Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable and non‐invasive. The longstanding needs of the eDNA community are modular informatics tools, comprehensive and customizable reference databases, flexibility across high‐throughput sequencing platforms, fast multilocus metabarcode processing and accurate taxonomic assignment. Improvements in bioinformatics tools make addressing each of these demands within a single toolkit a reality. The new modular metabarcode sequence toolkit Anacapa ( https://github.com/limey-bean/Anacapa/) addresses the above needs, allowing users to build comprehensive reference databases and assign taxonomy to raw multilocus metabarcode sequence data. A novel aspect of Anacapa is its database building module, “Creating Reference libraries Using eXisting tools” (CRUX), which generates comprehensive reference databases for specific user‐defined metabarcoding loci. The Quality Control and ASV Parsing module sorts and processes multiple metabarcoding loci and processes merged, unmerged and unpaired reads maximizing recovered diversity. DADA2 then detects amplicon sequence variants (ASVs) and the Anacapa Classifier module aligns these ASVs to CRUX‐generated reference databases using Bowtie2. Lastly, taxonomy is assigned to ASVs with confidence scores using a Bayesian Lowest Common Ancestor (BLCA) method. The Anacapa Toolkit also includes an r package, ranacapa, for automated results exploration through standard biodiversity statistical analysis. Benchmarking tests verify that the Anacapa Toolkit effectively and efficiently generates comprehensive reference databases that capture taxonomic diversity, and can assign taxonomy to both MiSeq and HiSeq‐length sequence data. We demonstrate the value of the Anacapa Toolkit in assigning taxonomy to seawater eDNA samples collected in southern California. The Anacapa Toolkit improves the functionality of eDNA and streamlines biodiversity assessment and management by generating metabarcode specific databases, processing multilocus data, retaining a larger proportion of sequencing reads and expanding non‐traditional eDNA targets. All the components of the Anacapa Toolkit are open and available in a virtual container to ease installation.

Plant species can show considerable morphological and functional variation along environmental gradients. This intraspecific trait variation (ITV) can have important consequences for community assembly, biotic interactions, ecosystem functions and responses to global change. However, directly measuring ITV across many species and wide geographic areas is often infeasible. Thus, a method to predict spatial variation in a species’ functional traits could be valuable. We measured specific leaf area (SLA), height and leaf area (LA) of grasses across California, covering 59 species at 230 sampling locations. We asked how these traits change along climate gradients within each species and used machine learning to predict local trait values for any species at any location based on phylogenetic position, local climate and that species’ mean traits. We then examined how much these local predictions alter patterns of assemblage‐level trait variation across the state. Most species exhibited higher SLA and grew taller at higher temperatures and produced larger leaves in drier conditions. The random forests predicted spatial variation in functional traits very accurately, with correlations up to 0.97. Because trait records were spatially biased towards warmer areas, and these areas tend to have higher SLA individuals within each species, species means of SLA were upwardly biased. As a result, using species means over‐estimates SLA in the cooler regions of the state. Our results also suggest that height may be substantially under‐predicted in the warmest areas. Synthesis. Using only species mean traits to characterize the functional composition of communities risks introducing substantial error into trait‐based estimates of ecosystem properties including decomposition rates or NPP. The high performance of random forests in predicting local trait values provides a way forward for estimating high‐resolution patterns of ITV without a massive data collection effort.

Climate change is leading to habitat shifts that threaten species persistence throughout California's unique ecosystems. Baseline biodiversity data would provide opportunities for habitats to be managed under short-term and long-term environmental change. Aiming to provide biodiversity data, the UC Conservation Genomics Consortium launched the California Environmental DNA (CALeDNA) program to be a citizen and community science biomonitoring initiative that uses environmental DNA (eDNA, DNA shed from organisms such as from fur, feces, spores, pollen or leaves). Now with results from 1,000 samples shared online, California biodiversity patterns are discoverable. Soil, sediment and water collected by researchers, undergraduates and the public reveal a new catalog of thousands of organisms that only slightly overlap with traditional survey bioinventories. The CALeDNA website lets users explore the taxonomic diversity in different ways, and researchers have created tools to help people new to eDNA to analyze community ecology patterns. Although eDNA results are not always precise, the program team is making progress to fit it into California's biodiversity management toolbox, such as for monitoring ecosystem recovery after invasive species removal or wildfire.

Although how rare species persist in communities is a major ecological question, the critical phenotypic dimension of rarity is broadly overlooked. Recent work has shown that evaluating functional distinctiveness, the average trait distance of a species to other species in a community, offers essential insights into biodiversity dynamics, ecosystem functioning, and biological conservation. However, the ecological mechanisms underlying the persistence of functionally distinct species are poorly understood. Here we propose a heterogeneous fitness landscape framework, whereby functional dimensions encompass peaks representing trait combinations that yield positive intrinsic growth rates in a community. We identify four fundamental causes leading to the persistence of functionally distinct species in a community. First, environmental heterogeneity or alternative phenotypic designs can drive positive population growth of functionally distinct species. Second, sink populations with negative growth can deviate from local fitness peaks and be functionally distinct. Third, species found at the margin of the fitness landscape can persist but be functionally distinct. Fourth, biotic interactions (either positive or negative) can dynamically alter the fitness landscape. We offer examples of these four cases and some guidelines to distinguish among them. In addition to these deterministic processes, we also explore how stochastic dispersal limitation can yield functional distinctiveness.

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Synthesis research in ecology and environmental science improves understanding, advances theory, identifies research priorities, and supports management strategies by linking data, ideas, and tools. Accelerating environmental challenges increases the need to focus synthesis science on the most pressing questions. To leverage input from the broader research community, we convened a virtual workshop with participants from many countries and disciplines to examine how and where synthesis can address key questions and themes in ecology and environmental science in the coming decade. Seven priority research topics emerged: (1) diversity, equity, inclusion, and justice (DEIJ), (2) human and natural systems, (3) actionable and use-inspired science, (4) scale, (5) generality, (6) complexity and resilience, and (7) predictability. Additionally, two issues regarding the general practice of synthesis emerged: the need for increased participant diversity and inclusive research practices; and increased and improved data flow, access, and skill-building. These topics and practices provide a strategic vision for future synthesis in ecology and environmental science.

17Soil microorganisms influence a variety of processes in plant communities. Many the-18 oretical and empirical studies have shown that dynamic feedbacks between plants and 19 soil microbes can stabilize plant coexistence by generating negative frequency-dependent 20 plant population dynamics. However, inferring the net effects of soil microbes on plant 21 coexistence requires also quantifying the degree to which they provide one species an av-22 erage fitness advantage, an effect that has received little empirical attention. We conducted 23 a greenhouse study to quantify microbially mediated stabilization and fitness differences 24 among fifteen pairs of annual plants that co-occur in southern California grasslands. We 25 found that although soil microbes frequently generate negative frequency-dependent 26 dynamics that stabilize plant interactions, they simultaneously mediate large average 27 fitness differences between species. The net result is that if the plant species are otherwise 28 competitively equivalent, the impact of plant-soil feedbacks is often to favor species exclu-29 sion over coexistence, a result that only becomes evident by quantifying the microbially 30 mediated fitness difference. Our work highlights that comparing the stabilizing effects of 31 plant-soil feedbacks to the fitness difference they generate is essential for understanding 32 the influence of soil microbes on plant diversity. 33 Keywords 34 coexistence, rhizosphere, annual plants, plant-microbe interactions, soil biota, competition 35 36 The dynamics of plants and soil microorganisms are tightly intertwined. The composition 37 of soil microbial communities responds strongly to different plant species, in large part due 38 to interspecific differences in root architecture and exudate profile (Berg and Smalla 2009). 39 Soil microorganisms in turn influence the growth of plant species, with the direction and 40 magnitude of their effect determined both by the composition of the microbial community 41 and by the genetic and functional characteristics of the plants (Laliberté et al. 2014, Keller 42 and Lau 2018). These plant-soil feedbacks can have important consequences for various 43 processes in plant communities (van der Putten et al. 2016), including species coexistence. 44 The effects of soil microorganisms on plant species coexistence are typically studied 45 in the context of a theoretical framework developed by Bever et al. (1997). This framework 46 isolated the effects of soil microbes by modeling the dynamics of plant species that differ 47 only in the soil microbial communities they cultivate and in how their growth is influenced 48 by these cultivated communities. Bever et al. (1997) showed that the soil microbial commu-49 nity stabilizes plant interactions when the microbial community cultivated by each plant 50 species limits the growth of the cultivating plant species more (or benefits it less) than that 51 of the other plant species in the system. When this condition is satisfied, the microbial com-52 munity gener...

Leaf drought tolerance traits influence plant survival in water deficit conditions, and these traits are influenced by both the plant’s evolutionary history and the environment in which the plant is currently growing. However, due to the substantial phenotypic plasticity in leaf traits, we still do not know to what degree variation in leaf traits is governed by species’ phylogenetic history or by their environment. To explore this question, we re-examined a drought tolerance dataset from 37 native Australian shrub species with varying climate origins growing in a common garden located in Melbourne, Australia. We previously measured seven leaf morphophysiological traits, and here, we estimated how phylogenetically conserved these traits are. We quantified phylogeny and the strength of correlation between the morphological traits and physiological traits before and after accounting for shared phylogenetic history. We also evaluated the relationship between species’ leaf traits and the climate of their native ranges. We present three main findings: (a) most leaf drought tolerance traits had weak phylogenetic signals, which is consistent with the convergent evolution of these traits. (b) There is weak but consistent coordination between distinct leaf drought tolerance traits, which can be masked due to species’ phylogenetic histories. (c) Leaf drought tolerance traits show strong correlations with the climate of species’ origins, and this relationship is only weakly impacted by phylogenetic signals. Therefore, the role of phylogeny on the coordination among leaf functional traits and their links to climate were limited. A better understanding of trait–environment relationships might be more pivotal than understanding the evolution of these traits for improving the predictions of species’ response to climate change–type drought, especially for shrub species that span substantial aridity gradients.