1. We used a factorial experimental design to test whether habitat fragmentation (two different fragment sizes) and connectivity (presence and absence of corridors between small fragments) affected population growth rate and two conventional measures of the demographic structure (proportion of reproductive adults and sex ratio) in 12 enclosed populations of root voles.
2. Because the matriline has been suggested to be a functional entity affecting the demography of Microtus populations, we employed a study protocol (including laboratory-raised founder animals and intensive live trapping combined with fluorescent powder techniques), which enabled us to track the matrilineal genealogy in the populations. Thus, the effect of habitat structure on the matrilineal structure of the populations, quantified by the Shannon–Wiener diversity index, could be tested for the first time.
3. Population growth rate was density dependent, but neither this population parameter nor sex ratio and proportion of reproductive adults differed between the habitat treatments. This was unexpected since the presumed determinants of Microtus demography, such as individual space use, dispersal distances and spatio-social organization had earlier been found to differ between the treatments.
4. The matrilineal structure (diversity) of the populations changed in response to the experimental habitat manipulations. In corridor-connected systems, some matrilines became numerically dominant, which lead to reduced matrilineal diversity compared to systems with isolated habitat fragments. We hypothesize that some matrilines were able to colonize and exploit corridor-connected fragments better than other matrilines. Matrilineal diversity was not related to any other demographic attribute (growth rate, sex ratio and functional stage structure) at the population level.
5. Our results suggest that fragmentation-induced changes of individual and matrilineal level attributes do not necessarily propagate into population level differences in vital rates. The notion that matrilines may be a functional entity in Microtus populations could not be supported.
6. Our experimental results suggest that population genetics, more than population demography, may be sensitive to habitat fragmentation and connectivity, within the specific temporal and spatial extent explored. In particular, the effect of corridors on matrilineal diversity imply that population genetic studies based on mtDNA markers should consider habitat connectivity when analysing genetic diversity.