Body size and abundance relationship: an index of diversity for herbivores

It is evident to any biologist that small-bodied species within a given higher taxon (order, class, phylum, etc.) tend to be represented by more individuals. Hence small-bodied species are generally more abundant than large-bodied species. We analyzed large herbivore species data collected in Kenyan rangelands. An index of biological diversity derived from the negative relation between animal species body size and its local abundance is proposed. We compared the new index with species abundances at landscape scale (10 × 10 km) in individual districts, as well as in the combined regional data. The results show a consistently strong positive relation between the new diversity index and species abundances. The proposed diversity index has the advantage of incorporating information on species abundances without the need for time-consuming surveys.     

A comparison of univariate and multivariate numerical and graphical techniques for determining inter- and intraspecific feeding relationships in estuarine fish

The advantages and disadvantages of various numerical and graphical techniques for the analysis of inter- and intraspecific feeding relationships of fishes were examined. All methods have been cited in the literature since 1988. The index of preponderance, the resultant index and graphical methods proposed by Costello and Tokeshi were used to illustrate the relative importance of prey species to an individual fish species with no differentiation between size classes. Inter- and intraspecific competition and niche overlap were determined from multivariate analysis [the ordination technique, detrended correspondence analysis, cluster analysis by the Bray-Curtis equation, per cent overlap and two-way indicator species analysis (TWINSPAN)]. The identity of the prey organisms are not lost in the comparisons, and the value of this is determined through comparison with techniques such as Shannon-Wiener which obscure these data. The Shannon-Wiener diversity index was combined with an analysis of 'evenness' to refine the technique further to assess niche breadth, as was the Levins index. The study shows that to give an estimate of competition within the community, it is important to assess the data with respect to seasonal and temporal patterns using multivariate analysis.     

Detecting outliers in species distribution data

Aim

Species distribution data play a pivotal role in the study of ecology, evolution, biogeography and biodiversity conservation. Although large amounts of location data are available and accessible from public databases, data quality remains problematic. Of the potential sources of error, positional errors are critical for spatial applications, particularly where these errors place observations beyond the environmental or geographical range of species. These outliers need to be identified, checked and removed to improve data quality and minimize the impact on subsequent analyses. Manually checking all species records within large multispecies datasets is prohibitively costly. This work investigates algorithms that may assist in the efficient vetting of outliers in such large datasets.

Location

We used real, spatially explicit environmental data derived from the western part of Victoria, Australia, and simulated species distributions within this same region.

Methods

By adapting species distribution modelling (SDM), we developed a pseudo‐SDM approach for detecting outliers in species distribution data, which was implemented with random forest (RF) and support vector machine (SVM) resulting in two new methods: RF_pdSDM and SVM_pdSDM. Using virtual species, we compared eight existing multivariate outlier detection methods with these two new methods under various conditions.

Results

The two new methods based on the pseudo‐SDM approach had higher true skill statistic (TSS) values than other approaches, with TSS values always exceeding 0. More than 70% of the true outliers in datasets for species with a low and intermediate prevalence can be identified by checking 10% of the data points with the highest outlier scores.

Main conclusions

Pseudo‐SDM‐based methods were more effective than other outlier detection methods. However, this outlier detection procedure can only be considered as a screening tool, and putative outliers must be examined by experts to determine whether they are actual errors or important records within an inherently biased set of data.     

Assessing endemism at multiple spatial scales, with an example from the Australian vascular flora

Aim  To develop an approach for assessing the spatial scale of centres of endemism among species level data.
Location Australia.
Methods  Endemism is inherently scale dependent. Therefore, the Corrected Weighted Endemism (CWE) index used by Crisp et al. [ J. Biogeogr. (2001)28:183] is extended to account for species samples in local neighbourhoods as a Spatial CWE index. This then allows an analysis of how the degree of endemism of a location (cell) changes with spatial scale. The quality of the Spatial CWE index results are assessed using three spatial randomizations at the species level with and without preserving species richness and distributional patterns. We show that CWE is equivalent to beta diversity and predict that it should show high rates of change around centres of endemism.
Results  Similar patterns to those found by Crisp et al. using a data set of vascular flora from Australia are retrieved, but the extent to which they are scale dependent is more easily identified. For example, the Central Australian centre discounted by Crisp et al. is identified when a three-cell radius neighbourhood is used. However, the level of endemism in this centre is no greater than in the margins of many of the coastal centres of endemism. Most of the identified centres of endemism are better than random at all scales and are increasingly so as the spatial scale increases. As predicted, the highest rate of change in Spatial CWE (beta diversity) is most often between zero- and one-cell radius neighbours in most centres of endemism.
Main conclusions  The explicit incorporation of geographical space in analyses allows for a greater understanding of the scale-dependence of phenomena, in this case endemism and beta diversity.     

贵州兴义实蝇类昆虫多样性特征

【目的】掌握贵州兴义实蝇的种类组成和不同生境中的发生规律及多样性变化。【方法】2010-2011年,在贵州兴义 5个不同生境的监测点,采用性诱剂、食物引诱剂及被害瓜果培养法对实蝇类昆虫种类和数量进行了系统调查和监测,并对监测数据进行分析。【结果】贵州兴义实蝇优势种包括桔小实蝇 Bactrocera dorsalis (Hendel)、瓜实蝇 B. cucurbitae (Coquillett)、南瓜实蝇 B. tau (Walker)及具条实蝇 B. scutellata (Hendel),且不同年份各监测点实蝇优势种及相似性系数(0.33~0.89)存在差异;但其年种群动态相似。聚类分析结果显示,两个农村生境果园中实蝇种群关系最近,城市混合果园与其他生境果园中实蝇种群关系最远;各监测点的多样性指数在不同年份也不同,监测的2年间 Simpson 指数、Shannon 指数和均匀度指数分别在0.11~0.68、0.28~1.25和0.18~0.62之间。【结论】贵州兴义实蝇种类丰富,种群发生规律与气候、寄主、生态位竞争等因素有关;相近生境混合果园诱捕到的实蝇种数和数量大于单一果园;离城区越近,实蝇发生期越早,数量越大。研究结果为了解该地区实蝇种类分布以及预防实蝇危害提供了科学依据。     

Invasiveness and homogenization: synergism of wide dispersal and high local abundance

Aim To determine whether invasive and locally abundant non‐native species have a more homogenizing effect on plant communities than non‐invasive and less abundant non‐native species. Location California and Florida counties, conservation areas in the USA, and eight US cities. Methods Species lists among counties, conservation areas and cities were compared to see whether invasive and abundant non‐native species increased the Jaccard index of similarity between localities beyond any increases caused by non‐invasive and less abundant non‐native species. Results For all comparisons, we found that invasive non‐native species have a significantly greater homogenizing effect than non‐invasive non‐native species. For the US conservation areas, we found that locally abundant invasive species tend to be more widespread and more widely shared than less abundant invasive species. There is also a positive relationship between homogenization by invasive species and the magnitude of human disturbance. Main conclusions Invasive non‐native species tend to be disproportionately shared among communities relative to non‐invasive non‐native species. This effect is enhanced by human disturbance, as measured by the ratio of non‐native to native species. There is a synergism between abundance and geographical range which enhances the homogenizing effects of abundant species. Invasive species, with wide ecological niches, are more widely shared among communities and more locally abundant. Abundant invasive species are thus more spatially homogenizing, and more ecologically dominant (functionally homogenizing). Also, ‘perceived homogenization’ is probably greater than homogenization measured by the increase in shared species. The abundant species typically seen by the casual observer in a biological community are probably more commonly shared between communities than less common species. Studies that lack abundance data and measure homogenization only on the basis of shared species, which includes most homogenization studies to date, probably underestimate the homogenizing impacts of non‐native species as perceived by people.     

不同林龄桉树人工林林下物种多样性和生物量的动态变化

采用空间代替时间法和典型抽样法,以四川省威远县桉树(Eucalyptus robusta)人工林为研究对象,综合分析其林下植被物种组成及重要值、灌木层和草本层地上、地下和全株生物量以及物种多样性指数(Shannon-Wiener多样性指数H、Simpson优势度指数H′、丰富度指数D和Pielou均匀度指数JSW),探究林下植被的物种多样性和生物量在5个不同林龄(4,5,6,7,8年生)下的动态变化及二者之间的相关性。结果表明:调查到植物共有210种,隶属79科151属,草本层物种数多于灌木层。草本层的五节芒(Miscanthus floridulus)、芒萁(Dicranop?teris pedata)和灌木层的野牡丹(Melastoma malabathricum)、戟叶悬钩子(Rubus hastifolius)在不同林龄下都占据主要优势地位。随着林龄的增大,郁闭度加大,灌木层的D、H和H′值均表现为先增后减的规律;草本层D、H和H′值均呈先增后减再增再减的双峰趋势。草本层各生物量呈先增后减再增的变化趋势;灌木层各生物量呈先增后减的变化趋势。物种多样性与生物量呈显著正相关,草本层的D、H指数是影响生物量的直接因子。桉树人工林林下植被物种分布、组成、物种多样性和生物量对林龄变化的响应不同,表现为不同的动态特征规律,相关结果为我国西南地区桉树林管理提供了数据支撑。     

生物群落多样性的测度方法 V.生物群落物种数目的估计方法

群落的物种数目,即物种丰富度,是最古老、同时也是最基本的一个多样性概念,从对它的估计中可以得到关于物种灭绝速率方面的信息,这对生物多样性保护是非常重要的。已经提出了很多方法来估计群落中的物种数目,这些方法可以分为两大类,即基于理论抽样的方法和基于数据分析的方法。前者包括经典估计方法和贝叶斯估计方法;后者包括对数正态分布的积分方法、再抽样方法和种－面积曲线的外推方法。发现：（１）有些方法适用于动物群落,如大多数基于理论抽样的方法;有些方法则适用于植物群落,如大多数基于数据分析的方法;（２）这些方法还没有经过全面而系统地比较;（３）还没有一个普遍认为比较好的方法。因此,建议采用野外调查与模拟研究相结合的方法对各种估计方法进行系统地评价。     

塔里木河下游植物群落的物种数量变化与生态系统动态研究

物种多样性是指物种及其集合体的生物学多样性。物种多样性研究的核心是物种的数量变化和物种的生物学多样性程度。本文根据野外采集的数据 ,运用Simpson指数、McIn tosh指数以及Margalef指数 ,对塔里木河下游英苏、阿布达勒、喀尔达依、阿拉干、依干不及麻等地区的物种多样性指数分别进行了计算 ,并根据计算得到的生物多样性指数探讨了干旱区退化生态系统的物种多样性以及在干旱区物种多样性与生态系统稳定性之间的关系。结果表明 ,塔里木河下游从英苏至依干不及麻 ,Simpson多样性指数的变化范围为 0 82～ 0 2 6 ,McIn tosh均匀度指数的变化范围为 0 6 0～ 0 1 8,Margalef丰富度指数的变化范围为 1 4 7～ 0 38,物种数的变化范围是 9～ 2。分析表明塔里木河下游生态系统退化十分严重 ,并据此讨论了塔里木河下游生态系统退化的特征、演替动态及稳定性     

长江上游支流南广河的鱼类多样性及资源现状

南广河是长江上游一级支流, 为全面了解该河流的鱼类多样性, 作者于2017年11月至2018年9月在南广河干流及支流28个采样点进行了6次调查, 共采集鱼类64种, 隶属于5目13科48属, 其中四川省重点保护鱼类有鲈鲤(Percocypris pingi)和岩原鲤(Procypris rabaudi) 2种, 长江上游特有鱼类17种, 列入《中国脊椎动物红色名录》的濒危和易危的鱼类有9种。南广河现有分布鱼类以小型种类为主, 宽鳍鱲(Zacco platypus)和鲤(Cyprinus carpio)为优势种。南广河鱼类多样性总体较高, Margalef丰富度指数、Shannon-Wiener多样性指数、Simpson优势度指数及Pielou均匀度指数分别为6.57、3.10、0.93、0.74; 中游河段的鱼类种类和数量较丰富, 分别占渔获物总种类和总数量的65.63%和28.98%; 支流镇舟河的鱼类种类和数量也较丰富, 分别占37.50%和20.48%。南广河不同河段的鱼类种类组成具有明显差异, 大坝建设和过度捕捞可能影响了鱼类分布并导致其资源量下降。     

秦岭太白红杉群落特征及其物种多样性的研究

选择太白红杉群落分布集中的太白山、长安光头山、玉皇山和冰晶顶等4个地段,设计18个样地,用样方法进行调查,共作样方280个。分析了太白红杉群落的种类组成、区系特点、群落外貌、垂直结构和水平结构等群落学特征,并对该群落的环境概况进行分析,计划了不同地段上群落的频、盖度指标和不同层次上的Shannon-Wiener指数,Simpson指数、Pielou指数和种间相遇指数。结果表是,太白红杉主要分布于秦岭海拔2800－3500m的高海拔山地,群落组成种类约85种,北温带分布属占优势,地面芽植物种类多,数量大,是该群落的优质层片。乔木层为太白红杉单优组成,平均高度约8．6m,多样性指数0．207－0．420,灌木层H值为1．779－2．363,草本层H值最高,为2．122－3．025。本研究为太白红杉可持续利用和保护提供了有益的参考。     

石门台自然保护区蝴蝶特种多样性研究

1999年6月～2003年4月间,对广东石门台自然保护区的蝴蝶进行了调查,共记录到蝴蝶361种,分隶于11科190属。其中中国特有种51 种,占总数的14.1%;国家保护种10种,占我国两次颁布（1989和2000年）的保护物种名录中蝴蝶总数量（83种）的12.0%。通过以人工林生境为主的试验区、次生林生境为主的缓冲区和原生林生境为主的核心区等3个功能区中选择样点进行的蝴蝶多样性分析表明,缓冲区的物种多样性及科、属多样性均较高,且有众多的珍稀物种,是一个重要的蝴蝶生息地,应加强管制。进一步说明了保护蝶类的根本在于护林,进而为保护好广东省目前面积最大的自然保护区——石门台自然保护区的生物多样性及不可多得的自然遗产——热带亚热带低地森林提供依据。此外,本文将科、属多样性与物种多样性综合起来考虑,同时使用Shannon-Wiener指数与G-F指数,较为全面地评价了该保护区蝴蝶的群落多样性。     

基于无人机多源遥感数据的亚热带森林树种分类

树种多样性是生态学研究的重要内容,树木的种类和空间分布信息可有效服务于可持续森林管理。但在复杂林分条件下,获取高精度分类结果的难度大。而无人机遥感可获取局域超精细数据,为树种分类精度的提高提供了可能。基于可见光、高光谱、激光雷达等多源无人机遥感数据,探究其在亚热带林分条件下的树种分类潜力。研究发现:(1)随机森林分类器总体精度和各树种的F1分数最高,适合亚热带多树种的分类制图,其区分13种类别(8乔木,4草本)的总体精度为95.63%,Kappa系数为0.948;(2)多源数据的使用可以显著提高分类精度,全特征模型精度最高,且高光谱和激光雷达数据显著影响全特征模型分类精度,可见光纹理数据作用较小;(3)分类特征重要性从大到小排序为结构信息,植被指数,纹理信息,最小噪声变换分量。     

Assessing the risk of freshwater fish introductions into the Iberian Peninsula

1. Preventing the introduction of species likely to become invaders is the best management option to deal with biological invasions. A data set consisting of native, introduced and species not currently present in Iberian Peninsula (n = 167 species) was used to identify freshwater fish species that are likely to be introduced and become successful invaders in the near future. 2. Principal component analysis (PCA) of species traits was used to determine species likely to be introduced, assuming that the traits of species introduced in the future will resemble those of previously introduced species. The likelihood of introduction was calculated as the proportion of neighbour species (in the space defined by the PCA) that have been introduced to the Iberian Peninsula and, together with metrics related to different stages of invasion, was used to construct a region‐specific risk index (Iberian risk index). 3. Introduced species had higher index values compared with native species or species currently absent from the region. The Iberian risk index was positively related to the results of an independent risk analysis for freshwater fish as well as to the geographical spread of species previously introduced to the Iberian Peninsula. 4. Iberian risk index values were used to establish a cut‐off value for estimating the probability of a successful invasion. This threshold value was used to construct a list of 20 species to be included in a ‘watch list’ to prevent freshwater fish invasions in the Iberian Peninsula.     

海南五指山热带山地雨林植物物种多样性研究

王指山热带山地雨林的物种种类十分丰富,在１ｈｍ＾２样地中共出现５４个科,１００个属的乔木树种１７７种,１３３７个个体。区系地理分析表明属的分布区类型以热带分布型成分占优,为８９．０％,充分体现了五指山山地雨林的热带性质。多样性指数分析结果为：样地１Ｍａｒｇａｌｅｆ指数１７．８２２,Ｓｈａｎｎｏｎ－Ｗｉｅｎｅｒ指数５．６２１,均匀度０．８２３,Ｓｉｍｐｓｏｎ指数０．０５０,均匀度６．７７５,表明五指     

“Forms” of water mites (Acari: Hydrachnidia): intraspecific variation or valid species?

In many groups of organisms, especially in the older literature, it has been common practice to recognize sympatrically occurring phenotypic variants of a species as “forms”. However, what these forms really represent often remains unclear, especially in poorly studied groups. With new algorithms for DNA‐based species delimitation, the status of forms can be explicitly tested with molecular data. In this study, we test a number of what is now recognized as valid species of water mites (Hydrachnidia), but have in the past been treated as forms sympatrically occurring with their nominate species. We also test a form without prior taxonomical status, using DNA and morphometrics. The barcoding fragment of COI, nuclear 28S and quantitative analyses of morphological data were used to test whether these taxa merit species status, as suggested by several taxonomists. Our results confirm valid species. Genetic distances between the form and nominate species (Piona dispersa and Piona variabilis, COI 11%), as well as likelihood ratio tests under the general mixed‐Yule coalescent model, supported that these are separately evolving lineages as defined by the unified species concept. In addition, they can be diagnosed with morphological characters. The study also reveals that some taxa genetically represent more than one species. We propose that P. dispersa are recognized as valid taxa at the species level. Unionicola minor (which may consist of several species), Piona stjordalensis, P. imminuta s. lat., and P. rotundoides are confirmed as species using this model. The results also imply that future studies of other water mite species complexes are likely to reveal many more genetically and morphologically distinct species.     

occAssess: An R package for assessing potential biases in species occurrence data

Species occurrence records from a variety of sources are increasingly aggregated into heterogeneous databases and made available to ecologists for immediate analytical use. However, these data are typically biased, i.e. they are not a probability sample of the target population of interest, meaning that the information they provide may not be an accurate reflection of reality. It is therefore crucial that species occurrence data are properly scrutinised before they are used for research. In this article, we introduce occAssess, an R package that enables straightforward screening of species occurrence data for potential biases. The package contains a number of discrete functions, each of which returns a measure of the potential for bias in one or more of the taxonomic, temporal, spatial, and environmental dimensions. Users can opt to provide a set of time periods into which the data will be split; in this case separate outputs will be provided for each period, making the package particularly useful for assessing the suitability of a dataset for estimating temporal trends in species'' distributions. The outputs are provided visually (as ggplot2 objects) and do not include a formal recommendation as to whether data are of sufficient quality for any given inferential use. Instead, they should be used as ancillary information and viewed in the context of the question that is being asked, and the methods that are being used to answer it. We demonstrate the utility of occAssess by applying it to data on two key pollinator taxa in South America: leaf‐nosed bats (Phyllostomidae) and hoverflies (Syrphidae). In this worked example, we briefly assess the degree to which various aspects of data coverage appear to have changed over time. We then discuss additional applications of the package, highlight its limitations, and point to future development opportunities.     

Rapid assessment in conservation research: a critique of avifaunal assessment techniques illustrated by Ecuadorian and Madagascan case study data

The urgency of conservation concerns in the tropics, linked with the limitations imposed on research efforts by the tropical environment has resulted in the development of methods for rapid assessment of biological communities. One such method, the MacKinnon list technique, has been increasingly applied in avifaunal surveys worldwide. Using paired tropical bird data sets from Ecuadorian cloud forest and Madagascan littoral forest, we compare the performance of the MacKinnon list with that of the more standard method of point counts in indicating when a site has been adequately surveyed, estimating the magnitude of species richness, quantifying relative species abundance, and providing an α‐index of diversity. In species‐rich Ecuadorian cloud forest, neither method produced data indicating adequate survey effort, despite extensive sampling, whereas in the relatively species‐poor Madagascan littoral forests, data collected by both methods indicated that the area had been sufficiently surveyed with comparable sampling effort. Species richness estimates generated from MacKinnon list data provided a more accurate estimate of the magnitude of the species richness for the Ecuadorian avifauna, whereas estimates for the Madagascan avifauna stabilised with relatively few samples using either method. Data collected by each method reflected different patterns of relative abundance among the five most abundant species, with MacKinnon list data showing a bias towards solitary and territorial species and against monospecific flocking species relative to the point count data. As a consequence of this bias, MacKinnon list data also fail to reflect accurately the structure of communities as quantified by an index of community evenness. Point counts, on the other hand, failed to capture the full species complement of the species‐rich Ecuadorian study area. As techniques for the rapid assessment of unsurveyed areas, both methods are subject to biases that limit their value, if used alone, in collecting data of scientific and management value. We propose a hybrid rapid assessment methodology that capitalises on the strengths of both techniques while compensating for their weaknesses.     

Changes in fish assemblages in catchments in north‐eastern Spain: biodiversity,conservation status and introduced species

1. North‐eastern Spain is a hot spot for the introduction of alien fish species, and its native fish fauna is one of the most endangered worldwide. We used an extensive data set from 2002 to 2003 and historical information from the area to characterize fish diversity and establish conservation priorities in river catchments. 2. Diversity indices were used to characterize fish diversity at the basin scale. An index of conservation status was applied for each species, which considers the occurrence, abundance and endemicity of each taxon. We used indirect ordination methods to test the relationship among basin features and to identify those variables most correlated with each other. To identify physical, biotic and environmental characteristics that seem to make a basin particularly susceptible to invasion, we performed a step‐wise multiple regression to examine the relationship between the number of native, translocated and introduced fish species (including the original native species richness of each basin), and landscape variables. 3. Over a period of approximately 50 years, the mean range size of native fish species has decreased by 60%. The greatest decline occurred in Gasterosteus gymnurus, Anguilla anguilla and Salaria fluviatilis, for which species over 75% of the original distribution area has been lost. The species with the highest conservation index were Gasterosteus gymnurus and Salaria fluviatilis. 4. Basin area and the catchment type explained 70% of variation in native species richness, whereas the number of dams and basin area accounted for more than 80% of variation in the number of introduced species. 5. The original native species richness and the number of introduced species at basin scale were not related, and thus there was no evidence of “biotic resistance” to invasion. The restoration of natural hydrologic processes and the development of specific management tools to protect native species, such as the prioritization of areas for fish conservation and the eradication of local populations of exotic species, are required to restore native fish fauna in these catchments.