Anthropogenic barriers, in particular transportation infrastructure, hunting and settlement, fragment wildlife habitats, preventing a continuous gene flow. The resulting isolation significantly impairs the genetic diversity of populations and therefore the long-term conservation of species. Even populations with large numbers of animals living side by side cannot benefit from each other as metapopulations, so that at the very least their adaptation to the habitat is at risk. The effective population size has been established in the relevant literature as a parameter for diversity and adaptability. The 100/1000 rule states that a population needs at least 1000 genetically diverse and reproductively active animals to maintain its adaptability. If this number falls below 100, inbreeding depression can no longer be absorbed and the animals in these genetically monotonous populations are very likely to suffer from inbreeding depression, which manifests itself particularly in reduced fertility, disease resistance and the insufficiency of other polygenic traits. The incidence of deformities also increases with increasing levels of homozygosity. To characterize and determine the genetic health status of the populations in Hesse (HE) and North Rhine-Westphalia (NRW), 2490 samples were taken in a total of 40 red deer areas. The samples were processed with the help of 16 representative and comparable microsatellites selected in preliminary studies. After Bayesian methods, Fst and the comparison of alleles were used to analyze the connectivity of the areas among each other, isolated areas could be identified and delimited from superordinate regions with connectivity. The metapopulations with existing connectivity were then examined for their allele richness and their allele potential and effective population size were calculated. In only two large areas, the Rothaargebirge (eight sample areas) and the Eifel (four sample areas), an effective population size of 1000 was reliably exceeded in the network of metapopulations, which seems to ensure long-term adaptability and survivability. Seven of the areas were below an effective population size of 100, Minden (52.5; NRW), Hünxe (53.4; NRW) and Wahner Heide (99.7; NRW), four areas even fell below an effective population size of 50, the Reichswald Kleve (8,7; NRW), the Nutscheid (17,7; NRW), the Ebbegebirge (19,3; NRW) and the Krofdorfer Forst (44,2; HE), so that they seem to be no longer able to react to short-term inbreeding depressions. The assumption that the higher human population density in NRW than in HE means that red deer areas are more isolated was confirmed by the current study. However, the direct comparison (Eifel - Waldhessen) also showed that the hunting management guidelines of the state of NRW are genetically and therefore biologically better adapted to red deer than those of the state of Hesse. Both long-term adaptable areas were completely (Eifel) or to a large extent (Rothaargebirge) in NRW. It became apparent that state-wide generalized management guidelines do not do justice to the individual conditions of the red deer areas, so that, as in NRW with the involvement of the Research Centre for Hunting Science and Game Damage Prevention, the hunting communities are of particular importance in the collection of evidence-based data on red deer populations. This data must be taken into account by red deer management, e.g. in order to promote genetically necessary age structures and migratory deer, especially males. Based on the results of the present study, particular importance should be attached to migratory stags aged 1-5 years in order to connect the 29 genetically suboptimally positioned red deer populations. The necessary migration corridors must be conserved and, if necessary, newly created in order to reconnect the separated red deer areas. Stags up to five years of age must therefore be protected in areas free of red deer and structural barriers, such as highways, must be passable. Holistically conceived concepts of multi-faceted red deer management with zoning for humans and animals, involvement of the population, a policy at eye level and consideration of climatic, ecological and economic conditions are an immense challenge but indispensable in order to preserve a future for our wild animals and especially for red deer. The seamless chain of evidence in this study on the development of isolated populations (STRUCTURE, DAPC, BAPS, TESS, Fst and allele comparison), genetic impoverishment (allele potential and effective population size) and significantly increased homozygosity values in malformed individuals from previous studies prove the problems of red deer despite locally often high populations and show suboptimal management to date. The emerging conflicts are mainly of an economic-human nature, but harm the red deer in the short term through hunting mortality and in the medium to long term through genetic lethality.
