*2.3. Common Alleles*

Common alleles were estimated to understand the phenomenon of cotton evolution and the gene flow mechanism. All six species of cotton considered in this study have common alleles at 114 loci, keeping *G. hirsutum* as fixed. The SSR marker DPL0330-A showed the maximum number of common alleles (124) among all tetraploid cottons except for *G. klotzschianum*, which is diploid, while DPL0249-C showed the minimum number of common alleles, which were only found in *G. barbadense*, *G. klotzschianum*, and *G. hirsutum*. The number of common alleles ranged from 21 to 123 in all six species of *Gossypium*. In this investigation, a total of 459 common loci were observed. Eighty-eight, 101, 82, 91, 67, and 30 loci having common alleles specific to *G. hirsutum* were observed in *G. barbadense*, *G. darwinii*, *G. tomentosum*, *G. ekmanianum*, *G. stephensii,* and *G. klotzschianum,* respectively (Supplementary Table S4). These *G. hirsutum*-specific alleles were amplified by 85 out of 111 SSR markers. The presence of *G. hirsutum*-specific alleles in all six species of *Gossypium* indicated a high level of natural introgression. The level of introgression was found to vary among these wild-type accessions [36,51].
