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．     

城市建成区自生草本植物群落的物种多样性与功能多样性——以深圳市为例

城市自生草本植物的物种多样性和功能多样性直接影响城市生态系统的功能和稳定性,但目前相关研究依然很缺乏。以深圳市为例,基于建成区600个1hm²样地的现场调查数据,分析自生草本植物的群落结构、物种多样性、群落功能特征及功能多样性。结果显示:①调查共记录自生草本植物61科178属273种,其中多年生草本占54.6%,乡土植物占65.6%。②占明显优势的功能特征有中小型叶(91.85%)、草质叶(42.59%)、纸质叶(32.96%)、叶片无毛或近无毛(56.67%)、中等密度绒毛(40.37%)、叶面较粗糙(52.59%)、花期4-6个月(50.78%)、果期4-6个月(49.22%)、干果(86.03%)。③群落类型间功能丰富度FDp、功能离散度Rao二次熵差异极显著(P ＜ 0.01)、功能均匀度FEve差异显著(P ＜ 0.05)。④公园绿地的物种多样性指数明显高于其他三类绿地;不同绿地类型间的功能丰富度和功能离散度在滞尘、降噪、降温增湿及生物多样性保护方面都有极显著差异(P ＜ 0.01),功能均匀度只在滞尘及生物多样性保护方面差异极显著(P ＜ 0.01)。⑤各功能多样性指数均与Margalef指数、Simpson指数及Shannon-Wiener指数呈极显著正相关关系(P ＜ 0.01)。研究结论和方法为维护城市生态系统稳定性、建设生态宜居城市、促进城市可持续发展提供理论依据。     

Impact of land-use intensity on the conservation of functional and phylogenetic diversity in temperate semi-natural plant communities

The earth is facing a worldwide decline in biodiversity, with land-use change identified as one of the most important drivers. There is evidence that the loss of diversity has a significant impact on ecosystem functioning. Earlier research focused on species richness, but more recent, functional and phylogenetic diversity came into the picture as the stronger determinants of ecosystem processes. The effects of increasing land-use intensity on functional (FD) and phylogenetic diversity (PD), however, are still poorly understood. We studied how FD and PD are affected by land-use intensity in temperate plant communities. Our results show that land-use intensity has a clear impact on species richness, but also affects functional and phylogenetic diversity. Intensive agricultural areas fail to support high and sustainable levels of functional and phylogenetic diversity. These results highlight the need for the protection of biodiversity in nature reserves and the conservation of areas with extensive agricultural practices. Because species richness may influence the measures of functional and phylogenetic diversity, we compared the observed FD and PD values with random values generated with a matrix-swap null model. The observed discrepancy between species loss and the loss of FD and PD calls for an integrated approach to biodiversity conservation, in which the different components of biodiversity are considered together.     

spacodiR: structuring of phylogenetic diversity in ecological communities

MOTIVATION: spacodiR is a cross-platform package, written for the R environment, for studying partitioning of diversity among natural communities in space and time. Complementing and extending existing software, spacodiR allows for hypothesis testing and parameter estimation in studying spatial structuring of species-, phylogenetic- and trait diversities. AVAILABILITY: Integrated with other software in the R environment and with well documented and demonstrated functions, spacodiR is an open-source package and available at http://cran.r-project.org. CONTACT: jonathan.eastman@gmail.com; ohardy@ulb.ac.be.     

Phylogenetic diversity of Sri Lankan freshwater crabs and its implications for conservation

As part of a Global Biodiversity Hotspot, the conservation of Sri Lanka's endemic biodiversity warrants special attention. With 51 species (50 of them endemic) occurring in the island, the biodiversity of freshwater crabs is unusually high for such a small area (65 600 km²). Freshwater crabs have successfully colonized most moist habitats and all climatic and elevational zones in Sri Lanka. We assessed the biodiversity of these crabs in relation to the different elevational zones (lowland, upland and highland) based on both species richness and phylogenetic diversity. Three different lineages appear to have radiated simultaneously, each within a specific elevational zone, with little interchange thereafter. The lowland and upland zones show a higher species richness than the highland zone while – unexpectedly – phylogenetic diversity is highest in the lowland zone, illustrating the importance of considering both these measures in conservation planning. The diversity indices for the species in the various IUCN Red List categories in each of the three zones suggest that risk of extinction may be related to elevational zone. Our results also show that overall more than 50% of Sri Lanka's freshwater crab species (including several as yet undescribed ones), or approximately 72 million years of evolutionary history, are threatened with extinction.     

Water-energy relationships shape the phylogenetic diversity of terricolous lichen communities in Mediterranean mountains: Implications for conservation in a climate change scenario

Lichens are symbiotic organisms sensitive to climate change and susceptible to a severe decline in diversity, especially in high elevation environments that are already threatened. In this study, we focused on water-energy relationships derived from climatic variables and phylogenetic diversity indices of terricolous lichen communities occurring on a representative Mediterranean mountain. We hypothesized that the variation of precipitation and temperature and their interaction along the altitudinal gradient will shape the phylogenetic diversity and structure of lichen communities. Our results reveal that dry and arid conditions lead to a strong loss in phylogenetic diversity with consequent impoverishment of high elevation lichen communities under a climate change scenario. The interaction between variables, reflecting water-energy relationships with phylogenetic and community diversity patterns, suggests that in a future climate change scenario, the novel climatic conditions may reduce the capability of the species to survive harsher conditions, and Mediterranean mountains may face a severe loss of genetic diversity in a climate change scenario.     

Phylogenetic diversity and the conservation biogeography of African primates

Aim Phylogenetics has an important role in conservation biogeography. However, there are few data on the phylogenetic diversity of African primates. The phylogenetic diversity (PD) of a species is a measure of its taxonomic distinctness and can be estimated by looking at the phylogenetic relationships among taxa. Species‐specific metrics on PD can then be used to determine conservation priorities at various biogeographical scales. We used PD metrics to rank 55 African primate species according to their conservation priorities at the country level and within six African biogeographical regions. We also addressed the following question: are there differences in conservation rankings between the IUCN Red List and our PD metrics? Location Africa. Methods We created a consensus phylogeny for all African primate clades based on genetic studies. Analyses of species distributions were determined using presence/absence scores at two levels: country and biogeographical region. A node‐based method that standardizes for widespread taxa and endemicity was used to calculate PD indices. Hierarchical cluster analysis was used to convert one of the standardized, phylogenetic indices into three clusters that could be ranked and compared with the main IUCN conservation rankings of endangered, vulnerable, and lower risk. Results At the country and region levels, the top‐priority species in terms of PD are Pan paniscus, Macaca sylvanus, Arctocebus calabarensis, Gorilla beringei, Arctocebus aureus, Allenopithecus nigroviridis, Gorilla gorilla, Procolobus verus, Cercopithecus solatus, Cercocebus galeritus, Colobus angolensis, Theropithecus gelada, Galagoides zanzibaricus, Galagoides granti, and Procolobus (Piliocolobus) badius. Geographic rankings were highest for the Democratic Republic of the Congo (country level) and Central Africa (region level). Although there were no overall differences between IUCN conservation ranks and the PD rankings, there were significant differences between the two systems for vulnerable and endangered primate taxa. Main conclusions There are few ecological and behavioural data on populations of some of the African primates that represent the highest levels of phylogenetic diversity. Studies of primate taxa with high PD rankings should focus on identifying sites suitable for intensive studies of population densities, feeding ecology, and reproductive behaviour. We suggest that PD metrics can serve as an important, complementary data set in the IUCN ranking system for primates.     

Assessing genetic diversity for conservation management: a case study of a threatened reptile

The consequences of inbreeding in small isolated populations are well documented, yet populations are often managed in isolation to avoid irreversibly mixing genetic lineages and to maintain the historic integrity of each population. Three remaining populations of Whitaker's skink ( Cyclodina whitakeri ) in New Zealand, remnants of a once wider distribution, illustrate the conflict between this genetic goal (separate management of populations) with the more tangible and immediate threats of small population size and inbreeding. Middle and Castle Islands harbour populations of C. whitakeri and have been separated from each other and from the mainland for ∼10 000 years. The single mainland population at Pukerua Bay is extremely small, declining and deemed a high priority for management. We sequenced a 550 bp region of mitochondrial DNA (mtDNA,ND2) and genotyped animals from all three populations at 13 microsatellite loci. The population of C. whitakeri at Pukerua Bay showed marked differences from the island populations at both mtDNA (unique, fixed haplotype) and microsatellite loci ( F _ST∼0.20), and private alleles were detected at a high frequency (24% of all alleles). However, we attribute this pattern to an historic genetic gradient coupled with rapid genetic drift. Further, animals in captivity show genetic signatures of both Pukerua Bay and island populations, despite the goal to maintain a pure Pukerua Bay stock. The mixed genetic stock in captivity provides an opportunity for the addition of skinks from Middle Island to evaluate the risks of further population hybridization, including the disruption of potential local adaptation, while mitigating the risks of inbreeding.     

Facilitation can increase the phylogenetic diversity of plant communities

With the advent of molecular phylogenies the assessment of community assembly processes has become a central topic in community ecology. These processes have focused almost exclusively on habitat filtering and competitive exclusion. Recent evidence, however, indicates that facilitation has been important in preserving biodiversity over evolutionary time, with recent lineages conserving the regeneration niches of older, distant lineages. Here we test whether, if facilitation among distant-related species has preserved the regeneration niche of plant lineages, this has increased the phylogenetic diversity of communities. By analyzing a large worldwide database of species, we showed that the regeneration niches were strongly conserved across evolutionary history. Likewise, a phylogenetic supertree of all species of three communities driven by facilitation showed that nurse species facilitated distantly related species and increased phylogenetic diversity.     

Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation

The value of biodiversity lies in its option value for the future, the greater the complement of contemporary biodiversity conserved today, the greater the possibilities for future biodiversity because of the diverse genetic resource needed to ensure continued evolution in a changing and uncertain world. From this perspective, biodiversity option value can be equated with richness in the different features expressed by species. An individual species of greater value is one contributing more novel features to a given subset. The feature diversity of species and communities is difficult to estimate directly, but can be predicted by the phylogenetic relationships among the species. The ‘Phylogenetic Diversity’ measure (PD) (Faith, 1992a) estimates the relative feature diversity of any nominated set of species by the sum of the lengths of all those branches spanned by the set. These branch lengths reflect patristic or path‐length distances. This study first reviews and expands on some of the properties of PD, and develops simple modifications of the measure (δnPD and enPD) to enable capture of both the phylogenetic relatedness of species and their abundances in each sample. Then the application of PD, δnPD and enPD to a wide range of conservation and resource management issues is demonstrated using avian case studies. Supertree construction procedures (matrix representation using parsimony analysis; average consensus) were used to combine the extensive DNA‐DNA hybridization tree of Sibley & Ahlquist (1990) with numerous, recently published phylogenetic reconstructions to derive a phylogenetic tree for the global avian fauna. Using this supertree as a systematic framework, the utility of PD was demonstrated in four case studies: (i) state of the environment reporting, with changes in avian faunas resulting from extinctions quantified as indicators of the state of biodiversity at Global, New Zealand and Waikato region scales, and changes in available habitat quantified as indicators of pressures on biodiversity in the Waikato region; (ii) setting priorities for threatened species management, with PD as a measure of option value integrated with information on survivorship expectations to develop a ranking among threatened New Zealand forest bird species; (iii) monitoring biotic response to management, with data from 5‐minute counts used to analyse changes in forest bird communities under three management regimes in New Zealand; and (iv) selection of indicator species, with PD used to objectively identify subsets of species in the Global, New Zealand and Waikato avian faunas that comprise a high proportion of the option value in those faunas.     

系统发育多样性测度及其在生物多样性保护中的应用

生物多样性保护面临两个基本问题：如何确定生物多样性测度以及如何保护生物多样性。传统的生物多样性测度是以物种概念为基础的,用生态学和地理学方法确定各种生物多样性指数。其测度依赖于样方面积的大小,并且所有的物种在分类上同等对待。系统发育多样性测度基于系统发育和遗传学的理论和方法,能确定某一物种对类群多样性的贡献大小。该方法比较复杂,只有在类群的系统发育或遗传资料比较齐全时方能应用。本文认为,物种生存力途径和系统发育多样性测度相结合有助于确定物种和生态系统保护的优先秩序。     

Microbial communities of urban stormwater sediments: the phylogenetic structure of bacterial communities varies with porosity

This study focuses on the distribution of bacterial and fungal communities within the microstructure of a multi-contaminated sedimentary layer resulting from urban stormwater infiltration. Fractionation was performed on the basis of differential porosity and aggregate grain size, resulting in five fractions: leachable fitting macroporosity, < 10, 10-160, 160-1000 μm fitting aggregates, > 1000 μm. Amounts of both bacterial and fungal biomasses are greater in the < 10 μm and leachable fractions. The aggregates contain numerous bacteria but very low amounts of fungal biomass. Single-strand conformational polymorphism molecular profiles highlighted the differences between bacterial and fungal communities of the leachable fraction and those of the aggregates. Random Sanger sequencing of ssu clones revealed that these differences were mainly because of the presence of Epsilonproteobacteria and Firmicutes in the leachable fractions, while the aggregates contained more Cyanobacteria. The Cyanobacteria phylotypes in the aggregates were dominated by the sequences related to Microcoleus vaginatus while the leachable fractions presented the sequences of chloroplastic origin. Therefore, more than 50% of the phylotypes observed were related to Proteobacteria while 40% were related to Cyanobacteria and Bacteroidetes. Preferential distribution of clades in almost all the phyla or classes detected was observed. This study provides insight into the identities of dominant members of the bacterial communities of urban sediments. Microcoleus vaginatus appeared to predominate in pioneer soils.     

Phylogenetic generalised dissimilarity modelling: a new approach to analysing and predicting spatial turnover in the phylogenetic composition of communities

Compared to species turnover, patterns of phylogenetic turnover provide extra information about the spatial structure of biodiversity, for example providing more informative comparisons between the biota of sites which share no species. To harness this information for broad‐scale spatial analysis, we present phylo‐GDM, a technique for interpolating the spatial structure of phylogenetic turnover between sampled locations in relation to environment, based on generalised dissimilarity modelling (GDM). Using a database of over 150 000 location records for 114 myobatrachid frog species in Australia, linked to a species‐level phylogeny inferred from 2467 base pairs of mitochondrial DNA, we calculated species and phylogenetic turnover between pairs of sites. We show how phylogenetic turnover extended the range of informative comparison of compositional turnover to more biologically and environmentally dissimilar sites. We generated GDM models which predict species and phylogenetic turnover across Australia, and tested the fit of models for different ages within the phylogeny to find the phylogenetic tree depth at which the relationship to current day environment is greatest. We also incorporated explanatory variables based on biogeographic patterns, to represent broad‐scale turnover resulting from divergent evolutionary histories. We found that while the predictive power of our models was lower for full phylogenetic turnover than for species turnover, models based on the more recent components of the phylogeny (closer to the tips) outperformed species models and full phylogenetic models. Phylo‐GDM has considerable potential as a method for incorporating phylogenetic relationships into biodiversity analyses in ways not previously possible. Because phylogenies do not require named taxa, phylo‐GDM may also provide a means of including lineages with poorly resolved taxonomy (e.g. from metagenomic sequencing) into biodiversity planning and phylogeographic analysis.