Loss of connectivity between habitat patches is particularly important for small, environmentally specialized species with short migratory capacity. Taking the root vole as an example, we studied whether variation in the landscape (its geomorphological evolution) may affect the genetic differentiation exhibited by a wetland species, and thus the resilience of its population. We did so by testing the genetic differentiation at 9 sites located in two areas in the peripheral zone of the root vole’s range limit in Poland (the Sandomierz Basin and Western Polesie), and confronted the results with the differing origins and geomorphological characteristics of the hydrogenic environments in those two areas. Based on the analyses of 12 microsatellite loci (N = 118) and the 908 bp of cytochrome b sequences (N = 107), higher genetic variability was found in individuals from Western Polesie than from the Sandomierz Basin. Geomorphological analysis conducted with the use of DTM, satellite images, geological maps and cartographic fieldwork showed that the habitats optimal for the root vole are configured differently in the two areas considered, occurring mainly in river valleys and in isolated wetlands of lake-land plains, respectively. Simultaneous analysis of both the spatial configuration and connectivity of habitats, and the voles’ evolutionary directions and genetic parameters, supports the conclusion that the linear character of highly fragmented riverine habitats, additionally inundated during episodic flooding, is less favorable for the gene dispersal of small mammals than extensive marshy wetlands, even despite locally occurring barriers. These findings indicate that the genesis and geomorphological evolution of the landscape may influence the ecological changes taking place there, including habitat reduction and fragmentation. They may therefore be important for the persistence/resilience of particular species and therefore should be taken into account in conservation management of hydrogenic habitat areas, especially those close to the range limit of species with demanding habitat requirements.
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