Genomic diversity of major tree species in the Eurasian relict forests of northern Iran.

We investigated population genetics of the native tree species Boiss., Lipsky, and C.A. Mey. in the Hyrcanian forests of northern Iran and also populations in the Euro-Siberian and Colchic subregions of northern Türkiye. We used the double-digest RADseq method and genotyped 90 populations and 1,589 individuals across the distribution range of the species. Genome-wide SNPs from 28 populations of , 32 populations of , and 30 revealed higher genetic differentiation among populations than among and . The global value was lowest for populations and highest for populations, while the global value was negative for . Demographic history analysis revealed a bottleneck during the last glacial period (11,500—115,000 Kya) for the populations with reduced effective population size ( ). All three species show multiple bottlenecks and reduced during the Quaternary. Pronounced genetic divergence among populations in the Hyrcanian forests compared to the other two species suggests cryptic speciation. Conversely, and populations showed low levels of genetic structure, suggesting that species-specific factors, such as pollen production and pollination efficiency, may have influenced the genetic patterns within these species in similar environments. The nucleotide diversity of populations in Iran is negatively correlated with altitude (p = 0.046). In contrast, populations show a significant correlation between nucleotide diversity and longitude (p = 0.008). Furthermore, the populations from Türkiye showed a distinct west–east genetic structure and were highly diverged from the Iranian populations.