Description of the microsatellite markers used.

The threat of isolation to red deer (Cervus elaphus) has been described in numerous European studies. The consequences range from reduced genetic diversity and increased inbreeding to inbreeding depression. It has been shown that the underlying factors cannot be generalised, but vary greatly in their effects depending on local conditions. The aim of this study was to analyse in detail the genetics of red deer in a large German federal state with a population density of 532 inhabitants per km2 and 23.8% settlement and traffic area, in order to generate data for future management of the region. 1199 individual samples of red deer were collected in all 20 Administrative Management Units (AMUs) and compared with existing results from the neighbouring state of Hesse (19 AMUs). All 2490 individuals from both states were clustered using Bayesian methods and connectivity between neighbouring AMUs was quantified. Overall, 30% of the AMUs were found to be highly isolated, mostly with effective population sizes (Ne)