Trophic resource partitioning drives fine-scale coexistence in cryptic bat species

Sequencing data generated from metabarcoding and high throughput sequencing on Illumina MiSeq of arthropod DNA in faecal smaples from Myotis escalerai and Myotis crypticus in the Iberian Peninsula in 2017. Raw sequencing data post removal of primers and low quality reads. Two different generic arthropod primers were used: ZBJ (Zeale et al. 2011, Mol. Ecol. Resour. 11: 236-244) and CFMRA (ANML; Jusino et al. 2019, Mol. Ecol. Resour. 19: 176–190).,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 the 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 from syntopic and allotopic locations within the sympatric region to describe the diets both taxonomically and functionally and compare prey consumption with prey availability. The two bat species had highly 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 syntopic populations, supporting trophic shift under fine-scale co-occurrence. Furthermore, the diet of M. escalerai had a marginally lower proportion of not nocturnally volant prey in syntopic populations, 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.,Dataset includes sample list with species identification and capture site location (Sample_ID_location.csv), and list of arthropod BINs identified in bat faecal samples and their presence in each of the two bat species (Novell-Fernandez_EcolEvol_Data file S1.csv).