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Mesas A, Aguilera VM, González CE, Giesecke R, Escribano R, Vargas CA. Molecular evidence for a new endemic species of Acartia (Copepoda, Calanoida) from the Southeast Pacific coast. Sci Rep 2024; 14:12366. [PMID: 38811606 PMCID: PMC11137159 DOI: 10.1038/s41598-024-62080-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
The loss of biodiversity in marine populations is one of the consequences of the increased events of extreme environmental conditions in the oceans, which can condition the persistence of populations to future scenarios of climate change. Therefore, it is extremely necessary to explore and monitor the genetic diversity of natural populations. In the Southeast Pacific Ocean (SEPO), specifically on the coast of Chile, the presence of the copepod Acartia tonsa has been indicated solely using morphological evidence, due to the absence of genetic information. In the present work, the genetic diversity, population structure and phylogenetic position within the genus Acartia, of populations identified morphologically as A. tonsa, was evaluated by amplification of the mitochondrial cytochrome c oxidase subunit I and nuclear marker 18 s. Our results showed that the populations identified as A. tonsa correspond to a new monophyletic group endemic to SEPO (GMYC = 1.00; PTP = 0.95). The populations showed moderate to high genetic diversity with an incipient structuring between populations and biogeographic zones. Our results suggest that despite the homogenizing effect of the Humboldt Current, isolation by distance and contrasting environmental conditions at different geographic scales have an important influence on the genetic diversity of zooplankton in the SEPO region.
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Affiliation(s)
- Andrés Mesas
- Millennium Institute of Oceanography, Universidad de Concepción, Concepción, Chile.
- Coastal Ecosystems and Global Environmental Change Lab (ECCALab), Department of Aquatic System, Faculty of Environmental Sciences, Universidad de Concepción, Concepción, Chile.
| | - Víctor M Aguilera
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Bernardo Ossandón #877, C.P. 1781681, Coquimbo, Chile
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
| | - Carolina E González
- Millennium Institute of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Ricardo Giesecke
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
- Centro de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - Rubén Escribano
- Millennium Institute of Oceanography, Universidad de Concepción, Concepción, Chile
- Department of Oceanography, Faculty of Natural and Oceanographic Sciences, University of Concepción, 4030000, Concepción, Chile
| | - Cristian A Vargas
- Millennium Institute of Oceanography, Universidad de Concepción, Concepción, Chile
- Coastal Ecosystems and Global Environmental Change Lab (ECCALab), Department of Aquatic System, Faculty of Environmental Sciences, Universidad de Concepción, Concepción, Chile
- Coastal Social-Ecological Millennium Institute (SECOS), Universidad de Concepción & P. Universidad Católica de Chile, Santiago, Chile
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2
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Jense C, Adams M, Raadik TA, Waters JM, Morgan DL, Barmuta LA, Hardie SA, Deagle BE, Burridge CP. Cryptic diversity within two widespread diadromous freshwater fishes (Teleostei: Galaxiidae). Ecol Evol 2024; 14:e11201. [PMID: 38799386 PMCID: PMC11116845 DOI: 10.1002/ece3.11201] [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: 07/04/2023] [Revised: 03/03/2024] [Accepted: 03/19/2024] [Indexed: 05/29/2024] Open
Abstract
Identification of taxonomically cryptic species is essential for the effective conservation of biodiversity. Freshwater-limited organisms tend to be genetically isolated by drainage boundaries, and thus may be expected to show substantial cryptic phylogenetic and taxonomic diversity. By comparison, populations of diadromous taxa, that migrate between freshwater and marine environments, are expected to show less genetic differentiation. Here we test for cryptic diversity in Australasian populations (both diadromous and non-diadromous) of two widespread Southern Hemisphere fish species, Galaxias brevipinnis and Galaxias maculatus. Both mtDNA and nuclear markers reveal putative cryptic species within these taxa. The substantial diversity detected within G. brevipinnis may be explained by its strong climbing ability which allows it to form isolated inland populations. In island populations, G. brevipinnis similarly show deeper genetic divergence than those of G. maculatus, which may be explained by the greater abundance of G. maculatus larvae in the sea allowing more ongoing dispersal. Our study highlights that even widespread, 'high-dispersal' species can harbour substantial cryptic diversity and therefore warrant increased taxonomic and conservation attention.
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Affiliation(s)
- Charlotte Jense
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Mark Adams
- Evolutionary Biology UnitSouth Australian MuseumAdelaideSouth AustraliaAustralia
- School of Biological SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Tarmo A. Raadik
- Department of Energy, Environment and Climate ActionArthur Rylah Institute for Environmental ResearchHeidelbergVictoriaAustralia
| | | | - David L. Morgan
- Centre for Sustainable Aquatic Ecosystems, Harry Butler InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Leon A. Barmuta
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Scott A. Hardie
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Bruce E. Deagle
- Australian National Fish CollectionCSIRO National Research Collections AustraliaHobartTasmaniaAustralia
| | - Christopher P. Burridge
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
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3
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Wall-Palmer D, Janssen AW, Goetze E, Choo LQ, Mekkes L, Peijnenburg KTCA. Fossil-calibrated molecular phylogeny of atlantid heteropods (Gastropoda, Pterotracheoidea). BMC Evol Biol 2020; 20:124. [PMID: 32957910 PMCID: PMC7507655 DOI: 10.1186/s12862-020-01682-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/06/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The aragonite shelled, planktonic gastropod family Atlantidae (shelled heteropods) is likely to be one of the first groups to be impacted by imminent ocean changes, including ocean warming and ocean acidification. With a fossil record spanning at least 100 Ma, atlantids have experienced and survived global-scale ocean changes and extinction events in the past. However, the diversification patterns and tempo of evolution in this family are largely unknown. RESULTS Based on a concatenated maximum likelihood phylogeny of three genes (cytochrome c oxidase subunit 1 mitochondrial DNA, 28S and 18S ribosomal rRNA) we show that the three extant genera of the family Atlantidae, Atlanta, Protatlanta and Oxygyrus, form monophyletic groups. The genus Atlanta is split into two groups, one exhibiting smaller, well ornamented shells, and the other having larger, less ornamented shells. The fossil record, in combination with a fossil-calibrated phylogeny, suggests that large scale atlantid extinction was accompanied by considerable and rapid diversification over the last 25 Ma, potentially driven by vicariance events. CONCLUSIONS Now confronted with a rapidly changing modern ocean, the ability of atlantids to survive past global change crises gives some optimism that they may be able to persist through the Anthropocene.
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Affiliation(s)
- Deborah Wall-Palmer
- Plankton Diversity and Evolution, Nauralis Biodiversity Center, Leiden, The Netherlands.
| | - Arie W Janssen
- Plankton Diversity and Evolution, Nauralis Biodiversity Center, Leiden, The Netherlands
| | - Erica Goetze
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, USA
| | - Le Qin Choo
- Plankton Diversity and Evolution, Nauralis Biodiversity Center, Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Lisette Mekkes
- Plankton Diversity and Evolution, Nauralis Biodiversity Center, Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Katja T C A Peijnenburg
- Plankton Diversity and Evolution, Nauralis Biodiversity Center, Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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González CE, Goetze E, Escribano R, Ulloa O, Victoriano P. Genetic diversity and novel lineages in the cosmopolitan copepod Pleuromamma abdominalis in the Southeast Pacific. Sci Rep 2020; 10:1115. [PMID: 31980660 PMCID: PMC6981114 DOI: 10.1038/s41598-019-56935-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 12/16/2019] [Indexed: 11/20/2022] Open
Abstract
Across boundary currents, zooplankton are subject to strong oceanographic gradients and hence strong selective pressures. How such gradients interact with the speciation process of pelagic organisms is still poorly understood in the open ocean realm. Here we report on genetic diversity within the pelagic copepod Pleuromamma abdominalis in the poorly known Southeast Pacific region, with samples spanning an ocean gradient from coastal upwelling to the oligotrophic South Pacific Subtropical Gyre. We assessed variation in fragments of the mitochondrial (mt) genes cytochrome c oxidase subunit I (COI) and Cytochrome b as well as in the nuclear internal transcribed spacer (ITS) region and 28 S rRNA. Phylogenetic analyses revealed the presence of 8 divergent lineages occurring across the gradient with genetic distances in the range of 0.036 and 0.44 (mt genes), and GMYC species delimitation methods support their inference as distinct (undescribed) species. Genetic lineages occurring across the zonal gradient showed strong genetic structuring, with the presence of at least two new lineages within the coastal upwelling zone, revealing an unexpectedly high level of endemism within the Humboldt Current System. Multivariate analyses found strong correlation between genetic variation and surface chlorophyll-a and salinity, suggesting an important role for hydrographic gradients in maintaining genetic diversity. However, the presence of cryptic lineages within the upwelling zone cannot be easily accounted for by environmental heterogeneity and poses challenging questions for understanding the speciation process for oceanic zooplankton.
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Affiliation(s)
- Carolina E González
- Graduate Program in Oceanography, Department of Oceanography, University of Concepción, PO Box 160, Barrio Universitario s/n Concepción, Concepción, 4030000, Chile. .,Instituto Milenio de Oceanografía (IMO) and Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, PO Box 160 C, Barrio Universitario s/n Concepción, Concepción, 4030000, Chile.
| | - Erica Goetze
- Department of Oceanography, University of Hawaii at Manoa, 1000 Pope Road, Honolulu, Hawaii, USA
| | - Rubén Escribano
- Instituto Milenio de Oceanografía (IMO) and Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, PO Box 160 C, Barrio Universitario s/n Concepción, Concepción, 4030000, Chile
| | - Osvaldo Ulloa
- Instituto Milenio de Oceanografía (IMO) and Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, PO Box 160 C, Barrio Universitario s/n Concepción, Concepción, 4030000, Chile
| | - Pedro Victoriano
- Department of Zoology, Faculty of Natural and Oceanographic Sciences, University of Concepción, PO Box 160 C, Barrio Universitario s/n Concepción, Concepción, 4030000, Chile
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Burridge AK, Van Der Hulst R, Goetze E, Peijnenburg KTCA. Assessing species boundaries in the open sea: an integrative taxonomic approach to the pteropod genus Diacavolinia. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Abstract
To track changes in pelagic biodiversity in response to climate change, it is essential to accurately define species boundaries. Shelled pteropods are a group of holoplanktonic gastropods that have been proposed as bio-indicators because of their vulnerability to ocean acidification. A particularly suitable, yet challenging group for integrative taxonomy is the pteropod genus Diacavolinia, which has a circumglobal distribution and is the most species-rich pteropod genus, with 24 described species. We assessed species boundaries in this genus, with inferences based on geometric morphometric analyses of shell-shape variation, genetic (cytochrome c oxidase subunit I, 28S rDNA sequences) and geographic data. We found support for a total of 13 species worldwide, with observations of 706 museum and 263 freshly collected specimens across a global collection of material, including holo‐ and paratype specimens for 14 species. In the Atlantic Ocean, two species are well supported, in contrast to the eight currently described, and in the Indo‐Pacific we found a maximum of 11 species, partially merging 13 of the described species. Distributions of these revised species are congruent with well-known biogeographic provinces. Combining varied datasets in an integrative framework may be suitable for many diverse taxa and is an important first step to predicting species-specific responses to global change.
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Affiliation(s)
- Alice K Burridge
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | | | - Erica Goetze
- Department of Oceanography, University of Hawai’i at Mānoa, Honolulu, Hawaii, USA
| | - Katja T C A Peijnenburg
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly. Mol Phylogenet Evol 2019; 135:86-97. [PMID: 30771513 DOI: 10.1016/j.ympev.2019.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/30/2019] [Accepted: 02/04/2019] [Indexed: 11/22/2022]
Abstract
The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 380 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively "trivial" aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic.
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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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Sommer SA, Van Woudenberg L, Lenz PH, Cepeda G, Goetze E. Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre. Mol Ecol 2017; 26:6136-6156. [PMID: 28792641 DOI: 10.1111/mec.14286] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 06/08/2017] [Accepted: 06/30/2017] [Indexed: 01/28/2023]
Abstract
Although metazoan animals in the mesopelagic zone play critical roles in deep pelagic food webs and in the attenuation of carbon in midwaters, the diversity of these assemblages is not fully known. A metabarcoding survey of mesozooplankton diversity across the epipelagic, mesopelagic and upper bathypelagic zones (0-1500 m) in the North Pacific Subtropical Gyre revealed far higher estimates of species richness than expected given prior morphology-based studies in the region (4,024 OTUs, 10-fold increase), despite conservative bioinformatic processing. Operational taxonomic unit (OTU) richness of the full assemblage peaked at lower epipelagic-upper mesopelagic depths (100-300 m), with slight shoaling of maximal richness at night due to diel vertical migration, in contrast to expectations of a deep mesopelagic diversity maximum as reported for several plankton groups in early systematic and zoogeographic studies. Four distinct depth-stratified species assemblages were identified, with faunal transitions occurring at 100 m, 300 m and 500 m. Highest diversity occurred in the smallest zooplankton size fractions (0.2-0.5 mm), which had significantly lower % OTUs classified due to poor representation in reference databases, suggesting a deep reservoir of poorly understood diversity in the smallest metazoan animals. A diverse meroplankton assemblage also was detected (350 OTUs), including larvae of both shallow and deep living benthic species. Our results provide some of the first insights into the hidden diversity present in zooplankton assemblages in midwaters, and a molecular reappraisal of vertical gradients in species richness, depth distributions and community composition for the full zooplankton assemblage across the epipelagic, mesopelagic and upper bathypelagic zones.
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Affiliation(s)
- Stephanie A Sommer
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Lauren Van Woudenberg
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Petra H Lenz
- Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Georgina Cepeda
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP), Mar del Plata, Argentina
| | - Erica Goetze
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Manoa, Honolulu, HI, USA
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9
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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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10
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Schiffer PH, Herbig HG. Endorsing Darwin: global biogeography of the epipelagic goose barnaclesLepas spp. (Cirripedia, Lepadomorpha) proves cryptic speciation. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12373] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Philipp H. Schiffer
- Institute for Genetics; University of Cologne; Zülpicher Strasse 47 D-50674 Köln Germany
- EMBL; Meyerhofstraße 1 D-69117 Heidelberg Germany
| | - Hans-Georg Herbig
- Institute of Geology and Mineralogy; University of Cologne; Zülpicher Strasse 49a D-50674 Köln Germany
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de Vargas C, Audic S, Henry N, Decelle J, Mahe F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horak A, Jaillon O, Lima-Mendez G, Luke J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki ME, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E, Boss E, Follows M, Karp-Boss L, Krzic U, Reynaud EG, Sardet C, Sullivan MB, Velayoudon D. Eukaryotic plankton diversity in the sunlit ocean. Science 2015; 348:1261605. [DOI: 10.1126/science.1261605] [Citation(s) in RCA: 1138] [Impact Index Per Article: 126.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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12
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Burridge AK, Goetze E, Raes N, Huisman J, Peijnenburg KTCA. Global biogeography and evolution of Cuvierina pteropods. BMC Evol Biol 2015; 15:39. [PMID: 25880735 PMCID: PMC4443520 DOI: 10.1186/s12862-015-0310-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 02/19/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Shelled pteropods are planktonic gastropods that are potentially good indicators of the effects of ocean acidification. They also have high potential for the study of zooplankton evolution because they are metazoan plankton with a good fossil record. We investigated phenotypic and genetic variation in pteropods belonging to the genus Cuvierina in relation to their biogeographic distribution across the world's oceans. We aimed to assess species boundaries and to reconstruct their evolutionary history. RESULTS We distinguished six morphotypes based on geometric morphometric analyses of shells from 926 museum and 113 fresh specimens. These morphotypes have distinct geographic distributions across the Atlantic, Pacific and Indian oceans, and belong to three major genetic clades based on COI and 28S DNA sequence data. Using a fossil-calibrated phylogeny, we estimated that these clades separated in the Late Oligocene and Early to Middle Miocene. We found evidence for ecological differentiation among all morphotypes based on ecological niche modelling with sea surface temperature, salinity and phytoplankton biomass as primary determinants. Across all analyses, we found highly congruent patterns of differentiation suggesting species level divergences between morphotypes. However, we also found distinct morphotypes (e.g. in the Atlantic Ocean) that were ecologically, but not genetically differentiated. CONCLUSIONS Given the distinct ecological and phenotypic specializations found among both described and undescribed Cuvierina taxa, they may not respond equally to future ocean changes and may not be equally sensitive to ocean acidification. Our findings support the view that ecological differentiation may be an important driving force in the speciation of zooplankton.
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Affiliation(s)
- Alice K Burridge
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands.
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94248, Amsterdam, 1090 GE, The Netherlands.
| | - Erica Goetze
- Department of Oceanography, University of Hawaii at Manoa, 1000 Pope Road, Honolulu, HI, 96822, USA.
| | - Niels Raes
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands.
| | - Jef Huisman
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94248, Amsterdam, 1090 GE, The Netherlands.
| | - Katja T C A Peijnenburg
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands.
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94248, Amsterdam, 1090 GE, The Netherlands.
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Pante E, Puillandre N, Viricel A, Arnaud-Haond S, Aurelle D, Castelin M, Chenuil A, Destombe C, Forcioli D, Valero M, Viard F, Samadi S. Species are hypotheses: avoid connectivity assessments based on pillars of sand. Mol Ecol 2015; 24:525-44. [DOI: 10.1111/mec.13048] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/06/2014] [Accepted: 12/13/2014] [Indexed: 01/31/2023]
Affiliation(s)
- Eric Pante
- Littoral, Environnement et Sociétés (LIENSs); UMR 7266 CNRS - Université de La Rochelle; 2 rue Olympe de Gouges 17042 La Rochelle France
| | - Nicolas Puillandre
- ISYEB - UMR 7205 - CNRS, MNHN; UPMC (University Paris 06); EPHE - Muséum national d'Histoire naturelle; Sorbonne Universités; CP26, 57 rue Cuvier F-75231 Paris Cedex 05 France
| | - Amélia Viricel
- Littoral, Environnement et Sociétés (LIENSs); UMR 7266 CNRS - Université de La Rochelle; 2 rue Olympe de Gouges 17042 La Rochelle France
| | | | - Didier Aurelle
- Aix Marseille Université; CNRS, IRD; Avignon Université, IMBE UMR 7263; 13397 Marseille France
| | - Magalie Castelin
- Aquatic Animal Health Section; Fisheries and Oceans Canada; Pacific Biological Station; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - Anne Chenuil
- Aix Marseille Université; CNRS, IRD; Avignon Université, IMBE UMR 7263; 13397 Marseille France
| | - Christophe Destombe
- Sorbonne Universités; UPMC; University Paris 06; Station Biologique de Roscoff F-29680 Roscoff France
- CNRS, Laboratory Evolutionary Biology and Ecology of Algae; Sorbonne Universités; Université Pierre et Marie Curie (UPMC) Univ Paris 06, UMI 3614, UPMC, PUCCh, UACh; Station Biologique de Roscoff F-29680 Roscoff France
| | - Didier Forcioli
- Faculté des Sciences; Université Nice-Sophia-Antipolis, Equipe Symbiose Marine UMR 7138; Parc Valrose 06108 Nice Cedex 2 France
- UMR 7138 Evolution Paris Seine; Université Pierre et Marie Curie - CNRS; 7 Quai St Bernard 75252 Paris Cedex 05 France
| | - Myriam Valero
- Sorbonne Universités; UPMC; University Paris 06; Station Biologique de Roscoff F-29680 Roscoff France
- CNRS, Laboratory Evolutionary Biology and Ecology of Algae; Sorbonne Universités; Université Pierre et Marie Curie (UPMC) Univ Paris 06, UMI 3614, UPMC, PUCCh, UACh; Station Biologique de Roscoff F-29680 Roscoff France
| | - Frédérique Viard
- Sorbonne Universités; UPMC; University Paris 06; Station Biologique de Roscoff F-29680 Roscoff France
- Centre National de la Recherche Scientifique (CNRS); Laboratory Adaptation and Diversity in the Marine Environment; Team Diversity and Connectivity in Coastal Marine Landscapes, UMR 7144; Station Biologique de Roscoff F-29680 Roscoff France
| | - Sarah Samadi
- ISYEB - UMR 7205 - CNRS, MNHN; UPMC (University Paris 06); EPHE - Muséum national d'Histoire naturelle; Sorbonne Universités; CP26, 57 rue Cuvier F-75231 Paris Cedex 05 France
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14
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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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