Data from: Strong decline of gene diversity in local populations of the highly endangered common hamster (Cricetus cricetus) in the western part of its european range.

Abstract

The Common hamster (Cricetus cricetus) has declined by more than 99% in the westernmost part of its range in Belgium, the Netherlands and the adjacent German federal state of North Rhine-Westphalia (BNN region) in the second half of the 20th century. To detect a decline in genetic variation as a result of inbreeding and genetic drift we have measured the genetic variation in current BNN hamster populations and compared the outcome with the genetic variation in museum samples from the historical, non-fragmented, population. Most of the current populations have lost the majority of their rare alleles and individual animals have become nearly homozygous. The total gene diversity of the remaining small populations combined is not much less than that of the historical population. Hence, the main genetic difference between historical and present is not in terms of total genetic variation or number of alleles in the BNN region, but in the distribution of this variation over the populations.

Samples This study is based on 250 DNA samples from hamster populations in the BNN region (n=85) and reference populations in France (n=68) and a population in Central Germany (n=97). The samples from the BNN region consisted of 52 samples from the five currently surviving populations in Belgium, the Netherlands and North Rhine–Westphalia and 33 samples from museum specimens. The museum samples consisted of pieces of dried skin, sometimes including hairs, that were taken from museum specimens that were collected or found in the wild in Belgium and the Netherlands during the period 1925-1985; 85% of the specimens were collected before 1970. In total 51 museum specimens from the museums of natural history in Leiden (Naturalis, the Netherlands) and Brussels (KBIN, Belgium) were sampled, but only 33 samples provided sufficient enough DNA for PCR amplification. The technical analysis of museum and current samples is described in detail in Neumann & Jansman (2004). Each museum sample was assigned either to the historical hamster population of Belgium (n=8) or to the historical population of the Netherlands (n=25).

Genotyping All samples were genotyped for a maximum of 11 microsatellite loci: Ccrμ3, Ccrμ4, Ccrμ6, Ccrμ10, Ccrμ11, Ccrμ12, Ccrμ13, Ccrμ15, Ccrμ17, Ccrμ19, and Ccrμ20. However, in our study we used only 9 of the 11 available microsatellites because there were too many missing values at loci Ccrμ6 and/or Ccrμ19, especially in the museum samples. Museum samples with less than 6 known loci were excluded from the analysis. Almost half of the 33 museum samples showed missing values (n=17, 51%), with 8 samples missing 1 locus, 8 samples missing 2 loci and 1 sample missing 3 loci.

Each row is a genotype from an individual. The dataset has the following columns: A) Population per country and period B) Unique individual number C) Population: historical or recent D-Y) alleles per locus for each individual Z) Specific sample location (in the wild) AA) Populations (assigned to) AB) Origin (wild) AC) Year of collection AD) Country