Extinction debt at the gene level: does current or historical habitat size explain extant genetic diversity in Succisa pratensis?

Loss of connectivity and habitat decline are considered as major threats for biodiversity because gene flow between populations is interrupted and the probability of extinction increases. Species extinction may occur long after habitat destruction, a phenomenon called extinction debt. While numerous studies have considered such delayed extinction at the species level, it has rarely been assessed whether extinction debt also occurs at the gene level. Here, we relate genetic diversity (allelic richness) with historical and current landscape configuration (historical/current habitat size, size development, historical/current habitat connectivity, connectivity development). We sampled 41 populations of Succisa pratensis, a widespread, perennial fen plant, in fragmented fen meadows of different sizes and degrees of connectivity in the canton of Zurich (Switzerland). We assessed present-day allelic richness at 11 nuclear microsatellite markers, which were newly developed using 454 sequencing, while landscape characteristics were estimated for the years 1850, 1900, 1950 and 2000. Habitat connectivity, connectivity decline and size did not explain allelic richness in S. pratensis. However, patches without size decline had a lower allelic richness than patches with intermediate or high decline. This could be an indication of the importance of former size because patches with a high size decline level were all formerly larger than 3 ha. An extinction debt at the gene level could exist since effects of habitat destruction and fragmentation is not yet clearly visible in the genetic diversity. Extant genetic diversity can also be explained by population size of S. pratensis. Large populations (>1000) are significantly more diverse than small populations (<100). Historical landscape configuration could explain extant genetic diversity in S. pratensis therefore the results of our study could be interpreted as an extinction debt at the gene level.