Whilst climate change is recognised as a major future threat to biodiversity, most species are currently threatened by extensive human-induced habitat loss, fragmentation and degradation. Tropical high altitude alpine and montane forest ecosystems and their biodiversity are particularly sensitive to temperature increases under climate change, but they are also subject to accelerated pressures from land conversion and degradation due to a growing human population. We studied the combined effects of anthropogenic land-use change, past and future climate changes and mountain range isolation on the endemic Ethiopian Highlands long-eared bat, Plecotus balensis, an understudied bat that is restricted to the remnant natural high altitude Afroalpine and Afromontane habitats. We integrated ecological niche modelling, landscape genetics and model-based inference to assess the genetic, geographic and demographic impacts of past and recent environmental changes. We show that mountain range isolation and historic climates shaped population structure and patterns of genetic variation, but recent anthropogenic land-use change and habitat degradation are associated with a severe population decline and loss of genetic diversity. Our models predict that the suitable niche of this bat has been progressively shrinking since the last glaciation period. This study highlights threats to tropical montane biodiversity, squeezed to higher altitudes under climate change while losing genetic diversity and suffering population declines due to anthropogenic land-use change. We conclude that assessments of threats to biodiversity under global change should adopt a holistic approach, simultaneously studying the effects of multiple threats across temporal scales based on genetic, ecological and geographic information.

Understanding the processes that enable species coexistence has important implications for assessing how ecological systems will respond to global change. Morphology and functional similarity increase the potential for competition, and therefore, co-occurring morphologically similar but genetically unique species are a good model system for testing coexistence mechanisms. We used DNA metabarcoding and High Throughput Sequencing to characterise for first time the trophic ecology of two recently-described cryptic bat species with parapatric ranges, Myotis escalerai and Myotis crypticus. We collected faecal samples from allopatric and sympatric regions and locations to describe the diet both taxonomically and functionally and compare prey consumption with prey availability. The two bat species had similar diets characterised by high arthropod diversity, particularly Lepidoptera, Diptera and Araneae, and a high proportion of prey that is not volant at night, which points to extensive use of gleaning. Diet overlap at the prey-item level was lower in locally sympatric than allopatric locations, supporting trophic shift under fine-scale sympatry. Furthermore, locally sympatric samples of M. escalerai had a marginally lower proportion of not nocturnally volant prey, suggesting that the shift in diet may be driven by a change in foraging mode. Our findings suggest that fine-scale coexistence mechanisms can have implications for maintaining broad-scale diversity patterns. This study highlights the importance of including both allopatric and sympatric populations and choosing meaningful spatial scales for detecting ecological patterns. We conclude that a combination of high taxonomic resolution with a functional approach helps identify patterns of niche shift.