Comparison of visual survey and seining methods for estimating abundance of an endangered,benthic stream fish

We compared visual survey and seining methods for estimating abundance of endangered Okaloosa darters, Etheostoma okaloosae, in 12 replicate stream reaches during August 2001. For each 20-m stream reach, two divers systematically located and marked the position of darters and then a second crew of three to five people came through with a small-mesh seine and exhaustively sampled the same area. Visual surveys required little extra time to complete. Visual counts (24.2 ± 12.0; mean ± one SD) considerably exceeded seine captures (7.4 ± 4.8), and counts from the two methods were uncorrelated. Visual surveys, but not seines, detected the presence of Okaloosa darters at one site with low population densities. In 2003, we performed a depletion removal study in 10 replicate stream reaches to assess the accuracy of the visual survey method. Visual surveys detected 59% of Okaloosa darters present, and visual counts and removal estimates were positively correlated. Taken together, our comparisons indicate that visual surveys more accurately and precisely estimate abundance of Okaloosa darters than seining and more reliably detect presence at low population densities. We recommend evaluation of visual survey methods when designing programs to monitor abundance of benthic fishes in clear streams, especially for threatened and endangered species that may be sensitive to handling and habitat disturbance.     

Minimum Sample Size Ensuring Validity of Classical Confidence Intervals for Means of Skewed and Platykurtic Distributions

COCHRAN (1953) and BARTCH (1957) gave formulae for the magnitude of the sample size (n) ensuring the validity of the limiting normal distribution of the sample mean x(ⁿ) obtained from a non-normal distribution with marked asymmetry and kurtosis. These formulae have been checked empirically in this paper using (a) simulated data with given asymmetry and kurtosis and (b) real data gathered from a coronary heart disease study. We find that our results are in general agreement with Bartch's formula. However, in a number of cases, the asymptotic normal distribution is attained for smaller sample size than that required by Bartch's formula.     

HPLC shadowing: Artifacts in peptide characterization monitored by RIA

High performance liquid chromatography (HPLC), a valuable tool for characterization of peptides, is frequently used in combination with sensitive radioimmunoassays (RIA). The shadow phenomenon, representing carry-over of the peptide from previous application of the standard, can appear to result in the presence of endogenous peptide in the test sample when none is actually there. With delta sleep-inducing peptide (DSIP), we found the shadowing to be as high as 10%, although it was only 1% with ¹²⁵I-Tyr-DSIP. Thus, when HPLC-RIA systems are used for identification of peptides, caution must be used to avoid false positive results.     

Population ecology of the southern cassowary Casuarius casuarius johnsonii , Mission Beach north Queensland

Little is known of the ecology and population dynamics of the world’s largest avian frugivore. This study investigated the population of endangered southern cassowary at Mission Beach, northeast Australia, and examined the problems associated with determining population size and density of this keystone species. Using the results of an intensive field survey aimed at estimating absolute numbers of individual cassowaries, the appropriate sampling methodology for rare and elusive species was explored. Approximately 102 km² of rainforest was surveyed using 346 km of search transects. Of a total of 110 cassowaries, there were 49 adults (28 male, 19 female, 2 unknown), 28 subadults, 31 chicks, and 2 independent birds of unknown status. This is approximately 35% of the adult population previously estimated for the Mission Beach area. Overall adult cassowary density was 0.48 adults/km²; the density of independent birds, i.e. adults and subadults, was 0.78 birds/km². Mean indicative home range (IHR) for adult females and males was 2.13 and 2.06 km², respectively. Mean IHR of subadults was smaller at 0.95 km². It was concluded that the previous practice of surveying small areas at Mission Beach (<4 km²) has led to consistent overestimation of cassowary population density, up to six times its real number. It is shown that a sample plot between 5 and 15 km² is necessary to approximate true cassowary density. These findings have significant application to the conservation of cassowaries in New Guinea and in the Wet Tropics World Heritage Area of Australia.     

红雪茶基源种的鉴定及资源分布

本研究通过对红雪茶基源种进行考证,并结合品种鉴定及野外生态调查,结果表明,红雪茶的基源种应为金丝刷（Lethariella cladonioides）和金丝带（L.zahlbruckneri）,在这两个种群内,存在化学多态现象。市售的“红雪茶”主要由这两个种的四个化学宗所组成。红雪茶的分布中心主要在藏东南,滇西北及川西地区,目前红雪茶的资源已经受到了极大的破坏,日渐濒危。为加强对野生红雪茶资源的有效保护,提出了开展红雪茶种质资源保护的建议。     

Quality control of microbiota metagenomics by k-mer analysis

Background

The biological and clinical consequences of the tight interactions between host and microbiota are rapidly being unraveled by next generation sequencing technologies and sophisticated bioinformatics, also referred to as microbiota metagenomics. The recent success of metagenomics has created a demand to rapidly apply the technology to large case–control cohort studies and to studies of microbiota from various habitats, including habitats relatively poor in microbes. It is therefore of foremost importance to enable a robust and rapid quality assessment of metagenomic data from samples that challenge present technological limits (sample numbers and size). Here we demonstrate that the distribution of overlapping k-mers of metagenome sequence data predicts sequence quality as defined by gene distribution and efficiency of sequence mapping to a reference gene catalogue.

Results

We used serial dilutions of gut microbiota metagenomic datasets to generate well-defined high to low quality metagenomes. We also analyzed a collection of 52 microbiota-derived metagenomes. We demonstrate that k-mer distributions of metagenomic sequence data identify sequence contaminations, such as sequences derived from “empty” ligation products. Of note, k-mer distributions were also able to predict the frequency of sequences mapping to a reference gene catalogue not only for the well-defined serial dilution datasets, but also for 52 human gut microbiota derived metagenomic datasets.

Conclusions

We propose that k-mer analysis of raw metagenome sequence reads should be implemented as a first quality assessment prior to more extensive bioinformatics analysis, such as sequence filtering and gene mapping. With the rising demand for metagenomic analysis of microbiota it is crucial to provide tools for rapid and efficient decision making. This will eventually lead to a faster turn-around time, improved analytical quality including sample quality metrics and a significant cost reduction. Finally, improved quality assessment will have a major impact on the robustness of biological and clinical conclusions drawn from metagenomic studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1406-7) contains supplementary material, which is available to authorized users.     

Catechol–rhodanine derivatives: Specific and promiscuous inhibitors of Escherichia coli deoxyxylulose phosphate reductoisomerase (DXR)

To develop more effective inhibitors than fosmidomycin, a natural compound which inhibits the deoxyxylulose 5-phosphate reductoisomerase (DXR), the second enzyme of the MEP pathway, we designed molecules possessing on the one hand a catechol that is able to chelate the magnesium dication and on the other hand a group able to occupy the NADPH recognition site. Catechol–rhodanine derivatives (1–6) were synthesized and their potential inhibition was tested on the DXR of Escherichia coli. For the inhibitors 1 and 2, the presence of detergent in the enzymatic assays led to a dramatic decrease of the inhibition suggesting, that these compounds are rather promiscuous inhibitors. The compounds 4 and 5 kept their inhibition capacity in the presence of Triton X100 and could be considered as specific inhibitors of DXR. Compound 4 showed antimicrobial activity against Escherichia coli. The only partial protection of NADPH against the inhibition suggested that the catechol–rhodanine derivatives did not settle in the coenzyme binding site. This paper points out the necessity to include a detergent in the DXR enzymatic assays to avoid false positive when putative hydrophobic inhibitors are tested and especially when the IC₅₀, are in the micromolar range.     

The reproductive ecology of two subspecies of the bitterling Rhodeus atremius (Cyprinidae, Acheilognathinae)

The reproductive ecology of two endangered subspecies of the bitterling Rhodeus atremius was investigated in two rivers in Okayama and Fukuoka Prefectures, Japan. Several other bitterling species, R. ocellatus, Tanakia limbata, T. lanceolata, Acheilognathus tabira and A. rhombeus, are also found in these rivers. Spawning of both R. atremius subspecies was recorded between late March and August 2007, peaking between April and July. Females of R. atremius began to mature at small body size (minimum 25 mm). They had small clutch sizes (maximum 16 eggs) and developed a short ovipositor (mean 13.6 mm), which was used to deposit a bulb-shaped egg of comparatively large size (3.2 mm³, major and minor axes 2.8 and 1.5 mm). Clutch size, ovipositor length and egg size appear to be a function of female body size. Both the body size and ovipositor length of R. atremius with ripe ova and the size and shape of the eggs varied seasonally. Rhodeus a. suigensis achieved maturity at a smaller body size, had a longer ovipositor and produced smaller eggs, with the minor axis being wider relative to the major axis than those of R. a. atremius. Rhodeus atremius may be adapted for depositing small numbers of eggs in a much shallower position inside the gills of smaller host mussels than other bitterling species.     

A nested-intensity design for surveying plant diversity

Managers of natural landscapes need cost-efficient, accurate, and precise systems to inventory plant diversity. We investigated a nested-intensity sampling design to assess local and landscape-scale heterogeneity of plant species richness in aspen stands in southern Colorado, USA. The nested-intensity design used three vegetation sampling techniques: the Modified-Whittaker, a 1000-m² multiple-scale plot (n = 8); a 100-m² multiple-scale Intensive plot (n = 15); and a 100-m² single-scale Extensive plot (n = 28). The large Modified-Whittaker plot (1000 m²) recorded greater species richness per plot than the other two sampling techniques (P < 0.001), estimated cover of a greater number of species in 1-m² subplots (P < 0.018), and captured 32 species missed by the smaller, more numerous 100-m² plots of the other designs. The Intensive plots extended the environmental gradient sampled, capturing 17 species missed by the other techniques, and improved species–area calculations. The greater number of Extensive plots further expanded the gradient sampled, and captured 18 additional species. The multi-scale Modified-Whittaker and Intensive designs allowed quantification of the slopes of species–area curves in the single-scale Extensive plots. Multiple linear regressions were able to predict the slope of species–area curves (adj R ² = 0.64, P < 0.001) at each Extensive plot, allowing comparison of species richness at each sample location. Comparison of species–accumulation curves generated with each technique suggested that small, single-scale plot techniques might be very misleading because they underestimate species richness by missing locally rare species at every site. A combination of large and small multi-scale and single-scale plots greatly improves our understanding of native and exotic plant diversity patterns.     

湖北南河国家级自然保护区及周边七子花群落特征与种群结构

七子花（Heptacodium miconioides Rehder）为我国特有的落叶灌木或小乔木,被列入国家重点保护野生植物名录和世界自然保护联盟（IUCN）受威胁植物名录。2022年8月,被认为在湖北消失115年的七子花,在谷城南河国家级自然保护区及其周边被重新发现。本研究以新发现的3个七子花种群（傅家寨、玉皇阁和李庙镇）为研究对象,分析其生境特征、伴生群落物种组成、种群结构和受威胁因素。分布区的植被为典型的落叶阔叶林,以小叶鹅耳枥（Carpinus stipulata H. J. P. Winkl.）、化香树（Platycarya strobilacea Siebold & Zucc.）、七子花和栓皮栎（Quercus variabilis Blume）为优势种。新发现种群共记录到151株七子花,基本都分布于海拔1 000~1 300 m的山脊或崖壁上。七子花的大小级结构图呈纺锤型,表明新发现种群为衰退型,实生苗更新不足。新发现的151株个体中有137株（91%）产生萌蘖,共产生936个萌蘖,平均每株6.83个。大量的萌蘖在很大程度上弥补了幼苗的不足,使该物种能够占领其生态位,利于种群的维持。新发现种群位于偏远山区的山脊和崖壁上,人为干扰较小,因此可以推测内因是其种群衰退的主要驱动力。建议对周边区域开展更大规模的调查,同时采用包括就地保护、人工扩繁、迁地保护和野外回归在内的整合保护计划加强对七子花的保护和可持续利用。     

A euryhaline fish,lost in the desert: The unexpected metapopulation structure of Coptodon guineensis (Günther, 1862) in the Sebkha of Imlili

Euryhaline Cichlid fish of the species Coptodon guineensis are present in different water holes situated in a dried depression in the desert in the extreme South of Morocco, the Sebkha of Imlili. A genetic survey of this population, using complete sequences of the ND2 gene (mtDNA) and sixteen microsatellite loci, revealed that the fish in the sebkha did not form a single population, but rather a metapopulation. This metapopulational structure may be regarded as good news from the point of view of the conservation of fish in the sebkha. Although small individual populations may have short, finite life spans, the metapopulation as a whole is more stable, because immigrants from one population are likely to re-colonize the habitat, left open by the extinction of another.     

Clinical and radiological features of breast tumors according to history of false-positive results in mammography screening

BackgroundWomen with a false-positive result after a screening mammogram have an increased risk of cancer detection in subsequent participations, especially after assessments involving cytology or biopsy. We aimed to compare women's personal characteristics, tumoral features and the radiological appearance of cancers with and without a previous false-positive result generated by additional imaging or invasive procedures.MethodsFrom 1996 to 2007, 111,098 women aged 45–69 years participated in four population-based breast cancer screening programs in Spain, and 1281 cancers were detected. We included all cancers detected in subsequent screenings (n = 703) and explored the occurrence of previous false-positive results. We identified false-positives requiring additional imaging or invasive procedures. Differences on tumoral features (invasiveness, tumor size, and lymph node status) and radiological appearance were assessed by Chi-square test, and agreement between the location of cancer and prior suspicious by Cohen's kappa coefficient. A multivariate analysis was preformed to evaluate the effect of previous screening results and age on the odds of presenting an in situ carcinoma.ResultsAmong the 703 cancers detected in subsequent screenings, 148 women (21.1%) had a previous false-positive result. Of these, 105 were by additional imaging and 43 by invasive procedures. Women with prior false-positive result requiring invasive assessment, compared to women with negative tests, and women with prior false-positive requiring additional imaging, had a higher proportion of in situ carcinomas (31.7%, 15.3%, 12.9%, respectively; p = 0.014) and microcalcifications (37.2%, 20.2%, 9.5%, respectively; p = 0.003). The proportion of in situ carcinomas was even higher in women over 60 years (39.2%, 12.5%, 13.0%, respectively; p = 0.001). Ipsilateral cancer was observed in 65.7% of cases with prior cytology or biopsy (k = 0.479; 95%CI: 0.330–0.794).ConclusionA large number of in situ malignancies and calcification patterns were found among women with prior false-positive result in mammography screening requiring cytology or biopsies, suggesting progression from a previously benign lesion.     

Limited genetic structure and evidence for dispersal among populations of the endangered Florida grasshopper sparrow, Ammodramus savannarum floridanus

The Florida grasshopper sparrow, Ammodramus savannarum floridanus, is a non-migratory, endangered subspecies endemic to the prairie region of south-central Florida. It has experienced significant population declines and is currently restricted to five locations. We found substantial levels of variation in microsatellites and mtDNA control region sequences, estimates of inbreeding genetic effective population sizes that were much larger than the estimated census size, and no evidence of inbreeding within five sampled populations (n = 105). We also found a lack of genetic structure among populations (F _ST = 0.0123 for microsatellites and θ = 0.008 for mtDNA), and evidence for dispersal between populations, with 7.6% of all individuals identified as immigrants to their population of capture. We suggest that the subspecies be managed as a single management unit on a regional scale rather than as multiple management units on a local subpopulation scale. There is still a limited opportunity to preserve much of the present genetic variation in this subspecies, if immediate measures are taken to reverse the current population decline before this variation is reduced by genetic drift.     

中国的濒危物种及其保护

重点分析了濒危物种的概念，确定原则，阐述了物种保护的三种基因类型，即自养保护、圈养保护和基因保护。简要介绍了国家自然科学基金资助的与物种保护有关的项目。初步探讨限各种不同保护类型中存在的重要科学问题、可能研究领域和方向，以促进我国物种保护和研究的发展。     

Species richness of exotic and endangered fishes in Japan’s reservoirs

We analyzed the patterns of total, endangered and exotic fish species richness in 80 reservoirs throughout Japan using Generalized Linear Models (GLMs) with variables of dam characteristics (e.g. reservoir size, isolated period, altitude, DO, pH, rainfall, and air temperature) and watershed characteristics (e.g. watershed area, human population, and land-use patterns). Exotic species richness was positively correlated with total species richness but negatively correlated with endangered species richness. Largemouth bass, rainbow trout, and bluegill were the three most widely distributed species, occupying 47.5, 37.5, and 33.8% of the reservoirs, respectively. The patterns of total and endangered species richness were largely explained by watershed area and annual air temperature. Exotic species richness was determined primarily by the proportion of developed areas within each watershed. Therefore, reservoirs in more developed areas tend to support more exotic fish species that in turn threaten endangered fish species more severely.