The spatial configuration and management of agricultural and other land-use practices can affect ecological assemblages, but how resident and migratory species respond to land uses is not well known, hindering our understanding of the effects of land use on biodiversity. Here, we compare alpha and beta diversity and ecosystem functioning for resident and migratory birds across three land uses: (1) primary forest, (2) secondary forest, and (3) cattle pasture. Compositionally, resident bird assemblages exhibited gradual shifts across habitats with diversity steadily declining with increasing distance from a protected area and reductions in understory vegetation. In contrast, migratory bird community composition clustered into five distinct groups, shifting 50-60% less than resident assemblages across the same gradients with no declines in richness. We found that migratory bird abundance was greater in secondary forest and cattle pasture, and migratory insectivores compensated for 68% of the abundance losses of resident forest insectivores in secondary forests and cattle pastures. Among the insectivores, increases of migratory birds in secondary forest and cattle pasture compensated for the abundance declines of resident birds that utilize foliage gleaning and sallying foraging methods. Our findings underscore the importance of local landscape evaluation and management around protected areas, highlighting the unique responses of resident and migratory birds to land use and the potential mechanisms sustaining ecosystem functions in modified habitats.

Priority effects, where the order and timing of species arrival influence the assembly of ecological communities, have been observed in a variety of taxa and habitats. However, the genetic and molecular basis of priority effects remains unclear, hindering the mechanistic understanding of priority effects. We sought to gain such an understanding for the nectar yeast Metschnikowia reukaufii, commonly found in the nectar of our study plant, the hummingbird-pollinated Diplacus (Mimulus) aurantiacus. In this plant, M. reukaufii experiences strong priority effects when it reaches flowers after other nectar yeasts, such as M. rancensis. After inoculation into two contrasting types of synthetic nectar simulating early arrival of M. rancensis, we conducted whole-transcriptome sequencing of 108 strains of M. reukaufii. We found that several genes were differentially expressed in M. reukaufii strains when the nectar had been conditioned by growth of M. rancensis. Many of these genes were associated with amino acid metabolism, consistent with our previous finding that early-arriving species limit late-arriving species’ growth by reducing amino acid availability. Furthermore, investigation of expression quantitative trait loci (eQTLs) revealed that genes involved in amino acid transport and resistance to antifungal compounds were enriched in genetic variants, with differing effects on gene expression caused by M. rancensis. We also found that gene expression was associated with population growth rate, particularly when amino acids were limited. These results suggest that intraspecific genetic variation in the ability of nectar yeasts to respond to nutrient limitation and direct fungal competition underpins the molecular mechanisms of priority effects.