Genomic variation in parthenogenetic lizard Darevskia armeniaca: evidence from DNA fingerprinting data

New records and geographic distribution of the sympatric zones of unisexual and bisexual rock lizards of the genus Darevskia in Armenia and adjacent territories

Background

Caucasian rock lizards of the genus Darevskia are unique taxa, including both bisexual and parthenogenetic species. The parthenogenetic species have originated as a result of natural hybridisation between females and males of different bisexual species. The species involved in interspecific hybridisation are called parental. However, sympatric zones (SZ) of unisexual and bisexual rock lizards of the Caucasus are still poorly studied, although they are very important for understanding the role of hybrid individuals of different origin in reticulate evolution. This paper presents the location of the SZs of parthenogenetic and their parental bisexual rock lizards of the genus Darevskia in Armenia and adjacent territories of Georgia and Nagorno-Karabakh. We summarised the locations of the SZs identified from 1957 to the present, based on our field survey data gathered in 2018-2019 and records from publications and museum collections. This dataset includes 39 SZs of three types: SZ of parental bisexual species, SZ of parental species with unisexual species and SZ of the parthenogenetic species. For each zone, species composition, geographical and altitudinal distribution are presented. New records expand our knowledge of the geographical and altitudinal distribution of SZs in these species and provide additional data for understanding the mechanisms of reticulate evolution and hybridogeneous speciation in the past, present and future.

New information

The new records, including geographical and altitudinal distributions of three types of SZs, are presented, which expand the previously-known list to 39 locations of contact zones for parthenogenetic and its bisexual parental species of rock lizards of the genus Darevskia in Armenia and the adjacent territories of Georgia and Nagorno-Karabakh.

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

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.

DNA damage and micronuclei in parthenogenetic and bisexual Darevskia rock lizards from the areas with different levels of soil pollution

Natural species are widely used as indicator organisms to estimate of the impact of environmental pollution. Here we present the results of first study of a reliability of parthenogenetic Darevskia аrmeniaca and bisexual Darevskia raddei rock lizards as sentinels for monitoring of environmental genotoxicity. The comet assay and micronucleus test were applied to the lizards sampled in six areas in Armenia and Artsakh with different levels of soil contamination. The results obtained showed a clear relationship between the pollution level of lizards' habitats and the frequency of DNA damage in the comet assay. Low baseline frequency of micronuclei in D. аrmeniaca and D. raddei, however, makes this parameter ineffective for environmental genotoxicity evaluation. The parthenogenetic lizards D. аrmeniaca showed higher sensitivity toward genotoxic pollutions compared with bisexual D. raddei living in the same environment. The correlations between soil content of heavy metals Cr, Cu, Zn, Mo, Pb and DNA damage in D. аrmeniaca and between Cu, As, Mo, Pb and DNA damage in D. raddei were revealed. Overall, the lizards D. raddei and D. аrmeniaca appeared to be sensitive species in detecting soil pollution in natural environment. The application of the comet assay in Darevskia lizard species can be considered as a more appropriate method than a micronucleus test. The use of parthenogenetic lizards D. аrmeniaca as bioindicator will permit to assess the environmental genotoxicity independent of the genetic polymorphism of bisexual species.

DNA fingerprinting in zoology: past, present, future

In 1962, Thomas Kuhn famously argued that the progress of scientific knowledge results from periodic 'paradigm shifts' during a period of crisis in which new ideas dramatically change the status quo. Although this is generally true, Alec Jeffreys' identification of hypervariable repeat motifs in the human beta-globin gene, and the subsequent development of a technology known now as 'DNA fingerprinting', also resulted in a dramatic shift in the life sciences, particularly in ecology, evolutionary biology, and forensics. The variation Jeffreys recognized has been used to identify individuals from tissue samples of not just humans, but also of many animal species. In addition, the technology has been used to determine the sex of individuals, as well as paternity/maternity and close kinship. We review a broad range of such studies involving a wide diversity of animal species. For individual researchers, Jeffreys' invention resulted in many ecologists and evolutionary biologists being given the opportunity to develop skills in molecular biology to augment their whole organism focus. Few developments in science, even among the subsequent genome discoveries of the 21st century, have the same wide-reaching significance. Even the later development of PCR-based genotyping of individuals using microsatellite repeats sequences, and their use in determining multiple paternity, is conceptually rooted in Alec Jeffreys' pioneering work.