RESEARCH ARTICLE Genetic monitoring and effects of stocking practices on small Cyprinus carpio populations Nikoleta Karaiskou • Maria Lappa • Stefanos Kalomoiris • George Oikonomidis • Chariklia Psaltopoulou • Theodore J. Abatzopoulos • Costas Triantaphyllidis • Alexander Triantafyllidis Received: 21 July 2010 / Accepted: 26 May 2011 / Published online: 10 June 2011 Ó Springer Science+Business Media B.V. 2011 Abstract The ability to detect genetic differences both in space and time is crucial for conserving genetic variation. It can reveal genetic diversity and genetic composition changes of declining native populations that are supported through stocking with captive bred individuals. The present study was designed to analyse the temporal stability of a declining common carp (Cyprinus carpio) population from Lake Volvi (North Greece). Polymorphism was evaluated using seven microsatellite loci at two sampling time points (separated by 12 years). The genetic variability of four additional populations (from two rivers and two lakes) in Northern Greece was also investigated for comparison. Heterozygosity values (0.692–0.868) and allelic richness (8.530–11.148) were high for all studied populations and comparable to other European populations. However, the analysis of temporal common carp samples from Lake Volvi revealed a significant change in their genetic com- position and admixture analysis demonstrated significant introgression of stocked individuals into the native population. Both temporal and point estimate methods revealed low effective size (Ne = 61–171.3) for this pop- ulation, possibly a result of an ancient genetic bottleneck that led to population decline and/or recent anthropogenic interventions. This low Ne has rendered the native popu- lation vulnerable to alteration of its genetic composition. Our study demonstrates that enhancement programs should be applied cautiously, especially for small populations. Moreover, it underlines the need for temporal analyses, which may contribute to the evaluation of previous man- agement policies and to future decision making. Keywords Temporal analysis Á Effective population size Á Wild common carp Á Stocking impact Introduction Ecosystems worldwide are undergoing significant degra- dation with negative impacts to biodiversity. The devel- opment of molecular genetic analyses and new statistical programs in recent years have made it possible to gain a greater understanding of genetic differentiation across landscapes, both within and between species as well as of the forces that shape them such as genetic drift, gene flow and selection (Luikart and England 1999). Therefore, in addition to ecosystem restoration practices, conservation and sustainable development programs should also use data on the genetic structure of populations. Genetic analyses that use samples collected only from a single period of time provide a narrow perspective of demographic processes. Anthropogenic induced changes (e.g., overexploitation, population translocation, and stocking) that can severely affect the genetic composition of natural populations cannot be monitored easily without Nikoleta Karaiskou and Maria Lappa contributed equally for this study. Electronic supplementary material The online version of this article (doi:10.1007/s10592-011-0231-z) contains supplementary material, which is available to authorized users. N. Karaiskou Á M. Lappa Á S. Kalomoiris Á T. J. Abatzopoulos Á C. Triantaphyllidis Á A. Triantafyllidis (&) Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Macedonia, Greece e-mail: atriant@bio.auth.gr G. Oikonomidis Á C. Psaltopoulou Department of Freshwater Fisheries, Prefecture of Thessaloniki, Fisheries Direction, Loutron 14, 57200 Lagadas, Macedonia, Greece 123 Conserv Genet (2011) 12:1299–1311 DOI 10.1007/s10592-011-0231-z