The extreme rarity of asexual vertebrates in nature is generally explained by genomic decay due to absence of meiotic recombination, thus leading to extinction of such lineages. We explore features of a vertebrate asexual genome, the Amazon molly, Poecilia formosa, and find few signs of genetic degeneration but unique genetic variability and ongoing evolution. We uncovered a substantial clonal polymorphism and, as a conserved feature from its interspecific hybrid origin, a 10-fold higher heterozygosity than in the sexual parental species. These characteristics seem to be a principal reason for the unpredicted fitness of this asexual vertebrate. Our data suggest that asexual vertebrate lineages are scarce not because they are at a disadvantage, but because the genomic combinations required to bypass meiosis and to make up a functioning hybrid genome are rarely met in nature.

This work was supported by grants to W.C.W. (NIH: 2R24OD011198-04A1), M.W.H. (NSF DBI-1564611), M.S. (German Research Foundation DFG projects Scha408/10-1 and Scha408/12-1), M.St. (Heisenberg-Fellowship STO 493/2-2 of the German Science Foundation/DFG), T.M.B.(MINECO BFU2014-55090-P (FEDER), U01 MH106874 grant, Howard Hughes International Early Career, Obra Social ‘La Caixa’ and Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya) and R.B.W. (NIH: R24OD011120). The genome annotation work carried out by NCBI was supported by the Intramural Research Program of the NIH, National Library of Medicine. The genome annotation work by Ensembl was supported by funding from the Wellcome Trust (WT108749/Z/15/Z and WT098051), the National Institutes of Health (R24 RR032658-01) and the European Molecular Biology Laboratory