Dataset Information

Mitochondrial cytochrome c oxidase subunit I gene analysis of the yellowfin snapper, Lutjanus xanthopinnis in the Indo-Pacific region and a note on Lutjanus lutjanus population structure.

ABSTRACT: The yellowfin snapper, Lutjanus xanthopinnis, was recorded as a newly described species in the Indo-Pacific region in 2015. However, the knowledge of its biology, biogeography and ecology is scarcely understood, and, hence, its current conservation status is categorized as Data Deficient. The mitochondrial cytochrome c oxidase subunit I (COI) gene was examined to confirm species identification. We also examined the COI gene haplotypes of L. xanthopinnis in Brunei Darussalam and Malaysia together with other waters, i.e., Bangladesh, Indonesia, Japan, Singapore, Sri Lanka and Taiwan. Our molecular analyses found that Brunei Darussalam and eastern Peninsular Malaysia samples were genetically similar. However, the former showed higher genetic diversity than the latter. The samples from these two sites also showed signatures of population expansion. Furthermore, identical haplotypes could be found in different locations, suggesting the absence of spatial genetic structure. On the other hand, Lutjanus lutjanus showed a population structure associated with geographical locations, i.e., western Pacific Ocean, Indian Ocean and Maluku in Indonesia.

SUBMITTER: Arai T

PROVIDER: S-EPMC10474401 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

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Mitochondrial cytochrome c oxidase subunit I gene analysis of the yellowfin snapper, Lutjanus xanthopinnis in the Indo-Pacific region and a note on Lutjanus lutjanus population structure.

Arai Takaomi T Taha Hussein H Alidon Najihah N Jumat Juhaidah J Azmey Syakirah S Zan Nur Dhabitah ND Aimi Mat Jaafar Tun Nurul TN Habib Ahasan A

Heliyon 20230822 9

The yellowfin snapper, Lutjanus xanthopinnis, was recorded as a newly described species in the Indo-Pacific region in 2015. However, the knowledge of its biology, biogeography and ecology is scarcely understood, and, hence, its current conservation status is categorized as Data Deficient. The mitochondrial cytochrome c oxidase subunit I (COI) gene was examined to confirm species identification. We also examined the COI gene haplotypes of L. xanthopinnis in Brunei Darussalam ...[more]

PMID: 37662727

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Project description:In the tropical Indo-Pacific, most phylogeographic studies have focused on the shallow-water taxa that inhabit reefs to approximately 30 m depth. Little is known about the large predatory fishes, primarily snappers (subfamily Etelinae) and groupers (subfamily Epinephelinae) that occur at 100-400 m. These long-lived, slow-growing species support fisheries across the Indo-Pacific, yet no comprehensive genetic surveys within this group have been conducted. Here we contribute the first range-wide survey of a deepwater Indo-Pacific snapper, Pristipomoides filamentosus, with special focus on Hawai'i. We applied mtDNA cytochrome b and 11 microsatellite loci to 26 samples (N=1,222) collected across 17,000 km from Hawai'i to the western Indian Ocean. Results indicate that P. filamentosus is a highly dispersive species with low but significant population structure (mtDNA Φ(ST)=0.029, microsatellite F(ST)=0.029) due entirely to the isolation of Hawai'i. No population structure was detected across 14,000 km of the Indo-Pacific from Tonga in the Central Pacific to the Seychelles in the western Indian Ocean, a pattern rarely observed in reef species. Despite a long pelagic phase (60-180 days), interisland dispersal as adults, and extensive gene flow across the Indo-Pacific, P. filamentosus is unable to maintain population connectivity with Hawai'i. Coalescent analyses indicate that P. filamentosus may have colonized Hawai'i 26 K-52 K y ago against prevailing currents, with dispersal away from Hawai'i dominating migration estimates. P. filamentosus harbors low genetic diversity in Hawai'i, a common pattern in marine fishes, and our data indicate a single archipelago-wide stock. However, like the Hawaiian Grouper, Hyporthodus quernus, this snapper had several significant pairwise comparisons (F(ST)) clustered around the middle of the archipelago (St. Rogatien, Brooks Banks, Gardner) indicating that this region may be isolated or (more likely) receives input from Johnston Atoll to the south.

Project description:BackgroundThe lack of barriers in the marine environment has promoted the idea of panmixia in marine organisms. However, oceanographic conditions and habitat characteristics have recently been linked to genetic structure in marine species. The Tropical Eastern Pacific (TEP) is characterized by dynamic current systems and heterogeneous oceanographic conditions. The Gulf of Panama (part of the equatorial segment for the TEP) is influenced by a complex current system and heterogeneous environment, which has been shown to limit the gene flow for shoreline species. Next Generation Sequencing (NGS) has contributed to detect genetic differences in previously reported panmictic species by the assessment of loci associated with selection and to understand how selection acts affects marine populations. Lutjanus guttatus is a species distributed in the TEP for which previous studies using mitochondrial data recovered a panmictic pattern along its distributional range. In this study, we used SNP data of L. guttatus individuals sampled along its range to evaluate population genetic structure and investigate whether oceanographic factors influence the species' genetic architecture. Finally, we assessed the role of adaptive selection by evaluating the contribution of outlier and neutral loci to genetic divergence.MethodsThe RADcap method was used to obtain 24 million paired reads for 123 individuals of L. guttatus covering nearly all its distributional area. Genetic variation was assessed using both spatial and non-spatial methods by comparing three different data sets: (i) a Combined Loci (CL dataset = 2003 SNPs); a search for putative loci under selection allowed the evaluation of (ii) Neutral Loci (NL dataset = 1858 SNPs) and (iii) Outlier Loci (OL dataset = 145 SNPs). We used the estimating effective migration surface (EEMS) approach to detect possible barriers to gene flow.ResultsGenetic differences were found in the OL dataset, showing two clusters (Northern and Southern), whereas NL showed no differences. This result may be related to the Selection-Migration balance model. The limit between the Northern and Southern groups was in the Gulf of Panama, which has been previously identified as a barrier to gene flow for other species, mainly due to its heterogeneous oceanographic conditions. The results suggest that selection plays an important role in generating genetic differences in Lutjanus guttatus. A migration corridor was detected that coincides with the Costa Rica Coastal Current that flows from Central America to the Gulf of California, allowing the homogenization of the northern population. In the Southern cluster, a migration corridor was observed with the OL from Panama to Colombia, which could be associated with the currents found in the Gulf of Panama. Genetic variation found in the OL of Lutjanus guttatus highlights the usefulness of NGS data in evaluating the role of selection in population differentiation.

Dataset Information

Mitochondrial cytochrome c oxidase subunit I gene analysis of the yellowfin snapper, Lutjanus xanthopinnis in the Indo-Pacific region and a note on Lutjanus lutjanus population structure.

Publications

Mitochondrial cytochrome c oxidase subunit I gene analysis of the yellowfin snapper, <i>Lutjanus xanthopinnis</i> in the Indo-Pacific region and a note on <i>Lutjanus lutjanus</i> population structure.

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