Genetic diversity and spatial population structure of a deepwater snapper, Pristipomoides filamentosus in the south-west Indian Ocean

Mzingirwa, Fatuma Ali; Mkare, Thomas K.; Nyingi, Dorothy Wanja; Njiru, James

doi:10.1007/s11033-019-04962-w

Cited by 4 publications

(4 citation statements)

References 49 publications

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“…Atoll is in the direct path of one of the bifurcated arms of the South Equatorial Current as it passes through the Mascarene Plateau [124,133]. The South Equatorial Current pushes water westward, which may create a barrier to gene flow to islands south of Seychelles such as Mauritius and Réunion [129,130,133]. Although there are currently no bonefishor even elopomorph -larval dispersal models for the Indian Ocean, pelagic larval dispersal simulation models of coral species in the SWIO corroborate the biogeographic break between Seychelles and Mauritius, suggesting connectivity is limited even when the pelagic larval duration is between 50-60 days [124,133].…”

Section: Discussionmentioning

confidence: 99%

Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish

et al. 2022

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The roundjaw bonefish, Albula glossodonta, is the most widespread albulid in the Indo-Pacific and is vulnerable to extinction. We assembled the genome of a roundjaw bonefish from Hawai‘i, USA, which will be instrumental for effective transboundary management and conservation when paired with population genomics datasets. The 1.05 gigabase pair (Gbp) contig-level assembly had a 4.75 megabase pair (Mbp) NG50 and a maximum contig length of 28.2 Mbp. Scaffolding yielded an LG50 of 20 and an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. The genome comprised 6.5% repetitive elements and was annotated with 28.3 K protein-coding genes. We then evaluated population genetic connectivity between six atolls in the Western Indian Ocean with 38,355 SNP loci across 66 A. glossodonta individuals. We discerned shallow population structure and observed genetic homogeneity between atolls in Seychelles and reduced gene flow between Seychelles and Mauritius. The South Equatorial Current might be the limiting mechanism of this reduced gene flow. The genome assembly will be useful for addressing taxonomic uncertainties of bonefishes globally.

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Section: Discussionmentioning

confidence: 99%

Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish

et al. 2022

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“…This genetic structuring was unexpected, given the long pelagic larval duration of A. glossodonta . However, there is evidence of limited gene flow between Seychelles and Mauritius in other marine fish species with pelagic larvae, such as Lutjanid kasmira [129], Lethrinus nebulosus [130], and Pristipomoides filamentous [131].…”

Section: Discussionmentioning

confidence: 99%

“…St. Brandon’s Atoll is in the direct path of one of the bifurcated arms of the South Equatorial Current as it passes through the Mascarene Plateau [125, 134]. The South Equatorial Current pushes water westward, which may create a barrier to gene flow to islands south of Seychelles such as Mauritius and Réunion [130, 131, 134]. Although there are currently no bonefish – or even elopomorph – larval dispersal models for the Indian Ocean, pelagic larval dispersal simulation models of coral species in the southwestern Indian Ocean corroborate the biogeographic break between Seychelles and Mauritius, suggesting connectivity is limited even when the pelagic larval duration is between 50–60 days [125, 134].…”

Section: Discussionmentioning

confidence: 99%

Genome Assembly of the Roundjaw Bonefish (Albula glossodonta), a Vulnerable Circumtropical Sportfish

Pickett

Talma

Glass

et al. 2021

Preprint

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Background: Bonefishes are cryptic species indiscriminately targeted by subsistence and recreational fisheries worldwide. The roundjaw bonefish, Albula glossodonta is the most widespread bonefish species in the Indo-Pacific and is listed as vulnerable to extinction by the IUCN's Red List due to anthropogenic activities. Whole-genome datasets allow for improved population and species delimitation, which – prior to this study – were lacking for Albula species. Results: We generated a high-quality genome assembly of an A. glossodonta individual from Hawai'i, USA. The assembled contigs had an NG50 of 4.75 Mbp and a maximum length of 28.2 Mbp. Scaffolding yielded an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. Half the genome was contained in 20 scaffolds. The genome was annotated with 28.3 K protein-coding genes. We then analyzed 66 A. glossodonta individuals and 38,355 SNP loci to evaluate population genetic connectivity between six atolls in Seychelles and Mauritius in the Western Indian Ocean. We observed genetic homogeneity between atolls in Seychelles and evidence of reduced gene flow between Seychelles and Mauritius. The South Equatorial Current could be one mechanism limiting gene flow of A. glossodonta populations between Seychelles and Mauritius. Conclusions: Quantifying the spatial population structure of widespread fishery species such as bonefishes is necessary for effective transboundary management and conservation. This population genomic dataset mapped to a high-quality genome assembly allowed us to discern shallow population structure in a widespread species in the Western Indian Ocean. The genome assembly will be useful for addressing the taxonomic uncertainties of bonefishes globally.

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“…Fin clip collection was performed during November 2020. Clipping of pectoral fin [16,40] from dead fish was done with a sterilized pair of scissors and thereafter stored in sterilized 1.8 ml serum vials filled with 95% ethanol and kept at −20° C until the laboratory analysis. A pair of scissors/scalpel and forceps were subjected to 30% bleach and rinsed in distilled water between individual fish and sampling sites.…”

Section: Sample Collectionmentioning

confidence: 99%

DNA barcoding affirms the presence of invasiveParachanna obscuraand new records of some species in the Mweru-Luapula fishery

Seemani,

Katongo,

Bloomer

et al. 2024

Preprint

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DNA barcoding has recently been instrumental in identifying both invasive and undetected species in aquatic environments. This study aimed at analysing collected fish fin clips to ascertain the identity of native species and the Parachanna species that have invaded the Mweru-Luapula (ML) fishery of Zambia. The identification process was carried out through field phenotypic analysis using species guides and DNA barcoding, with the mitochondrial DNA (mtDNA) cytochrome C oxidase 1 (COI) gene fragment. Of the 28 specimens for which DNA was successfully PCR amplified, five matched the reference sequences of species and 22 matched the reference sequences of genera on the NCBI GenBank. Five unexpected species, namely Oreochromis niloticus, Coptodon zillii, Mormyrus kannume, Thoracochromis buysi and Tylochromis polylepis were identified. The study further affirmed the presence of invasive Parachanna obscura in the fishery and its interconnected water bodies. Parachanna obscura invaded the fishery through annual flooding from aquacultural facilities in the Democratic Republic of Congo (DRC). There is a need to investigate this invasion further by using large sample sizes and also by applying the gonadosomatic index (GSI) to determine invasive species occupancy and impact on native species throughout the fishery. This study provides a platform for further detailed taxonomic verification and species inventory of the entire ML fishery. This will facilitate the development of a viable and sustainable strategy to appropriately curb the impact of invasive species, and will thus contribute to the conservation of the ML aquatic biodiversity.

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Genetic diversity and spatial population structure of a deepwater snapper, Pristipomoides filamentosus in the south-west Indian Ocean

Cited by 4 publications

References 49 publications

Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish

Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish

Genome Assembly of the Roundjaw Bonefish (Albula glossodonta), a Vulnerable Circumtropical Sportfish

DNA barcoding affirms the presence of invasiveParachanna obscuraand new records of some species in the Mweru-Luapula fishery

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