Spatial and temporal variation in genetic diversity of an endangered freshwater seal

Molecular-genetic assessments of demographic history, population structure, and loss of genetic variation in small natural populations are often hampered by a lack of information on initial diversity, isolation time, and migration rates. The landlocked population of currently less than 300 ringed seals inhabiting Lake Saimaa in southeastern Finland offers a unique model for studying these questions in small populations. It has remained completely isolated since the last ice age, information on its initial genetic diversity can be inferred from the large marine source population in the Baltic Sea, and its ecology is well studied. We analyzed the mitochondrial DNA diversity of 215 Saimaa ringed seals spanning three decades in order to assess long- and short-term changes in the gene pool of this critically endangered subspecies. The mtDNA diversity of the Saimaa ringed seal is low, consisting of only eight haplotypes. Nevertheless, coalescent simulations show that the diversity is unexpectedly high when contrasted with the over 800 generations of isolation and the estimated historical carrying capacity of the lake. In the short term, marked temporal and spatial differentiation was observed among three decades and four regions of Lake Saimaa, suggesting extremely low effective subpopulation sizes and limited migration of females within the lake. Our study strongly suggests that enhancing gene flow and population growth is crucial for maintaining the remaining genetic diversity of the Saimaa ringed seal.