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Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols1to generate, to our knowledge, the first reference-quality genomes of six bat species (Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhliiand Molossus molossus). We integrated gene projections from our ‘Tool to infer Orthologs from Genome Alignments’ (TOGA) software with de novo and homology gene predictions as well as short- and long-read transcriptomics to generate highly complete gene annotations. To resolve the phylogenetic position of bats within Laurasiatheria, we applied several phylogenetic methods to comprehensive sets of orthologous protein-coding and noncoding regions of the genome, and identified a basal origin for bats within Scrotifera. Our genome-wide screens revealed positive selection on hearing-related genes in the ancestral branch of bats, which is indicative of laryngeal echolocation being an ancestral trait in this clade. We found selection and loss of immunity-related genes (including pro-inflammatory NF-κB regulators) and expansions of anti-viral APOBEC3 genes, which highlights molecular mechanisms that may contribute to the exceptional immunity of bats. Genomic integrations of diverse viruses provide a genomic record of historical tolerance to viral infection in bats. Finally, we found and experimentally validated bat-specific variation in microRNAs, which may regulate bat-specific gene-expression programs. Our reference-quality bat genomes provide the resources required to uncover and validate the genomic basis of adaptations of bats, and stimulate new avenues of research that are directly relevant to human health and disease1.

Female greater horseshoe bats form maternity colonies each summer in order to give birth and raise young. During the mating period, females visit males occupying territorial sites, copulation takes place and sperm are stored until ovulation occurs, normally in April. Using microsatellite markers and a likelihood method of parentage analysis, we studied breeding behaviour and male reproductive success over a five–year period in a population of bats in south–west Britain. Paternity was assigned with 80 confidence to 44 of young born in five successive cohorts. While a small annual skew in male reproductive success was detected, the variance increased over five years due to the repeated success of a few individuals. Mating was polygynous, although some females gave birth to offspring sired by the same male in separate years. Such repeated partnerships probably result from fidelity for either mating sites or individuals or from sperm competition. Females mated with males born both within and outside their own natal colony; however, relatedness between parents was no less than the average recorded for male–female pairs. Gene flow between colonies is likely to be primarily mediated by both female and male dispersal during the mating period rather than more permanent movements.

Activity patterns of greater horseshoe bats Rhinolophus ferrumequinum were investigated at caves in Cheddar (south-west England) during the hibernation season. An ultrasound detector and datalogger were used to monitor and record the number of echolocation calls in a single cave. Activity of R. ferrumequinum remained largely nocturnal throughout winter, and the mean time of activity over 24 h was 88 to 369 min after sunset. There was an increase in diurnal activity from late May to early June, probably because bats remained active after foraging at dawn towards the end of the hibernation season. Visits to the cave did not increase bat activity. Cave air temperature reflected external climatic temperature, although there was variation in cave temperature and its range within and among caves. Individual R. ferrumequinum are usually dispersed in caves in regions where temperature fluctuations correlate with climatic variations in temperature. There was a positive correlation between the number of daily bat passes monitored by the bat detector and datalogger (= daily activity) and cave temperature. Nocturnal activity may be sometimes associated with winter feeding. Neither date nor barometric pressure had a significant effect on daily activity. Activity patterns largely reflected the findings from individual R. ferrumequinum studied by telemetry (Park, 1998), in that bat activity increased with cave and climatic temperatures, and the temporal pattern of activity remained consistently nocturnal throughout winter, starting at dusk.