Climate and Species Richness Predict the Phylogenetic Structure of African Mammal Communities

We have little knowledge of how climatic variation (and by proxy, habitat variation) influences the phylogenetic structure of tropical communities. Here, we quantified the phylogenetic structure of mammal communities in Africa to investigate how community structure varies with respect to climate and species richness variation across the continent. In addition, we investigated how phylogenetic patterns vary across carnivores, primates, and ungulates. We predicted that climate would differentially affect the structure of communities from different clades due to between-clade biological variation. We examined 203 communities using two metrics, the net relatedness (NRI) and nearest taxon (NTI) indices. We used simultaneous autoregressive models to predict community phylogenetic structure from climate variables and species richness. We found that most individual communities exhibited a phylogenetic structure consistent with a null model, but both climate and species richness significantly predicted variation in community phylogenetic metrics. Using NTI, species rich communities were composed of more distantly related taxa for all mammal communities, as well as for communities of carnivorans or ungulates. Temperature seasonality predicted the phylogenetic structure of mammal, carnivoran, and ungulate communities, and annual rainfall predicted primate community structure. Additional climate variables related to temperature and rainfall also predicted the phylogenetic structure of ungulate communities. We suggest that both past interspecific competition and habitat filtering have shaped variation in tropical mammal communities. The significant effect of climatic factors on community structure has important implications for the diversity of mammal communities given current models of future climate change.     

Climate Change Risks and Conservation Implications for a Threatened Small-Range Mammal Species

Background

Climate change is already affecting the distributions of many species and may lead to numerous extinctions over the next century. Small-range species are likely to be a special concern, but the extent to which they are sensitive to climate is currently unclear. Species distribution modeling, if carefully implemented, can be used to assess climate sensitivity and potential climate change impacts, even for rare and cryptic species.

Methodology/Principal Findings

We used species distribution modeling to assess the climate sensitivity, climate change risks and conservation implications for a threatened small-range mammal species, the Iberian desman (Galemys pyrenaicus), which is a phylogenetically isolated insectivore endemic to south-western Europe. Atlas data on the distribution of G. pyrenaicus was linked to data on climate, topography and human impact using two species distribution modeling algorithms to test hypotheses on the factors that determine the range for this species. Predictive models were developed and projected onto climate scenarios for 2070–2099 to assess climate change risks and conservation possibilities. Mean summer temperature and water balance appeared to be the main factors influencing the distribution of G. pyrenaicus. Climate change was predicted to result in significant reductions of the species'' range. However, the severity of these reductions was highly dependent on which predictor was the most important limiting factor. Notably, if mean summer temperature is the main range determinant, G. pyrenaicus is at risk of near total extinction in Spain under the most severe climate change scenario. The range projections for Europe indicate that assisted migration may be a possible long-term conservation strategy for G. pyrenaicus in the face of global warming.

Conclusions/Significance

Climate change clearly poses a severe threat to this illustrative endemic species. Our findings confirm that endemic species can be highly vulnerable to a warming climate and highlight the fact that assisted migration has potential as a conservation strategy for species threatened by climate change.     

Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices

Yams (Dioscorea spp.) consist of approximately 600 species. Presently, these species are threatened by genetic erosion due to many factors such as pest attacks and farming practices. In parallel, complex taxonomic boundaries in this genus makes it more challenging to properly address the genetic diversity of yam and manage its germplasm. As a first step toward evaluating and preserving the genetic diversity yam species, we use a phylogenetic diversity (PD) approach that has the advantage to investigate phylogenetic relationships and test hypotheses of species monophyly while alleviating to the problem of ploidy variation within and among species. The Bayesian phylogenetic analysis of 62 accessions from 7 species from three regions of Cameroon showed that most Dioscorea sections were monophyletic, but species within sections were generally non-monophyletic. The wild species D. praehensilis and cultivated D. cayenensis were the species with the highest PD. At the opposite, D. esculenta has a low PD and future studies should focus on this species to properly address its conservation status. We also show that wild species show a stronger genetic structure than cultivated species, which potentially reflects the management of the yam germplasm by farmers. These findings show that phylogenetic diversity is a promising approach for an initial investigation of genetic diversity in a crop consisting of closely related species.     

Systematic Conservation Planning for Groundwater Ecosystems Using Phylogenetic Diversity

Aquifer ecosystems provide a range of important services including clean drinking water. These ecosystems, which are largely inaccessible to humans, comprise a distinct invertebrate fauna (stygofauna), which is characterized by narrow distributions, high levels of endemism and cryptic species. Although being under enormous anthropogenic pressure, aquifers have rarely been included in conservation planning because of the general lack of knowledge of species diversity and distribution. Here we use molecular sequence data and phylogenetic diversity as surrogates for stygofauna diversity in aquifers of New South Wales, Australia. We demonstrate how to incorporate these data as conservation features in the systematic conservation planning software Marxan. We designated each branch of the phylogenetic tree as a conservation feature, with the branch length as a surrogate for the number of distinct characters represented by each branch. Two molecular markers (nuclear 18S ribosomal DNA and mitochondrial cytochrome oxidase subunit I) were used to evaluate how marker variability and the resulting tree topology affected the site-selection process. We found that the sites containing the deepest phylogenetic branches were deemed the most irreplaceable by Marxan. By integrating phylogenetic data, we provide a method for including taxonomically undescribed groundwater fauna in systematic conservation planning.     

Decline of Mammal Species Diversity Along the Yungas Forest of Argentina

The southernmost extension of tropical Andean–Amazonian forests protrudes into the arid to semiarid habitats in northwestern Argentina. We analyzed the decline of species richness of forest mammals along these Yungas forests. In particular, we tested whether species decline is due to a general latitudinal effect and whether the drop of species from the assemblages was independent from species' traits and environmental variables. For these tests, we estimated the geographic range edges of 39 species of forest mammal and estimated the species richness with bands of 30'. First, we compared the slope of the decline of species richness from north to south (5.8 species/degree) with the decline expected from the latitudinal species gradient (1–3 species/degree). The decline in species richness of forest mammals along the Yungas was significantly steeper than expected. Second, with a null model assuming a random drop of mammal species we derived confidence limits for the expected species richness and number of range edges within the bands. None of the forest mammals reached the tip of the forest, in marked contrast to nonforest mammals. More range edges than expected from the null model fell within the bands 23°30'–24°00' S and a band near the tip of the Yungas indicating a nonrandom drop of species. The correlation between vulnerability traits and range edges suggests that processes associated with the availability of resources influence the drop of species. We propose that a suite of macroecological attributes interacting with a decrease in habitat quality determines the pattern of species richness in the Yungas forest.     

Mammal Diversity and Conservation in a Secondary Forest in Peninsular Malaysia

A comprehensive survey on large mammal diversity from a disturbed forest in Peninsular Malaysia has been carried out for over a period of 21 months. A total of 24 camera traps which accumulated to 5972 trap days. A total of 33 species 27 genera and 15 families of mammals were recorded via camera trapping and observations. The use of camera traps provides detailed information on diversity of some cryptic and secretive mammals. Secondary forest may support a wide diversity of mammals at a stable condition where intrusion, excision and fragmentation are reduced or avoided. The threats to mammals in the study are also discussed.     

Plant-Pollinator Coextinctions and the Loss of Plant Functional and Phylogenetic Diversity

Plant-pollinator coextinctions are likely to become more frequent as habitat alteration and climate change continue to threaten pollinators. The consequences of the resulting collapse of plant communities will depend partly on how quickly plant functional and phylogenetic diversity decline following pollinator extinctions. We investigated the functional and phylogenetic consequences of pollinator extinctions by simulating coextinctions in seven plant-pollinator networks coupled with independent data on plant phylogeny and functional traits. Declines in plant functional diversity were slower than expected under a scenario of random extinctions, while phylogenetic diversity often decreased faster than expected by chance. Our results show that plant functional diversity was relatively robust to plant-pollinator coextinctions, despite the underlying rapid loss of evolutionary history. Thus, our study suggests the possibility of uncoupled responses of functional and phylogenetic diversity to species coextinctions, highlighting the importance of considering both dimensions of biodiversity explicitly in ecological studies and when planning for the conservation of species and interactions.     

Converting Endangered Species Categories to Probabilities of Extinction for Phylogenetic Conservation Prioritization

Background

Categories of imperilment like the global IUCN Red List have been transformed to probabilities of extinction and used to rank species by the amount of imperiled evolutionary history they represent (e.g. by the Edge of Existence programme). We investigate the stability of such lists when ranks are converted to probabilities of extinction under different scenarios.

Methodology and Principal Findings

Using a simple example and computer simulation, we show that preserving the categories when converting such list designations to probabilities of extinction does not guarantee the stability of the resulting lists.

Significance

Care must be taken when choosing a suitable transformation, especially if conservation dollars are allocated to species in a ranked fashion. We advocate routine sensitivity analyses.     

Using Phylogenetic,Functional and Trait Diversity to Understand Patterns of Plant Community Productivity

Background

Two decades of research showing that increasing plant diversity results in greater community productivity has been predicated on greater functional diversity allowing access to more of the total available resources. Thus, understanding phenotypic attributes that allow species to partition resources is fundamentally important to explaining diversity-productivity relationships.

Methodology/Principal Findings

Here we use data from a long-term experiment (Cedar Creek, MN) and compare the extent to which productivity is explained by seven types of community metrics of functional variation: 1) species richness, 2) variation in 10 individual traits, 3) functional group richness, 4) a distance-based measure of functional diversity, 5) a hierarchical multivariate clustering method, 6) a nonmetric multidimensional scaling approach, and 7) a phylogenetic diversity measure, summing phylogenetic branch lengths connecting community members together and may be a surrogate for ecological differences. Although most of these diversity measures provided significant explanations of variation in productivity, the presence of a nitrogen fixer and phylogenetic diversity were the two best explanatory variables. Further, a statistical model that included the presence of a nitrogen fixer, seed weight and phylogenetic diversity was a better explanation of community productivity than other models.

Conclusions

Evolutionary relationships among species appear to explain patterns of grassland productivity. Further, these results reveal that functional differences among species involve a complex suite of traits and that perhaps phylogenetic relationships provide a better measure of the diversity among species that contributes to productivity than individual or small groups of traits.     

The Role of DNA Barcodes in Understanding and Conservation of Mammal Diversity in Southeast Asia

Background

Southeast Asia is recognized as a region of very high biodiversity, much of which is currently at risk due to habitat loss and other threats. However, many aspects of this diversity, even for relatively well-known groups such as mammals, are poorly known, limiting ability to develop conservation plans. This study examines the value of DNA barcodes, sequences of the mitochondrial COI gene, to enhance understanding of mammalian diversity in the region and hence to aid conservation planning.

Methodology and Principal Findings

DNA barcodes were obtained from nearly 1900 specimens representing 165 recognized species of bats. All morphologically or acoustically distinct species, based on classical taxonomy, could be discriminated with DNA barcodes except four closely allied species pairs. Many currently recognized species contained multiple barcode lineages, often with deep divergence suggesting unrecognized species. In addition, most widespread species showed substantial genetic differentiation across their distributions. Our results suggest that mammal species richness within the region may be underestimated by at least 50%, and there are higher levels of endemism and greater intra-specific population structure than previously recognized.

Conclusions

DNA barcodes can aid conservation and research by assisting field workers in identifying species, by helping taxonomists determine species groups needing more detailed analysis, and by facilitating the recognition of the appropriate units and scales for conservation planning.     

仙草植物内生芽胞杆菌种群多样性研究

为了研究仙草植株内生芽胞杆菌种群的多样性,利用营养琼脂培养基分离仙草根、茎、叶中的内生芽胞杆菌,采用16SrRNA序列鉴定法对分离获得的芽胞杆菌进行鉴定。同一组织内,对16SrRNA序列及形态完全一样的菌株合并冗余,用ClustalX对分离得到的菌株16SrRNA进行排序,构建Neighbor-Joining系统进化树,并计算多样性指数。实验结果显示,共分离得到58株仙草内生芽胞杆菌(根29株、茎28株、叶1株),分属于芽胞杆菌属(Bacillus)、类芽胞杆菌属(Paenibacillus)和赖氨酸芽胞杆菌属(Lysinibacillus),共3个属的11个种,其中与阿氏芽胞杆菌B.aryabhattai、简单芽胞杆菌B.simplex和B.flexus 3个种最接近的内生芽胞杆菌占总分离芽胞杆菌株数的62%;根部内生芽胞杆菌数量及种属均最丰富,其多样性指数高于茎和叶。     

A Population Accounting Approach to Assess Tourism Contributions to Conservation of IUCN-Redlisted Mammal Species

Over 1,000 mammal species are red-listed by IUCN, as Critically Endangered, Endangered or Vulnerable. Conservation of many threatened mammal species, even inside protected areas, depends on costly active day-to-day defence against poaching, bushmeat hunting, invasive species and habitat encroachment. Many parks agencies worldwide now rely heavily on tourism for routine operational funding: >50% in some cases. This puts rare mammals at a new risk, from downturns in tourism driven by external socioeconomic factors. Using the survival of individual animals as a metric or currency of successful conservation, we calculate here what proportions of remaining populations of IUCN-redlisted mammal species are currently supported by funds from tourism. This proportion is ≥5% for over half of the species where relevant data exist, ≥15% for one fifth, and up to 66% in a few cases. Many of these species, especially the most endangered, survive only in one single remaining subpopulation. These proportions are not correlated either with global population sizes or recognition as wildlife tourism icons. Most of the more heavily tourism-dependent species, however, are medium sized (>7.5 kg) or larger. Historically, biological concern over the growth of tourism in protected areas has centered on direct disturbance to wildlife. These results show that conservation of threatened mammal species has become reliant on revenue from tourism to a previously unsuspected degree. On the one hand, this provides new opportunities for conservation funding; but on the other, dependence on such an uncertain source of funding is a new, large and growing threat to red-listed species.     

Edge-Related Loss of Tree Phylogenetic Diversity in the Severely Fragmented Brazilian Atlantic Forest

Deforestation and forest fragmentation are known major causes of nonrandom extinction, but there is no information about their impact on the phylogenetic diversity of the remaining species assemblages. Using a large vegetation dataset from an old hyper-fragmented landscape in the Brazilian Atlantic rainforest we assess whether the local extirpation of tree species and functional impoverishment of tree assemblages reduce the phylogenetic diversity of the remaining tree assemblages. We detected a significant loss of tree phylogenetic diversity in forest edges, but not in core areas of small (<80 ha) forest fragments. This was attributed to a reduction of 11% in the average phylogenetic distance between any two randomly chosen individuals from forest edges; an increase of 17% in the average phylogenetic distance to closest non-conspecific relative for each individual in forest edges; and to the potential manifestation of late edge effects in the core areas of small forest remnants. We found no evidence supporting fragmentation-induced phylogenetic clustering or evenness. This could be explained by the low phylogenetic conservatism of key life-history traits corresponding to vulnerable species. Edge effects must be reduced to effectively protect tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest.     

系统发育多样性与系统发育结构在岛屿植物群落保护中的意义——以蜈支洲岛为例

为探讨系统发育多样性和系统发育结构在岛屿植物群落保护决策制定中的作用,以海南三亚蜈支洲岛被子植物群系为例,分析物种丰富度和系统发育多样性的相关性。结果表明,蜈支洲岛植被可分为10种群系类型,22个样方的物种丰富度与系统发育多样性呈显著正相关,但系统发育多样性与物种丰富度对植物多样性保护优先顺序的指示有差异。森林群系的物种丰富度和系统发育多样性普遍高于灌木和草本群系,4个森林群系样方表现为系统发育结构发散,3个森林群系样方表现为系统发育结构聚集。灌木群系中露兜树(Pandanus tectorius)灌丛和草海桐(Scaevola sericea)灌丛系统发育多样性较高,草本群系中厚藤(Vitex trifolia)灌草丛系统发育多样性较高,灌木和草本群系大多倾向于系统发育结构聚集。距海或人类活动区较近的群系可能受环境过滤的作用,而远离海和人类活动区的群系主要受竞争排斥作用影响。因此,在岛屿植物多样性保护策略制定中应当综合考虑物种和系统发育维度,以及环境、演替阶段及用岛方式等因素的影响。     

3种杓兰属植物菌根真菌系统发育和多样性分析

兰科植物菌根真菌(Orchid mycorrhizal fungi, OrMF)在兰科植物种子萌发和后续生长发育过程中具有重要作用。该研究采用培养(菌丝团分离)和非培养(克隆文库)2种方法获得同一栖息地3种不同杓兰属植物根中菌根真菌ITS序列并划分可操作分类单元(Operational taxonomic units, OTUs),分析其系统发育关系和多样性。结果表明:(1)所有根段中都有菌丝团定植,共分离出菌根真菌64株,其中63株为胶膜菌科(Tulasnellaceae)真菌,1株为角担菌科(Ceratobasidiaceae)真菌;可划分为7个OUT,每个OTU代表菌株的菌丝都能形成OrMF典型的近球形或椭球形链状排列的念珠状细胞;分离出来的菌根真菌均为无性型菌丝且不产生无性孢子。(2) 非培养法得到的3种杓兰属植物的根中OrMF分别隶属于胶膜菌科(Tulasnellaceae),腊壳菌科(Sebacinaceae)、角担菌科(Ceratobasidiaceae)和革菌科(Thelephoraceae),其中胶膜菌科OTU在种类和数量上占有绝对优势,培养和非培养2种方法得到的OrMF OTU类型和数量均为西藏杓兰(Cypripedium tibeticum)>无苞杓兰(C. flavum)>黄花杓兰(C. bardolphianum),但培养法少于非培养法。(3)对胶膜菌进行系统发育分析显示,优势和非优势OTU均分布在系统发育树的3个不同分支上,这种与多种亲缘关系较远的OrMF共生的现象可能与杓兰属植物对环境的适应性有关,且不同杓兰的OrMF物种丰富度没有显著差异,但群落结构存在差异。     

Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation

Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package “traitor” to facilitate assessments of missing trait data.     

Phylogenetic Resolution and Quantifying the Phylogenetic Diversity and Dispersion of Communities

Conservation biologists and community ecologists have increasingly begun to quantify the phylogenetic diversity and phylogenetic dispersion in species assemblages. In some instances, the phylogenetic trees used for such analyses are fully bifurcating, but in many cases the phylogenies being used contain unresolved nodes (i.e. polytomies). The lack of phylogenetic resolution in such studies, while certainly not preferred, is likely to continue particularly for those analyzing diverse communities and datasets with hundreds to thousands of taxa. Thus it is imperative that we quantify potential biases and losses of statistical power in studies that use phylogenetic trees that are not completely resolved. The present study is designed to meet both of these goals by quantifying the phylogenetic diversity and dispersion of simulated communities using resolved and gradually ‘unresolved’ phylogenies. The results show that: (i) measures of community phylogenetic diversity and dispersion are generally more sensitive to loss of resolution basally in the phylogeny and less sensitive to loss of resolution terminally; and (ii) the loss of phylogenetic resolution generally causes false negative results rather than false positives.     

Severe Loss of Suitable Climatic Conditions for Marsupial Species in Brazil: Challenges and Opportunities for Conservation

A wide range of evidences indicate climate change as one the greatest threats to biodiversity in the 21st century. The impacts of these changes, which may have already resulted in several recent species extinction, are species-specific and produce shifts in species phenology, ecological interactions, and geographical distributions. Here we used cutting-edge methods of species distribution models combining thousands of model projections to generate a complete and comprehensive ensemble of forecasts that shows the likely impacts of climate change in the distribution of all 55 marsupial species that occur in Brazil. Consensus projections forecasted range shifts that culminate with high species richness in the southeast of Brazil, both for the current time and for 2050. Most species had a significant range contraction and lost climate space. Turnover rates were relatively high, but vary across the country. We also mapped sites retaining climatic suitability. They can be found in all Brazilian biomes, especially in the pampas region, in the southern part of the Brazilian Atlantic Forest, in the north of the Cerrado and Caatinga, and in the northwest of the Amazon. Our results provide a general overview on the likely effects of global climate change on the distribution of marsupials in the country as well as in the patterns of species richness and turnover found in regional marsupial assemblages.