Multiple scales of genetic connectivity in a brooding coral on isolated reefs following catastrophic bleaching, Western Australia

Data on the variation of microsatellite markers and changes in coral cover at 6 sites at Scott Reef were used to identify:1. At which sites were Seriatopora hystrix worst affected by bleaching.2. The scale of genetic subdivision of S. hystrix at Scott Reef 5 years after the bleaching event, and to what extent had the majority of larvae dispersed (metres or tens of kilometres).3. Whether new recruits at the most severely bleached sites were produced locally (from a few remaining colonies), from other sites on the same reef, or from other reefs within the Scott Reef system.All sites consisted of 5 permanent 50 m transects on the reef slope at about 9 m depth. Transects were filmed 6 months before (October 1997), 6 months after (October 1998), and approximately 5 years after (November 2003) a bleaching event which occurred in February 1998. Percentage cover (estimated using a point intercept method) was calculated from the mean percent cover over the 5 transects at each site for each year.In January 2004, 287 samples from individual colonies of S. hystrix were collected from 6 sites within the Scott system: south Scott (SL1, SL2 and SS1), north Scott (SL4), Sandy Islet Reef (SL5), and Seringapatam Reef (SS3). At each site, the exact location of each sampled colony along a permanent 300 m transect was recorded, along with the global positioning system coordinates at the beginning of each transect. Between 45 and 50 colonies were sampled at regular intervals along each transect.Genotyping of the 287 individuals was carried out. Because only two pairs of individuals shared the same diploid multilocus genotype, one individual from each of these pairs was removed from subsequent analyses so that each unique genotype was represented only once.Characteristics of the 9 Seriatopora hystrix microsatellite markers recorded were: the number of unique multilocus genotypes (N), the number of alleles (A), the proportion of observed (HO) and expected (HE) heterozygotes per locus and site, and the FIS calculated for each locus and each site (FIS All). Loci: Sh2-002, Sh2-006, Sh4-001, Sh4-010, Sh3-003, Sh3-004, Sh3-007, Sh3-008, Sh3-009, Sh4-001, Sh4-010. Allelic frequencies, allelic patterns and expected heterozygosities under Hardy-Weinberg equilibrium, and the number of private alleles were calculated in Genalex v6.Tests for Hardy-Weinberg and linkage disequilibrium were conducted using FSTATv2.9.3a spatial autocorrelation analysis, applied within each site.
To explore the fine-scale processes influencing the local genetic structure and assess present day migration patterns over larger scales for S. hystrix at the Scott Reef system using high resolution genetic markers in combination with a detailed sampling design.To explore the influence of larval dispersal and adult abundances on rates of recruitment and recovery of this species following a catastrophic disturbance (bleaching) in an isolated system.

本数据集采用斯科特礁（Scott Reef）6个站位的微卫星标记（microsatellite markers）变异数据与珊瑚盖度变化数据，旨在明确三项核心科学问题：1. 哪些站位的杯形珊瑚（Seriatopora hystrix）受白化影响最为严重；2. 1998年白化事件发生5年后，斯科特礁杯形珊瑚的遗传分化程度，以及多数幼体的扩散规模（以米或数十公里计）；3. 受白化影响最严重站位的新补充个体，究竟是源自当地残存的少量群体、同一礁体的其他站位，还是斯科特礁系统内的其他礁体。
所有站位均设置于礁坡约9米水深区域，每条站位包含5条固定50米的样带（transect）。分别在1998年2月爆发的珊瑚白化事件发生前6个月（1997年10月）、后6个月（1998年10月）以及约5年后（2003年11月）对样带进行拍摄记录。采用样点拦截法（point intercept method）估算珊瑚盖度，以每个站位5条样带的平均盖度百分比作为各年度的盖度统计值。
2004年1月，研究团队从斯科特礁系统的6个站位共采集287个杯形珊瑚群体样本，涉及站位包括南斯科特礁（SL1、SL2与SS1）、北斯科特礁（SL4）、沙岛礁（Sandy Islet Reef，SL5）以及塞林加帕坦礁（Seringapatam Reef，SS3）。在每个站位中，记录每个采样群体沿固定300米样带的精确位置，并同步记录每条样带起点的全球定位系统（Global Positioning System, GPS）坐标。每条样带按固定间隔采样45至50个珊瑚群体。
研究团队对287个个体进行了基因分型。由于仅有两对个体拥有完全一致的二倍体多位点基因型（multilocus genotype），故从每对中移除1个个体，确保每个独特基因型仅在后续分析中保留一次。
本次研究涉及的9个杯形珊瑚微卫星标记特征参数包括：独特多位点基因型数量（N）、等位基因数（A）、每个位点与站位的观测杂合度（HO）与期望杂合度（HE），以及针对每个位点和站位计算的群体内近交系数FIS（FIS All）。所用扩增位点为：Sh2-002、Sh2-006、Sh4-001、Sh4-010、Sh3-003、Sh3-004、Sh3-007、Sh3-008、Sh3-009、Sh4-001、Sh4-010（原文存在位点重复，保留原始标注）。使用GenAlEx v6软件计算等位基因频率、等位基因模式、哈迪-温伯格平衡（Hardy-Weinberg equilibrium）下的期望杂合度，以及私有等位基因（private alleles）数量；使用FSTAT v2.9.3a软件开展哈迪-温伯格平衡与连锁不平衡（linkage disequilibrium）检验，并在每个站位内进行空间自相关（spatial autocorrelation）分析。
本研究的核心目标有二：其一，结合高分辨率遗传标记与精细化采样设计，探究影响斯科特礁系统杯形珊瑚局地遗传结构的精细尺度过程，并评估该物种当前在更大尺度上的迁移模式；其二，探索在孤立礁体系统中，幼体扩散与成体丰度对灾难性扰动（珊瑚白化）后该物种的种群补充与恢复速率的影响。