Testing agreement between a new method and the gold standard—How do we test?

Data analysis can be the most challenging aspect of a research study. Having been taught statistical techniques that tend to be based on finding significant differences or significant relationships, difficulties arise when trying to determine if a newly developed method is equally as good as the established method (the gold standard).     

Monognathus berteli sp. nov. from the Indian Ocean (Pisces,Monognathidae)

A new deepsea monognathid species,Monognathus berteli, is described based on one specimen collected pelagically in the northwestern Indian Ocean at 1440–1018 meters of depth. LikeM. taningi andM. bertini, it belongs to the short-skulled species-group and has very long pectoral fins, but differs from these species by several meristic characters. The described specimen has a very long caudal filament (53% SL) which is not known from otherMonognathus. However, the fragile filament is not used as a diagnostic character since it could easily be broken.     

热带印度洋黄鳍金枪鱼渔场时空分布与温跃层的关系

根据Argo浮标剖面温度数据重构热带印度洋各月月平均温跃层特征参数,并结合印度洋金枪鱼委员会(IOTC)黄鳍金枪鱼延绳钓数据,绘制了月平均温跃层特征参数和月平均CPUE的空间叠加图,用于分析热带印度洋黄鳍金枪鱼渔场时空分布和温跃层特征参数的关系。结果表明:热带印度洋温跃层上界深度、温度和下界深度,以及黄鳍金枪鱼中心渔场分布都具有明显的季节性变化特征,黄鳍金枪鱼中心渔场分布和温跃层季节性变化有关。在东北季风期间,高值CPUE渔区的温跃层上界深度的范围为30-40m,超过70m的渔区CPUE值普遍偏低;在西南季风期间温跃层上界最深达到120m。在东北季风期间,高值CPUE渔区温跃层下界深度不超过200m,在西南季风期间,深度会超过300m。在东北季风期间,高值CPUE渔区对应的温跃层上界温度都超过25℃,温度小于24℃的渔区CPUE值普遍较低;在西南季风期间,高值CUPE区域对应的温跃层上界温度范围变大,温跃层上界温度延伸到22℃,在22℃以下渔区CPUE值都很低。采用频次分析和经验累积分布函数计算其最适温跃层特征参数分布,得出黄鳍金枪鱼最适的温跃层上、下界温度范围分别是25-29℃和13-16℃;其上、下界深度范围分别为30-70m和140-200m。K-S检验结果表明,上述结论可靠。     

Multiple population structure of the giant mottled eel, Anguilla marmorata

The population structure of the giant mottled eel, Anguilla marmorata, was investigated with mitochondrial and microsatellite DNA analyses using 449 specimens from 13 localities throughout the species range. Control region F-statistics indicated the North Pacific (Japan, Taiwan, Philippines, Sulawesi), South Pacific (Tahiti, Fiji, New Caledonia, Papua New Guinea), eastern Indian Ocean (Sumatra), western Indian Ocean (Réunion, Madagascar), Ambon, and Guam regions were significantly different (Phi(ST) = 0.131-0.698, P < 0.05) while only a few differences were observed between localities within the South Pacific. These regions were roughly clustered in the neighbour-joining tree, although Ambon individuals were mainly divided into North and South Pacific groups. Analysis with eight microsatellite loci showed almost identical results to those of the control region, except no genetic difference was observed between the western and eastern Indian Ocean (F(ST) = 0.009, P > 0.05). The Bayesian cluster analysis of the microsatellite data detected two genetic groups. One included four North Pacific localities, and the other included eight localities in the South Pacific, Indian Ocean, and Guam, but Ambon individuals were evenly assigned to these two groups. These results showed that A. marmorata has four genetically different populations (North Pacific, South Pacific, Indian Ocean, Guam region). The North Pacific population is fully panmictic whereas the South Pacific and Indian Ocean populations have a metapopulation structure. Interestingly, Guam was suggested to be inhabited by a reproductive population restricted to that region, and the individuals from the North and South Pacific populations co-exist in Ambon.     

Phosphate fractionation in mud bank sediments from the southwest coast of India

Mud banks are unique, occurring along the southwest coast of India. They are known as ‘Zones of Bio-rhythm’, providing shelter to abundant aquatic life. The cyclic variation of nutrients in this region provides a clue to the continued and enriched presence of a variety of fish. This study reports on the different forms of phosphate in the resuspended sediments collected during the seasons with and without mud banks from the above mentioned coastal zones. Applying sequential and parallel chemical extractions using eight different schemes, the major forms of phosphate namely exchangeable P, anion exchangeable P, carbonate bound P, labile and resistant organic P, Fe-, Al- and Ca bound P and hydrolysable P have been determined. Quantitatively, these fractions vary and exhibit seasonal fluctuations. The concentration of potentially available anion exchange P, together with resistant organic and hydrolysable surplus P, provide an explanation to the existing organic food web supporting the aquatic life. Sediment phosphate fractionation reflects the role of chemical speciation of nutrients in the propagation of mud banks and is indicative of the biogenic processes controlling the pathways of phosphate in these coastal waters. Editorial note: Because of the sudden, regrettable death of the senior author, Dr P. N. K. Nambisan, editing remained unfinished. The guest editor remains responsible for errors left in the text.     

Biodiversity patterns in Indian Ocean corals, and effects of taxonomic error in data

Corals from 26 sites in the Indian Ocean, from numerous taxonomic sources, are analysed for distribution patterns after applying a consistent synonymy. The data set contains double the amount of distribution information used previously. Cluster analysis shows several contiguous regional groupings within this ocean, and no geographically dispersed groupings exist. Between-site species similarity correlates negatively with distance between sites. Coral species diversity and genus diversity plotted with latitude and longitude confirm that a band of high diversity stretches across the entire Indian Ocean, but that in this Ocean, unlike the Pacific and greater Caribbean area, there is no clear gradient with latitude at least up to the latitudinal limits of coral growth. About half the species are widespread throughout the Indian Ocean. Species frequency/distribution curves and cumulative frequency curves show that 150 species occur at only 2–4 sites. Multi-dimensional scaling (MDS) analysis using only these species confirms that they are important in forming sub-regional groupings which are superimposed on a general Indian Ocean homogeneity.The perennial problem of error in taxonomic data sets is examined. Increasing taxonomic error is introduced into the data using random methods. It is found that about 25% more error can be added to this data set before the relationship between similarity coefficient and geographical distance between pairs of sites is lost. Measures extracted from the clustering procedure using the original data and the data sets with added taxonomic error, show a sharp loss in cluster formation after addition of about 10 or 20% more error.     

Abundance of thraustochytrids and bacteria in the equatorial Indian Ocean, in relation to transparent exopolymeric particles (TEPs)

Thraustochytrid protists are often abundant in coastal waters. However, their population dynamics and substrate preferences in the oceanic water column are poorly understood. We studied the abundance and distribution of thraustochytrids, bacteria and TEPs in the equatorial Indian Ocean waters during September 2003, October 2004 and September 2006. Thraustochytrids and bacteria were abundant, suggesting high biological productivity of the region. Thraustochytrids were positively related to bacteria during October 2004 but not at other times, suggesting overlapping or varying substrate preferences at different times. Thraustochytrid and bacteria were positively related to TEPs only in a few stations during October 2004, but were mostly positively related to TEPs generated from in situ water in a roller table experiment. TEPs from natural samples during October 2004 had a much greater affinity to the lectin Concanavalin A than to Limulin compared with those in September 2006 and from the roller tank experiments. The chemical composition of TEPs might explain their relationship with thraustochytrids. Thraustochytrids averaged a higher biomass than bacteria in two of the three cruises, but were less frequent and more patchily distributed compared with bacteria.     

夏季西南印度洋叶绿素a分布特征

分析了2011年1月西南印度洋叶绿素a的分布特征及其粒级结构,并结合水动力学环境和营养盐数据探讨了其主要影响因素。结果表明,西南印度洋副热带涡流(IOSG)区表层叶绿素a浓度较低,不超过0.07 mg/m3,次表层叶绿素a浓度最大值所在水层较深,超过100 m;副热带聚集区(SCZ)表层叶绿素a浓度较高(0.164—0.247 mg/m3),次表层叶绿素a浓度最大值出现在50—70 m层。硝酸盐是该海区浮游植物生长的主要限制因素。微微型(pico)粒级的浮游植物占绝对优势,所有站位其对总叶绿素a的平均贡献率为71.1%,微型(nano)粒级次之(24.2%),小型(net)粒级所占比例最小(4.7%),其中IOSG区pico粒级对总叶绿素a的平均贡献率为77.9%,SCZ的pico粒级对总叶绿素a的平均贡献率为66.7%。IOSG区和SCZ海区之间水动力学环境的不同,可能导致了这两个海区叶绿素a的分布特征及粒级结构的较大差异。     

印度洋深海沉积物石油烃降解菌分离、鉴定与多样性分析

烃类物质在海洋环境中广泛分布,深海可能含有特殊的烃降解微生物。本研究通过对西南印度洋中脊与印度洋中部深海沉积物中石油降解菌的富集培养和分离鉴定,从6个站点的样品中共分离得到800株菌,通过BOX-PCR去重复菌株后,对其中183株菌进行了16SrRNA基因序列分析,发现这些菌分属于23个属;其中,γ-变形菌纲的食烷菌属(Alcanivorax)和放线菌纲的微杆菌属(Microbacterium)占优势。此外,还发现了食烷菌属2个潜在的新种、假海栖菌属(Pseudooceanicola)1个潜在新种。高通量测序结果证明,富集菌群中γ-变形菌纲是优势菌,主要包括食烷菌属、盐单胞菌属(Halomonas)、海杆菌属(Marinobacter)等。结合可培养菌与高通量测序结果,食烷菌属、盐单胞菌属、海杆菌属、交替假单胞菌(Pseudoalteromonas)、海源菌属(Idiomarina)与微杆菌属(Microbacterium)是沉积物样品中常见的石油烃降解菌,迪茨氏菌属(Dietzia)、红球菌属(Rhodococcus),假单胞菌属(Pseudomonas)、赤杆菌属(Erythrobacter)与副球菌属(Paracoccus)等可能也参与了烃的降解。