidence of cryptic or undescribed species. Moreover, our results indicate weak population differentiation among widely separated aggregations with genetic indices showing only subtle genetic discontinuities across all oceans of the world (RADseq F ST = 0.08-0.16). The results of this study provide unprecedented resolution of the systematics and global biogeography of this group and contribute valuable information to our understanding of how theoretical dispersal potential relates to actual population differentiation and diversification among marine organisms. Moreover, these results demonstrate the limitations of single gene analyses and the value of genomic-level resolution for estimating contemporary population structure in organisms with large, highly connected populations.
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Affiliation(s)
- Joseph B. Pfaller
- Department of Biology, Archie Carr Center for Sea Turtle ResearchUniversity of FloridaGainesvilleFlorida
- Caretta Research ProjectSavannahGeorgia
| | - Adam C. Payton
- Department of BiologyUniversity of FloridaGainesvilleFlorida
| | - Karen A. Bjorndal
- Department of Biology, Archie Carr Center for Sea Turtle ResearchUniversity of FloridaGainesvilleFlorida
| | - Alan B. Bolten
- Department of Biology, Archie Carr Center for Sea Turtle ResearchUniversity of FloridaGainesvilleFlorida
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Sugier K, Vacherie B, Cornils A, Wincker P, Jamet JL, Madoui MA. Chitin distribution in the Oithona digestive and reproductive systems revealed by fluorescence microscopy. PeerJ 2018; 6:e4685. [PMID: 29780666 PMCID: PMC5957050 DOI: 10.7717/peerj.4685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/10/2018] [Indexed: 11/20/2022] Open
Abstract
Among copepods, which are the most abundant animals on Earth, the genus Oithona is described as one of the most numerous and plays a major role in the marine food chain and biogeochemical cycles, particularly through the excretion of chitin-coated fecal pellets. Despite the morphology of several Oithona species is well known, knowledge of its internal anatomy and chitin distribution is still limited. To answer this problem, Oithona nana and O. similis individuals were stained by Wheat Germ Agglutinin-Fluorescein IsoThioCyanate (WGA-FITC) and DiAmidino-2-PhenylIndole (DAPI) for fluorescence microscopy observations. The image analyses allowed a new description of the organization and chitin content of the digestive and reproductive systems of Oithona male and female. Chitin microfibrils were found all along the digestive system from the stomach to the hindgut with a higher concentration at the peritrophic membrane of the anterior midgut. Several midgut shrinkages were observed and proposed to be involved in faecal pellet shaping and motion. Amorphous chitin structures were also found to be a major component of the ducts and seminal vesicles and receptacles. The rapid staining protocol we proposed allowed a new insight into the Oithona internal anatomy and highlighted the role of chitin in the digestion and reproduction. This method could be applied to a wide range of copepods in order to perform comparative anatomy analyses.
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Affiliation(s)
- Kevin Sugier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Benoit Vacherie
- Commissariat à l'Energie Atomique (CEA), Institut François Jacob, Genoscope, Evry, France
| | - Astrid Cornils
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Polar Biological Oceanography, Bremerhaven, Germany
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Louis Jamet
- Université de Toulon, Aix Marseille Université, CNRS/INSU, IRD, MIO UM 110, Mediterranean Institute of Oceanography, La Garde, France
| | - Mohammed-Amin Madoui
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
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18
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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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19
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20
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Wall-Palmer D, Burridge AK, Goetze E, Stokvis FR, Janssen AW, Mekkes L, Moreno-Alcántara M, Bednaršek N, Schiøtte T, Sørensen MV, Smart CW, T.C.A. Peijnenburg K. Biogeography and genetic diversity of the atlantid heteropods. PROGRESS IN OCEANOGRAPHY 2018; 160:1-25. [PMID: 29479121 PMCID: PMC5819870 DOI: 10.1016/j.pocean.2017.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 09/15/2017] [Accepted: 11/03/2017] [Indexed: 06/08/2023]
Abstract
The atlantid heteropods are regularly encountered, but rarely studied marine planktonic gastropods. Relying on a small (<14 mm), delicate aragonite shell and living in the upper ocean means that, in common with pteropods, atlantids are likely to be affected by imminent ocean changes. Variable shell morphology and widespread distributions indicate that the family is more diverse than the 23 currently known species. Uncovering this diversity is fundamental to determining the distribution of atlantids and to understanding their environmental tolerances. Here we present phylogenetic analyses of all described species of the family Atlantidae using 437 new and 52 previously published cytochrome c oxidase subunit 1 mitochondrial DNA (mtCO1) sequences. Specimens and published sequences were gathered from 32 Atlantic Ocean stations, 14 Indian Ocean stations and 21 Pacific Ocean stations between 35°N and 43°S. DNA barcoding and Automatic Barcode Gap Discovery (ABGD) proved to be valuable tools for the identification of described atlantid species, and also revealed ten additional distinct clades, suggesting that the diversity within this family has been underestimated. Only two of these clades displayed obvious morphological characteristics, demonstrating that much of the newly discovered diversity is hidden from morphology-based identification techniques. Investigation of six large atlantid collections demonstrated that 61% of previously described (morpho) species have a circumglobal distribution. Of the remaining 39%, two species were restricted to the Atlantic Ocean, five occurred in the Indian and Pacific oceans, one species was only found in the northeast Pacific Ocean, and one occurred only in the Southern Subtropical Convergence Zone. Molecular analysis showed that seven of the species with wide distributions were comprised of two or more clades that occupied distinct oceanographic regions. These distributions may suggest narrower environmental tolerances than the described morphospecies. Results provide an updated biogeography and mtCO1 reference dataset of the Atlantidae that may be used to identify atlantid species and provide a first step in understanding their evolutionary history and accurate distribution, encouraging the inclusion of this family in future plankton research.
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Affiliation(s)
- Deborah Wall-Palmer
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth PL4 8AA, UK
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Alice K. Burridge
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Erica Goetze
- Department of Oceanography, University of Hawai‘i at Mānoa, Honolulu, HI 96822, USA
| | - Frank R. Stokvis
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Arie W. Janssen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Lisette Mekkes
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - María Moreno-Alcántara
- Departamento de Plancton y Ecología Marina, Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, La Paz C.P. 23096, Mexico
| | - Nina Bednaršek
- Southern California Coastal Waters Research Project, Harbor Blvd #110, Costa Mesa, CA 92626, USA
| | - Tom Schiøtte
- The Natural History Museum of Denmark, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Christopher W. Smart
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Katja T.C.A. Peijnenburg
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1090 GE Amsterdam, The Netherlands
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21
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Deagle BE, Clarke LJ, Kitchener JA, Polanowski AM, Davidson AT. Genetic monitoring of open ocean biodiversity: An evaluation of DNA metabarcoding for processing continuous plankton recorder samples. Mol Ecol Resour 2017; 18:391-406. [PMID: 29171158 DOI: 10.1111/1755-0998.12740] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/07/2017] [Accepted: 11/16/2017] [Indexed: 10/18/2022]
Abstract
DNA metabarcoding is an efficient method for measuring biodiversity, but the process of initiating long-term DNA-based monitoring programmes, or integrating with conventional programs, is only starting. In marine ecosystems, plankton surveys using the continuous plankton recorder (CPR) have characterized biodiversity along transects covering millions of kilometres with time-series spanning decades. We investigated the potential for use of metabarcoding in CPR surveys. Samples (n = 53) were collected in two Southern Ocean transects and metazoans identified using standard microscopic methods and by high-throughput sequencing of a cytochrome c oxidase subunit I marker. DNA increased the number of metazoan species identified and provided high-resolution taxonomy of groups problematic in conventional surveys (e.g., larval echinoderms and hydrozoans). Metabarcoding also generally produced more detections than microscopy, but this sensitivity may make cross-contamination during sampling a problem. In some samples, the prevalence of DNA from large plankton such as krill masked the presence of smaller species. We investigated adding a fixed amount of exogenous DNA to samples as an internal control to allow determination of relative plankton biomass. Overall, the metabarcoding data represent a substantial shift in perspective, making direct integration into current long-term time-series challenging. We discuss a number of hurdles that exist for progressing DNA metabarcoding from the current snapshot studies to the requirements of a long-term monitoring programme. Given the power and continually increasing efficiency of metabarcoding, it is almost certain this approach will play an important role in future plankton monitoring.
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Affiliation(s)
- Bruce E Deagle
- Australian Antarctic Division, Kingston, Tas., Australia.,Antarctic Climate & Ecosystems Cooperative Research Centre, University of Tasmania, Hobart, Tas., Australia
| | - Laurence J Clarke
- Australian Antarctic Division, Kingston, Tas., Australia.,Antarctic Climate & Ecosystems Cooperative Research Centre, University of Tasmania, Hobart, Tas., Australia
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Madoui MA, Poulain J, Sugier K, Wessner M, Noel B, Berline L, Labadie K, Cornils A, Blanco-Bercial L, Stemmann L, Jamet JL, Wincker P. New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepodOithona. Mol Ecol 2017. [DOI: 10.1111/mec.14214] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Mohammed-Amin Madoui
- Commissariat à l'Energie Atomique (CEA); Institut de Biologie François Jacob, Genoscope; Evry France
- Centre National de la Recherche Scientifique; UMR 8030 Université d'Evry val d'Essonne; Evry France
- Université d'Evry Val D'Essonne; Evry France
| | - Julie Poulain
- Commissariat à l'Energie Atomique (CEA); Institut de Biologie François Jacob, Genoscope; Evry France
| | - Kevin Sugier
- Commissariat à l'Energie Atomique (CEA); Institut de Biologie François Jacob, Genoscope; Evry France
- Centre National de la Recherche Scientifique; UMR 8030 Université d'Evry val d'Essonne; Evry France
- Université d'Evry Val D'Essonne; Evry France
| | - Marc Wessner
- Commissariat à l'Energie Atomique (CEA); Institut de Biologie François Jacob, Genoscope; Evry France
| | - Benjamin Noel
- Commissariat à l'Energie Atomique (CEA); Institut de Biologie François Jacob, Genoscope; Evry France
| | - Leo Berline
- CNRS/INSU/IRD; Mediterranean Institute of Oceanography (MIO); Aix-Marseille Université; Marseille France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA); Institut de Biologie François Jacob, Genoscope; Evry France
| | - Astrid Cornils
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung; Polar Biological Oceanography; Bremerhaven Germany
| | | | - Lars Stemmann
- INSU-CNRS; Laboratoire D'Océanographie de Villefranche; UPMC Univ Paris 06; Sorbonne Universités; Villefranche-Sur-Mer France
| | - Jean-Louis Jamet
- Laboratoire PROTEE-EBMA E.A. 3819; Université de Toulon; La Garde Cedex France
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA); Institut de Biologie François Jacob, Genoscope; Evry France
- Centre National de la Recherche Scientifique; UMR 8030 Université d'Evry val d'Essonne; Evry France
- Université d'Evry Val D'Essonne; Evry France
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Han CC, Fang LS, Chang IM, Lin HD. Genetic variation of the land-locked freshwater shrimp Caridina pseudodenticulata (Decapoda: Atyidae: Caridina) in Taiwan. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:687-694. [PMID: 28712317 DOI: 10.1080/24701394.2017.1350948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Caridina pseudodenticulata is a land-locked freshwater shrimp, which is endemic to North and West Taiwan. It is listed as Vulnerable under criteria A1ce in the IUCN Red List. Our study used mitochondrial DNA fragment sequences of the cytochrome oxidase subunit I (COI) gene to examine its genetic structure. In total, 204 sequences were analyzed from 22 populations, and all 39 haplotypes were identified. Our study (1) found that the genetic diversity within population of this species was similar to that of other land-locked freshwater prawn in Taiwan; (2) displayed that during glaciation, the Taiwan Strait was largely above water, an event which created opportunities for colonization Taiwan and dispersal widely; (3) showed that although the phylogenetic analysis showed the lack of a population genetic structure, the AMOVA and haplotypes distribution pattern revealed geographically divided; (4) indicated that C. pseudodenticulata could across to neighbor rivers through the mouths of rivers, which confluent with each other during floods.
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Affiliation(s)
- Chiao-Chuan Han
- a National Museum of Marine Biology and Aquarium , Checheng , Pingtung , Taiwan.,b Graduate Institute of Marine Biology , National Dong Hwa University , Checheng , Pingtung , Taiwan
| | - Lee-Shing Fang
- c Department of Leisure and Sport Management , Cheng Shiu University , Kaohsiung , Taiwan
| | - I-Ming Chang
- d General Education Center, Wenzao Ursuline University of Languages , Kaohsiung , Taiwan
| | - Hung-Du Lin
- e The Affiliated School of National Tainan First Senior High School , Tainan , Taiwan
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