Bias in freshwater biodiversity sampling: the case of Iberian water beetles

Extensive distributional data bases are key tools in ecological research, and good-quality data are required to provide reliable conservation strategies and an understanding of biodiversity patterns and processes. Although the evaluation of data bases requires the incorporation of estimates of sampling effort and bias, no studies have focused on these aspects for freshwater biodiversity data. We used here a comprehensive data base of water beetles from the Iberian Peninsula and the Balearic Islands, and examine whether these data provide an unbiased, reliable picture of their diversity and distribution in the study area. Based on theoretical estimates using the Clench function on the accumulated number of records as a surrogate of sampling effort, about a quarter of the Iberian and Balearic 50 × 50 km Universal Transverse Mercator grid cells can be considered well prospected, with more than 70% of the theoretical species richness actually recorded. These well-surveyed cells are not evenly distributed across biogeographical and physicoclimatic subregions, reflecting some geographical bias in the distribution of sampling effort. Our results suggest that recording was skewed by relatively simple variables affecting collector activity, such as the perceived 'attractiveness' of mountainous landscapes and protected areas with recently described species, and accessibility of sampling sites (distance from main research centres). We emphasize the importance of these evaluation exercises, which are useful to locate areas needed of further sampling as well as to identify potential biases in the distribution of current biodiversity patterns.     

Variable reporting and quantitative reviews: a comparison of three meta-analytical techniques

Variable reporting of results can influence quantitative reviews by limiting the number of studies for analysis, and thereby influencing both the type of analysis and the scope of the review. We performed a Monte Carlo simulation to determine statistical errors for three meta‐analytical approaches and related how such errors were affected by numbers of constituent studies. Hedges’d and effect sizes based on item response theory (IRT) had similarly improved error rates with increasing numbers of studies when there was no true effect, but IRT was conservative when there was a true effect. Log response ratio had low precision for detecting null effects as a result of overestimation of effect sizes, but high ability to detect true effects, largely irrespective of number of studies. Traditional meta‐analysis based on Hedges’d are preferred; however, quantitative reviews should use various methods in concert to improve representation and inferences from summaries of published data.     

On comparison of mixture models for closed population capture-recapture studies

Summary .  A mixture model is a natural choice to deal with individual heterogeneity in capture–recapture studies. Pledger (2000, Biometrics 56, 434–442; 2005, Biometrics 61, 868–876) advertised the use of the two-point mixture model. Dorazio and Royle (2003, Biometrics 59, 351–364; 2005, Biometrics 61, 874–876) suggested that the beta-binomial model has advantages. The controversy is related to the nonidentifiability of the population size ( Link, 2003 , Biometrics 59, 1123–1130) and certain boundary problems. The total bias is decomposed into an intrinsic bias, an approximation bias, and an estimation bias. We propose to assess the approximation bias, the estimation bias, and the variance, with the intrinsic bias excluded when comparing different estimators. The boundary problems in both models and their impacts are investigated. Real epidemiological and ecological examples are analyzed.     

Biometric sex discrimination is unreliable when sexual dimorphism varies within and between years: an example in Eurasian Oystercatchers Haematopus ostralegus

Molecular sexing of birds has been possible for over a decade, but for practical reasons many studies still use biometric data for sex discrimination. In some species, the sexes are easy to distinguish but sexual dimorphism is often more subtle, requiring the use of statistical analyses of biometric measurements to discriminate sexes. These models are usually parameterized and validated using data from a limited number of sites and years. However, the resulting discriminant functions are often applied to other populations and periods. A crucial, but usually untested, assumption is that sexual dimorphism does not vary in time and space. Here we illustrate the consequences of violation of this assumption in Eurasian Oystercatchers Haematopus ostralegus , a species for which most studies have relied on biometric sexing. Using biometric data from captures of known-sex birds, we show that sexual dimorphism varied substantially in time and even reversed in some months and years. Furthermore, some biometric traits used in sexing changed gradually over time, causing a reduction in sexual dimorphism. We show that the consequences of this variation on sex discrimination in Oystercatchers are subtle and easily overlooked, but can result in inaccurate and strongly male- or female-biased sex-ratio estimates. We recommend that biometric sexing should be avoided in Oystercatchers unless specific calibration for each month, year and area is carried out. This recommendation also applies to other species where biometric traits may depend on environmental conditions. We argue that this condition might apply to many bird species and therefore advise caution when interpreting results based on biometric sex discrimination.     

果蝇Drosophila saltans种亚组(双翅目:果蝇科)系统发育关系:形态学能否解决分子冲突?(英文)

正确的系统发生重建对于理解进化事件至关重要。尽管分子系统学对于解决此类问题取得了极大的成功,由于一些诸如密码子使用偏性等的内在约束,来源于DNA的信息可能仍然存在着局限。因为发生在祖先的替代性转换,果蝇Drosophila saltans 5个种亚组由不同基因构建的分子系统树之间存在着冲突（在以往发表的分子系统学研究中,这些种组的每一个种亚组至少有一个代表）。本文用40个形态学特征重新分析了这些种组。不同于以前发表的大多数假说,本研究支序分类学的结果表明,果蝇sturtevanti种亚组是一个较早的分支, 而剩下的4个亚组形成一个支持度较高的类群;后者又可以再分为两个姐妹群：一个包含cordata 和elliptica 亚组,另一个包含parasaltans和saltans亚组。本研究结果修正了果蝇saltans种组的分子进化（密码子使用偏性）,并强调形态学对于系统发生重建和理解分子进化现象的重要作用。     

基于结构信息的蛋白质相互作用规律的研究

蛋白质-蛋白质相互作用是蛋白质发挥其功能的重要途径之一。作者基于相互作用蛋白质数据库、基因本体数据库和蛋白质结构分类数据库（structural classification of proteins, SCOP）,结合SWISS-PROT等相关数据库中蛋白质功能注释信息,定义描述蛋白质相互作用倾向性的参数,对酿酒酵母定位于不同细胞器蛋白、部分膜蛋白,以及酿酒酵母、线虫和大肠杆菌按SCOP分类的不同结构类蛋白质之间相互作用规律进行研究。结果表明各种细胞器、膜和结构类蛋白质之间相互作用确实存在明显的偏向性。     

A new cost‐distance model for human accessibility and an evaluation of accessibility bias in permanent vegetation plots in Great Smoky Mountains National Park,USA

Question: Can a new cost‐distance model help us to evaluate the potential for accessibility bias in ecological observations? How much accessibility bias is present in the vegetation monitoring plots accumulated over the last three decades in Great Smoky Mountains National Park? Location: Great Smoky Mountains National Park, North Carolina and Tennessee, USA. Methods: Distance, slope, stream crossings, and vegetation density were incorporated into a least‐cost model of energetic expenditure for human access to locations. Results: Estimated round‐trip energy costs for the park ranged from 0 to 1.62 × 10⁵ J kg^?1. The estimated round‐trip energetic expenditure for the surveys ranged from 53 to 1.51 × 10⁵ J kg^?1. Their distribution was more accessible than the random expectation. Ten (17%) of the vegetation types in the park are significantly under‐sampled relative to their area, and 16 (29%) are over‐sampled. Plots in 18 of the 40 vegetation types exhibited a significant positive correlation with accessibility. Conclusions: The least‐cost model is an improvement over previous attempts to quantify accessibility. The bias in plot locations suggests using a least‐cost model to test for bias in cases in which human accessibility is confounded with other sources of ecosystem variation.     

Evolutionary rate variation in Old World monkeys

We analysed over 8 million base pairs of bacterial artificial chromosome-based sequence alignments of four Old World monkeys and the human genome. Our findings are as follows. (i) Genomic divergences among several Old World monkeys mirror those between well-studied hominoids. (ii) The X-chromosome evolves slower than autosomes, in accord with ‘male-driven evolution’. However, the degree of male mutation bias is lower in Old World monkeys than in hominoids. (iii) Evolutionary rates vary significantly between lineages. The baboon branch shows a particularly slow molecular evolution. Thus, lineage-specific evolutionary rate variation is a common theme of primate genome evolution. (iv) In contrast to the overall pattern, mutations originating from DNA methylation exhibit little variation between lineages. Our study illustrates the potential of primates as a model system to investigate genome evolution, in particular to elucidate molecular mechanisms of substitution rate variation.     

Deficiency in African plant distribution data – missing pieces of the puzzle

Biodiversity is spatially unevenly distributed and so is the information on its spatial patterns. This uneven distribution of information on species occurrences is an important impediment to the conservation of biodiversity. Based on 185 427 collection records of 5873 plant species in sub-Saharan Africa, we analyse the availability of distribution data suitable for the GIS-based mapping of plant diversity patterns at a one-degree resolution. Using the bioclimatic model GARP, distribution ranges for each species were modelled. In order to identify data-deficient areas, the documented and modelled diversity patterns were compared. Only for a few, well-known centres of plant diversity are there comparatively many data collection records available. For several of the areas with very few collection records, such as the Guinean montane forests, the north-western Congolian lowland forests, and the southern Albertine Rift montane forests, the model predicts a species richness much higher than currently documented. In many of the data deficient areas, difficult conditions for scientific research appear to have limited collection activities for decades. Only strategic field collections can fill these gaps. Another cause of data deficiency is that data collected and digitized do not match the quality requirements for GIS-based work at the super-regional scale. In particular, regional databases documenting partial ranges of species are rarely connected. One challenge for the Global Strategy for Plant Conservation is therefore to establish international collaborative structures and technical standards that will allow analysis of biogeographical patterns across political boundaries.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 355–368.