Multigene barcoding and phylogeny of selected Engraulidae species

Gangan, Shardul S.; Pavan‐Kumar, A.; Jaiswar, A. K.

doi:10.1080/24701394.2019.1570175

Cited by 7 publications

(8 citation statements)

References 38 publications

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“…This study also confirms that COI is a useful genetic marker because it is broadly sequenced across different phyla, making it a good candidate gene for identifying species in an environmental sample. Nonetheless, relying only on one DNA fragment may lead to misidentification of pooled samples due to possible sequence similarity; this is why multigene approaches should be preferred in molecular biomonitoring studies (Zou et al 2012;Chesters et al 2015;Gangan et al 2019). Phytobenthos could be the first group to apply this approach, having 30% of species already barcoded with rbcL but not with COI.…”

Section: Discussionmentioning

confidence: 99%

Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

Zangaro¹,

Saccomanno²,

Tzafesta³

et al. 2021

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The biodiversity of the Mediterranean Sea is currently threatened by the introduction of Non-Indigenous Species (NIS). Therefore, monitoring the distribution of NIS is of utmost importance to preserve the ecosystems. A promising approach for the identification of species and the assessment of biodiversity is the use of DNA barcoding, as well as DNA and eDNA metabarcoding. Currently, the main limitation in the use of genomic data for species identification is the incompleteness of the DNA barcode databases. In this research, we assessed the availability of DNA barcodes in the main reference libraries for the most updated inventory of 665 confirmed NIS in the Mediterranean Sea, with a special focus on the cytochrome oxidase I (COI) barcode and primers. The results of this study show that there are no barcodes for 33.18% of the species in question, and that 45.30% of the 382 species with COI barcode, have no primers publicly available. This highlights the importance of directing scientific efforts to fill the barcode gap of specific taxonomic groups in order to help in the effective application of the eDNA technique for investigating the occurrence and the distribution of NIS in the Mediterranean Sea.

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Section: Discussionmentioning

confidence: 99%

Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

Zangaro¹,

Saccomanno²,

Tzafesta³

et al. 2021

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Section: Discussionmentioning

confidence: 99%

“…Here, our molecular analyses showed that specimens collected in Sepetiba Bay are genetically similar (>99.9%) to O. beta samples from Alabama/USA and Gulf of Mexico/USA, confirming their identity. However, the intraspecific split of three subclusters, with a maximum K2P divergence of 6.5%, might indicate taxonomic problems in this group, such as cryptic species or even misidentification of species (Ribeiro et al ., 2012; Gangan et al ., 2019). In this context, a deeper taxonomic and population knowledge about this group is necessary, since multiple records of O. beta in the Brazilian coast were reported in the last few years (Ribeiro et al ., 2012; Tomás et al ., 2012; Carvalho et al ., 2020; Cordeiro et al ., 2020) and whether these samples represent unique taxonomic units remains to be answered.…”

Section: Discussionmentioning

confidence: 99%

Opsanus beta (Goode & Bean, 1880) (Acanthopterygii: Batrachoididae), a non-indigenous toadfish in Sepetiba Bay, south-eastern Brazil

et al. 2021

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The introduction of non-native predator fish is thought to have important negative effects on native prey populations. Opsanus beta is a non-native toadfish that was originally described in the Gulf of Mexico, between the west coast of Florida and Belize. In the present study, we describe, for the first time, the occurrence of O. beta in Sepetiba Bay (22°55′S), south-eastern Brazil, probably brought into the bay through ships' ballast water. Thirteen specimens were recorded in this area near to Sepetiba Port. Similarly, three other records of this species in the Brazilian coast were also reported near to port areas at Rio de Janeiro (22°49′S), Santos (23°59′S) and Paranaguá (25°33′S) ports. To confirm the species identity, we employed DNA barcoding and compared our samples with sequences deposited on public databases, which indicated that our samples are highly similar (>99.9% of genetic similarity) to O. beta samples collected near its type locality. Several individuals were found in the capable spawning phase, according to histological analysis of the reproductive cell stages. The environmental plasticity of this species and the favourable local environmental conditions probably enabled the establishment of O. beta in this region. This raises concerns of potential high invasion impact due to this species' diet and reproductive capacity.

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“…The mitochondrial partial (648 bp) cytochrome oxidase I (COI) gene was newly sequenced for the holotype (SMF 35899 [KAU14-0575]) and two paratypes (SMF 34979 [KAU12-0682] and SMF 35369 [KAU13-0662]) of S. meteorum , new species. The resulting data were combined and compared with COI sequences examined by Steinke et al (2016), Gangan et al (2019), Afrand et al (2020), Hata et al (2021), and Jaonalison et al (2022). The dataset includes 22 specimens of S. balinensis , 6 specimens of S. belaerius , and 17 specimens of S. indicus (Table S1; see Data Accessibility).…”

Section: Methodsmentioning

confidence: 99%

A New Stolephorus (Teleostei: Clupeiformes: Engraulidae: Engraulinae) from the Red Sea

Hata

Lavoué

Bogorodsky

et al. 2023

Ichthyology & Herpetology

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The new anchovy Stolephorus meteorum, formerly confused with Stolephorus indicus, is described on the basis of 19 specimens collected from the southern Red Sea. Four other species, previously confused with or placed in the synonymy of S. indicus, have been either redescribed (Stolephorus commersonnii), described as new (Stolephorus belaerius), or resurrected from its synonymy (Stolephorus balinensis and Stolephorus scitulus). The new species shares with the latter four species, plus S. indicus, a relatively short maxilla and pelvic fins, and six or fewer prepelvic scutes but differs from them in the combination of some other characters, including intermediate numbers of gill rakers (total gill rakers on first gill arch 40-43, modally 41), 41 vertebrae, a large head and narrower interorbital area, and longer pelvic fins. A genetic analysis of the mitochondrial cytochrome oxidase I gene (COI) of S. meteorum, new species, S. balinensis, S. belaerius, and S. indicus revealed each species to be genetically divergent from the others by 2.5-3.6% uncorrected distance. STOLEPHORUS, an Indo-Pacific genus of marine and/or brackish water anchovies (Clupeiformes: Engraulidae), comprises 43 valid species (

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Multigene barcoding and phylogeny of selected Engraulidae species

Cited by 7 publications

References 38 publications

Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

Opsanus beta (Goode & Bean, 1880) (Acanthopterygii: Batrachoididae), a non-indigenous toadfish in Sepetiba Bay, south-eastern Brazil

A New Stolephorus (Teleostei: Clupeiformes: Engraulidae: Engraulinae) from the Red Sea

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Multigene barcoding and phylogeny of selected Engraulidae species

Cited by 7 publications

References 38 publications

﻿Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

﻿Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

Opsanus beta (Goode & Bean, 1880) (Acanthopterygii: Batrachoididae), a non-indigenous toadfish in Sepetiba Bay, south-eastern Brazil

A New Stolephorus (Teleostei: Clupeiformes: Engraulidae: Engraulinae) from the Red Sea

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Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA