Papillomaviruses (PVs) are widespread pathogens. However, the extent of PV infections in bats remains largely unknown. This work represents the first comprehensive study of PVs in Iberian bats. We identified four novel PVs in the mucosa of free-ranging Eptesicus serotinus (EserPV1, EserPV2, and EserPV3) and Rhinolophus ferrumequinum (RferPV1) individuals and analyzed their phylogenetic relationships within the viral family. We further assessed their prevalence in different populations of E. serotinus and its close relative E. isabellinus. Although it is frequent to read that PVs co-evolve with their host, that PVs are highly species-specific, and that PVs do not usually recombine, our results suggest otherwise. First, strict virus–host co-evolution is rejected by the existence of five, distantly related bat PV lineages and by the lack of congruence between bats and bat PVs phylogenies. Second, the ability of EserPV2 and EserPV3 to infect two different bat species (E. serotinus and E. isabellinus) argues against strict host specificity. Finally, the description of a second noncoding region in the RferPV1 genome reinforces the view of an increased susceptibility to recombination in the E2-L2 genomic region. These findings prompt the question of whether the prevailing paradigms regarding PVs evolution should be reconsidered.

To determine what shapes the distributions of cryptic species, we aimed to unravel ecological niches and geographical distributions of three cryptic bat species complexes in Iberia, Plecotus auritus/begognae, Myotis mystacinus/alcathoe and Eptesicus serotinus/isabellinus (with 44, 69, 66, 27, 121 and 216 records, respectively), considering ecological interactions and biogeographical patterns. Species distribution models (SDMs) were built using a presence‐only technique (Maxent), incorporating genetically identified species records with environmental variables (climate, habitat, topography). The most relevant variables for each species’ distribution and respective response curves were then determined. SDMs for each species were overlapped to assess the contact zones within each complex. Niche analyses were performed using niche metrics and spatial principal component analyses to study niche overlap and breadth. The Plecotus complex showed a parapatric distribution, although having similar biogeographical affinities (Eurosiberian), possibly explained by competitive exclusion. The Myotis complex also showed Eurosiberian affinities, with high overlap between niches and distribution, suggesting resource partitioning between species. Finally, E. serotinus was associated with Eurosiberian areas, while E. isabellinus occurred in Mediterranean areas, suggesting possible competition in their restricted contact zone. This study highlights the relevance of considering potential ecological interactions between similarly ecological species when assessing species distributions. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112,150–162.

Cryptic speciation and hybridization are two key processes that affect the origin and maintenance of biodiversity and our ability to understand and estimate it. To determine how these two processes interact, we studied allopatric and sympatric colonies of two cryptic bat species (Eptesicus serotinus and Eptesicus isabellinus) with parapatric distribution in the Iberian Peninsula. These species are the main reservoir for the most commonly rabies virus found in bats in Europe: the European bat Lyssavirus type 1 (EBLV‐1). We used mtDNA and nuclear microsatellite markers to confirm the taxonomic status of both species and to show a more pronounced and geographically based genetic structure in E. isabellinus than in its sibling E. serotinus. Using approximate Bayesian computation (ABC), we inferred rapid range expansion in both species after the Last Glacial Maximum until reaching their present distributions. ABC analysis also supported interspecific differences in genetic diversity and structure, pointing to an earlier expansion of E. isabellinus northward. We found no evidence of mitochondrial introgression between species, but nuclear markers identified a male‐mediated ongoing asymmetric hybridization from E. isabellinus to E. serotinus (28% hybrids in E. serotinus and 5% in E. isabellinus) in the contact zone. Although none of the bats studied tested positive for Lyssavirus RNA, the asymmetric hybridization supports the potential for the recently suggested interspecific transmission of EBLV‐1 from E. isabellinus into E. serotinus.

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