Anthropogenic pressures are causing the widespread loss of wildlife species and populations, with adverse consequences for ecosystem functioning. This phenomenon has been widely but inconsistently referred to as defaunation. A cohesive, quantitative framework for defining and evaluating defaunation is necessary for advancing biodiversity conservation. Likening defaunation to deforestation, we propose an operational framework for defaunation that defines it and related terms, situates defaunation relative to intact communities and faunal degradation, and encourages quantitative, ecologically reasonable, and equitable measurements. We distinguish between defaunation, the conversion of an ecosystem from having wild animals to not having wild animals, and faunal degradation, the process of losing animals or species from an animal community. The quantification of context-relevant defaunation boundaries or baselines is necessary to compare faunal communities over space and time. Situating a faunal community on the degradation curve can promote Global Biodiversity Framework targets, advancing the 2050 Vision for Biodiversity.

Frugivore‐mediated seed dispersal drives ecological functioning across tropical forests. The biological mechanisms affecting seed dispersal outcomes, as well as the role of specific functional traits in plants and their dispersers, is still not well understood. To address this gap, we conducted germination experiments in eight species of captive and two species of wild lemurs, which disperse different plant species. We (1) quantified the effects of pulp removal, seed priming, and feces effects (nutrient/microbial fertilization) through gut passage as mechanisms, (2) determined the effect of frugivore species on germination, and (3) assessed how individual plant and animal traits affected two seed germination outcomes: success rates and time‐to‐germination. Accounting for phylogenetic non‐independence of plants and estimating phylogenetic signal, we evaluated the effects of lemur gut passage and functional traits in a Bayesian framework. Seed priming during gut passage was the primary mechanism through which lemurs improved germination rates and decreased time‐to‐germination. Gut passage influenced the effect of seed length on germination probability but not time‐to germination. Germination outcomes varied by disperser species and seed size. Furthermore, seeds passed by male lemurs were 40% more likely to germinate than those passed by female lemurs. Germination probability was more similar for closely related plant species compared to those that were more distantly related, while the plant phylogenetic effects on time‐to‐germination were weaker. Moreover, germination depended on experimental setting; for example, lemur gut passage decreased time‐to‐germination in captive, but not wild settings. Our results highlight the complexity of biological mechanisms determining seed dispersal outcomes; ecological and evolutionary factors were important drivers of germination. Considering a diversity of potential effects is critical for advancing a mechanistic understanding of species interactions and their outcomes.

Anelloviruses are circular, negative-sense single-stranded DNA viruses that have remarkable diversity and ubiquity across mammals. However, few studies have attempted to determine anellovirus diversity and dynamics across a biodiverse landscape. Madagascar offers a unique opportunity to study anellovirus diversity, with speciose, endemic mammalian lineages that have evolved in geographic isolation for millions of years. These endemic animals frequently interact with more recently introduced populations of non-native small mammals. From oral swab samples taken from natural populations of lemurs, rodents and shrews in the Manombo Special Reserve and surrounding area in southeastern Madagascar, we determined the complete genomes of anelloviruses from black rats ( n =647 genomes), Webb’s tufted-tailed rats ( n =2), mouse lemurs ( n =4), a woolly lemur ( n =1) and a house shrew ( n =3). We observed distinct anellovirus lineages in the endemic lemurs and tufted-tailed rats, which we infer to be the result of their long-term geographic isolation in Madagascar. Lemur-infecting anelloviruses, in particular, do not cluster with other primate-infecting anelloviruses. In contrast, anellovirus diversity in widespread, non-native rodents (i.e. black rats) was similar to that of closely related, globally dispersed rodent species, concordant with their later introduction to Madagascar. With our large anellovirus dataset from black rats, we examined anellovirus alpha- and beta-diversity and viral co-occurrence networks. Black rat anellovirus populations showed high intra-individual variation, but the overall pool of circulating anelloviruses was consistent across age classes and sexes. Adult relative to juvenile/subadult black rats harboured richer anellovirus populations and were more connected within the co-occurrence network. Proximity between individuals and greater intra-individual viral diversity were also linked to more virus-sharing between black rats.