Gene flow of Holothuria scabra populations along the north-east coast of Australia, Torres Strait and the Solomon Islands

17 to 141 individuals were collected from 8 populations of the fished holothurian species Holothuria scabra (Echinodermata: Holothuroidea), from north-east Australia, the Torres Strait, and the Solomon Islands and investigated by allozyme electrophoresis of 7 polymorphic loci.Two shallow populations of Holothuria scabra were sampled in the area of Hervey Bay (Urangan, Tin Can Bay) in south Queensland during June 1998. Individuals from a deeper population in Hervey Bay (18-20 m) were obtained during 3 trawl shots using commercial prawn-trawling equipment.One intertidal population was sampled ca. 800 km north Upstart Bay in 1998. Data from these samples were used in a previous study investigating the relationship between 2 colour morphs and the gene flow between deep and shallow populations. This population was re-sampled in May 2000 to investigate whether gene frequencies and the small size of individuals (as found in 1998) were stable over time.During August 1999, samples were obtained from 2 reefs in the Torres Strait at the northern end of the GBR (Warrior Reef, Dungeness Reef). Two locations in the Solomon Islands, Kohinggo Island (Solomon Island A) and Kolombangarra Island (Solomon Island B), were sampled in December 1999.Samples from intertidal populations were taken during low tides by walking on the mud flats. During these periods, holothurians in shallow tide pools, usually with at least a sparse seagrass cover, migrate to the surface of the sediment. Since large areas had to be covered to obtain sufficient individuals, no effort was made to obtain subsamples within each of the populations. The length of all individuals was recorded to the nearest centimetre. A subsample of the gut lining (cleaned from sediments) was snap frozen in liquid nitrogen for later analyses.Seven polymorphic enzyme loci were surveyed using allozyme electrophoresis: PGM, HK, GPI, MDH, PEP-1, PEP-2 and PEP-3. Full details of staining and electrophoresis methods are given in:Ballment E, Uthicke S, Peplow L, Benzie JAH (1997) Techniques for enzyme electrophoretic analysis of the holothurians Holothuria atra and Stichopus chloronotus (Holothuroidea: Aspidochirotida). Aust Inst Mar Sci (AIMS) Tech Rep Ser 27:1-47Basic analyses of genetic variability were carried out using programs in the BIOSYS-1. F-statistics, cluster analyses and tests of conformation to Hardy-Weinberg expectations were performed using the TFPGA package. The contribution of asexual reproduction to each population was calculated as described in detail in:Uthicke S, Benzie JAH, Ballment E (1998) Genetic structure of fissiparous populations of Holothuria (Halodeima) atra on the Great Barrier Reef. Mar Biol 132:141-151. Deviations from Hardy-Weinberg equilibrium for each locus at each reef were tested by an exact-test, using the conventional Monte Carlo method with the default settings in TFPGA. To test for evidence of isolation by distance, Mantel¿s tests were performed on transformed (log + 1) geographic distance (km) and Rogers' genetic distances. The significance of Mantel's normalised Z was tested by 10000 random permutations using NTSYS-PC software. The aim of the study was to investigate gene flow between populations separated by different geographic scales (~20-2000 km), along the north-east coast of Australia, Torres Strait and the Solomon Islands, to provide information on connectivity to assist management and add to fundamental knowledge on the biology of this ecologically and economically important species.

本研究从澳大利亚东北部、托雷斯海峡以及所罗门群岛的8个捕捞用海参物种糙海参（Holothuria scabra，棘皮动物门（Echinodermata）：海参纲（Holothuroidea））种群中采集了17至141号个体，通过7个多态位点（polymorphic loci）的等位酶电泳（allozyme electrophoresis）开展分析。
1998年6月，研究团队在昆士兰州南部赫维湾（Urangan、Tin Can Bay区域）采集了2个糙海参浅海种群样本；同时借助商用虾拖网设备开展3次拖网作业，获取了赫维湾内18~20米水深的深海种群个体。同年，在阿普斯特特湾以北约800公里处的一个潮间带种群（intertidal population）进行了采样，该样本数据曾用于此前一项探究2种颜色形态与深浅海种群间基因流关系的研究。为验证基因频率以及1998年观测到的个体小型化特征是否随时间保持稳定，研究团队于2000年5月对该种群进行了重新采样。
1999年8月，在大堡礁（Great Barrier Reef）北端的托雷斯海峡的2个礁体（沃里克礁、邓杰内斯礁）采集了样本；同年12月，在所罗门群岛的2个点位——Kohinggo岛（所罗门群岛A）与Kolombangarra岛（所罗门群岛B）开展了采样工作。
潮间带种群样本于低潮期在泥滩上采集：此时浅潮池（通常覆盖有稀疏海草）内的海参会迁移至沉积物表面。由于需要覆盖大片区域以获取足够数量的个体，研究未在每个种群内部设置子样本采集环节。所有个体的体长均记录至最近1厘米，同时取肠道内衬的子样本（已清除沉积物）置于液氮中快速冷冻，以供后续分析使用。
本研究通过等位酶电泳检测了7个多态酶位点：PGM、HK、GPI、MDH、PEP-1、PEP-2与PEP-3。染色与电泳方法的详细细节参见：Ballment E、Uthicke S、Peplow L、Benzie JAH（1997）《海参类酶电泳分析技术：Holothuria atra与Stichopus chloronotus（海参纲：楯手目（Aspidochirotida））》，澳大利亚海洋科学研究所（Australian Institute of Marine Science, AIMS）技术报告系列27：1-47。
遗传变异的基础分析借助BIOSYS-1软件中的程序完成；F统计量、聚类分析以及哈迪-温伯格平衡（Hardy-Weinberg equilibrium）契合度检验均通过TFPGA工具包执行。种群内无性繁殖（asexual reproduction）的贡献比例计算方法详见：Uthicke S、Benzie JAH、Ballment E（1998）《大堡礁上裂体繁殖的糙海参（Holothuria (Halodeima) atra）种群遗传结构》，《海洋生物学（Marine Biology）》132：141-151。
针对每个礁体的每个位点，研究采用TFPGA工具包中默认设置的常规蒙特卡洛方法（Monte Carlo method）精确检验，检测其是否偏离哈迪-温伯格平衡。为检验距离隔离（isolation by distance）效应，研究对经过（log+1）转换的地理距离（单位：公里）与罗杰斯遗传距离（Rogers' genetic distances）进行了曼特尔检验（Mantel’s tests）；利用NTSYS-PC软件通过10000次随机置换（random permutations）检验曼特尔标准化Z值的显著性。
本研究的目的为：探究澳大利亚东北海岸、托雷斯海峡与所罗门群岛范围内、地理尺度介于约20~2000公里的种群间的基因流，以期为种群连通性相关的管理工作提供参考，并丰富这一兼具生态与经济重要性物种的基础生物学认知。