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Background  The parthenogenetic Caucasian rock lizard  Darevskia armeniaca , like most other parthenogenetic vertebrate species, originated through interspecific hybridization between the closely related sexual  Darevskia mixta  and  Darevskia valentini .  Darevskia armeniaca  was shown to consist of one widespread allozyme clone and a few rare ones, but notwithstanding the origin of clonal diversity remains unclear. We conduct genomic analysis of  D. armeniaca  and its parental sexual species using microsatellite and SNP markers to identify the origin of parthenogenetic clonal lineages.    Results  Four microsatellite-containing loci were genotyped for 111 specimens of  D. armeniaca , 17  D. valentini , and four  D. mixta . For these species, a total of 47 alleles were isolated and sequenced. Analysis of the data revealed 13 genotypes or presumptive clones in parthenogenetic  D. armeniaca , including one widespread clone, two apparently geographically restricted clones, and ten rare clones. Comparisons of genotype-specific markers in  D. armeniaca  with those of its parental species revealed three founder-events including a common and two rare clones. All other clones appeared to have originated via post-formation microsatellite mutations in the course of evolutionary history of  D. armeniaca .    Conclusion  Our new approach to microsatellite genotyping reveals allele-specific microsatellite and SNP markers for each locus studied. Interspecies comparison of these markers identifies alleles inherited by parthenospecies from parental species, and provides new information on origin and evolution of clonal diversity in  D. armeniaca . SNP analyses reveal at least three interspecific origins of  D. armeniaca , and microsatellite mutations in these initial clones give rise to new clones. Thus, we first establish multiple origins of  D. armeniaca.  Our study identifies the most effective molecular markers for elucidating the origins of clonal diversity in other unisexual species that arose via interspecific hybridization.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5359-5) contains supplementary material, which is available to authorized users.

Multiple interspecific hybridization and microsatellite mutations provide clonal diversity in the parthenogenetic rock lizard Darevskia armeniaca