Microsatellite-based genetic variability and differentiation of domesticated, wild and feral common carp (Cyprinus carpio L.) populations

In the past, the genetics of common carp populations has mainly been studied on regional levels using traditional protein markers. We analysed four microsatellite loci of 577 individuals from 22 domesticated, wild and feral populations spanning a geographical area as wide as from Europe through Central Asia to East and South-East Asia. The variability of these loci was much higher than that of the allozyme loci examined in our previous studies. A total number of 143 alleles were recorded across loci ranging from 27 at MFW28 to 47 at MFW7. However, the mean number of alleles per locus was remarkably lower: from 2.50 in a captive stock of River Amur wild carp to 14.25 in a wild population from Lake Arnasaiskie, Uzbekistan, and domesticated Chinese carp from Wuhan. The variability of populations did not show a clear geographical pattern but a highly significant difference was found in allelic richness between the 13 domesticated/captive stocks (average Ar = 4.436) and the nine wild−caught populations (average Ar = 8.221). The prevalence of different alleles in different populations resulted in a high degree of population differentiation: the FST values for all but four pairwise comparisons of Central Asian wild populations were significant. Within geographical regions the DA distances between populations were smallest in Central Asia (average DA = 0.139), intermediate in Europe (average DA = 0.434) and largest in East/South-East Asia (average DA = 0.833). Between geographical regions the European and Central Asian populations showed the smallest distances (average DA = 0.484) whereas the distances of these two regions and East/South-East Asia were almost identical but substantially larger (Europe vs. East/South-East Asia: average DA = 0.801, and Central Asia vs. East/South-East Asia: average DA = 0.806). All populations clustered into only two highly divergent major groups with 91% bootstrap support: Europe/Central Asia and East/South-East Asia. Thus, the microsatellite data also suggest an ancient separation of European/Central Asian from East/South-East Asian carp and a single origin of European carp in Central Asia as already inferred from our previous allozyme and mtDNA RFLP studies. The taxonomic status of subspecies assigned to European (C. c. carpio) and East Asian carp (C. c. haematopterus) is supported. However, because of their close relationship to European carp the Central Asian carp do not deserve a separate subspecies status (C. c. aralensis).