Summary
The subdiscipline of ‘community phylogenetics’ is rapidly growing and influencing thinking regarding community assembly. In particular, phylogenetic dispersion of co‐occurring species within ...a community is commonly used as a proxy to identify which community assembly processes may have structured a particular community: phylogenetic clustering as a proxy for abiotic assembly, that is habitat filtering, and phylogenetic overdispersion as a proxy for biotic assembly, notably competition.
We challenge this approach by highlighting (typically) implicit assumptions that are, in reality, only weakly supported, including (i) phylogenetic dispersion reflects trait dispersion; (ii) a given ecological function can be performed only by a single trait state or combination of trait states; (iii) trait similarity causes enhanced competition; (iv) competition causes species exclusion; (v) communities are at equilibrium with processes of assembly having been completed; (vi) assembly through habitat filtering decreases in importance if assembly through competition increases, such that the relative balance of the two can be thus quantified by a single parameter; and (vii) observed phylogenetic dispersion is driven predominantly by local and present‐day processes.
Moreover, technical sophistication of the phylogenetic‐patterns‐as‐proxy approach trades off against sophistication in alternative, potentially more pertinent approaches to directly observe or manipulate assembly processes.
Despite concerns about using phylogenetic dispersion as a proxy for community assembly processes, we suggest there are underappreciated benefits of quantifying the phylogenetic structure of communities, including (i) understanding how coexistence leads to the macroevolutionary diversification of habitat lineage‐pools (i.e. phylogenetic‐patterns‐as‐result approach); and (ii) understanding the macroevolutionary contingency of habitat lineage‐pools and how it affects present‐day species coexistence in local communities (i.e. phylogenetic‐patterns‐as‐cause approach).
We conclude that phylogenetic patterns may be little useful as proxy of community assembly. However, such patterns can prove useful to identify and test novel hypotheses on (i) how local coexistence may control macroevolution of the habitat lineage‐pool, for example through competition among close relatives triggering displacement and diversification of characters, and (ii) how macroevolution within the habitat lineage‐pool may control local coexistence of related species, for example through origin of close relatives that can potentially enter in competition.
Lay Summary
Anthropogenic disturbance has generated a significant loss of biodiversity worldwide and grazing by domestic herbivores is a contributing disturbance. Although the effects of grazing on plants are ...commonly explored, here we address the potential multi‐trophic effects on animal biodiversity (e.g. herbivores, pollinators and predators). We conducted a meta‐analysis on 109 independent studies that tested the response of animals or plants to livestock grazing relative to livestock excluded. Across all animals, livestock exclusion increased abundance and diversity, but these effects were greatest for trophic levels directly dependent on plants, such as herbivores and pollinators. Detritivores were the only trophic level whose abundance decreased with livestock exclusion. We also found that the number of years since livestock was excluded influenced the community and that the effects of grazer exclusion on animal diversity were strongest in temperate climates. These findings synthesise the effects of livestock grazing beyond plants and demonstrate the indirect impacts of livestock grazing on multiple trophic levels in the animal community. We identified the potentially long‐term impacts that livestock grazing can have on lower trophic levels and consequences for biological conservation. We also highlight the potentially inevitable cost to global biodiversity from livestock grazing that must be balanced against socio‐economic benefits.
Livestock grazing reduces the abundance and diversity of animals, but the effects are dependent on trophic level of responding species. Herbivores and pollinators are most impacted, while detritivores increase with livestock present. There is also an effect of livestock exclusion over time on the animal community.
Fungi play vital regulatory roles in terrestrial ecosystems. Local community assembly mechanisms, including deterministic and stochastic processes, as well as the size of regional species pools ...(gamma diversity), typically influence overall soil microbial community beta diversity patterns. However, there is limited evidence supporting their direct and indirect effects on beta diversity of different soil fungal functional groups in forest ecosystems. To address this gap, we collected 1606 soil samples from a 25-ha subtropical forest plot in southern China. Our goal was to determine the direct effects and indirect effects of regional species pools on the beta diversity of soil fungi, specifically arbuscular mycorrhizal (AM), ectomycorrhizal (EcM), plant-pathogenic, and saprotrophic fungi. We quantified the effects of soil properties, mycorrhizal tree abundances, and topographical factors on soil fungal diversity. The beta diversity of plant-pathogenic fungi was predominantly influenced by the size of the species pool. In contrast, the beta diversity of EcM fungi was primarily driven indirectly through community assembly processes. Neither of them had significant effects on the beta diversity of AM and saprotrophic fungi. Our results highlight that the direct and indirect effects of species pools on the beta diversity of soil functional groups of fungi can significantly differ even within a relatively small area. They also demonstrate the independent and combined effects of various factors in regulating the diversities of soil functional groups of fungi. Consequently, it is crucial to study the fungal community not only as a whole but also by considering different functional groups within the community.
In this study, we used data from temperate grassland plant communities in Alberta, Canada to test two longstanding hypotheses in ecology: 1) that there has been correlated evolution of the leaves and ...roots of plants due to selection for an integrated whole-plant resource uptake strategy, and 2) that trait diversity in ecological communities is generated by adaptations to the conditions in different habitats. We tested the first hypothesis using phylogenetic comparative methods to test for evidence of correlated evolution of suites of leaf and root functional traits in these grasslands. There were consistent evolutionary correlations among traits related to plant resource uptake strategies within leaf tissues, and within root tissues. In contrast, there were inconsistent correlations between the traits of leaves and the traits of roots, suggesting different evolutionary pressures on the above and belowground components of plant morphology. To test the second hypothesis, we evaluated the relative importance of two components of trait diversity: within-community variation (species trait values relative to co-occurring species; α traits) and among-community variation (the average trait value in communities where species occur; β traits). Trait diversity was mostly explained by variation among co-occurring species, not among-communities. Additionally, there was a phylogenetic signal in the within-community trait values of species relative to co-occurring taxa, but not in their habitat associations or among-community trait variation. These results suggest that sorting of pre-existing trait variation into local communities can explain the leaf and root trait diversity in these grasslands.
Field ecology has been included in a ‘replication crisis’ that extends across many scientific disciplines. However, the underlying concepts of replication, reproducibility and replicability are not ...always clearly distinguished, and complicate the identification of best practices. Furthermore, conducting experiments under the high variability of natural field conditions reduces the capacity for replication relative to other biological disciplines working under controlled conditions. Field ecologists are therefore facing a significant challenge in assessing the replicability of their research with implications for overall confidence in study outcomes.
Through a review of the literature, we discuss several related aspects of experimental design that can enhance confidence in scientific outcomes. Specifically, we describe sample replication (repeat sample), within‐study replication (repeat experiment) and between‐study replication (repeat study) and how each can be used within field ecology. Since perfect between‐study replication (i.e. direct replication) is generally not possible in field ecology, we suggest more explicit use of conceptual replication would enhance confidence in scientific outcomes. However, such changes require cultural shifts in practice among all participants in the scientific enterprise.
We suggest several tangible steps could be taken to improve confidence in ecological research: (a) increase the use of within‐study replication before publication, (b) increase replicability for aspects that we can control (e.g. pre‐register experiments, open data, publish code), (c) divest from novelty as the primary criterion for publication in leading ecological journals and invest in experimental design, (d) be sceptical of contradictory findings from studies testing similar research questions and (e) create a publishing environment that encourages more conceptual replication studies.
We believe adopting these practices will increase the confidence in results for field ecology. There are critical obstacles that could prevent some scientists from increasing within‐study or between‐study replication, including short‐term funding mechanisms and the prospect of fewer publications. We suggest strategies to mitigate negative impacts to researchers, such as leading journals piloting new article categories and explicit mention of experimentally linked studies. We acknowledge that adopting greater replication in field ecology will require significant changes to cultural practices, but there are clear benefits for improving our confidence in science.
L'ecologia del campo è stata inclusa in una "crisi di replicazione" che si estende a molte discipline scientifiche. Tuttavia, i concetti sottostanti di replica, riproducibilità, e replicabilità non sono sempre chiaramente distinti e complicano l'identificazione delle migliori pratiche. Inoltre, condurre esperimenti sotto l'elevata variabilità delle condizioni del campo naturale riduce la capacità di replicazione rispetto ad altre discipline biologiche che lavorano in condizioni controllate. Gli ecologisti sul campo si trovano quindi ad affrontare una sfida significativa nel valutare la replicabilità della loro ricerca con implicazioni per la fiducia complessiva nei risultati dello studio.
Utilizzando recensione della letteratura, discutiamo diversi aspetti correlati del disegno sperimentale che possono aumentare la fiducia nei risultati scientifici. In particolare, descriviamo la replica del campione (ripetizione del campione), la replica all'interno dello studio (ripetizione dell'esperimento), e la replica tra gli studi (ripetizione dello studio) e come ciascuna può essere utilizzata nell'ecologia del campo. Poiché la replica perfetta tra gli studi (cioè la replica diretta) non è generalmente possibile nell'ecologia sul campo, suggeriamo che un uso più esplicito della replica concettuale aumenterebbe la fiducia nei risultati scientifici. Tuttavia, tali cambiamenti richiedono cambiamenti culturali nella pratica tra tutti i partecipanti all'impresa scientifica.
Suggeriamo che si potrebbero intraprendere diversi passi tangibili per migliorare la fiducia nella ricerca ecologica: (1) aumentare l'uso della replicazione all'interno dello studio prima della pubblicazione, (2) aumentare la replicabilità per gli aspetti che possiamo controllare (ad es. Esperimenti pre‐registrati, dati aperti, pubblicazione codice), (3) disinvestire dalla novità come criterio principale per la pubblicazione nelle principali riviste ecologiche e investire nella progettazione sperimentale, (4) essere scettici sui risultati contraddittori di studi che testano domande di ricerca simili, e (5) creare un ambiente di pubblicazione che incoraggia una replica più concettuale studi.
Riteniamo che l'adozione di queste pratiche aumenterà la fiducia nei risultati per l'ecologia sul campo. Esistono ostacoli critici che potrebbero impedire ad alcuni scienziati di aumentare la replica all'interno dello studio o tra gli studi, compresi i meccanismi di finanziamento a breve termine e la prospettiva di un minor numero di pubblicazioni. Suggeriamo strategie per mitigare gli impatti negativi ai ricercatori, come le principali riviste che sperimentano nuove categorie di articoli e la menzione esplicita di studi collegati sperimentalmente. Riconosciamo che l'adozione di una maggiore replica nell'ecologia sul campo richiederà cambiamenti significativi alle pratiche culturali, ma ci sono chiari vantaggi per migliorare la nostra fiducia nella scienza.
Plant–plant interactions, often studied in the context of plant traits, are considered crucial assembly mechanisms for plant communities and offer insights into how neighbours affect growth. Three ...key questions regarding these interactions have theoretical importance but limited empirical support: (1) does similarity in plant traits enhance competitive interactions among species, (2) is the “competitive environment” determined through plant traits of the resident species, and (3) do greater species diversity and niche use result in increased competition among co‐occurring species. Here we use a simple experimental design to directly test these foundational questions.
In a mesocosm experiment using native grassland fragments, we investigated our questions simultaneously by manipulating trait relationships among resident and colonizing plants. To assess the net impact of neighbours on plant growth, we measured the degree of suppression experienced by focal plants compared to growth in the absence of neighbours. We further tested whether trait‐function relationships are context‐dependent by modifying available resources.
Contrary to the limiting similarity hypothesis, we found that reduced overall dissimilarity mitigated neighbour‐induced growth suppression, with more negative effects occurring among dissimilar neighbours. The influence of trait dissimilarity depended on nutrient context and was stronger under increased resource availability. We found little support for the idea that specific plant traits are “functional” in creating competitive environments: no community traits (community weighted means) were associated with net neighbour effects. In contrast, resource supply significantly affected species interactions, with increased resources exacerbating negative neighbour effects on plant growth.
We found that plant trait dissimilarity does function in competition but is contingent on resource context. However, trait values were not inherently competitive: traits may have physiological functions but did not function in focal plants' competitive response. We provide some of the limited data directly testing the core mechanisms of community assembly. We encourage such direct experimental tests as they are essential to building an understanding of ecological processes.
Read the free Plain Language Summary for this article on the Journal blog.
Read the free Plain Language Summary for this article on the Journal blog.
Competition is often highlighted as a major force influencing plant species diversity. However, there are multiple facets of competition (e.g., strength, intransitivity, and size asymmetry) that may ...have independent and differential impacts on diversity, making understanding the degree to which competition structures communities difficult. Unfortunately, field‐based experiments that decouple multiple facets of competition are lacking, limiting our ability to test theoretical frameworks and reducing understanding of the actual linkages among competition and coexistence. Here, we experimentally manipulate the size structure of local grassland communities to examine the relative impacts of competitive size asymmetry (i.e., competitive advantage based on relative size) and intensity (i.e., mean effect of neighbors on plant growth) on species loss and gain. Increased competitive size asymmetry was associated with increased species loss and decreased species gain, while no relationship was found between competitive intensity and species loss and gain. Furthermore, the probability of loss was not dependent on a species initial size, suggesting that small species may not always be the losers of size‐asymmetric interactions. Instead, loss was dependent on species rarity, where loss was higher for rare species. Overall, these results suggest that competitive size asymmetry may be more important for species loss than intensity in some plant communities and demonstrates the importance of decoupling different aspects of competition to better understand their drivers and ecological consequences.
Root‐centric studies have revealed fast taxonomic turnover across root neighborhoods, but how such turnover is accompanied by changes in species functions and phylogeny (i.e., β diversity) remains ...largely unknown. As β diversity can reflect the degree of community‐wide biotic homogenization, such information is crucial for better inference of below‐ground assembly rules, community structuring, and ecosystem processes. We collected 2480 root segments from 625 0–30 cm soil profiles in a subtropical forest in China. Root segments were identified into 138 species with DNA‐barcoding with six root morphological and architectural traits measured per species. By using the mean pairwise (Dpw) and mean nearest neighbor distance (Dnn) to quantify species ecological differences, we first tested the non‐random functional and phylogenetic turnover of root neighborhoods that would lend more support to deterministic over stochastic community assembly processes. Additionally, we examined the distance‐decay pattern of β diversity, and finally partitioned β diversity into geographical and environmental components to infer their potential drivers of environmental filtering, dispersal limitation, and biotic interactions. We found that functional turnover was often lower than expected given the taxonomic turnover, whereas phylogenetic turnover was often higher than expected. Phylogenetic Dpw (e.g., interfamily species) turnover exhibited a distance‐decay pattern, likely reflecting limited dispersal or abiotic filtering that leads to the spatial aggregation of specific plant lineages. Conversely, both functional and phylogenetic Dnn (e.g., intrageneric species) exhibited an inverted distance‐decay pattern, likely reflecting strong biotic interactions among spatially and phylogenetically close species leading to phylogenetic and functional divergence. While the spatial distance was generally a better predictor of β diversity than environmental distance, the joint effect of environmental and spatial distance usually overrode their respective pure effects. These findings suggest that root neighborhood functional homogeneity may somewhat increase forest resilience after disturbance by exhibiting an insurance effect. Likewise, root neighborhood phylogenetic heterogeneity may enhance plant fitness by hindering the transmission of host‐specific pathogens through root networks or by promoting interspecific niche complementarity not captured by species functions. Our study highlights the potential role of root‐centric β diversity in mediating community structures and functions largely ignored in previous studies.
Oxytocin (OXT; hereafter OT) and arginine vasopressin or vasotocin (AVP or VT; hereafter VT) are neurotransmitter ligands that function through specific receptors to control diverse functions
. Here ...we performed genomic analyses on 35 species that span all major vertebrate lineages, including newly generated high-contiguity assemblies from the Vertebrate Genomes Project
. Our findings support the claim
that OT (also known as OXT) and VT (also known as AVP) are adjacent paralogous genes that have resulted from a local duplication, which we infer was through DNA transposable elements near the origin of vertebrates and in which VT retained more of the parental sequence. We identified six major oxytocin-vasotocin receptors among vertebrates. We propose that all six of these receptors arose from a single receptor that was shared with the common ancestor of invertebrates, through a combination of whole-genome and large segmental duplications. We propose a universal nomenclature based on evolutionary relationships for the genes that encode these receptors, in which the genes are given the same orthologous names across vertebrates and paralogous names relative to each other. This nomenclature avoids confusion due to differential naming in the pre-genomic era and incomplete genome assemblies, furthers our understanding of the evolution of these genes, aids in the translation of findings across species and serves as a model for other gene families.
Animals regularly integrate information about the location of resources and the presence of competitors, altering their foraging behavior accordingly. We studied the annual plant Abutilon theophrasti ...to determine whether a plant can demonstrate a similarly complex response to two conditions: presence of a competitor and heterogeneous resource distributions. Individually grown plants fully explored the pot by using a broad and uniform rooting distribution regardless of soil resource distributions. Plants with competitors and uniform soil nutrient distributions exhibited pronounced reductions in rooting breadth and spatial soil segregation among the competing individuals. In contrast, plants with competitors and heterogeneous soil nutrient distributions reduced their root growth only modestly, indicating that plants integrate information about both neighbor and resource distributions in determining their root behavior.
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