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Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other reference. However, these do not include the phenotypic trait or attribute categories required for the annotation of genome-wide association studies (GWAS), Quantitative Trait Loci (QTL) mappings or any population-focused measurable trait data. Moreover, variations in gene expression in response to environmental disturbances even without any genetic alterations can also be associated with particular biological attributes. The integration of trait and biological attribute information with an ever increasing body of chemical, environmental and biological data greatly facilitates computational analyses and it is also highly relevant to biomedical and clinical applications.The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. OBA has a modular design which provides several benefits for users and data integrators, including an automated and meaningful classification of trait terms computed on the basis of logical inferences drawn from domain-specific ontologies for cells, anatomical and other relevant entities. The logical axioms in OBA also provide a previously missing bridge that can computationally link Mendelian phenotypes with GWAS and quantitative traits. The term components in OBA provide semantic links and enable knowledge and data integration across specialised research community boundaries, thereby breaking silos.

Shark teeth are one of the most abundant vertebrate fossils, and because tooth size generally correlates with body size, their accumulations document the size structure of populations. Understanding how ecological and environmental processes influence size structure, and how this extends to influence these dental distributions, may offer a window into the ecological and environmental dynamics of past and present shark populations. Here, we examine the dental distributions of sand tigers, including extant Carcharias taurus and extinct Striatolamia macrota , to reconstruct the size structure for a contemporary locality and four Eocene localities. We compare empirical distributions against expectations from a population simulation to gain insight into potential governing ecological processes. Specifically, we investigate the influence of dispersal flexibility to and from protected nurseries. We show that changing the flexibility of initial dispersal of juveniles from the nursery and annual migration of adults to the nursery explains a large amount of dental distribution variability. Our framework predicts dispersal strategies of an extant sand tiger population, and supports nurseries as important components of sand tiger life history in both extant and Eocene populations. These results suggest nursery protection may be vital for shark conservation with increasing anthropogenic impacts and climate change.

Many mammalian populations conform spatially and temporally to Bergmann's rule. This ecogeographic pattern is driven by selection for larger body masses by cooler temperatures and smaller ones by warming temperatures. However, it is unclear whether the response to warming or cooling temperatures is (a)symmetrical. Studies of the evolutionary record suggest that mammals evolve smaller body sizes more rapidly than larger ones, suggesting that it may be “easier” to adapt to warming climates than cooling ones. Here, we examine the potential asymmetrical response of mammals to past temperature fluctuations. We use the fossil midden record of the bushy-tailed woodrat, Neotoma cinerea, a well-studied animal that generally conforms to Bergmann's rule, to test the ability of populations to respond to warming versus cooling climate throughout its modern range in western North America over the late Quaternary. We quantified the response to temperature change, as characterized by the Greenland Ice Sheet Project 2 temperature record, using N. cinerea presence/absence and “darwins.” Our results show that populations within the modern range of N. cinerea show little difference between warming and cooling events. However, northern, peripheral populations are absent during older, cooler periods, possibly due to climate or taphonomy. Our study suggests adaptation in situ may be an underestimated response to future climate change.

Understanding variation of traits within and among species through time and across space is central to many questions in biology. Many resources assemble species-level trait data, but the data and metadata underlying those trait measurements are often not reported. Here, we introduce FuTRES (Functional Trait Resource for Environmental Studies; pronounced few-tress), an online datastore and community resource for individual-level trait reporting that utilizes a semantic framework. FuTRES already stores millions of trait measurements for paleobiological, zooarchaeological, and modern specimens, with a current focus on mammals. We compare dynamically derived extant mammal species' body size measurements in FuTRES with summary values from other compilations, highlighting potential issues with simply reporting a single mean estimate. We then show that individual-level data improve estimates of body mass-including uncertainty-for zooarchaeological specimens. FuTRES facilitates trait data integration and discoverability, accelerating new research agendas, especially scaling from intra- to interspecific trait variability.

The late Quaternary of North America was marked by prominent ecological changes, including the end-Pleistocene megafaunal extinction, the spread of human settlements and the rise of agriculture. Here we examine the mechanistic reasons for temporal changes in mammal species association and body size during this time period. Building upon the co-occurrence results from Lyons et al. (2016) - wherein each species pair was classified as spatially aggregated, segregated or random - we examined body mass differences (BMD) between each species pair for each association type and time period (Late Pleistocene: 40 000(14)C-11 700(14)C ybp, Holocene: 11 700(14)C-50 ybp and Modern: 50-0 yr). In the Late Pleistocene and Holocene, the BMD of both aggregated and segregated species pairs was significantly smaller than the BMD of random pairs. These results are consistent with environmental filtering and competition as important drivers of community structure in both time periods. Modern assemblages showed a breakdown between BMD and co-occurrence patterns: the average BMD of aggregated, segregated and random species pairs did not differ from each other. Collectively, these results indicate that the late Quaternary mammalian extinctions not only eliminated many large-bodied species but were followed by a re-organization of communities that altered patterns of species coexistence and associated differences in body size.

Understanding variation of traits within and among species through time and across space is central to many questions in biology. Many resources have been developed to assemble trait data at the species level, but the underlying data and metadata about those trait measurements are often not reported, limiting broadest utility. Here we introduce FuTRES (Functional Trait Resource for Environmental Studies), a datastore and community resource for individual-level trait reporting that utilizes a strong semantic framework and best practices approach to overcome previous limitations. FuTRES already stores millions of trait measurements that span across multiple time scales, including zooarchaeological and paleobiological specimens, with a current focus on mammals. Two case studies showcase the promise of FuTRES. The first compares dynamically derived extant mammal species' body size estimates with summary values from other compilations, highlighting potential issues with simply reporting a single mean estimate. The second shows that FuTRES data improves estimates of body mass – including uncertainty – for zooarchaeological specimens. FuTRES facilitates trait data integration and discoverability, accelerating new research agendas, especially scaling from intra- to interspecific trait variability.

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles—open data, open source and open methods—is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges.

A Constraint-based model of Dynamic Island Biogeography: environmental history and species traits predict hysteresis in populations and communities We present a conceptual model that shows how hysteresis can emerge in dynamic island systems given simple constraints on trait-mediated processes. Over time, many islands cycle between phases of increasing and decreasing size and connectivity to a mainland species pool. As these phases alternate, the dominant process driving species composition switches between colonization and extinction. Both processes are mediated by interactions between organismal traits and environmental constraints: colonization probability is affected by a species’ ability to cross the intervening matrix between a population source and the island; population persistence (or extinction) is driven by the minimum spatial requirements for sustaining an isolated population. Because different suites of traits often mediate these two processes, similar environmental conditions can lead to differences in species compositions at two points of time. Thus, the Constraint-based model of Dynamic Island Biogeography (C-DIB) illustrates the possible role of hysteresis—the dependency of outcomes not only on the current system state but also the system’s history of environmental change—in affecting populations and communities in insular systems. The model provides a framework upon which additional considerations of lag times, biotic interactions, evolution, and other processes can be incorporated. Importantly, it provides a testable framework to study the physical and biological constraints on populations and communities across diverse taxa, scales, and systems.

Functional traits are the features of organisms that directly interact with the environment. Studying change and variation in these traits across space, time, and taxonomy can inform how species have responded to environmental and climatic change, how communities are assembled, and other eco-evolutionary questions. Trait data are collected at the individual level; however, animal trait databases often report these data at the species level, undermining their value for researchers who want to look at variation within species and rendering trait data ambiguous when taxonomy is updated. Additionally, these data are often recorded in auxiliary fields, such as “field notes” or hidden in supplementary materials or published tables, making them difficult to recover by researchers. Furthermore, animal trait data from paleontological, zooarchaeological (from archaeological sites), and neontological specimens are typically curated in separate forums and formats that are not easily integrated to provide perspective across the entire range of time. We are developing a toolkit to overcome these challenges called FuTRES: Functional Trait Resource for Environmental Studies. We seek to make these data accessible, standardize trait descriptions across Vertebrata, and teach (future) scientists how to create FAIR (findable, accessible, interoperable, and reusable) trait datasets. To make data more FAIR, FuTRES employs ontologies, a logical framework for relating terms to search datasets and standardizing traits across datasets. FuTRES builds off existing ontologies and standards, such as UBERON for anatomical terms and PATO and OBA for trait terms, as well as create new terms that are general enough to be used for all vertebrates and multiple disciplines. This talk will showcase the semantic framework underpinning FuTRES, describe how we are linking diverse trait datasets to ontologies and, therefore, each other, and report the results of a preliminary analysis of integrated datasets.

Synthesising trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Despite the well-recognised importance of traits for addressing ecological and evolutionary questions, trait-based approaches still struggle with several basic data requirements to deliver openly accessible, reproducible, and transparent science. Here, we introduce the Open Traits Network (OTN) – a decentralised alliance of international researchers and institutions focused on collaborative integration and standardisation of the exponentially increasing availability of trait data across all organisms. The OTN embraces the use of Open Science principles in trait research, particularly open data, open source, and open methodology protocols and workflows, to accelerate the synthesis of trait data across the Tree of Life. Increased efforts at all levels – from individual scientists, research networks, scientific societies, funding agencies, to publishers – are necessary to fully exploit the opportunities offered by Open Science in trait research. Democratising access to data, tools and resources will facilitate rapid advances in the biological sciences and our ability to address pressing environmental and societal demands.

The Geozoic encompasses the 3.6 Ga interval in Earth history when life has existed. Over this time, life has diversified from exclusively tiny, single-celled organisms to include large, complex multicellular forms. Just how and why this diversification occurred has been a major area of interest for paleontologists and evolutionary biologists for centuries. Here, we compile data on organism size throughout the Geozoic fossil record for the three domains of life. We describe canonical trends in the evolution of body size, synthesize current understanding of the patterns and causal mechanisms at various hierarchical scales, and discuss the biological and geological consequences of variation in organismal size.

In the version of this Perspective originally published, the first author of reference 39 was incorrectly listed as W. Cornwell and the publication year was incorrect. The reference should have read as follows: “Flores-Moreno, H. et al. fungaltraits aka funfun: a dynamic functional trait database for the world's fungi (GitHub, 2019); https://doi.org/10.5281/zenodo.1216257”. This has now been corrected.

AimWe present a Constraint-based Model of Dynamic Island Biogeography (C-DIB) that predicts how species functional traits interact with dynamic environments to determine the candidate species available for local community assembly on real and habitat islands through time.LocationReal and habitat islands globally.MethodsWe develop the C-DIB model concept, synthesize the relevant literature, and present a toolkit for evaluating model predictions for a wide variety of “island” systems and taxa.ResultsThe C-DIB model reveals that as islands cycle between phases of increasing or decreasing size and connectivity to a source pool, the dominant process driving species’ presence or absence switches between colonization and extinction. Both processes are mediated by interactions between organismal traits and environmental constraints. Colonization probability is predicted by a species’ ability to cross the intervening matrix between a population source and the island; population persistence (or extinction) is predicted by the minimum spatial requirements to sustain an isolated population. The non-random distributions of mammals on islands of the Sunda Shelf and Great Basin “sky islands” provide example study systems for evaluating the C-DIB model.Main conclusionsBecause different suites of traits impose constraints on the processes of colonization and extinction, similar environmental conditions can host different candidate species despite the same predicted richness. Thus, the model exemplifies the specific yet underappreciated role of hysteresis –the dependency of outcomes not only on the current system state –but also the historical contingency of environmental change in affecting populations and communities in insular systems.

Globally, large-bodied wild mammals are in peril. Because "megamammals" have a disproportionate influence on vegetation, trophic interactions, and ecosystem function, declining populations are of considerable conservation concern. However, this is not new; trophic downgrading occurred in the past, including the African rinderpest epizootic of the 1890s, the massive Great Plains bison kill-off in the 1860s, and the terminal Pleistocene extinction of megafauna. Examining the consequences of these earlier events yields insights into contemporary ecosystem function. Here, we focus on changes in methane emissions, produced as a byproduct of enteric fermentation by herbivores. Although methane is ∼ 200 times less abundant than carbon dioxide in the atmosphere, the greater efficiency of methane in trapping radiation leads to a significant role in radiative forcing of climate. Using global datasets of late Quaternary mammals, domestic livestock, and human population from the United Nations as well as literature sources, we develop a series of allometric regressions relating mammal body mass to population density and CH4 production, which allows estimation of methane production by wild and domestic herbivores for each historic or ancient time period. We find the extirpation of megaherbivores reduced global enteric emissions between 2.2-69.6 Tg CH4 y(-1) during the various time periods, representing a decrease of 0.8-34.8% of the overall inputs to tropospheric input. Our analyses suggest that large-bodied mammals have a greater influence on methane emissions than previously appreciated and, further, that changes in the source pool from herbivores can influence global biogeochemical cycles and, potentially, climate.

The extent to which different kinds of organisms have adapted to environmental temperature regimes is central to understanding how they respond to climate change. The Scholander-Irving (S-I) model of heat transfer lays the foundation for explaining how endothermic birds and mammals maintain their high, relatively constant body temperatures in the face of wide variation in environmental temperature. The S-I model shows how body temperature is regulated by balancing the rates of heat production and heat loss. Both rates scale with body size, suggesting that larger animals should be better adapted to cold environments than smaller animals, and vice versa. However, the global distributions of ∼9,000 species of terrestrial birds and mammals show that the entire range of body sizes occurs in nearly all climatic regimes. Using physiological and environmental temperature data for 211 bird and 178 mammal species, we test for mass-independent adaptive changes in two key parameters of the S-I model: basal metabolic rate (BMR) and thermal conductance. We derive an axis of thermal adaptation that is independent of body size, extends the S-I model, and highlights interactions among physiological and morphological traits that allow endotherms to persist in a wide range of temperatures. Our macrophysiological and macroecological analyses support our predictions that shifts in BMR and thermal conductance confer important adaptations to environmental temperature in both birds and mammals.

The extinct sharkCarcharocles megalodonis one of the largest marine apex predators ever to exist. Nonetheless, little is known about its body-size variations through time and space. Here, we studied the body-size trends ofC. megalodonthrough its temporal and geographic range to better understand its ecology and evolution. Given that this species was the last of the megatooth lineage, a group of species that shows a purported size increase through time, we hypothesized thatC. megalodonalso displayed this trend, increasing in size over time and reaching its largest size prior to extinction. We found thatC. megalodonbody-size distribution was left-skewed (suggesting a long-term selective pressure favoring larger individuals), and presented significant geographic variation (possibly as a result of the heterogeneous ecological constraints of this cosmopolitan species) over geologic time. Finally, we found that stasis was the general mode of size evolution ofC. megalodon(i.e., no net changes over time), contrasting with the trends of the megatooth lineage and our hypothesis. Given thatC. megalodonis a relatively long-lived species with a widely distributed fossil record, we further used this study system to provide a deep-time perspective to the understanding of the body-size trends of marine apex predators. For instance, our results suggest that (1) a selective pressure in predatory sharks for consuming a broader range of prey may favor larger individuals and produce left-skewed distributions on a geologic time scale; (2) body-size variations in cosmopolitan apex marine predators may depend on their interactions with geographically discrete communities; and (3) the inherent characteristics of shark species can produce stable sizes over geologic time, regardless of the size trends of their lineages.

Genetic variation within and among key species can have significant ecological consequences at the population, community, and ecosystem levels. In order to understand ecological properties of systems based on habitat-forming clonal plants, it is crucial to clarify which traits vary among plant genotypes and how they influence ecological processes, and to assess their relative contribution to ecosystem functioning in comparison to other factors. Here we used a mesocosm experiment to examine the relative influence of genotypic identity and extreme levels of nitrogen loading on traits that affect ecological processes (at the population, community, and ecosystem levels) for Zostera marina, a widespread marine angiosperm that forms monospecific meadows throughout coastal areas in the Northern Hemisphere. We found effects of both genotype and nitrogen addition on many plant characteristics (e.g., aboveground and belowground biomass), and these were generally strong and similar in magnitude, whereas interactive effects were rare. Genotypes also strongly differed in susceptibility to herbivorous isopods, with isopod preference among genotypes generally matching their performance in terms of growth and survival. Chemical rather than structural differences among genotypes drove these differences in seagrass palatability. Nitrogen addition uniformly decreased plant palatability but did not greatly alter the relative preferences of herbivores among genotypes, indicating that genotype effects are strong. Our results highlight that differences in key traits among genotypes of habitat-forming species can have important consequences for the communities and ecosystems that depend on them and that such effects are not overwhelmed by known environmental stressors. © 2011 by the Ecological Society of America.