This is the first analysis of the genetic population structure of crucian carp from Sweden, the aim being to discover whether historic ponds still hold populations of crucian carp, and secondly to study their genetic constitution, not only as a measure of relatedness between pond populations but also in comparison to wild populations. The sampling strategy was therefore not optimised for a rigorous and detailed analysis of the population genetics in each of these ponds and lakes.
The analysis of the population structure revealed that three pond populations, U5P, G1P and Ö1P, comprised members that were closest to be completely without detectable admixture events. This indicates that they have been isolated from other populations for a long time period and presumably genetic drift has led to unique allele frequencies not shared by the other populations in this study. In those ponds, having little or no admixture, there is the potential to become sources of future stocking and reservoirs of ancient/native crucian carp populations. In contrast, the populations in U1P, SK1P and SK3P were conspicuously mixed in terms of population structure and are therefore not likely to comprise only one, original, population. They may have been re-stocked several times with fish caught from different populations, or with fish from other ponds. Indeed, historic notes of medieval aquaculture suggest that wild fish were caught and put into ponds for later use (Bonow and Svanberg 2012).
The populations from two ponds in the province of Östergötland showed very different structures and were not closely related to the population genetic tree. Some individuals in each population belonged to several clusters according to STRUCTURE, indicating that they were admixed. The populations in ÖG2P seemed to be closely related to the coastal population from the province Uppland, U7W. These two populations also shared some population clusters. It is therefore possible that the ÖG2P pond has been stocked with fish from the coast of the Baltic Sea.
The two sampling sites Ö1P and the small creek near Kalmar S2W are separated by Kalmar Strait and could thus have a source population in common. Indeed, the population genetic tree showed a well-supported cluster of these two populations. The other sampled population from Kalmar Strait, S1W, did not belong to this cluster. However, the STRUCTURE analysis indicated that they shared population clusters with each other.
All populations from Scania and from the pond S3P in Småland uniquely belonged to the same neighbour-joining cluster. In all other populations, there was little or no correlation with the geographic location. This suggests that the fish used for stocking ponds came from the same source in Scania and were more diverse in the other provinces. Judging from available sources, the pond farming of crucian carp in Scania may have been established well before it became common in Uppland (Hofmeister 2004; Svanberg et al. 2012). Scania was until 1658 a province of Denmark, and the fish in these ponds might have been of Danish origin. However, there are no genetic data from Danish crucian carp to compare with.
In Scania, the populations from the lake and the ponds were part of the same neighbour-joining cluster, well supported by bootstrap analysis. This suggests that ponds were stocked with wild fish caught in nearby waters or that fish has been released from ponds into lakes. The wild populations on the other hand could be feral fish spread from the first man-made ponds in the late middle ages. This could be indicated by the small differences in allelic richness between wild and pond fish. If the wild fish were naturally colonised, one would expect a higher degree of allelic richness in these populations. The expected heterozygosity should also be higher in the wild population, but this was not the case if compared to some of the pond populations. Whether the fish has been moved to or from the lake requires further investigations with a larger number of populations included.
Even though it was a weak association between populations U5P and G1P in both genetic distance and population structure, it suggests that there has been some contact between these populations. A stronger association was on the other hand seen among the populations in Scania, especially the ponds SK4P and SK5P that are located quite far from each other (close to 70 km) and yet share a common population cluster as suggested by the STRUCTURE analysis. One possibility is that land owners shared their crucian carp populations with each other and therefore are populations spread over larger distances than would be the case if they have been spread naturally.
In conclusion, this is the first study of population genetics of crucian carp in Sweden and it shows that there are candidates for old populations present in historic ponds. These populations can be of great value should the aquaculture of crucian carp be re-introduced in Sweden.