Comparing species and evolutionary diversity metrics to inform conservation

Phylogenetic diversity (PD) is an important measure for identifying areas of conservation. Phylogenetic diversity is a robust biodiversity metric because it accounts for the relationships among species, and not just the number of species. For this reason, it is an essential element for conservation planning. Unfortunately, PD metrics are not used by many for conservation planning. In the case of Colombia, which is rich in crop and wild plant biodiversity, lacks information on genetic resources of Crop Wild Relatives (CWR). Due to deforestation and agriculture expansion, the habitat, where these crop wild relatives grow, is being reduced at an alarming rate and could be destroyed altogether. This study focuses on crop wild relatives in Colombia, comparing species diversity versus PD-based metrics to show the advantages of using evolutionary information for conservation planning. We identified new areas with high PD and endemism among CWR diversity which are important to establishing comprehensive conservation strategies.     

试论农业生态系统的多样性

探讨农业生态系统多样性的概念和性质,建立农业生态系统多样性研究的农业生态系统分类方法,研究描述农业生态系统多样性特征的一些指标,提出进一步加强农业生态系统多样性研究的建议。     

The partitioning of diversity: showing Theseus a way out of the labyrinth

A methodology for partitioning of biodiversity into α, β and γ components has long been debated, resulting in different mathematical frameworks. Recently, use of the Rao quadratic entropy index has been advocated since it allows comparison of various facets of diversity (e.g. taxonomic, phylogenetic and functional) within the same mathematical framework. However, if not well implemented, the Rao index can easily yield biologically meaningless results and lead into a mathematical labyrinth. As a practical guideline for ecologists, we present a critical synthesis of diverging implementations of the index in the recent literature and a new extension of the index for measuring β‐diversity. First, we detail correct computation of the index that needs to be applied in order not to obtain negative β‐diversity values, which are ecologically unacceptable, and elucidate the main approaches to calculate the Rao quadratic entropy at different spatial scales. Then, we emphasize that, similar to other entropy measures, the Rao index often produces lower‐than‐expected β‐diversity values. To solve this, we extend a correction based on equivalent numbers, as proposed by Jost (2007), to the Rao index. We further show that this correction can be applied to additive partitioning of diversity and not only its multiplicative form. These developments around the Rao index open up an exciting avenue to develop an estimator of turnover diversity across different environmental and temporal scales, allowing meaningful comparisons of partitioning across species, phylogenetic and functional diversities within the same mathematical framework. We also propose a set of R functions, based on existing developments, which perform different key computations to apply this framework in biodiversity science.     

Stochastic properties of generalised Yule models, with biodiversity applications

The Yule model is a widely used speciation model in evolutionary biology. Despite its simplicity many aspects of the Yule model have not been explored mathematically. In this paper, we formalise two analytic approaches for obtaining probability densities of individual branch lengths of phylogenetic trees generated by the Yule model. These methods are flexible and permit various aspects of the trees produced by Yule models to be investigated. One of our methods is applicable to a broader class of evolutionary processes, namely the Bellman-Harris models. Our methods have many practical applications including biodiversity and conservation related problems. In this setting the methods can be used to characterise the expected rate of biodiversity loss for Yule trees, as well as the expected gain of including the phylogeny in conservation management. We briefly explore these applications.     

Distribution of phylogenetic diversity under random extinction

Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the unknown subset of current species that will still be present at some future time, then this ‘future phylogenetic diversity’ provides a measure of the impact of various extinction scenarios in biodiversity conservation. In this paper, we study the distribution of future phylogenetic diversity under a simple model of extinction (a generalized ‘field of bullets’ model). We show that the distribution of future phylogenetic diversity converges to a normal distribution as the number of species grows, under mild conditions, which are necessary. We also describe an algorithm to compute the distribution efficiently, provided the edge lengths are integral, and briefly outline the significance of our findings for biodiversity conservation.     

Will hotspots conserve extra primate and carnivore evolutionary history?

Setting aside biodiversity hotspots would be especially compelling if they contained not just enormous numbers of species but also excessive evolutionary history. A recent study seemed to provide evidence for this incentive for hotspot conservation. Sechrest et al . (2002 ) reported that hotspots contain more endemic phylogenetic diversity (PD) than expected based on the numbers of primate and carnivore species they contain. We extend their analysis and revise some of their claims. For primates and threatened carnivores, we show that the original analysis was driven by a single hotspot (Madagascar) that contains an ancient endemic clade. The remaining hotspots harbour less rather than significantly more endemic PD than expected. Thus, while one hotspot contains an enormous excess of evolutionary history, the remaining hotspots do not. Our analysis reveals that the overriding influence of a single hotspot can create the misleading impression that hotspots generally contain excessive evolutionary history. Justification for the hotspot initiative should be based on robust evidence. We join others in endorsing an increased role for detailed phylogenetic analysis in conservation planning.     

Identifying hotspots of endemic woody seed plant diversity in China

Aim This study aimed to detect distribution patterns and identify diversity hotspots for Chinese endemic woody seed plant species (CEWSPS). Location China. Methods Presence of 6885 CEWSPS throughout China was mapped by taking the Chinese administrative county as the basic spatial analysis unit. The diversity was measured with five indices: endemic richness (ER), weighted endemism (WE), phylogenetic diversity (PD), phylogenetic endemism (PE) and biogeographically weighted evolutionary distinctiveness (BED). Three levels of area (i.e. 1, 5 and 10% of China’s total land area) were used to identify hotspots, but the 5% level was preferred when both the total area of the hotspots identified and the diversity of CEWSPS reached by the hotspots were considered. Results Distribution patterns of CEWSPS calculated with the five indices are consistent with each other over the national extent. However, the hotspots do not show a high degree of consistency among the results derived from the five indices. Those identified with ER and PD are very similar, and so are those with WE and BED. In total, 20 hotspots covering 7.9% of China’s total land area were identified, among which 11 were identified with all the five indices, including the Hengduan Mountains, Xishuangbanna Region, Hainan Island, and eight mountainous areas located in east Chongqing and west Hubei, in east Yunnan and west Guangxi, in north Guangxi, south‐east Guizhou and south‐west Hunan, in north Guangdong and south Hunan, in south‐east Tibet, and in south‐east Hubei and north‐west Jiangxi. Taiwan Island was also identified as a major hotspot with WE, PE and BED. Main conclusions Hotspots of CEWSPS were identified with five indices considering both distributional and phylogenetic information. They cover most of the key areas of biodiversity defined by previous researchers using other approaches. This further verifies the importance of these areas for China’s biodiversity conservation.     

Resemblance in phylogenetic diversity among ecological assemblages

Questions: How can a resemblance (similarity or dissimilarity) measure be formulated to include information on both the evolutionary relationships and abundances of organisms, and how does it compare to measures lacking such information? Methods: We extend the family of Phylogenetic Diversity (PD) measures to include a generalized method for calculating pair‐wise resemblance of ecological assemblages. Building on previous work, we calculate the matching/mismatching components of the 2 × 2 contingency table so as to incorporate information on both phylogeny and abundance. We refer to the class of measures so defined as “PD resemblance” and use the term “SD resemblance” for the traditional class of measures based on species diversity alone. As an illustration, we employ data on the diversity and stem density of shrubs of Toohey Forest, Australia, to compare PD resemblance to its SD resemblance equivalent for both incidence and abundance data. Results: While highly correlated, PD resemblance consistently measures assemblages as more similar than does SD resemblance, and tends to “smooth out” the otherwise skewed and truncated distribution of pair‐wise resemblance indices of our high‐turnover data set, resulting in nMDS ordinations with lower stress. Randomization of species distributions across assemblages indicates that phylogeny has made a significant contribution to the ordination pattern. Conclusions: PD resemblance measures, in addition to providing an evolutionary perspective, have great potential to improve distance‐based analyses of community patterns, particularly if species responses to ecological gradients are unimodal and phylogenetically conserved.     

The diversity and distribution of lianas in the Afromontane rain forests of Ethiopia

The diversity and distribution of lianas were studied in five Afromontane rain forests of Ethiopia. Quadrats of 20 × 20 m were laid down along transects in the Bonga, Berhane‐Kontir, Harenna, Yayu and Maji forests. In all forests, 30,917 liana individuals belonging to 123 species in 87 genera and 40 plant families were recorded. The most species‐rich families were Asclepiadaceae (14), Fabaceae (9), Annonaceae (7) and Cucurbitaceae (7). The top 10 dominant families represented 56% of the total number of species. Over 400 other plant species representing different life forms were recorded growing together with lianas. The lianas accounted for over 30% of the total woody plant diversity and over 20% of the total floral diversity in the study areas. The analysis of floristic composition of the forests indicates that the Berhane‐Kontir Forest had the highest Fisher's diversity index α, and Yayu the lowest. Generally, there were low similarities between the forests in terms of species composition. Although lianas were abundant in almost all forests, there was a considerable variation among the forests in terms of density and spatial distribution. The major dispersal modes of lianas were anemochory (30%), mammaliochory (30%), ornithochory and autochory, and the four mechanisms of climbing of lianas were twining (54%), hooking (24%), rooting and use of tendrils. Altitude and human disturbance were found to be important factors affecting liana distribution. The need for sustainable management and use of lianas in the Afromontane rain forests is emphasized.     

Process‐Based Species Action Plans: an approach to conserve contemporary evolutionary processes that sustain diversity in taxonomically complex groups

Many endemic plant species belong to taxonomically complex groups. These endemics have often arisen as a consequence of recent and rapid evolutionary divergence facilitated by processes such as hybridization, polyploidy and/or breeding system transitions. The rapid and dynamic nature of divergence in taxonomically complex groups leads to problems in the implementation of traditional species‐based approaches for the conservation of the biodiversity that they contain. Firstly, the taxa of interest can be difficult to define and identify, leading to practical difficulties in implementing conservation measures. Secondly, a species‐based approach often fails to capture the complexity of diversity present in the taxonomically complex group. To accommodate these challenges, we have developed a Process‐Based Species Action Plan approach. This is designed to conserve the processes leading to the generation of biodiversity, rather than focusing on the preservation of individual named taxa. We illustrate the approach using a group of endemic tree species (Sorbus) on the Scottish island of Arran that have originated via a combination of multiple recent hybridization events and apomixis. The plan focuses on the optimization of habitat management to ensure the reproduction and regeneration of Sorbus in the zone in which these evolutionary processes operate, and to facilitate hybridization that will ensure the continued generation of diversity in this group. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 194–203.     

微生物多样性及其保育

大量实验证明因原始环境的改变使放线菌多样性急剧减少。在对微生物资源的特点及保护微生物资源的必要性进行分析的基础上,提出了保护微生物资源及其多样性的若干措施。     

Maximal ecological diversity exceeds evolutionary diversity in model ecosystems

Understanding community saturation is fundamental to ecological theory. While investigations of the diversity of evolutionary stable states (ESSs) are widespread, the diversity of communities that have yet to reach an evolutionary endpoint is poorly understood. We use Lotka–Volterra dynamics and trait-based competition to compare the diversity of randomly assembled communities to the diversity of the ESS. We show that, with a large enough founding diversity (whether assembled at once or through sequential invasions), the number of long-time surviving species exceeds that of the ESS. However, the excessive founding diversity required to assemble a saturated community increases rapidly with the dimension of phenotype space. Additionally, traits present in communities resulting from random assembly are more clustered in phenotype space compared to random, although still markedly less ordered than the ESS. By combining theories of random assembly and ESSs we bring a new viewpoint to both the saturation and random assembly literature.     

Variable history of land use reduces the relationship to specific habitat requirements of a threatened aquatic insect

The hutchinsonian realized niche of a species is the most common tool for selecting the actions needed when restoring habitats and establishing conservation areas of species. However, defining the realized niche of a species is problematic due to variation across spatial and temporal scales. In this study we tested the hypothesis that habitat parameters defining the realized niche of a species can be derived from a regional study and that national changes in land use influence the perception of the realized niche across different landscapes. We described the realized habitat niche of the threatened dragonfly Leucorrhinia pectoralis, in four Estonian landscapes which all have undergone more than 20 years of habitat degradations. We recorded the presence/absence of L. pectoralis and measured 7 habitat variables for 140 lakes and ponds located in one restored and three un-restored landscapes. Lake size and proportion of short riparian vegetation were significantly positive parameters determining the presence of L. pectoralis across landscape types. The species was much more habitat specific in the restored landscape, with larger influence of other habitat parameters. Our data suggest that the realized niche of the species in the un-restored landscapes was constrained by the present-day habitats. The study demonstrate that if a species realized niche is derived from local distribution patterns without incorporating landscape history it can lead to an erroneous niche definition. We show that landscape restoration can provide knowledge on a species’ habitat dependencies before habitat degradation has occurred, provided that restoration mitigation reflects the former landscape characteristics.     

采用未培养技术对荷斯坦奶牛瘤胃细菌多样性进行初步分析

采用未培养(Culture independent)技术直接从荷斯坦奶牛瘤胃液中提取瘤胃细菌微生物混合DNA(也叫元基因组DNA),利用细菌16SrDNA通用引物27F与1492R,扩增瘤胃混合微生物的16SrDNA,根据16SrDNA序列对瘤胃细菌多样性进行初步分析。通过16SrDNA序列同源性分析,发现有多于一半以上的序列与可培养的菌株的同源性小于90%,属于不可培养的菌株。选用45条测得序列与已知序列构建系统发育树,分析结果表明,它们分属于两大类LGCGPB(the lowG CGram positivebac teria)和CFB(Cytophaga_Flexibacter $CBacteroides group),剩下的克隆尚难确定其分类地位,可能是代表新属和种的序列,这些序列已向GenBank提交并得到序列号(AY986777_AY986791)。     

微生物系统发育多样性及其保护生物学意义

近年来,分子系统发育分析方法,特别是rBNA基因同源性分析方法,在微生物多样性的研究中发挥着越来越重要的作用．它克服了传统的微生物分离培养方法的限制,极大地促进了人们对微生物多样性的理解．在遗传信息同源性分析基础上得出的微生物系统发育多样性为多样性的保护提供了新的视点．它不但可以作为微生物多样性评价的手段,而且为多样性保护中优先秩序的确定提供了依据．同时也为生物多样性保护确定了目标,即最大程度地保护系统发育关系中所包含的信息．本文对微生物系统发育多样性的特点及其保护生物学意义进行了简要评述．     

Biodiversity conservation in a fast-growing metropolitan area in China: a case study of plant diversity in Beijing

As the capital of China, Beijing has experienced extensive urbanization in the past two decades. To explore the effect of urbanization on plant diversity, we investigated the vascular plant diversity of the whole Beijing Municipality in three different functional (urban, suburban and exurban) regions. For its geo-diversity, Beijing has a rather abundant vascular plant diversity (2,276 species), including 207 species of conservation concern such as endemic, threatened and protected species. The exurban region had not only the highest species diversity (1,998 species), but also the most species of conservation concern (194 species). Urban region possessed the maximum alien species in terms of both absolute number and proportional representation, while the suburban region had the least species diversity (1,026 species). Some problems, such as wetland shrink and biological invasions, were common in the whole Beijing Municipality. However, primary threats to biodiversity differed in the three functional regions. The urban and suburban regions mainly suffered from habitat loss and fragmentation due to urban sprawl, while the exurban region faced serious ecosystem degradation from increasing disturbance from both local and urban people. Based on our investigation, we put forward conservation strategies for the three regions: improving the structure and ecological function of green spaces in urban region, preserving as much remnant natural habitats in the suburban region, and restricting the rural tourism and establishing a biosphere reserve in the exurban region. In addition, improving public education and orientating that more to social aspects of conservation practice is strongly recommended.     

Effects of different land use patterns on nifH genetic diversity of soil nitrogen-fixing microbial communities in Leymus Chinensis steppe

Biological nitrogen fixation through prokaryotic microbe is an important source of nitrogen been input into many natural ecosystems. In this study the active diazotrophic community was investigated in the three treatments of mowed, grazed and enclosed Leymus chinensis steppes in Hulunbeier grassland of Inner Mongolia by using approaches of polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE) and sequence analysis. The community structure and diversity of the bacterial groups from the different samples was further analyzed by using different techniques, such as statistical analysis and diversity index evaluation of the band patterns etc. The results showed that grazing activity significantly reduced the number of species and quantities of nitrogen-fixing microorganisms, as well as the nifH gene diversity. However, enclosed plots had the lowest diversity of nifH gene. While the highest one found in mowing plots. A total of 30 sequences representing 25 different sequence types were recovered from the DGGE gels after phylogenetic constructions. The results also revealed that most sequences were coming from Alphaproteobacteria of Proteobacteria, and characterized by sequences of members of Rhodobacter, Bradyrhizobium, Mesorhizobium, Rhodopseudomonas, Xanthomonas, Azospirillum, Gluconacetobacter, Methylobacterium and Methylocystis. Symbiotic nitrogen-fixers existed in grazing, mowing and enclosed plots accounted for 21.4%, 47.3% and 31.3% respectively in their dominant nitrogen-fixing bacteria. The result of principal components analysis showed that the influence of different land use patterns on nitrogen-fixing microbial communities composition can be ordered as grazing plots > enclosed plots > mowing plots. Nitrogen-fixing microbial communities in L. chinensis steppe were significantly (P < 0.05) influenced by the levels of nitrate nitrogen, total phosphorus, available phosphorus contents and pH value when canonical correspondence analysis was employed to identify relationship between nifH gene and soil physicochemical factors under different land use patterns. The result obtained from correlation analysis showed that there was a significant (P < 0.05) negative relationship between the nitrate nitrogen and the total phosphorus content, furthermore, the available phosphorus content was strongly correlated (P < 0.01) with the pH value.