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Apomys, a Philippine endemic genus of forest mice, occurs throughout most oceanic portions of the archipelago and is its most speciose mammal genus, with 18 species currently recognized. Recent extensive surveys of mammals on Mindoro Island have produced specimens that document the presence of three genetically and morphologically distinct candidate species of Apomys (subgenus Megapomys) previously unknown. These three, plus one previously described relative from Mindoro, constitute a clade of well-supported, reciprocally monophyletic units based on cytochrome b sequence data, all of which are strongly supported using BPP species delimitation. Data from three nuclear genes show less divergence, but species delimitation analyses are consistent with results from cytochrome b. These four taxa are easily diagnosed on the basis of pelage and cranial morphology. Each of the four species occurs allopatrically, though two occur along a single elevational gradient. In this paper, we formally describe the three new species. We estimate that the common ancestor of the four species arrived on Mindoro from Luzon roughly 4.7 Ma, with initial diversification beginning roughly 2.7 Ma, and increasing to the current four species about 1.3 Ma. The three new species increase the number of mammals currently recognized as endemics on Mindoro from nine to twelve. This is a remarkably high number of endemic mammals from an island of its size, and reflects Mindoro’s status as a geologically old island permanently isolated from other oceanic islands in the Philippines by deep water, while also corroborating Mindoro as the smallest island within which endemic speciation by small mammals is known to have occurred.   

Abstract Island ecosystems provide natural laboratories to assess the impacts of isolation on population persistence. However, most studies of persistence have focused on a single species, without comparisons to other organisms they interact with in the ecosystem. The case study of moose and gray wolves on Isle Royale allows for a direct contrast of genetic variation in isolated populations that have experienced dramatically differing population trajectories over the past decade. Whereas the Isle Royale wolf population recently declined nearly to extinction due to severe inbreeding depression, the moose population has thrived and continues to persist, despite having low genetic diversity and being isolated for ∼120 years. Here, we examine the patterns of genomic variation underlying the continued persistence of the Isle Royale moose population. We document high levels of inbreeding in the population, roughly as high as the wolf population at the time of its decline. However, inbreeding in the moose population manifests in the form of intermediate-length runs of homozygosity suggestive of historical inbreeding and purging, contrasting with the long runs of homozygosity observed in the smaller wolf population. Using simulations, we confirm that substantial purging has likely occurred in the moose population. However, we also document notable increases in genetic load, which could eventually threaten population viability over the long term. Overall, our results demonstrate a complex relationship between inbreeding, genetic diversity, and population viability that highlights the use of genomic datasets and computational simulation tools for understanding the factors enabling persistence in isolated populations.