Bat pluripotent stem cells reveal unusual entanglement between host and viruses.

Bats are distinctive among mammals due to their ability to fly, use laryngeal echolocation, and tolerate viruses. However, there are currently no reliable cellular models for studying bat biology or their response to viral infections. Here, we created induced pluripotent stem cells (iPSCs) from two species of bats: the wild greater horseshoe bat (Rhinolophus ferrumequinum) and the greater mouse-eared bat (Myotis myotis). The iPSCs from both bat species showed similar characteristics and had a gene expression profile resembling that of cells attacked by viruses. They also had a high number of endogenous viral sequences, particularly retroviruses. These results suggest that bats have evolved mechanisms to tolerate a large load of viral sequences and may have a more intertwined relationship with viruses than previously thought. Further study of bat iPSCs and their differentiated progeny will provide insights into bat biology, virus host relationships, and the molecular basis of bats' special traits.

Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae).

The family Pteropodidae (Old World fruit bats) comprises $>$200 species distributed across the Old World tropics and subtropics. Most pteropodids feed on fruit, suggesting an early origin of frugivory, although several lineages have shifted to nectar-based diets. Pteropodids are of exceptional conservation concern with $>$50% of species considered threatened, yet the systematics of this group has long been debated, with uncertainty surrounding early splits attributed to an ancient rapid diversification. Resolving the relationships among the main pteropodid lineages is essential if we are to fully understand their evolutionary distinctiveness, and the extent to which these bats have transitioned to nectar-feeding. Here we generated orthologous sequences for $>$1400 nuclear protein-coding genes (2.8 million base pairs) across 114 species from 43 genera of Old World fruit bats (57% and 96% of extant species- and genus-level diversity, respectively), and combined phylogenomic inference with filtering by information content to resolve systematic relationships among the major lineages. Concatenation and coalescent-based methods recovered three distinct backbone topologies that were not able to be reconciled by filtering via phylogenetic information content. Concordance analysis and gene genealogy interrogation show that one topology is consistently the best supported, and that observed phylogenetic conflicts arise from both gene tree error and deep incomplete lineage sorting. In addition to resolving long-standing inconsistencies in the reported relationships among major lineages, we show that Old World fruit bats have likely undergone at least seven independent dietary transitions from frugivory to nectarivory. Finally, we use this phylogeny to identify and describe one new genus. [Chiroptera; coalescence; concordance; incomplete lineage sorting; nectar feeder; species tree; target enrichment.].

Considering adaptive genetic variation in climate change vulnerability assessment reduces species range loss projections.

Local adaptations can determine the potential of populations to respond to environmental changes, yet adaptive genetic variation is commonly ignored in models forecasting species vulnerability and biogeographical shifts under future climate change. Here we integrate genomic and ecological modeling approaches to identify genetic adaptations associated with climate in two cryptic forest bats. We then incorporate this information directly into forecasts of range changes under future climate change and assessment of population persistence through the spread of climate-adaptive genetic variation (evolutionary rescue potential). Considering climate-adaptive potential reduced range loss projections, suggesting that failure to account for intraspecific variability can result in overestimation of future losses. On the other hand, range overlap between species was projected to increase, indicating that interspecific competition is likely to play an important role in limiting species' future ranges. We show that although evolutionary rescue is possible, it depends on a population's adaptive capacity and connectivity. Hence, we stress the importance of incorporating genomic data and landscape connectivity in climate change vulnerability assessments and conservation management.

Concealed by darkness: interactions between predatory bats and nocturnally migrating songbirds illuminated by DNA sequencing.

Recently, several species of aerial-hawking bats have been found to prey on migrating songbirds, but details on this behaviour and its relevance for bird migration are still unclear. We sequenced avian DNA in feather-containing scats of the bird-feeding bat Nyctalus lasiopterus from Spain collected during bird migration seasons. We found very high prey diversity, with 31 bird species from eight families of Passeriformes, almost all of which were nocturnally flying sub-Saharan migrants. Moreover, species using tree hollows or nest boxes in the study area during migration periods were not present in the bats' diet, indicating that birds are solely captured on the wing during night-time passage. Additional to a generalist feeding strategy, we found that bats selected medium-sized bird species, thereby assumingly optimizing their energetic cost-benefit balance and injury risk. Surprisingly, bats preyed upon birds half their own body mass. This shows that the 5% prey to predator body mass ratio traditionally assumed for aerial hunting bats does not apply to this hunting strategy or even underestimates these animals' behavioural and mechanical abilities. Considering the bats' generalist feeding strategy and their large prey size range, we suggest that nocturnal bat predation may have influenced the evolution of bird migration strategies and behaviour.

Circum-Mediterranean phylogeography of a bat coupled with past environmental niche modeling: A new paradigm for the recolonization of Europe?

The isolation of populations in the Iberian, Italian and Balkan peninsulas during the ice ages define four main paradigms that explain much of the known distribution of intraspecific genetic diversity in Europe. In this study we investigated the phylogeography of a wide-spread bat species, the bent-winged bat, Miniopterus schreibersii around the Mediterranean basin and in the Caucasus. Environmental Niche Modeling (ENM) analysis was applied to predict both the current distribution of the species and its distribution during the last glacial maximum (LGM). The combination of genetics and ENM results suggest that the populations of M. schreibersii in Europe, the Caucasus and Anatolia went extinct during the LGM, and the refugium for the species was a relatively small area to the east of the Levantine Sea, corresponding to the Mediterranean coasts of present-day Syria, Lebanon, Israel, and northeastern and northwestern Egypt. Subsequently the species first repopulated Anatolia, diversified there, and afterwards expanded into the Caucasus, continental Europe and North Africa after the end of the LGM. The fossil record in Iberia and the ENM results indicate continuous presence of Miniopterus in this peninsula that most probably was related to the Maghrebian lineage during the LGM, which did not persist afterwards. Using our results combined with similar findings in previous studies, we propose a new paradigm explaining the general distribution of genetic diversity in Europe involving the recolonization of the continent, with the main contribution from refugial populations in Anatolia and the Middle East. The study shows how genetics and ENM approaches can complement each other in providing a more detailed picture of intraspecific evolution.

Unravelling the evolutionary history and future prospects of endemic species restricted to former glacial refugia.

The contemporary distribution and genetic composition of biodiversity bear a signature of species' evolutionary histories and the effects of past climatic oscillations. For many European species, the Mediterranean peninsulas of Iberia, Italy and the Balkans acted as glacial refugia and the source of range recolonization, and as a result, they contain disproportionately high levels of diversity. As these areas are particularly threatened by future climate change, it is important to understand how past climatic changes affected their biodiversity. We use an integrated approach, combining markers with different evolutionary rates and combining phylogenetic analysis with approximate Bayesian computation and species distribution modelling across temporal scales. We relate phylogeographic processes to patterns of genetic variation in Myotis escalerai, a bat species endemic to the Iberian Peninsula. We found a distinct population structure at the mitochondrial level with a strong geographic signature, indicating lineage divergence into separate glacial refugia within the Iberian refugium. However, microsatellite markers suggest higher levels of gene flow resulting in more limited structure at recent time frames. The evolutionary history of M. escalerai was shaped by the effects of climatic oscillations and changes in forest cover and composition, while its future is threatened by climatically induced range contractions and the role of ecological barriers due to competition interactions in restricting its distribution. This study warns that Mediterranean peninsulas, which provided refuge for European biodiversity during past glaciation events, may become a trap for limited dispersal and ecologically limited endemic species under future climate change, resulting in loss of entire lineages.

A new species of the Miniopterus schreibersii species complex (Chiroptera: Miniopteridae) from the Maghreb Region, North Africa.

We used an integrative approach combining cranio-dental characters, mitochondrial and nuclear data and acoustic data to show the presence in the genus Miniopterus of a cryptic species from the Maghreb region. This species was previously recognised as Miniopterus schreibersii (Kuhl, 1817). Miniopterus maghrebensis sp. nov. can be differentiated from M. schreibersii sensu stricto on the basis of cranial characters and from mitochondrial DNA and microsatellite evidence. Although slight external morphological and acoustic differences were noted between the two species, these criteria alone did not allow reliable species identification from live animals. Based on the specimens identified morphologically and/or genetically, the distribution range of M. maghrebensis sp. nov. extends from northern Morocco to south of the High Atlas Mountains and northern Tunisia. The new cryptic species is found in sympatry with M. schreibersii s.str. near coastal regions of North Africa.

The shaping of genetic variation in edge-of-range populations under past and future climate change.

With rates of climate change exceeding the rate at which many species are able to shift their range or adapt, it is important to understand how future changes are likely to affect biodiversity at all levels of organisation. Understanding past responses and extent of niche conservatism in climatic tolerance can help predict future consequences. We use an integrated approach to determine the genetic consequences of past and future climate changes on a bat species, Plecotus austriacus. Glacial refugia predicted by palaeo-modelling match those identified from analyses of extant genetic diversity and model-based inference of demographic history. Former refugial populations currently contain disproportionately high genetic diversity, but niche conservatism, shifts in suitable areas and barriers to migration mean that these hotspots of genetic diversity are under threat from future climate change. Evidence of population decline despite recent northward migration highlights the need to conserve leading-edge populations for spearheading future range shifts.

Novel lyssavirus in bat, Spain.

A new tentative lyssavirus, Lleida bat lyssavirus, was found in a bent-winged bat (Miniopterus schreibersii) in Spain. It does not belong to phylogroups I or II, and it seems to be more closely related to the West Causasian bat virus, and especially to the Ikoma lyssavirus.

Detection of rhabdovirus viral RNA in oropharyngeal swabs and ectoparasites of Spanish bats.

Rhabdoviruses infect a variety of hosts, including mammals, birds, reptiles, fish, insects and plants. As bats are the natural host for most members of the genus Lyssavirus, the specificity of the amplification methods used for active surveillance is usually restricted to lyssaviruses. However, the presence of other rhabdoviruses in bats has also been reported. In order to broaden the scope of such methods, a new RT-PCR, able to detect a diverse range of rhabdoviruses, was designed. The method detected 81 of 86 different rhabdoviruses. In total, 1488 oropharyngeal bat swabs and 38 nycteribiid samples were analysed, and 17 unique rhabdovirus-related sequences were detected. Phylogenetic analysis suggested that those sequences detected in bats did not constitute a monophyletic group, even when originating from the same bat species. However, all of the sequences detected in nycteribiids and one sequence obtained from a bat did constitute a monophyletic group with Drosophila melanogaster sigma rhabdovirus.

Discovery of an ebolavirus-like filovirus in europe.

Filoviruses, amongst the most lethal of primate pathogens, have only been reported as natural infections in sub-Saharan Africa and the Philippines. Infections of bats with the ebolaviruses and marburgviruses do not appear to be associated with disease. Here we report identification in dead insectivorous bats of a genetically distinct filovirus, provisionally named Lloviu virus, after the site of detection, Cueva del Lloviu, in Spain.

Phylogeography and postglacial recolonization of Europe by Rhinolophus hipposideros: evidence from multiple genetic markers.

The demographic history of Rhinolophus hipposideros (lesser horseshoe bat) was reconstructed across its European, North African and Middle-Eastern distribution prior to, during and following the most recent glaciations by generating and analysing a multimarker data set. This data set consisted of an X-linked nuclear intron (Bgn; 543 bp), mitochondrial DNA (cytb-tRNA-control region; 1630 bp) and eight variable microsatellite loci for up to 373 individuals from 86 localities. Using this data set of diverse markers, it was possible to determine the species' demography at three temporal stages. Nuclear intron data revealed early colonization into Europe from the east, which pre-dates the Quaternary glaciations. The mtDNA data supported multiple glacial refugia across the Mediterranean, the largest of which were found in the Ibero-Maghreb region and an eastern location (Anatolia/Middle East)-that were used by R. hipposideros during the most recent glacial cycles. Finally, microsatellites provided the most recent information on these species' movements since the Last Glacial Maximum and suggested that lineages that had diverged into glacial refugia, such as in the Ibero-Maghreb region, have remained isolated. These findings should be used to inform future conservation management strategies for R. hipposideros and show the power of using a multimarker data set for phylogeographic studies.

A new Pipistrelle bat from the oceanic Island of Príncipe (Western Central Africa).

We describe a population of pipistrelle-like bats from Príncipe Island (Gulf of Guinea, Western Central Africa) as a new species based on the molecular and morphological characteristics of six specimens collected more than 30 years ago. The description of this new species was not possible until the traditionally entangled systematics of the whole pipistrelle group was clarified in recent years with the inclusion of molecular techniques and adequate species sampling. In this new taxonomic framework, the new species was clearly included within the dark-winged group of the recently described genus Pseudoromicia. The pipistrelles from Príncipe Island present a moderately inflated skull in lateral view with inner upper incisors that are moderately bicuspids and a baculum distinctly long with expanded tips. Besides these morphological characters, the new bat species is distinguished by its dwarfism, being the smallest species recognized within the genus. The ecology and conservation status of this endemic island species are unknown and field studies are urgently needed to evaluate the situation and conservation threats to this new species in its natural habitat.

A species-level trait dataset of bats in Europe and beyond.

Knowledge of species' functional traits is essential for understanding biodiversity patterns, predicting the impacts of global environmental changes, and assessing the efficiency of conservation measures. Bats are major components of mammalian diversity and occupy a variety of ecological niches and geographic distributions. However, an extensive compilation of their functional traits and ecological attributes is still missing. Here we present EuroBaTrait 1.0, the most comprehensive and up-to-date trait dataset covering 47 European bat species. The dataset includes data on 118 traits including genetic composition, physiology, morphology, acoustic signature, climatic associations, foraging habitat, roost type, diet, spatial behaviour, life history, pathogens, phenology, and distribution. We compiled the bat trait data obtained from three main sources: (i) a systematic literature and dataset search, (ii) unpublished data from European bat experts, and (iii) observations from large-scale monitoring programs. EuroBaTrait is designed to provide an important data source for comparative and trait-based analyses at the species or community level. The dataset also exposes knowledge gaps in species, geographic and trait coverage, highlighting priorities for future data collection.

Genetic and phenotypic differentiation between the critically endangered Balearic shearwater and neighboring colonies of its sibling species.

Understanding the demographic and evolutionary processes within and between populations is essential for developing effective management strategies. Thus, for establishing good conservation policies both genetic and phenotypic studies are crucial. We carried out an integrated analysis of genetic and phenotypic characters of the critically endangered Balearic shearwater Puffinus mauretanicus (182 individuals) and compared them with those of 2 nearby colonies of Yelkouan shearwater P. yelkouan (40 individuals), a species for which hybridization has been hypothesized. The results of the microsatellite analyses were compared with previous mitochondrial DNA analyses. Genetic variability was low in the Balearic shearwater and high levels of inbreeding were revealed at local scale. Most dispersal in Balearic shearwaters was to neighboring sites, even though low levels of population structure were found. The admixture between the 2 species was much higher at nuclear than at mitochondrial level, but phenotypic characters would seem to indicate that a lower level of admixture exists. Individual nuclear DNA, mtDNA, and phenotype did not match at individual level, showing that migration alone cannot explain this phenomenon. We suggest that these 2 young shearwater species could have been involved in processes of divergence and admixing. However, due to the longer coalescence times in nuclear markers, incomplete lineage sorting cannot be ruled out.

Counteracting forces of introgressive hybridization and interspecific competition shape the morphological traits of cryptic Iberian Eptesicus bats.

Cryptic species that coexist in sympatry are likely to simultaneously experience strong competition and hybridization. The first phenomenon would lead to character displacement, whereas the second can potentially promote morphological similarity through adaptive introgression. The main goal of this work was to investigate the effect of introgressive hybridization on the morphology of cryptic Iberian Eptesicus bats when facing counteracting evolutionary forces from interspecific competition. We found substantial overlap both in dentition and in wing morphology traits, though mainly in individuals in sympatry. The presence of hybrids contributes to a fifth of this overlap, with hybrids showing traits with intermediate morphometry. Thus, introgressive hybridization may contribute to species adaptation to trophic and ecological space responding directly to the macro-habitats characteristics of the sympatric zone and to local prey availability. On the other hand, fur shade tended to be browner and brighter in hybrids than parental species. Colour differences could result from partitioning of resources as an adaptation to environmental factors such as roost and microhabitats. We argue that a balance between adaptive introgression and niche partitioning shapes species interactions with the environment through affecting morphological traits under selection.

The role of forest structure and composition in driving the distribution of bats in Mediterranean regions.

Forests are key native habitats in temperate environments. While their structure and composition contribute to shaping local-scale community assembly, their role in driving larger-scale species distributions is understudied. We used detailed forest inventory data, an extensive dataset of occurrence records, and species distribution models integrated with a functional approach, to disentangle mechanistically how species-forest dependency processes drive the regional-scale distributions of nine forest specialist bats in a Mediterranean region in the south of Spain. The regional distribution patterns of forest bats were driven primarily by forest composition and structure rather than by climate. Bat roosting ecology was a key trait explaining the strength of the bat-forest dependency relationships. Tree roosting bats were strongly associated with mature and heterogeneous forest with large trees (diameters > 425 mm). Conversely, and contrary to what local-scale studies show, our results did not support that flight-related traits (wing loading and aspect ratio) drive species distributional patterns. Mediterranean forests are expected to be severely impacted by climate change. This study highlights the utility of disentangling species-environment relationships mechanistically and stresses the need to account for species-forest dependency relationships when assessing the vulnerability of forest specialists towards climate change.

Phylogeny of European bat Lyssavirus 1 in Eptesicus isabellinus bats, Spain.

To better understand the epidemiology of European bat lyssavirus 1 (EBLV-1) in Europe, we phylogenetically characterized Lyssavirus from Eptesicus isabellinus bats in Spain. An independent cluster of EBLV-1 possibly resulted from geographic isolation and association with a different reservoir from other European strains. EBLV-1 phylogeny is complex and probably associated with host evolutionary history.

Detection of alpha and betacoronaviruses in multiple Iberian bat species.

Bat coronaviruses (CoV) are putative precursors of the severe acute respiratory syndrome (SARS) CoV and other CoV that crossed the species barrier from zoonotic reservoirs into the human population. To determine the presence and distribution of CoV in Iberian bats, 576 individuals of 26 different bat species were captured in 13 locations in Spain. We report for the first time the presence of 14 coronaviruses in 9 Iberian bat species. Phylogenetic analysis of a conserved CoV genome region (RdRp gene) shows a wide diversity and distribution of alpha and betacoronavirus in Spain. Interestingly, although some of these viruses are related to other European BatCoV, or to Asian CoV, some of the viruses found in Spain cluster in new groups of α and ß CoV.

Assessing survival in a multi-population system: a case study on bat populations.

In long-lived animals, adult survival is among the most important determinants of population dynamics. Although it may show considerable variation both in time and among populations and sites, a single survival estimate per species is often used in comparative evolutionary studies or in conservation management to identify threatened populations. We estimated adult survival of the isabelline serotine bat Eptesicus isabellinus using capture-recapture data collected on six maternity colonies scattered over a large area (distance 8-103 km) during periods varying from 8 to 26 years. We modelled temporal and inter-colony variations as random effects in a Bayesian framework and estimated mean annual adult survival of females on two scales and a single survival value across all colonies. On a coarse scale, we grouped colonies according to two different habitat types and investigated the effect on survival. A difference in adult survival was detected between the two habitat types [posterior mean of annual survival probability 0.71; 95% credible interval (CI) 0.51-0.86 vs. 0.60; 0.28-0.89], but it was not statistically supported. On a fine scale, survival of the six colonies ranged between 0.58 (95% CI 0.23-0.92) and 0.81 (0.73-0.88), with variation between only two colonies being statistically supported. Overall survival was 0.72 (95% CI 0.57-0.93) with important inter-colony variability (on a logit scale 0.98; 95% CI 0.00-8.16). Survival varied temporally in a random fashion across colonies. Our results show that inference based solely on single colonies should be treated with caution and that a representative unbiased estimate of survival for any species should ideally be based on multiple populations.