Reproducibility of Vibrionaceae population structure in coastal bacterioplankton

How reproducibly microbial populations assemble in the wild remains poorly understood. Here, we assess evidence for ecological specialization and predictability of fine-scale population structure and habitat association in coastal ocean Vibrionaceae across years. We compare Vibrionaceae lifestyles in the bacterioplankton (combinations of free-living, particle, or zooplankton associations) measured using the same sampling scheme in 2006 and 2009 to assess whether the same groups show the same environmental association year after year. This reveals complex dynamics with populations falling primarily into two categories: (i) nearly equally represented in each of the two samplings and (ii) highly skewed, often to an extent that they appear exclusive to one or the other sampling times. Importantly, populations recovered at the same abundance in both samplings occupied highly similar habitats suggesting predictable and robust environmental association while skewed abundances of some populations may be triggered by shifts in ecological conditions. The latter is supported by difference in the composition of large eukaryotic plankton between years, with samples in 2006 being dominated by copepods, and those in 2009 by diatoms. Overall, the comparison supports highly predictable population-habitat linkage but highlights the fact that complex, and often unmeasured, environmental dynamics in habitat occurrence may have strong effects on population dynamics.     

Systematic relationships within the Vibrionaceae (Bacteria: Gammaproteobacteria): steps toward a phylogenetic taxonomy

A phylogenetic hypothesis is presented for all 95 species of the family Vibrionaceae (Bacteria: Gammaproteobacteria) based on a combined analysis of eight molecular loci (16S rRNA, gyrB, recA, rpoA, gapA, mreB, topA, atpA) for up to 9337 nucleotide characters. Members of this taxon exhibit diverse life histories, including bioluminescence, pathogenicity to human and marine organisms, symbiosis, quorum sensing and extremophilic environment living, making a hypothesis of phylogenetic history important to studies addressing these traits from an evolutionary perspective. It is proposed that this phylogenetic set of relationships replaces previous phenetic hypotheses and be used to construct a phylogenetic taxonomy. Recent taxonomic proposals, including the validity of four, instead of one, families representing the 95 species and historical notions of genera within the group are compared with the presented phylogenetic hypothesis. Character support is traced through the tree and is used to address these taxonomic proposals. Photobacterium is not a monophyletic group as it is currently delimited. Aliivibrio is found within Photobacterium, suggesting a new definition for Photobacterium that includes all species of Aliivibrio. Enterovibrio, Salinivibrio and Grimontia, previously thought to be distinct from and basal to Photobacterium and Vibrio, are found nested deeply within a large Vibrio clade. © The Willi Hennig Society 2010.     

A method of deriving subgroups of a population: a study of craniofacial taxonomy

Subgroups within a population are often difficult to discover and describe except by subjective methods. In this study, cluster analysis (numerical taxonomy) methods were used on selected craniofacial measurements obtained from 308 North American White children of both sexes in the age range 6–18 to derive categories of skeletal facial types. Two different cluster analysis approaches were used in conjunction with a separate overall evaluation of facial balance, an independent measure of maxillo-mandibular relationship (AB/FOP), and a traditional classification (Angle). The categories derived rest on corroborative and overlapping evidence from each of those methods. The categories were examined to determine if it is possible to classify a sample by means of cluster analysis, the size and discreteness of each class, how they compare with the Angle classification of the same sample, and the percentage of individuals that may be identified unequivocally by this classification scheme. Five categories were obtained. Labeled Category A — Category E, they show some correspondence to the Angle Classes I, II, and III, but categories A, B, and C appear to be subgroups, heretofore undetected, of Angle Class II. Categories D and E correspond to Angle Classes I and III, respectively. The categories are more realistic and informative than the Angle classes. Each category is reported along with its distinguishing skeletal characteristics.     

Reverse taxonomy for elucidating diversity of insect-associated nematodes: a case study with termites

Background

The molecular operational taxonomic unit (MOTU) has recently been applied to microbial and microscopic animal biodiversity surveys. However, in many cases, some of the MOTUs cannot be definitively tied to any of the taxonomic groups in current databases. To surmount these limitations, the concept of “reverse taxonomy” has been proposed, i.e. to primarily list the MOTUs with morphological information, and then identify and/or describe them at genus/species level using subsamples or by re-isolating the target organisms. Nevertheless, the application of “reverse taxonomy” has not been sufficiently evaluated. Therefore, the practical applicability of “reverse taxonomy” is tested using termite-associated nematodes as a model system for phoretic/parasitic organisms which have high habitat specificity and a potential handle (their termite host species) for re-isolation attempts.

Methodology

Forty-eight species (from 298 colonies) of termites collected from the American tropics and subtropics were examined for their nematode associates using the reverse taxonomy method and culturing attempts (morphological identification and further sequencing efforts). The survey yielded 51 sequence types ( =  MOTUs) belonging to 19 tentatively identified genera. Within these, four were identified based on molecular data with preliminary morphological observation, and an additional seven were identified or characterized from successful culturing, leaving eight genera unidentified.

Conclusions

That 1/3 of the genera were not successfully identified suggests deficiencies in the depth of available sequences in the database and biological characters, i.e. usually isolated as phoretic/parasitic stages which are not available for morphological identification, and too many undiscovered lineages of nematodes. Although there still is the issue of culturability of nematodes, culturing attempts could help to make reverse taxonomy methods more effective. However, expansion of the database, i.e., production of more DNA barcodes tied to biological information by finding and characterizing additional new and known lineages, is necessary for analyzing functional diversity.     

Further study on polyamine compositions in Vibrionaceae

It has previously been reported that norspermidine, one of the unusual polyamines, is present in Vibrio species. To expand this observation, the cellular polyamine compositions of additional species and strains in the family Vibrionaceae (Vibrio, Photobacterium, Listonella, and Shewanella) as well as Aeromonas species and Plesiomonas shigelloides, which have been proposed to be excluded from Vibrionacea, were determined by using gas-liquid chromatography. Some Vibrio species previously reported were reexamined under the same conditions, and their results are included in this report. Norspermidine was detected as a major triamine in 23 of 24 Vibrio species, all of 4 Listonella species, and 3 of 5 Photobacterium species. Vibrio costicola, Photobacterium fischeri, and Photobacterium phosphoreum contained no norspermidine. Listonella species were indistinguishable from Vibrio species in their polyamine profiles. However, Schewanella putrefaciens ATCC 8071, formerly allocated in the genus Alteromonas, contained no norspermidine, and its polyamine profile was similar to those of four Aeromonas species, in which putrescine was exclusively found. Plesiomonas shigelloides was very similar to Escherichia coli in that putrescine and spermidine were predominant polyamines. Our data indicate that the occurrence of norspermidine may be very helpful as a generic marker in identification and classification of Vibrio and Listonella species. A gas-liquid chromatographic method with a nitrogen-selective detector was presented for rapid and sensitive detection of cellular norspermidine.     

Analyzing spatial-temporal dynamics of the ecological niche: a marten (Martes martes) population case study

A potential of discriminant analysis is demonstrated in a case study of the common marten (Martes martes L., 1758) ecological niche within the Central Forest Reserve and its buffer zone. The analysis is aimed at identifying how the probability to encounter a marten's footprint along a walking route depends on the relief and other parameters of the environment discerned by remote sensing. The analyses that were done individually for each of the eleven months from a three-year observation period have revealed the pattern of the species spatial distribution and a measure of its association with the environment to be dependent, to a large extent, on the weather conditions. In general, associations with the environment do increase under unfavorable conditions. The methods are suggested that integrate outcomes of the monthly analyses into a general map of habitat types. The technique presented has wide application opportunities in studying the ecology of populations and solving problems of practical ecology.     

Numerical taxonomy of Vibrionaceae isolated from cultured amberjack (Seriola dumerili) and surrounding water

A numerical taxonomic study was performed on 148 isolates of Gram-negative, heterotrophic, facultative anaerobic bacteria isolated from amberjack (Seriola dumerili) and its surrounding culture water. The study included 30 type and reference strains belonging to genera Vibrio, Listonella, and Photobacterium. The strains were characterized by 109 morphological, biochemical, physiological, and nutritional tests. Cluster analysis of similarity matrices obtained with S(SM) and S(J) coefficients was carried out. UPGMA (unweighted pair group mathematical average) analysis defined 11 phena at S(SM) values > or = 86%. Nine phena were identified as Vibrio alginolyticus, V. fischeri, V. harveyi, V. carchariae, V. mediterranei, V. splendidus, V. furnissii, V. parahaemolyticus, and Photobacterium damselae subsp. damselae. The two latter comprised strains isolated from diseased fish.     

基于ARIMA模型的生态足迹动态模拟和预测——以甘肃省为例

生态足迹(EF)是一种定量测量人类对自然利用程度的方法。然而目前对其发展趋势准确的定量分析尚不多见。可采用自回归综合移动平均模型(ARIMA)来模拟并预测区域生态足迹。综合运用生态足迹方法和ARIMA模型对甘肃省1949-2009年的生态足迹和生态承载力进行了动态模拟和分析,在此基础上预测了2010-2015年的生态足迹变化趋势。结果表明:1949-2009年,人均生态足迹呈现上升趋势,预计2010-2015年上升趋势明显加快,2015年会增加到2.6051 hm²/人,是2009年的1.67倍;1997-2004年人均生态承载力逐年减少,2005年之后逐年增加,预计2010-2015年仍会增加;预计2010-2015年所有人均生态足迹组成类型均呈现上升趋势,尤以人均化石能源生态足迹增长显著;1997-2009年人均生态承载力均小于人均生态足迹,导致生态赤字,甘肃省生态环境处于不可持续状态,预计2010-2015年人均生态承载力略有增长,但仍小于人均生态足迹,生态赤字不断增大,预计2015年增长到-2.0468 hm²/人,约为2009年(-1.0262 hm²/人)的两倍,甘肃省生态环境不断恶化;经济的发展依赖于化石能源的消耗而造成对自然资源的过度利用,大量耕地转换为建设用地,草地荒漠化是引起甘肃省生态赤字的主要原因;改变经济发展和资源消费模式,控制人口规模,减少人均生态足迹消耗,优化配置和集约节约利用自然资源,提高生态承载力是促进社会经济和资源环境可持续发展的有效途经。     

Physiology and taxonomy of scleractinian corals: a case study in the genus Stylophora

The morphology and skeletal characteristics of colonies of the coral genus Stylophora living on the reef edge at 1 m depth on the Jordanian coast of the Gulf of Aqaba (Red Sea) are those of S. mordax (Dana 1846) which has not been reported previously from that area. These colonies were considered earlier as ecomorphs of S. pistillata (Esper 1797) which lives down to at least 67 m on the reef slopes. Growth, organic content and metabolism were compared in colonies living at different depths (1,5,10 and 30 m). The trends of twelve parameters between 1 and 5 m were different from the variation observed between 5 and 30 m. Colonies living at 1 m have a higher chlorophyll content but a lower metabolic activity and growth rate than colonies living at 5 m. Most of these pecularities cannot be explained by the influence of environmental factors. It is therefore suggested that S. mordax is a valid taxon.     

新疆生态足迹与环境压力的时空分异

提高生态现代化总体水平是改善区域生态环境承载力的核心和关键。利用生态环境质量指数和生态现代化指数(EM I)对我国西部生态环境脆弱区的新疆维吾尔自治区生态足迹和环境压力的变动态势进行了系统分析。结果表明:2004年新疆生态现代化指数在全国排名为27位,仍然为我国生态现代化水平落后的地区之一。1980—2005年,新疆综合现代化水平远低于高收入国家、世界平均水平和中等发达国家。1998年新疆人均生态足迹由25957hm2增加到2007年的40551hm2,人均生态承载力由3.1270hm2减少到2.8266 hm2。区域环境水平呈下降趋势。资源转化率、生态保护指数呈明显上升态势。环境治理指数呈剧烈变动,1996-2003年呈N型变动态势,区域生态脆弱性没有明显逆转。     

The complimentary role of genetic and ecological data in understanding population structure: a case study using moose (Alces alces)

Landscape features can influence animal movements and gene flow, so rigorous analysis of population structure should include both levels of analysis. We conducted individual-based landscape genetic analysis, using data from eight microsatellite loci, on adult female moose (Alces alces; n = 92) from two areas in southern Ontario, and also monitored movements of a subsample of animals (n = 38) to gauge complementarity of the data sources (genetic and telemetry data) in understanding patterns of population structure. Genetic data indicated that female moose constituted a single panmictic population encompassing both areas, with no evidence of isolation by Euclidean (Mantel test p > 0.38) or least-cost (Mantel test p > 0.19) distances, even when such distances were calculated from costs extracted from resource selection functions of the radio-collared individuals. In contrast, throughout the 2.5-year study radio-telemetry data failed to reveal large-scale movement of female moose. In fact, although moose tended to occupy home ranges in a wide range of sizes, their locations were largely fixed at a larger spatial scale encompassing both study areas. This finding implies that radio-telemetry data alone would not have revealed the extent of connectivity between moose populations, whereas least-cost genetic measures in the absence of telemetry data would not have shown the localised movements of adult females. Our contrasting results highlight the importance of multiple sources of information when assessing population connectivity of large mammals.     

Torosaurus is not Triceratops: ontogeny in chasmosaurine ceratopsids as a case study in dinosaur taxonomy

Background

In horned dinosaurs, taxonomy is complicated by the fact that the cranial ornament that distinguishes species changes with age. Based on this observation, it has been proposed that the genera Triceratops and Torosaurus are in fact synonymous, with specimens identified as Torosaurus representing the adult form of Triceratops. The hypothesis of synonymy makes three testable predictions: 1) the species in question should have similar geographic and stratigraphic distributions, 2) specimens assigned to Torosaurus should be more mature than those assigned to Triceratops, and 3) intermediates should exist that combine features of Triceratops and Torosaurus. The first condition appears to be met, but it remains unclear whether the other predictions are borne out by the fossil evidence.

Methodology/Principal Findings

We assessed the relative maturity of Torosaurus and Triceratops specimens by coding skulls for characters that vary with maturity, and then using a clustering analysis to arrange them into a growth series. We found that a well-defined sequence of changes exists in horned dinosaurs: development of cranial ornament occurs in juveniles, followed by fusion of the skull roof in subadults, and finally, the epoccipitals, epijugals, and rostral fuse to the skull in adults. Using this scheme, we identified mature and immature individuals of both Torosaurus and Triceratops. Furthermore, we describe the ventral depressions on the frill of Triceratops, and show that they differ in shape and position from the parietal fenestrae of Torosaurus. Thus, we conclude that these structures are not intermediates between the solid frill of Triceratops and the fenestrated frill of Torosaurus.

Conclusions/Significance

Torosaurus is a distinct genus of horned dinosaur, not the adult of Triceratops. Our method provides a framework for assessing the hypothesis of synonymy through ontogeny in the fossil record.     

Updating risk prediction tools: a case study in prostate cancer

Online risk prediction tools for common cancers are now easily accessible and widely used by patients and doctors for informed decision-making concerning screening and diagnosis. A practical problem is as cancer research moves forward and new biomarkers and risk factors are discovered, there is a need to update the risk algorithms to include them. Typically, the new markers and risk factors cannot be retrospectively measured on the same study participants used to develop the original prediction tool, necessitating the merging of a separate study of different participants, which may be much smaller in sample size and of a different design. Validation of the updated tool on a third independent data set is warranted before the updated tool can go online. This article reports on the application of Bayes rule for updating risk prediction tools to include a set of biomarkers measured in an external study to the original study used to develop the risk prediction tool. The procedure is illustrated in the context of updating the online Prostate Cancer Prevention Trial Risk Calculator to incorporate the new markers %freePSA and [-2]proPSA measured on an external case-control study performed in Texas, U.S.. Recent state-of-the art methods in validation of risk prediction tools and evaluation of the improvement of updated to original tools are implemented using an external validation set provided by the U.S. Early Detection Research Network.     

Genomic,ecological, and morphological approaches to investigating species limits: A case study in modern taxonomy from Tropical Eastern Pacific surgeonfishes

A wide variety of species are distinguished by slight color variations. However, molecular analyses have repeatedly demonstrated that coloration does not always correspond to distinct evolutionary histories between closely related groups, suggesting that this trait is labile and can be misleading for species identification. In the present study, we analyze the evolutionary history of sister species of Prionurus surgeonfishes in the Tropical Eastern Pacific (TEP), which are distinguished by the presence or absence of dark spots on their body. We examined the species limits in this system using comparative specimen‐based approaches, a mitochondrial gene (COI), more than 800 nuclear loci (Ultraconserved Elements), and abiotic niche comparisons. The results indicate there is a complete overlap of meristic counts and morphometric measurements between the two species. Further, we detected multiple individuals with intermediate spotting patterns suggesting that coloration is not diagnostic. Mitochondrial data recovered a single main haplotype shared between the species and all locations resulting in a complete lack of structure (Φ_ST = 0). Genomic analyses also suggest low levels of genetic differentiation (F_ST = 0.013), and no alternatively fixed SNPs were detected between the two phenotypes. Furthermore, niche comparisons could not reject niche equivalency or similarity between the species. These results suggest that these two phenotypes are conspecific and widely distributed in the TEP. Here, we recognize Prionurus punctatus Gill 1862 as a junior subjective synonym of P. laticlavius (Valenciennes 1846). The underlying causes of phenotypic variation in this species are unknown. However, this system gives insight into general evolutionary dynamics within the TEP.     

生态安全格局构建及景观生态风险预测——以赛罕乌拉国家级自然保护区为例

自然保护区生态风险评价与预测对区域自然资源保护及规划管理具有重要意义。研究以赛罕乌拉国家级自然保护区为例,利用2000、2010、2020年三期土地利用数据,基于景观生态风险指数(ERI)评价研究区景观生态风险,结合最小累积阻力模型(MCR)构建生态安全格局,并借助斑块生成土地利用变化模拟模型(PLUS)模拟2030-2050年土地利用及景观生态风险演变状况,对研究区的风险管控与格局优化提出相应策略与措施。结果表明:(1)研究区景观生态风险呈北低南高的空间分布特征,以较低风险区为主,2000-2020年景观生态风险整体呈先下降后上升趋势; (2)重要生态功能"点"——56处生态源地、49个生态节点,"轴"——144条生态廊道,"面"——生态保育区、生态过渡区、合理利用区等3个生态功能区,共同构成了研究区的生态安全格局;(3)2030-2050年研究区主要以较低风险区为主,呈现北低南高的空间分布特征。从时空演变上看,2020-2050年赛罕乌拉国家级自然保护区景观生态风险呈下降趋势。研究成果可为自然保护区生态保护与治理提供决策参考。     

生态足迹理论在生态市建设规划中的应用——以海口市为例

生态市建设规划是促进区域可持续发展的有效措施,而生态足迹理论作为定量测度发展的可持续状态的一类生物物理方法对于定量描述区域发展现状、判断发展中的基本问题具有重要的借鉴作用。生态足迹分析应用到生态市建设规划中可以（1）分析可持续发展进程,明确城市可持续发展状态;（2）明确城市一定人口的消费对环境产生的后果以及与可持续发展相关的重要资源问题;（3）为合理开展生态市建设规划、减少生态足迹提供决策信息。本研究根据海口生态市建设规划实践剖析了生态足迹理论在明确上述3个方面中的应用。结果表明：海口市2002年生态足迹为生态承载力的5．6倍,处于不可持续状态。出现赤字的土地类型依次为耕地、水域、化石燃料用地和草地,其中耕地赤字为各项需求之首。海口市2002年万元GDP的生态足迹为0．93hm^2,表现为资源利用效率较低,但海口市生态占用率较小,生态环境压力相对较小。根据海口市生态环境现状,减少生态足迹、提高可持续发展能力的规划途径主要为：通过保护土地资源和提高科技发展水平改善耕地和草地赤字的现状;通过构建城市生态交通和构建生态建筑与节能体系来缓解化石燃料用地的压力;通过发展循环经济和转变消费模式来提高资源利用效率;通过控制人口增长来提高人均生态承载力。