Depleted genetic variation of the European ground squirrel in Central Europe in both microsatellites and the major histocompatibility complex gene: implications for conservation

Abstract

Habitat fragmentation may influence the genetic make-up and adaptability of endangered populations. To facilitate genetic monitoring of the endangered European ground squirrel (EGS), we analyzed 382 individuals from 16 populations in Central Europe, covering almost half of its natural range. We tested how fragmentation affects the genetic architecture of presumably selectively neutral (12 microsatellites) and non-neutral (the major histocompatibility class II DRB gene) loci. Spatial genetic analyses defined two groups of populations, “western” and “eastern”, with a significantly higher level of habitat fragmentation in the former group. The highly fragmented western populations had significantly lower genetic diversity in both types of markers. Only one allele of the DRB gene predominated in populations of the western group, while four alleles were evenly distributed across the eastern populations. Coefficient of inbreeding values (F IS) calculated from microsatellites were significantly higher in the western (0.27–0.79) than in eastern populations (−0.060–0.119). Inter-population differentiation was very high, but similar in both groups (western F ST = 0.23, eastern F ST = 0.25). The test of isolation by distance was significant for the whole dataset, as well as for the two groups analyzed separately. Comparison of genetic variability and structure on microsatellites and the DRB gene does not provide any evidence for contemporary selection on MHC genes. We suggest that genetic drift in small bottlenecked and fragmented populations may overact the role of balancing selection. Based on the resulting risk of inbreeding depression in the western populations, we support population management by crossbreeding between the western and eastern populations.

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Acknowledgments

We would like to thank to Ľudovít Ďureje for a substantial help in analysis of microsatellites and to Max Galan for his help with DRB analysis. Also we thank other colleagues who helped in the field work, namely Ivan Baláž, Ervin Hapl and Bedřich Hájek. We thank to David Hardekopf for an improvement of English. This research was supported by the European Science Foundation grant (ConGen EX/1141), South Bohemia University Grant Agency (53/2006/P-BF), GA of the ASCR (KJB601410816) and Ministry of Education CR (MSM 6007665801). JB was partially supported by Ministry of Education CR (Biodiversity Research Centre no. LC06073 and Long-term research plan MSM 0021622416). LC was supported from grant IRP IAPG AV0Z 50450515 provided by the Academy of Sciences of the Czech Republic and by the Biodiversity Research Centre no. LC06073.

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Correspondence to Štěpánka Říčanová.

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10592_2011_213_MOESM1_ESM.doc

Supplementary Table A List of microsatellite loci tested. NA = number of alleles. Letter above the name of a locus identifies the same amplification set (set A, B and C) (DOC 43 kb)

10592_2011_213_MOESM2_ESM.doc

Supplementary Table B Estimation of the presence of null alleles in each population and for each microsatellite locus and the DRB gene using FreeNA software (Chapuis and Estoup 2007). Only values higher than 0.15 are marked in grey, which are considered to represent a high probability of the presence of a null allele (DOC 55 kb)

10592_2011_213_MOESM3_ESM.doc

Supplementary Table C Pairwise F ENAST values (from FreeNA, Chapuis and Estoup 2007) between EGS populations based on microsatellite data are above the diagonal, and values of F′ ST (according to Hedrick 2005) are below. Note: Marks of significance: * P < 0.05, NS-non significant (P > 0.05) (DOC 60 kb)

10592_2011_213_MOESM4_ESM.doc

Supplementary Table D Comparison of values of F ST in microsatellites and in MHC (DRB) using different corrections of F ST and confidential intervals for F ST in microsatellites (DOC 30 kb)

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Říčanová, Š., Bryja, J., Cosson, JF. et al. Depleted genetic variation of the European ground squirrel in Central Europe in both microsatellites and the major histocompatibility complex gene: implications for conservation. Conserv Genet 12, 1115–1129 (2011). https://doi.org/10.1007/s10592-011-0213-1

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Keywords

  • Souslik
  • Endangered species
  • Sciuridae
  • Habitat fragmentation
  • DRB
  • MHC Class II