Application of a SSR‐GBS marker system on investigation of European Hedgehog species and their hybrid zone dynamics. Issue 5 (14th February 2019)

• Record Type: Journal Article
• Authors: Curto, Manuel; Winter, Silvia; Seiter, Anna; Schmid, Lukas; Scheicher, Klaus; Barthel, Leon M. F.; Plass, Jürgen; Meimberg, Harald
• Is Part Of: Ecology and evolution. Volume 9:Issue 5(2019)
• Page Start: 2814
• Page End: 2832
• Publication Date: 2019-02-14
• Subjects: European hedgehog -- hybridzone -- microsatellites -- SSR‐GBS -- white‐breasted hedgehog; Ecology -- Periodicals; Evolution -- Periodicals; 577.05
• DOI: 10.1002/ece3.4960
• Languages: English
• ISSNs: 2045-7758

Abstract

Abstract: By applying second‐generation sequencing technologies to microsatellite genotyping, sequence information is produced which can result in high‐resolution population genetics analysis populations and increased replicability between runs and laboratories. In the present study, we establish an approach to study the genetic structure patterns of two European hedgehog species Erinaceaus europaeus and E. roumanicus . These species are usually associated with human settlements and are good models to study anthropogenic impacts on the genetic diversity of wild populations. The short sequence repeats genotyping by sequence (SSR‐GBS) method presented uses amplicon sequences to determine genotypes for which allelic variants can be defined according to both length and single nucleotide polymorphisms (SNPs). To evaluate whether complete sequence information improved genetic structure definition, we compared this information with datasets based solely on length information. We identified a total of 42 markers which were successfully amplified in both species. Overall, genotyping based on complete sequence information resulted in a higher number of alleles, as well as greater genetic diversity and differentiation between species. Additionally, the structure patterns were slightly clearer with a division between both species and some potential hybrids. There was some degree of genetic structure within species, although only in E. roumanicus was this related to geographical distance. The statistically significant results obtained by SSR‐GBS demonstrate that it is superior to electrophoresis‐based methods for SSR genotyping. Moreover, the greater reproducibility and throughput with lower effort which can be obtained with SSR‐GBS and the possibility to include degraded DNA into the analysis, allow for continued relevance of SSR markers during the genomic era. Abstract : Microsatellite genotyping based on Illumina MiSeq sequencing recovered genetic structure patterns in the European hedgehog species, Erinaceus europaeus, and E. roumanicus . As main advantages of this approach, sequence information is available allowing allele call based on length variation and on SNPs in the flaking regions, resulting in a higher discriminatory power in the assessment of genetic structure. The applicability of the method considering the high replicability and simplification of laboratory procedure is discussed, and a procedure for bioinformatics for allele call is presented.