Length-based assessment of Nemipterus bathybius in northern South China Sea
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摘要:
深水金线鱼 (Nemipterus bathybius) 是南海北部重要的底层经济鱼类，但近年来其资源呈现过度开发的态势。利用2014—2019年在南海北部底拖网调查中采集的3 059尾深水金线鱼生物学数据，使用基于长度的贝叶斯生物量评估 (Length-based Bayesian biomass estimation method, LBB) 和基于长度的繁殖潜力比(Length-based spawning potential ratio, LBSPR) 2种数据缺乏条件下的资源评估模型，对其资源状况进行了评估，为其种群科学管理和可持续利用提供技术支撑。结果表明，2014—2019年南海北部深水金线鱼的渐近体长 (Linf)、相对自然死亡率 (M/K) 和50%性成熟体长 (L50) 分别为23.7 cm、2.33和11.76 cm。LBB模型评估结果显示，其种群资源量水平 (B/BMSY)、50%渔获长度与最适可捕长度的比值 (Lc/Lc_opt) 分别为0.89、0.85，表明深水金线鱼处于轻度过度开发状态和生长型过度捕捞状态。LBSPR模型评估结果显示繁殖潜力比 (SPR) 为0.19，说明深水金线鱼正处于过度捕捞状态。通过先验参数的不确定性分析，发现LBB和LBSPR对参数Linf的设置极为敏感，对参数M/K的设置比较敏感，因此在使用LBB和LBSPR模型进行评估时应谨慎设置以上2种参数。
Abstract:Yellowbelly threadfin bream (Nemipterus bathybius), an economically important demersal fish species in the northern South China Sea, has been overexploited in recent years. To provide technical support for the scientific management and sustainable utilization of N. bathybius stocks, based on the biological data of 3 059 individuals of N. bathybius collected during bottom trawl surveys in the northern South China Sea from 2014 to 2019, we assessed the stock status by using two assessment models [Length-based Bayesian biomass (LBB) and length-based spawning potential ratio (LBSPR)] under data-poor conditions. Results show that the asymptotic fork length (Linf), relative natural mortality (M/K), and 50% sexually mature body length (L50) of N. bathybius in the northern South China Sea from 2014 to 2019 were 23.7 cm, 2.33 and 11.76 cm, respectively. The LBB assessment results show that the relative biomass level (B/BMSY) and ratio of length of 50% of the individuals captured by the gear to optimal length-at-first-capture (Lc/Lc_opt) were 0.89 and 0.85, respectively, indicating that N. bathybius was experiencing moderate overfishing and growth overfishing. The LBSPR results show a spawning potential ratio (SPR) of 0.19, indicating that N. bathybius was experiencing overfishing. Uncertainty analysis of the priori parameters reveals that LBB and LBSPR results were extremely sensitive to the setting of Linf and sensitive to the setting of M/K. Therefore, the above two parameters should be set with caution when using LBB and LBSPR.
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Keywords:
- Nemipterus bathybius /
- Stock assessment /
- Data-poor /
- Uncertainty /
- Biomass /
- Spawning potential ratio
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鲮(Cirrhinus molitorella)，属鲤科(Cyprinidae)、野鲮亚科(Labeoninae)，是两广地区的四大家鱼(鳙、草、鲢、鲮)之一，在广东省的淡水养殖业中占有重要的地位。四大家鱼繁殖成功以来，普遍存在的近亲繁殖使得亲鱼性成熟提前、个体越变越小、鱼苗病害增多、生长减慢等问题出现[1]，养殖群体遗传多样性下降。因此，收集保存野生原种，了解其遗传多样性状况并从中筛选出具有优良性状的个体或群体进行苗种生产对于水产养殖业的持续稳定发展具有重要意义。
AFLP技术首先由荷兰科学家ZABEAU和VOS提出[2-3]，此项技术兼具了RAPD和RFLP的优点，既有前者的简便灵敏和高效性也有后者的可靠性，是迄今为止最有效的分子标记之一。广东鲮鱼原种场2000和2003年先后2次从西江流域肇庆段采捞野生鲮鱼苗，作为鲮原种保存。饲养过程中发现该批鲮原种存在体色及生长速率差异。为了比较该批原种2个不同体色的子群体间的遗传差异，我们采用AFLP方法对其进行了研究。
1. 材料
1.1 实验用鱼
2005年7月，从广东鲮鱼原种场取保种样品，对体色不同的2个子群体(体色青，q; 体色淡黄，h)各取29尾，共58尾，分别编号为q1~29、h1~29。剪尾鳍保存于95%的乙醇中，4 h后更换1次95%的乙醇，保存用于总DNA抽提。
1.2 AFLP分析中使用的接头及引物序列
参照VOS等[3]方法并稍作修改进行AFLP分析，研究中使用的接头及引物序列见表 1。
表 1 AFLP分析的寡核苷酸接头和引物序列Table 1. The oligo nucleotide adaptors and primers used for the AFLP analysis接头或引物
adaptor or Primer序列(5′→3′)
sequence(5′→3′)adaptor EcoRI-1 CTC GTA GAC TGC GTA CC EcoRI-2 AAT TGG TAC GCA GTC TAC MseI-1 GAC GAT GAG TCC TGA G MseI-2 TAC TCA GGA CTC AT primers of pre-amplication EcoRI+1 GTA GAC TGC GTA CCA ATT CA MseI+1 GAC GAT GAG TCC TGA GTA AC primers of selective amplification E-NNN GAC TGC GTA CCA ATT C NNN NNN AAG，AGC，AGT，ATC，ACG M-NN(N) GAT GAG TCC TGA GTA A NN(N) NN(N) CAA，ACG，CTC，CAG，CGT 注: ‘E-NNN’和‘M-NN(N)’各自代表一条引物序列，其中的一个‘N’代表一个选择性碱基。‘NNN’为引物‘E-NNN’的选择性碱基，而‘NN(N)’为引物‘M-NN(N)’的选择性碱基
Note: ‘E-NNN’ and ‘M-NN(N)’ represented a primer sequence respectively，and an ‘N’ represented one selective nucleotide in the primer.‘NNN’was the selective nucleotides for the primer‘E-NNN’，whereas‘NN(N)’for the primer‘M-NN(N)’.2. 方法
2.1 鲮总DNA的提取及定量
采用本实验室改进的Tris-饱和酚法进行鲮总DNA抽提[4]。在德国Biometra核酸定量仪上测定基因组DNA的吸光值，测定核酸浓度。选取光密度OD260/OD280比值在1.8~2.0之间的基因组DNA，将其浓度稀释至50 ng · μL-1，-20℃保存备用。
2.2 总DNA的消化、连接、扩增
实验方法及操作过程参照夏军红[5]博士论文并稍做修改进行。所做修改如下，在DNA样品限制性消化中，DNA用量为250 ng，+1/+1 PCR预扩增中，+1引物用量为100 ng，+3/+3 PCR选择性扩增中，+3引物用量为150 ng。
2.3 PAGE电泳
+3/+3循环结束后，1.5% Agrose胶检测扩增结果。等体积2×上样缓冲液终止反应，点样，6%变性聚丙烯酰胺凝胶电泳分离，银染法显色(Premega银染试剂盒操作说明书)，数码相机拍照记录。
2.4 数据分析
银染之后得到的谱带应用软件Labimage(Ver 2.6，by Kapelan)分析，相对于分子量标记100 bp DNA ladder确定等位基因大小。数据统计所有清晰可见的条带，有带记为1，无带记为0，获得0~1矩阵。利用Popgene(Ver.3.1)进行数据分析[6]。
3. 结果与分析
3.1 AFLP引物筛选及扩增图谱
从25对AFLP引物组合(表 1)中选取6对扩增条带丰富、带型清晰、有差异性条带的AFLP引物用于进一步分析。引物组合为E1M3、E1M4、E2M4、E4M3、E5M1、E5M2。以上6对AFLP引物对子群体h和子群体q共58个个体进行PCR扩增，共产生173条扩增条带，分子量范围在50~400 bp之间，平均每对引物产生29条扩增条带，其中多态性条带数为72条，多态位点比例为41.5%。子群体q、h的多态位点数分别为61和70，多态性片段的比例分别为35.11%、40.43%。在6对引物产生的173条扩增条带中，有1条编号为E2M4-1的条带在子群体h中的频率远远高于在子群体q中的出现频率，该条带在2个子群体间的出现频率差别很大，子群体h中的出现频率为72.4%，而子群体q中的出现频率仅为20.6%。图 1为引物E2M4扩增的AFLP图谱，从图谱中可以看出鲮个体间的差异。标注位点为子群体h的高频位点。
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图 1 引物组合E2M4对原种群体的扩增图谱q1~29. 子群体q; h1~29. 子群体h; M. 100 bp分子量标准Figure 1. AFLP-PCR pattern of primer pair E2M4 on original populationq1~29. sub-stock q; h1~29. sub-stock h; M. 100 bp DNA ladder3.2 鲮原种群体的遗传多样性分析
对所取鲮原种群体进行遗传多样性分析结果，鲮原种群体的遗传多样性指数为0.1254，其子群体h与子群体q的遗传多样性指数分别为0.1367和0.0998，子群体h的遗传多样性指数远高于子群体q。
4. 讨论
本研究采用AFLP方法对广东鲮鱼原种场的鲮原种群体进行了遗传多样性分析。对鲮原种群体2个子群体遗传多样性分析表明，子群体h的遗传多样性水平高于子群体q(0.1367>0.0998)，2个子群体间的遗传分化较为明显。这一结果与笔者此前采用RAPD方法研究的结果[4]一致。广东鲮鱼原种场在对该批鲮原种的饲养观察中已发现，子群体h的生长性能优于子群体q，因而获得子群体h相对于子群体q的特异性分子标记对于培育具有生长优势的鲮优良品系具有重要意义。AFLP标记能够提供大量且高密度的信息位点，因此，有可能在表型不同的2个鲮原种子群体间筛选出具有群体特异性的分子标记。夏军红等[5]采用AFLP方法从36对引物组合中筛选到一对长江江豚性连锁分子标记的引物组合，找到一个与性别相关的标记性位点。本研究从25对引物组合中选取了6对扩增中显示出有差异条带的引物组合对该批鲮原种的2个子群体进行扩增，获得了1条在子群体h中的出现频率绝对高于子群体q的条带E2M4-1(72.4%>20.6%)。体色是由多基因控制的性状，条带E2M4-1有可能与控制体色的某基因位点呈不完全连锁。进一步扩大筛选范围，采用更多引物组合做进一步研究有希望获得2个子群体间的特异性分子标记。
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图 1 南海北部近海研究区域及站点分布
Figure 1. Study area and station distribution in offshore northern South China Sea
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图 2 南海北部雄性、雌性、整体深水金线鱼体长-体质量关系
Figure 2. Length-body mass relationship among male, female and all N. bathybius in northern South China Sea
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图 3 南海北部深水金线鱼性成熟比例与体长拟合的逻辑斯蒂曲线
Figure 3. Logistic model fitted for relationship between body length and percentage of mature N. bathybius in northern South China Sea
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图 4 南海北部深水金线鱼基于LBB方法的分析结果
注：左图为模型对体长数据的拟合曲线，右图为LBB方法的预测；Lc是50%个体被渔具捕获的体长；Lopt为未开发种群获得最大生物量的捕捞体长。
Figure 4. Estimated values for N. bathybius in northern South China Sea by length-based Bayesian biomass assessment model
Note: The left figure shows the fits of the model to length data, and the right figure shows the predictions of the LBB analysis; Lc. Length of 50% of the individuals captured by the gear; Lopt. Fishing body length for obtaining maximum biomass in undeveloped populations.
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图 5 南海北部深水金线鱼基于LBSPR方法的分析结果
注：a. 长度-频率分布(柱状图)，预测的种群大小组成(折线图)；b. LBSPR模型拟合的性成熟和选择性曲线，其中L50=11.76 cm和L95=12.94 cm时；c. 选择性参数($S_{L_{50}}$和 $S_{L_{95}} $)、捕捞死亡率与自然死亡率的比值(F/M)和繁殖潜力比的估计值；d. 在目标SPR=0.4时，观测到的长度-频率数据与预期的大小组成。
Figure 5. Length-based spawning potential ratio for N. bathybius in northern South China Sea
Note: a. Length-frequency distribution (Pillars), and predicted fished size composition (Line chart); b. Maturity and selectivity curves from the fitted LBSPR model when L50 was 11.76 cm and L95 was 12.94 cm; c. Distribution of mean selectivity parameters ($S_{L_{50}} $ and $S_{L_{95}} $), fishing mortality to natural mortality (F/M), and spawning potential ratio; d. Observed length-frequency data against an expected size composition at a target SPR of 0.4.
表 1 南海北部深水金线鱼的样品信息
Table 1 Sample information of N. bathybius in northern South China Sea
年份
Year月份
Month样本数
Sampling
number体长 Body length/mm 范围
Range均值±标准差
Mean±Standard
deviation2014 7 293 93~193 121.2±16.3 10 225 77~184 119.9±21.6 2015 1 120 73~172 121.8±18.7 4 330 75~189 111.4±19.2 2016 7 304 84~200 121.8±19.4 10 78 74~178 122.1±23.8 2017 1 71 72~176 109.3±18.7 4 197 72~158 115.0±15.3 2018 3 220 75~176 113.8±19.0 8 87 78~182 126.0±24.2 2019 3 524 73~176 106.6±16.8 9 610 65~192 117.3±19.0 
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表 2 LBB和LBSPR方法所需数据目录
Table 2 Data for LBB and LBSPR methods
参数
Parameter估算值
Estimated value基于长度的繁殖潜力比模型
Length-based spawning potential ratio
(LBSPR) assessment model基于长度的贝叶斯估计模型
Length-based Bayesian biomass
(LBB) assessment model长度-频率数据
Length–frequency data/ √ √ 渐近体长 (Linf)
Asymptotic length/cm23.7 cm √ 〇 生长系数 (K)
Growth coefficient0.326 〇 自然死亡率 (M)
Natural mortality0.762 〇 相对自然死亡率M/K 2.33 √ 〇 50%性成熟体长 (L50)
Body length at 50% sexual maturity/cm11.76 √ 〇 95%性成熟体长 (L95)
Body length at 95% sexual maturity/cm12.94 √ 渐近体长的变异系数
Coefficient of variation of Linf0.1 √ 长度-体质量关系参数 (a)
Length-body mass relationship parameter6.854 0×10−5 〇 长度-体质量关系参数 (b)
Length-body mass relationship parameter2.797 4 〇 注：“√” 代表必需数据；“〇”代表可选数据。 Note: "√" represents required data; "〇" represents optional data.
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表 3 LBB和LBSPR在不同先验参数下的评估结果
Table 3 Estimated results of LBB and LBSPR parameters with different priors
组号
Group No.先验参数
Prior parameterLBSPR结果
Results of LBSPRLBB结果
Results of LBBLinf/mm L50/mm M/K F/M SPR B/BMSY F/M Lc/Lc_opt 1 237 117.6 2.33 1.71 0.19 0.89 1.00 0.85 2 232 1.73 0.20 0.99 0.90 0.87 3 234 1.76 0.20 0.94 0.97 0.86 4 236 1.71 0.19 0.90 1.00 0.85 5 238 1.84 0.18 0.87 1.10 0.84 6 240 1.73 0.19 0.84 1.10 0.83 7 242 1.94 0.17 0.81 1.10 0.82 8 237 112.6 2.33 1.71 0.21 0.89 1.00 0.85 9 114.6 1.71 0.21 0.89 1.00 0.85 10 116.6 1.71 0.20 0.89 1.00 0.85 11 118.6 1.71 0.19 0.89 1.00 0.85 12 120.6 1.71 0.18 0.89 1.00 0.85 13 122.6 1.71 0.17 0.89 1.00 0.85 14 237 117.6 2.28 1.77 0.19 0.84 1.10 0.83 15 2.30 1.75 0.19 0.87 1.00 0.84 16 2.32 1.73 0.19 0.87 1.00 0.84 17 2.34 1.70 0.20 0.89 1.00 0.84 18 2.36 1.68 0.20 0.92 1.00 0.86 19 2.38 1.66 0.20 0.92 0.99 0.86
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表 4 不同时期深水金线鱼种群参数
Table 4 Population parameters of N. bathybius in different periods
参数
Parameter年份 Year 1992 1997 2009 2017 渐近体长 Asymptotic length (Linf)/mm 242 220 235 237 生长系数Growth coefficient (K) 0.39 0.45 0.48 0.326 50%性成熟体长Body length at 50% sexual maturity (L50)/mm 128.6 116.5 110.5 117.6
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