Archaeal diversity in naturally occurring and impacted environments from a tropical region

AIMS: To evaluate archaeal diversity in natural and impacted habitats from Rio de Janeiro state, Brazil, a tropical region of South America. METHODS AND RESULTS: 16S rRNA gene was amplified directly by polymerase chain reaction (PCR) from genomic DNA, extracted from Guanabara Bay (GB) water, halomarine sediment (HS), municipal landfill leachate, agricultural soil and wastewater treatment (WT) system. Five archaeal 16S rDNA clone libraries were constructed. A total of 123 clones, within the five libraries analysed, were clustered into 29 operational taxonomic units, related to cultivated (24%) and uncultivated (76%) organisms. Rarefaction analysis showed that the libraries contained different levels of diversity. PCR-denaturing gradient gel electrophoresis (DGGE) of 16S-23S intergenic spacer regions confirmed the presence of a dominant phylotype, revealed by the WT system clone library. CONCLUSIONS: Archaeal communities of impacted environments seem to be confined to specific ecosystems with similar physicochemical properties, while communities from natural environments appear to be widely distributed. The presence of a high number of phylotypes related to uncultivated organisms suggests new archaeal lineages. SIGNIFICANCE AND IMPACT OF THE STUDY: This study reports, for the first time, the analysis of archaeal diversity in tropical environments from Brazil, and adds sequences from this region to the developing database of 16S rRNA clone libraries from environmental samples.     

Phylogenetic assemblage structure of North American trees is more strongly shaped by glacial–interglacial climate variability in gymnosperms than in angiosperms

How fast does biodiversity respond to climate change? The relationship of past and current climate with phylogenetic assemblage structure helps us to understand this question. Studies of angiosperm tree diversity in North America have already suggested effects of current water–energy balance and tropical niche conservatism. However, the role of glacial–interglacial climate variability remains to be determined, and little is known about any of these relationships for gymnosperms. Moreover, phylogenetic endemism, the concentration of unique lineages in restricted ranges, may also be related to glacial–interglacial climate variability and needs more attention. We used a refined phylogeny of both angiosperms and gymnosperms to map phylogenetic diversity, clustering and endemism of North American trees in 100‐km grid cells, and climate change velocity since Last Glacial Maximum together with postglacial accessibility to recolonization to quantify glacial–interglacial climate variability. We found: (1) Current climate is the dominant factor explaining the overall patterns, with more clustered angiosperm assemblages toward lower temperature, consistent with tropical niche conservatism. (2) Long‐term climate stability is associated with higher angiosperm endemism, while higher postglacial accessibility is linked to to more phylogenetic clustering and endemism in gymnosperms. (3) Factors linked to glacial–interglacial climate change have stronger effects on gymnosperms than on angiosperms. These results suggest that paleoclimate legacies supplement current climate in shaping phylogenetic patterns in North American trees, and especially so for gymnosperms.     

The macroevolution of climatic niches and its role in ant diversification

1. Investigating how climatic niches change over evolutionary timescales is a necessary step to understanding the current distribution of lineages, yet few studies have addressed this issue using comprehensive datasets. In this study, the evolution of ant climatic niches is investigated at a global scale based on bioclimatic data associated with 163 481 ant occurrence records. The resulting dataset was subjected to principal component analysis, and the scores obtained were used to characterise the main axes of ant climatic niche evolution. 2. Principal component axis 1 (PC1) reflected variation in average temperature and seasonality – consistent with typical tropical/temperate gradients – whereas PC2 was associated with varying levels of aridity. Evolution along these two niche axes was markedly different: differences in the amount of explained variance between PC1 (65%) and PC2 (19%) suggest that climatic niche evolution was nearly three times more pronounced along a tropical–temperate climate axis. 3. There was statistically significant phylogenetic signal on PC1, with genera occupying more tropical conditions diversifying at a faster rate, yet neither of these results is significant on PC2. In addition, most of the ancient ant lineages are associated with conditions of low seasonality and high temperatures. 4. These results provide partial support for the tropical conservatism hypothesis as an explanation for geographical patterns of ant species richness.     

Phylogenetic structure of angiosperm communities during tropical forest succession

The phylogenetic structure of ecological communities can shed light on assembly processes, but the focus of phylogenetic structure research thus far has been on mature ecosystems. Here, I present the first investigation of phylogenetic community structure during succession. In a replicated chronosequence of 30 sites in northeastern Costa Rica, I found strong phylogenetic overdispersion at multiple scales: species present at local sites were a non-random assemblage, more distantly related than chance would predict. Phylogenetic overdispersion was evident when comparing the species present at each site with the regional species pool, the species pool found in each age category to the regional pool or the species present at each site to the pool of species found in sites of that age category. Comparing stem size classes within each age category, I found that during early succession, phylogenetic overdispersion is strongest in small stems. Overdispersion strengthens and spreads into larger size classes as succession proceeds, corroborating an existing model of forest succession. This study is the first evidence that succession leaves a distinct signature in the phylogenetic structure of communities.     

Life span variation in 13 Drosophila species: a comparative study on life span,environmental variables and stress resistance

Recently, heterogeneity of the environment has been suggested as an important player in the evolution of life span variation. Established ageing theories propose that life span variation is the result of coevolution with other traits, such as stress resistance. This study aimed to compare these alternative hypotheses by examining the relationship between four environmental variables and different types of stress resistance traits with life span in 13 Drosophila species originating from tropical, subtropical and temperate environments (ecotypes). Average life span was found to differ significantly both between species and sexes, but only male life span correlated with the environment and cold resistance. While controlling for phylogeny, the environmental variable precipitation seasonality and resistance against cold‐induced stress explained most variation in male life span. Furthermore, male life span varied between species in a manner represented by environmental variables linked to the different ecotypes, such that tropical species lived longer and were less cold resistant. The current results suggest that general mechanisms underlying stress resistance and life span are unlikely. In addition, our results point to the environment independently shaping variation in life span and cold resistance rather than genetic interactions.     

Buttress trees in a 20-hectare tropical dipterocarp rainforest in Xishuangbanna,SW China

Aims Buttresses are prevalent and are important to many ecological processes in tropical rainforests but are overlooked in many rainforest studies. Based on a buttress survey in a 20-hectare plot, this study aims to answer the following questions: (I) Is buttress forming a fixed species characteristic? (ii) Is there any phylogenetic signal for buttress forming across a broad taxonomic scale? (iii) Is buttress forming an inherent feature or simply induced by environmental factors, and how is this relevant to the size of the tree?Methods We surveyed buttresses for all 95940 trees with diameter at breast height (DBH) ≥10mm in a 20-ha tropical dipterocarp rainforest in Xishuangbanna, SW China. The occurrence of buttresses was compared across different taxa and across different tree-size classes. A phylogenetic analysis was conducted among buttressed and non-buttressed species in order to understand the evolutionary background of buttress formation.Important findings This preliminary study showed that buttress trees are very abundant (making up 32% of trees with ≥100mm DBH) in this 20-ha tropical rainforest situated at the northern edge of the tropics. Fifty-one percent of the 468 tree species in the plot had stems that produced buttresses. Large trees were more likely to develop buttresses than smaller ones. We found that although buttress formation is not a fixed species characteristic, there is a strong phylogenetic signal for buttress formation in larger species.     

The early evolution of the mega‐diverse genus Begonia (Begoniaceae) inferred from organelle DNA phylogenies

Begonia L. is one of the largest flowering plant genera, a ubiquitous component of many tropical forests and an economically important ornamental plant. In the present study, we address the early evolution of Begonia by generating molecular phylogenies from approximately 7000 bases of chloroplast DNA and approximately 6000 bases of mitochondrial DNA for each of 30 exemplar Begonia species. Broadscale biogeographic patterns found in the phylogenies, together with previously estimated divergence dates, indicated that extant Begonia lineages first diversified in Africa and then subsequently in America and Asia. The phylogenies also revealed that the closest African relatives of the American and Asian Begonia are seasonally‐adapted species. Moderate to strong incongruence between the phylogenies suggested that they differ genealogically. These differences could have been the result of either interspecific hybridization and/or incomplete lineage sorting. The results obtained in the present study provide a much needed genus‐wide framework for future evolutionary studies of this exceptionally diverse tropical genus. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 243–250.     

Seed viability in Bursera: The relative contribution of environmental variation and phylogenetic relatedness

Seed viability is a crucial factor affecting the regeneration potential of seeds, but there is little information on how this trait varies across habitats, populations, species, and higher taxonomic units, as well as on the relative contributions of evolutionary history and environmental factors to this trait. Here we evaluate the relative contributions of climatic variability and phylogenetic history to seed viability in a group of species of Bursera that belong to two distinct lineages (sections Bursera and Bullockia). We analyzed 39 seed lots from 11 species, comprising several populations and 2 years, and estimated embryo presence and viability in each lot. We examined spatial and temporal variation in viability and analyzed the relationship between this trait and water availability using regression models; the amount of phylogenetic signal in seed viability was also estimated. Mean seed viability was consistently low in species of section Bursera (mean 29.7%) and substantially higher in species of section Bullockia (mean 79.6%). A high proportion of unviable seeds were embryoless. Spatial and temporal variation in seed viability was significant but usually low among populations and species. The relationship between water availability and seed viability was not significant, but the amount of phylogenetic signal in seed viability was high and significant (λ = 0.74). There is a clear difference in seed viability among the two sections of Bursera. During the split of the two sections in the middle Eocene, the reorganization of the genome may have involved changes in fruit morphology associated with differences in parthenocarpy among them.     

Evolutionary history of the flora of Mexico: Dry forests cradles and museums of endemism

Mexico is considered an exceptional biogeographic area with a varied endemic flora, however spatial phylogenetic measures of biodiversity have not yet been estimated to understand how its flora assembled to form the current vegetation. Patterns of species richness, endemism, phylogenetic diversity, phylogenetic endemism and centers of neo‐ and paleo‐endemism were determined to examine differences and congruence among these measures, and their implications for conservation. Of 24 360 vascular plant species 10 235 (42%) are endemic. Areas of endemism and phylogenetic endemism were associated with dry forests in zones of topographic complexity in mountain systems, in deserts, and in isolated xeric vegetation. Every single locality where seasonally tropical dry forests have been reported in Mexico was identified as an area of endemism. Significant phylogenetic diversity was the most restricted and occurred in the Trans‐Mexican Volcanic Belt and in the Sierra de Chiapas. Notably, the highest degree of phylogenetic clustering comprising neo‐, paleo‐, and super‐endemism was identified in southernmost Mexico. Most vascular plant lineages diverged in the Miocene (5–20 mya) when arid environments expanded across the world. The location of Mexico between two very large landmasses and the fact that more than fifty percent of its surface is arid favored the establishment of tropical lineages adapted to extreme seasonality and aridity. These lineages were able to migrate from both North and South America across Central America presumably during the Miocene and to diversify, illustrating the signature of the flora of Mexico of areas of endemism with a mixture of neo‐ and paleo‐endemism.     

Environmental correlates for tropical tree diversity and distribution patterns in Borneo

Aim Identify environmental correlates for tropical tree diversity and composition. Location Borneo, Southeast Asia. Methods A GIS‐environmental database with 5 arc minute (c. 10 × 10 km) resolution was combined with tree inventory data. Tree diversity, phylogenetic diversity (PD) and the two main compositional gradients were determined for 46 tree inventories. Akaike's information criterion and a data jackknifing procedure were used to select 50 explanatory models for diversity and composition gradients. The average of these models was used as our final diversity and compositional model. We applied Moran's I to detect spatial autocorrelation of residuals. Results Tree diversity, PD and the two main compositional gradients in Borneo were all significantly correlated with the environment. Tree diversity correlated negatively with elevation, soil depth, soil coarseness (texture) and organic carbon content, whereas it correlated positively with soil C:N ratio, soil pH, moisture storage capacity and annual rainfall. Tree PD was correlated positively with elevation and temperature seasonality and was largely determined by gymnosperms. However, angiosperm PD also correlated positive with elevation. Compositional patterns were strongly correlated with elevation but soil texture, cation‐exchange‐capacity, C:N ratio, C and N content and drainage were also important next to rainfall seasonality and El Niño Southern Oscillation drought impact. Main conclusions Although elevation is the most important correlate for diversity and compositional gradients in Borneo, significant additional variability is explained by soil characteristics (texture, carbon content, pH, depth, drainage and nutrient status) and climate (annual rainfall, rainfall seasonality and droughts). The identified environmental correlates for diversity and composition gradients correspond to those found in other tropical regions of the world. Differences between the regions are mainly formed by differences in the relative importance of the environmental variables in explaining diversity and compositional gradients.     

The influence of historical dispersal on the phylogenetic structure of tree communities in the tropical Andes

We test for evidence of the Tropical Niche Conservatism or the Out of The Tropics hypotheses in structuring patterns of tree community composition along a 2000 + meter elevational gradient in the northern tropical Andes. By collecting and integrating data on the presence–absence of tree species within plots with phylogenetic information, we analyzed the following: (a) patterns of phylogenetic dispersion and species diversity along the elevational gradient based on indexes of net relatedness, nearest taxon relatedness, and species richness (α‐diversity); and (b) the replacement of lineages along the gradient using the PhyloSorensen metric (β‐diversity). More specifically, we established 20 0.25‐ha permanent tree inventory plots between 750 and 2,802 m asl where all individuals with diameter at breast height (DBH) ≥ 10 cm were measured and identified. We then used a series of linear models to test for changes in α and β diversity between plots in relation to elevation. Neither the net relatedness index nor the nearest taxon index showed a significant relationship with elevation. However, there was greater phylogenetic overdispersion at intermediate elevations; this likely reflects the mixing of species with contrasting origins from tropical and temperate lineages. β‐diversity between plots was negatively related to the corresponding difference in elevation, indicating that closely related lineages occupy similar ranges of elevation and temperature. We conclude that the immigration of lineages from extra‐tropical regions has significant effects in determining the phylogenetic structure of tree communities in tropical Andean forests. Abstract in Spanish is available with online material.     

Soil phosphorus heterogeneity promotes tree species diversity and phylogenetic clustering in a tropical seasonal rainforest

The niche theory predicts that environmental heterogeneity and species diversity are positively correlated in tropical forests, whereas the neutral theory suggests that stochastic processes are more important in determining species diversity. This study sought to investigate the effects of soil nutrient (nitrogen and phosphorus) heterogeneity on tree species diversity in the Xishuangbanna tropical seasonal rainforest in southwestern China. Thirty‐nine plots of 400 m² (20 × 20 m) were randomly located in the Xishuangbanna tropical seasonal rainforest. Within each plot, soil nutrient (nitrogen and phosphorus) availability and heterogeneity, tree species diversity, and community phylogenetic structure were measured. Soil phosphorus heterogeneity and tree species diversity in each plot were positively correlated, while phosphorus availability and tree species diversity were not. The trees in plots with low soil phosphorus heterogeneity were phylogenetically overdispersed, while the phylogenetic structure of trees within the plots became clustered as heterogeneity increased. Neither nitrogen availability nor its heterogeneity was correlated to tree species diversity or the phylogenetic structure of trees within the plots. The interspecific competition in the forest plots with low soil phosphorus heterogeneity could lead to an overdispersed community. However, as heterogeneity increase, more closely related species may be able to coexist together and lead to a clustered community. Our results indicate that soil phosphorus heterogeneity significantly affects tree diversity in the Xishuangbanna tropical seasonal rainforest, suggesting that deterministic processes are dominant in this tropical forest assembly.     

A trait-based approach to determining principles of plant biogeography

Lineage-specific traits determine how plants interact with their surrounding environment. Unrelated species may evolve similar phenotypic characteristics to tolerate, persist in, and invade environments with certain characteristics, resulting in some traits becoming relatively more common in certain types of habitats. Analyses of these general patterns of geographical trait distribution have led to the proposal of general principles to explain how plants diversify in space over time. Trait–environment correlation analyses quantify to what extent unrelated lineages have similar evolutionary responses to a given type of habitat. In this synthesis, I give a short historical overview on trait–environment correlation analyses, from some key observations from classic naturalists to modern approaches using trait evolution models, large phylogenies, and massive data sets of traits and distributions. I discuss some limitations of modern approaches, including the need for more realistic models, the lack of data from tropical areas, and the necessary focus on trait scoring that goes beyond macromorphology. Overcoming these limitations will allow the field to explore new questions related to trait lability and niche evolution and to better identify generalities and exceptions in how plants diversify in space over time.     

功能多样性和谱系多样性对热带云雾林群落构建的影响

近年来, 功能多样性和谱系多样性为探究群落构建机制提供了新方法。为了更准确地了解海南岛高海拔热带云雾林群落构建机制, 该研究以海南岛霸王岭热带云雾林为对象, 测定7个环境因子和13个植物功能性状。利用主成分分析(PCA)筛选环境因子, 以霸王岭、尖峰岭和黎母山热带云雾林分布物种建立区域物种库, 结合模型, 分析Rao二次熵(RaoQ)和平均成对谱系距离(MPD)变化对植物群落构建的影响。结果表明: 林冠开阔度、土壤全磷含量和坡度是影响植物群落构建的关键环境因子。多数功能性状的系统发育信号很低且不显著, 说明热带云雾林群落的系统发育关系与功能性状随历史进程变化不一致。RaoQ和MPD的实际观测值都显著低于期望值, 且其标准效应值与土壤磷含量显著相关, 说明生境过滤是驱动热带云雾林群落构建的关键因子, 土壤磷含量是群落构建的关键环境筛。     

海南岛3个林区热带云雾林植物多样性变化

以分布在海南岛西部(霸王岭国家级自然保护区, 21个样方)、西南部(尖峰岭国家级自然保护区, 12个样方)和中部(黎母山省级自然保护区, 15个样方)的热带云雾林为研究对象, 研究α及β物种多样性、功能多样性、谱系多样性的变化, 为植物多样性的保护提供科学依据。结果表明: 尖峰岭群落树木个体多度、物种丰富度最大, 黎母山群落树木个体多度、物种丰富度最小; 黎母山群落间物种组成差异最大, 霸王岭群落间物种组成差异最小, 海南岛霸王岭(西部)、尖峰岭(西南部)和黎母山(中部) 3个林区热带云雾林物种多样性差异可能与空气温度和相对湿度有关。尖峰岭群落内功能丰富度、Rao’s二次熵最低, 功能均匀度最高, 群落间平均成对性状距离最小, 反映群落构建主要受环境筛影响; 霸王岭群落Rao’s二次熵最高, 功能均匀度最低, 群落间平均成对性状距离最大, 反映群落构建主要受限制相似性影响; 黎母山群落内功能丰富度最高, 群落间平均最近性状距离最大, 表明限制相似性在黎母山热带云雾林群落构建中的作用更重要。霸王岭群落内谱系多样性、物种间平均最近相邻谱系距离均较大, 反映物种间谱系关系趋于发散; 黎母山群落内谱系多样性、物种间平均成对谱系距离及群落间平均成对谱系距离均最小, 反映物种间谱系关系趋于聚集; 而尖峰岭群落内物种间平均成对谱系距离、群落间平均成对谱系距离最大, 但物种间平均最近相邻谱系距离最小, 反映物种间谱系关系既具有发散又具有聚集的共存格局。因此, 海南岛热带云雾林群落植物多样性变化格局与环境及物种间相互作用有关。     

Evolutionary heritage shapes tree distributions along an Amazon‐to‐Andes elevation gradient

Understanding how evolutionary constraints shape the elevational distributions of tree lineages provides valuable insight into the future of tropical montane forests under global change. With narrow elevational ranges, high taxonomic turnover, frequent habitat specialization, and exceptional levels of endemism, tropical montane forests and trees are predicted to be highly sensitive to environmental change. Using plot census data from a gradient traversing > 3,000 m in elevation on the Amazonian flank of the Peruvian Andes, we employ phylogenetic approaches to assess the influence of evolutionary heritage on distribution trends of trees at the genus‐level. We find that closely related lineages tend to occur at similar mean elevations, with sister genera pairs occurring a mean 254 m in elevation closer to each other than the mean elevational difference between non‐sister genera pairs. We also demonstrate phylogenetic clustering both above and below 1,750 m a.s.l, corresponding roughly to the cloud‐base ecotone. Belying these general trends, some lineages occur across many different elevations. However, these highly plastic lineages are not phylogenetically clustered. Overall, our findings suggest that tropical montane forests are home to unique tree lineage diversity, constrained by their evolutionary heritage and vulnerable to substantial losses under environmental changes, such as rising temperatures or an upward shift of the cloud‐base.     

Long-term reproductive behaviour of woody plants across seven Bornean forest types in the Gunung Palung National Park (Indonesia): suprannual synchrony, temporal productivity and fruiting diversity

For 68 months, we observed the reproductive behaviour of 7288 woody plants (172 figs, 1457 climbers and 5659 trees) spanning major soil and elevational gradients. Two 2–3 month community-wide supra-annual fruiting events were synchronized across five forest types, coinciding with ENSO events. At least 27 genera in 24 families restricted their reproduction to these events, which involved a substantial proportion of tree diversity (> 80% of phylogenetic diversity). During these events, mean reproductive levels (8.5%) represented an almost four-fold increase compared with other months. These patterns indicate a strong behavioural advantage to this unusual reproductive behaviour. Montane forest experienced a single, separate fruiting peak while the peat swamp forest did not participate. Excluding these events, no temporal reproductive pattern was detectible, at either the landscape or forest type. These phenological patterns have major implications for the conservation of frugivore communities, with montane and swamp forests acting as 'keystone' forests.     

Phylogenetic turnover in tropical tree communities: impact of environmental filtering,biogeography and mesoclimatic niche conservatism

Aim We addressed the roles of environmental filtering, historical biogeography and evolutionary niche conservatism on the phylogenetic structure of tropical tree communities with the following questions. (1) What is the impact of mesoclimatic gradients and dispersal limitation on phylogenetic turnover and species turnover? (2) How does phylogenetic turnover between continents compare in intensity with the turnover driven by climatic gradients at a regional scale? (3) Are independent phylogenetic reconstructions of the mesoclimatic niche of clades congruent between continents? Location Panama Canal Watershed and Western Ghats (India), two anciently divergent biogeographic contexts but with comparable rainfall gradients. Methods Using floristic data for 50 1‐ha plots in each region, independent measures of phylogenetic turnover (Π_ST) and species turnover (Jaccard) between plots were regressed on geographic and ecological distances. Mesoclimatic niches were reconstructed for each node of the phylogeny and compared between the two continents. Results (1) The phylogenetic turnover within each region is best explained by mesoclimatic differences (environmental filtering), while species turnover depends both on mesoclimatic differences and geographic distances (dispersal limitation). (2) The phylogenetic turnover between continents (Π_ST = 0.009) is comparable to that caused by mesoclimatic gradients within regions (Π_ST = 0.010) and both effects seem cumulative. (3) Independent phylogenetic reconstructions of the mesoclimatic niches were strongly correlated between the two continents (r = 0.61), despite the absence of shared species. Main conclusions Our results demonstrate a world‐wide deep phylogenetic signal for mesoclimatic niche within a biome, indicating that positive phylogenetic turnover at a regional scale reflects environmental filtering in plant communities.     

Phylogenetic Composition of Angiosperm Diversity in the Cloud Forests of Mexico

Several members of the most ancient living lineages of flowering plants (angiosperms) inhabit humid, woody, mostly tropical habitats. Here we assess whether one of these forest types, the cloud forests of Mexico (CFM), contain a relatively higher proportion of phylogenetically early-diverging angiosperm lineages. The CFM houses an extraordinary plant species diversity, including members of earliest-diverging angiosperm lineages. The phylogenetic composition of CFM angiosperm diversity was evaluated through the relative representation of orders and families with respect to the global flora, and the predominance of phylogenetically early- or late-diverging lineages. Goodness-of-fit tests indicated significant differences in the proportional local and global representation of angiosperm clades. The net difference between the percentage represented by each order and family in the CFM and the global flora allowed identification of clades that are overrepresented and underrepresented in the CFM. Early-diverging angiosperm orders and families were found to be neither over- nor underrepresented in the CFM. A slight predominance of late-diverging phylogenetic levels among overrepresented clades, however, was encountered in the CFM. The resulting pattern suggests that cloud forests provide habitats where the most ancient angiosperm lineages have survived in the face of accumulating species diversity belonging to phylogenetically late-diverging lineages.