Dealing with many correlated covariates in capture–recapture models

Capture–recapture models for estimating demographic parameters allow covariates to be incorporated to better understand population dynamics. However, high-dimensionality and multicollinearity can hamper estimation and inference. Principal component analysis is incorporated within capture–recapture models and used to reduce the number of predictors into uncorrelated synthetic new variables. Principal components are selected by sequentially assessing their statistical significance. We provide an example on seabird survival to illustrate our approach. Our method requires standard statistical tools, which permits an efficient and easy implementation using standard software.     

A cautionary note on the use of hypervolume kernel density estimators in ecological niche modelling

Blonder et al. ( 2014 , Global Ecology and Biogeography, 23, 595–609) introduced a new multivariate kernel density estimation (KDE) method to infer Hutchinsonian hypervolumes in the modelling of ecological niches. The authors argued that their KDE method matches or outperforms several methods for estimating hypervolume geometries and for conducting species distribution modelling. Further clarification, however, is appropriate with respect to the assumptions and limitations of KDE as a method for species distribution modelling. Using virtual species and controlled environmental scenarios, we show that KDE both under‐ and overestimates niche volumes depending on the dimensionality of the dataset and the number of occurrence records considered. We suggest that KDE may be a viable approach when dealing with large sample sizes, limited sampling bias and only a few environmental dimensions.     

基于叶绿体DNA atpB-rbcL片段的典型樱亚属部分种的亲缘关系及分类地位探讨

蔷薇科典型樱亚属植物（Subg.Cerasus Koehne）（樱花类）具有重要的观赏价值,深入研究其种间亲缘关系及分类地位,对于国产樱属植物系统发育与种质资源创新具有重要的理论指导意义。基于PCR扩增与测序技术研究了从云南、江西、福建采集的典型樱亚属3个种（含变种）的叶绿体DNA非编码区atpB-rbcL片段,结合GenBank数据库已经提交的其它4个种的同源序列,共获得7个种的30条序列矩阵,以此构建了单倍型中介网络图与系统发育树,分析和探讨了它们的亲缘关系与分类地位。（1）在atpB-rbcL序列矩阵中,774个有效位点中共发现15个多态性位点,占分析序列的1.94%,（A+T）含量为70.50%,存在明显的碱基偏好;（2）DNASP 5共检测到9个单倍型,物种间平均单倍型多样性（H_d=0.880 5±0.026）,平均核苷酸多态性（π=0.007 11±0.000 54）,除尾叶樱桃（Prunus dielsiana）外（Hap5~Hap7）,其余物种拥有各自独特的1个单倍型,具有较丰富的遗传多样性;（3）综合Network中介图与系统发育重建结果：推测磐安樱桃（P.pananensis）处于较原始的进化阶段,相比尾叶樱桃,与浙闽樱桃（P.schneideriana）亲缘关系较近;长柱尾叶樱桃（P.dielsiana var.longistyla）与尾叶樱桃互为姊妹支,并共同构成独立进化单元。综上,叶绿体atpB-rbcL片段在典型樱亚属下种间的适用效果较好,可以优先选为DNA条形码;分子证据结合形态学特征支持将长柱尾叶樱桃作为尾叶樱桃变种的处理意见,而磐安樱桃的分类地位则需要更多的证据。     

大气校正对毛竹林生物量遥感估算的影响

基于Landsat TM影像对毛竹林生物量进行了估算,并利用6种大气校正方法(FLAASH、6S、DOS1～DOS4)分析了大气校正对毛竹林生物量遥感估算的影响.结果表明：6种大气校正模型均能有效地消除大气影响;不同大气校正模型校正后,归一化植被指数(NDVI)与毛竹林生物量之间的关系得到很好改善;对于同一种大气校正方法而言,NDVI、红外指数（II）和近红外指数（MI）与生物量之间关系的差异较大,说明在探讨植被指数的生物物理意义时必须进行大气校正;与其他5种模型相比,DOS3模型校正后的Landsat TM数据与毛竹林生物量之间具有最高的相关系数,但6种校正模型校正前后Landsat TM数据与毛竹林生物量之间的相关系数没有显著差异,说明采用单一时相遥感影像建立多元线性回归模型估算生物量时,可以不进行大气校正.     

Historic distribution and driving factors of human-caused fires in the Chinese boreal forest between 1972 and 2005

Aims The pattern and driving factors of forest fires are of interest for fire occurrence prediction and forest fire management. The aims of the study were: (i) to describe the history of human-caused fires by season and size of burned area over time; (ii) to identify the spatial patterns of human-caused fires and test for the existence of 'hotspots' to determine their exact locations in the Daxing'an Mountains; (iii) to determine the driving factors that determine the spatial distribution and the possibility of human-caused fire occurrence.Methods In this study, K -function and Kernel density estimation were used to analyze the spatial pattern of human-caused fires. The analysis was conducted in S-plus and ArcGIS environments, respectively. The analysis of driving factors was performed in SPSS 19.0 based on a logistic regression model. The variables used to identify factors that influence fire occurrence included vegetation types, meteorological conditions, socioeconomic factors, topography and infrastructure factors, which were extracted and collected through the spatial analysis mode of ArcGIS and from official statistics, respectively.Important findings The annual number of human-caused fires and the area burnt have declined since 1987 due to the implementation of a forest fire protection act. There were significant spatial heterogeneity and seasonal variations in the distribution of human-caused fires in the Daxing'an Mountains. The heterogeneity was caused by elevation, distance to the nearest railway, forest type and temperature. A logistic regression model was developed to predict the likelihood of human-caused fire occurrence in the Daxing'an Mountains; its global accuracy attained 64.8%. The model was thus comparable to other relevant studies.     

Retrospective Estimation of Genetic Diversity of an Extinct Oriental White Stork (Ciconia boyciana) Population in Japan Using Mounted Specimens and Implications for Reintroduction Programs

The Japanese regional population of the Oriental white stork (Ciconia boyciana) became extinct in 1986. Mitochondrial DNA (mtDNA) D-loop region from 20 mounted specimens preserved at public facilities in Toyooka City, Hyogo Prefecture, Japan and its vicinity (n = 17), the area inhabited by the last of the Japanese population, and samples originating from China (n = 3) which were kept at a zoo was analyzed. After extracting DNA from small pieces of skin from mounted specimens, a 1210-bp region of the mtDNA D-loop region was analyzed. The haplotypes among 11 specimens of storks captured or found dead at Toyooka City just before the population became extinct were completely identical. Four haplotypes observed among the mounted specimens preserved in the vicinity of Toyooka City were differentiated from those of captive storks originating from China and Russia in a previous study. Therefore, the last Japanese population might have been a genetically unique group. However, phylogenetic analysis using the maximum likelihood method showed that haplotypes found in the Japanese regional population were closely related to the Chinese and Russian lineages (sequence difference = 2.1%). One mounted specimen collected in 1935 at Izushi village, in the vicinity of Toyooka City, showed the same haplotype as the captive storks from China, suggesting that genetic flow may have historically occurred between the populations of Japan and the continent. Recently, reintroduction for the Oriental white stork has been planned in Toyooka City. The planning for the recovery of extinct populations should not only involve translocation of species to the range from which it disappeared, but also reconstruction of regional populations while considering the genetic lineage between the extinct and introduced populations.     

Interference of Thiomersal in Biologicals During Protein Estimation

In the present report thiomersal was detected as interfering substance in hepatitis B vaccines during the total protein estimation by Lowry's protein assay. The thiomersal at different concentrations of 0.005%, 0.0075%, 0.01%, 0.02%, 0.05% and 0.1% was found to reduce the Folin Ciocalteu's phenol reagent and produce colour development between 0.024 O.D to 1.023 O.D. values. Further, the thiomersal was shown to interfere between 34.55% to 52.73% with Folin Ciocalteu's phenol reagent, when 10 batches of different hepatitis B vaccines were subjected to estimation of total protein content by Lowry's protein assay.     

Estimation of the Consumption of Nekton and Plankton by the Minke Whale Balaenoptera acutorostrata

This is a review of the data available on the population subdivision and life cycle of the Minke whale, the most abundant whalebone whale in the World Ocean. Different methods of estimation and calculation of the rate of food consumption by this species, the latter including those developed for the Sea of Okhotsk, are compared.