raits, broadly speaking, are measurable attributes or characteristics of organisms. Traits related to function (for example, leaf size, body mass, tooth size or growth form) are often used to understand how organisms interact with their environment and other species via key vital rates such as survival, development and reproduction 1-5. Trait-based approaches have long been used in systematics and macroevolution to delineate taxa and reconstruct ancestral morphology and function 6-8 and to link candidate genes to phentoypes 9-11. The broad appeal of the trait concept is its ability to facilitate quantitative comparisons of biological form and function. Traits also allow us to mechanistically link organismal responses to abiotic and biotic factors with measurements that are, in principle, relatively easy to capture across large numbers of individuals. For example, appropriately chosen and defined traits can help identify lineages that share similar life-history strategies for a given environmental regime 12,13. Documenting and understanding the diversity and composition of traits in ecosystems directly contributes to our understanding of organismal and ecosystem processes, functionality, productivity and resilience in the face of environmental change 14-19. In light of the multiple applications of trait data to address challenges of global significance (Box 1), a central question remains: How can we most effectively advance the synthesis of trait data within and across disciplines? In recent decades, the collection, compilation and availability of trait data for a variety of organisms has accelerated rapidly. Substantial trait databases now exist for plants 20-23 , reptiles 24,25 , invertebrates 23,26-29 , fish 30,31 , corals 32 , birds 23,33,34 , amphibians 35 , mammals 23,36-38 and fungi 23,39 , and parallel efforts are no doubt underway for other taxa. Though considerable effort has been made to quantify traits for some groups (for example, Fig. 1), substantial work remains. To develop and test theory in biodiversity science, much greater effort is needed to fill in trait data across the Tree of Life by combining and integrating data and trait collection efforts.

Summary Dietary inferences are a key foundation for paleoecological, ecomorphological and macroevolutionary studies because they inform us about the direct relationships between the components of an ecosystem. However, we need to consider the range of dietary variation we want to investigate and characterize before choosing a proxy. The goal of the present work is to evaluate the differences in dietary discrimination power between our new method, the multidimensional multi‐proxy dental morphology analysis (MPDMA) and unidimensional dental morphology proxies such as orientation patch count (OPCR), relief index (RI) or slope. In order to do that, we three‐dimensionally scanned the dentitions of 134 extant mammals including 28 marsupials (order Diprotodontia) and 106 placentals (orders Carnivora, Primates and Rodentia) and classified their diets using a new classification scheme that emphasizes the primary resource in a given diet. Diet categories included herbivory, carnivory, frugivory, granivory, insectivory, fungivory, gumivory and generalist. Unidimensional proxies significantly discriminate (P < 0·05) between one or two diet categories on the one hand and the rest on the other. For example, OPCR discriminates well between carnivorous and non‐carnivorous species. However, none of the individual proxies discriminate all eight dietary categories. Multi‐proxy dental morphology analysis demonstrates significant morphological differences across diets (MANOVA, d.f. = 7; F = 7·56; P < 0·05) and correctly discriminates diet for 67–82% of the specimens in the data set including and excluding rodents respectively. Combining different morphological variables makes it possible to draw better dietary inferences and fully represent the multidimensional nature of dental morphology and dietary specializations. Our results have important applications in ecological, paleoecological and evolutionary research.

Understanding the feeding behaviour of the species that make up any ecosystem is essential for designing further research. Mammals have been studied intensively, but the criteria used for classifying their diets are far from being standardized. We built a database summarizing the dietary preferences of terrestrial mammals using published data regarding their stomach contents. We performed multivariate analyses in order to set up a standardized classification scheme. Ideally, food consumption percentages should be used instead of qualitative classifications. However, when highly detailed information is not available we propose classifying animals based on their main feeding resources. They should be classified as generalists when none of the feeding resources constitute over 50% of the diet. The term ‘omnivore’ should be avoided because it does not communicate all the complexity inherent to food choice. Moreover, the so-called omnivore diets actually involve several distinctive adaptations. Our dataset shows that terrestrial mammals are generally highly specialized and that some degree of food mixing may even be required for most species.

Diets estimated from different proxies such as stable isotopes, stomach contents, and dental microwear often disagree, leading to nominally well‐supported but greatly differing estimates of diet for both extinct and extant species that complicate our understanding of ecology. We show that these perceived incongruences can be caused by proxies recording diet over vastly different timescales. Field observations reveal a diet averaged over minutes or hours, whereas dental morphology may reflect the diet of a lineage over millions of years of evolution. Failing to explicitly consider the scale of proxies and the potentially large temporal variability in diet can cause erroneous predictions in any downstream analyses such as conservation planning or paleohabitat reconstructions. We propose a cross‐scale framework for conceptualizing diet suitable for both modern ecologists and paleontologists and provide recommendations for any studies involving dietary data. Treating diet in this temporally explicit framework and matching the scale of our questions with the scale of our data will lead to a much richer and clearer understanding of ecological and evolutionary processes.

Diet and body mass are highly important factors in mammalian ecology, and they have also proven to be powerful paleoecological indicators. Our previous research has proposed a new classification scheme for mammals with more dietary divisions that emphasizes the primary resource in a given diet. We analyzed a database summarizing the dietary preferences of 139 species of marsupial and placental terrestrial mammals (including 14 orders) and their average body masses in order to explore whether this new classification better highlights ecomorphological differences between species. Additionally, the dietary diversity of every species in the data set was quantified by applying the inverse Simpson index to stomach content percentages. We observed a decrease in maximum dietary diversity with increasing body mass. Having lower requirements for energy and nutrients per unit of body weight or ecological advantages such as larger home ranges allows larger mammals to feed on less nutritive feeding resources (i.e., structural plant material). Our results also suggest that body-size ranges are different across dietary specializations. Smaller mammals (<1 kg) are mainly insectivores, granivores, or mixed feeders, while bigger animals (>30 kg) are usually either carnivores or herbivores that feed specifically on grasses and leaves. The medium-size range (1–30 kg) is mostly composed of frugivorous species that inhabit tropical and subtropical rain forests. Thus, the near absence of medium-sized mammals in open environments such as savannas can be linked to the decreasing density of fruit trees needed to support a pure frugivorous diet year-round. In other words, seasonality of precipitation prevents species from specializing on a totally frugivorous diet. Our results suggest that this new classification scheme correlates well with body mass, one of the most studied morphological variables in paleoecology and ecomorphology. Therefore, the classification should serve as a useful basis for future paleoclimatological studies.

Large mammals are at high risk of extinction globally. To understand the consequences of their demise for community assembly, we tracked community structure through the end-Pleistocene megafaunal extinction in North America. We decomposed the effects of biotic and abiotic factors by analyzing co-occurrence within the mutual ranges of species pairs. Although shifting climate drove an increase in niche overlap, co-occurrence decreased, signaling shifts in biotic interactions. Furthermore, the effect of abiotic factors on co-occurrence remained constant over time while the effect of biotic factors decreased. Biotic factors apparently played a key role in continental-scale community assembly before the extinctions. Specifically, large mammals likely promoted co-occurrence in the Pleistocene, and their loss contributed to the modern assembly pattern in which co-occurrence frequently falls below random expectations.

Understanding how ecological communities are organized and how they change through time is critical to predicting the effects of climate change. Recent work documenting the co-occurrence structure of modern communities found that most significant species pairs co-occur less frequently than would be expected by chance. However, little is known about how co-occurrence structure changes through time. Here we evaluate changes in plant and animal community organization over geological time by quantifying the co-occurrence structure of 359,896 unique taxon pairs in 80 assemblages spanning the past 300 million years. Co-occurrences of most taxon pairs were statistically random, but a significant fraction were spatially aggregated or segregated. Aggregated pairs dominated from the Carboniferous period (307 million years ago) to the early Holocene epoch (11,700 years before present), when there was a pronounced shift to more segregated pairs, a trend that continues in modern assemblages. The shift began during the Holocene and coincided with increasing human population size and the spread of agriculture in North America. Before the shift, an average of 64% of significant pairs were aggregated; after the shift, the average dropped to 37%. The organization of modern and late Holocene plant and animal assemblages differs fundamentally from that of assemblages over the past 300 million years that predate the large-scale impacts of humans. Our results suggest that the rules governing the assembly of communities have recently been changed by human activity.

No abstract