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Abstract Islands make up a large proportion of Earth's biodiversity, yet are also some of the most sensitive systems to environmental perturbation. Biogeographic theory predicts that geologic age, area, and isolation typically drive islands' diversity patterns, and thus potentially impact non‐native spread and community homogenization across island systems. One limitation in testing such predictions has been the difficulty of performing comprehensive inventories of island biotas and distinguishing native from introduced taxa. Here, we use DNA metabarcoding and statistical modelling as a high throughput method to survey community‐wide arthropod richness, the proportion of native and non‐native species, and the incursion of non‐natives into primary habitats on three archipelagos in the Pacific – the Ryukyus, the Marianas and Hawaii – which vary in age, isolation and area. Diversity patterns largely match expectations based on island biogeography theory, with the oldest and most geographically connected archipelago, the Ryukyus, showing the highest taxonomic richness and lowest proportion of introduced species. Moreover, we find evidence that forest habitats are more resilient to incursions of non‐natives in the Ryukyus than in the less taxonomically rich archipelagos. Surprisingly, we do not find evidence for biotic homogenization across these three archipelagos: the assemblage of non‐native species on each island is highly distinct. Our study demonstrates the potential of DNA metabarcoding to facilitate rapid estimation of biogeographic patterns, the spread of non‐native species, and the resilience of ecosystems. 

ABSTRACT Anthropogenic pressures such as hunting are increasingly driving the localised functional extinctions of large‐ and medium‐sized wildlife in tropical forests, a phenomenon broadly termed ‘defaunation’. Concurrently in these areas, smaller‐bodied species benefit from factors such as competitive release and increase in numbers. This transformation of the wildlife community can impact species interactions and ecosystem services such as seed dispersal and seed‐mediated geneflow with far‐reaching consequences. Evidence for negative genetic effects following defaunation is well‐documented in large‐seeded plants that require large frugivores for long‐distance seed dispersal. However, how defaunation affects plants with small or medium‐small seeds (< 1.5 cm), which tend to be consumed and dispersed by frugivorous mutualists of a range of body sizes and responses to anthropogenic threats, is not well understood. To better understand defaunation's impacts on tropical plant communities, we investigated spatial and genetic patterns in a hyperabundant medium‐to‐small‐seeded palm,Euterpe precatoriain three sites with different defaunation levels. Results indicate that defaunation is associated with higher fine‐scale spatial genetic structure among seedlings and increased spatial clustering within seedling cohorts and between seedlings and conspecific adults, as well as a reduction in nearest‐neighbour distances between seedlings and conspecific adults. There were no clear effects on inbreeding or genetic diversity. However, we caution these trends may indicate that defaunation reduces seed dispersal services for species previously presumed to be robust to deleterious effects of losing large frugivores by virtue of having smaller seeds and broad suites of dispersal agents, and negative downstream effects on genetic diversity could occur.