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138 results for “community phylogenetic”
Phylogenetic restriction of plant invasion in drought-stressed environments: implications for insect-pollinated plant communities in water-limited ecosystems
<p><span><strong>Background</strong>: Plant-pollinator community diversity has been found to decrease under conditions of drought stress, however research into the temporal dimensions of this phenomenon remains limited. In this study, we investigated the effect of seasonal drought on the temporal niche dynamics of entomophilous flowering plants in a water-limited ecosystem. We hypothesized that closely related native and exotic plants would tend to share similar life history, and that peak flowering events would therefore coincide with phylogenetic clustering in plant communities based on expected phenological responses of plant functional types to limitations in soil moisture availability.</span></p> <p><span><strong>Location</strong>:<b> </b>Galiano Island, British Columbia, Canada</span></p> <p><span><strong>Methods</strong>:<b> </b>Combining methods from pollinator research and phylogenetic community ecology, we tested the influence of environmental filtering over plant community phenology across gradients of landscape disturbance and soil moisture. Floral resource availability and community structure were quantified by counts of flowering shoots. We constructed a robust phylogeny to analyze spatial and temporal variation in phylogenetic patterns across the landscape, testing the significance of the observed patterns against a randomly generated community phylogeny. Phylogenetic metrics were then regressed against factors of disturbance and soil moisture availability. </span></p> <p><span><strong>Results</strong>:<b> </b>Critical seasonal fluctuations in floral resources coincided with significant phylogenetic clustering in plant communities, with decreasing plant diversity observed under conditions of increasing drought stress. Exotic plant species in the Asteraceae became increasingly pervasive across the landscape, occupying a late season temporal niche in drought-stressed environments.</span></p> <p><span><strong>Main conclusion</strong>:<b> </b>Results suggest that environmental filtering is the dominant assembly process structuring the temporal niche of plant communities in this water-limited ecosystem. Based on these results, and trends seen elsewhere, the overall diversity of plant-pollinator communities may be expected to decline with the increasing drought stress predicted under future climate scenarios.</span></p>
Data from: Geography and ecology shape the phylogenetic composition of Amazonian tree communities
<p><strong>Aim:</strong> Amazonia hosts more tree species, from numerous evolutionary lineages both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonised multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types.</p> <p><strong>Location:</strong> Amazonia.</p> <p><strong>Taxon:</strong> Angiosperms (Magnoliids; Monocots; Eudicots).</p> <p><strong>Methods:</strong> Data for the abundance of 5,082 tree species in 1,989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran's eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny.</p> <p><strong>Results:</strong> In the terra firme and várzea forest types, phylogenetic composition varies by geographic region, but the igapó and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate, and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R <sup>2</sup> = 19% overall for combined spatial/environmental effects). Phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R <sup>2</sup> = 28%). A greater number of lineages were significant indicators of geographic regions than forest types.</p> <p><strong>Main conclusions:</strong> Numerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization on specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions. </p>
Phylogenetic α- and β-diversities jointly reveal leaf-litter ant community assembly mechanisms along a tropical elevational gradient
<p>This study was conducted along the eastern slope of the Cofre de Perote mountain, in Veracruz, Mexico. This region is located at the junction of the Trans-Mexican volcanic belt and the Sierra Madre Oriental. We selected eight study sites spanning an elevational gradient of 3500 meters of altitude. Regardless of the geographical distance, all sites were systematically separated with an elevational difference of 500 meters on average between each other. We placed our study sites at the following elevations above sea level: 30-50 m, 610-670 m, 900-1010 m, 1470-1650 m, 2020-2230 m, 2470-2600 m, 3070-3160 m and 3480-3540 m, however, for simplicity, we will refer to each site as discrete units (i.e. 0, 600, 1000, 1500, 2100, 2500, 3100, 3500 m).</p> <p>Sampling sites were old-growth forests characterized by no obvious forest use and highly dominance of mature forests, except in the case of the lowest site (i.e., La Mancha), where most of its original vegetation has been transformed. To overcome the effect of perturbation in the studied patterns, we sampled La Mancha in a secondary forest with up to 30 years of regeneration. All sampling sites were closed-canopy forests in which a leaf-litter layer could be guaranteed. During the rainy season (July-September) of 2018 one 300-m transversal transect was located at each one of the eight study locations where we established 10 equidistantly sampling points (i.e., 30 meters between each other). Two independent 1-m2 samples were taken perpendicularly to each sampling point: one 10 meters on the right side and the other 10 meters from the left side. This procedure was repeated in a second transect placed during the dry season (March-May) of 2019 to increase community characterization as well as reduce any seasonality effect on our diversity patterns. Transects within an elevational site were separated at least 1 km away from each other. Thus, we obtained 320 m<sup>2</sup> leaf-litter samples characterized the whole mountain (8 study sites x 20 m<sup>2 </sup>per transect x 2 transects = 320 m<sup>2</sup>). In each 1-m<sup>2</sup> quadrat, we collected the leaf litter inside and sifted it through a coarse mesh screen of 1-cm grid size to remove the largest fragments and concentrate the fine litter. The concentrated fine litter from each sample was suspended in independent mini-Winkler sacks for 3 days in the laboratory. Falling arthropods were collected into a container with 95% ethanol. Ant workers were removed from each container for identification. When possible, specimens were identified at the species level. If not, we assigned a morphospecies number.</p> <p> </p> <p><strong>Phylogenetic tree constructions</strong></p> <p>Ideally, one would use a complete, species-level phylogeny of all ant species present in your study area to calculate phylogenetic diversity, yet our current understanding of ant relationships is still limited. As an alternative, we built a genus-level phylogeny based on the tree by Moreau & Bell, (2013), but using the phylogenetic relationships and divergence times within Myrmicinae from Ward et al. (2015). This phylogeny was then pruned to keep only a single species per genus to generate a genus-level phylogeny. To maximize taxonomic coverage, we replaced genera that were missing from those studies by closely-related lineages that were not present in our dataset using other phylogenetic studies (Borowiec, 2016; Lapolla et al., 2010; Schmidt & Shattuck, 2014). We then used the list of species (Supporting Information Table S1) in our dataset to simulate a species-level phylogeny in which the relationships within genera were obtained from a Yule (pure-birth) process using the <em>genus.to.species.tree</em> function in the “phytools” package (Revell, 2012). A total of 1000 simulated trees were obtained to account for phylogenetic uncertainty [see Arnan et al. (2018) and Divieso et al. (2020) for similar approach]. Additionally, we constructed a maximum clade credibility tree (hereafter MCC tree) which was used to summarize the uncertainty of the 1000 simulated trees. The MCC tree was constructed from the sample of the 1000 trees with the <em>maxCladeCred</em> function incorporated in the “ape” package (Paradis et al., 2019). Both the 1000 hypothetical trees and the MCC tree were used in downstream analyses (Supporting Information Fig. 1).</p>
Both source and recipient range phylogenetic community structure can predict the outcome of avian introductions
<p>Competing phylogenetic models have been proposed to explain the success of species introduced to other communities. Here, we present a study predicting the establishment success of birds introduced to Florida, Hawaii, and New Zealand using several alternative models, considering species' phylogenetic relatedness to source and recipient range taxa, propagule pressure, and traits. We find consistent support for the predictive ability of source region phylogenetic structure. However, we find that the effects of recipient region phylogenetic structure vary in sign and magnitude depending on inclusion of source region phylogenetic structure, delineation of the recipient species pool, and the use of phylogenetic correction in the models. We argue that tests of alternative phylogenetic hypotheses including the both source and recipient community phylogenetic structure, as well as important covariates such as propagule pressure, are likely to be critical for identifying general phylogenetic patterns in introduction success, predicting future invasions, and for stimulating further exploration of the underlying mechanisms of invasibility.</p>
Nuanced qualitative trait approaches reveal environmental filtering and phylogenetic constraints on lichen communities
<p>We propose that a qualitative trait approach based on more detailed nuanced traits may reveal previously overlooked patterns, especially when combined with phylogenetic perspectives. By sampling epiphytic lichens and using a functional approach based on nuanced qualitative traits, such as a much greater resolution over photobiont identity, type of cortex and chemical compounds, we evaluated the effects of environmental filtering and phylogenetic constraints on community assembly along natural succession of Atlantic rainforest. We found changes in taxonomic, functional and phylogenetic composition, structure and diversity. Functional traits such as photobiont genera, type of cortex, reproductive structures, propagule size and protection strategies showed strong responses to succession. Mature forests with a closed canopy impose strong environment filtering that is reflected in lichen species turnover, limiting diversity, but also holding different functional and phylogenetic composition. The use of a nuanced qualitative trait approach may overcome some of the limitations of using this type of traits and show the importance of often overlooked key lichen functional traits, including presence of carbon concentrating mechanisms in photobionts and cortex properties. Furthermore, this is the first study showing how patterns of phylogenetic assembly along forest succession structure lichen communities.</p>
Long-term nitrogen fertilization alters arbuscular mycorrhizal fungi community phylogenetic structure in plant roots across fine spatial scales
<p><span>Purpose:</span><span> Nitrogen deposition due to human activities is known to have a substantial impact on arbuscular mycorrhizal fungi (AMF) community in plant roots. However, the influence of elevated nitrogen on the phylogenetic structure of AMF across fine spatial scales, as well as the mechanisms behind such alterations, are remained poorly understood. </span></p> <p><span>Results:</span><span> Nitrogen addition significantly increased the phylogenetic alpha diversity (diversity within a plot) and the 'within-treatment' phylogenetic beta diversity (dissimilarity among replicate plots) of AMF communities, which resulted in an increased 'within-treatment' phylogenetic gamma diversity (overall diversity among all the replicate plots within a treatment). These changes were caused by the relative abundance decline of a dominant genus (</span><span>Glomus</span><span>) and an increase in non-dominant genera. Mechanically, nitrogen addition affected phylogenetic alpha diversity mainly by influencing soil properties. Likewise, the increased 'within-treatment' dissimilarity of plant community composition and changes in soil properties caused by nitrogen addition and plot distance contributed to an increase in within-treatment phylogenetic beta diversity. </span></p> <p><span>Conclusions:</span><span> We conclude that deterministic environmental filtering (both abiotic and biotic) and dispersal limitation effect played critical roles in AMF community assembly under global change scenarios. Insightfully, this study provides a mechanistic understanding of the response of AMF to nitrogen addition across fine scales.</span></p>
Spatial phylogenetic and phenotypic patterns reveal ontogenetic shifts in ecological processes of plant community assembly
The analysis of spatial phylogenetic and phenotypic structure of plant communities provides insight into the underlying processes and interactions governing their assembly, and how these may change during plant ontogeny. We used point pattern analysis to find out if saplings and adult plants are surrounded by phylogenetically and phenotypically more similar or dissimilar neighbours than expected by chance, and whether these associations change from the sapling to the adult stage. To this end, we combined information on the phylogenetic structure and eight phenotypic traits of 15 woody plant species in two Mediterranean mixed forests of southeastern Spain. At the community level, we found that the sapling bank at both sites did not show phylogenetic or phenotypic spatial patterns, but adults showed phylogenetic clustering (i.e., heterospecific neighbours were more similar than expected). At the species level, we found frequently repulsive patterns in the sapling bank of less abundant species (i.e., heterospecific sapling or adult neighbours were more dissimilar than expected) in both, phylogenetic and phenotypic analyses. For the adult stage, we found phylogenetic attraction (i.e., more similar neighbours) in just one species and phenotypic clustering in four species. The processes driving the assembly of the communities of saplings and adults leave detectable signals in the spatial phylogenetic and phenotypic structure of our two forest communities. Our findings reinforce the existence of ontogenetic shifts in the mechanisms involved in plant community assembly. Facilitation between phylogenetically distant and phenotypically divergent species favours the recruitment of less abundant species. However, processes acting later in the ontogeny ameliorate the competition between close relatives and determine the spatial structure of adult plants. Nevertheless, the role of phenotype in shaping adult-adult interactions was context- and trait-dependent. The use of spatial point pattern analysis allowed a nuanced interpretation of the phylogenetic and phenotypic structures of the plant community.
The Community Coevolution Model with application to the study of evolutionary relationships between genes based on phylogenetic profiles
<p>Organismal traits can evolve in a coordinated way, with correlated patterns of gains and losses reflecting important evolutionary associations. Discovering these associations can reveal important information about the functional and ecological linkages among traits. Phylogenetic profiles treat individual genes as traits distributed across sets of genomes and can provide a fine-grained view of the genetic underpinnings of evolutionary processes in a set of genomes. Phylogenetic profiling has been used to identify genes that are functionally linked, and to identify common patterns of lateral gene transfer in microorganisms. However, comparative analysis of phylogenetic profiles and other trait distributions should take into account the phylogenetic relationships among the organisms under consideration.</p> <p>Here we propose the Community Coevolution Model (CCM), a new coevolutionary model to analyze the evolutionary associations among traits, with a focus on phylogenetic profiles. In the CCM, traits are considered to evolve as a community with interactions, and the transition rate for each trait depends on the current states of other traits. Surpassing other comparative methods for pairwise trait analysis, CCM has the additional advantage of being able to examine multiple traits as a community to reveal more dependency relationships. We also develop a simulation procedure to generate phylogenetic profiles with correlated evolutionary patterns that can be used as benchmark data for evaluation purposes.</p> <p>A simulation study demonstrates that CCM is more accurate than other methods including the Jaccard Index and three tree-aware methods. The parameterization of CCM makes the interpretation of the relations between genes more direct, which leads to Darwin's scenario being identified easily based on the estimated parameters. We show that CCM is more efficient and fits real data better than other methods resulting in higher likelihood scores with fewer parameters. An examination of 3786 phylogenetic profiles across a set of 659 bacterial genomes highlights linkages between genes with common functions, including many patterns that would not have been identified under a non-phylogenetic model of common distribution. We also applied the CCM to 44 proteins in the well-studied Mitochondrial Respiratory Complex I and recovered associations that mapped well onto the structural associations that exist in the complex.</p>
Data from: Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions
1.Heterogeneity within pathogen species can have important consequences for how pathogens transmit across landscapes; however, discerning different transmission routes is challenging. 2.Here we apply both phylodynamic and phylogenetic community ecology techniques to examine the consequences of pathogen heterogeneity on transmission by assessing subtype specific transmission pathways in a social carnivore. 3.We use comprehensive social and spatial network data to examine transmission pathways for three subtypes of feline immunodeficiency virus (FIVPle) in African lions (Panthera leo) at multiple scales in the Serengeti National Park, Tanzania. We used FIVPle molecular data to examine the role of social organization and lion density in shaping transmission pathways and tested to what extent vertical (i.e., father and/or mother offspring relationships) or horizontal (between unrelated individuals) transmission underpinned these patterns for each subtype. Using the same data, we constructed subtype specific FIVPle co-occurrence networks and assessed what combination of social networks, spatial networks, or co-infection best structured the FIVPle network. 4.While social organization (i.e., pride) was an important component of FIVPle transmission pathways at all scales, we find that FIVPle subtypes exhibited different transmission pathways at within- and between-pride scales. A combination of social and spatial networks, coupled with consideration of subtype co-infection, was likely to be important for FIVPle transmission for the two major subtypes, but the relative contribution of each factor was strongly subtype specific. 5.Our study provides evidence that pathogen heterogeneity is important in understanding pathogen transmission, which could have consequences for how endemic pathogens are managed. Furthermore, we demonstrate that community phylogenetic ecology coupled with phylodynamic techniques can reveal insights into the differential evolutionary pressures acting on virus subtypes, which can manifest into landscape-level effects.
Intra-specific variation in plant associated herbivore communities is phylogenetically structured in Brassicaceae
<p>As a result of co-evolution between plants and herbivores, related plants often interact with similar herbivore communities. Variation in plant-herbivore interactions is determined by variation in underlying functional traits and by ecological and stochastic processes. Hence, typically only a subset of possible interactions is realized on individual plants. We show that insect herbivore communities assembling on individual plants are structured by plant phylogeny among twelve species in two phylogenetic lineages of Brassicaceae. This community sorting to plant phylogeny was retained when splitting the community according to herbivore feeding guilds. Relative abundance of herbivores as well as the size of the community structured community dissimilarity among plant species. Importantly, the amount of intra-specific variation in realized plant-herbivore interactions is also phylogenetically structured. We argue that variability in realized interactions that is not directly structured by plant traits is ecologically relevant and must be considered in the evolution of plant defences.</p>
Unravelling the factors affecting taxonomic, phylogenetic and functional beta diversity of stream macroinvertebrate communities in the World's Third Pole
<p><span><strong>Aim</strong>: </span><span>Disentangling how</span><span> stochastic and deterministic processes contribute to variation in beta diversity is a common goal for ecologists and biogeographers. However, such studies are scarce in alpine streams, especially when different diversity facets are considered. Here, we combined different approaches to examine the drivers of taxonomic, phylogenetic and functional beta diversities and discussed how our results can inform community assembly and biodiversity conservation in Tibetan streams.</span></p> <p><span><strong>Location</strong>: </span><span>Tibet </span><span>Plateau</span></p> <p><span><strong>Taxon</strong>: </span><span>Macroinvertebrates</span></p> <p><span><strong>Methods</strong>: </span><span>We first partitioned multiple facets of beta diversity (B<sub>total</sub>) into species replacement (B<sub>repl</sub>) and richness difference (B<sub>rich</sub>) as well as local (LCBD) or species (SCBD) contributions. Then, we applied ordination methods to examine the relative importance of local, climatic and spatial factors on </span><span>B<sub>total</sub></span><span>, </span><span>B<sub>repl</sub></span><span> and </span><span>B<sub>rich</sub></span><span>, respectively. We explored community assembly rules using null models based on trait and phylogeny structure. </span></p> <p><span><strong>Results</strong>: </span><span>B<sub>total</sub></span><span> displayed high values and was primarily driven by B<sub>repl</sub>. Local, climatic and spatial factors were poor predictors of the different facets of beta diversity. Null models showed that the diversity metrics did not differ from those of null expectations, suggesting that most individual streams might be occupied by species that were merely random draws from the functional or phylogenetic pools available in this region. Partitioning beta diversity into LCBD and SCBD implied that the upper canyon streams were more unique than those at lower elevations and can be valuable for biodiversity conservation.</span></p> <p><span><strong>Main conclusions</strong>: </span><span>Analyzing multiple facets of beta diversity provide important insights into community assembly that cannot be acquired by focusing on taxonomic diversity only. Using a multi-faceted approach involving species, phylogenetic and trait data, our study not only sheds light on the assembly mechanisms of macroinvertebrate communities in alpine streams but also bring inspiration for biodiversity conservation in the 'World's Third Pole' that is highly sensitive to global change. </span></p>
Environment differentially affects the functional and phylogenetic structures of plant communities in a dry evergreen Afromontane tropical forest
<p class="MsoNormal"><span>Testing how local environmental conditions influence plant community assembly is important to understand the underlying mechanisms that promote and/or maintain biodiversity. Functional traits are used to find the broad spectrum of resource use strategies that plants use to</span><span> respond to environmental variation</span><span>. The patterns and drivers of plant community assembly through the lens of traits and phylogeny, however, remain to be studied in a uniquely biodiversity rich but poorly known fragmented dry Afromontane forest of Ethiopia. Here, we combined trait and community phylogenetic data from thirty sampling plots of 20 × 20 m size to determine the functional and phylogenetic structures and their drivers in a fragmented, human-dominated dry evergreen Afromontane forest. We found phylogenetic and functional clustering of plants in which the effect of environment was found to be trait specific. A weak phylogenetic signal for traits was detected suggesting that species resource use strategies may not be inferred using species phylogenetic distance. Additionally, we found functional traits to be weak in predicting species abundance distribution. Overall, while this study shows a non-random community assembly pattern, it also highlights the importance of deterministic processes being trait specific. </span></p>
Data from: Nitrogen fertilization, not water addition, alters plant phylogenetic community structure in a semi-arid steppe
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Intra-specific variation in plant associated herbivore communities is phylogenetically structured in Brassicaceae
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Nuanced qualitative trait approaches reveal environmental filtering and phylogenetic constraints on lichen communities
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Data from: Local adaptation, geographical distance and phylogenetic relatedness: assessing the drivers of siderophore-mediated social interactions in natural bacterial communities
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Data from: Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions
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Phylogenetic restriction of plant invasion in drought-stressed environments: implications for insect-pollinated plant communities in water-limited ecosystems
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Data from: Grassland restoration characteristics influence phylogenetic and taxonomic structure of plant communities and suggest assembly mechanisms
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Environment differentially affects the functional and phylogenetic structures of plant communities in a dry evergreen Afromontane tropical forest
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