Combining genetic gain and diversity by considering average coancestry in clonal selection of Norway spruce

 Genetic relationship within a population can be measured by average coancestry. This can also be expressed as an effective number which represents the relative genetic diversity of the population. The goal of breeding can be formulated to maximise genetic value minus average coancestry times a constant (the “penalty constant”). An iterative search algorithm can then be used to find the best selections for meeting this goal. Two such algorithms, one for a fixed number of selections and the other for a variable optimum number, were applied to select a mixture of field-tested Norway spruce clones with known parents. The results were compared with those from the conventional method of restricting parental contributions to the selected population as a means to control diversity. Coancestry-adjusted selection always yielded more gain than restricted selection at a given effective population size (except under circumstances where the methods were equivalent). Expressed another way, at any given level of gain, coancestry-adjusted selection maintained a larger effective population size than did restricted selection. The relative superiority of coancestry-adjusted selection declined when the effective population size approached the lowest value, that at which no penalty or restriction was applied. The method was extended by the second search algorithm to optimise the selected number of clones. The optimal number of clones can be rather large when diversity is heavily valued, but the reduction in genetic gain becomes large. Received: 7 April 1997 / Accepted: 9 June 1997     

Methods to estimate effective population size using pedigree data: Examples in dog,sheep, cattle and horse

Background

Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate.

Results

Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species.

Conclusions

When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied.     

Genetic management of captive populations: the advantages of circular mating

We performed computer simulations to evaluate the effectiveness of circular mating as a genetic management option for captive populations. As a benchmark, we used the method proposed by Fernández and Caballero according to which parental contributions are set to produce minimum coancestry among the offspring and matings are performed so as to minimize mean pairwise coancestry (referred to as the Gc/mc method). In contrast to other methods, fitness does not vary with population size in the case of circular mating, and can be higher than under random mating. Whether circular mating is an effective method in conserving captive populations depends on the trade-off between different considerations. On the one hand, circular mating shows the highest allelic diversity and the lowest mean pairwise coancestry for all population sizes. It also shows a relatively higher efficiency of purging deleterious alleles. More importantly, circular mating can significantly increase the success probability of populations released to the wild relative to the Gc/mc method. On the other hand, circular mating has the drawback of showing high inbreeding rates and low fitness in early generations, which can result to an increase in the extinction probability of the captive populations. However, this increase is slight unless population size and litter size are both very low. Overall, if the slight increase in extinction probability can be tolerated then circular mating fulfils the primary goals of a captive breeding program, i.e., it maintains high levels of genetic diversity and increases the success probability of reintroduced populations.     

Maintaining genetic diversity using molecular coancestry: the effect of marker density and effective population size

Background

The most efficient method to maintain genetic diversity in populations under conservation programmes is to optimize, for each potential parent, the number of offspring left to the next generation by minimizing the global coancestry. Coancestry is usually calculated from genealogical data but molecular markers can be used to replace genealogical coancestry with molecular coancestry. Recent studies showed that optimizing contributions based on coancestry calculated from a large number of SNP markers can maintain higher levels of diversity than optimizing contributions based on genealogical data. In this study, we investigated how SNP density and effective population size impact the use of molecular coancestry to maintain diversity.

Results

At low SNP densities, the genetic diversity maintained using genealogical coancestry for optimization was higher than that maintained using molecular coancestry. The performance of molecular coancestry improved with increasing marker density, and, for the scenarios evaluated, it was as efficient as genealogical coancestry if SNP density reached at least 3 times the effective population size.However, increasing SNP density resulted in reduced returns in terms of maintained diversity. While a benefit of 12% was achieved when marker density increased from 10 to 100 SNP/Morgan, the benefit was only 2% when it increased from 100 to 500 SNP/Morgan.

Conclusions

The marker density of most SNP chips already available for farm animals is sufficient for molecular coancestry to outperform genealogical coancestry in conservation programmes aimed at maintaining genetic diversity. For the purpose of effectively maintaining genetic diversity, a marker density of around 500 SNPs/Morgan can be considered as the most cost effective density when developing SNP chips for new species. Since the costs to develop SNP chips are decreasing, chips with 500 SNPs/Morgan should become available in a short-term horizon for non domestic species.     

Genome-Wide Estimates of Coancestry and Inbreeding in a Closed Herd of Ancient Iberian Pigs

Maintaining genetic variation and controlling the increase in inbreeding are crucial requirements in animal conservation programs. The most widely accepted strategy for achieving these objectives is to maximize the effective population size by minimizing the global coancestry obtained from a particular pedigree. However, for most natural or captive populations genealogical information is absent. In this situation, microsatellites have been traditionally the markers of choice to characterize genetic variation, and several estimators of genealogical coefficients have been developed using marker data, with unsatisfactory results. The development of high-throughput genotyping techniques states the necessity of reviewing the paradigm that genealogical coancestry is the best parameter for measuring genetic diversity. In this study, the Illumina PorcineSNP60 BeadChip was used to obtain genome-wide estimates of rates of coancestry and inbreeding and effective population size for an ancient strain of Iberian pigs that is now in serious danger of extinction and for which very accurate genealogical information is available (the Guadyerbas strain). Genome-wide estimates were compared with those obtained from microsatellite and from pedigree data. Estimates of coancestry and inbreeding computed from the SNP chip were strongly correlated with genealogical estimates and these correlations were substantially higher than those between microsatellite and genealogical coefficients. Also, molecular coancestry computed from SNP information was a better predictor of genealogical coancestry than coancestry computed from microsatellites. Rates of change in coancestry and inbreeding and effective population size estimated from molecular data were very similar to those estimated from genealogical data. However, estimates of effective population size obtained from changes in coancestry or inbreeding differed. Our results indicate that genome-wide information represents a useful alternative to genealogical information for measuring and maintaining genetic diversity.     

Optimum contribution selection in large general tree breeding populations with an application to Scots pine

Development of selection methods that optimises selection differential subject to a constraint on the increase of inbreeding (or coancestry) in a population is an important part of breeding programmes. One such method that has received much attention in animal breeding is the optimum contribution (OC) dynamic selection method. We implemented the OC algorithm and applied it to a diallel progeny trial of Pinus sylvestris L. (Scots pine) focussing on two traits (total tree height and stem diameter). The OC method resulted in a higher increase in genetic gain (8–30%) compared to the genetic gain achieved using standard restricted selection method at the same level of coancestry constraint. Genetic merit obtained at two different levels of restriction on coancestry showed that the benefit of OC was highest when restriction was strict. At the same level of genetic merit, OC decreased coancestry with 56 and 39% for diameter and height, respectively, compared to the level of coancestry obtained using unrestricted truncation selection. Inclusion of a dominance term in the statistical model resulted in changes in contribution rank of trees with 7 and 13% for diameter and height, respectively, compared to results achieved by using a pure additive model. However, the genetic gain was higher for the pure additive model than for the model including dominance for both traits.     

Population structure of <Emphasis Type="Italic">Nouelia insignis</Emphasis> (Asteraceae), an endangered species in southwestern China,based on chloroplast DNA sequences: recent demographic shrinking

Nouelia insignis, an endangered species, is distributed in the Jinsha and Nanpan drainage areas in southwestern China. In this study, we examined the genetic diversity and population structure based on the sequences of the cpDNA rpL 16 intron. Low levels of genetic variation were detected within all populations of the endemic species. A gene genealogy of 11 haplotypes recovered two major lineages I and II, with haplotypes H1 and H6 nested as interior nodes, respectively. Haplotype H1 was widespread in all populations, while haplotype H6 was restricted to populations southern of the Jinsha River. Low levels of genetic differentiation were detected, as most F _st values between populations were zero. This result, however, contradicts previous studies based on allozymes and fingerprinting. Genetic analyses suggested that coancestry due to low evolutionary rates resulted in the lack of geographical subdivision. Molecular dating estimated that the two lineages split about 3.224 MYA (95% CI 1.070–6.089 MYA). Maintenance of ancestral polymorphisms was possibly attributable to a long-standing large effective population size until recently. Postglacial demographic expansion was supported by a unimodal mismatch distribution and star-like phylogenies.     

Population structure of the Trakehner Horse breed

The objective of this study was to examine the population structure of the Trakehner Horse breed. A total of 13 793 pedigree records were used for analysing the active breeding population and their ancestors dating back to 1950. Ancestors that were born before 1950 were called as base animals. The average generation interval was calculated as 10.2 years. The effective population size (Ne) was estimated by the increase in average year-wise inbreeding coefficient and average coancestry, respectively. Two methods were applied to estimate the effective population size: 1. Numerator-relationship-matrix (NRM), which did not consider missing ancestries. 2. Uncertain-parentage-matrix (UPM), which considered a probabilistic correction for unknown ancestors. There were no major differences between these two methods with respect to the rate of increase in inbreeding although the global levels using the UPM method were observed to be higher. Estimates for the inbreeding coefficients and the average coancestries varied little between both methods. The estimates of the effective population size per generation based on the rate of inbreeding ranged from 169 (NRM) to 150 (UPM) and 158 (NRM) to 144 (UPM) calculated by the average coancestry. From the early 1990s onwards, a strong increase in the rate of inbreeding was observed. This may be due to an increasing variance of the family size of sires and may be interpreted as a consequence of the growing use of artificial insemination. Analysing coancestries within and between the centrally managed regional breeding societies in Germany further revealed the Trakehner horse breed to be a genetically fragmented population with a main partition corresponding to formerly divided East and West Germany. The average rate of gene contributions (Thoroughbred (xx), Arab Horse breed (ox)) to the defined actual breeding population was calculated to be 22.3% xx-genes and 11.7% ox-genes.     

Using genomic tools to maintain diversity and fitness in conservation programmes

Conservation programmes aim at maximizing the survival probability of populations, by minimizing the loss of genetic diversity, which allows populations to adapt to changes, and controlling inbreeding increases. The best known strategy to achieve these goals is optimizing the contributions of the parents to minimize global coancestry in their offspring. Results on neutral scenarios showed that management based on molecular coancestry could maintain more diversity than management based on genealogical coancestry when a large number of markers were available. However, if the population has deleterious mutations, managing using optimal contributions can lead to a decrease in fitness, especially using molecular coancestry, because both beneficial and harmful alleles are maintained, compromising the long‐term viability of the population. We introduce here two strategies to avoid this problem: The first one uses molecular coancestry calculated removing markers with low minor allele frequencies, as they could be linked to selected loci. The second one uses a coancestry based on segments of identity by descent, which measures the proportion of genome segments shared by two individuals because of a common ancestor. We compare these strategies under two contrasting mutational models of fitness effects, one assuming many mutations of small effect and another with few mutations of large effect. Using markers at intermediate frequencies maintains a larger fitness than using all markers, but leads to maintaining less diversity. Using the segment‐based coancestry provides a compromise solution between maintaining diversity and fitness, especially when the population has some inbreeding load.     

Gene and QTL detection in a three-way barley cross under selection by a mixed model with kinship information using SNPs

Quantitative trait locus (QTL) detection is commonly performed by analysis of designed segregating populations derived from two inbred parental lines, where absence of selection, mutation and genetic drift is assumed. Even for designed populations, selection cannot always be avoided, with as consequence varying correlation between genotypes instead of uniform correlation. Akin to linkage disequilibrium mapping, ignoring this type of genetic relatedness will increase the rate of false-positives. In this paper, we advocate using mixed models including genetic relatedness, or ‘kinship’ information for QTL detection in populations where selection forces operated. We demonstrate our case with a three-way barley cross, designed to segregate for dwarfing, vernalization and spike morphology genes, in which selection occurred. The population of 161 inbred lines was screened with 1,536 single nucleotide polymorphisms (SNPs), and used for gene and QTL detection. The coefficient of coancestry matrix was estimated based on the SNPs and imposed to structure the distribution of random genotypic effects. The model incorporating kinship, coancestry, information was consistently superior to the one without kinship (according to the Akaike information criterion). We show, for three traits, that ignoring the coancestry information results in an unrealistically high number of marker–trait associations, without providing clear conclusions about QTL locations. We used a number of widely recognized dwarfing and vernalization genes known to segregate in the studied population as landmarks or references to assess the agreement of the mapping results with a priori candidate gene expectations. Additional QTLs to the major genes were detected for all traits as well.     

Demographic and genetic status of an isolated population of bog turtles (<Emphasis Type="Italic">Glyptemys muhlenbergii</Emphasis>): implications for managing small populations of long-lived animals

In this study, we sought to determine the population stability and genetic diversity of one isolated population of the federally-threatened bog turtle (Glyptemys muhlenbergii) in North Carolina. Using capture–recapture data, we estimated adult survival and population growth rate from 1992 to 2007. We found that the population decreased from an estimated 36 adult turtles in 1994 to approximately 11 adult turtles in 2007. We found a constant adult survival of 0.893 (SE = 0.018, 95% confidence interval, 0.853–0.924) between 1992 and 2007. Using 18 microsatellite markers, we compared the genetic status of this population with five other bog turtle populations. The target population displayed allelic richness (4.8 ± 0.5) and observed heterozygosity (0.619 ± 0.064) within the range of the other bog turtle populations. Coalescent analysis of population growth rate, effective population size, and timing of population structuring event also indicated the genetics of the target population were comparable to the other populations studied. Estimates of effective population size were a proportion of the census size in all populations except the target population, in which the effective population size was larger than the census size (30 turtles vs. 11 turtles). We attribute the high genetic diversity in the target population to the presence of multiple generations of old turtles. This study illustrates that the demographic status of populations of long-lived species may not be reflected genetically if a decline occurred recently. Consequently, the genetic integrity of populations of long-lived animals experiencing rapid demographic bottlenecks may be preserved through conservation efforts effective in addressing demographic problems.     

Variable rates of random genetic drift in protected populations of English yew: implications for gene pool conservation

Protecting populations in their natural habitat allows for the maintenance of naturally evolved adaptations and ecological relationships. However, the conservation of genetic resources often requires complementary practices like gene banks, translocations or reintroductions. In order to minimize inbreeding depression and maximize the adaptive potential of future populations, populations chosen for ex situ conservation should be selected according to criteria that will result in a reduction of global coancestry in the population. Generally, large populations should reveal lower coancestry and higher genetic variation than small populations. If detailed knowledge about coancestry is lacking, census population number (N _c ) can be used as a proxy for required characteristics. However, a simple measure of N _c may be misleading in particular cases as genetic processes rely on effective population size (N _e ) rather than N _c and these two measures may differ substantially due to demographic processes. We used an example of English yew to address whether N _c can be a good predictor of genetic parameters when used in conservation programs. Using microsatellite markers, we estimated allelic richness, inbreeding and coancestry coefficients of six relatively large yew populations in Poland. Each population was characterized by N _e using the linkage disequilibrium method. Our results showed that populations of English yew were subject to substantial divergence and genetic drift, with both being inversely proportional to the effective subpopulation size (N _e ). Additionally, allelic richness appeared proportional to N _e but not to N _c . However, the N _e /N ratio differed greatly among populations, which was possibly due to different population histories. From the results we concluded that choosing source populations based only on their census size can be fairly misleading. Implications for conservation are briefly discussed.     

Removing exogenous information using pedigree data

Management of certain populations requires the preservation of its pure genetic background. When, for different reasons, undesired alleles are introduced, the original genetic conformation must be recovered. The present study tested, through computer simulations, the power of recovery (the ability for removing the foreign information) from genealogical data. Simulated scenarios comprised different numbers of exogenous individuals taking part of the founder population and different numbers of unmanaged generations before the removal program started. Strategies were based on variables arising from classical pedigree analyses such as founders’ contribution and partial coancestry. The efficiency of the different strategies was measured as the proportion of native genetic information remaining in the population. Consequences on the inbreeding and coancestry levels of the population were also evaluated. Minimisation of the exogenous founders’ contributions was the most powerful method, removing the largest amount of genetic information in just one generation. However, as a side effect, it led to the highest values of inbreeding. Scenarios with a large amount of initial exogenous alleles (i.e. high percentage of non native founders), or many generations of mixing became very difficult to recover, pointing out the importance of being careful about introgression events in populations where these are undesired.     

Effective population size of a population with stochastically varying size

For a Wright–Fisher model with mutation whose population size fluctuates stochastically from generation to generation, a heterozygosity effective population size is defined by means of the equilibrium average heterozygosity of the population. It is shown that this effective population size is equal to the harmonic mean of population size if and only if the stochastic changes of population size are uncorrelated. The effective population size is larger (resp. smaller) than the harmonic mean when the stochastic changes of population size are positively (resp. negatively) autocorrelated. These results and those obtained so far for other stochastic models with fluctuating population size suggest that the property that effective population sizes are always larger than the harmonic mean under the fluctuation of population size holds only for continuous time models such as diffusion and coalescent models, whereas effective population sizes can be equal to or smaller than the harmonic mean for discrete time models.     

Asymmetric gene flow and the evolutionary maintenance of genetic diversity in small,peripheral Atlantic salmon populations

Small populations may be expected to harbour less genetic variation than large populations, but the relation between census size (N), effective population size (N _e), and genetic diversity is not well understood. We compared microsatellite variation in four small peripheral Atlantic salmon populations from the Iberian peninsula and three larger populations from Scotland to test whether genetic diversity was related to population size. We also examined the historical decline of one Iberian population over a 50-year period using archival scales in order to test whether a marked reduction in abundance was accompanied by a decrease in genetic diversity. Estimates of effective population size (N _e) calculated by three temporal methods were consistently low in Iberian populations, ranging from 12 to 31 individuals per generation considering migration, and from 38 to 175 individuals per generation if they were regarded as closed populations. Corresponding N _e/N ratios varied from 0.02 to 0.04 assuming migration (mean=0.03) and from 0.04 to 0.18 (mean=0.10) assuming closed populations. Population bottlenecks, inferred from the excess of heterozygosity in relation to allelic diversity, were detected in all four Iberian populations, particularly in those year classes derived from a smaller number of returning adults. However, despite their small size and declining status, Iberian populations continue to display relatively high levels of heterozygosity and allelic richness, similar to those found in larger Scottish populations. Furthermore, in the R. Asón no evidence was found for a historical loss of genetic diversity despite a marked decline in abundance during the last five decades. Thus, our results point to two familiar paradigms in salmonid conservation: (1)␣endangered populations can maintain relatively high levels of genetic variation despite their small size, and (2) marked population declines may not necessarily result in a significant loss of genetic diversity. Although there are several explanations for such results, microsatellite data and physical tagging suggest that high levels of dispersal and asymmetric gene flow have probably helped to maintain genetic diversity in these peripheral populations, and thus to avoid the negative consequences of inbreeding.     

Considerations for monitoring population trends of colonial waterbirds using the effective number of breeders and census estimates

Detecting trends in population size fluctuations is a major focus in ecology, evolution, and conservation biology. Populations of colonial waterbirds have been monitored using demographic approaches to determine annual census size (N_a). We propose the addition of genetic estimates of the effective number of breeders (N_b) as indirect measures of the risk of loss of genetic diversity to improve the evaluation of demographics and increase the accuracy of trend estimates in breeding colonies. Here, we investigated which methods of the estimation of N_b are more precise under conditions of moderate genetic diversity, limited sample sizes and few microsatellite loci, as often occurs with natural populations. We used the wood stork as a model species and we offered a workflow that researchers can follow for monitoring bird breeding colonies. Our approach started with simulations using five estimators of N_b and the theoretical results were validated with empirical data collected from breeding colonies settled in the Brazilian Pantanal wetland. In parallel, we estimated census size using a corrected method based on counting active nests. Both in simulations and in natural populations, the approximate Bayesian computation (ABC) and sibship assignment (SA) methods yielded more precise estimates than the linkage disequilibrium, heterozygosity excess, and molecular coancestry methods. In particular, the ABC method performed best with few loci and small sample sizes, while the other estimators required larger sample sizes and at least 13 loci to not underestimate N_b. Moreover, according to our N_b/N_a estimates (values were often ≤0.1), the wood stork colonies evaluated could be facing the loss of genetic diversity. We demonstrate that the combination of genetic and census estimates is a useful approach for monitoring natural breeding bird populations. This methodology has been recommended for populations of rare species or with a known history of population decline to support conservation efforts.     

Controlling genetic variability by mathematical programming in a selection scheme on an open-pollinated population in Eucalyptus globulus

A model using integer quadratic mathematical programming has been developed to control the inbreeding level (or genetic diversity) through group coancestry in a selection programme for a forestry population structured in terms of maternal families coming from different locations. A method to calculate the average group coancestry between- and within-families for these open-pollinated populations is also proposed. This model has been applied to data from a breeding programme of Australian Eucalyptus globulus. The strategy proved to be effective as reductions of up to 50% for the group coancestry of the selected individuals were reached with a loss of only 5% of the maximum attainable selection differential (corresponding to truncation selection). Received: 14 October 1999 / Accepted: 26 July 2000     

How to monitor elusive lizards: comparison of capture–recapture methods on giant day geckos (Gekkonidae, Phelsuma madagascariensis grandis) in the Masoala rainforest exhibit, Zurich Zoo

Rapid and reliable estimation of population size is needed for the efficient monitoring of animal populations of conservation concern. Unfortunately, technical advances in this area have not been paralleled in uptake in conservation, which may be due to difficulties in implementation or the lack of general guidelines for application. Here we tested five different methods used to estimate population size [capture–mark–recapture (CMR), finite-mixture models, model averaging of finite-mixture models, accumulation curve methods (ACM), and the line transect method (LT)] using extensive capture–recapture data of the giant day gecko (Gekkonidae, Phelsuma madagascariensis grandis, Gray 1870) at the Masoala rainforest exhibit, Zurich Zoo. When the complete data were analyzed [30 sessions (and 27 sessions for the LT)], all methods except the LT produced similar estimates of population size. The simple ACM gave a small coefficient of variation (CV), but did not cover the most likely value of population size at moderate sampling effort. Nevertheless, the ACM was the only method that showed a reasonable convergence when subsets of data were used. CMR and Pledger models included the reference value in their confidence intervals (CI) after 25 and 30 sessions, respectively. Although model averaging did slightly improve the estimate, the CV was still high for the full dataset. Our method of using subsets of data to test the robustness of estimates is simple to apply and could be adopted more widely in such analyzes to evaluate sensitivity to method of evaluation. In conclusion, simple accumulation methods showed similar efficiency to more complex statistical models, and are likely to be sufficiently precise for most conservation monitoring purposes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Advantages of using molecular coancestry in the removal of introgressed genetic material

Background

When introgression of undesired exogenous genetic material occurs in a population intended to remain pure, actions are necessary to recover the original background. It has been shown that genome-wide information can replace pedigree information for different objectives and is a valuable tool in the fields of genetic conservation and breeding. In this simulation study, molecular information provided by 50 000 SNP was used to minimise the molecular coancestry between individuals of an admixed population and the foreign individuals that originally introgressed a native population in order to remove the exogenous DNA.

Results

This management method, which detects the ‘purest’ individuals to be used as parents for the next generation, allowed recovery of the native genetic background to a great extent in all simulated scenarios. However, it also caused an increase in inbreeding larger than expected because of the lower number of individuals selected as parents and the higher coancestry between them. In scenarios involving several introgression events the method was more efficient than in those involving a single introgression event because part of the genetic information was mixed with the native genetic material for a shorter period.

Conclusions

Genome-wide information can be used to identify the purest individuals via the minimisation of molecular coancestry between individuals of the admixed and exogenous populations. Removal of the undesired genetic material is more efficient with a molecular-based approach than with a pedigree-based approach.     

Genetic monitoring and effects of stocking practices on small <Emphasis Type="Italic">Cyprinus carpio</Emphasis> populations

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 composition 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 population, 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 population 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 management policies and to future decision making.