Molecular phylogeny of the Calanoida (Crustacea: Copepoda)

Blanco-Bercial, Leocadio; Bradford‐Grieve, Janet M.; Bucklin, Ann

doi:10.1016/j.ympev.2011.01.008

Cited by 107 publications

(74 citation statements)

References 60 publications

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“…The use of conservative nuclear markers such as 18S and 28S is widely applied when investigating the monophyly and reciprocal relationships of higher taxa in copepods, while it is known to have loose resolution for the discrimination of infra-generic taxa (Braga et al, 1999;Thum, 2004;Blanco-Bercial et al, 2011;Figueroa, 2011). In the frame of this study, the tree topologies based on the nuclear ribosomal DNA fragments support the monophyly of the genus Hemidiaptomus (Fig.…”

Section: Systematicsmentioning

confidence: 55%

“…Analyses were performed following a hierarchical taxonomical approach: (i) conservative nuclear ribosomal DNA genes (18S and 28S), which are widely used to resolve relationships at the genusand family-rank in copepods (e.g. : Bucklin et al, 2003;Braga et al, 1999;Wyngaard et al, 2010;Blanco-Bercial et al, 2011), were used to investigate the taxonomical rank to be assigned to the taxon Occidodiaptomus in the frame of the family Diaptomidae, (ii) species grouping based on a matrix of morphological characters was compared to that obtained through molecular analyses, (iii) fragments of the mitochondrial genes 16S and Cyt-b were used to check for the monophyly of Occidodiaptomus and to investigate the relationships among the taxa belonging to it. Finally, the COI gene was chosen as an additional mitochondrial marker for further testing the monophyly of the clades singled out with the other mitochondrial markers in the only H. ingens s.l.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Overlooked cryptic endemism in copepods: Systematics and natural history of the calanoid subgenus Occidodiaptomus Borutzky 1991 (Copepoda, Calanoida, Diaptomidae)

Marrone

Brutto

Hundsdoerfer

et al. 2013

Molecular Phylogenetics and Evolution

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a b s t r a c tOur comprehension of the phylogeny and diversity of most inland-water crustaceans is currently hampered by their pronounced morphological bradytely, which contributed to the affirmation of the ''Cosmopolitanism Paradigm'' of freshwater taxa. However, growing evidence of the existence of cryptic diversity and molecular regionalism is available for calanoid copepods, thus stressing the need for careful morphological and molecular studies in order to soundly investigate the systematics, diversity and distribution patterns of the group.Diaptomid copepods were here chosen as model taxa, and the morphological and molecular diversity of the species belonging to the west-Mediterranean diaptomid subgenus Occidodiaptomus were investigated with the aim of comparing the patterns of morphological and molecular evolution in freshwater copepods. Three species currently lumped under the binomen Hemidiaptomus (Occidodiaptomus) ingens and two highly divergent clades within H. (O.) roubaui were distinguished, thus showing an apparent discordance between the molecular distances recorded and Occidodiaptomus morphological homogeneity, and highlighting a noteworthy decoupling between the morphological and molecular diversity in the subgenus.Current Occidodiaptomus diversity pattern is ascribed to a combined effect of ancient vicariance and recent dispersal events. It is stressed that the lack of sound calibration points for the molecular clock makes it difficult to soundly temporally frame the diversification events of interest in the taxon studied, and thus to asses the role of morphological bradytely and of accelerated molecular evolutionary rates in shaping the current diversity of the group.

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Section: Systematicsmentioning

confidence: 55%

Section: Introductionmentioning

confidence: 99%

Overlooked cryptic endemism in copepods: Systematics and natural history of the calanoid subgenus Occidodiaptomus Borutzky 1991 (Copepoda, Calanoida, Diaptomidae)

Marrone

Brutto

Hundsdoerfer

et al. 2013

Molecular Phylogenetics and Evolution

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“…Indeed, in copepods, insufficient and only partial sequences have been used and showed a limitation for certain order-level [21, 73, 74]. Blanco-Bercial et al [75] discussed that the use of a single gene at the family or superfamily level of copepods contributed to the disparate results, and the relationships in the superfamily Centropagoidea (Order Calanoida) were still unresolved using the four concatenated genes (18S rRNA, 28S rRNA, cytochrome c oxidase subunit I, and cytochrome b ) [75]. Therefore, the phylogenomic approach will make notable contributions to a better resolution of copepod evolution and then can be anchored to certain taxonomic clades.…”

Section: Discussionmentioning

confidence: 99%

Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies

Eyun

2017

BMC Evol Biol

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BackgroundCopepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level.ResultsThis study attempted to resolve phylogenetic relationships among and within four major copepod orders including Harpacticoida and the phylogenetic position of Copepoda among five other crustacean groups (Anostraca, Cladocera, Sessilia, Amphipoda, and Decapoda) using 24 nuclear protein-coding genes. Phylogenomics has confirmed the monophyly of Copepoda and Podoplea. However, this study reveals surprising differences with the majority of the copepod phylogenies and unexpected similarities with postembryonic characters and earlier proposed morphological phylogenies; More precisely, Cyclopoida is more closely related to Siphonostomatoida than to Harpacticoida which is likely the most basally-branching group of Podoplea. Divergence time estimation suggests that the origin of Harpacticoida can be traced back to the Devonian, corresponding well with recently discovered fossil evidence. Copepoda has a close affinity to the clade of Malacostraca and Thecostraca but not to Branchiopoda. This result supports the hypothesis of the newly proposed clades, Communostraca, Multicrustacea, and Allotriocarida but further challenges the validity of Hexanauplia and Vericrustacea.ConclusionsThe first phylogenomic study of Copepoda provides new insights into taxonomic relationships and represents a valuable resource that improves our understanding of copepod evolution and their wide range of ecological adaptations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0883-5) contains supplementary material, which is available to authorized users.

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“…Thus, the MiSeq-based analysis with respect to taxonomic compositions of non-calanoid copepods was superior. The reference database is incomplete, especially for non-calanoid copepods, as shown in Fig 5, and their phylogenetic relationships are not well resolved compared with those of calanoid copepods [43]. Additional barcoding and phylogenetic studies, especially of non-calanoid copepods, would lead to better taxonomic assignments in metagenetic analysis.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of metagenetic community analysis of planktonic copepods using Illumina MiSeq: Comparisons with morphological classification and metagenetic analysis using Roche 454

2017

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Metagenetics is a rapid and taxonomically comprehensive method for revealing community structures within environmental samples, based on large amounts of sequence data produced by high-throughput sequencers. Because community structures of planktonic copepods are important in the ocean owing to their high diversity and abundance, a metagenetic analysis of the 28S D2 region using Roche 454 was previously developed. However, the Illumina MiSeq platform with a high sequence output is being used more frequently in metagenetics, and non-calanoid copepods have not previously been fully evaluated. Here, we evaluated an Illumina MiSeq-based metagenetic analysis using a mock community and field-collected samples that were examined in a previous study using Roche 454, and the community structure, including non-calanoid copepods, was compared among morphological and metagenetic analyses. We removed a singleton read and applied an appropriate abundance threshold to remove erroneous Molecular Operational Taxonomic Units (MOTUs) with low-abundance sequences in the MiSeq-based analysis. Results showed that the copepod community was successfully characterized using Illumina MiSeq. Higher-quality sequences were obtained using MiSeq than by Roche 454, which reduced the overestimation of diversity, especially at a strict 99% similarity threshold for MOTU clustering. Taxonomic compositions in terms of both biomass and presence/absence of species, including non-calanoids, were more appropriately represented in the MiSeq- than in Roche 454-based analysis. Our data showed that metagenetic analysis using Illumina MiSeq is more useful for revealing copepod communities than Roche 454, owing to the lower cost and higher quality.

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Molecular phylogeny of the Calanoida (Crustacea: Copepoda)

Cited by 107 publications

References 60 publications

Overlooked cryptic endemism in copepods: Systematics and natural history of the calanoid subgenus Occidodiaptomus Borutzky 1991 (Copepoda, Calanoida, Diaptomidae)

Overlooked cryptic endemism in copepods: Systematics and natural history of the calanoid subgenus Occidodiaptomus Borutzky 1991 (Copepoda, Calanoida, Diaptomidae)

Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies

Evaluation of metagenetic community analysis of planktonic copepods using Illumina MiSeq: Comparisons with morphological classification and metagenetic analysis using Roche 454

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