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Choi HY, Kim S, Choi HC, Youn SH. The complete mitochondrial genome of sleek unicornfish, Naso hexacanthus (Acanthuridae, Perciformes). Mitochondrial DNA B Resour 2023; 8:274-275. [PMID: 36845009 PMCID: PMC9946333 DOI: 10.1080/23802359.2022.2160666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The complete mitochondrial DNA sequence of sleek unicornfish, Naso hexacanthus was first determined in this study. The complete mitogenome is 16,611 bp in length composed of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The nucleotides consist of 33.8% A, 20.6% C, 25.0% G, 20.6% T. The gene order and direction are identical to those of N. lopezi and the species of Acanthuridae. The result would be useful to investigate genetic relationships among the species of Naso.
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Affiliation(s)
- Hae-young Choi
- Fisheries Resources and Environment Division, South Sea Fisheries Research Institute, Yeosu, Korea
| | - Sung Kim
- Marine Ecosystem Research Center, Korea Institute of Ocean Science & Technology, Busan, Korea
| | - Hee-chan Choi
- Fisheries Resources and Environment Division, East Sea Fisheries Research Institute, Gangwon, Korea
| | - Seok-hyun Youn
- Fisheries Resources and Environment Division, East Sea Fisheries Research Institute, Gangwon, Korea,CONTACT Seok-hyun Youn Oceanic Climate & Ecology Research Division, National Institute of Fisheries Science, Busan, 46083, Korea
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2
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Vargas-Fonseca OA, Yates P, Kirkman SP, Pistorius PA, Moore DM, Natoli A, Cockcroft V, Hoelzel AR. Population structure associated with bioregion and seasonal prey distribution for Indo-Pacific bottlenose dolphins (Tursiops aduncus) in South Africa. Mol Ecol 2021; 30:4642-4659. [PMID: 34289192 DOI: 10.1111/mec.16086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/19/2021] [Accepted: 06/29/2021] [Indexed: 11/28/2022]
Abstract
Many marine species exhibit fine-scale population structure despite high mobility and a lack of physical barriers to dispersal, but the evolutionary drivers of differentiation in these systems are generally poorly understood. Here we investigate the potential role of habitat transitions and seasonal prey distributions on the evolution of population structure in the Indo-Pacific bottlenose dolphin, Tursiops aduncus, off South Africa's coast, using double-digest restriction-site associated DNA sequencing. Population structure was identified between the eastern and southern coasts and correlated with the habitat transition between the temperate Agulhas (southern) and subtropical Natal (eastern) Bioregions, suggesting differentiation driven by resource specializations. Differentiation along the Natal coast was comparatively weak, but was evident in some analyses and varied depending on whether the samples were collected during or outside the seasonal sardine (Sardinops sagax) run. This local abundance of prey could influence the ranging patterns and apparent genetic structure of T. aduncus. These findings have significant and transferable management implications, most importantly in terms of differentiating populations inhabiting distinct bioregions and seasonal structural patterns within a region associated with the movement of prey resources.
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Affiliation(s)
- O Alejandra Vargas-Fonseca
- Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa.,Marine Apex Predator Research Unit (MAPRU), Institute for Coastal and Marine Research, Nelson Mandela University, Port Elizabeth, South Africa
| | - Paige Yates
- Department of Biosciences, University of Durham, Durham, UK
| | - Stephan P Kirkman
- Marine Apex Predator Research Unit (MAPRU), Institute for Coastal and Marine Research, Nelson Mandela University, Port Elizabeth, South Africa.,Branch: Oceans and Coasts, Department of Environment, Forestry and Fisheries (DEFF), Cape Town, South Africa
| | - Pierre A Pistorius
- Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa.,Marine Apex Predator Research Unit (MAPRU), Institute for Coastal and Marine Research, Nelson Mandela University, Port Elizabeth, South Africa
| | - Daniel M Moore
- Department of Biosciences, University of Durham, Durham, UK
| | - Ada Natoli
- Department of Life and Environmental Sciences, College of Natural and Health Sciences, Zayed University, United Arab Emirates.,UAE Dolphin Project, Dubai, United Arab Emirates
| | - Victor Cockcroft
- Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa
| | - A Rus Hoelzel
- Department of Biosciences, University of Durham, Durham, UK
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Neves JMM, Almeida JPFA, Sturaro MJ, FabrÉ NN, Pereira RJ, Mott T. Deep genetic divergence and paraphyly in cryptic species of Mugil fishes (Actinopterygii: Mugilidae). SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1729892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Jessika M. M. Neves
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - JoÃo P. F. A. Almeida
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - Marcelo J. Sturaro
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Nidia N. FabrÉ
- Laboratório de Ecologia, Peixes e Pesca, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - Ricardo J. Pereira
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - TamÍ Mott
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
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Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea. PLoS One 2018; 13:e0193220. [PMID: 29466431 PMCID: PMC5821360 DOI: 10.1371/journal.pone.0193220] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 02/07/2018] [Indexed: 11/19/2022] Open
Abstract
The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P < 0.001); (2) low frequency of later-generation hybrids; (3) significant association with mitochondrial Clade A and Clade B, respectively; and (4) subtle yet significant body shape differences as inferred from geometric morphometric analysis. The divergence between mitochondrial Clade C and the two other clades was not matched by genetic differences at microsatellite marker loci. The occurrence of discordant mitonuclear combinations (20.5% of the total number of individuals) is thought to result from mitochondrial introgression, consistent with a scenario of demographic, and presumably spatial, post-Pleistocene expansion of populations from northern regions into a secondary contact zone in the South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region.
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Bertrand JAM, Borsa P, Chen WJ. Phylogeography of the sergeants Abudefduf sexfasciatus and A. vaigiensis reveals complex introgression patterns between two widespread and sympatric Indo-West Pacific reef fishes. Mol Ecol 2017; 26:2527-2542. [PMID: 28160340 DOI: 10.1111/mec.14044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/19/2017] [Accepted: 01/25/2017] [Indexed: 01/02/2023]
Abstract
On evolutionary timescales, sea level oscillations lead to recurrent spatio-temporal variation in species distribution and population connectivity. In this situation, applying classical concepts of biogeography is challenging yet necessary to understand the mechanisms underlying biodiversity in highly diverse marine ecosystems such as coral reefs. We aimed at studying the outcomes of such complex biogeographic dynamics on reproductive isolation by sampling populations across a wide spatial range of a species-rich fish genus: the sergeants (Pomacentridae: Abudefduf). We generated a mutlilocus data set that included ten morpho-species from 32 Indo-West Pacific localities. We observed a pattern of mito-nuclear discordance in two common and widely distributed species: Abudefduf sexfasciatus and Abudefduf vaigiensis. The results showed three regional sublineages (Indian Ocean, Coral Triangle region, western Pacific) in A. sexfasciatus (0.6-1.5% divergence at cytb). The other species, A. vaigiensis, is polyphyletic and consists of three distinct genetic lineages (A, B and C) (9% divergence at cytb) whose geographic ranges overlap. Although A. vaigiensis A and A. sexfasciatus were found to be distinct based on nuclear information, A. vaigiensis A was found to be nested within A. sexfasciatus in the mitochondrial gene tree. A. sexfasciatus from the Coral Triangle region and A. vaigiensis A were not differentiated from each other at the mitochondrial locus. We then used coalescent-based simulation to characterize a spatially widespread but weak gene flow between the two species. We showed that these fishes are good candidates to investigate the evolutionary complexity of the discrepancies between phenotypic and genetic similarity in closely related species.
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Affiliation(s)
- Joris A M Bertrand
- Institute of Oceanography, National Taiwan University, N°1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Philippe Borsa
- Institut de recherche pour le développement, UMR 250 'Ecologie marine tropicale des océans Pacifique et Indien', 101 promenade Roger-Laroque Anse Vata, BP A5, 98848 Nouméa cedex, New Caledonia
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, N°1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
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Firidin S, Eroglu O, Altinok I. Genetic characterization of brown meagre (Sciaena umbra) and Shi Drum (Umbrina cirrosa) populations. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Lack of Spatial Subdivision for the Snapper Lutjanus purpureus (Lutjanidae - Perciformes) from Southwest Atlantic Based on Multi-Locus Analyses. PLoS One 2016; 11:e0161617. [PMID: 27556738 PMCID: PMC4996478 DOI: 10.1371/journal.pone.0161617] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 08/09/2016] [Indexed: 11/25/2022] Open
Abstract
The Caribbean snapper Lutjanus purpureus is a marine species fish commonly found associated with rocky seabeds and is widely distributed along of Western Atlantic. Data on stock delineation and stock recognition are essential for establishing conservation measures for commercially fished species. However, few studies have investigated the population genetic structure of this economically valuable species, and previous studies (based on only a portion of the mitochondrial DNA) provide an incomplete picture. The present study used a multi-locus approach (12 segments of mitochondrial and nuclear DNA) to elucidate the levels of genetic diversity and genetic connectivity of L. purpureus populations and their demographic history. L. purpureus has high levels of genetic diversity, which probably implies in high effective population sizes values for the species. The data show that this species is genetically homogeneous throughout the geographic region analyzed, most likely as a result of dispersal during larval phase. Regarding demographic history, a historical population growth event occurred, likely due to sea level changes during the Pleistocene.
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Barrow LN, Bigelow AT, Phillips CA, Lemmon EM. Phylogeographic inference using Bayesian model comparison across a fragmented chorus frog species complex. Mol Ecol 2015; 24:4739-58. [DOI: 10.1111/mec.13343] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 07/24/2015] [Accepted: 08/08/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Lisa N. Barrow
- Department of Biological Science Florida State University 319 Stadium Drive, P.O. Box 3064340 Tallahassee FL 32306‐4340 USA
| | - Alyssa T. Bigelow
- Department of Biological Science Florida State University 319 Stadium Drive, P.O. Box 3064340 Tallahassee FL 32306‐4340 USA
| | - Christopher A. Phillips
- Illinois Natural History Survey Prairie Research Institute University of Illinois 185 Natural Resources Bldg, 607 E. Peabody Drive Champaign IL 61820 USA
| | - Emily Moriarty Lemmon
- Department of Biological Science Florida State University 319 Stadium Drive, P.O. Box 3064340 Tallahassee FL 32306‐4340 USA
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Temporal Stability of Genetic Structure in a Mesopelagic Copepod. PLoS One 2015; 10:e0136087. [PMID: 26302332 PMCID: PMC4547763 DOI: 10.1371/journal.pone.0136087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 07/29/2015] [Indexed: 11/19/2022] Open
Abstract
Although stochasticity in oceanographic conditions is known to be an important driver of temporal genetic change in many marine species, little is known about whether genetically distinct plankton populations can persist in open ocean habitats. A prior study demonstrated significant population genetic structure among oceanic gyres in the mesopelagic copepod Haloptilus longicornis in both the Atlantic and Pacific Oceans, and we hypothesized that populations within each gyre represent distinct gene pools that persist over time. We tested this expectation through basin-scale sampling across the Atlantic Ocean in 2010 and 2012. Using both mitochondrial (mtCOII) and microsatellite markers (7 loci), we show that the genetic composition of populations was stable across two years in both the northern and southern subtropical gyres. Genetic variation in this species was partitioned among ocean gyres (FCT = 0.285, P < 0.0001 for mtCOII, FCT = 0.013, P < 0.0001 for microsatellites), suggesting strong spatial population structure, but no significant partitioning was found among sampling years. This temporal persistence of population structure across a large geographic scale was coupled with chaotic genetic patchiness at smaller spatial scales, but the magnitude of genetic differentiation was an order of magnitude lower at these smaller scales. Our results demonstrate that genetically distinct plankton populations persist over time in highly-dispersive open ocean habitats, and this is the first study to rigorously test for temporal stability of large scale population structure in the plankton.
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Thinking outside the barrier: neutral and adaptive divergence in Indo-Pacific coral reef faunas. Evol Ecol 2014. [DOI: 10.1007/s10682-014-9724-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Hubert N, Espiau B, Meyer C, Planes S. Identifying the ichthyoplankton of a coral reef using DNA barcodes. Mol Ecol Resour 2014; 15:57-67. [PMID: 24935524 DOI: 10.1111/1755-0998.12293] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/28/2014] [Accepted: 05/30/2014] [Indexed: 11/30/2022]
Abstract
Marine fishes exhibit spectacular phenotypic changes during their ontogeny, and the identification of their early stages is challenging due to the paucity of diagnostic morphological characters at the species level. Meanwhile, the importance of early life stages in dispersal and connectivity has recently experienced an increasing interest in conservation programmes for coral reef fishes. This study aims at assessing the effectiveness of DNA barcoding for the automated identification of coral reef fish larvae through large-scale ecosystemic sampling. Fish larvae were mainly collected using bongo nets and light traps around Moorea between September 2008 and August 2010 in 10 sites distributed in open waters. Fish larvae ranged from 2 to 100 mm of total length, with the most abundant individuals being <5 mm. Among the 505 individuals DNA barcoded, 373 larvae (i.e. 75%) were identified to the species level. A total of 106 species were detected, among which 11 corresponded to pelagic and bathypelagic species, while 95 corresponded to species observed at the adult stage on neighbouring reefs. This study highlights the benefits and pitfalls of using standardized molecular systems for species identification and illustrates the new possibilities enabled by DNA barcoding for future work on coral reef fish larval ecology.
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Affiliation(s)
- Nicolas Hubert
- Institut de Recherche pour le Développement (IRD), UMR226 ISE-M, Bât. 22 - CC065, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
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Horne JB, van Herwerden L, Abellana S, McIlwain JL. Observations of Migrant Exchange and Mixing in a Coral Reef Fish Metapopulation Link Scales of Marine Population Connectivity. J Hered 2013; 104:532-46. [DOI: 10.1093/jhered/est021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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