Genetic diversity, gene flow and drift in Bavarian red deer populations (Cervus elaphus)

The red deer (Cervus elaphus) population of Bavaria in Southern Germany was severely reduced during the 19th century due to over-hunting. The species has since recovered within designated areas. Subsequent habitat fragmentation presumably has changed the genetic structure of Bavarian red deer. In order to assess the genetic diversity, we analysed samples obtained from nine different Bavarian and two adjacent (Thueringen and Czech-Republic) red deer populations, genotyping 19 microsatellite loci. Our analyses revealed moderate and significant differences in diversity. Referring to assignment tests, the genetic differentiation of Bavarian red deer was sufficient to assign an individual's origin to the correct population at an average of 91.6%. The correlation of genetic and geographic distance matrices revealed no evidence for isolation by distance. The coalescent model analysis suggests that the genetic structure used to be characterized by a drift-gene flow equilibrium and is now influenced by drift and disruption of the gene flow. Only three of the examined populations showed a probability of less than 10% that two genes within these populations share a common ancestor (F_IS-value). Two populations had high F_IS values, indicating the influence of drift. Additionally, the intrapopulation indices revealed a low variability in these populations. The estimated effective population sizes (N_e) were generally in the same range as the actual population sizes. The inbreeding rates, based on the estimated N_e, and the inbreeding coefficients suggested that the Bavarian red deer populations are in a stable state.