We report a massive region-wide decline of corals across the entire Caribbean basin, with the average hard coral cover on reefs being reduced by 80%, from about 50% to 10% cover, in three decades. Our meta-analysis shows that patterns of change in coral cover are variable across time periods but largely consistent across subregions, suggesting that local causes have operated with some degree of synchrony on a region-wide scale. Although the rate of coral loss has slowed in the past decade compared to the 1980s, significant declines are persisting. The ability of Caribbean coral reefs to cope with future local and global environmental change may be irretrievably compromised.

2008年5–6月在徐闻西岸设置了25个站点, 运用截线样带法调查了造礁石珊瑚的种类多样性和空间分布。本次研究共发现造礁石珊瑚57种, 每个站位的种类数均不超过30种。Shannon-Wiener多样性指数和Pielou均匀度指数均值分别为1.79和0.42。二异角孔珊瑚(Goniopora duofasciata)、盾形陀螺珊瑚(Turbinaria peltata)和锯齿刺星珊瑚(Cyphastrea serailia)是优势种, 其中二异角孔珊瑚为绝对优势种。造礁石珊瑚覆盖率在0–38%之间, 大部分站位介于10–20%, 平均为12.1%。调查区珊瑚礁分布不规则, 呈斑块状分布。

Marine fishes exhibit spectacular phenotypic changes during their ontogeny, and the identification of their early stages is challenging due to the paucity of diagnostic morphological characters at the species level. Meanwhile, the importance of early life stages in dispersal and connectivity has recently experienced an increasing interest in conservation programmes for coral reef fishes. This study aims at assessing the effectiveness of DNA barcoding for the automated identification of coral reef fish larvae through large-scale ecosystemic sampling. Fish larvae were mainly collected using bongo nets and light traps around Moorea between September 2008 and August 2010 in 10 sites distributed in open waters. Fish larvae ranged from 2 to 100 mm of total length, with the most abundant individuals being <5 mm. Among the 505 individuals DNA barcoded, 373 larvae (i.e. 75%) were identified to the species level. A total of 106 species were detected, among which 11 corresponded to pelagic and bathypelagic species, while 95 corresponded to species observed at the adult stage on neighbouring reefs. This study highlights the benefits and pitfalls of using standardized molecular systems for species identification and illustrates the new possibilities enabled by DNA barcoding for future work on coral reef fish larval ecology.© 2014 John Wiley & Sons Ltd.

Barcoding has proven a useful tool in the rapid identification of all life stages of fish species. Such information is of critical importance for fisheries management and conservation, especially in high-diversity regions, such as Mexico’s marine waters, where more than 2200 species occur. The present study reports the barcode analysis of 1392 specimens from the Yucatan Peninsula, corresponding to 610 adults and juveniles, 757 larvae and 25 eggs, representing 181 species (179 teleosts and 2 rays), 136 genera and 74 families. Barcoding results revealed major range extensions and overlooked taxa, including three sympatric species of Albula (one likely undescribed) and a new taxon of Floridichthys. In total, six species of eggs and 34 species of larvae were identified through their barcode match with adults. These cases enabled the first discrimination of the larvae of four species of Eucinostomus, and new information about spawning locality and time was obtained from egg records for the hogfish, Lachnolaimus maximus, which is one of the most commercially important species in the Mexican Caribbean. Also, barcodes revealed mistakes in species recognition during a sport-fish contest. In the future, barcodes will help avoid similar errors and protect rare or endangered species, and will aid regulation of fisheries quotas.

Quantifying and classifying ichthyoplankton is one of the most effective ways of monitoring the recruitment process in fishes. However, correctly identifying the fish based on morphological characters is extremely difficult, especially in the early stages of development. We examined ichthyoplankton from tributaries and reservoirs along the middle stretch of the Paranapanema River, one of the areas most impacted by hydroelectric projects in the Neotropics. Matching DNA sequences of the COI gene (628-648 bp) allowed us to identify 99.25% of 536 samples of eggs (293) and larvae (243) subjected to BOLD-IDS similarity analysis with a species-level threshold of 1.3%. The results revealed 37 species in 27 genera, 15 families and four orders, some 23.8% of documented fish species in the Paranapanema River. Molecular identification meant that we could include data from egg samples that accounted for about 30% of the species richness observed. The results in this study confirm the efficacy of DNA barcoding in identifying Neotropical ichthyoplankton and show how the data produced provide valuable information for preparing plans for conserving and managing inland waters. © 2015 John Wiley & Sons Ltd.

Delimiting ichthyoplankton is fundamental work for monitoring the recruitment process and identifying the spawning and nursing grounds of fishes. Nevertheless, it is extremely difficult to identify the fish during the early stages at the species level based on morphological characters because of the paucity of diagnostic features. In this study, we investigated the fish larval community through large-scale ecosystemic sampling in South China Sea (SCS) during 2013 and 2017 using DNA barcodes. To maintain the morphologies of fish larvae, we preserved the larvae in formalin and developed a technique to recover their DNA. Among the 3,500 chosen larvae, we successfully extracted DNA from 2,787 larval samples and obtained 1,006 high-quality sequences. Blast searches showed that 408 larvae (i.e., 40.5%) could be unambiguously identified to species, 413 larvae (i.e., 41.1%) were ambiguously species delimitation, and 185 larvae (i.e., 18.4%) showed a low match similarity with target sequences. A total of 101 species were identified, among which 38 and 33 species corresponded to demersal and reef-associated species, whereas the remaining 30 species corresponded to benthopelagic, pelagic-oceanic, bathypelagic, and pelagic-neritic species. High-quality larval photographs of the 101 diagnosed species showed intact morphological characters and thus provided a reference for identifying fish species during the early stages based on morphological characters. Our study highlighted the possibility of recovering and amplifying DNA from formalin-fixed samples and provided new insight into the fish larval community in the SCS.

Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or "transition" type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or "transversion" type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = -(1/2) ln [(1-2P-Q) square root of 1-2Q]. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = -(1/2) ln (1-2P-Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.

本研究选取2017年4月采集的厦门湾鱼卵、仔稚鱼样品进行DNA 条形码分析。获得鱼卵、仔稚鱼的COI 基因序列27 条, 共鉴定种类11种,全部鉴定到种，隶属于4目9科11 属。在系统进化树的分析中, 同一种类的不同个体都聚在一支, 所有物种都分别聚为独立的一支, 这些物种都能有效地区分开来，说明利用COI基因可以进行有效的仔稚鱼物种鉴定。同时获取11种鱼类浮游生物高清图像，并描述其甄别性的形态特征。以上结果表明, 线粒体COI基因作为DNA 条形码可以实现鱼卵和仔稚鱼的物种鉴定, 且较多能鉴定到种的水平。

本文基于线粒体细胞色素C氧化酶亚基 I（COI）基因和16S rRNA基因片段对采集于厦门海域的仔稚鱼样品进行种类鉴定，探究其在仔稚鱼种类鉴定中的适用性。研究共获得64条COI基因序列和74条16S rRNA基因序列，通过序列比对，COI基因将仔稚鱼样品鉴定为26个种类，其中19个种类鉴定到种、6个鉴定到属、1个种类仅鉴定到科；16S rRNA基因将仔稚鱼样品鉴定为29个种类，其中23个种类鉴定到种、6个鉴定到属。COI基因的平均种内遗传距离为0.001 5，平均种间遗传距离为0.197 6，16S rRNA基因的平均种内遗传距离为0.000 3，平均种间遗传距离为0.089 2，COI和16S rRNA基因的平均种间遗传距离都为平均种内遗传距离的10倍以上，两者都可以进行有效的仔稚鱼种类鉴定。在基于COI和16S rRNA基因构建的系统进化树上，所有物种都分别单独聚为一支，同一个种类的不同个体都能聚在同一个分支，这些物种均能得到有效区分。以上结果表明，COI和16S rRNA基因均可以实现仔稚鱼的种类鉴定，两种基因结合使用可以提高仔稚鱼种类鉴定的准确性。

Ichthyoplankton assemblages and their relationship with environmental variables are investigated in waters off the Pearl River Estuary in spring and autumn of 2019. Of 80 ichthyoplankton taxa identified using DNA barcode and morphological methods, 61 are identified to species. The most abundance families (Carangidae, Trichiuridae, Mullidae, and Scombridae) account for 61.34% of the horizontal total catch in spring, while Menidae and Carangidae are the most abundant families identified in autumn, accounting for 89.72% of the horizontal total catch. Cluster analysis identifies three species assemblages in spring, and four in autumn based on horizontal trawls. Relationships between assemblage structure and environmental variables (in situ and remote sensed) are determined by canonical correspondence analysis. Ichthyoplankton assemblage structure appears to be strongly influenced by sea level anomalies, salinity, water depth, temperature at 10 m depth, and distance from shore. We demonstrate the efficacy of using DNA barcode to identify ichthyoplankton, and suggest how these data can be used to protect fish spawning grounds in waters off the Pearl River Estuary.