Length–weight relationship of nine fish species from Skadar Lake (Adriatic catchment area of Montenegro)

This study provides data on the length–weight relationships (LWR) of nine fish species sampled between 2010 and 2014 from Skadar Lake, Montenegro. Also provided are the first comprehensive data of LWRs for three freshwater fishes for which no LWR information was available in the FishBase data bank. The b parameter values ranged from 2.936 to 3.271, while values of the a parameter ranged from 0.002 to 0.014.     

傀儡湖18种鱼类全长与体重关系研究

为了了解中国长江中下游湖泊——傀儡湖(N 31o24′, E 120o51′)鱼类生长的特性, 于2013年4月至2015年4月利用地笼、多网目复合刺网和网簖等工具对该水域鱼类进行了月度调查。共捕获鱼类18种, 隶属于3科, 主要以鲤科鱼类为主。运用最小二乘法对这18种鱼类的全长和体重的回归关系进行拟合, 其中3种鱼类全长与体重的回归方程为首次拟合。此外, 15种鱼类的最大全长超过世界鱼类数据库(FishBase)中记录的最大全长。研究提供的鱼类全长与体重回归方程及其参数填补了世界鱼类数据库的空白。     

Length‐weight and length‐length relationships of five fish species from the Zigui section of the lower Three Gorges Reservoir,Hubei Province,China

This paper provides the length‐weight and length–length relationships for five fish species in the Zigui section of the lower Three Gorges Reservoir of the Yangtze River. Specimens were collected from December 2014 to January 2017, using various types of fishing gear and electroshock fishing techniques. Length‐weight relationships (LWRs) for one fish species and Length–length relationships (LLRs) for five fish species are unknown to FishBase. New maximum total lengths for four species were also recorded for FishBase. Moreover, standard‐length to total‐length equations for converting size measurements for these five species are presented.     

Preliminary estimates of the population parameters of major fish species in Lake Ayamé I (Bia basin; Côte d'Ivoire)

Length frequency data collected from artisanal fisheries in Lake Ayamé I (Côte d'Ivoire) from August 2004 to 2005 were analysed with F isat software using the E lefan package to estimate the population parameters of 11 fish species. Asymptotic values for total length ( L∞ ) ranged from 20.5 cm for Brycinus imberi to 78 cm for Mormyrops anguilloides . Growth rates ( k ) varied from 0.24 year⁻¹ for Chrysichthys nigrodigitatus to 0.57 year⁻¹ for Hemichromis fasciatus . The growth performance estimates were close to the values found by others authors and reported in FishBase 2008. Fishing mortality ( F ) and exploitation rate ( E ) were found to be below optimum levels of exploitation for most fish species. Recruitment was noted as year–round and bimodal for most studied populations. The data sets were limited in most cases, thus this study provides preliminary population parameters only, but for species for which information is scarce. For application in stock assessment, the growth parameters and especially the natural mortality data require further confirmation.     

Length–weight and length–length relationships for common fish and crayfish species in the Everglades,Florida, USA

Length–weight and length–length relationships are reported for 18 species of fish and two species of crayfish within the Everglades, FL, USA. This study provides updated relationships for native species, as well as initial relationships for established exotic species in this region. Additionally, 14 length–weight and two length–length relationships are presented to FishBase for the first time.     

limma powers differential expression analyses for RNA-sequencing and microarray studies

limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.     

Length–weight relationships of 21 fishes from the Xiangjiang River,China

This paper provides the length–weight relationships for 21 fish species belonging to four families and 19 genera from the Xiangjiang River, a tributary of the middle Yangtze River in China. Among them, the length–weight relationships for 14 fishes are first‐time reports for FishBase, and new maximum total lengths of 13 fishes are also reported.     

affy--analysis of Affymetrix GeneChip data at the probe level

MOTIVATION: The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used. RESULTS: The affy package is an R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. The package is currently in its second release, affy provides the user with extreme flexibility when carrying out an analysis and make it possible to access and manipulate probe intensity data. In this paper, we present the main classes and functions in the package and demonstrate how they can be used to process probe-level data. We also demonstrate the importance of probe-level analysis when using the Affymetrix GeneChip platform.     

Length‐weight relationships of six fishes from the Anning River,China

This paper provides the length–weight relationships for six fish species collected from the Anning River, one of the biggest tributaries of the Yalong River in China. A total of 1096 specimens belonging to six fish species were analyzed. Among them, the length–weight relationships for 4 fish species are first‐time reports for FishBase and new maximum lengths of one fish species is also reported.     

Length–weight relationships of four small fish species caught in the Heishui River,China

In the present paper the length–weight relationships (LWRs) were determined for Jinshaia sinensis Sauvage & Dabry de Thiersant, 1874; Triplophysa anterodorsalis Zhu & Cao, 1989; Liobagrus marginatus Günther, 1892; and Glyptothorax sinensis Regan, 1908 caught in the Heishui River in July 2014. The specimens were caught with fishing gear including drifting gillnets (mesh size 4 cm) and shrimp cages. This paper provides new data on LWRs for FishBase.     

Length-weight relationships of 10 fish species from the coastal waters of the East China Sea

The present study provides the length-weight relationships (LWRs) for 10 marine fish species collected from the coastal waters of the East China Sea by bottom trawl surveys. The open width of the sampling net was 40 m and the mesh size of the codend was 20 mm. Specimens were collected from November 2015 to November 2019 at seasonal intervals. The measurement accuracy of weight and length were 0.1 grams and 0.1 centimeters, respectively. This study provides new information of LWRs for nine species which have not yet been reported in FishBase. Also, this study updates the information of maximum length for two species.     

samc: an R package for connectivity modeling with spatial absorbing Markov chains

Quantifying landscape connectivity is fundamental to better understand and predict how populations respond to environmental change. Currently, popular methods to quantify landscape connectivity emphasize how landscape features provide resistance to movement. While many tools are available to quantify landscape resistance, these do not discern between two fundamentally different sources of resistance: movement behavior and mortality. To address this issue, we developed the samc R package that quantifies landscape connectivity using absorbing Markov chain theory. Within this mathematical framework, movements are represented as transient states in the Markov chain, while mortality is represented by transitions to absorbing states. Not only does this framework explicitly account for these different issues, it provides a probabilistic approach that can incorporate both short-term and long-term dynamics, as well as species distribution and abundance. The package includes functions to quantify life expectancy, long-term visitation rates, and various spatially and temporally explicit measures of mortality and movement at the local and landscape scales. These functions in samc have been optimized to find computationally practical solutions in landscapes comprised of > 2 × 10⁶ cells. Here, we illustrate the workflow of the samc package with publicly available movement and mortality data on the endangered Florida panther Puma concolor coryi. This analysis showed that movement and mortality are generally correlated except for locations near roads (areas of high mortality risk) that are within the dispersal range of source locations. This pattern would have been undetectable with current methods that quantify movement resistance. Overall, the samc package provides a means for implementing spatial absorbing Markov chains that can distinguish between movement behavior and mortality resulting in more reliable landscape connectivity measures.     

RAPD数据分析软件RAPDDIST V1.0的使用

介绍了RAPDDISTV1 0软件包中的 7个程序 ,并以已发表论文中的数据分析为例介绍了该软件程序的使用 ,目的是为使用此软件的同行提供一些帮助     

Taxonomic and Distributional Databases of Fishes in Taiwan

The fishes of Taiwan comprise total 2450 species in 250 families, about 1/10 of the world's fishes. Curatorial and distributional data of Taiwanese fish have been integrated into a database that can be accessed interactively on the Internet at http://fishdb.sinica.edu.tw. The database includes the following items: basic information and specimen photo of each species, distributional database, bibliographic database, curatorial database, inquiring system for Chinese fish names of the world fishes, and new version of erratum of Fishes of Taiwan. The above regional database of Taiwanese fishes provides hyperlinks to fish data for each species in the global fish data, FishBase, of ICLARM (http://www.fishbase.org). Through the collaboration with FishBase and other global networks for taxonomic purposes, like Species 2000, BioNet, or GBIF (Global Biodiversity Information Facilities), users in the world can also obtain updated data provided by Taiwan. We hope our experience with database establishment can be used as a model to help other countries to develop their own regional fish databases or even to build up databases of other groups of organisms. There should be one good approach for all people in the world for sharing complete and updated biodiversity information via the Internet.     

New features in the dendroTools R package: Bootstrapped and partial correlation coefficients for monthly and daily climate data

Climate-growth relationships are usually analysed using monthly climate data. The dendroTools R package also provides methodological approaches that enable climate-growth analysis for daily climate data. Such analysis reveals more complete climate signal patterns. In this article, new functions of the dendroTools R package are presented. Partial correlation coefficients are now implemented and can be used to calculate the strength of a linear relationship between two variables, while controlling for a third variable. Bootstrapped correlations can then be used to provide insights into the confidence intervals of statistical estimates. The calculation of partial and bootstrapped correlations is available for daily and monthly data. Finally, data transformation, S3 generic plotting and summary functions are also presented here.     

TURBOVEG,a comprehensive data base management system for vegetation data

Abstract. The computer software package TURBOVEG (for Microsoft® Windows®) was developed in The Netherlands for the processing of phytosociological data. This package comprises an easy‐to‐use data base management system. The data bank to be managed can be divided into several data bases which may consist of up to 100 000 relevés each. The program provides methods for input, import, selection, and export of relevés. In 1994, TURBOVEG was accepted as the standard computer package for the European Vegetation Survey. Currently it has been installed in more than 25 countries throughout Europe and overseas.     

Generation of synthetic data and experimental designs in evaluating interactions for association studies

Complex diseases, by definition, involve multiple factors, including gene-gene interactions and gene-environment interactions. Researchers commonly rely on simulated data to evaluate their approaches for detecting high-order interactions in disease gene mapping. A publicly available simulation program to generate samples involving complex genetic and environmental interactions is of great interest to the community. We have developed a software package named gs1.0, which has been widely used since its publication. In this article, we present an upgraded version gs2.0, which not only inherits its capacity to generate realistic genotype data but also provides great functionality and flexibility to simulate various interaction models. In addition to a standalone version, a user-friendly web server (http://cbc.case.edu/gs) has been set up to help users to build complex interaction models. Furthermore, by utilizing three three-locus models as an example, we have shown how realistic model parameters can be chosen in generating simulated data.     

Length–weight relationships of three freshwater cyprinid fish species from Chalakudy River,South Western Ghats,India

This paper provides length‐weight relationships (LWRs) for three freshwater cyprinid fish species: Barbodes carnaticus (Jerdon, 1849), Hypselobarbus kolus (Sykes, 1839) and Tor khudree (Sykes, 1839) from the Chalakduy River in South Western Ghats of India. Fish samples were collected on a monthly basis between April 2011 to March 2012 using gill nets of different mesh sizes (3.5–10 cm). LWRs for these three species had not been previously reported in FishBase.     

Length‐weight relationships of 19 freshwater fishes from the Daechung Reservoir in South Korea

The length‐weight relationships for nineteen freshwater fish species in the Daechung Reservoir, South Korea, were analyzed. LWR data for fourteen of these species were not yet listed in FishBase.     

Length–weight relationships of eight cyprinid fishes from the Geum River in South Korea

The length‐weight relationships for eight native freshwater fish species collected in the Geum River, South Korea, were analysed. LWR data for six of the species were not available in FishBase.