Functional traits of the world’s late Quaternary large-bodied avian and mammalian herbivores

Prehistoric and recent extinctions of large-bodied terrestrial herbivores had significant and lasting impacts on Earth’s ecosystems due to the loss of their distinct trait combinations. The world’s surviving large-bodied avian and mammalian herbivores remain among the most threatened taxa. As such, a greater understanding of the ecological impacts of large herbivore losses is increasingly important. However, comprehensive and ecologically-relevant trait datasets for extinct and extant herbivores are lacking. Here, we present HerbiTraits, a comprehensive functional trait dataset for all late Quaternary terrestrial avian and mammalian herbivores ≥10 kg (545 species). HerbiTraits includes key traits that influence how herbivores interact with ecosystems, namely body mass, diet, fermentation type, habitat use, and limb morphology. Trait data were compiled from 557 sources and comprise the best available knowledge on late Quaternary large-bodied herbivores. HerbiTraits provides a tool for the analysis of herbivore functional diversity both past and present and its effects on Earth’s ecosystems.

Herbivores affect numerous ecological and ecosystem processes. The traits contained in HerbiTraits encapsulate major dimensions of herbivore ecology and its effect on the environment, from affecting local vegetation and soils to influencing global climate. Linkages indicate direct and indirect effects of traits on ecological processes or components, scaling from traits (left-hand side) to globe (right-hand side).  www.nature.com/scientificdata www.nature.com/scientificdata/ case of severe droughts, as consumption does not necessarily mean the species has the capacity to survive on these alternative diets. In these cases, we have noted the evidence and justified our decision-making process.
In cases where no dietary data were available (n = 26 species), we imputed diet values based on a posterior distribution of 1,000 equally-likely phylogenies for mammals ≥10 kg from PHYLACINE v1.2.1 29,43 . We used the R package "Rphylopars" v0.3.0 with a Brownian motion evolutionary model and took the median value from the 1,000 phylogenetic trees 44,45 . This model accounted for both the evolutionary correlation of the individual dietary values across the full phylogeny as well as the probability of diet values based on other traits, as some trait combinations (e.g. arboreality and grazing) are very rare. Given that this imputation was conducted across full mammal phylogenies (≥10 kg), we used life history traits from PHYLACINE v1.2.1 29,43 , so that imputation for species only distantly related to other herbivores (e.g. bears) would be robust.
Fermentation type. Digestive physiology controls the quantity and quality of vegetation (e.g., fiber and nutrient content) that herbivores consume. Fermentation type therefore shapes effects on vegetation, gut passage rate, seed and nutrient dispersal distances, water requirements, and the resulting stoichiometry of excreta 19,[46][47][48][49] (Fig. 1). Following Hume 46 , fermentation type was collected as a categorical variable consisting of simple gut, hindgut colon, hindgut caecum, foregut non-ruminant, and ruminant (Table 1). These variables capture the range of fermentation adaptations across avian and mammalian herbivores. Based on these classifications and Hume 46 , we also ranked fermentation efficiencies (0-3) on an ordinal scale to these various digestive strategies, to facilitate quantitative functional diversity analyses (Table 1).
Fermentation types show strong phylogenetic conservatism at the family level. Therefore, for the most part, if direct anatomical evidence was not available, we inferred fermentation types from extant relatives. However, some extinct herbivores possess no close modern relatives and may have been functionally non-analog (e.g. 23 extinct ground sloths, 3 notoungulates, 4 diprotodons, 16 glyptodonts, and 12 giant lemurs). In these cases, closest living relatives, expert opinions, and craniodental morphology were used to determine the most likely fermentation system. For example, notoungulates, an extinct group from South America, possess no close relatives yet their craniodental and appendicular morphology resemble extant hindgut fermenting taxa (rhinos), and hindgut fermentation is widely considered to be ancestral in ungulates 50 . In all cases, we describe our justification and the state of the debate in the current literature.
Habitat use. Habitat use determines the components of ecosystems that herbivores interact with and is central to understanding their effects on vegetation, soils, and processes like nutrient dispersal (e.g. moving nutrients from terrestrial to aquatic environments 51 ). We classified habitat with three non-exclusive binary variables (0 or 1) for the use of arboreal, terrestrial, and aquatic environments. We further classified this variable categorically as semi-aquatic, terrestrial, semi-arboreal, and arboreal. Defining habitat use is challenging as many terrestrial species use aquatic or arboreal environments opportunistically, and percentage habitat use data is unavailable for most species. To ensure habitat designations were consistent for extant and extinct species, we classified taxa on the basis of obligate habitat use across their geographic range and/or the possession of specialized adaptations (e.g. climbing ability) that would be evident in the morphology of fossil specimens. Further proof of habitat use by extinct species was inferred from close relatives or isotopic proxy data, when relevant. In cases where no specific information was available, we inferred habitat use from absence of evidence (e.g. there is no specific data regarding aquatic or arboreal habitat use by gemsbok Oryx gazella).

Diet Value Interpretation
Textual description 3 The food source is a major (51-100%) and essential part of the species' diet.

2
The food source is an important but not major part (21-50%) of the species diet. It is generally a non-essential part of the species diet.
"also consumes" "seasonally consumes" "may consume" 1 The food source is a relatively small (11-20%) and unimportant part of the species diet.
"occasionally consumes" "sometimes consumes" "opportunistically consumes" "has been reported to eat" 0 This food source is an insignificant part (0-10%) of the species diet.
"does not consume" "has once been seen consuming" The text does not mention the food source www.nature.com/scientificdata www.nature.com/scientificdata/ Limb morphology. Limb morphology is broadly associated with herbivore habitat preferences, locomotion (e.g., cursoriality, fossoriality, climbing), anti-predator responses, and rates of body size evolution [52][53][54] . Limb morphology also controls disturbance-related trampling effects on soils, with hoofed unguligrade taxa having stronger influences on soils than those with other morphologies 55 . Trampling has important effects on soils, hydrology, albedo, and vegetation 7,56 and is often considered an essentially novel aspect of introduced herbivores in Australia and North America (e.g 10,57,58 .). Limb morphology was collected as a three-level categorical variable consisting of plantigrade (walking on soles of feet), digitigrade (walking on toes), and unguligrade (walking on hoof). For example, plantigrade species are more likely to be fossorial or scansorial in habit, digitigrade species are likely to be saltatory or ambulatory (e.g. extant kangaroos), while unguligrade species are often adapted for rocky, vertiginous terrain or cursoriality 53,54 . Limb morphology shows high phylogenetic conservatism across herbivore lineages and thus was primarily collected at the genus or family level from primary and secondary literature.

Data Records
HerbiTraits consists of an Excel workbook containing metadata (column names and descriptions), the trait dataset, and references as three separate sheets. The dataset is open-access and is hosted on Figshare 59 as well as on GitHub (https://github.com/MegaPast2Future/HerbiTraits).

technical Validation
The majority of functional trait data were collected from primary peer-reviewed literature ( (39), conference proceedings (9), and grey literature (5). For transparency, justifications for trait designations (particularly relevant for extinct species) are described in the Notes columns and the highest quality evidence is ranked in trait-specific Reliability columns. Contradictions between sources have been noted and values have been based on the most empirically-robust methods or by averaging values across studies (see above). All data designations have been cross-checked (by EJL, SDS, JR, MD, and OM). We aim to maintain HerbiTraits with the best available data. We urge users to report errors or updates on newly published data for integration into HerbiTraits by filing an Issue on our GitHub (https://github.com/MegaPast2Future/HerbiTraits) repository page, or by emailing the corresponding authors. Furthermore, the GitHub (https://github.com/ MegaPast2Future/HerbiTraits) page includes an incomplete trait file, which contains other ecologically relevant traits, such as adaptations for digging and free water dependence 60 . These traits remain unavailable for many taxa, but provide a starting point for further data collection and analysis.

Usage notes
Please cite this publication when using HerbiTraits. As the taxonomy and phylogeny is derived from PHYLACINE v1.2.1, that data is compatible with PHYLACINE v1. www.nature.com/scientificdata www.nature.com/scientificdata/