Phylogenetic Community Research Articles

Propagule pressure increase and phylogenetic diversity decrease community\u2019s susceptibility to invasion

BackgroundInvasions pose a large threat to native species, but the question of why some species are more invasive, and some communities more prone to invasions than others, is far from solved. Using 10 different three-species bacterial communities, we tested experimentally if the phylogenetic relationships between an invader and a resident community and the propagule pressure affect invasion probability.ResultsWe found that greater diversity in phylogenetic distances between the members of resident community and the invader lowered invasion success, and higher propagule pressure increased invasion success whereas phylogenetic distance had no clear effect. In the later stages of invasion, phylogenetic diversity had no effect on invasion success but community identity played a stronger role.ConclusionsTaken together, our results emphasize that invasion success does not depend only on propagule pressure, but also on the properties of the community members. Our results thus indicate that invasion is a process where both invader and residing community characters act in concert.

Range shifting species reduce phylogenetic diversity in high latitude communities via competition.

Under anthropogenic climate change, many species are expanding their ranges to higher latitudes and altitudes, resulting in novel species interactions. The consequences of these range shifts for native species, patterns of local biodiversity and community structure in high latitude ecosystems are largely unknown but critical to understand in light of widespread poleward expansions by many warm-adapted generalists. Using niche modelling, phylogenetic methods, and field and laboratory studies, we investigated how colonization of Scotland by a range expanding damselfly, Ischnura elegans, influences patterns of competition and niche shifts in native damselfly species, and changes in phylogenetic community structure. Colonization by I.elegans was associated with reduced population density and niche shifts in the resident species least related to I.elegans (Lestes sponsa), reflecting enhanced competition. Furthermore, communities colonized by I.elegans exhibited phylogenetic underdispersion, reflecting patterns of relatedness and competition. Our results provide a novel example of a potentially general mechanism whereby climate change-mediated range shifts can reduce phylogenetic diversity within high latitude communities, if colonizing species are typically competitively superior to members of native communities that are least-closely related to the colonizer.

Taxonomic, phylogenetic and functional diversity of an urban Amazonian avifauna

Amazonia is undergoing rapid urbanisation, but nothing has been published on the structure and function of urban Amazonian avifaunas. Here we present the results of a year-long survey of the avifauna of an Amazonian city, exploring temporal variation in its taxonomic, phylogenetic and functional diversity. We found urban bird communities to be taxonomically depauperate and dominated by a small subset of common species typical of second growth and river-edge habitats. Broad patterns of phylogenetic community similarity typically resembled those found in other studies on urban Neotropical bird assemblages, with insectivores the dominant guild. There was significant temporal variation in taxonomic and phylogenetic structure owing to the seasonal arrival and departure of a regionally over-represented minority of migratory species. Although the urban avian assemblage is of limited regional conservation value, it may still offer significant biodiversity services and represent one of few points of contact for local people with biodiversity.

Spatial analysis of phylogenetic community structure: New version of a classical method

The increasing availability of phylogenetic information facilitates the use of evolutionary methods in community ecology to reveal the importance of evolution in the species assembly process. However, while several methods have been applied to a wide range of communities across different spatial scales with the purpose of detecting non-random phylogenetic patterns, the spatial aspects of phylogenetic community structure have received far less attention. Accordingly, the question for this study is: can point pattern analysis be used for revealing the phylogenetic structure of multi-species assemblages? We introduce a new individual-centered procedure for analyzing the scale-dependent phylogenetic structure of multi-species point patterns based on digitized field data. The method uses nested circular plots with increasing radii drawn around each individual plant and calculates the mean phylogenetic distance between the focal individual and all individuals located in the circular ring delimited by two successive radii. This scale-dependent value is then averaged over all individuals of the same species and the observed mean is compared to a null expectation with permutation procedures. The method detects particular radius values at which the point pattern of a single species exhibits maximum deviation from the expectation towards either phylogenetic aggregation or segregation. Its performance is illustrated using data from a grassland community in Hungary and simulated point patterns. The proposed method can be extended to virtually any distance function for species pairs, such as functional distances.

Life cycle matters: DNA barcoding reveals contrasting community structure between fern sporophytes and gametophytes

AbstractFerns are the only major lineage of vascular plants that have nutritionally independent sporophyte (diploid) and gametophyte (haploid) life stages. However, the implications of this unique life cycle for fern community ecology have rarely been considered. To compare patterns of community structure between fern sporophytes and gametophytes, we conducted a survey of the ferns of the islands of Moorea and Tahiti (French Polynesia). We first constructed a DNA barcode library (plastid rbcL and trnH‐psbA) for the two island floras including 145 fern species. We then used these DNA barcodes to identify more than 1300 field‐collected gametophytes from 25 plots spanning an elevational gradient from 200 to 2000 m. We found that species richness of fern sporophytes conforms to the well‐known unimodal (i.e., mid‐elevation peak) pattern, reaching a maximum at ~1000–1200 m. Moreover, we found that fern sporophyte communities become increasingly phylogenetically clustered at high elevations. In contrast, species richness of fern gametophytes was consistent across sites, and gametophytes showed no correlation of phylogenetic community structure with elevation. Turnover of sporophyte and gametophyte communities was closely linked with elevation at shallow phylogenetic levels, but not at deeper nodes in the tree. Finally, we found several species for which gametophytes had broader ranges than sporophytes, including a vittarioid fern with abundant gametophytes but extremely rare sporophytes. Our study highlights the importance of including diverse life history stages in surveys of community structure, and has implications for the possible impacts of climate change on the distribution of fern diversity.

IMPACTS OF PHYLOGENETIC DILUTION AND CONCENTRATION EFFECTS ON SPECIES DIVERSITY AND DISTRIBUTION PATTERNS

In theoretical ecology and community ecology, it is still unclear how phylogenetic community structure and species distributions are linked together. In this paper, a neutral model for evaluating phylogenetic constraints on species diversity and distribution patterns is developed to address these issues. To accomplish this, temporal species distribution and diversity patterns are evaluated and simulated by considering the impact of phylogenetic relatedness of species in a lattice landscape with square grids. A continuous patch for the resultant distributional range map of a species is defined as a group of grids in which the interior grids are adjacent to each other while the edge grids of the patch are isolated from other remaining grids in the range map. The adjacency or isolation of a grid with respect to another grid follows the von Neumann neighborhood criterion. The hypothesis tested is: phylogenetically closely related species tend to avoid each other (phylogenetic dilution), which produces a phylogenetic overdispersion pattern. In this case, all species have similar species abundances and distribution-patch size patterns. In contrast, if closely related species tend to associate together (phylogenetic concentration), a phylogenetic clustering pattern emerges: phylogenetically distinct species tend to have higher abundances and more large distribution patches. Using simulations, this paper presents results which demonstrate the reverse phenomenon: if it is assumed that phylogenetic relatedness of species is modeled as a dilution effect, the resultant distributional maps for evolutionarily distinct species present significantly increased numbers of continuous large patches. An evolutionarily distinct clade tends to have significantly higher relative abundance than other clades in all simulations. It was also found that if phylogenetic relatedness of species is modeled as a concentration effect, the simulated distributional map of each species would present a similar percentage of large patches for both evolutionarily unique and common clades for many cases when the community size is large enough. However, being similar to dilution effect, the resultant species relative abundance for evolutionarily unique clade is significantly higher than that for evolutionarily common clade. In conclusion, evolutionary distinct species will have more chances to survive with high populations and less fragmented distributional range in environments where the phylogenetic dilution effect is functioning. It is hoped that these results contributed to clarifying the complex associations generated by phylogenetic community structure in future ecological and evolutionary studies.

The Tropical Forests of Southern China and Conservation of Biodiversity

Species-rich tropical forests once occurred along much of China’s southern border, from southeastern Xizang (Tibet) and southern Yunnan to southwestern Guangxi, southern Taiwan and Hainan, mainly south of 22°30’N latitude. These Chinese forests are similar to Southeast Asian lowland tropical forests in their profiles and physiognomic characteristics, floristic composition and species richness. Studies of these southern forests in China are reviewed. Complete vegetation studies on the physiognomy and floristic composition have been done in southern Yunnan, Hainan and southwestern Guangxi. Forest fragmentation, dispersal patterns of trees, and the maintenance, population dynamics, phylogenetic community structure, tree functionality and phylogenetic diversity and conservation of these tropical Chinese forests have also been studied. Major changes in land use in China have resulted in an increase in rubber and Eucalyptus plantations and a decrease in the extent of southern forests. The direct results have been fragmentation and loss of biodiversity. The underplanting of economic crops in native forests also threatens to destroy saplings and seedlings, causing the forest to lose its regenerative capacity. Limiting further expansion of monoculture tree plantations, restricting underplanting, and promoting multi-species agroforestry systems are needed in China to conserve the biodiversity of its forests.

Linking the community structure of arbuscular mycorrhizal fungi and plants: a story of interdependence?

Arbuscular mycorrhizal fungi (AMF) are crucial to plants and vice versa, but little is known about the factors linking the community structure of the two groups. We investigated the association between AMF and the plant community structure in the nearest neighborhood of Festuca brevipila in a semiarid grassland with steep environmental gradients, using high-throughput sequencing of the Glomeromycotina (former Glomeromycota). We focused on the Passenger, Driver and Habitat hypotheses: (i) plant communities drive AMF (passenger); (ii) AMF communities drive the plants (driver); (iii) the environment shapes both communities causing covariation. The null hypothesis is that the two assemblages are independent and this study offers a spatially explicit novel test of it in the field at multiple, small scales. The AMF community consisted of 71 operational taxonomic units, the plant community of 47 species. Spatial distance and spatial variation in the environment were the main determinants of the AMF community. The structure of the plant community around the focal plant was a poor predictor of AMF communities, also in terms of phylogenetic community structure. Some evidence supports the passenger hypothesis, but the relative roles of the factors structuring the two groups clearly differed, leading to an apparent decoupling of the two assemblages at the relatively small scale of this study. Community phylogenetic structure in AMF suggests an important role of within-assemblage interactions.

Advances of Community-Level Plant DNA Barcoding in China.

DNA barcoding is a commonly used bio-technology in multiple disciplines including biology, environmental science, forensics and inspection, etc. Forest dynamic plots provide a unique opportunity to carry out large-scale, comparative, and multidisciplinary research for plant DNA barcoding. The paper concisely reviewed four previous progresses in China; specifically, species discrimination, community phylogenetic reconstruction, phylogenetic community structure exploration, and biodiversity index evaluation. Further, we demonstrated three major challenges; specifically, building the impetus to generate DNA barcodes using multiple plant DNA markers for all woody species at forest community levels, analyzing massive DNA barcoding sequence data, and promoting theoretical innovation. Lastly, we raised five possible directions; specifically, proposing a “purpose-driven barcode” fit for multi-level applications, developing new integrative sequencing strategies, pushing DNA barcoding beyond terrestrial ecosystem, constructing national-level DNA barcode sequence libraries for special plant groups, and establishing intelligent identification systems or online server platforms. These efforts will be potentially valuable to explore large-scale biodiversity patterns, the origin and evolution of life, and will also facilitate preservation and utilization of biodiversity resources.

Phylogenetic community structure of fungal endophytes in seagrass species

AbstractA total of 81 fungal endophytes were isolated from four seagrass species:

Disturbance by an endemic rodent in an arid shrubland is a habitat filter: effects on plant invasion and taxonomical, functional and phylogenetic community structure.

Disturbance often drives plant invasion and may modify community assembly. However, little is known about how these modifications of community patterns occur in terms of taxonomic, functional and phylogenetic structure. This study evaluated in an arid shrubland the influence of disturbance by an endemic rodent on community functional divergence and phylogenetic structure as well as on plant invasion. It was expected that disturbance would operate as a habitat filter favouring exotic species with short life cycles. Sixteen plots were sampled along a disturbance gradient caused by the endemic fossorial rodent Spalacopus cyanus , measuring community parameters and estimating functional divergence for life history traits (functional dispersion index) and the relative contribution to functional divergence of exotic and native species. The phylogenetic signal (Pagel's lambda) and phylogenetic community structure (mean phylogenetic distance and mean nearest taxon phylogenetic distance) were also estimated. The use of a continuous approach to the disturbance gradient allowed the identification of non-linear relationships between disturbance and community parameters. The relationship between disturbance and both species richness and abundance was positive for exotic species and negative for native species. Disturbance modified community composition, and exotic species were associated with more disturbed sites. Disturbance increased trait convergence, which resulted in phylogenetic clustering because traits showed a significant phylogenetic signal. The relative contribution of exotic species to functional divergence increased, while that of natives decreased, with disturbance. Exotic and native species were not phylogenetically distinct. Disturbance by rodents in this arid shrubland constitutes a habitat filter over phylogeny-dependent life history traits, leading to phylogenetic clustering, and drives invasion by favouring species with short life cycles. Results can be explained by high phenotypic and phylogenetic resemblance between exotic and native species. The use of continuous gradients when studying the effects of disturbance on community assembly is advocated.

Can functional traits account for phylogenetic signal in community composition?

Phylogenetic and functional trait-based analyses inform our understanding of community composition, yet methods for quantifying the overlap in information derived from functional traits and phylogenies remain underdeveloped. Does adding traits to analyses of community composition reduce the phylogenetic signal in the residual variation? If not, then measured functional traits alone may be insufficient to explain community assembly. We propose a general statistical framework to quantify the proportion of phylogenetic pattern in community composition that remains after including measured functional traits. We then illustrate the framework with applications to two empirical data sets. Both data sets showed strong phylogenetic attraction, with related species likely to co-occur in the same communities. In one data set, including traits eliminated all phylogenetic signals in the residual variation of both abundance and presence/absence patterns. In the second data set, including traits reduced phylogenetic signal in residuals by 25% and 98% for abundance and presence/absence data, respectively. Our framework provides an explicit way to estimate how much phylogenetic community pattern remains in the residual variation after including measured functional traits. Knowing that functional traits account for most of the phylogenetic pattern should provide confidence that important traits for phylogenetic community structure have been identified. Conversely, knowing that there is unexplained residual phylogenetic information should spur the search for additional functional traits or other processes underlying community assembly.

Phylogenetic occupancy models integrate imperfect detection and phylogenetic signal to analyze community structure.

Biological communities are structured phylogenetically-closely related species are typically more likely to be found at the same sites. This may be, in part, because they respond similarly to environmental gradients. Accurately surveying biological communities is, however, made difficult by the fact that detection of species is not perfect. In recent years, numerous statistical methods have been developed that aim to overcome deficiencies in the species detection process. However, these methods do not allow investigators to assess phylogenetic community structure. Here, we introduce the phylogenetic occupancy model (POM), which accounts for imperfect species detection while assessing phylogenetic patterns in community structure. Using simulated data sets we show that the POM grants less biased estimates of phylogenetic structure than models without imperfect detection, and can correctly ascertain the effects of species traits on community composition while accounting for evolutionary non-independence of taxa. Integrating phylogenetic methods into widely used occupancy models will help clarify how evolutionary history influences modern day communities.

Radiating despite a Lack of Character: Ecological Divergence among Closely Related, Morphologically Similar Honeyeaters (Aves: Meliphagidae) Co-occurring in Arid Australian Environments.

Quantifying the relationship between form and function can inform use of morphology as a surrogate for ecology. How the strength of this relationship varies continentally can inform understanding of evolutionary radiations; for example, does the relationship break down when certain lineages invade and diversify in novel habitats? The 75 species of Australian honeyeaters (Meliphagidae) are morphologically and ecologically diverse, with species feeding on nectar, insects, fruit, and other resources. We investigated Meliphagidae ecomorphology and community structure by (1) quantifying the concordance between morphology and ecology (foraging behavior), (2) estimating rates of trait evolution in relation to the packing of ecological space, and (3) comparing phylogenetic and trait community structure across the broad environmental gradients of the continent. We found that morphology explained 37% of the variance in ecology (and 62% vice versa), and we uncovered well-known bivariate relationships among the multivariate ecomorphological data. Ecological trait diversity declined less rapidly than phylogenetic diversity along a gradient of decreasing precipitation. We employ a new method (trait fields) and extend another (phylogenetic fields) to show that while species in phylogenetically clustered, arid-environment assemblages are similar morphologically, they are as varied in foraging behavior as those from more diverse assemblages. Thus, although closely related and similar morphologically, these arid-adapted species have diverged in ecological space to a similar degree as their mesic counterparts.

Phylogenetic clustering found in lichen but not in plant communities in European heathlands

Species richness is a widespread measure to evaluate the effect of different management histories on plant communities and their biodiversity. However, analysing the phylogenetic structure of plant communities could provide new insights into the effects of different management methods on community assemblages and provide further guidance for conservation decisions. Heathlands require permanent management to ensure the existence of such a cultural landscape. While traditional management with grazing is time consuming, mechanical methods are often applied but their consequences on the phylogenetic community assemblages are still unclear. We sampled 60 vegetation plots in dry sandy heathlands (EU habitat type 2310) in northern Germany stratified by five different heathland management histories: fire, plaggen (turf cutting), mowing, deforestation and intensive grazing. Due to the distant relationship of vascular plants and lichens, we assembled two phylogenetic trees, one for vascular plants and one for lichens. We then calculated phylogenetic diversity (PD) and measures of phylogenetic community structure for vascular plant and lichen communities. Deforested areas supported significantly higher PD values for vascular plant communities. We found that PD was strongly correlated with species richness (SR) but the calculation of rarefied PD was uncorrelated to SR leading to a different ranking of management histories. We observed phylogenetic clustering in the lichen communities but not for vascular plants. Thus, management by mowing and intensive grazing promotes habitat filtering of lichens, while management histories that cause greater disturbance such as fire and plaggen do not seem to affect phylogenetic community structure. The set of management strategies fulfilled the goals of the managers in maintaining a healthy heathland community structure. However, management strategies that cause less disturbance can offer an additional range of habitat for other taxonomic groups such as lichen communities.

Environmental filtering and neutral processes shape octocoral community assembly in the deep sea.

The ecological and evolutionary processes that interact to shape community structure are poorly studied in the largest environment on earth, the deep sea. Phylogenetic data and morphological traits of octocorals were coupled with environmental factors to test hypotheses of community assembly in the deep (250-2500m) Gulf of Mexico. We found lineage turnover at a depth of 800-1200m, with isidids and chrysogorgiids at deeper depths and a diversity of species from across the phylogeny occupying shallower depths. Traits, including axis type, polyp shape, and polyp retraction, differed among species occupying the shallowest (250-800m) and deepest (1200-2500m) depths. Results also indicated that octocoral species sort along an environmental gradient of depth. Closely related octocoral species sorted into different depth strata on the upper to middle slope, likely due to barriers imposed by water masses followed by adaptive divergence. Within any given depth zone down to 2000m, the phylogenetic relatedness of co-existing octocorals was random, indicating that stochastic processes, such as recruitment, also shape community structure. At depths >2000m, octocorals were more closely related than expected by chance due to the diversification of chrysogorgiids and isidids, which retain conserved traits that impart survival at deeper and/or colder depths. Polyp density, size, and inter-polyp distance were significantly correlated with depth, particularly in plexaurids and isidids, highlighting trait lability across depth and supporting that environmental gradients influence octocoral morphology. Our community phylogenetics approach indicates that both environmental filtering and neutral processes shape community assembly in the deep sea.

Environmental filtering of eudicot lineages underlies phylogenetic clustering in tropical South American flooded forests.

The phylogenetic community assembly approach has been used to elucidate the role of ecological and historical processes in shaping tropical tree communities. Recent studies have shown that stressful environments, such as seasonally dry, white-sand and flooded forests tend to be phylogenetically clustered, arguing for niche conservatism as the main driver for this pattern. Very few studies have attempted to identify the lineages that contribute to such assembly patterns. We aimed to improve our understanding of the assembly of flooded forest tree communities in Northern South America by asking the following questions: are seasonally flooded forests phylogenetically clustered? If so, which angiosperm lineages are over-represented in seasonally flooded forests? To assess our hypotheses, we investigated seasonally flooded and terra firme forests from the Magdalena, Orinoco and Amazon Basins, in Colombia. Our results show that, regardless of the river basin in which they are located, seasonally flooded forests of Northern South America tend to be phylogenetically clustered, which means that the more abundant taxa in these forests are more closely related to each other than expected by chance. Based on our alpha and beta phylodiversity analyses we interpret that eudicots are more likely to adapt to extreme environments such as seasonally flooded forests, which indicates the importance of environmental filtering in the assembly of the Neotropical flora.

Soil bacterial community and functional shifts in response to altered snowpack in moist acidic tundra of northern Alaska

Abstract. Soil microbial communities play a central role in the cycling of carbon (C) in Arctic tundra ecosystems, which contain a large portion of the global C pool. Climate change predictions for Arctic regions include increased temperature and precipitation (i.e. more snow), resulting in increased winter soil insulation, increased soil temperature and moisture, and shifting plant community composition. We utilized an 18-year snow fence study site designed to examine the effects of increased winter precipitation on Arctic tundra soil bacterial communities within the context of expected ecosystem response to climate change. Soil was collected from three pre-established treatment zones representing varying degrees of snow accumulation, where deep snow ∼ 100 % and intermediate snow ∼ 50 % increased snowpack relative to the control, and low snow ∼ 25 % decreased snowpack relative to the control. Soil physical properties (temperature, moisture, active layer thaw depth) were measured, and samples were analysed for C concentration, nitrogen (N) concentration, and pH. Soil microbial community DNA was extracted and the 16S rRNA gene was sequenced to reveal phylogenetic community differences between samples and determine how soil bacterial communities might respond (structurally and functionally) to changes in winter precipitation and soil chemistry. We analysed relative abundance changes of the six most abundant phyla (ranging from 82 to 96 % of total detected phyla per sample) and found four (Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi) responded to deepened snow. All six phyla correlated with at least one of the soil chemical properties (% C, % N, C : N, pH); however, a single predictor was not identified, suggesting that each bacterial phylum responds differently to soil characteristics. Overall, bacterial community structure (beta diversity) was found to be associated with snow accumulation treatment and all soil chemical properties. Bacterial functional potential was inferred using ancestral state reconstruction to approximate functional gene abundance, revealing a decreased abundance of genes required for soil organic matter (SOM) decomposition in the organic layers of the deep snow accumulation zones. These results suggest that predicted climate change scenarios may result in altered soil bacterial community structure and function, and indicate a reduction in decomposition potential, alleviated temperature limitations on extracellular enzymatic efficiency, or both. The fate of stored C in Arctic soils ultimately depends on the balance between these mechanisms.

The influence of climate on species distribution over time and space during the late Quaternary

Understanding the effect of climate on the composition of communities and its change over time and space is one of the major aims in ecology and paleoecology. Herein, we tackled on this issue by studying late Quaternary large mammal paleocommunities of Eurasia. The late Quaternary was a period of strong environmental instability, especially characterized by the occurrence of the last glacial maximum (LGM). We used community phylogenetics and joint species distribution models in order to understand the factors determining paleocommunity composition in the late Quaternary. Our results support the existence of strong climatic selection operating on the LGM fauna, both through the disappearance of warm-adapted species such as Elephas antiquus, Hippopothamus amphibious, and Stephanorhinus hemitoechus, and by setting the stage for the existence of a community characterized by cold-adapted large mammals. Patterns of abundance in the fossil record, co-occurrence between species pairs, and the extent of climatic forcing on faunal composition, differ between paleocommunities, but not between extinct and extant species, which is consistent with the idea that climate change, rather than the presence of humans, exerted a major effect on the survival of the late Quaternary megafauna.

구멍갈파래(Ulva pertusa)에 서식하는 해양세균의 계통학적 다양성 및 군집구조 분석

구멍갈파래(Ulva pertusa)에 서식하는 해양세균의 계통학적 다양성 및 군집구조 분석