Otolith chemistry indicates large-scale connectivity in Chilean jack mackerel (Trachurus murphyi), a highly mobile species in the Southern Pacific Ocean

Chemistry in material laid down prior to capture along the edges of otoliths of Chilean jack mackerel (Trachurus murphyi) showed strong spatial heterogeneity corresponding to hydrographic structure across putative population boundaries between (i) the western and eastern South Pacific Ocean, and (ii) Chile and Peru. Yet the chemistry of the otolith nucleus, in material laid down during early life, showed no evidence supporting the existence of these boundaries. Instead, jack mackerel from New Zealand had similar nucleus chemistry to most sampling areas off South America; and those off southern Peru showed similar nucleus chemistry to most sampling areas off Chile. Strong differences were found between southern and northern Peru, and cluster analysis indicated this was caused by a group of fish off northern Peru with chemistry found nowhere else. Most other fish grouped in two clusters, which showed properties suggesting correspondence with a major spawning zone in oceanic water off central Chile, and a smaller area in coastal water off northern Chile, characterized by similar sea surface temperature, lack of westward transport, and low kinetic energy. Rather than discrete populations separated by boundaries, these results suggest complex spatial structure defined by environmentally mediated survival and connectivity: fish caught off New Zealand may be of South American origin; the spawning zone off central Chile may supply fisheries around the South Pacific; and spawning off northern Chile may be an important source of fish caught locally and in Peru. However, northern Peru does not supply areas further south.     

气候变化对东南太平洋智利竹筴鱼渔获量的影响

为了探讨气候变化对智利竹筴鱼(Trachurus murphyi)渔获量的长期影响, 采集 1900—2016 年北大西洋涛动

(North Atlantic Oscillation, NAO)、太平洋年代际涛动(Pacific Decadal Oscillation, PDO)、厄尔尼诺(El Ni?o)等 8 个

低频气候变化参数, 全球海气温度异常指标时间序列数据和 1970—2016 年东南太平洋智利竹筴鱼总渔获量数据,

在对其进行相关性分析的基础上, 运用 BP 神经网络模型构建了东南太平洋智利竹筴鱼渔获量预测模型, 并以效率

系数为评价规则对预测模型进行评价, 进而得到了最优预测模型。最后对最优预测模型进行了因子敏感性分析, 提

取了对东南太平洋智利竹筴鱼(Trachurus murphyi)影响较大的因子。最优预测模型拟合效果显示, 渔获量拟合值与

观测值有基本一致的变化趋势, 两个序列的线性相关系数为 0.745, 模型拟合效果良好。最优模型因子敏感性分析

表明, 在研究期间, 影响东南太平洋智利竹筴鱼渔获量的气候变化表征因子主要为北大西洋涛动、太平洋年代际涛

动和北太平洋指数。     

3.

Population structure of long tailed hake Macruronus magellanicus in the Pacific and Atlantic oceans: Implications for fisheries management     

G. Machado-Schiaffino  E. Garcia-Vazquez 《Fisheries Research》2011,111(3):164-169

Pre-spawning adult samples of long tailed hake, Macruronus magellanicus, were obtained from fisheries vessels in one location in the southeast Pacific Ocean and three in the southwest Atlantic Ocean, at different latitudes. Population structure was determined based on six nuclear hypervariable microsatellite loci and on mitochondrial DNA sequence variation at the locus COI. Paired tests of genic differentiation for microsatellite loci indicate the existence of genetic population structure for this species, where significant differences exist between some southern and northern samples. Multivariate analysis (factorial correspondence analysis) of microsatellite variation showed differentiation between the Pacific and the Atlantic populations. Analysis of the mitochondrial variation confirmed the microsatellite analysis of population structure, and revealed some additional differentiation between northern and southern Atlantic samples and exclusive haplotypes in each region. These findings suggest that the species should be managed as north–south separate stocks in the Atlantic Ocean.     

4.

Genetic connectivity of the South American fur seal (Arctocephalus australis) across Atlantic and Pacific oceans revealed by mitochondrial genes          下载免费PDF全文

Pedro Rodrigues  Mauricio Seguel  Josefina Gutiérrez  Héctor Pavés  Claudio Verdugo 《水产资源保护:海洋与淡水生态系统》2018,28(2):315-323

相似文献   

5.

西北太平洋鸢乌贼种群遗传结构   总被引：3，自引：1，他引：3  

刘连为  周永东  陆化杰  刘必林  陈新军 《水产学报》2017,41(9):1355-1364

为检测西北太平洋鸢乌贼种群遗传结构,采用线粒体DNA细胞色素b基因(Cytb)序列分析方法对鸢乌贼东海群体、南海群体与菲律宾海群体进行遗传变异分析。结果显示,(1)所有群体总的单倍型多样度与核苷酸多样度分别为0.982±0.006、0.012±0.006;菲律宾海群体对应的遗传多样度均最高,分别为0.973±0.014、0.015±0.008;南海群体与东海群体的单倍型多样度分别为0.959±0.026、0.943±0.031,核苷酸多样度均为0.006±0.003。3个地理群体均具有较高的遗传多样性水平。(2)分子方差分析结果显示,34.6%的遗传变异来自于群体间,群体间遗传分化极显著。两两群体间Fst分析表明,西北太平洋鸢乌贼群体间均具有极显著的遗传分化。构建的单倍型邻接系统树和最小跨度树显示,西北太平洋鸢乌贼群体存在明显的系统发育谱系结构(谱系A、B、C),3个谱系单倍型类群间也存在极显著的遗传分化(Fst=0.735~0.805)。(3)中性检验和核苷酸不配对分析结果均表明,谱系B可能经历过近期群体扩张事件,发生群体扩张的时间在10.3~12.5万年前。综合分析认为,西北太平洋鸢乌贼的种群遗传结构模式及系统发育地理格局模式是由其栖息地海洋环境与更新世气候变化共同塑造的。建议在渔业管理上将3个地理群体划分为3个独立的管理单元。     

6.

环境因子对东南太平洋智利竹䇲鱼渔场时空分布异质性影响     

白思琦  邹晓荣  张鹏  丁鹏 《南方水产科学》2021,17(1):17-24

基于2012—2018 年4—8 月我国东南太平洋智利竹?鱼 (Trachurus murphyi) 渔捞日志数据,应用地理权重回归模型 (GWR) 探究智利竹?鱼渔场资源分布与环境因子的空间异质性关系.结果表明,环境因子海面温度基于GWR 模型回归的拟合优度为0.54,校正的拟合优度为0.34,赤池信息准则 (Aka...     

7.

Concurrent habitat fluctuations of two economically important marine species in the Southeast Pacific Ocean off Chile in relation to ENSO perturbations     

Zhiping Feng  Wei Yu  Xinjun Chen 《Fisheries Oceanography》2022,31(1):123-134

ENSO-driven concurrent habitat fluctuations of two economically important marine species jumbo squid Dosidicus gigas and jack mackerel Trachurus murphyi in the Southeast Pacific Ocean off Chile during 1950–2017 were examined using a habitat suitability index (HSI) modeling approach. The optimal HSI models sourced from 10 weighing-based scenarios were developed, selected and validated using the crucial factors water temperature at 400 m depth (Temp_400m), sea surface height anomaly (SSHA) and sea surface salinity (SSS) for D. gigas and sea surface temperature (SST), Temp_400m, and mixed layer depth (MLD) for T. murphyi. Results suggested that the optimal HSI model could accurately predict the habitat hotspots for D. gigas and T. murphyi. The ENSO event (indicated by Niño 3.4 index, NI) was significantly related to environmental conditions off Chile. Cross-correlation revealed positive relationships between NI and SST, SSHA, SSS, and Temp_400m and negative correlation between NI and MLD. Synchronous opposite habitat fluctuations were shown between D. gigas and T. murphyi under different ENSO events. The NI was significantly negatively related to the HSI of D. gigas and positively correlated with the HSI of T. murphyi. Comparing with the El Niño years, suitable habitats of D. gigas and T. murphyi dramatically enlarged and contracted, respectively, during the La Niña years. Both suitable habitats moved southwestward under this climate conditions. Our finding suggested that ENSO-driven environmental changes played important roles in the concurrent habitat fluctuations of D. gigas and T. murphyi. Such studies are conducive to the effective utilization and management of multiple related species.     

8.

大泷六线鱼放流群体与野生群体遗传多样性比较     

郭婷  宋娜  刘淑德  涂忠  胡发文  高天翔  陈健 《水产学报》2020,44(12):1976-1986

基于线粒体DNA控制区高变区部分序列和4对微卫星标记,对大泷六线鱼放流群体及自然海域群体的遗传多样性与遗传差异进行了比较分析。线粒体DNA控制区序列分析的结果显示,413尾个体共检测到单倍型117种,其中仅Hap₃、 Hap₇和Hap₁7为共享单倍型,占总单倍型数目的 2.5%;放流、野生群体特有单倍型分别为20种和66种,分别占总单倍型数的17.09%和56.41%,放流群体特有单倍型数明显低于野生群体;放流群体和野生群体核苷酸多样性分别为0.005 1～0.006 7和0.005 8～0.007 5,单倍型多样性分别为0.856 7～0.949 9和0.883 1～0.954 9,遗传多样性均较高。微卫星标记分析结果显示,放流、野生群体平均等位基因数(Na)分别为13～44和13～27,平均多态信息含量为0.885 6和0.874 0,均具较高的遗传多态性;群体遗传结构分析结果表明,放流、野生群体间遗传分化水平较低。研究表明,山东近海大泷六线鱼放流群体与野生群体均具有较丰富的遗传多样性,且遗传结构未存在显著的群体分化...     

9.

Genetic diversity,population structure,and historical demography of a highly vagile and human-impacted seabird in the Pacific Ocean: The red-tailed tropicbird,Phaethon rubricauda     

Andrea I. Varela  Katherina Brokordt  Stefanie M.H. Ismar-Rebitz  Chris P. Gaskin  Nicholas Carlile  Terence O'Dwyer  Josh Adams  Eric A. VanderWerf  Guillermo Luna-Jorquera 《水产资源保护:海洋与淡水生态系统》2021,31(2):367-377

1. Many seabird breeding colonies have recovered from heavy anthropogenic disturbance after conservation actions. The widely distributed red-tailed tropicbird, Phaethon rubricauda, was used as a model species to assess potential anthropogenic impacts on the genetic diversity of breeding colonies in the Pacific Ocean.
2. Cytochrome c oxidase subunit I and control region sequences analyses were conducted across the range of the species in the Pacific Ocean. The study sites were at islands without human-related disturbance (non-impacted islands) and with human-related disturbance (impacted islands). We hypothesized that (i) breeding colonies of the red-tailed tropicbird on impacted islands have lower genetic diversity compared with colonies on non-impacted islands, and (ii) breeding colonies of the red-tailed tropicbird show significant fine and broad-scale genetic structure across the Pacific Ocean. Bayesian skyline analyses were conducted to infer past changes in population sizes.
3. Genetic diversity was similar between impacted and non-impacted islands. There was significant broad-scale genetic structure among colonies separated by over 6,000 km, but a lack of significant fine-scale genetic structure within Australasia and Hawai'i, although a significant level of differentiation was found within Chile with Φ_ST analyses. Skyline analyses showed that effective population sizes remained relatively constant through time, but experienced either a slight decrease or the end of an expansion event through the last 1,000 years. These changes may be related to the arrival of humans on Pacific islands.
4. Impacted islands may have received immigrants from other relatively close islands, buffering the loss of genetic diversity. However, it is also possible that colonies have retained ancestral variation or that a large effective population size coupled with a long generation time (13 years) has prevented the loss of genetic diversity in human-impacted islands. Future research using higher-resolution markers is needed to resolve the population genetic structure of the red-tailed tropicbird in an ecological time-scale.

     

10.

Australian sperm whales from different whaling stocks belong to the same population     

Joanna Day  David Power  Rosemary Gales  John Bannister  Maxine P. Piggott  Kerstin Bilgmann  Robert Harcourt  Luciano B. Beheregaray  Luciana M. Möller 《水产资源保护:海洋与淡水生态系统》2021,31(6):1452-1465

1. Understanding the factors driving population structure in marine mammals is needed to evaluate the impacts of previous exploitation, current anthropogenic threats, conservation status, and success of population recovery efforts.
2. Sperm whales are characterized by a worldwide distribution, low genetic diversity, complex patterns of social and genetic structure that differ significantly within and between ocean basins, and a long history of being commercially whaled. In Australia, sperm whales from the (International Whaling Commission assigned) southern hemisphere ‘Division 5’ stock were very heavily exploited by whaling.
3. The present study assessed the potential effects of whaling on the genetic diversity of sperm whales in Australia and the population genetic structure of these whales within a global context. A combination of historical and contemporary sperm whale samples (n = 157) were analysed across six regions, from south-eastern Australia (‘Division 6’ stock in the Pacific Ocean) to south-western Australia (‘Division 5’ stock in the Indian Ocean).
4. Sperm whales sampled from the ‘Division 5’ and ‘Division 6’ stocks belong to the same population based on nuclear and mitochondrial DNA (mtDNA) analyses. Four novel sperm whale mtDNA haplotypes were identified in animals from Australian waters. Levels of genetic diversity were low in Australian sperm whales but were similar to those previously reported for populations in the Indian and Pacific Oceans.
5. Given the genetic distinctiveness of sperm whales in Australian waters from other regions in the Pacific and Indian Oceans, and the lack of recovery in population numbers, further scientific studies are needed to increase our understanding of population dynamics and the effectiveness of threat management strategies in this species.

     

11.

Modelling South Pacific jack mackerel spatial population dynamics and fisheries          下载免费PDF全文

A.‐C. Dragon  I. Senina  N.T. Hintzen  P. Lehodey 《Fisheries Oceanography》2018,27(2):97-113

Since the 1970s, South Pacific jack mackerel (Trachurus murphyi) is one of the world's most important commercial exploited fish stock. The peak in the catch was achieved in the 1990s, after which the catch for all fleets steadily decreased due to strong fishing mortality and potentially unfavourable environmental conditions. An application of the ecosystem and fish population model SEAPODYM was developed for this species in the South Pacific Ocean to determine the extent of environmental and fisheries drivers on the stock dynamics. We combined publicly available fishing data, acoustic biomass estimates and expert knowledge to optimise fish population dynamics parameters (habitats, movements, natural and fishing mortality). Despite a large proportion of missing catch over the simulation period, the model provides realistic distributions of biomass, a good fit‐to‐data and is in agreement with the literature. The feeding habitat is predicted to be delineated by water temperature between 15°C for the first cohorts and 8.5°C for the oldest and dissolved oxygen concentration above 1.8 ml/L. Optimal spawning temperature is estimated to 15.57°C (S.E.: 0.75°C). The core habitat is predicted off Central Chile which is also the main fishing ground. There are other areas of higher fish concentration east of New Zealand, in the eastern part of the southern convergence and off Peru and northern Chile. However, there is a clear continuity between these different large sub‐populations. Fishing is predicted to have by far the highest impact, a result that should be reinforced if all fishing mortality could be included.     

12.

Genetic characteristics of Pacific cod populations in Korea based on microsatellite markers     

Mi-Jung Kim  Hye Suck An  Kwang-Ho Choi 《Fisheries Science》2010,76(4):595-603

Pacific cod (Gadus macrocephalus) is a commercially important species in Korea. However, overfishing in the 1990s caused a strong decline in catch, and in response, artificially cultured juveniles have been released annually to enhance the stocks. Cod fishing has recently increased in Korea, and the variation within the cod population necessitates the study of their genetic characteristics. In this study, we utilized two newly developed and eight previously reported microsatellite markers to examine the genetic characteristics of Pacific cod populations. We compared the genetic diversity and genetic structure of three cod populations from the Korean coasts with three populations from the North Pacific Ocean. Genetic differences were identified in the eastern sea cod population from Korea. These genetic differences included a large number of alleles per locus, a large number of unique alleles, higher frequencies of the most common alleles, and lower gene diversity compared to the other Korean populations. Additionally, the eastern sea cod population was genetically significantly differentiated from the southern and western sea populations in Korea, in which no significant genetic differentiation was detected (F _ST = 0.033 and 0.031, respectively, P < 0.005).     

13.

Genetic diversity of wild mekong giant catfish Pangasianodon gigas collected from Thailand and Cambodia     

Thawatchai Ngamsiri  Masamichi Nakajima  Srijanya Sukmanomon  Naruepon Sukumasavin  Wongphatom Kamonrat  Uthairat Na-Nakorn  Nobuhiko Taniguchi 《Fisheries Science》2007,73(4):792-799

The Mekong giant catfish Pangasianodon gigas is endemic to the Mekong River and is a critically endangered species. The genotypes of the microsatellite DNA (msDNA) and mitochondrial DNA (mtDNA) markers (right domain of the control region) were detected to evaluate the present status of genetic divergence of this species from the Mekong River in Thailand and Cambodia. The observed and expected heterozygosity values of Mekong giant catfish in Thailand and Cambodia were relatively low in comparison with those of other nonendangered freshwater fish species. These two populations from Thailand and Cambodia showed similar levels of genetic diversity, as evaluated by the 384 nucleotides of the mtDNA control region with 13 haplotypes. The pairwise F _ST value between the two populations based on the genotype frequencies of msDNA and mtDNA markers suggested a close genetic relationship between the populations in Thailand and Cambodia. The results of this study support the conclusion that the Mekong giant catfish is critically endangered. Care should be taken to sustain the genetic diversity of this species, as the level of genetic variability has already decreased in the wild population. This species is a target species for an ongoing stock enhancement program in the Mekong River in Thailand. It is proposed to apply these markers for proper broodstock management, such as for minimal kinship selective breeding in the hatchery.     

14.

Genetic population structure of the bigeye tuna Thunnus obesus in the central Pacific Ocean based on mtDNA Cytb sequences     

Zhichao Wu  Qianghua Xu  Jiangfeng Zhu  Xiaojie Dai  Liuxiong Xu 《Fisheries Science》2014,80(3):415-426

Bigeye tuna Thunnus obesus is considered an important fishery species around the world. There is no adequate genetic data available for the T. obesus population. Polymorphism of sequence variations in mitochondrial Cytb genes were assessed to explore the level of genetic variability and differentiation among eight populations of T. obesus sampled from the central Pacific Ocean. Overall, a total of 44 mtDNA haplotypes and 26 variable sites were detected in the 686 bp segment of mtDNA Cytb gene. Nucleotide diversity ranged from 0.17 to 0.27 % and the haplotype diversity ranged from 0.604 to 0.793. An analysis of molecular variance (AMOVA) test of bigeye tuna revealed that 99.38 % of the genetic variation occurred within populations. Both the maximum likelihood tree and the haplotype network indicated that two lineages of bigeye tuna coexisted in the central Pacific Ocean. Hierarchical AMOVA tests and pairwise analysis revealed no geographical isolation among haplotypes within the two lineages. High Nm values from this investigation indicated high rates of gene flow between the two sampling regions. Furthermore, tests of neutrality and mismatch distribution suggested that T. obesus might have experienced a population expansion, one that possibly occurred 110,000 years ago. Our study firstly unraveled the population genetic structure of the T. obesus in the central Pacific Ocean, and addressed the related fishery management issues including fishery stock identification, management, and conservation.     

15.

Wild stock structure of <Emphasis Type="Italic">Girella punctata</Emphasis> in Japan revealed shallow genetic differentiation but subtle substructure in subsidiary distributions     

Tetsuya Umino  Teruyuki Kajihara  Hiroshi Shiozaki  Toshiyuki Ohkawa  Dal-Sang Jeong  Kenichi Ohara 《Fisheries Science》2009,75(4):909-919

Twelve populations of Girella punctata, from widespread locations of the species’ range in Japan and Korea, were screened for sequence variability within the mitochondrial DNA (mtDNA) control region (n = 128) and at five polymorphic microsatellite loci (n = 547) to determine the genetic structure maintaining population integrity. mtDNA variability of 132 variable sites within a 334-bp region reveals shallow genetic differentiation across populations. The weak differentiation of G. punctata was partly supported by the screening of five polymorphic microsatellite loci. However, hierarchical analysis of molecular variance and principal component analysis on the basis of allele frequencies in microsatellite loci extracted a subtle substructure in a subsidiary population and in near-subsidiary populations in the semi-enclosed Seto Inland Sea.     

16.

Genetic population structure of the Pacific bluefin tuna Thunnus orientalis and the yellowfin tuna Thunnus albacares in the North Pacific Ocean     

Shohei Nomura  Toru Kobayashi  Yasuo Agawa  Daniel Margulies  Vernon Scholey  Yoshifumi Sawada  Naoki Yagishita 《Fisheries Science》2014,80(6):1193-1204

The genetic population structure of the Pacific bluefin tuna (PBF) Thunnus orientalis and the yellowfin tuna (YFT) T. albacares in the North Pacific Ocean was investigated. The polymorphism of microsatellite (SSR) loci and sequences of mitochondrial DNA control region (mtCR) were analyzed for 71 samples of PBF from Japan and Mexico and 45 samples of YFT from Japan and Panama. In the SSR analyses, both single-locus (?0.010 to 0.008 in PBF and ?0.023 to 0.020 in YFT) and global multilocus (0.003 in PBF and ?0.002 in YFT) F _ST values among the geographic populations were low and not significant in these species. In the mtCR analyses, neither the neighbor-joining tree nor the minimum spanning network showed genetic differentiation among the geographic populations in each species. The pairwise F _ST values among the geographic populations of them (?0.005 in PBF and ?0.020 to ?0.014 in YFT) were low and not significant. Our SSR and mtCR data suggested that genetic differentiations were not evident among the eastern and western populations in the North Pacific Ocean either in PBF or in YFT. Mismatch distributions, demographic parameters, and neutrality tests suggested that sudden population expansion of PBF and YFT in the North Pacific Ocean occurred 628,000–731,000 and 450,000–525,000 years ago, respectively.     

17.

基于线粒体COⅠ和Cytb基因序列的北太平洋柔鱼种群遗传结构研究   总被引：2，自引：1，他引：1  

刘连为  许强华  陈新军 《水产学报》2012,36(11):1675-1684

为准确掌握柔鱼的种群遗传结构,拟通过线粒体DNA的COI和Cytb基因序列分析方法对柔鱼不同产卵季节群体的遗传多样性和遗传结构进行研究。经PCR扩增与测序分别获得600 bp COI与481 bp Cytb基因序列。基于COI基因序列分析得到的单倍型数、单倍型多样性指数、核苷酸多样性指数及平均核苷酸差异数分别为24、(0.729 ±0.033)、(0.005 70 ± 0.003 25)和3.421。基于Cytb基因序列分析得到的单倍型数、单倍型多样性指数、核苷酸多样性指数及平均核苷酸差异数分别为28、(0.852 ± 0.016)、(0.006 45 ± 0.003 73)和3.101。分析认为, 北太平洋柔鱼2个产卵季节群体均具有较高的单倍型多样性指数和较低的核苷酸多样性指数。单倍型邻接树、两两群体间的F_st值以及AMOVA分析结果均表明, 北太平洋柔鱼2个产卵季节群体间的遗传差异不显著, 不存在显著的群体遗传结构。初步认为, 该海域因缺乏地理上的障碍, 加之北太平洋海流的作用以及柔鱼个体较强的游泳能力, 使得群体之间具有较强的基因流。     

18.

南海大眼金枪鱼和黄鳍金枪鱼的群体遗传结构   总被引：1，自引：0，他引：1  

王中铎  郭昱嵩  颜云榕  侯刚  范艳波  冯波  卢伙胜  刘楚吾 《水产学报》2012,36(2):191-201

测定了南海西沙和南沙群岛附近海区(11～12°N,15°N;110～112°E)黄鳍金枪鱼61尾(17尾成鱼、44尾幼鱼)和大眼金枪鱼26尾(22尾成鱼、4尾幼鱼)的线粒体基因组控制区部分序列(D-loop),结合GenBank数据库中印度洋、太平洋和大西洋群体的同源数据,分析结果:(1)黄鳍金枪鱼与大眼金枪鱼均具极高的单倍型多样性(Hd>99%),聚类树及群体间分化指数(FST和Snn)表明大眼金枪鱼群体分化程度明显高于黄鳍金枪鱼群体;(2)大眼金枪鱼和黄鳍金枪鱼的南海群体与印度洋群体之间基因流最强(Nm=51.638和261.280 10),其次为太平洋群体(Nm=10.868 8和-50.801 81);(3)黄鳍金枪鱼和大眼金枪鱼都基本服从群口扩张模型,而mismatch分布分别呈单、双峰,其中大眼金枪鱼的南海群体扩张较晚(Tau=7.902)且最为明显(θ1/θ0=99 999/14.752)。     

19.

Genetic diversity and population history of Tanichthys albonubes (Teleostei: Cyprinidae): Implications for conservation          下载免费PDF全文

《水产资源保护:海洋与淡水生态系统》2018,28(2):422-434

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20.

南海北部近海竹荚鱼资源密度的概率分布型特征     

晏然  范江涛  陈作志  蔡研聪  张魁  许友伟  徐姗楠 《中国水产科学》2019,26(1):91-98

竹荚鱼(Trachurusjaponicus)是中国南海北部近海主要渔获物之一,其空间分布具有非均匀性。根据2014—2017年南海北部近海两个周期(2014—2015年为第1周期, 2016—2017年为第2周期)的底拖网调查数据,以单位捕捞努力量(catchperuniteffort,CPUE)表征资源密度,采用柯尔莫可洛夫-斯米洛夫检验(Kolmogorov-Smirnov,K-S test)探索了11种概率分布特征。结果表明,南海北部陆架区竹荚鱼不具明显的概率分布特征,而北部湾海域竹荚鱼资源密度服从对数正态分布型且第二周期较第一周期更为显著。同时,采用基于对数正态理论模型法(对数正态模型与Delta模型)与调查设计法(均值法)对该海域进行资源密度估值比较,发现基于对数正态理论模型更切合竹荚鱼资源密度结构分布特征,而在对数正态理论模型中Delta模型法更适用于该物种资源密度估值。     

Population structure of long tailed hake Macruronus magellanicus in the Pacific and Atlantic oceans: Implications for fisheries management

Pre-spawning adult samples of long tailed hake, Macruronus magellanicus, were obtained from fisheries vessels in one location in the southeast Pacific Ocean and three in the southwest Atlantic Ocean, at different latitudes. Population structure was determined based on six nuclear hypervariable microsatellite loci and on mitochondrial DNA sequence variation at the locus COI. Paired tests of genic differentiation for microsatellite loci indicate the existence of genetic population structure for this species, where significant differences exist between some southern and northern samples. Multivariate analysis (factorial correspondence analysis) of microsatellite variation showed differentiation between the Pacific and the Atlantic populations. Analysis of the mitochondrial variation confirmed the microsatellite analysis of population structure, and revealed some additional differentiation between northern and southern Atlantic samples and exclusive haplotypes in each region. These findings suggest that the species should be managed as north–south separate stocks in the Atlantic Ocean.     

Genetic connectivity of the South American fur seal (Arctocephalus australis) across Atlantic and Pacific oceans revealed by mitochondrial genes

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西北太平洋鸢乌贼种群遗传结构

为检测西北太平洋鸢乌贼种群遗传结构,采用线粒体DNA细胞色素b基因(Cytb)序列分析方法对鸢乌贼东海群体、南海群体与菲律宾海群体进行遗传变异分析。结果显示,(1)所有群体总的单倍型多样度与核苷酸多样度分别为0.982±0.006、0.012±0.006;菲律宾海群体对应的遗传多样度均最高,分别为0.973±0.014、0.015±0.008;南海群体与东海群体的单倍型多样度分别为0.959±0.026、0.943±0.031,核苷酸多样度均为0.006±0.003。3个地理群体均具有较高的遗传多样性水平。(2)分子方差分析结果显示,34.6%的遗传变异来自于群体间,群体间遗传分化极显著。两两群体间Fst分析表明,西北太平洋鸢乌贼群体间均具有极显著的遗传分化。构建的单倍型邻接系统树和最小跨度树显示,西北太平洋鸢乌贼群体存在明显的系统发育谱系结构(谱系A、B、C),3个谱系单倍型类群间也存在极显著的遗传分化(Fst=0.735~0.805)。(3)中性检验和核苷酸不配对分析结果均表明,谱系B可能经历过近期群体扩张事件,发生群体扩张的时间在10.3~12.5万年前。综合分析认为,西北太平洋鸢乌贼的种群遗传结构模式及系统发育地理格局模式是由其栖息地海洋环境与更新世气候变化共同塑造的。建议在渔业管理上将3个地理群体划分为3个独立的管理单元。     

环境因子对东南太平洋智利竹䇲鱼渔场时空分布异质性影响

基于2012—2018 年4—8 月我国东南太平洋智利竹?鱼 (Trachurus murphyi) 渔捞日志数据,应用地理权重回归模型 (GWR) 探究智利竹?鱼渔场资源分布与环境因子的空间异质性关系.结果表明,环境因子海面温度基于GWR 模型回归的拟合优度为0.54,校正的拟合优度为0.34,赤池信息准则 (Aka...     

Concurrent habitat fluctuations of two economically important marine species in the Southeast Pacific Ocean off Chile in relation to ENSO perturbations

ENSO-driven concurrent habitat fluctuations of two economically important marine species jumbo squid Dosidicus gigas and jack mackerel Trachurus murphyi in the Southeast Pacific Ocean off Chile during 1950–2017 were examined using a habitat suitability index (HSI) modeling approach. The optimal HSI models sourced from 10 weighing-based scenarios were developed, selected and validated using the crucial factors water temperature at 400 m depth (Temp_400m), sea surface height anomaly (SSHA) and sea surface salinity (SSS) for D. gigas and sea surface temperature (SST), Temp_400m, and mixed layer depth (MLD) for T. murphyi. Results suggested that the optimal HSI model could accurately predict the habitat hotspots for D. gigas and T. murphyi. The ENSO event (indicated by Niño 3.4 index, NI) was significantly related to environmental conditions off Chile. Cross-correlation revealed positive relationships between NI and SST, SSHA, SSS, and Temp_400m and negative correlation between NI and MLD. Synchronous opposite habitat fluctuations were shown between D. gigas and T. murphyi under different ENSO events. The NI was significantly negatively related to the HSI of D. gigas and positively correlated with the HSI of T. murphyi. Comparing with the El Niño years, suitable habitats of D. gigas and T. murphyi dramatically enlarged and contracted, respectively, during the La Niña years. Both suitable habitats moved southwestward under this climate conditions. Our finding suggested that ENSO-driven environmental changes played important roles in the concurrent habitat fluctuations of D. gigas and T. murphyi. Such studies are conducive to the effective utilization and management of multiple related species.     

大泷六线鱼放流群体与野生群体遗传多样性比较

基于线粒体DNA控制区高变区部分序列和4对微卫星标记,对大泷六线鱼放流群体及自然海域群体的遗传多样性与遗传差异进行了比较分析。线粒体DNA控制区序列分析的结果显示,413尾个体共检测到单倍型117种,其中仅Hap₃、 Hap₇和Hap₁7为共享单倍型,占总单倍型数目的 2.5%;放流、野生群体特有单倍型分别为20种和66种,分别占总单倍型数的17.09%和56.41%,放流群体特有单倍型数明显低于野生群体;放流群体和野生群体核苷酸多样性分别为0.005 1～0.006 7和0.005 8～0.007 5,单倍型多样性分别为0.856 7～0.949 9和0.883 1～0.954 9,遗传多样性均较高。微卫星标记分析结果显示,放流、野生群体平均等位基因数(Na)分别为13～44和13～27,平均多态信息含量为0.885 6和0.874 0,均具较高的遗传多态性;群体遗传结构分析结果表明,放流、野生群体间遗传分化水平较低。研究表明,山东近海大泷六线鱼放流群体与野生群体均具有较丰富的遗传多样性,且遗传结构未存在显著的群体分化...     

Genetic diversity,population structure,and historical demography of a highly vagile and human-impacted seabird in the Pacific Ocean: The red-tailed tropicbird,Phaethon rubricauda

1. Many seabird breeding colonies have recovered from heavy anthropogenic disturbance after conservation actions. The widely distributed red-tailed tropicbird, Phaethon rubricauda, was used as a model species to assess potential anthropogenic impacts on the genetic diversity of breeding colonies in the Pacific Ocean.
2. Cytochrome c oxidase subunit I and control region sequences analyses were conducted across the range of the species in the Pacific Ocean. The study sites were at islands without human-related disturbance (non-impacted islands) and with human-related disturbance (impacted islands). We hypothesized that (i) breeding colonies of the red-tailed tropicbird on impacted islands have lower genetic diversity compared with colonies on non-impacted islands, and (ii) breeding colonies of the red-tailed tropicbird show significant fine and broad-scale genetic structure across the Pacific Ocean. Bayesian skyline analyses were conducted to infer past changes in population sizes.
3. Genetic diversity was similar between impacted and non-impacted islands. There was significant broad-scale genetic structure among colonies separated by over 6,000 km, but a lack of significant fine-scale genetic structure within Australasia and Hawai'i, although a significant level of differentiation was found within Chile with Φ_ST analyses. Skyline analyses showed that effective population sizes remained relatively constant through time, but experienced either a slight decrease or the end of an expansion event through the last 1,000 years. These changes may be related to the arrival of humans on Pacific islands.
4. Impacted islands may have received immigrants from other relatively close islands, buffering the loss of genetic diversity. However, it is also possible that colonies have retained ancestral variation or that a large effective population size coupled with a long generation time (13 years) has prevented the loss of genetic diversity in human-impacted islands. Future research using higher-resolution markers is needed to resolve the population genetic structure of the red-tailed tropicbird in an ecological time-scale.

     

Australian sperm whales from different whaling stocks belong to the same population

1. Understanding the factors driving population structure in marine mammals is needed to evaluate the impacts of previous exploitation, current anthropogenic threats, conservation status, and success of population recovery efforts.
2. Sperm whales are characterized by a worldwide distribution, low genetic diversity, complex patterns of social and genetic structure that differ significantly within and between ocean basins, and a long history of being commercially whaled. In Australia, sperm whales from the (International Whaling Commission assigned) southern hemisphere ‘Division 5’ stock were very heavily exploited by whaling.
3. The present study assessed the potential effects of whaling on the genetic diversity of sperm whales in Australia and the population genetic structure of these whales within a global context. A combination of historical and contemporary sperm whale samples (n = 157) were analysed across six regions, from south-eastern Australia (‘Division 6’ stock in the Pacific Ocean) to south-western Australia (‘Division 5’ stock in the Indian Ocean).
4. Sperm whales sampled from the ‘Division 5’ and ‘Division 6’ stocks belong to the same population based on nuclear and mitochondrial DNA (mtDNA) analyses. Four novel sperm whale mtDNA haplotypes were identified in animals from Australian waters. Levels of genetic diversity were low in Australian sperm whales but were similar to those previously reported for populations in the Indian and Pacific Oceans.
5. Given the genetic distinctiveness of sperm whales in Australian waters from other regions in the Pacific and Indian Oceans, and the lack of recovery in population numbers, further scientific studies are needed to increase our understanding of population dynamics and the effectiveness of threat management strategies in this species.

     

Modelling South Pacific jack mackerel spatial population dynamics and fisheries

Since the 1970s, South Pacific jack mackerel (Trachurus murphyi) is one of the world's most important commercial exploited fish stock. The peak in the catch was achieved in the 1990s, after which the catch for all fleets steadily decreased due to strong fishing mortality and potentially unfavourable environmental conditions. An application of the ecosystem and fish population model SEAPODYM was developed for this species in the South Pacific Ocean to determine the extent of environmental and fisheries drivers on the stock dynamics. We combined publicly available fishing data, acoustic biomass estimates and expert knowledge to optimise fish population dynamics parameters (habitats, movements, natural and fishing mortality). Despite a large proportion of missing catch over the simulation period, the model provides realistic distributions of biomass, a good fit‐to‐data and is in agreement with the literature. The feeding habitat is predicted to be delineated by water temperature between 15°C for the first cohorts and 8.5°C for the oldest and dissolved oxygen concentration above 1.8 ml/L. Optimal spawning temperature is estimated to 15.57°C (S.E.: 0.75°C). The core habitat is predicted off Central Chile which is also the main fishing ground. There are other areas of higher fish concentration east of New Zealand, in the eastern part of the southern convergence and off Peru and northern Chile. However, there is a clear continuity between these different large sub‐populations. Fishing is predicted to have by far the highest impact, a result that should be reinforced if all fishing mortality could be included.     

Genetic characteristics of Pacific cod populations in Korea based on microsatellite markers

Pacific cod (Gadus macrocephalus) is a commercially important species in Korea. However, overfishing in the 1990s caused a strong decline in catch, and in response, artificially cultured juveniles have been released annually to enhance the stocks. Cod fishing has recently increased in Korea, and the variation within the cod population necessitates the study of their genetic characteristics. In this study, we utilized two newly developed and eight previously reported microsatellite markers to examine the genetic characteristics of Pacific cod populations. We compared the genetic diversity and genetic structure of three cod populations from the Korean coasts with three populations from the North Pacific Ocean. Genetic differences were identified in the eastern sea cod population from Korea. These genetic differences included a large number of alleles per locus, a large number of unique alleles, higher frequencies of the most common alleles, and lower gene diversity compared to the other Korean populations. Additionally, the eastern sea cod population was genetically significantly differentiated from the southern and western sea populations in Korea, in which no significant genetic differentiation was detected (F _ST = 0.033 and 0.031, respectively, P < 0.005).     

Genetic diversity of wild mekong giant catfish Pangasianodon gigas collected from Thailand and Cambodia

The Mekong giant catfish Pangasianodon gigas is endemic to the Mekong River and is a critically endangered species. The genotypes of the microsatellite DNA (msDNA) and mitochondrial DNA (mtDNA) markers (right domain of the control region) were detected to evaluate the present status of genetic divergence of this species from the Mekong River in Thailand and Cambodia. The observed and expected heterozygosity values of Mekong giant catfish in Thailand and Cambodia were relatively low in comparison with those of other nonendangered freshwater fish species. These two populations from Thailand and Cambodia showed similar levels of genetic diversity, as evaluated by the 384 nucleotides of the mtDNA control region with 13 haplotypes. The pairwise F _ST value between the two populations based on the genotype frequencies of msDNA and mtDNA markers suggested a close genetic relationship between the populations in Thailand and Cambodia. The results of this study support the conclusion that the Mekong giant catfish is critically endangered. Care should be taken to sustain the genetic diversity of this species, as the level of genetic variability has already decreased in the wild population. This species is a target species for an ongoing stock enhancement program in the Mekong River in Thailand. It is proposed to apply these markers for proper broodstock management, such as for minimal kinship selective breeding in the hatchery.     

Genetic population structure of the bigeye tuna Thunnus obesus in the central Pacific Ocean based on mtDNA Cytb sequences

Bigeye tuna Thunnus obesus is considered an important fishery species around the world. There is no adequate genetic data available for the T. obesus population. Polymorphism of sequence variations in mitochondrial Cytb genes were assessed to explore the level of genetic variability and differentiation among eight populations of T. obesus sampled from the central Pacific Ocean. Overall, a total of 44 mtDNA haplotypes and 26 variable sites were detected in the 686 bp segment of mtDNA Cytb gene. Nucleotide diversity ranged from 0.17 to 0.27 % and the haplotype diversity ranged from 0.604 to 0.793. An analysis of molecular variance (AMOVA) test of bigeye tuna revealed that 99.38 % of the genetic variation occurred within populations. Both the maximum likelihood tree and the haplotype network indicated that two lineages of bigeye tuna coexisted in the central Pacific Ocean. Hierarchical AMOVA tests and pairwise analysis revealed no geographical isolation among haplotypes within the two lineages. High Nm values from this investigation indicated high rates of gene flow between the two sampling regions. Furthermore, tests of neutrality and mismatch distribution suggested that T. obesus might have experienced a population expansion, one that possibly occurred 110,000 years ago. Our study firstly unraveled the population genetic structure of the T. obesus in the central Pacific Ocean, and addressed the related fishery management issues including fishery stock identification, management, and conservation.     

Wild stock structure of <Emphasis Type="Italic">Girella punctata</Emphasis> in Japan revealed shallow genetic differentiation but subtle substructure in subsidiary distributions

Twelve populations of Girella punctata, from widespread locations of the species’ range in Japan and Korea, were screened for sequence variability within the mitochondrial DNA (mtDNA) control region (n = 128) and at five polymorphic microsatellite loci (n = 547) to determine the genetic structure maintaining population integrity. mtDNA variability of 132 variable sites within a 334-bp region reveals shallow genetic differentiation across populations. The weak differentiation of G. punctata was partly supported by the screening of five polymorphic microsatellite loci. However, hierarchical analysis of molecular variance and principal component analysis on the basis of allele frequencies in microsatellite loci extracted a subtle substructure in a subsidiary population and in near-subsidiary populations in the semi-enclosed Seto Inland Sea.     

Genetic population structure of the Pacific bluefin tuna Thunnus orientalis and the yellowfin tuna Thunnus albacares in the North Pacific Ocean

The genetic population structure of the Pacific bluefin tuna (PBF) Thunnus orientalis and the yellowfin tuna (YFT) T. albacares in the North Pacific Ocean was investigated. The polymorphism of microsatellite (SSR) loci and sequences of mitochondrial DNA control region (mtCR) were analyzed for 71 samples of PBF from Japan and Mexico and 45 samples of YFT from Japan and Panama. In the SSR analyses, both single-locus (?0.010 to 0.008 in PBF and ?0.023 to 0.020 in YFT) and global multilocus (0.003 in PBF and ?0.002 in YFT) F _ST values among the geographic populations were low and not significant in these species. In the mtCR analyses, neither the neighbor-joining tree nor the minimum spanning network showed genetic differentiation among the geographic populations in each species. The pairwise F _ST values among the geographic populations of them (?0.005 in PBF and ?0.020 to ?0.014 in YFT) were low and not significant. Our SSR and mtCR data suggested that genetic differentiations were not evident among the eastern and western populations in the North Pacific Ocean either in PBF or in YFT. Mismatch distributions, demographic parameters, and neutrality tests suggested that sudden population expansion of PBF and YFT in the North Pacific Ocean occurred 628,000–731,000 and 450,000–525,000 years ago, respectively.     

基于线粒体COⅠ和Cytb基因序列的北太平洋柔鱼种群遗传结构研究

为准确掌握柔鱼的种群遗传结构,拟通过线粒体DNA的COI和Cytb基因序列分析方法对柔鱼不同产卵季节群体的遗传多样性和遗传结构进行研究。经PCR扩增与测序分别获得600 bp COI与481 bp Cytb基因序列。基于COI基因序列分析得到的单倍型数、单倍型多样性指数、核苷酸多样性指数及平均核苷酸差异数分别为24、(0.729 ±0.033)、(0.005 70 ± 0.003 25)和3.421。基于Cytb基因序列分析得到的单倍型数、单倍型多样性指数、核苷酸多样性指数及平均核苷酸差异数分别为28、(0.852 ± 0.016)、(0.006 45 ± 0.003 73)和3.101。分析认为, 北太平洋柔鱼2个产卵季节群体均具有较高的单倍型多样性指数和较低的核苷酸多样性指数。单倍型邻接树、两两群体间的F_st值以及AMOVA分析结果均表明, 北太平洋柔鱼2个产卵季节群体间的遗传差异不显著, 不存在显著的群体遗传结构。初步认为, 该海域因缺乏地理上的障碍, 加之北太平洋海流的作用以及柔鱼个体较强的游泳能力, 使得群体之间具有较强的基因流。     

南海大眼金枪鱼和黄鳍金枪鱼的群体遗传结构

测定了南海西沙和南沙群岛附近海区(11～12°N,15°N;110～112°E)黄鳍金枪鱼61尾(17尾成鱼、44尾幼鱼)和大眼金枪鱼26尾(22尾成鱼、4尾幼鱼)的线粒体基因组控制区部分序列(D-loop),结合GenBank数据库中印度洋、太平洋和大西洋群体的同源数据,分析结果:(1)黄鳍金枪鱼与大眼金枪鱼均具极高的单倍型多样性(Hd>99%),聚类树及群体间分化指数(FST和Snn)表明大眼金枪鱼群体分化程度明显高于黄鳍金枪鱼群体;(2)大眼金枪鱼和黄鳍金枪鱼的南海群体与印度洋群体之间基因流最强(Nm=51.638和261.280 10),其次为太平洋群体(Nm=10.868 8和-50.801 81);(3)黄鳍金枪鱼和大眼金枪鱼都基本服从群口扩张模型,而mismatch分布分别呈单、双峰,其中大眼金枪鱼的南海群体扩张较晚(Tau=7.902)且最为明显(θ1/θ0=99 999/14.752)。     

Genetic diversity and population history of Tanichthys albonubes (Teleostei: Cyprinidae): Implications for conservation

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南海北部近海竹荚鱼资源密度的概率分布型特征

竹荚鱼(Trachurusjaponicus)是中国南海北部近海主要渔获物之一,其空间分布具有非均匀性。根据2014—2017年南海北部近海两个周期(2014—2015年为第1周期, 2016—2017年为第2周期)的底拖网调查数据,以单位捕捞努力量(catchperuniteffort,CPUE)表征资源密度,采用柯尔莫可洛夫-斯米洛夫检验(Kolmogorov-Smirnov,K-S test)探索了11种概率分布特征。结果表明,南海北部陆架区竹荚鱼不具明显的概率分布特征,而北部湾海域竹荚鱼资源密度服从对数正态分布型且第二周期较第一周期更为显著。同时,采用基于对数正态理论模型法(对数正态模型与Delta模型)与调查设计法(均值法)对该海域进行资源密度估值比较,发现基于对数正态理论模型更切合竹荚鱼资源密度结构分布特征,而在对数正态理论模型中Delta模型法更适用于该物种资源密度估值。