Phylogenetic Community Research Articles

Endemicity and evolutionary value: a study of Chilean endemic vascular plant genera

This study uses phylogeny-based measures of evolutionary potential (phylogenetic diversity and community structure) to evaluate the evolutionary value of vascular plant genera endemic to Chile. Endemicity is regarded as a very important consideration for conservation purposes. Taxa that are endemic to a single country are valuable conservation targets, as their protection depends upon a single government policy. This is especially relevant in developing countries in which conservation is not always a high resource allocation priority. Phylogeny-based measures of evolutionary potential such as phylogenetic diversity (PD) have been regarded as meaningful measures of the “value” of taxa and ecosystems, as they are able to account for the attributes that could allow taxa to recover from environmental changes. Chile is an area of remarkable endemism, harboring a flora that shows the highest number of endemic genera in South America. We studied PD and community structure of this flora using a previously available supertree at the genus level, to which we added DNA sequences of 53 genera endemic to Chile. Using discrepancy values and a null model approach, we decoupled PD from taxon richness, in order to compare their geographic distribution over a one-degree grid. An interesting pattern was observed in which areas to the southwest appear to harbor more PD than expected by their generic richness than those areas to the north of the country. In addition, some southern areas showed more PD than expected by chance, as calculated with the null model approach. Geological history as documented by the study of ancient floras as well as glacial refuges in the coastal range of southern Chile during the quaternary seem to be consistent with the observed pattern, highlighting the importance of this area for conservation purposes.

Disentangling the phylogenetic and ecological components of spider phenotypic variation.

An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhabitat scale, although phylogenic signal is present in both scales. Taken together, these results suggest that whereas at the habitat scale selective colonization affect spider body size and shape, at fine scales both selective colonization and adaptive evolution determine spider body shape. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape. We also discussed the relevance in considering multiple scales when studying phylogenetic community structure.

Microbial community structure and function of Nitrobenzene reduction biocathode in response to carbon source switchover

The stress of poised cathode potential condition and carbon source switchover for functional biocathode microbial community influences is poorly understood. Using high-throughput functional gene array (GeoChip v4.2) and Illumina 16S rRNA gene MiSeq sequencing, we investigated the phylogenetic and functional microbial community of the initial inoculum and biocathode for bioelectrochemical reduction of nitrobenzene to less toxic aniline in response to carbon source switchover (from organic glucose to inorganic bicarbonate). Selective transformation of nitrobenzene to aniline maintained in the bicarbonate fed biocathode although nitrobenzene reduction rate and aniline formation rate were significantly decreased compared to those of the glucose-fed biocathode. When the electrical circuit of the glucose-fed biocathode was disconnected, both rates of nitrobenzene reduction and of aniline formation were markedly decreased, confirming the essential role of an applied electric field for the enhancement of nitrobenzene reduction. The stress of poised cathode potential condition led to clear succession of microbial communities from the initial inoculum to biocathode and the carbon source switchover obviously changed the microbial community structure of biocathode. Most of the dominant genera were capable of reducing nitroaromatics to the corresponding aromatic amines regardless of the performance mode. Heterotrophic Enterococcus was dominant in the glucose-fed biocathode while autotrophic Paracoccus and Variovorax were dominant in the bicarbonate-fed biocathode. Relatively higher intensity of diverse multi-heme cytochrome c (putatively involved in electrons transfer) and carbon fixation genes was observed in the biocarbonate-fed biocathode, likely met the requirement of the energy conservation and maintained the nitrobenzene selective reduction capability after carbon source switchover. Extracellular pilin, which are important for biofilm formation and potential conductivity, had a higher gene abundance in the glucose-fed biocathode might explain the enhancement of electro-catalysis activity for nitrobenzene reduction with glucose supply. Dominant nitroaromatics-reducing or electrochemically active bacteria and diverse functional genes related to electrons transfer and nitroaromatics reduction were associated with nitrobenzene reduction efficiency of biocathode communities in response to carbon source switchover.

Niche filtering rather than partitioning shapes the structure of temperate forest ant communities

An ever-increasing number of studies use tools from community phylogenetics to infer the processes underlying the assembly of communities. However, very few studies simultaneously use experimental approaches to characterize the ecological niches of species and directly assess the importance of these structuring processes. In this study, we developed an experimental approach for quantifying the use of four types of food resources and three habitat templets in temperate forest ant assemblages. We then used null models to assess whether niches overlapped more or less than expected by chance. Finally, we integrated comparative phylogenetic methods with experimental data on niche use to assess the degree of phylogenetic signal in several key components of the niche. We found that niche filtering, rather than partitioning, was the predominant structuring force. Niche filtering resulted from conservatism in habitat niches in evolutionary time and limitations in the availability of food resources in ecological time. Our study thus supports the idea that similarities in niches among species, rather than the differences, drive the assembly of ant communities.

Phylogenetic diversity stabilizes community biomass

Aims The relationship between biodiversity and ecological stability is a long-standing issue in ecology. Current diversity–stability studies, which have largely focused on species diversity, often report an increase in the stability of aggregate community properties with increasing species diversity. Few studies have examined the linkage between phylogenetic diversity, another important dimension of biodiversity, and stability. By taking species evolutionary history into account, phylogenetic diversity may better capture the diver sity of traits and niches of species in a community than species diversity and better relate to temporal stability. In this study, we investigated whether phylogenetic diversity could affect temporal stability of community biomass independent of species diversity. Methods We performed an experiment in laboratory microcosms with a pool of 12 bacterivorous ciliated protist species. To eliminate the possibility of species diversity effects confounding with phylogenetic diversity effects, we assembled communities that had the same number of species but varied in the level of phylogenetic diversity. Weekly disturbance, in the form of short-term temperature shock, was imposed on each microcosm and species abundances were monitored over time. We examined the relationship between temporal stability of community biomass and phylogenetic diversity and evaluated the role of several stabilizing mechanisms for explaining the influence of phylogenetic diversity on temporal stability. Important Findings Our results showed that increasing phylogenetic diversity promoted temporal stability of community biomass. Both total community biomass and summed variances showed a U-shaped relationship with phylogenetic diversity, driven by the presence of large, competitively superior species that attained large biomass and high temporal variation in their biomass in both low and high phylogenetic diversity communities. Communities without these species showed patterns consistent with the reduced strength of competition and increasingly asynchronous species responses to environmental changes under higher phylogenetic diversity, two mechanisms that can drive positive diversity–stability relationships. These results support the utility of species phylogenetic knowledge for predicting ecosystem functions and their stability.

Phylogenetic community ecology: integrating community ecology and evolutionary biology

Phylogenetic community ecology: integrating community ecology and evolutionary biology

Diversity and phylogenetic community structure of ants along a Costa Rican elevational gradient

The diversity and phylogenetic community structure of many organisms is negatively affected by factors that covary with elevation. On the Pacific slope of the Cordillera Guanacaste within Area de Conservación Guanacaste (ACG) in northwestern Costa Rica we found a negative relationship between elevation and ant diversity on each of three volcanos. This pattern was evident when diversity was measured through molecular operational taxonomic units (MOTU) or by phylogenetic diversity (PD) based on DNA barcodes or a multi‐gene phylogeny. We observed an asymmetrical mid‐elevation peak at approximately 600–800 m and we found high species turnover between sites on the same mountain and among the three mountains. At the highest elevation cloud forest sites we found evidence of significant phylogenetic clustering, the expected result of environmental filtering. The narrow elevational range of each species, coupled with the high diversity at each sampling point, emphasizes that climate change will bring strong changes in the location and composition of biodiversity on these mountains. The structure and composition of the hyperdiverse communities present at any one elevation is extremely vulnerable to a changing climate.

White-tailed deer are a biotic filter during community assembly, reducing species and phylogenetic diversity.

Community assembly entails a filtering process, where species found in a local community are those that can pass through environmental (abiotic) and biotic filters and successfully compete. Previous research has demonstrated the ability of white-tailed deer (Odocoileus virginianus) to reduce species diversity and favour browse-tolerant plant communities. In this study, we expand on our previous work by investigating deer as a possible biotic filter altering local plant community assembly. We used replicated 23-year-old deer exclosures to experimentally assess the effects of deer on species diversity (H'), richness (SR), phylogenetic community structure and phylogenetic diversity in paired browsed (control) and unbrowsed (exclosed) plots. Additionally, we developed a deer-browsing susceptibility index (DBSI) to assess the vulnerability of local species to deer. Deer browsing caused a 12 % reduction in H' and 17 % reduction in SR, consistent with previous studies. Furthermore, browsing reduced phylogenetic diversity by 63 %, causing significant phylogenetic clustering. Overall, graminoids were the least vulnerable to deer browsing based on DBSI calculations. These findings demonstrate that deer are a significant driver of plant community assembly due to their role as a selective browser, or more generally, as a biotic filter. This study highlights the importance of knowledge about the plant tree of life in assessing the effects of biotic filters on plant communities. Application of such knowledge has considerable potential to advance our understanding of plant community assembly.

Phylogenetic community structure of subtropical forests along elevational gradients in Ailao Mountains of southwest China

Understanding the maintenance of biodiversity and community assembly is a central issue in community ecology. Here, we examined patterns of the community phylogenetic structure of subtropical forests along an elevational gradient in the Ailao Mountains of southwest China. We surveyed all trees with diameter at breast height ≥1 cm in 16 plots, and constructed a community phylogeny from DNA barcode sequence data with a constraint tree based on Angiosperm Phylogeny Group (APG) III. We found that the community structure changed from phylogenetically clustered to phylogenetically overdispersed with increasing elevation. Co-occurring trees at low-elevation communities tended to be more closely related than expected by chance, implying that these communities were structured primarily by habitat filtering. Clustered and over-dispersed phylogenetic compositions were showed in mid-elevation communities, suggesting that these communities are structured by habitat filtering or competitive exclusion. At high-elevation sites, NRI (Net Relatedness Index) showed clustering, but NTI (Nearest Taxon Index) showed randomness or over-dispersion. We therefore interpreted our results with caution. It is possible that convergent evolution 第 4 期 卢孟孟等: 沿海拔梯度变化的哀牢山亚热带森林群落系统发育结构 439 may be occurred independently in distantly related lineages under higher environmental stress at high elevations. Taken together, the results of our study provide insight into the potential role of elevational gradients in shaping community composition and phylogenetic diversity.

Plant functional and phylogenetic turnover correlate with climate and land use in the Western Swiss Alps

Understanding the relative importance of historical and environmental processes in the structure and composition of communities is one of the longest quests in ecological research. Increasingly, researchers are relying on the functional and phylogenetic β-diversity of natural communities to provide concise explanations on the mechanistic basis of community assembly and the drivers of trait variation among species. The present study investigated how plant functional and phylogenetic β-diversity change along key environmental and spatial gradients in the Western Swiss Alps. Methods Using the quadratic diversity measure based on six functional traits: specific leaf area (SLA), leaf dry matter content (LDMC), plant height (H), leaf carbon content (C), leaf nitrogen content (N), and leaf carbon to nitrogen content (C/N) alongside a species-resolved phylogenetic tree, we relate variations in climate, spatial geographic, land use and soil gradients to plant functional and phylogenetic turnover in mountain communities of the Western Swiss Alps. Important findings Our study highlights two main points. First, climate and land use factors play an important role in mountain plant community turnover. Second, the overlap between plant functional and phylogenetic turnover along these gradients correlates with the low phylogenetic signal in traits, suggesting that in mountain landscapes, trait lability is likely an important factor in driving plant community assembly. Overall, we demonstrate the importance of climate and land use factors in plant functional and phylogenetic community turnover, and provide valuable complementary insights into understanding patterns of β-diversity along several ecological gradients.

Integrating phylogenetic community structure with species distribution models: an example with plants of rock barrens

Approaches using phylogenetic pattern in ecological communities to deduce processes of community assembly have been criticised as disconnected from foundations in ecological mechanism, especially with respect to lack of data about abiotic and biotic niches. These criticisms can be addressed with analyses of organismal traits that underlie environmental filtering, competitive exclusion, and other candidate processes; however, the difficulty of assembling large trait databases means that such studies remain uncommon. We suggest a synthesis of phylogenetic community structure analysis and species distribution modeling that we believe can allow inference about community processes without prohibitive data requirements. We illustrate this method for angiosperm communities of rock barrens in eastern Canada. First, we analyzed phylogenetic community structure of four rock‐barren sites at three nested spatial scales (quadrat to region). For the nine most common species in our barrens, we used regional occurrence records to build species distribution models identifying environmental drivers of the nine species’ distributions. Coefficients of these models represent implicit trait data that summarize each species’ response to the environmental drivers in the model. We then tested for phylogenetic signal in these traits, to ask whether ecological forces acting on them could be generating phylogenetic community structure. We found strong phylogenetic clustering at the quadrat level, while patterns at larger scales were complex. Our distribution model suggested drought stress as the dominant driver for distributions of all the species, consistent with local correlations with soil depth, and the species’ responses to drought showed strong phylogenetic signal. The convergence of results from phylogenetic community structure and species distribution modeling suggests that barren communities are structured at the quadrat level by environmental filtering effects of moisture stress, to which species have phylogenetically patterned responses.

Plant DNA barcodes promote the development of phylogenetic commu- nity ecology

Plant DNA barcodes promote the development of phylogenetic commu- nity ecology

Anthropogenic disturbance shapes phylogenetic and functional tree community structure in a subtropical forest

Forests across the world are increasingly affected by human activities, with unmanaged forests often in early- and mid-successional phases after anthropogenic disturbances. In consequence, it is important to obtain a better understanding of these successional dynamics and their implications for the functioning of forest ecosystems. Here, we investigate this issue for a highly diverse subtropical forest in China, as it is particularly relevant here. China naturally harbors large forested areas and much forest biodiversity, but its forests are also subject to strong anthropogenic pressures, with only 2% of its forest remaining undisturbed. We assess how anthropogenic disturbance shapes two important aspects of forest biodiversity, namely phylogenetic and functional community structure. Comparing plots that have not been disturbed within the last 100years, plots clear-cut ∼50years ago, and plots clear-cut ∼50years ago and then selectively cut ∼20years ago, we find that the abundant gymnosperm species which are important pioneer species in southern China strongly affect phylogenetic structure, causing over-dispersion among large stems in disturbed stands. A tendency for decreasingly clumped phylogenetic structure over succession when considering only angiosperms may reflect an initial filtering by disturbance whose legacy decreases during succession. Multi-trait functional structure, which was not significantly affected by gymnosperms, has similar patterns to the phylogenetic structure without gymnosperms. Phylogenetic and functional structure differs among stem size classes, but with partially divergent trends. Functional structure is more strongly linked to a disturbance indicator, the proportion of light-demanding species, than phylogenetic structure. Our results illustrate that past tree harvesting has left strong legacies in the phylogenetic and functional structure of tree stands in a highly diverse southern Chinese forest and thus may also shape their functioning.

Bacterial Communities in Soil Under Moss and Lichen-Moss Crusts

Biological soil crusts are symbiotic microbial communities formed by green algae, mosses, fungi, lichens, cyanobacteria and bacteria in different proportions. Crusts contribute to soil fertility and favour water retention and infiltration. However, little is known about the bacterial community structure in soil under the crusts. Soil was sampled under a moss crust (considered the MOSS group), lichen plus moss (considered the LICHEN group) and bare soil (considered the BARE group) and the microbial communities determined using nearly full 16S rRNA gene libraries. Bacteria belonging to seven different phyla were found and the Acidobacteria and Alphaproteobacteria were the dominant in each group. The crusts affected negatively the abundance of the Burkholderiales. The phylogenetic diversity and bacterial community membership were different in the LICHEN group compared to the BARE and MOSS groups, but not species richness and community structure. The beta diversity analysis also revealed a different bacterial community structure beneath the LICHEN and MOSS crusts, suggesting species-specific influence. This is a first insight into the effect of a biological soil crust on the bacterial community structure in an organic matter rich soil of a high altitude mountain forest.

Barro Colorado Island's phylogenetic assemblage structure across fine spatial scales and among clades of different ages

Phylogenetic analyses of assemblage membership provide insight into how ecological communities are structured. However, despite the scale-dependency of many ecological processes, little is known about how assemblage and source pool size definitions can be altered, either alone or together, to provide insight into how ecological diversity is maintained. Moreover, although studies have acknowledged that different clades within an assemblage may be structured by different forces, there has been no attempt to relate the age of a clade to its community phylogenetic structure. Using assemblage phylogenies and spatially explicit data for trees from Barro Colorado Island (BCI), we show that larger assemblages, and assemblages with larger source pools, are more phylogenetically clustered. We argue that this reflects competition, the influence of pathogens, and chance assembly at smaller spatial scales, all operating within the context of wider-scale habitat filtering. A community phylogenetic measure that is based on a null model derived explicitly from trait evolution theory, D, is better able to detect these differences than commonly used measures such as SES(MPD) and SES(MNTD). We also detect a moderate tendency for stronger phylogenetic clustering in younger clades, which suggests that coarse analyses of diverse assemblages may be missing important variation among clades. Our results emphasize the importance of spatial and phylogenetic scale in community phylogenetics and show how varying these scales can help to untangle complex assembly processes.

Specificity and temporal dynamics of complex bacteria–sponge symbiotic interactions

Microbes are known to form intricate and intimate relationships with most animal and plant taxa. Microbe--host symbiotic associations are poorly explored in comparison with other species interaction networks. The current paradigm on symbiosis research stems from species-poor systems where pairwise and reciprocally specialized interactions between a single microbe and a single host that coevolve are the norm. These symbioses involving just a few species are fascinating in their own right, but more diverse and complex host-associated microbial communities are increasingly found, with new emerging questions that require new paradigms and approaches. Here we adopt an intermediate complexity approach to study the specificity, phylogenetic community structure, and temporal variability of the subset of the most abundant bacteria associated with different sponge host species with diverse eco-evolutionary characteristics. We do so by using a monthly resolved annual temporal series of host-associated and free-living bacteria. Bacteria are very abundant and diverse within marine sponges, and these symbiotic interactions are hypothesized to have a very ancient origin. We show that host-bacteria reciprocal specialization depends on the temporal scale and level of taxonomic aggregation considered. Sponge hosts with similar eco-evolutionary characteristics (e.g., volume of tissue corresponding to microbes, water filtering rates, and microbial transmission type) have similar bacterial phylogenetic community structure when looking at interactions aggregated over time. In general, sponge hosts hypothesized to form more intricate relationships with bacteria show a remarkably persistent bacterial community over time. Other hosts, however, show a large turnover similar to that observed for free-living bacterioplankton. Our study highlights the importance of exploring temporal variability in host--microbe interaction networks if we aim to determine how specific and persistent these poorly explored but extremely common interactions are.

Phylogenetic plant community structure along elevation is lineage specific.

The trend of closely related taxa to retain similar environmental preferences mediated by inherited traits suggests that several patterns observed at the community scale originate from longer evolutionary processes. While the effects of phylogenetic relatedness have been previously studied within a single genus or family, lineage-specific effects on the ecological processes governing community assembly have rarely been studied for entire communities or flora. Here, we measured how community phylogenetic structure varies across a wide elevation gradient for plant lineages represented by 35 families, using a co-occurrence index and net relatedness index (NRI). We propose a framework that analyses each lineage separately and reveals the trend of ecological assembly at tree nodes. We found prevailing phylogenetic clustering for more ancient nodes and overdispersion in more recent tree nodes. Closely related species may thus rapidly evolve new environmental tolerances to radiate into distinct communities, while older lineages likely retain inherent environmental tolerances to occupy communities in similar environments, either through efficient dispersal mechanisms or the exclusion of older lineages with more divergent environmental tolerances. Our study illustrates the importance of disentangling the patterns of community assembly among lineages to better interpret the ecological role of traits. It also sheds light on studies reporting absence of phylogenetic signal, and opens new perspectives on the analysis of niche and trait conservatism across lineages.

Highly diverse and spatially heterogeneous mycorrhizal symbiosis in a rare epiphyte is unrelated to broad biogeographic or environmental features

Symbiotic interactions are common in nature. In dynamic or degraded environments, the ability to associate with multiple partners (i.e. broad specificity) may enable species to persist through fluctuations in the availability of any particular partner. Understanding how species interactions vary across landscapes is necessary to anticipate direct and indirect consequences of environmental degradation on species conservation. We asked whether mycorrhizal symbiosis by populations of a rare epiphytic orchid (Epidendrum firmum) is related to geographic or environmental heterogeneity. The latter would suggest that interactions are governed by environmental conditions rather than historic isolation of populations and/or mycorrhizal fungi. We used DNA-based methods to identify mycorrhizal fungi from eleven E.firmum populations in Costa Rica. We used molecular and phylogenetic analyses to compare associations. Epidendrum firmum exhibited broad specificity, associating with diverse mycorrhizal fungi, including six Tulasnellaceae molecular operational taxonomic units (MOTUs), five Sebacinales MOTUs and others. Notably, diverse mycorrhizal symbioses formed in disturbed pasture and roadside habitats. Mycorrhizal fungi exhibited significant similarity within populations (spatial and phylogenetic autocorrelation) and significant differences among populations (phylogenetic community dissimilarity). However, mycorrhizal symbioses were not significantly associated with biogeographic or environmental features. Such unexpected heterogeneity among populations may result from complex combinations of fine-scale environmental factors and macro-evolutionary patterns of change in mycorrhizal specificity. Thus, E.firmum exhibits broad specificity and the potential for opportunistic associations with diverse fungi. We suggest that these characteristics could confer symbiotic assurance when mycorrhizal fungi are stochastically available, which may be crucial in dynamic or disturbed habitats such as tropical forest canopies.

Patterns of species diversity and phylogenetic structure of vascular plants on the Qinghai‐Tibetan Plateau

Large-scale patterns of species richness and the underlying mechanisms regulating these patterns have long been the central issues in biogeography and macroecology. Phylogenetic community structure is a result of combined effects of contemporary ecological interactions, environmental filtering, and evolutionary history, and it links community ecology with biogeography and trait evolution. The Qinghai-Tibetan Plateau provides a good opportunity to test the influence of contemporary climate on shaping species richness because of its unique geological history, cold climate, and high biodiversity. In this study, based on high-resolution distributions of ˜9000 vascular plant species, we explored how species richness and phylogenetic structure of vascular plants correlate with climates on the highest (and species rich) plateau on the Earth. The results showed that most of the vascular plants were distributed on the eastern part of the plateau; there was a strong association between species richness and climate, even after the effects of habitat heterogeneity were controlled. However, the responses of richness to climate remarkably depended on life-forms. Richness of woody plants showed stronger climatic associations than that of herbaceous plants; energy and water availability together regulated richness pattern of woody plants; whereas water availability predominantly regulated richness pattern of herbaceous plants. The phylogenetic structure of vascular species clustered in most areas of the plateau, suggesting that rapid speciation and environment filtering dominated the assembly of communities on the plateau. We further propose that biodiversity conservation in this area should better take into account ecological features for different life-forms and phylogenetic lineages.

Soil conditions and phylogenetic relatedness influence total community trait space during early plant succession

Aims The total space of traits covered by the members of plant communities is an important parameter of ecosystem functioning and complexity. We trace the variability of trait space during early plant succession and ask how trait space co-varies with phylogenetic community structure and soil conditions. Particularly, we are inter ested in the small-scale variability in trait space and the influence of biotic and abiotic filters. Methods We use data on species richness and soil conditions from the first 7 years of initial succession of an artificial catchment in north-eastern Germany. Total functional attribute diversity serves as a proxy to total trait space. Important Findings Total trait space steadily increased during succession. We observed high small-scale variability in total trait space that was positively cor related with species richness and phylogenetic segregation and negatively correlated with total plant cover. Trait space increased with soil carbonate content, while pH and the fraction of sandy material behaved indifferently. Our results indicate that during early succession, habitat filtering processes gain importance leading to a lesser increase in trait space than expected from the increase in species richness alone.