A survey of the availability of primary bioinformatics web resources

The explosive growth of the bioinformatics field has led to a large amount of data and software applications publicly available as web resources. However, the lack of persistence of web references is a barrier to a comprehensive shared access. We conducted a study of the current availability and other features of primary bioinforo matics web resources （such as software tools and databases）. The majority （95%） of the examined bioinformatics web resources were found running on UNIX/Linux operating systems, and the most widely used web server was found to be Apache （or Apache-related products）. Of the overall 1,130 Uniform Resource Locators （URLs） examined, 91% were highly available （more than 90% of the time）, while only 4% showed low accessibility （less than 50% of the time） during the survey. Furthermore, the most common URL failure modes are presented and analyzed.     

福建省安溪县药用植物资源调查与分析

依托第四次全国中药资源普查,采用代表区域-样地-样方-样方套,结合样线调查方法,通过野外调查、走访调查及查阅相关资料等,对福建安溪药用植物资源种类和分布进行分析。结果显示,安溪县药用植物有1515种,隶属215科844属,草本为主要生活类型,药用部位主要以根及根茎类和全草类为主;其中福建重点药材115种、特色药材46种。安溪县药用植物资源丰富,物种多样性高,今后应加强资源保护与规划,合理开发利用该地药用植物资源。     

Evolutionary constraints on polyembryony in parasitic wasps: a simulation model

Polyembryony involves the production of several genetically identical progeny from a single egg through clonal division. Although polyembryonic development allows highly efficient reproduction, especially in some parasitoid wasps, it is far less common than monoembryony (development of one embryo per egg). To understand what might constrain the evolutionary success of polyembryony in parasitoids, we developed Monte Carlo models that simulate the competition between polyembryonic females and their monoembryonic counterparts. We investigated which simulated life‐history traits of the females allow the monoembryonic mode of development to succeed. Published empirical studies were surveyed to explore whether these traits indeed differ between polyembryonic parasitoids and related monoembryonic species. The simulations predict an advantage to monoembryony in parasitoids whose reproduction is limited by host availability rather than by egg supply, and that parasitize small‐bodied hosts. Comparative data on the parasitoid families Encyrtidae and (to a lesser extent) Braconidae, but not the data from Platygastridae, circumstantially support these predictions. The model also predicts monoembryony to outcompete polyembryony when: 1) hosts vary considerably in quality, 2) polyembryonic development carries high physiological costs, and 3) monoembryonic females make optimal clutch size decisions upon attacking hosts. These multiple constraints may account for the rarity of polyembryony among parasitoid species.     

Environmental DNA metabarcoding as an effective and rapid tool for fish monitoring in canals

We focus on a case study along an English canal comparing environmental DNA (eDNA) metabarcoding with two types of electrofishing techniques (wade-and-reach and boom-boat). In addition to corroborating data obtained by electrofishing, eDNA provided a wider snapshot of fish assemblages. Given the semi-lotic nature of canals, we encourage the use of eDNA as a fast and cost-effective tool to detect and monitor whole fish communities.     

Ecology,conservation, and phylogenetic position of the Madagascar Jacana Actophilornis albinucha

The Madagascar Jacana Actophilornis albinucha (Jacanidae) is an endemic shorebird found in the threatened wetlands of western Madagascar. This species is presumed to exhibit classical polyandry; however, few data are available to support that assumption. More generally, a lack of basic understanding of this species hinders conservation efforts. We conducted the most extensive study of the Madagascar Jacana to date, and report on its: 1) distribution, population size and density; 2) degree of sexual size dimorphism; and 3) phylogenetic position. The surveys were conducted at 54 lakes, between January and October in 2016. Madagascar Jacana were found at 22 lakes, and within these were distributed at a mean density of 3.5 ± 0.74 [SE] individuals per hectare of surveyed habitat. We estimate the global population size to be between 975 and 2 064 individuals, and habitat destruction appears to be the main threat to the species. Females were significantly larger than males, consistent with reports for other Jacanidae species. Using a mitochondrial DNA fragment, we expanded the Jacanidae genetic phylogeny, and confirmed that Madagascar Jacana is the sister species to the African Jacana Actophilornis africanus. Further studies are urgently needed to thoroughly re-assess the threat status and population trend of the Madagascar Jacana.     

Entanglement‐scar acquisition rates and scar frequency for Bering‐Chukchi‐Beaufort Seas bowhead whales using aerial photography

The Bering‐Chukchi‐Beaufort Seas (BCBS) bowhead whale (Balaena mysticetus) has been considered at low‐risk for entanglement injuries and ship strikes because their range is mainly north of commercial fisheries; nevertheless, changes to their arctic habitat, including a longer open water period and declining sea ice, have resulted in increasing commercial activity and concern about fisheries interactions. We examined interyear matches (between 1985 and 2011) from a photo identification project and identified whales that had acquired entanglement injuries. We estimated the probability of a bowhead acquiring an entanglement injury using two statistical methods: interval censored survival analysis and a simple binomial model. Both methods give similar results, suggesting a 2.2% (95% CI: 1.1%–3.3%) annual probability of acquiring a scar. We also include an entanglement scar frequency analysis of aerial photographs from the 2011 spring and fall surveys near Point Barrow, Alaska, which suggest 12.4% of live bowheads show evidence of entanglement scarring. Entanglement rates for the BCBS bowhead stock are lower than many other large whale stocks, and abundance has increased over the past 35 yr; however, our findings indicate that fishing gear entanglement is a more serious concern for the BCBS bowhead whale population than previously thought.     

Evaluating food availability and nest predation risk as sources of bias in aural bird surveys

ABSTRACT The use of aural surveys to estimate population parameters is widespread in avian studies. Despite efforts to increase the efficacy of this method, the potential for ecological context to bias population estimates remains largely unexplored. For example, food availability and nest predation risk can influence singing activity independent of density and, therefore, may bias aural estimates where these ecological factors vary systematically among habitats or other categories of ecological interest. We used a natural fire event in a mixed‐conifer forest that experienced variation in fire severity (low, intermediate, and high) to determine if aural surveys produce accurate density estimates of Dark‐eyed Juncos ( Junco hyemalis) independent of ecological context. During the first 2‐yr postfire, we censused junco populations in each burn type with intensive spot‐mapping and nest searching, locating 168 nests. Simultaneously, we conducted fixed‐radius point‐count surveys and estimated food availability and nest predation risk in each burn type to test whether ecological context may influence aural detection probability independent of actual density. We found no difference in nesting densities among patches burned at different severity. Arthropod food availability was inversely related to fire severity during the first postfire breeding season, but increased to higher levels across all severities during the second. In both years, aural detections were significantly greater in intermediate severity patches that consistently represented the habitat with the lowest nest predation risk. These results suggest that nest predation risk may significantly bias aural estimates of avian populations. Although traditional aural survey methods such as the Breeding Bird Survey measure habitat attributes, our findings highlight the difficulty in assessing relevant covariates in estimates of avian population. Future research must consider the potential for nest predation and other ecological factors to drive interannual or interhabitat variation in avian population estimates independent of true changes in population size.     

Assessing internet survey data collection methods with ethnic nurse shift workers

An increasing number of ethnic minorities are expected to enter the United States workforce based on projected demographic changes. This includes American Indian/Alaskan Native (AI/AN) nurses. Sociocultural influences on sleep disturbances, sleepiness, and other aspects related to shift-work tolerance are of unrecognized importance. More minority nurses are needed to provide culturally congruent care; however, AI/AN nurses represent less than 1% of nurses located throughout the American workforce. This article aims to verify the feasibility of Internet data collection (Web-based survey) methods and instrument stability as the first part of a two-phase study comparing individual differences and shift-work-related sleep disturbances between AI/AN and White non-Hispanic (WNH) nurses. In the first phase, an Internet survey was used to reach a cross-section of AI/AN and WNH nurses. The on-line survey was composed of accepted shift-work-related instruments. Items estimating sleep disturbances, sociocultural choices, time awareness, polychronicity, morningness/eveningness, ethnic identity, and demographic questions were asked. The survey was linked to a series of Web pages describing the study purpose, inclusion and exclusion criteria, consent form, Web survey, and the second phase of the study in which subjects were invited to participate in actigraphy measurements. The survey was pilot-tested for error codes, item confusion, length, and completion time. Forced-answer questions were added asking ethnicity, age group, license type, state where licensed, and legal name on nursing license before accessing the survey. Data were saved periodically, cued by the word “continue.” The database was located on a secure server and password protected. Nurses were recruited using published articles and printed advertisements, hospital e-mail systems, national nursing organization Web sites (minoritynurse.com; NANAINA.org), nursing Web site discussion groups, snow-balling, and word of mouth. The site was accessed 656 times with the Internet survey being completed by 138 WNH and 56 AI/AN nurses meeting the inclusion criteria. Except for the polychronicity measure (PAI3), instruments measuring time awareness, chronotype, and situational sleepiness achieved acceptable reliability coefficients with Internet data collection. Using pull-down menus would improve questions asking specific times. Internet data collection with different ethnic groups is possible; however, accessing the target population may be difficult. Despite extensive recruitment efforts, few AI/AN nurses participated. Computer literacy and failing to relate to the study's purpose may have limited the interest of the AI/AN nurses. It is possible to recruit nurse shift workers and collect individual difference and sleep disturbance data through the Internet; however, the researcher must remain vigilant throughout the process.     

Sampling accuracy of reef resource inventory technique

A new technique called the reef resource inventory (RRI) was developed to map the distribution and abundance of benthos and substratum on reefs. The rapid field sampling technique uses divers to visually estimate the percentage cover of categories of benthos and substratum along 2×20 m plotless strip-transects positioned randomly over the tops, and systematically along the edge of reefs. The purpose of this study was to compare the relative sampling accuracy of the RRI against the line intercept transect technique (LIT), an international standard for sampling reef benthos and substratum. Analysis of paired sampling with LIT and RRI at 51 sites indicated sampling accuracy was not different (P>0.05) for 8 of the 12 benthos and substratum categories used in the study. Significant differences were attributed to small-scale patchiness and cryptic coloration of some benthos; effects associated with sampling a sparsely distributed animal along a line versus an area; difficulties in discriminating some of the benthos and substratum categories; and differences due to visual acuity since LIT measurements were taken by divers close to the seabed whereas RRI measurements were taken by divers higher in the water column. The relative cost efficiency of the RRI technique was at least three times that of LIT for all benthos and substratum categories and as much as 10 times higher for two categories. These results suggest that the RRI can be used to obtain reliable and accurate estimates of relative abundance of broad categories of reef benthos and substratum.

Understanding population history for conservation purposes: population genetics of Saxifraga aizoides (Saxifragaceae) in the lowlands and lower mountains north of the Alps

Several alpine species have outlying populations in the lowlands and lower mountains north of the Alps. These small, isolated populations are usually described as either (1) glacial relics, (2) descendants from populations living on forelands and moraines during the ice ages, or (3) populations founded by long-distance dispersal after glaciation. A floristic survey of the historic and present distributions and an allozyme investigation were performed on one of these relic species, Saxifraga aizoides. The species was historically more abundant and had more stations in more regions of northeastern Switzerland. The former population structures within regions, nowadays destroyed, were still reflected in distinct and high regional genetic diversity and variation. There was weak evidence of increased inbreeding in outlying populations, but populations did not deviate from Hardy-Weinberg equilibrium. No geographic pattern of genetic variation above the regional scale (>10 km) was found. Based on the spatial and genetic structures found, it was not possible to discriminate between the abovementioned hypotheses. Nevertheless, the study shows how a thorough evaluation of distribution and abundance data aids the interpretation of genetic data with respect to population history, biogeography, and conservation biology.