Evaluation of ITS2-28S as a molecular marker for identification of calanoid copepods in the subtropical western North Pacific

Hirai, Junya; Shimode, Shinji; Tsuda, Atsushi

doi:10.1093/plankt/fbt016

Cited by 40 publications

(40 citation statements)

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“…Dawson ; Chen & Hare ; Hirai et al . ). However, the evolutionary history of one or two markers may not reflect the evolutionary history of populations and species (Takahata ; Ball et al .…”

Section: Introductionmentioning

confidence: 97%

Multilocus evidence for globally distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod

et al. 2014

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Zooplanktonic taxa have a greater number of distinct populations and species than might be predicted based on their large population sizes and open-ocean habitat, which lacks obvious physical barriers to dispersal and gene flow. To gain insight into the evolutionary mechanisms driving genetic diversification in zooplankton, we developed eight microsatellite markers to examine the population structure of an abundant, globally distributed mesopelagic copepod, Haloptilus longicornis, at 18 sample sites across the Atlantic and Pacific Oceans (n = 761). When comparing our microsatellite results with those of a prior study that used a mtDNA marker (mtCOII, n = 1059, 43 sample sites), we unexpectedly found evidence for the presence of a cryptic species pair. These species were globally distributed and apparently sympatric, and were separated by relatively weak genetic divergence (reciprocally monophyletic mtCOII lineages 1.6% divergent; microsatellite FST ranging from 0.28 to 0.88 across loci, P < 0.00001). Using both mtDNA and microsatellite data for the most common of the two species (n = 669 for microsatellites, n = 572 for mtDNA), we also found evidence for allopatric barriers to gene flow within species, with distinct populations separated by continental landmasses and equatorial waters in both the Atlantic and Pacific Ocean basins. Our study shows that oceanic barriers to gene flow can act as a mechanism promoting allopatric diversification in holoplanktonic taxa, despite the high potential dispersal abilities and pelagic habitat for these species.

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Section: Introductionmentioning

confidence: 97%

Multilocus evidence for globally distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod

et al. 2014

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“…; Hirai et al . ); the divergent sequences within this family do not form a single phylogenetic group. The Acartiidae showed primer mismatches and short sequence length of the LSU‐D2 region.…”

Section: Discussionmentioning

confidence: 93%

“…; Hirai et al . ). It is simple to design primer pairs for PCR amplification of LSU sequences (Machida & Knowlton ); however, the rate of evolution of nuclear LSU sequences is slow in comparison with mitochondrial DNA, and some closely related species are underestimated in metagenetic analyses because of insufficient taxonomic resolution (Porazinska et al .…”

Section: Discussionmentioning

confidence: 97%

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A metagenetic approach for revealing community structure of marine planktonic copepods

Hirai

Kuriyama

Ichikawa

et al. 2014

Molecular Ecology Resources

106

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Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We determined an appropriate similarity threshold for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) using an artificial community containing 33 morphologically identified species. The 99% similarity threshold had high species-level resolution for MOTU clustering but overestimated species richness. The artificial community was appropriately clustered into MOTUs at 97% similarity, with little inflation in MOTU numbers and with relatively high species-level resolution. The number of sequence reads of each MOTU was correlated with dry weight of that taxon, suggesting that sequence reads could be used as a proxy for biomass. Next, we applied the method to field-collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97% similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. Further, MOTUs were successfully classified into taxonomic groups at the family level at 97% similarity; similar patterns of species richness and biomass were revealed within families with metagenetic and morphological analyses. At the 99% similarity threshold, MOTUs with high proportions of sequence reads were identified as biomass-dominant species in each field-collected sample. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure.

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“…Phylogenetic studies of Sivakumar, Anandan, Muthupriya, Gopikrishna, & Altaff (2013) with reference to 18S rDNA of Thermocyclops decipiens also suggested no interpopulation variability in the 3' end fragment of the 18S rDNA molecule was observed in T. decipiens, T. crassus, M. darwini, M. Nevertheless, more than one aspects of the organism must be considered in order to make a reasonable conclusion about the mtCOI similarity and divergence among N. meggiti. In order to make a more accurate conclusion several alternative molecular techniques such as DNA sequences of nuclear introns, internal transcribed spacer 2 or large subunit ribosomal DNA (ITS2-28S) may be combined to resolve diaptomid phylogenies at the species level as suggested by Hirai, Shimode, and Atsushi (2013).…”

Section: Discussionmentioning

confidence: 99%

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BEGUM¹,

DHARANI²,

ALTAFF³

2018

GenAqua

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Calanoid copepods belonging to the family Diaptomidae occur commonly and abundantly in different types of freshwater environment. Based on morphological taxonomic key characters 48 diaptomid species belonging to 13 genera were reported from India. Taxonomic discrimination of many species of these genera is difficult due to their high morphological similarities and minute differences in key characters. In the present study two species of the genus, Neodiaptomus, N. meggiti and N. schmackeri from Andaman Islands were examined based on morphological and molecular characters which showed low variation in morphology and differences in their distributions. The morphological taxonomy of Copepoda with genetic analysis has shown complementing values in understanding the genetic variation and phylogeny of the contemporary populations. In this study, a molecular phylogenetic analysis of N. meggiti and N. schmackeri is performed on the basis of mitochondrial Cytochrome c oxidase subunit I (COI) gene. The mtDNA COI sequence of N. meggiti and N. schmackeri is 650 bp long. The mtDNA COI 1 gene sequence data of N. meggiti exhibits a remarkable constancy throughout its distributional area ranging from North to south Andaman. Similarity of N. meggiti with other genera of the family varies from 67.6 to 75.5% while of N. schmackeri varies from 65.5 to 72.6% on the basis of COI gene sequences. While N. meggiti and N. schmackeri share a similarity of 92.3%, high COI gene sequence similarity among each other supports the morphological based data that they belong to the same genus. The phylogenetic relationship elucidated using three different tree-making algorithms, the neighbour joining, minimum evolution and maximum parsimony showed that five plankton specimens under study form two clusters and constituted a deeply rooted, evolutionarily distinct group, separated from the other related genera used in the analysis. The phylogenetic relationship of the two diaptomid copepod N. meggiti and N. schmackeri of Andaman is remarkably accurate when the Neighbor joining phylogenetic tree and as well as maximum parsimony phylogenetic tree are considered.

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Evaluation of ITS2-28S as a molecular marker for identification of calanoid copepods in the subtropical western North Pacific

Cited by 40 publications

References 42 publications

Multilocus evidence for globally distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod

Multilocus evidence for globally distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod

A metagenetic approach for revealing community structure of marine planktonic copepods

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