Conservation biology of Malagasy strepsirhines: a phylogenetic approach

The phylogenetic diversity of extant lemurs represents one of the most important but least studied aspects of the conservation biology of primates. The phylogenetic diversity of a species is inversely proportional to the relative number and closeness of its phylogenetic relatives. Phylogenetic diversity can then be used to determine conservation priorities for specific biogeographic regions. Although Malagasy strepsirhines represent the highest phylogenetic diversity among primates at the global level, there are few phylogenetic data on species-specific and regional conservation plans for lemurs in Madagascar. Therefore, in this paper the following questions are addressed for extant lemurs: 1) how does the measure of taxonomic uniqueness used by Mittermeier et al. (1992 Lemurs of Madagascar; Gland, Switzerland: IUCN) equate with an index of phylogenetic diversity, 2) what are the regional conservation priorities based on analyses of phylogenetic diversity in extant lemurs, and 3) what conservation recommendations can be made based on analyses of phylogenetic diversity in lemurs? Taxonomic endemicity standardized weight (TESW) indices of phylogenetic diversity were used to determine the evolutionary component of biodiversity and to prioritize regions for conserving lemur taxa. TESW refers to the standardization of phylogenetic diversity indices for widespread taxa and endemicity of species. The phylogenetic data came from recent genetic studies of Malagasy strepsirhines at the species level. Lemur species were assigned as being either present or absent in six biogeographic regions. TESW indices were combined with data on lemur complementarity and protected areas to assign conservation priorities at the regional level. Although there were no overall differences between taxonomic ranks and phylogenetic rankings, there were significant differences for the top-ranked taxa. The phylogenetic component of lemur diversity is greatest for Daubentonia madagascariensis, Allocebus trichotis, Lepilemur septentrionalis, Indri indri, and Mirza coquereli. Regional conservation priorities are highest for lemurs that range into northeast humid forests and western dry forests. Expansion of existing protected areas in these regions may provide the most rapid method for preserving lemurs. In the long term, new protected areas must be created because there are lemur species that: 1) are not found in existing protected areas, 2) exist only in one or two protected areas, and 3) are still being discovered outside the current network of protected areas. Data on the population dynamics and feeding ecology of phylogenetically important species are needed to ensure that protected areas adequately conserve lemur populations in Madagascar.     

An assessment of the hypervariable domains of the 16S rRNA genes for their value in determining microbial community diversity: the paradox of traditional ecological indices

Amplicon length heterogeneity PCR (LH-PCR) was investigated for its ability to distinguish between microbial community patterns from the same soil type under different land management practices. Natural sagebrush and irrigated mouldboard-ploughed soils from Idaho were queried as to which hypervariable domains, or combinations of 16S rRNA gene domains, were the best molecular markers. Using standard ecological indices to measure richness, diversity and evenness, the combination of three domains, V1, V3 and V1+V2, or the combined V1 and V3 domains were the markers that could best distinguish the undisturbed natural sagebrush communities from the mouldboard-ploughed microbial communities. Bray-Curtis similarity and multidimensional scaling were found to be better metrics to ordinate and cluster the LH-PCR community profiling data. The use/misuse of traditional ecological indices such as diversity and evenness to study microbial community profiles will remain a major point to consider when performing metagenomic studies.     

红火蚁对新入侵龙眼园和荒草地蚂蚁类群多样性的影响

于2007年7月至2008年2月期间在增城龙眼园及周边的荒草地人工移殖1蚁巢及10蚁巢红火蚁,并采用陷阱法和诱饵诱集法调查研究红火蚁对新入侵龙眼园区和荒草地区蚂蚁类群多样性的影响。结果表明,在荫蔽、少干扰的龙眼园和杂草茂密、少干扰的未割草区,红火蚁难以成功定殖,对这两种生境蚂蚁类群的多样性几乎没有影响;在红火蚁成功定殖的1蚁巢割草区和10蚁巢割草区,红火蚁以这两种密度入侵对蚂蚁类群多样性的影响程度不同。在1蚁巢割草区,红火蚁入侵后5个月期间,由于其数量占蚂蚁个体总数的比例很少,对蚂蚁类群多样性的影响很小;在红火蚁成功定殖5个月后,第6—7个月其工蚁所占比例增加,蚂蚁类群个体数和优势度下降,多样性和均匀度增加;第8—9个月其工蚁所占比例继续增加,而蚂蚁个体数、多样性和均匀度下降,优势度增加。在10蚁巢割草区,红火蚁入侵后,蚂蚁类群个体数、多样性和均匀度下降,优势度增加。红火蚁入侵对1蚁巢割草区和10蚁巢割草区蚂蚁物种数的影响较小。     

Integrating phylogenetic and functional biodiversity facets to guide conservation: a case study using anurans in a global biodiversity hotspot

The Cerrado is one of the most threatened biomes in Brazil, with little spatial representation within the Protected Area network. Recently, proposed conservation plans worldwide have advocated for the use of multiple biodiversity facets to protect unique evolutionary and functional processes. Our aim was to identify areas with high biodiversity representativeness applying this multifaceted perspective, and propose conservation plans based on the joint analysis of taxonomic, functional and phylogenetic diversity. We used a database of the Brazilian National Program for Research in Biodiversity, which employs a standard protocol for sampling tadpoles. The Cerrado database includes samples from 165 water bodies spread over 15 localities, covering most of the Central Brazilian Cerrado. We selected four morphological traits to calculate functional diversity and used a dated phylogeny available in the literature to compute phylogenetic diversity. Our approach selected five priority areas for conservation, one of which is already protected. Our results highlighted the importance of four new areas which show high values of diversity, including original lineages and traits, and urgently need conservation prioritization. Furthermore, unlike the current protected network, our approach performs significantly better than random at protecting sites with high phylogenetic and functional diversity. We therefore discuss how the multifaceted indices considered can help protect key ecosystem functions and evolutionary legacy in anuran communities of the Brazilian Cerrado.     

Phylogenetic measures of biodiversity uncover pteridophyte centres of diversity and hotspots in Tuscany

Biodiversity studies traditionally use species as their analysis unit. However, observed biodiversity is not necessarily an indicator of significant biodiversity and therefore, should not be used alone, particularly when the results will be employed for conservation planning. Here, we examine pteridophyte diversity in Tuscany using 4668 geo-referenced pteridophyte records stored in Wikiplantbase #Toscana and calculating standard richness measures and phylogenetic indices; in addition, we assessed the environmental predictors of each diversity metric. Finally, we identified which areas hosting significantly high diversity are not adequately covered by protected areas or intersected by human activities. Although considerable diversity is distributed along Tuscany within areas traditionally recognised as biodiversity hotspots, important areas of diversity are identified only after the application of randomisation tests and through the phylogenetic metrics. Topographic ruggedness resulted the single most important variable predicting high value of all indices; temperature seasonality and temperature continentality resulted the secondary explanatory variables with a significant negative effect on most diversity indices.     

Earthworm communities a bioindicator of arable land management practices: A case study in semiarid region of India

The abundances and activities of earthworms in arable lands depend strongly on management practices and; therefore earthworm can act as a potential bioindicator of land use practices. In this study earthworm diversity and abundances was measured in three differently managed agro-ecosystems i.e. conventional, integrated and organic, in some sites of northern semiarid region of India. The maximal numbers of earthworm occurrence were in integrated farming system (100%, all studied sites showed the presence) followed by organically managed (70%) and conventional (18.9%) agro-ecosystems. A total of six species belonging to four different families were identified during this survey and all recorded earthworm species were present in organically managed agro-ecosystems, while integrated and conventional arable lands exhibited only three earthworm species. The abundance of earthworms in arable system was also directly related to the management practices. The values of ecological indices e.g. Shannon diversity (H′), species dominance (C), the species richness (S) and evenness (E) indicated the anthropogenic pressure on earthworm communities in arable lands of northern India.     

半干旱黄土区不同管理措施下草地群落结构对短期氮、水添加的响应

氮沉降和降水变异显著影响草地群落结构和功能,但缺乏对不同管理措施下草地群落结构对氮沉降和降水变异响应的研究。为模拟不同管理措施下草地群落结构对氮沉降和降水变异的响应特征,以半干旱黄土区云雾山国家自然保护区典型草原为研究对象,系统分析了在封育、刈割和火烧三种管理措施下,氮添加和水添加对群落地上生物量、功能群组成和群落多样性的影响。结果表明,氮添加和水添加对地上生物量、功能群组成和群落多样性指数的影响因管理措施不同有所差异。（1）在封育草地上,氮添加显著降低物种多样性,对地上生物量影响较小;水添加显著增加物种多样性指数,氮添加和水添加的交互作用显著增加地上生物量、禾本科所占比例和莎草科所占比例;物种多样性指数均与地上生物量无显著相关,与不同功能群所占比例显著相关。（2）在刈割草地上,氮添加和水添加显著提高草地群落地上生物量,氮添加和水添加交互作用尤为显著;氮添加和水添加显著增加物种丰富度指数,对物种均匀度影响较小;杂草类所占比例和地上生物量对Shannon-Weiner多样性指数的贡献率较大。（3）在火烧草地上,氮添加和水添加显著提高群落地上生物量,对物种多样性的影响因年份不同有所差异,氮添加和水添加交互作用具有累加效应;Shannon-Weiner多样性指数与地上生物量呈显著负相关,与莎草科所占比例呈显著正相关。研究表明管理措施显著影响群落结构对氮添加和水添加的响应特征,亦改变生产力和物种多样性的关系模式,为更好地应对全球变化进行草地管理提供数据支撑。     

生物多样性和均匀度显著性的随机化检验及计算软件

多样性指数和均匀度以其简单易用而被广泛应用于群落生物学和生物多样性等研究中,然而由于缺乏合适的统计检验方法等原因,其分析的可信性往往较低,因而限制了其应用。鉴于生物多样性研究中广泛应用主观和直接的比较不,有必要建立和使用较为严格的多样性统计检验。本研究建立和应用了如下随机化检验方法：单群落多样性指数和均匀度的显著性检验,单群落多样性指数和均匀度的置认区间,群落间多群样和均匀度的差异显著性检验。随机化方法已被成功地应用于群落生态学研究,其原理是：随机排序某一向量中的元素,或随机交换两向量中的对应元素。计算该随机化数据的多样性和均匀度,重复该过程多次,统计和计算显著性检验的p值,由向量中的对应元素。计算该随机化数据的多样性和均匀度,重复该过程多次,统计和显著性检验的p值。由此可确定多样性和差异的统计显著性。同时,研制了相应的Internet计算软件BiodiverisytTest。该软件由7个Java类和1个HTML文件组成,可运行于多种操作系统和网络浏览器上,可读取多种类型的ODBC数据库文件如Access,Excel,FoxPro,Dbase等。该软件中包括Shannon-Wiener多样性指数,Simpson多样性指数,McIntosh多样性指数,Berger-Parker多样性指数,Hrlbert多样性指数以及Brillouin多样性指数。基于Shannon-Wiener多样性指数和Berger-Parker多样性指数,用BiodiversityTest软件对水稻田节肢动物群落多样性（15个地点,17个功能群,125个节肢动物种）进行了比较和分析。结果显示,两组结果可较好地反映水稻节肢动物群落多样性的差异显著性,这些检验方法可有效地反映多样性指数和均匀度的变化。与水稻田节肢动物群落间多样性的直接比较法相比,该随机化检验方法获得更客观的结果。本算法与软件有助于改进生物多样性研究中使用的某些不甚严格的分析方法,为随机化检验方法在生物多样性研究中的进一步应用提供了一种可用的工具。     

Assessing habitat diversity and potential areas of similarity across protected areas globally

Biophysical characterization analyses of protected areas (PA) that provide information on their ecological values and potential areas with similar characteristics are needed to make informed PA network planning and management decisions. This study combines and further develops methodologies that use remote sensing and modelling to identify habitat functional types in PAs and map similar areas at the ecoregion level. The study also develops new terrestrial habitat diversity and irreplaceability indices at habitat and PA scale that allow the comparison and ranking of PAs in terms of biophysical gradients and singular environmental conditions. Six PAs were selected to highlight and discuss the results of the proposed methodology. Both individual and composite indices should be considered when trying to compare PAs to understand the overall complexity and ecological values of each PA. Results can inform planning and management of individual and protected area networks as well as identify new areas for conservation. The information provided by the model about similar habitats outside protected areas can also help assess their representativeness and support studies to strengthen ecological connectivity. Besides systematic comparisons, detailed assessments of protected areas can also be performed using medium and high-resolution input variables. This is especially relevant for protected areas in developing countries where undertaking fieldwork is very difficult and the budget devoted to conservation is limited.     

The importance of species diversity and its components as criteria for selecting nature conservation areas

The failure of one of the traditional approaches for selecting sites where economic activities should be restricted is shown based on a simple example. Species richness cannot serve as a criterion for the creation of protected areas and species diversity is poorly suited for this as well. The other component of biodiversity, species evenness, is more informative: the lower its value is, the more scarce species are prone to extinction due to anthropogenic impact. It is necessary to support the existence of substantial parts of habitats of endemic, rare, and endangered species in areas with low species evenness, where dominant species are actively harvested. The restriction of economic activities in those areas is more effective for the conservation of the global species richness than simply protecting the diversity hotspots.     

Comparison of taxonomic, colony morphotype and PCR-RFLP methods to characterize microfungal diversity

We compared three methods for estimating fungal species diversity in soil samples. A rapid screening method based on gross colony morphological features and color reference standards was compared with traditional fungal taxonomic methods and PCR-RFLP for estimation of ecological indices of soil microfungal community composition. Normalized counts of colony morphotypes on dichloran rose bengal medium were used to estimate species richness (S) and evenness (J) and to calculate Shannon's diversity (H) and Simpson's (SI) dominance indices. Isolates were obtained by dilution plating techniques from litter and soil layer samples taken from Douglas-fir forest and clear-cut areas at two locations in the Cascade Mountains. The highest correspondence (97%) was observed between taxonomic identification and RFLP patterns (32:33). Cladistic analyses of PCR-RFLP patterns indicated an 81% correspondence between RFLP patterns:colony morphotypes (33:41). A correspondence of 78% was observed between traditional taxonomic identification:colony morphotypes (32:41). Statistical analyses of ecological indices based on quantitative application of the colony morphotyping method indicated significant differences (P < 0.05) in fungal community composition between forested and clear-cut areas at the Toad Road site but not at the Falls Creek site. Comparisons of ecological indices based on traditional identification of taxa by microscopic characterization on defined culture media resulted in identical findings of statistical significance. The colony morphotyping approach is proposed as a screening method to identify potential effects of land management practices, edaphic factors and pollutants on microfungal diversity.     

山西翅果油树群落的多样性研究

用丰富度指数、多样性指数和均匀度指数对山西翅果油树群落的多样性进行了研究 ,并用相关分析研究了海拔与多样性指数及多样性指数间的关系 ,结果表明 :1 )在干扰强烈的生境中 ,翅果油树群落具有较低的丰富度指数、多样性指数的均匀性 ,而接近顶极群落阶段 ,多样性指数和丰富度指数也较低 ,但具有较高的均匀性 ;干扰强度较小的生境中 ,群落具有较高的丰富度指数、多样性指数和均匀性。2 )灌木层和草本层的丰富度、多样性指数和均匀度指数呈现多元化的趋势。 3)海拔对山西翅果油树群落多样性的影响不显著。     

渭河底栖动物性状和功能对空间尺度环境变量响应的生态区差异性

以我国中部渭河南部流域山区和平原生态区的底栖动物为研究对象,通过计算29个生物性状类别和7个功能多样性指数,比较了不同生态区的生物性状组成和功能与性状多样性指数差异性;应用综合RLQ和fourth-corner方法探索底栖动物生物性状组成与土地利用和理化变量的关系;通过广义线性模型(GLM)比较不同空间尺度环境变量对底栖动物功能与性状多样性指数影响的生态区差异性。研究发现,共18个底栖动物性状组成在山区和平原间存在显著差异性,其中具有无庇护所和以叶片为庇护所材料、外骨骼轻微骨化和骨化良好、草食性、捕食性等生物性状的底栖动物栖息于栖境状况较好的山区,体壁呼吸、虫体柔软、集食者等生物性状更多的集中在人类活动较严重的平原区。除了功能均匀度指数外,山区的性状和功能多样性指数均显著高于平原,说明平原环境干扰显著降低了底栖动物性状和功能多样性。综合RLQ和fourth-corner方法表明底栖动物生物性状对环境胁迫的响应存在可预测性。GLM模型结果表明,山区和平原生物性状和功能多样性指数受到不同空间尺度土地利用和理化环境变量的影响:流域尺度城镇用地、水温和TN含量是影响山区功能和性状多样性指数模型的重要环境变量,但平原区河段尺度农业用地面积百分比和平均水深是影响功能和性状多样性的主要因子。     

Negative relationships between species richness and evenness render common diversity indices inadequate for assessing long-term trends in butterfly diversity

Species richness and evenness, the two principle components of species diversity, are frequently used to describe variation in species assemblages in space and time. Compound indices, including variations of both the Shannon–Wiener index and Simpson’s index, are assumed to intelligibly integrate species richness and evenness into all-encompassing measures. However, the efficacy of compound indices is disputed by the possibility of inverse relationships between species richness and evenness. Past studies have assessed relationships between various diversity measures across survey locations for a variety of taxa, often finding species richness and evenness to be inversely related. Butterflies are one of the most intensively monitored taxa worldwide, but have been largely neglected in such studies. Long-term butterfly monitoring programs provide a unique opportunity for analyzing how trends in species diversity relate to habitat and environmental conditions. However, analyzing trends in butterfly diversity first requires an assessment of the applicability of common diversity measures to butterfly assemblages. To accomplish this, we quantified relationships between butterfly diversity measures estimated from 10 years of butterfly population data collected in the North Saskatchewan River Valley in Edmonton, Alberta, Canada. Species richness and evenness were inversely related within the butterfly assemblage. We conclude that species evenness may be used in conjunction with richness to deepen our understandings of assemblage organization, but combining these two components within compound indices does not produce measures that consistently align with our intuitive sense of species diversity.     

山西五鹿山森林群落木本植物功能多样性

通过选取群落中木本植物种子的扩散方式、传粉方式、植株高度和盖度等13个功能性状,计算出群落的6个功能多样性指数:功能性状距离、功能性状平均距离、功能体积、功能均匀度、功能分散指数和Rao二次熵指数,结合群落物种丰富度指数、Shannon-Wiener指数和物种均匀度指数对山西五鹿山森林群落木本植物功能多样性进行研究。结果表明:(1)功能性状距离、功能性状平均距离、功能体积与物种丰富度、Shannon-Wiener指数显著正相关;功能均匀度与Shannon-Wiener指数、物种均匀度指数显著正相关;功能分散指数、Rao二次熵指数与物种均匀度指数、Shannon-Wiener指数显著正相关;(2)功能多样性的差异很大程度上是由于物种差异所引起的;(3)6个功能多样性指数可分为三类:功能性状距离、功能性状平均距离、功能体积为功能丰富度指数;功能均匀度为功能均匀度指数;功能分散指数和Rao二次熵指数为功能离散度指数。该分类结果符合指数的计算方法和生态学意义,以及相互独立的标准。     

Tree Diversity in Western Kenya: Using Profiles to Characterise Richness and Evenness

Species diversity is a function of the number of species and the evenness in the abundance of the component species. We calculated diversity and evenness profiles, which allowed comparing the diversity and evenness of communities. We applied the methodology to investigate differences in diversity among the main functions of trees on western Kenyan farms. Many use-groups (all trees and species that provide a specific use) could not be ranked in diversity or evenness. No use-group had perfectly even distributions. Evenness could especially be enhanced for construction materials, fruit, ornamental, firewood, timber and medicine, which included some of the most species-rich groups of the investigated landscape. When considering only the evenness in the distribution of the dominant species, timber, medicine, fruit and beverage ranked lowest (> 60% of trees belonged to the dominant species of these groups). These are also use-groups that are mainly grown by farmers to provide cash through sales. Since not all communities can be ranked in diversity, studies that attempt to order communities in diversity should not base the ordering on a single index, or even a combination of several indices, but use techniques developed for diversity ordering such as the Rényi diversity profile. The rarefaction of diversity profiles described in this article could be used in studies that compare results from surveys with different sample sizes.     

太湖流域土地利用与景观格局演变研究

基于遥感、GIS技术和景观生态学方法,以太湖流域为研究区域,在1985年、1995年和2000年的土地利用图基础上,分析了土地利用与景观格局演变.结果表明,15年间,太湖流域农田呈减少趋势,建设用地、林地、草地、水体呈增加趋势,其中农田的减少占土地利用总减少量的89.64%,建设用地的增加占土地利用总增加量的79.21%;由于人类活动的干预,太湖流域景观结构与景观异质性发生了较大变化.从景观尺度上看,斑块密度、多样性指数和均匀度指数呈降低趋势,边界密度、优势度指数、景观形状指数呈增加趋势;从斑块尺度上看,各景观组分的异质性指数及其变化过程有较大的差异,体现了景观生态系统的复杂性.人口增长、经济、政策等因素是太湖流域近15年景观格局动态变化的主要驱动力.太湖流域土地利用变化产生了景观碎化、边缘效应、生境退化等景观生态效应.可通过调整景观尺度上的土地利用方式,使太湖流域生态建设及水土资源实现可持续发展.     

Comparing tree diversity and composition in coffee farms and sacred forests in the Western Ghats of India

Expansion of coffee cultivation is one of the causes of deforestation and biodiversity loss. However, shade grown coffee has been promoted as a means for preserving biodiversity in the tropics. In this study we compared tree diversity in two types of coffee management regimes with the sacred groves in the Western Ghats of India. We computed species accumulation curves, species diversity indices and evenness indices to compare the different management regimes. Results of diversity indices showed that shade coffee had less diversity compared to sacred groves. Exotic species dominated the tree diversity in lands where the tree harvesting rights are with the growers. Native trees dominated the tree diversity when growers had no ownership rights on trees. A species accumulation curve suggested that the sacred grove had higher species richness compared to other two habitats. Lack of incentive to preserve endemic species as shade trees is forcing growers to plant more exotic species in shade grown coffee plots. If encouraged, shade grown coffee can preserve some biodiversity, but cannot provide all ecological benefits of a natural forest.