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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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Burridge AK, Hörnlein C, Janssen AW, Hughes M, Bush SL, Marlétaz F, Gasca R, Pierrot-Bults AC, Michel E, Todd JA, Young JR, Osborn KJ, Menken SBJ, Peijnenburg KTCA. Time-calibrated molecular phylogeny of pteropods. PLoS One 2017; 12:e0177325. [PMID: 28604805 PMCID: PMC5467808 DOI: 10.1371/journal.pone.0177325] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 04/04/2017] [Indexed: 11/19/2022] Open
Abstract
Pteropods are a widespread group of holoplanktonic gastropod molluscs and are uniquely suitable for study of long-term evolutionary processes in the open ocean because they are the only living metazoan plankton with a good fossil record. Pteropods have been proposed as bioindicators to monitor the impacts of ocean acidification and in consequence have attracted considerable research interest, however, a robust evolutionary framework for the group is still lacking. Here we reconstruct their phylogenetic relationships and examine the evolutionary history of pteropods based on combined analyses of Cytochrome Oxidase I, 28S, and 18S ribosomal rRNA sequences and a molecular clock calibrated using fossils and the estimated timing of the formation of the Isthmus of Panama. Euthecosomes with uncoiled shells were monophyletic with Creseis as the earliest diverging lineage, estimated at 41-38 million years ago (mya). The coiled euthecosomes (Limacina, Heliconoides, Thielea) were not monophyletic contrary to the accepted morphology-based taxonomy; however, due to their high rate heterogeneity no firm conclusions can be drawn. We found strong support for monophyly of most euthecosome genera, but Clio appeared as a polyphyletic group, and Diacavolinia grouped within Cavolinia, making the latter genus paraphyletic. The highest evolutionary rates were observed in Heliconoides inflatus and Limacina bulimoides for both 28S and 18S partitions. Using a fossil-calibrated phylogeny that sets the first occurrence of coiled euthecosomes at 79-66 mya, we estimate that uncoiled euthecosomes evolved 51-42 mya and that most extant uncoiled genera originated 40-15 mya. These findings are congruent with a molecular clock analysis using the Isthmus of Panama formation as an independent calibration. Although not all phylogenetic relationships could be resolved based on three molecular markers, this study provides a useful resource to study pteropod diversity and provides general insight into the processes that generate and maintain their diversity in the open ocean.
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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
| | - Christine Hörnlein
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
- Koninklijk Nederlands Instituut voor Onderzoek der Zee (NIOZ), Yerseke, The Netherlands
| | | | - Martin Hughes
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
- Natural History Museum (NHM), Cromwell Road, London, United Kingdom
| | - Stephanie L. Bush
- Smithsonian Institution National Museum of Natural History, Washington DC, United States of America
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, California, United States of America
| | - Ferdinand Marlétaz
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Onna-son, Japan
| | - Rebeca Gasca
- El Colegio de la Frontera Sur (ECOSUR), Unidad Chetumal, Quintana Roo, Chetumal, Mexico
| | - Annelies C. Pierrot-Bults
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Ellinor Michel
- Natural History Museum (NHM), Cromwell Road, London, United Kingdom
| | - Jonathan A. Todd
- Natural History Museum (NHM), Cromwell Road, London, United Kingdom
| | - Jeremy R. Young
- Department of Earth Sciences, University College London, London, United Kingdom
| | - Karen J. Osborn
- Smithsonian Institution National Museum of Natural History, Washington DC, United States of America
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, California, United States of America
| | - Steph B. J. Menken
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - 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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Votrubova-Dubska J, Vanek D, Zikmund J, Mestek O, Urbanova V, Brzobohata H, Brestovansky P. Technical note: Efficient removal of a PCR inhibitory agent (vivianite) found on excavated bones. Forensic Sci Int 2016; 261:8-13. [DOI: 10.1016/j.forsciint.2015.12.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/28/2015] [Accepted: 12/29/2015] [Indexed: 11/30/2022]
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Trivedi S, Aloufi AA, Ansari AA, Ghosh SK. Role of DNA barcoding in marine biodiversity assessment and conservation: An update. Saudi J Biol Sci 2016; 23:161-71. [PMID: 26980996 PMCID: PMC4778524 DOI: 10.1016/j.sjbs.2015.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/09/2014] [Accepted: 01/05/2015] [Indexed: 12/18/2022] Open
Abstract
More than two third area of our planet is covered by oceans and assessment of marine biodiversity is a challenging task. With the increasing global population, there is a tendency to exploit marine resources for food, energy and other requirements. This puts pressure on the fragile marine environment and necessitates sustainable conservation efforts. Marine species identification using traditional taxonomical methods is often burdened with taxonomic controversies. Here we discuss the comparatively new concept of DNA barcoding and its significance in marine perspective. This molecular technique can be useful in the assessment of cryptic species which is widespread in marine environment and linking the different life cycle stages to the adult which is difficult to accomplish in the marine ecosystem. Other advantages of DNA barcoding include authentication and safety assessment of seafood, wildlife forensics, conservation genetics and detection of invasive alien species (IAS). Global DNA barcoding efforts in the marine habitat include MarBOL, CeDAMar, CMarZ, SHARK-BOL, etc. An overview on DNA barcoding of different marine groups ranging from the microbes to mammals is revealed. In conjugation with newer and faster techniques like high-throughput sequencing, DNA barcoding can serve as an effective modern tool in marine biodiversity assessment and conservation.
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Affiliation(s)
- Subrata Trivedi
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Abdulhadi A. Aloufi
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Abid A. Ansari
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Sankar K. Ghosh
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
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Lin J, Kong L, Li Q. DNA barcoding of true limpets (Order Patellogastropoda) along coast of China: a case study. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2310-4. [PMID: 25812056 DOI: 10.3109/19401736.2015.1022758] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we applied a partial sequence of mitochondrial COI gene as DNA barcode to assess the viability of DNA barcoding for distinguishing Patellogastropoda. One-hundred thirty-five COI gene sequences were obtained from 13 species belonging to Nacellidae (Cellana) and Lottiidae (Lottia, Patelloida and Nipponacmea) along the coast of China. The alignment result of these sequences indicated the existence of insertions in mitochondrial COI gene of Patellogastropoda. The Kimura 2-parameter (K2P) distances within species and genera were 0.00-1.01% (average 0.07%) and 18.09-37.80% (average 24.07%), respectively, an obvious barcoding gap existed. All species in our study were clearly discriminated in all trees (neighbor-joining (NJ), Bayesian, and maximum likelihood (ML) tree) with a highly supported clade node. The character-based barcode method successfully identified 100% of the Patellogastropod species included, and performed well in discriminating Patellogastropod genera. The results of this study affirm that DNA barcoding based on the COI gene can identify species belonging to Patellogastropoda rapidly and accurately.
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Affiliation(s)
- Jiping Lin
- a Key Laboratory of Mariculture, Ministry of Education, Ocean University of China , Qingdao , China
| | - Lingfeng Kong
- a Key Laboratory of Mariculture, Ministry of Education, Ocean University of China , Qingdao , China
| | - Qi Li
- a Key Laboratory of Mariculture, Ministry of Education, Ocean University of China , Qingdao , China
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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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High cryptic diversity across the global range of the migratory planktonic copepods Pleuromamma piseki and P. gracilis. PLoS One 2013; 8:e77011. [PMID: 24167556 PMCID: PMC3805563 DOI: 10.1371/journal.pone.0077011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/28/2013] [Indexed: 11/25/2022] Open
Abstract
Although holoplankton are ocean drifters and exhibit high dispersal potential, a number of studies on single species are finding highly divergent genetic clades. These cryptic species complexes are important to discover and describe, as identification of common marine species is fundamental to understanding ecosystem dynamics. Here we investigate the global diversity within Pleuromamma piseki and P. gracilis, two dominant members of the migratory zooplankton assemblage in subtropical and tropical waters worldwide. Using DNA sequence data from the mitochondrial gene cytochrome c oxidase subunit II (mtCOII) from 522 specimens collected across the Pacific, Atlantic and Indian Oceans, we discover twelve well-resolved genetically distinct clades in this species complex (Bayesian posterior probabilities >0.7; 6.3–17% genetic divergence between clades). The morphologically described species P. piseki and P. gracilis did not form monophyletic groups, rather they were distributed throughout the phylogeny and sometimes co-occurred within well-resolved clades: this result suggests that morphological characters currently used for taxonomic identification of P. gracilis and P. piseki may be inaccurate as indicators of species’ boundaries. Cryptic clades within the species complex ranged from being common to rare, and from cosmopolitan to highly restricted in distribution across the global ocean. These novel lineages appear to be ecologically divergent, with distinct biogeographic distributions across varied pelagic habitats. We hypothesize that these mtDNA lineages are distinct species and suggest that resolving their systematic status is important, given the ecological significance of the genus Pleuromamma in subtropical-tropical waters worldwide.
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