Sexual reproduction is almost ubiquitous among extant eukaryotes. As most asexual lineages are short-lived, abandoning sex is commonly regarded as an evolutionary dead end. Still, putative anciently asexual lineages challenge this view. One of the most striking examples are bdelloid rotifers, microscopic freshwater invertebrates believed to have completely abandoned sexual reproduction tens of Myr ago. Here, we compare whole genomes of 11 wild-caught individuals of the bdelloid rotifer Adineta vaga and present evidence that some patterns in its genetic variation are incompatible with strict clonality and lack of genetic exchange. These patterns include genotype proportions close to Hardy-Weinberg expectations within loci, lack of linkage disequilibrium between distant loci, incongruent haplotype phylogenies across the genome, and evidence for hybridization between divergent lineages. Analysis of triallelic sites independently corroborates these findings. Our results provide evidence for interindividual genetic exchange and recombination in A. vaga, a species previously thought to be anciently asexual.

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15 7 8 Sexual reproduction which involves alternation of meiosis and syngamy is the 9 ancestral condition of extant eukaryotes. Transitions to asexual reproduction 10 were numerous, but most of the resulting eukaryotic lineages are rather short-11 lived. Still, there are several exceptions to this rule including darwinulid 12 ostracods 1,2 and timema stick insects 3 . The most striking of them is bdelloid 13 rotifers 4-6 , microscopic freshwater invertebrates which underwent an extensive 14 adaptive radiation after apparently losing meiosis over 10 Mya. Indeed, both the 15 lack of males in numerous bdelloid species and the lack of proper homology 16 between chromosomes 6 rule out ordinary sex. However, this does not exclude the 17 possibility of some other mode of interindividual genetic exchange and 18 recombination in their populations 7 . Recent analyses based on a few loci 19suggested genetic exchanges in this group 8,9 , although this has been 20 controversial 10 . Here, we compare complete genomes of 11 individuals from the 21 wild population of the bdelloid rotifer Adineta vaga, and show that its genetic 22 structure, which involves Hardy-Weinberg proportions of genotypes within loci 23 and lack of linkage disequilibrium between distant loci, is incompatible with 24 strictly clonal reproduction. Instead, it can emerge only under ongoing 25 recombination between different individuals within this species, possibly through 26 transformation. Such a genetic structure makes the population immune to 27

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