Systematic Status of Bonefishes (Albula spp.) From the Eastern Pacific Ocean Inferred from Analyses of Allozymes and Mitochondrial DNA

Pfeiler, Edward; Colborn, Jeff; Douglas, Marlis R.; Douglas, Michael E.

doi:10.1023/a:1014263528547

Cited by 9 publications

(2 citation statements)

References 20 publications

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“…The threat to A. glossodonta and other bonefish species will persist unless identification is made easier and population genomics techniques are employed to understand and identify evolutionarily significant units, areas of overlap between species, presence and extent of hybridization, and life-history traits, especially migration and spawning [4]. Genetic identification has previously been accomplished using only a portion of the mitochondrial cytochrome b gene and some microsatellite markers [6,9,15,19,[26][27][28][29][30][31][32][33], which probably sequencing was performed in rapid run mode for 250 cycles in one lane on the Illumina (San Diego, California, USA) Hi-Seq 2500 at the DNASC after sonication with Covaris (Woburn, Massachusetts, USA) Adaptive Focus Acoustics technology and preparation with New England Biolabs (Ipswich, Massachusetts, USA) NEBNext Ultra II End Repair and Ligation kits with adapters from Integrated DNA Technologies (Coralville, Iowa, USA).…”

Section: Contextmentioning

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: Contextmentioning

confidence: 99%

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

et al. 2022

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“…The threat to A. glossodonta and other bonefish species will persist unless identification is made easier and population genomics techniques are employed to understand and identify evolutionarily significant units, areas of overlap between species, presence and extent of hybridization, and life-history traits, especially migration and spawning [4]. Genetic identification has hitherto been accomplished using only a portion of the mitochondrial cytochrome b gene and some microsatellite markers [6, 9, 15, 18, 25-32], which likely provide an insufficient taxonomic history [4, 33-35]. To contribute to a more robust capacity for identification and enable more complex genomics-based analyses, we present a high-quality genome assembly of an A. glossodonta individual.…”

Section: Introductionmentioning

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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Lingering Taxonomic Challenges Hinder Conservation and Management of Global Bonefishes

et al. 2020

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Despite expanding research on the popular recreational fishery, bonefish taxonomy remains murky. The genus Albula, comprising these iconic circumtropical marine sportfishes, has a complex taxonomic history driven by highly conserved morphology. Presently, 12 putative species are spread among 3 species complexes. The cryptic morphology hinders visual identification, requiring genetic species identification in some cases. Unclear nomenclature can have unintended consequences, including exacerbating taxonomic uncertainty and complicating resolution efforts. Further, ignoring this reality in publications may erode management and conservation efforts. In the Indian and Pacific oceans, ranges and areas of overlap are unclear, precluding certainty about which species support the fishery and hindering conservation efforts. Species overlap, at both broad and localized spatial scales, may mask population declines if one is targeted primarily (as demonstrated in the western Atlantic fishery). Additional work is necessary, especially to increase our understanding of spatiotemporal ecology across life history stages and taxa. If combined with increased capacity to discern between cryptic species, population structure may be ascertained, and fisheries stakeholders will be enabled to make informed decisions. To assist in such efforts, we have constructed new range maps for each species and species complex. For bonefishes, conservation genomic approaches may resolve lingering taxonomic uncertainties, supporting effective conservation and management efforts. These methods apply broadly to taxonomic groups with cryptic diversity, aiding species delimitation and taxonomic revisions.

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Systematic Status of Bonefishes (Albula spp.) From the Eastern Pacific Ocean Inferred from Analyses of Allozymes and Mitochondrial DNA

Cited by 9 publications

References 20 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

Lingering Taxonomic Challenges Hinder Conservation and Management of Global Bonefishes

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