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Introduction: Often, bioinformatics uses summary sketches to analyze next-generation sequencing data, but most sketches are not well understood statistically. Under a simple mutation model, Blanca et al. analyzed complete sketches, that is, the complete set of unassembled k-mers, from two closely related sequences. The analysis extracted a point mutation parameter θ quantifying the evolutionary distance between the two sequences. Methods: We extend the results of Blanca et al. for complete sketches to parametrized syncmer sketches with downsampling. A syncmer sketch can sample k-mers much more sparsely than a complete sketch. Consider the following simple mutation model disallowing insertions or deletions. Consider a reference sequence A (e.g., a subsequence from a reference genome), and mutate each nucleotide in it independently with probability θ to produce a mutated sequence B (corresponding to, e.g., a set of reads or draft assembly of a related genome). Then, syncmer counts alone yield an approximate Gaussian distribution for estimating θ. The assumption disallowing insertions and deletions motivates a check on the lengths of A and B. The syncmer count from B yields an approximate Gaussian distribution for its length, and a p-value can test the length of B against the length of A using syncmer counts alone. Results: The Gaussian distributions permit syncmer counts alone to estimate θ and mutated sequence length with a known sampling error. Under some circumstances, the results provide the sampling error for the Mash containment index when applied to syncmer counts. Conclusions: The approximate Gaussian distributions provide hypothesis tests and confidence intervals for phylogenetic distance and sequence length. Our methods are likely to generalize to sketches other than syncmers and may be useful in assembling reads and related applications. [ABSTRACT FROM AUTHOR]

Niche partitioning promotes species coexistence. Yet, it remains unclear how phylogeny and morphology influence the trophic niches of closely related aquatic species with shared feeding modes. Freshwater mussels (Family: Unionidae) are a group of filter‐feeding bivalves that are ideal for investigating mechanisms of niche partitioning. Particle size selection and patterns of ingestion are controlled by gill latero‐frontal cirri density (CD) and the number of cilia per cirrus (CC). We investigated trophic assimilation and niche area using stable isotope signatures (훿13C and 훿15N) and gill morphology with scanning‐electron microscopy for a diverse mussel assemblage from the Sipsey River, Alabama, USA. We predicted that (1) trophic niches and gill morphology would differ within and among species across sites; (2) co‐occurring species would partition food resources; (3) greater phylogenetic distances among species would result in increased trophic dissimilarity; (4) more CC and higher CD would result in a narrower trophic niche area, or more constrained range of food items assimilated. We found that (1) species identity and site influenced gill morphology and stable isotope signatures but that the trophic niche area of a species was only affected by species identity; (2) the average proportion of niche area overlap between co‐occurring species was low across sites (0.04 to 0.18); (3) trophic dissimilarity among species increased with phylogenetic distance; (4) CD but not the number of CC negatively related to trophic niche area. Our results indicate that gill morphology and evolutionary history are likely key factors governing the trophic niches of mussels. In addition, intraspecific variation in gill morphology across sites may either reflect a phenotypic response to differences in local resource availability or suggest that other mechanisms shape particle selection. Examining the interplay among the trophic niche, phylogeny, and morphology among functionally similar species further informs our understanding of the mechanisms facilitating their coexistence. [ABSTRACT FROM AUTHOR]

The mechanisms underlying plant species distribution and abundance have been long studied in ecology. However, the role of heterospecific pollen interference in shaping these patterns needs more attention. Species distribution and abundance are important factors determining whether a species is endangered or not; thus, understanding the impact of heterospecific pollen interference on rare species could help to inform conservation strategies aimed at preserving plant communities. In this study, we conducted a multispecies experiment using eight co‐occurring and co‐flowering plant species with varying rarity levels in Switzerland. We performed cross‐pollinations by hand between nearly all species pairs and measured seed set (whether a flower produces seed) and seed number (number of seeds per flower) as outcomes. We looked at the effects of rarity status, self‐compatibility, and recipient‐donor relatedness on heterospecific pollen interference. Contrary to expectations, neither seed set nor seed number were affected by heterospecific pollen deposition. Self‐compatible species had a higher seed set probability, but this was independent from species rarity. In our study setting, heterospecific pollen interference seems to have only minor effects on seed set and seed number, and consequently on recruitment. Thus, heterospecific pollen interference seems to play only a minor role in shaping plant species distribution and abundance. Nevertheless, the higher impact of heterospecific pollen deposition on rare and closely related species, as well as the importance of conspecific pollen loss, might need further investigation for both in situ and ex‐situ conservation strategies. [ABSTRACT FROM AUTHOR]

The timing and order of species arrival have been shown to be a significant factor in the assembly of biotic communities. Therefore, understanding priority effects, which refer to the impact of an early‐arriving species on a later‐arriving one, can help us better predict community assembly processes. However, little is known about the role of phylogenetic distance (PD) in priority effects and how they are mediated by the biogeographic history (BH) and the life stages (LSs) of interacting species.To shed light on the role of PD in priority effects, we conducted a multispecies greenhouse experiment. We created 10 allopatric and 10 sympatric species pairs, representing a PD gradient between early‐ and late‐arriving species from 5 to 270 Myr in evolutionary history and tested the priority effect of early‐arriving species on the late‐arriving species at multiple LSs.We found evidence of stronger competition between closely related species, as late‐arriving plants produced less above‐ground biomass when the PD was low. However, priority effects varied across the development of late‐arriving plants, as there were no effects on seedling emergence and survival, independent of PD. Regardless of PD, the pairs of allopatric and sympatric species did not differ in their responses.Synthesis. While many studies have produced contradictory results regarding the effect of PD on plant–plant interactions, our study provides experimental evidence that priority effects can be stronger when PD is small. This effect was independent of BH but varied across different LSs of late‐arriving plants. The dependence of the effect of PD on the LS of late‐arriving species highlights the importance of the timing of interactions for the assembly of plant communities, which could also have significant implications for the fields of invasion and restoration ecology. [ABSTRACT FROM AUTHOR]

Broad‐scale assessments of plant–frugivore interactions indicate the existence of a latitudinal gradient in interaction specialization. The specificity (i.e. the similarity of the interacting partners) of plant–frugivore interactions could also change latitudinally given that differences in resource availability could favour species to become more or less specific in their interactions across latitudes.Species occurring in the tropics could be more taxonomically, phylogenetically and functionally specific in their interactions because of a wide range of resources that are constantly available in these regions that would allow these species to become more specialized in their resource usage.We used a data set on plant–avian frugivore interactions spanning a wide latitudinal range to examine these predictions, and we evaluated the relationship between latitude and taxonomic, phylogenetic and functional specificity of plant and frugivore interactions. These relationships were assessed using data on population interactions (population level), species means (species level) and community means (community level).We found that the specificity of plant–frugivore interactions is generally not different from null models. Although statistically significant relationships were often observed between latitude and the specificity of plant–frugivore interactions, the direction of these relationships was variable and they also were generally weak and had low explanatory power. These results were consistent across the three specificity measures and levels of organization, suggesting that there might be an interplay between different mechanisms driving the interactions between plants and frugivores across latitudes. [ABSTRACT FROM AUTHOR]

ABSTRACT The mechanisms underlying plant species distribution and abundance have been long studied in ecology. However, the role of heterospecific pollen interference in shaping these patterns needs more attention. Species distribution and abundance are important factors determining whether a species is endangered or not; thus, understanding the impact of heterospecific pollen interference on rare species could help to inform conservation strategies aimed at preserving plant communities. In this study, we conducted a multispecies experiment using eight co‐occurring and co‐flowering plant species with varying rarity levels in Switzerland. We performed cross‐pollinations by hand between nearly all species pairs and measured seed set (whether a flower produces seed) and seed number (number of seeds per flower) as outcomes. We looked at the effects of rarity status, self‐compatibility, and recipient‐donor relatedness on heterospecific pollen interference. Contrary to expectations, neither seed set nor seed number were affected by heterospecific pollen deposition. Self‐compatible species had a higher seed set probability, but this was independent from species rarity. In our study setting, heterospecific pollen interference seems to have only minor effects on seed set and seed number, and consequently on recruitment. Thus, heterospecific pollen interference seems to play only a minor role in shaping plant species distribution and abundance. Nevertheless, the higher impact of heterospecific pollen deposition on rare and closely related species, as well as the importance of conspecific pollen loss, might need further investigation for both in situ and ex‐situ conservation strategies.

ABSTRACT Niche partitioning promotes species coexistence. Yet, it remains unclear how phylogeny and morphology influence the trophic niches of closely related aquatic species with shared feeding modes. Freshwater mussels (Family: Unionidae) are a group of filter‐feeding bivalves that are ideal for investigating mechanisms of niche partitioning. Particle size selection and patterns of ingestion are controlled by gill latero‐frontal cirri density (CD) and the number of cilia per cirrus (CC). We investigated trophic assimilation and niche area using stable isotope signatures (𝛿13C and 𝛿15N) and gill morphology with scanning‐electron microscopy for a diverse mussel assemblage from the Sipsey River, Alabama, USA. We predicted that (1) trophic niches and gill morphology would differ within and among species across sites; (2) co‐occurring species would partition food resources; (3) greater phylogenetic distances among species would result in increased trophic dissimilarity; (4) more CC and higher CD would result in a narrower trophic niche area, or more constrained range of food items assimilated. We found that (1) species identity and site influenced gill morphology and stable isotope signatures but that the trophic niche area of a species was only affected by species identity; (2) the average proportion of niche area overlap between co‐occurring species was low across sites (0.04 to 0.18); (3) trophic dissimilarity among species increased with phylogenetic distance; (4) CD but not the number of CC negatively related to trophic niche area. Our results indicate that gill morphology and evolutionary history are likely key factors governing the trophic niches of mussels. In addition, intraspecific variation in gill morphology across sites may either reflect a phenotypic response to differences in local resource availability or suggest that other mechanisms shape particle selection. Examining the interplay among the trophic niche, phylogeny, and morphology among functionally similar species further informs our understanding of the mechanisms facilitating their coexistence.

A concern in weed biological control research is the potential for candidate biocontrol agents to impact not only the target weed but also native or economically important flora. The degree of evolutionary relatedness between the target weed species and a non-target species is a key predictor of the susceptibility of the non-target to the biocontrol agent. To manage this risk, biocontrol practitioners need to understand the phylogenetic position of the host weed relative to non-target plant species. However, comprehensively sampled phylogenetic trees are often unavailable, with incomplete information scattered across multiple publications. Further, older published phylogenies based on Sanger sequence data often lack branch resolution and support, which increases uncertainty in biocontrol decision making. Decreasing sequencing cost and technological advances have led to phylogenomic approaches being more widely used to understand evolutionary relationships between species. For example, target capture sequencing methods using bait kits such as Angiosperms353 enable cost-effective and timely phylogenomic-level analysis of flowering plant groups at different scales. Here, we introduce a workflow to embed a comprehensive understanding of evolutionary relationships into the efficient development of host test lists in weed biological control. We demonstrate the effectiveness of the workflow through a case study on the major crop weed flaxleaf fleabane (Erigeron bonariensis). Phylogenomic analysis was conducted on 280 species of the tribe Astereae (family Asteraceae) occurring in Australia and New Zealand, clarifying relationships between the target species and related clades of native and non-native Astereae. We consider the phylogenetic tree in the context of a previously proposed host test list and discuss taxonomic implications, highlighting avenues of future molecular-based work to uncover the origin of Australian fleabanes. This study provides a workflow and demonstrates the practical application of target sequence capture for phylogenomic inference to support risk analysis and decision making in classical weed biological control.

Climate change has become one of the most critical threats to global biodiversity. However, whether phylogenetically related species respond to climate change in similar ways remains controversial. The answer to this question is crucial for understanding the impacts of climate change and the conservation on the tree of life. By integrating species distribution models with a molecular phylogeny of 50 threatened plant species from one of the global biodiversity hotspots, Gongga Mountains (Mt. Gongga) in southwest China, we evaluated the responses of threatened plant species to future climate change, and estimated whether species responses are phylogenetically conserved. Phylogenetic reconstruction was used to calculate the phylogenetic distance and null model to verify the reliability of the results. We found that correlations between responses of different species to future climate change decreased with the increase in their phylogenetic distance in the monocotyledonous or herbaceous species, but not in the dicotyledonous and woody species. Our results suggested that the responses of herbaceous and monocotyledonous threatened species in Mt. Gongga to future climate change tend to be phylogenetically conserved, while the responses of woody and dicotyledonous threatened species are not. Our study provides evidence for the existence of phylogenetically non-random extinction in the monocotyledonous herbs in Mt. Gongga and highlights the importance of integrating phylogenetic information and evolutionary history into conservation planning. We also provide theoretical basis and technical support for designing effective conservation schemes for the protection of biodiversity under anthropogenic climate change. [ABSTRACT FROM AUTHOR]

Over the past fifty years, the distribution patterns of C4 species, across large spatial scales, are largely ignored. Here, we endeavored to examine patterns in the taxonomic and phylogenetic diversity of species with C4 photosynthetic pathways across the broad spatial extent of China and relate those to climatic gradients. We built a database of all plants with the C4 photosynthetic pathway in China. We analyzed the geographic distributions, taxonomic diversity, phylogenetic diversity, and phylogenetic structure of all C4 species, as well as the three families with the most C4 species (Poaceae, Amaranthaceae and Cyperaceae), and compared their values along temperature and precipitation gradients at two scales--the level of the province and at the 100 x 100 km grid cell. We found 644 C4 plants (belonging to 23 families 165 genera) in China, with Poaceae (57%), Amaranthaceae (17%), Cyperaceae (13%) accounting for the majority of species. Standardized effect size values of phylogenetic distances were negative overall, indicating that C4 species showed a phylogenetic clustering pattern. Southern China had the highest species richness and the highest degree of phylogenetic clustering. C4 tended to be more phylogenetically over-dispersed in regions with colder and/or drier climates, but more clustered in warmer and/or wetter climates. Patterns within individual families were more nuanced. The distribution of C4 species and its phylogenetic structure across China was constrained by temperature and precipitation. C4 species showed a phylogenetic clustering pattern across China, while different families showed more nuanced responses to climate variation, suggesting a role for evolutionary history. [ABSTRACT FROM AUTHOR]

Context: Environmental filtering is an important assembly process that structures plant communities and is commonly inferred from taxonomic, functional trait and phylogenetic patterns. However, while these approaches can be informative, the influence of other co-occurring processes on community diversity, such as competitive exclusion, remains poorly understood. Objectives: By combing functional traits and a phylogeny of woody plants across anthropogenically created islands, we aim to explore the ways in which environmental filtering and competitive exclusion can simultaneously influence community assembly processes. We expect that communities on smaller islands, where competition for limited space and resources is more intense, should be functionally and phylogenetically less clustered than those on larger islands because this more intense competition should reduce the coexistence of the most closely related or functionally similar species. Methods: We used ten functional traits and a phylogeny of 76 woody plant species to assess species diversity and similarity within communities across an island area gradient. We combed functional traits and phylogeny into a functional–phylogenetic distance matrix and calculated the communities' mean functional-phylogenetic distance (MFPD) and its standardized effect size (SES.MFPD) as measures of ecological similarity. Results: As expected, species were more phylo-functionally similar to one another than expected by chance within islands and this underdispersion grew stronger with island area, indicating that while islands generally contained clustered communities, environmental filtering and competitive exclusion were both likely occurring. By integrating species abundance distributions with community similarity, we found that the most abundant species were phylo-functionally similar to the least abundant species. Species richness increased with island area, as expected, but the additional species found only on larger islands tended to have low abundances, providing opportunities for rare species to persist. Conclusions: With environmental filtering narrowing the number of species that can persist, the loss of phylo-functionally closely related rare species on smaller islands was likely caused by competition or stochastic removals, leading to greater species dissimilarity than on larger islands. On larger islands, the clustered patterns are likely to be the result of a combination of competitive exclusion caused by resource limitation and environmental filtering. [ABSTRACT FROM AUTHOR]

Over the past fifty years, the distribution patterns of C4 species, across large spatial scales, are largely ignored. Here, we endeavored to examine patterns in the taxonomic and phylogenetic diversity of species with C4 photosynthetic pathways across the broad spatial extent of China and relate those to climatic gradients. We built a database of all plants with the C4 photosynthetic pathway in China. We analyzed the geographic distributions, taxonomic diversity, phylogenetic diversity, and phylogenetic structure of all C4 species, as well as the three families with the most C4 species (Poaceae, Amaranthaceae and Cyperaceae), and compared their values along temperature and precipitation gradients at two scales—the level of the province and at the 100 x 100 km grid cell. We found 644 C4 plants (belonging to 23 families 165 genera) in China, with Poaceae (57%), Amaranthaceae (17%), Cyperaceae (13%) accounting for the majority of species. Standardized effect size values of phylogenetic distances were negative overall, indicating that C4 species showed a phylogenetic clustering pattern. Southern China had the highest species richness and the highest degree of phylogenetic clustering. C4 tended to be more phylogenetically over-dispersed in regions with colder and/or drier climates, but more clustered in warmer and/or wetter climates. Patterns within individual families were more nuanced. The distribution of C4 species and its phylogenetic structure across China was constrained by temperature and precipitation. C4 species showed a phylogenetic clustering pattern across China, while different families showed more nuanced responses to climate variation, suggesting a role for evolutionary history.

Although phylogenetic distance between native and exotic species has a close link with their interactions, it is still unclear how environmental stresses and species interactions influence the relationship between phylogenetic distance and biological invasions. Here we assessed the effect of invader–native phylogenetic distance on the growth of the invader (Symphyotrichum subulatum) under three levels of drought (no, moderate, or intense drought). Under no drought, interspecific competition between close relatives was the dominant process and native communities more closely related to the invader showed higher resistance to invasion, supporting Darwin's naturalization hypothesis. In contrast, under intense drought, facilitation between close relatives by mutualism with arbuscular mycorrhizal fungi (AMF) became more important, and the invader became more successful in their more closely related native communities, supporting the preadaptation hypothesis. The colonization rate of AMF of the invader was higher in more closely related native communities regardless of the drought treatment, but it was only positively related to invader biomass under intense drought. Therefore, the shift of species interactions from competition to facilitation may be ascribed to the promotion of AMF to invasion occurring under intense drought, which leads to the effect of closely related natives on the invader shifting from negative to positive. Our results provide a new angle to resolve Darwin's naturalization conundrum from the change of species interactions along a stress gradient, and provide important clues for invasion management when species interactions change in response to global climatic change. [ABSTRACT FROM AUTHOR]

Aim: Our main aim was to identify the distribution of, and potential mechanisms underpinning, hybrid‐rich zones – regions with a disproportionate number of unique interspecific hybrids. We investigated whether coral reef fish hybrids coincided with factors such as phylogenetic relatedness, biogeographic barriers, species richness, geographic isolation, endemism, and oceanic currents. Location: Global. Time period: Contemporary. Major taxa studied: Coral reef fishes. Methods: We conducted a literature review and mapping to assess the taxonomic and global prevalence of hybridisation in coral reef fishes. We then fit Generalised additive models using a full‐subsets and Bayesian framework to assess which variables are associated with hybrid‐rich zones. Results: We found 143 unique interspecific coral reef fish hybrids involving 204 species – which accounts for approximately 7% of coral reef fish species, indicating that hybridisation is as common in the sea as it is on land. Characteristic coral reef fish families were not homogeneously represented in our dataset, with particularly colourful groups standing out. Mapping our dataset revealed that coral reef fish hybrids are found worldwide, though some ecoregions (e.g., the Christmas and Cocos (Keeling) Islands, South Kuroshio, Hawaii, and Eastern Philippines) are more hybrid‐rich than others. Our analysis revealed that mean surface current velocity, phylogenetic relatedness, and geographic isolation were the best predictors of hybrid richness in a given location. Main conclusions: Phylogenetic distance between coral reef fish species may serve as a pre‐condition for hybridisation to occur, lying between introgression and reproductive incompatibility. We also propose a novel mechanism, with oceanic currents driving long‐distance larval dispersal events, transporting stray species to geographically remote sinks to maintain hybrid‐rich zones. [ABSTRACT FROM AUTHOR]

Biological invasions are key to understanding ecological processes that determine the formation of novel interactions. Alien species can negatively impact floral visitation to native species, but native species may also facilitate early establishment of closely related alien species by providing a preadapted pollinator community. We tested whether floral visitation to alien species depended on phylogenetic relatedness and floral similarity to native species.In a field experiment, we simulated the early stages of an invasion by adding potted alien plants into co‐flowering native communities. We paired each alien plant with a host native plant, and recorded floral visitation to them for 3,068 hr (totalling 84,814 visits). We used 34 alien and 20 native species in 151 species combinations. We tested whether the number of floral visits to alien plants, the proportion of visits to alien plant relative to visits to both alien and native plants, and the similarity in flower visitor compositions of alien and native plants depended on phylogenetic and floral trait distances between alien and native species.Floral visitation to alien species was highest when they had intermediate floral trait distances to native species, and either low or high phylogenetic distances. Alien species received more similar flower‐visitor groups to natives when they had low phylogenetic and either low or high floral trait distances to native species.Co‐flowering native species may facilitate floral visitation to closely related alien species, and distantly related alien plants seem to avoid competition for flower visitors with native plants. Alien species with similar floral traits to natives compete with them for flower visitors, and alien species with dissimilar floral traits may not share flower visitors with native species. Alien species with intermediate floral trait distances to natives are most likely to receive flower visitors, as they are not too dissimilar and may still share flower visitors with native species, but not too similar to compete for flower visitors with them.The non‐linear patterns between floral visitation and similarity of the alien and native species suggest that an interplay of facilitation and competition simultaneously drives the formation of novel plant‐pollinator interactions. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Since Darwin's time, degree of ecological similarity between exotic and native species has been assumed to affect the establishment success or failure of exotic species. However, a direct test of the effect of exotic–native similarity on establishment of exotics is scarce because of the difficulty in recognizing failures of species to establish in the field. Here, using a database on the establishment success and failure of exotic fish species introduced into 673 freshwater lakes, we evaluate the effect of similarity on the establishment of exotic fishes by combining phylogenetic and functional information. We illustrate that, relative to other biotic and abiotic factors, exotic–native phylogenetic and functional similarities were the most important correlates of exotic fish establishment. While phylogenetic similarity between exotic and resident fish species promoted successful establishment, functional similarity led to failure of exotics to become established. Those exotic species phylogenetically close to, but functionally distant from, native fishes were most likely to establish successfully. Our findings provide a perspective to reconcile Darwin's naturalization conundrum and suggest that, while phylogenetic relatedness allows exotic fish species to pre‐adapt better to novel environments, they need to possess distinct functional traits to reduce competition with resident native fish species. [ABSTRACT FROM AUTHOR]

The phylogenetic distance between species often predicts differences in ecologically important traits. The phylogenetic diversity and structure of biological communities can inform our understanding of the processes that shape those communities, and there is a well-developed framework for comparing phylogenetic structures of communities. However, particularly in studies of phylogenetic distances from one focal species to other members of its assemblage (a one-to-many framework), the standard metrics of community-wide studies encounter significant limitations due to the left-skewed distribution of pairwise phylogenetic distances in most biological communities. For studies that require estimating the degree of phylogenetic isolation of a focal taxon, the mean phylogenetic distance (MPD) usually provides little power to distinguish among taxa because it is heavily weighted by the many ways to be distantly related, whereas the nearest taxon distance (NTD) is highly idiosyncratic and ignores cases where multiple close relatives may contribute equally strongly to influence the focal species. Here we highlight the value of examining the cumulative distribution of phylogenetic distances in studies that take a focal-species approach. We describe and discuss the benefits of two new metrics. An integrated metric of phylogenetic distances (AUPhyDC) uses information from the whole cumulative distribution, whereas the tenth quantile (PD10) is an extremely simple metric that improves on NTD by capturing the influence of multiple close relatives on ecological interactions. Several recent examples found that PD10 did a better job of revealing ecological patterns than NTD or MPD. We provide R code to facilitate the use of these approaches and advocate for the inclusion of PD10 along with NTD and MPD in statistical packages for phylogenetic ecology. [ABSTRACT FROM AUTHOR]

Global food security is heavily reliant on crop pollination. However, evidence on pollinator decline has been reported in all continents. Globally affordable conservation strategies need to be developed, as high-cost measures like European agri-environment schemes are not scalable in all countries. Here, we test, if a low-cost conservation approach named "Farming with Alternative Pollinators" (FAP) can benefit wild pollinator abundance and richness in agro-ecosystems and in crops, through establishment of marketable habitat enhancement plants (MHEP). The study was carried out in four Moroccan agro-climatic regions, during two years, using 6 main crops (pumpkin, zucchini, faba bean, tomato, eggplant and apple) and 201 sites. Additionally, we investigated how crop type, crop-MHEP composition (i.e. phylogenetic distances among crop and MHEP) and local climate can drive the success of the approach in comparison to monocultural fields. Based on 7097 recorded specimens, our results show that the wild pollinators of the entire FAP fields (i.e. 75% main crop and 25% MHEP) were significantly more abundant and species-rich than those of control fields (i.e. 100% main crop). Considering the main crop wild pollinators, FAP did not display any significant effect either on wild pollinator abundance or on pollinator richness. The mean phylogenetic distance between the main crop and MHEP, and climatic variables were not correlated with increase in wild pollinator abundance and richness in FAP fields. The crop type was found to influence the effect of the FAP approach. Our study provides strong evidence that FAP constitutes a relevant method for wild pollinator conservation in agro-ecosystems. Further research on additional environmental factors is necessary to outline the circumstances under which the FAP approach can positively affect wild pollinator communities. • Marketable habitat plants support pollinator abundance and richness in agro-ecosystems. • Marketable habitat plants does not promote crop pollinator abundance and richness. • Phylogeny of habitat plants and crop does not affect pollinator abundance and richness. • The climate does not shape the effect of habitat plants on pollinator communities. • The crop type modulates the impact of marketable habitat plants on pollinators. [ABSTRACT FROM AUTHOR]

Premise: Pollinator sharing of co‐flowering plants may result in interspecific pollen receipt with a fitness cost. However, the underlying factors that determine the effects of heterospecific pollen (HP) are not fully understood. Moreover, the cost of stigma closure induced by HP may be more severe for plants with special touch‐sensitive stigmas than for plants with non‐touch‐sensitive stigmas. Very few studies have assessed HP effects on stigma behavior. Methods: We conducted hand‐pollination experiments with 10 HP donors to estimate HP effects on stigma behavior and stigmatic pollen germination in Campsis radicans (Bignoniaceae) at low and high pollen loads. We assessed the role of phylogenetic distance between donor and recipient, pollen size, and pollen aperture number in mediating HP effects. Additionally, we observed pollen tube growth to determine the conspecific pollen‐tube‐growth advantage. Results: Stigma behavior differed significantly with HP of different species. Pollen load increased, while pollen size decreased, the percentage of permanent closure and stigmatic germination of HP. Stigmatic HP germination increased with increasing aperture number. However, HP effects did not depend on phylogenetic distance. In addition, conspecific pollen had a pollen‐tube‐growth advantage over HP. Conclusions: Our results provide a good basis for understanding the stigma‐pollen recognition process of plant taxa with touch‐sensitive stigmas. We concluded that certain flowering traits drive the HP effects on the post‐pollination period. To better understand the impact of pollinator sharing and interspecific pollen transfer on plant evolution, we highlight the importance of evaluating more factors that determine HP effects at the community level. [ABSTRACT FROM AUTHOR]

Multiple studies have investigated bibliometric factors predictive of the citation count a research article will receive. In this article, we go beyond bibliometric data by using a range of machine learning techniques to find patterns predictive of citation count using both article content and available metadata. As the input collection, we use the CORD-19 corpus containing research articles—mostly from biology and medicine—applicable to the COVID-19 crisis. Our study employs a combination of state-of-the-art machine learning techniques for text understanding, including embeddings-based language model BERT, several systems for detection and semantic expansion of entities: ConceptNet, Pubtator and ScispaCy. To interpret the resulting models, we use several explanation algorithms: random forest feature importance, LIME, and Shapley values. We compare the performance and comprehensibility of models obtained by "black-box" machine learning algorithms (neural networks and random forests) with models built with rule learning (CORELS, CBA), which are intrinsically explainable. Multiple rules were discovered, which referred to biomedical entities of potential interest. Of the rules with the highest lift measure, several rules pointed to dipeptidyl peptidase4 (DPP4), a known MERS-CoV receptor and a critical determinant of camel to human transmission of the camel coronavirus (MERS-CoV). Some other interesting patterns related to the type of animal investigated were found. Articles referring to bats and camels tend to draw citations, while articles referring to most other animal species related to coronavirus are lowly cited. Bat coronavirus is the only other virus from a non-human species in the betaB clade along with the SARS-CoV and SARS-CoV-2 viruses. MERS-CoV is in a sister betaC clade, also close to human SARS coronaviruses. Thus both species linked to high citation counts harbor coronaviruses which are more phylogenetically similar to human SARS viruses. On the other hand, feline (FIPV, FCOV) and canine coronaviruses (CCOV) are in the alpha coronavirus clade and more distant from the betaB clade with human SARS viruses. Other results include detection of apparent citation bias favouring authors with western sounding names. Equal performance of TF-IDF weights and binary word incidence matrix was observed, with the latter resulting in better interpretability. The best predictive performance was obtained with a "black-box" method—neural network. The rule-based models led to most insights, especially when coupled with text representation using semantic entity detection methods. Follow-up work should focus on the analysis of citation patterns in the context of phylogenetic trees, as well on patterns referring to DPP4, which is currently considered as a SARS-Cov-2 therapeutic target. [ABSTRACT FROM AUTHOR]

Elton's biotic resistance hypothesis, which posits that diverse communities should be more resistant to biological invasions, has received considerable experimental support. However, it remains unclear whether such a negative diversity–invasibility relationship would persist under anthropogenic environmental change. By using the common ragweed (Ambrosia artemisiifolia) as a model invader, our 4‐year grassland experiment demonstrated consistently negative relationships between resident species diversity and community invasibility, irrespective of nitrogen addition, a result further supported by a meta‐analysis. Importantly, our experiment showed that plant diversity consistently resisted invasion simultaneously through increased resident biomass, increased trait dissimilarity among residents, and increased community‐weighted means of resource‐conservative traits that strongly resist invasion, pointing to the importance of both trait complementarity and sampling effects for invasion resistance even under resource enrichment. Our study provides unique evidence that considering species' functional traits can help further our understanding of biotic resistance to biological invasions in a changing environment. [ABSTRACT FROM AUTHOR]

Plants and arbuscular mycorrhizal fungi (AMF) can form complex symbiotic networks based on functional trait selection, contributing to the maintenance of ecosystem biodiversity and stability. However, the selectivity of host plants on AMF and the characteristics of plant-AMF networks remain unclear in Tibetan alpine meadows. In this study, we studied the AMF communities in 69 root samples from 23 plant species in a Tibetan alpine meadow using Illumina-MiSeq sequencing of the 18S rRNA gene. The results showed a significant positive correlation between the phylogenetic distances of plant species and the taxonomic dissimilarity of their AMF community. The plant-AMF network was characterized by high connectance, high nestedness, anti-modularity, and anti-specialization, and the phylogenetic signal from plants was stronger than that from AMF. The high connected and nested plant-AMF network potentially promoted the interdependence and stability of the plant-AMF symbioses in Tibetan alpine meadows. This study emphasizes that plant phylogeny and plant-AMF networks play an important role in the coevolution of host plants and their mycorrhizal partners and enhance our understanding of the interactions between aboveground and belowground communities. [ABSTRACT FROM AUTHOR]

Understanding the mechanism shaping species assemblages 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-occur in similar niches. The other is the competitive exclusion hypothesis, where related species are driven far apart by competition such that they overdisperse across various niches. Here, we investigate the relationship between species assemblages and their phylogenetic relatedness from a network perspective by using five separate ecosystems ranging from oceans to an inland lake. We quantified the similarity in species network positions in a food web and clustered them into different trophic role groups; using an online database, we quantified their phylogenetic distances. We then investigated whether related species tend to underdisperse or overdisperse across different trophic role groups. In general, our results suggest that 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. [ABSTRACT FROM AUTHOR]

Plants and arbuscular mycorrhizal fungi (AMF) can form complex symbiotic networks based on functional trait selection, contributing to the maintenance of ecosystem biodiversity and stability. However, the selectivity of host plants on AMF and the characteristics of plant-AMF networks remain unclear in Tibetan alpine meadows. In this study, we studied the AMF communities in 69 root samples from 23 plant species in a Tibetan alpine meadow using Illumina-MiSeq sequencing of the 18S rRNA gene. The results showed a significant positive correlation between the phylogenetic distances of plant species and the taxonomic dissimilarity of their AMF community. The plant-AMF network was characterized by high connectance, high nestedness, anti-modularity, and anti-specialization, and the phylogenetic signal from plants was stronger than that from AMF. The high connected and nested plant-AMF network potentially promoted the interdependence and stability of the plant-AMF symbioses in Tibetan alpine meadows. This study emphasizes that plant phylogeny and plant-AMF networks play an important role in the coevolution of host plants and their mycorrhizal partners and enhance our understanding of the interactions between aboveground and belowground communities.

Understanding how functional and phylogenetic patterns vary among scales and along ecological gradients within a given species pool is critical for inferring community assembly processes. However, we lack a clear understanding of these patterns in stressful habitats such as Mediterranean high mountains where ongoing global warming is expected to affect species fitness and species interactions, and subsequently species turnover. In this study, we investigated 39 grasslands with the same type of plant community and very little species turnover across an elevation gradient above the treeline at Sierra de Guadarrama National Park in central Spain. In particular, we assessed functional and phylogenetic patterns, including functional heterogeneity, using a multi-scale approach (cells, subplots, and plots) and determined the relevance of key ecological factors (i.e., elevation, potential solar radiation, pH, soil organic carbon, species richness, and functional heterogeneity) that affect functional and phylogenetic patterns at each spatial scale. Overall, at the plot scale, coexisting species tended to be more functionally and phylogenetically similar. By contrast, at the subplot and cell scales, species tended to be more functionally different but phylogenetically similar. Functional heterogeneity at the cell scale was comparable to the variation across plots along the gradient. The relevance of ecological factors that regulate diversity patterns varied among spatial scales. An increase in elevation resulted in functional clustering at larger scales and phylogenetic overdispersion at a smaller scale. The soil pH and organic carbon levels exhibited complex functional patterns, especially at small spatial scales, where an increase in pH led to clustering patterns for the traits related to the leaf economic spectrum (i.e., foliar thickness, specific leaf area, and leaf dry matter content). Our findings confirm the presence of primary environmental filters (coldness and summer drought at our study sites) that constrain the regional species pool, suggesting the presence of additional assembly mechanisms that act at the smallest scale (e.g., micro-environmental gradients and/or species interactions). Functional and phylogenetic relatedness should be determined using a multi-scale approach to help interpret community assembly processes and understand the initial community responses to environmental changes, including ongoing global warming.

• Introduces a contemporary molecular analytics workflow centered on evolutionary relationships into biocontrol risk analysis. • Recommends the use of patristic (phylogenetic) distance over degrees of separation. • Employed target sequence capture for tribal-level phylogenomic analysis on flaxleaf fleabane case study. A concern in weed biological control research is the potential for candidate biocontrol agents to impact not only the target weed but also native or economically important flora. The degree of evolutionary relatedness between the target weed species and a non-target species is a key predictor of the susceptibility of the non-target to the biocontrol agent. To manage this risk, biocontrol practitioners need to understand the phylogenetic position of the host weed relative to non-target plant species. However, comprehensively sampled phylogenetic trees are often unavailable, with incomplete information scattered across multiple publications. Further, older published phylogenies based on Sanger sequence data often lack branch resolution and support, which increases uncertainty in biocontrol decision making. Decreasing sequencing cost and technological advances have led to phylogenomic approaches being more widely used to understand evolutionary relationships between species. For example, target capture sequencing methods using bait kits such as Angiosperms353 enable cost-effective and timely phylogenomic-level analysis of flowering plant groups at different scales. Here, we introduce a workflow to embed a comprehensive understanding of evolutionary relationships into the efficient development of host test lists in weed biological control. We demonstrate the effectiveness of the workflow through a case study on the major crop weed flaxleaf fleabane (Erigeron bonariensis). Phylogenomic analysis was conducted on 280 species of the tribe Astereae (family Asteraceae) occurring in Australia and New Zealand, clarifying relationships between the target species and related clades of native and non-native Astereae. We consider the phylogenetic tree in the context of a previously proposed host test list and discuss taxonomic implications, highlighting avenues of future molecular-based work to uncover the origin of Australian fleabanes. This study provides a workflow and demonstrates the practical application of target sequence capture for phylogenomic inference to support risk analysis and decision making in classical weed biological control. [ABSTRACT FROM AUTHOR]

Coexisting plant species frequently exhibit marked differences in leaf damage caused by chewing insects. Such variation in leaf herbivory has often been attributed to interspecific differences in leaf defensive traits, leaf nutritional quality and leaf abundance. We aimed to investigate the hypothesis that plants surrounded by more similar neighbours tend to exhibit higher levels of herbivory than plants surrounded by less similar neighbours. We sampled 27 tree and shrub species in 49 plots of 10 m2 located in a Neotropical savanna. For each of the 815 plants sampled, we quantified leaf damage, specific leaf area, leaf toughness, height, and conspecific abundance. We analysed the relationship between herbivory levels and plant traits comparing each individual with its neighbouring plants. The effect of phylogenetic similarity was addressed using the mean phylogenetic distance between a focal plant individual and its neighbours (i.e., the phylogenetic isolation). Leaf herbivory damage ranged from zero to 29.6%. We found that phylogenetic isolation, specific leaf area, plant height, and plant abundance were not related to differences in leaf herbivory at the individual level in a neighbourhood. Our findings show that leaf herbivory damage of individual plants was not consistently influenced either by phylogenetic or by trait similarity with neighbours. [ABSTRACT FROM AUTHOR]

Species' evolutionary histories shape their present‐day ecologies, but the integration of phylogenetic approaches in ecology has had a contentious history. The field of ecophylogenetics promised to reveal the process of community assembly from simple indices of phylogenetic pairwise distances – communities shaped by environmental filtering were composed of closely related species, whereas communities shaped by competition were composed of less closely related species. However, the mapping of ecology onto phylogeny proved to be not so straightforward, and the field remains mired in controversy. Nonetheless, ecophylogenetic methods provided important advances across ecology. For example the phylogenetic distances between species is a strong predictor of pest and pathogen sharing, and can thus inform models of species invasion, coexistence and the disease dilution/amplification effect of biodiversity. The phylogenetic structure of communities may also provide information on niche space occupancy, helping interpret patterns of facilitation, succession and ecosystem functioning – with relevance for conservation and restoration – and the dynamics among species within foodwebs and metacommunities. I suggest leveraging advances in our understanding of the process of evolution on phylogenetic trees would allow the field to progress further, while maintaining the essence of the original vision that proved so seductive. [ABSTRACT FROM AUTHOR]

The phylogenetic distance between species often predicts differences in ecologically important traits. The phylogenetic diversity and structure of biological communities can inform our understanding of the processes that shape those communities, and there is a well-developed framework for comparing phylogenetic structures of communities. However, particularly in studies of phylogenetic distances from one focal species to other members of its assemblage (a one-to-many framework), the standard metrics of community-wide studies encounter significant limitations due to the left-skewed distribution of pairwise phylogenetic distances in most biological communities. For studies that require estimating the degree of phylogenetic isolation of a focal taxon, the mean phylogenetic distance (MPD) usually provides little power to distinguish among taxa because it is heavily weighted by the many ways to be distantly related, whereas the nearest taxon distance (NTD) is highly idiosyncratic and ignores cases where multiple close relatives may contribute equally strongly to influence the focal species. Here we highlight the value of examining the cumulative distribution of phylogenetic distances in studies that take a focal-species approach. We describe and discuss the benefits of two new metrics. An integrated metric of phylogenetic distances (AUPhyDC) uses information from the whole cumulative distribution, whereas the tenth quantile (PD10) is an extremely simple metric that improves on NTD by capturing the influence of multiple close relatives on ecological interactions. Several recent examples found that PD10 did a better job of revealing ecological patterns than NTD or MPD. We provide R code to facilitate the use of these approaches and advocate for the inclusion of PD10 along with NTD and MPD in statistical packages for phylogenetic ecology.

Investigating the factors that determine whether interactions are competitive or facilitative is essential to understanding community structure and trait evolution. Co-flowering plants interact indirectly through shared pollinators, and meta-analyses suggest that phylogenetic relatedness and floral trait similarity may predict the outcome of these interactions. In a comparative approach, we manipulated the floral community across five focal species to assess how floral similarity and phylogenetic relatedness affect the outcome of interactions. To assess the extent of pollinator-mediated competition versus facilitation, we compared pollen limitation in five focal species growing with floral neighbors (either congeners or neighbors from a different family) relative to a control (growing alone). We measured floral morphology, color, and nectar traits to calculate multivariate floral similarity between species pairs and inferred a phylogeny to calculate phylogenetic distance. Pollinator-mediated interaction values were regressed against floral similarity and phylogenetic distance. We found evidence of pollinator-mediated facilitation in nine of 13 species pairs. Furthermore, floral similarity and phylogenetic distance reduced facilitative interactions, but the latter relationship was not significant when controlling for the identity of the focal species. Our results suggest that facilitative pollinator sharing is more common than reported in the literature, but co-flowering plant species with similar floral traits are less likely to facilitate pollination. A better understanding of the factors that promote facilitation versus competition has important potential applications for managing rare and invasive species. [ABSTRACT FROM AUTHOR]

Freshwater ecosystems are of the most diverse ecosystems in the world, but anthropogenic disturbance and climate change are threatening the biodiversity of these habitats, particularly in the highly vulnerable arid regions. Understanding the compositional patterns in aquatic biota and discovering factors responsible for these patterns enable researchers to predict the impacts of environmental changes and reduce their destructive effects. As a first step for evaluating the conservation value of freshwater ecosystems in the arid areas of Central Iran, we investigated the phylogenetic beta diversity of Odonata assemblages and their response to climate, landscape, and local predictors. A total of 41 water bodies were surveyed and 42 species of Odonata were recorded. The distance matrices related to the total phylogenetic beta diversity of Odonata and the replacement and richness difference components were computed. Each of the three dissimilarity matrices were modelled by generalized dissimilarity modelling (GDM). The average phylogenetic beta diversity was high, and the replacement component had a higher contribution rather than the richness difference component. GDMs results showed that total phylogenetic beta diversity was strongly associated with climate and local predictors. The most influential variables observed were climate variables. Our findings indicated that even in extreme conditions, the freshwater ecosystems could support species with various phylogenetic histories. We emphasize the importance of man-made water bodies in supporting freshwater biodiversity in arid areas. Given the growing threat of habitat degradation and climate change, with no conservation plan, many vulnerable species may be in danger of localized extinction within the region. [ABSTRACT FROM AUTHOR]

Microbe-disease association relationship mining is drawing more and more attention due to its potential in capturing disease-related microbes. Hence, it is essential to develop new tools or algorithms to study the complex pathogenic mechanism of microbe-related diseases. However, previous research studies mainly focused on the paradigm of “one disease, one microbe,” rarely investigated the cooperation and associations between microbes, diseases or microbe-disease co-modules from system level. In this study, we propose a novel two-level module identifying algorithm (MDNMF) based on nonnegative matrix tri-factorization which integrates two similarity matrices (disease and microbe similarity matrices) and one microbe-disease association matrix into the objective of MDNMF. MDNMF can identify the modules from different levels and reveal the connections between these modules. In order to improve the efficiency and effectiveness of MDNMF, we also introduce human symptoms-disease network and microbial phylogenetic distance into this model. Furthermore, we applied it to HMDAD dataset and compared it with two NMF-based methods to demonstrate its effectiveness. The experimental results show that MDNMF can obtain better performance in terms of enrichment index (EI) and the number of significantly enriched taxon sets. This demonstrates the potential of MDNMF in capturing microbial modules that have significantly biological function implications.

In plant communities, some mechanisms maintain differences in species' abundances, while other mechanisms promote coexistence. Asymmetry in conspecific negative density dependence (CNDD) and/or habitat preference is hypothesized to shape relative species abundance, whereas community compensatory trends (CCTs) induced by community-level CNDD and heterospecific facilitation are hypothesized to promote coexistence. We use survey data from three 1-ha permanent dynamic plots in a subtropical forest over the course of a decade to find out which of these processes are important and at which life-history stages (the seedling, sapling, and juvenile stages) they exert their effects. CNDD was not related to abundance in any of the life-history stages. Suitable habitats positively influenced plant abundance at all tested life stages, but especially so for juveniles. Community-level CNDD of seedling neighbors was detected at the seedling stage, while heterospecific facilitation was detected across all tested life-history stages. A CCT in seedling survival was detected, but there was no evidence for such trends across the other life-history stages. Altogether, our results suggest that habitat specificity increases the rarity of species, whereas a CCT at the seedling stage, which is likely to be induced by CNDD and heterospecific facilitation, enables such species to maintain their populations. [ABSTRACT FROM AUTHOR]

Multiple invaders commonly co‐occur in native ecosystems and in some cases have been shown to facilitate each other thus exacerbating impacts on native species, while in other cases one invader may reduce the impact of another due to competition. We therefore aimed at identifying mechanisms driving alien species interactions. We conducted a common garden experiment investigating all pairwise combinations of 20 alien annual plant species in Germany. We first tested whether competition or facilitation occurred more often. Secondly, we determined whether individual traits, hierarchical or absolute trait distances, multivariate trait or phylogenetic distance explained alien plant interactions best. Thirdly, we assessed whether accounting for trait plasticity explains plant performance better than species‐level trait averages. While the magnitude of interspecific competition compared to intraspecific competition was on average larger across the 190 alien species combinations, interspecific facilitation still occurred in 24% of cases. Interactions could be better explained by hierarchical trait distances which reflect competitive ability, compared to phylogenetic and multivariate trait distance (reflecting niche differences). This finding supports criticisms about the applicability of testing limiting similarity versus environmental filtering and the community phylogenetic approach. Specifically, when growing taller and having a lower specific leaf area than the co‐occurring alien neighbour, biomass and seed number of individuals in mixture increased compared to growing alone. Effects of seed mass, root:shoot ratio and flowering time depended on the performance measure. In contrast to recent suggestions, accounting for trait plasticity did not necessarily explain plant performance better than models using species‐level trait averages. These results advance our fundamental understanding of trait‐interaction relationships, strengthening recent findings on the importance of competitive hierarchy in shaping interactions and community structure. In particular, applying these concepts to the novel case of alien‐alien interactions, is crucial given the continuing accumulation of alien species around the globe. [ABSTRACT FROM AUTHOR]

Microbe-disease association relationship mining is drawing more and more attention due to its potential in capturing disease-related microbes. Hence, it is essential to develop new tools or algorithms to study the complex pathogenic mechanism of microbe-related diseases. However, previous research studies mainly focused on the paradigm of "one disease, one microbe," rarely investigated the cooperation and associations between microbes, diseases or microbe-disease co-modules from system level. In this study, we propose a novel two-level module identifying algorithm (MDNMF) based on nonnegative matrix tri-factorization which integrates two similarity matrices (disease and microbe similarity matrices) and one microbe-disease association matrix into the objective of MDNMF. MDNMF can identify the modules from different levels and reveal the connections between these modules. In order to improve the efficiency and effectiveness of MDNMF, we also introduce human symptoms-disease network and microbial phylogenetic distance into this model. Furthermore, we applied it to HMDAD dataset and compared it with two NMF-based methods to demonstrate its effectiveness. The experimental results show that MDNMF can obtain better performance in terms of enrichment index (EI) and the number of significantly enriched taxon sets. This demonstrates the potential of MDNMF in capturing microbial modules that have significantly biological function implications. [ABSTRACT FROM AUTHOR]

Agroecosystem diversification is often implemented to diminish herbivory and reduce yield losses. However, increasing plant richness does not always reduce herbivory levels, so there is a need for better understanding which polyculture characteristics are effective in deterring herbivores. Here, we evaluated the hypothesis that functional and phylogenetic distances between intercropped species reduce herbivory pressure and enhance natural enemy response. Diminishing herbivory would be brought about by the complementarity and synergy of traits that deter herbivores and benefit herbivore natural enemies, and as a result of a decrease in the availability of host plants for specialized herbivores. Using a meta-analytical approach, we observed lower herbivore abundance and herbivory damage in focal plants when they grew in polycultures. In addition, polycultures showed increased levels of herbivore parasitism and greater abundance of predators and parasitoids, although the effect of the latter two was negligible. Interestingly, the functional distance between crops affected herbivore abundance and herbivory damage in opposite ways, but had no effect on herbivore natural enemy response. Contrary to our expectations, neither herbivory pressure nor natural enemy response appeared to be influenced by phylogenetic distance between intercropped species. Overall, our study provides valuable insights for agroecosystem design aimed at reducing yield loss by strategically intercropping functionally similar species. • Polycultures reduce herbivory damage and herbivore abundance in focal crops. • Polycultures increase herbivore parasitism but not their natural enemies' abundance. • Greater functional distance reduces herbivore abundance but increases herbivory damage. • Natural enemies' response to polycultures is not influenced by functional distance. • Phylogenetic distance between crops does not promote herbivory reduction. [ABSTRACT FROM AUTHOR]

Abstract Background Invasions 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. Results We 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. Conclusions Taken 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.

Introduced exotic plant species that originate from other continents are known to alter soil microbial community composition and nutrient cycling. Plant species that expand range to higher latitudes and altitudes as a consequence of current climate warming might as well affect the composition and functioning of native soil communities in their new range. However, the functional consequences of plant origin have been poorly studied in the case of plant range shifts. Here, we determined rhizosphere bacterial communities of four intracontinental range-expanding plant species in comparison with their four congeneric natives grown in soils collected from underneath those plant species in the field and in soils that are novel to them. We show that, when controlling for both species relatedness and soil characteristics, range-expanding plant species in higher latitude ecosystems will influence soil bacterial community composition and nutrient cycling in a manner similar to congeneric related native species. Our results highlight the importance to include phylogenetically controlled comparisons to disentangle the effect of origin from the effect of contrasting plant traits in the context of exotic plant species.

Co‐occurrence network analysis based on amplicon sequences is increasingly used to study microbial communities. Patterns of co‐existence or mutual exclusion between pairs of taxa are often interpreted as reflecting positive or negative biological interactions. However, other assembly processes can underlie these patterns, including species failure to reach distant areas (dispersal limitation) and tolerate local environmental conditions (habitat filtering). We provide a tool to quantify the relative contribution of community assembly processes to microbial co‐occurrence patterns, which we applied to explore soil bacterial communities in two dry ecosystems. First, we sequenced a bacterial phylogenetic marker in soils collected across multiple plots. Second, we inferred co‐occurrence networks to identify pairs of significantly associated taxa, either co‐existing more (aggregated) or less often (segregated) than expected at random. Third, we assigned assembly processes to each pair: patterns explained based on spatial or environmental distance were ascribed to dispersal limitation (2%–4%) or habitat filtering (55%–77%), and the remaining to biological interactions. Finally, we calculated the phylogenetic distance between taxon pairs to test theoretical expectations on the linkages between phylogenetic patterns and assembly processes. Aggregated pairs were more closely related than segregated pairs. Furthermore, habitat‐filtered aggregated pairs were closer relatives than those assigned to positive interactions, consistent with phylogenetic niche conservatism and cooperativism among distantly related taxa. Negative interactions resulted in equivocal phylogenetic signatures, probably because different competitive processes leave opposing signals. We show that microbial co‐occurrence networks mainly reflect environmental tolerances and propose that incorporating measures of phylogenetic relatedness to networks might help elucidate ecologically meaningful patterns. [ABSTRACT FROM AUTHOR]

Summary: The tendency of closely related plant species to share natural enemies has been suggested to limit their co‐occurrence and performance, but we lack a deep understanding on how mutualistic interactions such as the mycorrhizal symbiosis affect plant–plant interactions depending on the phylogenetic relatedness of the interacting plants. We hypothesise that the effect of the mycorrhizal symbiosis on plant−plant facilitative interactions depends on the phylogenetic distance between the nurse and facilitated plants.A recently published meta‐analysis compiled the strength of plant facilitative interactions in the presence or absence (or reduced abundance) of mycorrhizal fungi. We use phylogenetically informed Bayesian linear models to test whether the effect size is influenced by the phylogenetic distance between the plant species involved in each plant facilitative interaction.Conspecific facilitative interactions are more strongly enhanced by mycorrhizal fungi than interactions between closely related species. In heterospecific interactions, the effect of the mycorrhizal symbiosis on plant facilitation increases with the phylogenetic distance between the nurse and facilitated plant species.Our result showing that the effect of mycorrhizal symbiosis on the facilitation interactions between plants depends on their phylogenetic relatedness provides new mechanisms to understand how facilitation is assembling ecological communities. [ABSTRACT FROM AUTHOR]

Questions: Do neighbourhood interactions in trees result in discernible spatial and phylogenetic signals among their nearest neighbours in a montane evergreen and deciduous forest? Are neighbourhood patterns of different species associated with their abundances and traits? Location: Badagongshan National Nature Reserve, Hunan, China. Methods: We used four nearest‐neighbour indices: average spatial distance to the nearest conspecific cohort‐mate (SNCC), average spatial distance to the nearest conspecific adult (SNCA), average phylogenetic distance to the nearest heterospecific cohort‐mate (PNHC), and average phylogenetic distance to the nearest heterospecific adult (PNHA). We focused on 77 abundant species in a 25‐ha plot. We evaluated whether the changes in SNCC, PNHC, SNCA and PNHA deviated significantly from expected values of spatially random mortality during two life stage transitions. Results: For more than one‐fourth of the tested species, the changes in SNCC and PNHC deviated significantly from the expectations of random mortality. Nearly one‐third of the tested species showed greater SNCC at the juvenile stage than expected of random mortality, which may be mainly explained by conspecific tree competition for space and resources. Approximately 60% and 40% of the tested species showed significantly smaller SNCA and PNHA than expected by random mortality, respectively, which suggests the effects of facilitation and habitat filtering. In addition, abundant and taller species were suppressed by conspecific cohorts to a greater degree than locally rarer and shorter species. Deciduous species were more negatively influenced by conspecifics and closely related heterospecifics than evergreen species. Conclusions: Our study focused on long‐term responses of individual species to their conspecific and phylogenetic neighbourhoods and revealed the associations between species traits and neighbourhood patterns. Such trait–neighbourhood interactions provide support for stabilizing mechanisms driving species coexistence in this species‐rich subtropical forest. [ABSTRACT FROM AUTHOR]

Summary: Established plants can affect the recruitment of young plants, filtering out some and allowing the recruitment of others, with profound effects on plant community dynamics. Recruitment networks (RNs) depict which species recruit under which others. We investigated whether species abundance and phylogenetic distance explain the structure of RNs across communities.We estimated the frequency of canopy–recruit interactions among woody plants in 10 forest assemblages to describe their RNs. For each RN, we determined the functional form (linear, power or exponential) best describing the relationship of interaction frequency with three predictors: canopy species abundance, recruit species abundance and phylogenetic distance. We fitted models with all combinations of predictor variables, from which we simulated RNs.The best functional form of each predictor was the same in most communities (linear for canopy species abundance, power for recruit species abundance and exponential for phylogenetic distance). The model including all predictor variables was consistently the best in explaining interaction frequency and showed the best performance in predicting RN structure.Our results suggest that mechanisms related to species abundance are necessary but insufficient to explain the assembly of RNs. Evolutionary processes affecting phylogenetic divergence are critical determinants of RN structure. [ABSTRACT FROM AUTHOR]

Studies on the highly pathogenic avian influenza (HPAI) H5N1 suggest that wild bird migration may facilitate its long‐distance spread, yet the role of wild bird community composition in its transmission risk remains poorly understood. Furthermore, most studies on the diversity–disease relationship focused on host species diversity without considering hosts' phylogenetic relationships, which may lead to rejecting a species diversity effect when the community has host species that are only distantly related.Here, we explored the influence of waterbird community composition for determining HPAI H5N1 occurrence in wild birds in a continental‐scale study across Europe. In particular, we tested the diversity–disease relationship using both host species diversity and host phylogenetic diversity.Our results provide the first demonstration that host community composition—compared with previously identified environmental risk factors—can also effectively explain the spatial pattern of H5N1 occurrence in wild birds. We further show that communities with more higher risk host species and more closely related species have a higher risk of H5N1 outbreaks. Thus, both host species diversity and community phylogenetic structure, in addition to environmental factors, jointly influence H5N1 occurrence.Our work not only extends the current theory on the diversity–disease relationship, but also has important implications for future monitoring of H5N1 and other HPAI subtypes. [ABSTRACT FROM AUTHOR]

Different components of biological diversity of larval Chironomidae, typically the most abundant and the most diverse of all lotic zoo-benthos, were assessed to determine their suitability in prediction of the environmental quality. Animals were collected as 73 samples at 62 riverine sites on the territory of Poland and identified morphologically. The analysis of nonlinear regression was used to compare the suitability of the seven indices of diversity. Traditional indices of taxonomic diversity (taxonomic richness, Margalef and Shannon indices) and indices of taxonomic distinctness were found to be unsuitable for this purpose because of the unimodal type of response of their values along with the gradient of the environmental quality. Contrary to them, values of two measures of phylogenetic diversity monotonically increased along with the values of environmental quality measured by official index MMI (Multimetric Macroinvertebrate Index) and were considered highly useful. The best fitted functions estimating relationships between MMI and both indices of phylogenetic diversity (total phylogenetic distance and quadratic entropy) were statistically highly significant and have high values of the fit-accuracy parameters. Original index of phylogenetic diversity ChiPDi based on total phylogenetic diversity, quadratic entropy and taxonomic richness has been presented as well as the proposal of related procedure using barcoding methods. [ABSTRACT FROM AUTHOR]

Interspecific interactions play an important role in community assembly. A basic ecological question is whether interactions are specialized (one to one) or generalized (many to many). Specialization of interactions should ideally be assessed across several populations because species could be specialists at a particular site but generalists when several sites are considered. Mycorrhizal interactions are fundamental for orchid life and distribution, but their level of specialization is still under debate. To understand the extent to which epiphytic orchids are specialists in their mycorrhizal interactions, we studied the richness and phylogenetic structure of mycobionts across different sites, and the similarity in the mycobiont composition between coexisting orchid species. We sequenced the nrDNA ITS2 region and explored the mycobiont communities associated with two epiphytic orchids, Epidendrum marsupiale and Cyrtochilum pardinum , at two elevations within two sites in Ecuador. We found 108 OTUs belonging to Serendipitaceae (66), Ceratobasidiaceae (22), Atractiellales (11) and Tulasnellaceae (9). Orchids at the highest elevations hosted the highest OTU richness. The two orchid species shared a high percentage of mycobionts between all sites. No phylogenetic structure within orchid mycorrhizal communities was found at any sites or elevations. Our results indicate that the studied orchids are generalists and share a broad group of mycobionts (16 OTUs) with no apparent niche segregation within or between sites. • E. marsupiale and C. pardinum were associated with a high mycobiont richness. • Serendipitaceae was the richest mycobiont group associated with tropical orchids. • The highest richness of mycobionts occurred at higher altitudes. • No phylogenetic structure was found within orchid mycobionts. • E. marsupiale and C. pardinum showed generalist interactions with mycobionts. [ABSTRACT FROM AUTHOR]

Highlights • We present a new approach for assessing biological dissimilarity among communities. • It provides a framework that integrates all aspects of biological dissimilarities. • It has a potential to be applied in studies aiming to discriminate among communities. Abstract Quantifying the compositional differences among communities is central to answering some of the most challenging questions in community ecology. Traditional species-based estimates of community dissimilarity convey little information regarding the biological heterogeneity of species. More refined phylogenetic- and functional-based measures can improve the understanding of ecological mechanisms that drive species composition. However, a generalized framework, which unifies taxonomic, phylogenetic, and functional information of communities is still lackling. We present a new general framework for assessing the biological dissimilarity among communities based on species frequencies and biological (including taxonomic, phylogenetic, and functional) distances between species. We used the observations collected in a 30-hectare forest plot in northeastern China to illustrate the application of the new approach and its ability to discriminate communities along spatial and environmental gradients. The results suggested that both spatial and environmental gradients play significant roles in driving the species composition of forest communities. Compared with spatial gradients, local environmental conditions had a greater influence. Conclusion: The ability to measure differences among communities, based on species frequency and biological distances is useful for estimating effects of habitat heterogeneity, for understanding the mechanism of community assembly, and for assessing disturbance effects or species invasions at local or global scales. The Avalanche approach presented in this study represents an effective framework for comparing different measures of biological dissimilarity in one compatible system. [ABSTRACT FROM AUTHOR]