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38 results for “phylogenetic relatedness”
The impact of species phylogenetic relatedness on invasion varies distinctly along resource versus nonresource environmental gradients
<p><span>Understanding why certain plant communities are vulnerable to alien invasive species is essential to predicting and controlling invasion in a changing environment. Darwin's naturalization hypothesis suggests that non-native species should be more successful in communities where their close relatives are absent. Empirical tests of this hypothesis, however, have produced mixed results. Using plot-level data from natural forests along elevational transects covering strong environmental gradients, we examined whether the invasion of the globally invasive species <em>Ageratina adenophora</em> can be explained by environmental filtering and/or competition from closely related species linked to environmental gradients. Abundant precipitation, warm temperatures, open canopies, and postfire environments facilitated <em>A. adenophora</em> invasion, whereas resident taxonomic richness suppressed its invasion. Importantly, we found that invader-resident relatedness had a strong negative effect on invader cover under resource scarcity conditions (e.g., low water availability), but not under nonresource environmental stress conditions (e.g., low temperature). Our findings help reconcile the varied applicability of Darwin's naturalization hypothesis to biological invasions in a changing world.</span></p>
Data & Analysis Script for: Phylogenetic relatedness to native congeners drives insect abundance and diversity hosted by non-native trees
<p>The dataset contains all necessary data to reproduce the findings presented in Schweiger et al. 2023 - Phylogenetic relatedness to native congeners drives insect abundance and diversity hosted by non-native trees (submitted).</p> <p>The code necessary to reproduce the findings is included within this repository. The code contains comments. Please note, if you want to reproduce the findings you will have to change file path information matching your personal computer to be able to re-run the code.</p> <p>This data includes the biodiversity raw data collected for the manuscript. It <strong>does not </strong>include data used to calculate geographic, climatic or phylogenetic distances, as these data are freely available and necessary information to reproduce calculations are given within the Material & Methods section.</p> <p>All data is provided within one Excel file. Please, pay attention to the provided ReadMe sheet containing metadata information on the dataset.</p> <p>Please carefully read provided information within ReadMe, Metadata and Code description.</p>
Data from: Phylogenetic relatedness drives protists assembly in marine and terrestrial environments
<p>Aim: Assembly of protists communities is known to be driven mainly by environmental filtering, but the imprint of phylogenetic relatedness is unknown. In this study, we aim to test the degree at which co-occurrences and co-exclusions of protists in different phylogenetic relatedness classes are deviating from random expectation in two ecosystems in order to link them to ecological processes.</p> <p>Location: Global open-oceans and Neotropical rainforest soils</p> <p>Major taxa: Protists</p> <p>Time period: 2009-2013</p> <p>Methods: Protist metabarcoding data originated from two large scale studies. Co-occurrence and co-exclusion networks were constructed using a recent method combining a null distribution model with Spearman's rank correlation coefficients among pairs of OTU. Phylogenetic relatedness was estimated using either global pairwise sequence distance or phylogenetic distance inferred from best maximum-likelihood trees derived from multiple alignments of OTU representative sequences. Significance of observed patterns relating networks and phylogenies were evaluated by distance classes against two null models in which either the tips of the phylogenetic trees or the network edges were randomized.</p> <p>Results: Closely-related protists co-occurred more often than expected by chance in all datasets, but also co-excluded less often than expected by chance in the marine dataset only. Concurrent excess of co-occurrences and co-exclusions were observed at intermediate phylogenetic distances in the marine dataset.</p> <p>Main conclusions: This suggest that environmental filtering and dispersal limitation are the dominant forces driving protists co-occurrences in both environments, while signal of competitive exclusion was only detected in the marine environment. Co-exclusion differences are potentially linked to the individual environments: marine waters are more homogeneous, while the rainforest soils contain a myriad of nutrient rich micro-environment reducing the strength of mutual exclusion.</p>
The impact of species phylogenetic relatedness on invasion varies distinctly along resource versus nonresource environmental gradients
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Data from: Phylogenetic relatedness drives protists assembly in marine and terrestrial environments
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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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Phylogenetic relatedness mediates persistence and density of soil seed banks
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Data from: Life expectancy in ants explains variation in helpfulness, regardless of phylogenetic relatedness
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Data from: Joint effect of phylogenetic relatedness and trait selection on the elevational distribution of Rhododendron species
<p>Congeneric species may coexist at fine spatial scales through niche differentiation, however, the magnitude to which the effects of functional traits and phylogenetic relatedness contribute to their distribution along elevational gradients remains understudied. To test the hypothesis that trait and elevational range overlap can affect local speciesʼ coexistence, we first compared phylogenetic relatedness and trait (including morphological traits and leaf elements) divergence among closely related species of <em>Rhododendron</em> L. on Yulong Mountain, China. We then assessed relationships between the overlap of multiple functional traits and the degree of elevational range overlap among species pairs in a phylogenetic context. We found that phylogeny was a good predictor for most functional traits, where closely related species showed higher trait similarity and occupied different elevational niches at our study site. Species pairs of <em>R</em>. subgen. <em>Hymenanthes</em> (Blume) K. Koch showed low elevational range overlap and some species pairs of <em>R</em>. subgen. <em>Rhododendron</em> showed obvious niche differentiation. Trait divergence is greater for species in <em>R.</em> subgen. <em>Rhododendron</em>, and it plays an important role between species pairs with low elevational range overlap. Trait convergent selection takes place between co-occurring closely related species that have high elevational range overlap, which share more functional trait space due to environmental filtering or ecological adaptation in more extreme habitats. Our results highlight the importance of evolutionary history and trait selection for species coexistence at fine ecological scales along environmental gradients.</p>
Data from: Functional dissimilarity, not phylogenetic relatedness, determines interspecific interactions among plants in the Tibetan alpine meadows
The hypotheses suggesting that the nature and strength of species interactions should be determined by phylogenetic relatedness have important implications for the understanding of community structure. However, to date, there is limited empirical evidence to support them. At least two basic conditions need to be met in order to expect species interactions to be determined by evolutionary relatedness: a phylogenetic signal in the traits involved in the interactions and changes in the interactions as species are more ecologically similar. Here, we report results of a removal experiment in the Chinese Tibetan plateau in which we directly assessed if the nature and/or strength of interactions among twelve alpine meadow plant species were influenced by their phylogenetic relatedness and/or their functional dissimilarity. For each plant species, we compared its biomass production when grown alone to its biomass in presence of another species and used it as a measure of species interactions. Competition between pairs of species was more frequent than facilitation, with 60% of interactions resulting in plants producing less biomass when a second species was present. We found no effect of phylogenetic relatedness on the prevalence or intensity of competition or facilitation, presumably as none of the studied traits showed phylogenetic signal. Functional dissimilarity based on maximum plant height alone was the best predictor of both the prevalence and strength of competition and facilitation, followed by functional dissimilarity using all five functional traits. Our results pinpoint the limited capacity of phylogenetic relatedness as predictor of species interactions; underlining the limitations of using phylogenetic dispersion patterns to infer mechanisms of community assembly. On the contrary, when the right functional traits are used, functional dissimilarity among species can predict both the nature and strength of their interactions; accentuating the relevance of trait-based approaches in community ecology research.
Data from: Contrasting effects of phylogenetic relatedness on plant invader success in experimental grassland communities
1. Identifying the factors determining the success of invasive species is critical for management of biological invasions. Darwin's naturalization conundrum states that exotic species closely related to natives should be successful because of a shared affinity for local environmental conditions, but at the same time close relatives often compete more intensively, limiting 'niche' opportunities for the invaders. Previous studies have generally considered these two 'opposing' hypotheses as mutually exclusive, yet evidence for both of them abounds, indicating a practical dilemma for management of biological invasions. 2. In this study, we sowed the seeds of the invasive exotic Ambrosia artemisiifolia L. into 369 experimental plant communities to mimic an introduction of the exotics into a series of new habitats. We further linked the establishment and growth performance of the invader in these experimental communities to the phylogenetic relatedness between the invader and the community residents where it was introduced. 3. We found that the probability of invader establishment declined with increasing phylogenetic distance between the invader and residents, whereas the average size of surviving invader individuals increased with the phylogenetic distance. 4. These results can be at least partly explained by the observations that close relatives tend to create similar soil microhabitat through harboring similar soil enzymes (e.g. alkaline and acid phosphatases) benefiting invader establishment, and that intense competitive interactions between the invader and its close relatives suppressed exotic growth. 5. Synthesis and applications. This study presents the first experimental evidence that phylogenetic relatedness has contrasting effects on different aspects of invader success, thus shedding light on the long-standing Darwin's naturalization conundrum. Moreover, our findings also have important implications for management of plant invasions: for controlling invasive species characterized by high establishment probability, native species distantly related to the invasive species can be planted in sites surrounding the invasion foci; whereas, the opposite seems to be true for controlling those characterized by large individual size.
Data from: SIDER: an R package for predicting trophic discrimination factors of consumers based on their ecology and phylogenetic relatedness
Stable isotope mixing models (SIMMs) are an important tool used to study species' trophic ecology. These models are dependent on, and sensitive to, the choice of trophic discrimination factors (TDF) representing the offset in stable isotope delta values between a consumer and their food source when they are at equilibrium. Ideally, controlled feeding trials should be conducted to determine the appropriate TDF for each consumer, tissue type, food source, and isotope combination used in a study. In reality however, this is often not feasible nor practical. In the absence of species-specific information, many researchers either default to an average TDF value for the major taxonomic group of their consumer, or they choose the nearest phylogenetic neighbour for which a TDF is available. Here, we present the SIDER package for R, which uses a phylogenetic regression model based on a compiled dataset to impute (estimate) a TDF of a consumer. We apply information on the tissue type and feeding ecology of the consumer, all of which are known to affect TDFs, using Bayesian inference. Presently, our approach can estimate TDFs for two commonly used isotopes (nitrogen and carbon), for species of mammals and birds with or without previous TDF information. The estimated posterior probability provides both a mean and variance, reflecting the uncertainty of the estimate, and can be subsequently used in the current suite of SIMM software. SIDER allows users to place a greater degree of confidence on their choice of TDF and its associated uncertainty, thereby leading to more robust predictions about trophic relationships in cases where study-specific data from feeding trials is unavailable. The underlying database can be updated readily to incorporate more stable isotope tracers, replicates and taxonomic groups to further increase the confidence in dietary estimates from stable isotope mixing models, as this information becomes available.
FIGURE 1 in Morphological similarities between Amphisbaena mitchelli Procter, 1923 and A. miringoera Vanzolini, 1971 (Squamata: Amphisbaenidae): phylogenetic relatedness or morphological convergence?
FIGURE 1. Phylogram of amphisbaenians recovered by a Bayesian inference using 1,068 base pairs of the genes16S rRNA and C- MOS. The clade formed by Amphisbaena mitchelli and Amphisbaena miringoera is highlighted in a gray background. Accession numbers are provided next to the species names for 16S rRNA and C-MOS, respectively. Asterisks indicate specimens included in the matrix as missing data for C-MOS. Amphisbaenids with two pre-cloacal pores are in bold. Posterior probabilities and bootstrap values are provided next to the nodes.
Data from: Exploring trophic role similarity and phylogenetic relatedness between species in food webs
<p>Understanding the mechanism shaping species assemblage is a fundamental goal in ecology. In the past two hypotheses have been suggested. One is the filtering hypothesis where environmental factors select for species of similar traits such that they co-occurring in similar niches. The other is the competitive exclusion hypothesis where related species are driven far apart by competition such that they over-disperse across different niches. Here, we investigate the relationship between species assemblage and their phylogenetic relatedness from the network perspective by using five different ecosystems ranging from oceans to an inland lake. We quantified the similarity in species'network positions in a food web and cluster them into different trophic role groups; and from an on-line database we quantified their phylogenetic distances. We then investigated whether related species tend to under or overdisperse across different trophic role groups. In general, our result suggests the environmental filtering process is the dominant force shaping the species assemblage of those ecosystems. However, there are some possible cases where related species are driven by competition such that they evolve to adopt different trophic roles in relatively closed ecosystems.</p>
Impacts of growth form and phylogenetic relatedness on seed germination: a large-scale analysis of a subtropical regional flora
<p>Plant regeneration strategy plays a critical role in species survival and can be used as a proxy for the evolutionary response of species to climate change. However, information on the effects of key plant traits and phylogenetic relatedness on seed germination is limited at large regional scales that vary in climate. To test the hypotheses that phylogenetic niche conservatism plays a critical force in shaping seed ecophysiological traits across species, and also drives their response to climatic fluctuation, we conducted a controlled experiment on seed germination and determined the percentage and rate of germination for 249 species in subtropical China under two temperature regimes (i.e., daily 25ºC; daily alternating 25/15ºC for each 12 h). Germination was low with a skewed distribution (mean = 38.9% at 25ºC, and 43.3% at 25/15ºC). One fifth of the species had low (<10%) and slow (4–30d) germination, and only a few (8%) species had a high (>80%) and rapid (1.2–6.6d) germination. All studied plant traits (including germination responses) showed a significant phylogenetic signal, with an exception of seed germination percentage under the alternating temperature scenario. Generalized linear models (GLMs) and phylogenetic generalized estimation equations (GEEs) demonstrated that growth form and seed dispersal mode were strong drivers of germination. Our experimental study highlights that integrating plant key traits and phylogeny is critical to predicting seed germination response to future climate change.</p>
Phylogenetic relatedness of food plants reveals highest insect herbivore specialization at intermediate temperatures along a broad climatic gradient
<p>Phytophagous insects differ in their degree of specialisation, biased by resource availability. The composition and richness of herbivore and plant assemblages change along climatic gradients, but knowledge about associated shifts in specialisation is scarce and lacks controlling for abundance and phylogeny of interaction partners. Thus, we aimed to test whether the specialisation of herbivores in insect- plant – interaction networks decreases towards cold habitats as predicted by the 'altitude niche-breadth hypothesis' to forecast possible consequences of interaction rewiring under climate change.</p> <p>We used a non-invasive, standardized metabarcoding approach to reconstruct dietary relationships of Orthoptera species as a major insect herbivore taxon along a broad temperature gradient (~12 °C) in southern Germany. Based on orthopteran surveys, direct feeding observations in field, collection of faecal pellets from > 3,000 individuals of 54 species, and parallel vegetation surveys on 41 grassland sites, we quantified plant resource availability and its use by herbivores. Faecal samples were pooled for each species per site.</p>
Data from: Functional dissimilarity, not phylogenetic relatedness, determines interspecific interactions among plants in the Tibetan alpine meadows
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Data from: Contrasting effects of phylogenetic relatedness on plant invader success in experimental grassland communities
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Phylogenetic relatedness of food plants reveals highest insect herbivore specialization at intermediate temperatures along a broad climatic gradient
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Impacts of growth form and phylogenetic relatedness on seed germination: a large-scale analysis of a subtropical regional flora
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