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.