Data from: No evidence for nuclear introgression despite complete mtDNA replacement in the Carpathian newt (Lissotriton montandoni)

Patterns of interspecific introgression may vary geographically, and the distribution of introgressed variants can yield insight into the historical dynamics of genetic interactions between hybridizing species. Urodele amphibians, often characterized by limited mobility, deep intraspecific genetic structuring and vulnerability to climatic changes, constitute suitable models for such historical inferences. Here, we combine an extensive survey of the mitochondrial (mtDNA) and nuclear (15 microsatellites) genomes in the Carpathian newt, Lissotriton montandoni (Lm) with species distribution modelling (SDM). Populations of the smooth newt, L. vulgaris (Lv) from the areas surrounding the Lm range were also sampled to test whether gene flow between these hybridizing species extends beyond the area of strict syntopy. The extent of introgression differs dramatically between the mitochondrial genome and the nuclear genome. While multiple, spatially and temporally distinct introgression events from Lv resulted in complete mtDNA replacement in Lm, there was little evidence of recent interspecific nuclear gene flow in the assayed markers. Microsatellite differentiation within Lm defines three units, probably derived from separate glacial refugia, located in the northern, eastern and southern part of the Carpathians. In situ survival and range fragmentation of Lm are supported by SDM, corroborating the role of the Carpathians as a major refugial area. Our results, in combination with previous reports of extensive introgression of the major histocompatibility complex (MHC) genes, emphasize the complexity of historical gene exchange between Lm and Lv.IMa2 input file, mtDNA lineage J, Lissotriton montandoni and L. vulgarisJ_mon_vul_input.txtIMa2 input file, mtDNA lineage G, Lissotriton montandoni and L. vulgarisG_mon_vul_input.txtGPS coordinates of Lissotriton montandoni localities used for species distribution modelingMontandoni_localities.xlsxMicrosatellite genotypesGenepop format; 000000 - missing data (may inbclude null homozygotes); 999999 - confirmed null homozygotesNewts_ms_data.xlsMicrosatellite genotypes and mtDNA haplotypesGenepop-like format; 000000 - missing data (may inbclude null homozygotes); 999999 - confirmed null homozygotes; for individuals with sequenced mtDNA haplotype and GenBank Accession are givenNewts_ms_data_IndID_GenbankAcc.xlsClimatic data used in species distribution modellingThe input layers used to make the Maxent modelInput_layer.zi