Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.

Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.

The commonness of rarity: Global and future distribution of rarity across land plants.

A key feature of life's diversity is that some species are common but many more are rare. Nonetheless, at global scales, we do not know what fraction of biodiversity consists of rare species. Here, we present the largest compilation of global plant diversity to quantify the fraction of Earth's plant biodiversity that are rare. A large fraction, ~36.5% of Earth's ~435,000 plant species, are exceedingly rare. Sampling biases and prominent models, such as neutral theory and the k-niche model, cannot account for the observed prevalence of rarity. Our results indicate that (i) climatically more stable regions have harbored rare species and hence a large fraction of Earth's plant species via reduced extinction risk but that (ii) climate change and human land use are now disproportionately impacting rare species. Estimates of global species abundance distributions have important implications for risk assessments and conservation planning in this era of rapid global change.

Skills and Knowledge for Data-Intensive Environmental Research.

The scale and magnitude of complex and pressing environmental issues lend urgency to the need for integrative and reproducible analysis and synthesis, facilitated by data-intensive research approaches. However, the recent pace of technological change has been such that appropriate skills to accomplish data-intensive research are lacking among environmental scientists, who more than ever need greater access to training and mentorship in computational skills. Here, we provide a roadmap for raising data competencies of current and next-generation environmental researchers by describing the concepts and skills needed for effectively engaging with the heterogeneous, distributed, and rapidly growing volumes of available data. We articulate five key skills: (1) data management and processing, (2) analysis, (3) software skills for science, (4) visualization, and (5) communication methods for collaboration and dissemination. We provide an overview of the current suite of training initiatives available to environmental scientists and models for closing the skill-transfer gap.

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.

BACKGROUND: The Environment Ontology (ENVO; http://www.environmentontology.org/ ), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description. We have thus expanded, enhanced, and generalised the ontology to support its increasingly diverse applications. METHODS: We have updated our development suite to promote expressivity, consistency, and speed: we now develop ENVO in the Web Ontology Language (OWL) and employ templating methods to accelerate class creation. We have also taken steps to better align ENVO with the Open Biological and Biomedical Ontologies (OBO) Foundry principles and interoperate with existing OBO ontologies. Further, we applied text-mining approaches to extract habitat information from the Encyclopedia of Life and automatically create experimental habitat classes within ENVO. RESULTS: Relative to its state in 2013, ENVO's content, scope, and implementation have been enhanced and much of its existing content revised for improved semantic representation. ENVO now offers representations of habitats, environmental processes, anthropogenic environments, and entities relevant to environmental health initiatives and the global Sustainable Development Agenda for 2030. Several branches of ENVO have been used to incubate and seed new ontologies in previously unrepresented domains such as food and agronomy. The current release version of the ontology, in OWL format, is available at http://purl.obolibrary.org/obo/envo.owl . CONCLUSIONS: ENVO has been shaped into an ontology which bridges multiple domains including biomedicine, natural and anthropogenic ecology, 'omics, and socioeconomic development. Through continued interactions with our users and partners, particularly those performing data archiving and sythesis, we anticipate that ENVO's growth will accelerate in 2017. As always, we invite further contributions and collaboration to advance the semantic representation of the environment, ranging from geographic features and environmental materials, across habitats and ecosystems, to everyday objects in household settings.

Functional trait space and the latitudinal diversity gradient.

The processes causing the latitudinal gradient in species richness remain elusive. Ecological theories for the origin of biodiversity gradients, such as competitive exclusion, neutral dynamics, and environmental filtering, make predictions for how functional diversity should vary at the alpha (within local assemblages), beta (among assemblages), and gamma (regional pool) scales. We test these predictions by quantifying hypervolumes constructed from functional traits representing major axes of plant strategy variation (specific leaf area, plant height, and seed mass) in tree assemblages spanning the temperate and tropical New World. Alpha-scale trait volume decreases with absolute latitude and is often lower than sampling expectation, consistent with environmental filtering theory. Beta-scale overlap decays with geographic distance fastest in the temperate zone, again consistent with environmental filtering theory. In contrast, gamma-scale trait space shows a hump-shaped relationship with absolute latitude, consistent with no theory. Furthermore, the overall temperate trait hypervolume was larger than the overall tropical hypervolume, indicating that the temperate zone permits a wider range of trait combinations or that niche packing is stronger in the tropical zone. Although there are limitations in the data, our analyses suggest that multiple processes have shaped trait diversity in trees, reflecting no consistent support for any one theory.

Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.

Habitat area and climate stability determine geographical variation in plant species range sizes.

Despite being a fundamental aspect of biodiversity, little is known about what controls species range sizes. This is especially the case for hyperdiverse organisms such as plants. We use the largest botanical data set assembled to date to quantify geographical variation in range size for ~ 85 000 plant species across the New World. We assess prominent hypothesised range-size controls, finding that plant range sizes are codetermined by habitat area and long- and short-term climate stability. Strong short- and long-term climate instability in large parts of North America, including past glaciations, are associated with broad-ranged species. In contrast, small habitat areas and a stable climate characterise areas with high concentrations of small-ranged species in the Andes, Central America and the Brazilian Atlantic Rainforest region. The joint roles of area and climate stability strengthen concerns over the potential effects of future climate change and habitat loss on biodiversity.

Challenges and opportunities of open data in ecology.

Ecology is a synthetic discipline benefiting from open access to data from the earth, life, and social sciences. Technological challenges exist, however, due to the dispersed and heterogeneous nature of these data. Standardization of methods and development of robust metadata can increase data access but are not sufficient. Reproducibility of analyses is also important, and executable workflows are addressing this issue by capturing data provenance. Sociological challenges, including inadequate rewards for sharing data, must also be resolved. The establishment of well-curated, federated data repositories will provide a means to preserve data while promoting attribution and acknowledgement of its use.

Advancing ecological research with ontologies.

Ecology is inherently cross-disciplinary, drawing together many types of information to address questions about the natural world. Finding and integrating relevant data to assist in these analyses is crucial, but is difficult owing to ambiguous terminology and the lack of sufficient information about datasets. Ontologies provide a formal mechanism for defining terms and their relationships, and can improve the location, interpretation and integration of data based on its inherent meaning. Ontologies have assisted other disciplines (e.g. molecular biology) in unifying and enriching descriptions of data, and ecology can benefit from similar approaches. We review ontology efforts in ecology, and describe how these can benefit research by enhancing the location and interpretation of relevant data for confronting crucial ecological questions.

THE COSTS OF CHANGING SEX AND THE ONTOGENY OF MALES UNDER CONTEST COMPETITION FOR MATES.

In its simplest form, the size-advantage hypothesis predicts that individuals should change sex in order to increase their reproductive success. In terms of lifetime expectations, this must be true for the hypothesis to hold. However, as we review here, some loss of reproductive success may occur immediately after sex change. Unavoidable costs (e.g., those resulting from a restructuring of the gonad) have not been adequately distinguished from adaptive allocations of resources which diminish current reproduction in favor of large increases in future mating success. This strategy can become particularly important for species in which a few males monopolize matings. To illustrate this idea, we describe the changes in mating frequency as mature females become sexually active males in three species of protogynous wrasses. In one species, a male defends a permanent, all-purpose territory composed of up to 12 females. When he is removed, a single female changes sex and successfully completes mating sequences with all females in the territory within an average of 5.6 days. This duration roughly corresponds to the time required for functional transformation of gonads; thus, individuals in this species suffer few reproductive losses as a result of changing sex. The largest males in two other species mate with an average of 25 to 50 females per day, but only by successfully defending reproductive territories. In one of those species, individuals that changed sex mated infrequently over a two-year period after sexual transformation and, by the end of the study, were still well below the average size of males that consistently obtained territories. Sex-changed individuals in the other species had very low reproductive success for up to 45% of the maximum lifespan as a male. It is improbable that the substantial cost of changing sex in the latter two species results from gonad restructuring or from mistakes due to imprecise cues for sex change. Instead, the cost appears to represent an investment in growth rather than current reproduction as a means of rapidly attaining a size advantage when individuals face intense competition for extraordinarily successful mating territories.