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Yorifuji M, Hayashi M, Ono T. Interactive effects of ocean deoxygenation and acidification on a coastal fish Sillago japonica in early life stages. MARINE POLLUTION BULLETIN 2024; 198:115896. [PMID: 38096697 DOI: 10.1016/j.marpolbul.2023.115896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/26/2023] [Accepted: 12/02/2023] [Indexed: 01/05/2024]
Abstract
Acidification and deoxygenation are major threats to ocean environments. Despite the possibilities of their co-occurrence, little is known about their interactive effects on marine organisms. The effects of low pH and low dissolved oxygen (DO) on the early life stages of the coastal fish Sillago japonica were investigated. Twenty-five experimental treatments fully crossed in five levels of pH 7.6-8.1 and DO 50-230 μmol/kg (20-100 % saturation degree) were tested, and hatching rate of the embryos and survivability of the larvae after 24 h at 25 °C were investigated. Low DO treatment significantly affected the embryos and larvae compared to low pH treatment. The 50 % lethal concentration of DO showed the highest value at pH 7.6 and the lowest value at pH 7.7 and 7.9 for embryos and larvae, respectively. Therefore, effects of deoxygenation on fishes were alleviated under acidified condition around pH 7.7-7.9.
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Affiliation(s)
- Makiko Yorifuji
- Demonstration Laboratory, Marine Ecology Research Institute, 4-7-17 Arahama, Kashiwazaki, Niigata 945-0017, Japan; Marine Geo-Environment Research Group, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan.
| | - Masahiro Hayashi
- Demonstration Laboratory, Marine Ecology Research Institute, 4-7-17 Arahama, Kashiwazaki, Niigata 945-0017, Japan.
| | - Tsuneo Ono
- Fisheries Resource Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
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Peng L, Hua W, Chen Y, Wang W, Xue Z. Comparative analysis of the population diversity of black rockfish (Sebastes schlegelii) in northern China. Mol Biol Rep 2023; 50:10015-10024. [PMID: 37902911 DOI: 10.1007/s11033-023-08821-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 11/01/2023]
Abstract
The nearshore marine fish known as black rockfish (Sebastes schlegelii) is found in the Yellow Sea, Bohai Sea, and East China Sea. The population structure and genetic diversity of S. schlegelii are vulnerable to the effects of artificial stocking, environmental pollution, overfishing, and climate change, so relevant studies are urgently needed. This study used comparative mtDNA loop (D-loop) analysis to examine the genetic diversity and natural population structure of 98 individuals from the northern Chinese cities of Qingdao, Jinzhou, and Dalian. A total of 22 haplotypes were identified in the three groups of samples, with the most common haplotypes being Hap-2, Hap-3, Hap-4, Hap-5, and Hap-6. The results of genetic diversity based on the D-LOOP sequence showed that the genetic diversity of S. schlegelii in the study area showed high Hd and low π type, indicating that the genetic diversity of S. schlegelii was low. Analyses of molecular variance (AMOVA) showed that the percentage of among population variation was - 0.29%, and the percentage of within population variation was 100.29%, indicating that the genetic variation was mainly from within the population. Between the three locations, the genetic differentiation index (Fst) was - 0.0113 ~ 0.0061, and there was no genetic differentiation among the populations. The results of gene flow (Nm) coefficients showed that the average Nm among the three populations was infinite (Nm = inf > > 4) and the three populations formed a stochastic unit. The results of the neutrality test (Tajima's D, Fu's Fs) and the frequency of nucleotide mismatch distribution demonstrated that the three geographic populations of S. schlegelii did not undergo a large population expansion in recent history. Based on the above conclusions, the S. schlegelii as a whole should be protected in situ.
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Affiliation(s)
- Lei Peng
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China
- College of Aquatic and Life Science, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China
| | - Wenyuan Hua
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China
- College of Aquatic and Life Science, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China
| | - Yan Chen
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China
- College of Aquatic and Life Science, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China
| | - Wei Wang
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China.
- College of Aquatic and Life Science, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China.
| | - Zhuang Xue
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China.
- College of Aquatic and Life Science, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China.
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Robalo JI, Farias I, Francisco SM, Avellaneda K, Castilho R, Figueiredo I. Genetic population structure of the Blackspot seabream ( Pagellus bogaraveo): contribution of mtDNA control region to fisheries management. Mitochondrial DNA A DNA Mapp Seq Anal 2021; 32:115-119. [PMID: 33576693 DOI: 10.1080/24701394.2021.1882445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Marine fisheries management models have traditionally considered biological parameters and geopolitical boundaries. The result is the existence of fisheries management units that do not match genetic populations. However, this panorama is changing with the contribution of genetic and genomic data. Pagellus bogaraveo is a commercially important sparid in the northeast Atlantic, with three stock components being considered by ICES: the Celtic Sea and Bay of Biscay, Atlantic Iberian waters and the Azores. The northern stock collapsed (1975-1985) and is essential to characterize the genetic makeup of the species, particularly in the Iberian Peninsula, where it is managed as a single stock. The mitochondrial control region was used to screen the intraspecific diversity and population structure of individuals from six locations across the species range. The genetic diversity found is similar among sites, and there is differentiation between the Azores and the remaining locations.
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Affiliation(s)
- Joana I Robalo
- MARE - Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Lisboa, Portugal
| | - Inês Farias
- Portuguese Institute for Sea and Atmosphere (IPMA), Algés, Portugal
| | - Sara M Francisco
- MARE - Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Lisboa, Portugal
| | - Karen Avellaneda
- MARE - Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Lisboa, Portugal
| | - Rita Castilho
- University of the Algarve, Faro, Portugal.,Faculty of Science and Technology, Centre of Marine Sciences (CCMAR), Faro, Portugal
| | - Ivone Figueiredo
- Portuguese Institute for Sea and Atmosphere (IPMA), Algés, Portugal
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Matumba TG, Oliver J, Barker NP, McQuaid CD, Teske PR. Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA. F1000Res 2020; 9:339. [PMID: 32934803 PMCID: PMC7475959 DOI: 10.12688/f1000research.23635.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/20/2020] [Indexed: 11/22/2023] Open
Abstract
Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. Nuclear rRNA is not usually used to study intraspecific variation in species that are not spatially structured, presumably because this marker is assumed to evolve so slowly that it is more suitable for phylogenetics. Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolution is more clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a 'barcoding gap', estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.
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Affiliation(s)
- Tshifhiwa G. Matumba
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
- Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa
| | - Jody Oliver
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Nigel P. Barker
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, 0028, South Africa
| | - Christopher D. McQuaid
- Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa
| | - Peter R. Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
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Niu SF, Wu RX, Zhai Y, Zhang HR, Li ZL, Liang ZB, Chen YH. Demographic history and population genetic analysis of Decapterus maruadsi from the northern South China Sea based on mitochondrial control region sequence. PeerJ 2019; 7:e7953. [PMID: 31681517 PMCID: PMC6822595 DOI: 10.7717/peerj.7953] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 09/26/2019] [Indexed: 11/24/2022] Open
Abstract
Late Pleistocene climate oscillations are believed to have greatly influenced the distribution, population dynamics, and genetic variation of many marine organisms in the western Pacific. However, the impact of the late Pleistocene climate cycles on the demographic history and population genetics of pelagic fish in the northern South China Sea (SCS) remains largely unexplored. In this study, we explored the demographic history, genetic structure, and genetic diversity of Decapterus maruadsi, a typical pelagic fish, over most of its range in the northern SCS. A 828–832 bp fragment of mitochondrial control region were sequenced in 241 individuals from 11 locations. High haplotype diversity (0.905–0.980) and low nucleotide diversity (0.00269–0.00849) was detected, revealing low levels of genetic diversity. Demographic history analysis revealed a pattern of decline and subsequent rapid growth in the effective population size during deglaciation, which showed that D. maruadsi experienced recent demographic expansion after a period of low effective population size. Genetic diversity, genetic structure, and phylogenetic relationship analysis all demonstrated that no significant genetic differentiation existed among the populations, indicating that D. maruadsi was panmictic throughout the northern SCS. Periodic sea-level changes, fluctuation of the East Asian Monsoon, and Kuroshio variability were responsible for the population decline and expansion of D. maruadsi. The demographic history was the primary reason for the low levels of genetic diversity and the lack of significant genetic structure. The life history characteristics and ocean currents also had a strong correlation with the genetic homogeneity of D. maruadsi. However, the genetic structure of the population (genetic homogeneity) is inconsistent with biological characteristics (significant difference), which is an important reminder to identify and manage the D. maruadsi population carefully.
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Affiliation(s)
- Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Yun Zhai
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Hao-Ran Zhang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Zhong-Lu Li
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Yu-Hang Chen
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
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