Food for everyone: Differential feeding habits of cryptic bat species inferred from DNA metabarcoding

Ecological theory postulates that niches of co‐occurring species must differ along some ecological dimensions in order to allow their stable coexistence. Yet, many biological systems challenge this competitive exclusion principle. Insectivorous bats from the Northern Hemisphere typically form local assemblages of multiple species sharing highly similar functional traits and pertaining to identical feeding guilds. Although their trophic niche can be accessed with unprecedented details using genetic identification of prey, the underlying mechanisms of resource partitioning remain vastly unexplored. Here, we studied the differential diet of three closely‐related bat species of the genus Plecotus in sympatry and throughout their entire breeding season using DNA metabarcoding. Even at such a small geographic scale, we identified strong seasonal and spatial variation of their diet composition at both intra‐ and interspecific levels. Indeed, while the different bats fed on a distinct array of prey during spring, they showed higher trophic niche overlap during summer and fall, when all three species switched their hunting behaviour to feed on few temporarily abundant moths. By recovering 19 ecological traits for over 600 prey species, we further inferred that each bat species used different feeding grounds and hunting techniques, suggesting that niche partitioning was primarily habitat‐driven. The two most‐closely related bat species exhibited very distinct foraging habitat preferences, while the third, more distantly‐related species was more generalist. These results highlight the need of temporally comprehensive samples to fully understand species coexistence, and that valuable information can be derived from the taxonomic identity of prey obtained by metabarcoding approaches.

The menu varies with metabarcoding practices: A case study with the bat Plecotus auritus

Metabarcoding of feces has revolutionized the knowledge of animal diets by providing unprecedented resolution of consumed resources. However, it is still unclear how different methodological approaches influence the ecological conclusions that can be drawn from such data. Here, we propose a critical evaluation of several data treatments on the inferred diet of the bat Plecotus auritus using guano regularly collected from various colonies throughout the entire active season. First and unlike previous claims, our data indicates that DNA extracted from large amounts of fecal material issued from guano accumulates yield broader taxonomic diversity of prey than smaller numbers of pellets would do, provided that extraction buffer volumes are adapted to such increased amounts of material. Second, trophic niche analyses based on prey occurrence data uncover strong seasonality in the bat’s diet and major differences among neighboring maternity colonies. Third, while the removal of rare prey items is not always warranted as it introduces biases affecting particularly samples with greater prey species richness. Fourth, examination of distinct taxonomic depths in diet analyses highlights different aspects of food consumption providing a better understanding of the consumer’s diet. Finally, the biologically meaningful patterns recovered with presence-absence approaches are virtually lost when attempting to quantify prey consumed using relative read abundances. Even in an ideal situation where reference barcodes are available for most potential prey species, inferring realistic patterns of prey consumption remains relatively challenging. Although best practice in metabarcoding analyses will depend on the aims of the study, several previous methodological recommendations seem unwarranted for studying such diverse diets as that of brown long-eared bats.

Porous barriers? Assessment of gene flow within and among sympatric long-eared bat species

Species are the basic units for measuring biodiversity and for comprehending biological interactions. Yet, their delineation is often contentious, especially in groups that are both diverse and phenotypically conservative. Three cryptic species of long-eared bats, Plecotus auritus, P. austriacus, and P. macrobullaris, co-occur over extensive areas of Western Europe. The latter is a fairly recent discovery, questioning the overall diversity of the entire Plecotus complex. Yet, high morphological and acoustic similarities compromise the reliable identification of long-eared bats in the field. We postulate that such extensive phenotypic overlap, along with the recurrent observation of morphologically intermediate individuals, may hide rampant interspecific hybridization. Based on a geographic sampling centered on areas of sympatry in the Alps and Corsica, we assessed the level of reproductive isolation of these three Plecotus species with mitochondrial and nuclear markers, looking at both inter- and intraspecific genetic population structuring. No sign of hybridization was detected between these three species that appear well separated biologically. Genetic structuring of populations, however, reflected different species-specific responses to environmental connectivity, that is, to the presence of orographic or sea barriers. While the Alpine range and the Ligurian Sea coincided with sharp genetic discontinuities in P. macrobullaris and P. austriacus, the more ubiquitous P. auritus showed no significant population structuration. There were clear phylogeographic discrepancies between microsatellite and mitochondrial markers at the intraspecific level, however, which challenges the reliance on simple barcoding approaches for the delineation of sound conservation units.

Two Mitochondrial Barcodes for one Biological Species: The Case of European Kuhl's Pipistrelles (Chiroptera)

The Kuhl's pipistrelle (Pipistrellus kuhlii) is a Western Palaearctic species of bat that exhibits several deeply divergent mitochondrial lineages across its range. These lineages could represent cryptic species or merely ancient polymorphism, but no nuclear markers have been studied so far to properly assess the taxonomic status of these lineages. We examined here two lineages occurring in Western Europe, and used both mitochondrial and nuclear markers to measure degrees of genetic isolation between bats carrying them. The sampling focused on an area of strict lineage sympatry in Switzerland but also included bats from further south, in North Africa. All individuals were barcoded for the COI gene to identify their mitochondrial lineages and five highly polymorphic microsatellite loci were used to cluster them according to their nuclear genotypes. Despite this low number of nuclear markers, all North African nuclear genotypes were grouped in a highly distinct subpopulation when compared with European samples sharing the same mitochondrial barcodes. The reverse situation prevailed in Switzerland where bats carrying distinct barcodes had similar nuclear genotypes. There was a weak east/west nuclear structure of populations, but this was independent of mitochondrial lineages as bats carrying either variant were completely admixed. Thus, the divergent mitochondrial barcodes present in Western Europe do not represent cryptic species, but are part of a single biological species. We argue that these distinct barcodes evolved in allopatry and came recently into secondary contact in an area of admixture north of the Alps. Historical records from this area and molecular dating support such a recent bipolar spatial expansion. These results also highlight the need for using appropriate markers before claiming the existence of cryptic species based on highly divergent barcodes.

Systematic position and taxonomy of Pipistrellus deserti (Chiroptera: Vespertilionidae)

is a small, pale-coloured bat occurring in the most arid parts of the Sahara, in Morocco, Algeria, Libya, Egypt, and the Sudan, and marginally also in sub-Saharan Africa. Although most authors consider