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Different waves of postglacial recolonisation and genomic structure of bank vole populations in NE Poland

Abstract

Previous studies indicated that in some species phylogeographic patterns obtained in the analysis of nuclear and mitochondrial DNA (mtDNA) markers can be different. Such mitonuclear discordance can have important evolutionary and ecological consequences. In the present study, we aimed to check whether there was any discordance between mtDNA and nuclear DNA in the bank vole population in the contact zone of its two mtDNA lineages. We analysed the population genetic structure of bank voles using genome-wide genetic data (SNPs) and diversity of sequenced heart transcriptomes obtained from selected individuals from three populations inhabiting areas outside the contact zone. The SNP genetic structure of the populations confirmed the presence of at least two genetic clusters, and such division was concordant with the patterns obtained in the analysis of other genetic markers and functional genes. However, genome-wide SNP analyses revealed the more detailed structure of the studied population, consistent with more than two bank vole recolonisation waves, as recognised previously in the study area. We did not find any significant differences between individuals representing two separate mtDNA lineages of the species in functional genes coding for protein-forming complexes, which are involved in the process of cell respiration in mitochondria. We concluded that the contemporary genetic structure of the populations and the width of the contact zone were shaped by climatic and environmental factors rather than by genetic barriers. The studied populations were likely isolated in separate Last Glacial Maximum refugia for insufficient amount of time to develop significant genetic differentiation.

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Fig. 1: Sampling localities of bank voles Myodes glareolus in NE Poland with results of SNP clustering indicated in BAPS analyses (spatial models).
Fig. 2: Distribution of different genomic clusters identified in ADMIXTURE analyses.
Fig. 3: Results of PCA based on the genomic data.
Fig. 4: Results of PCA based on the transcriptomic data.
Fig. 5: Distribution of FST values between BIA and WL populations, calculated for transcriptome-derived SNPs.

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Data availability

Data has been archived in the Dryad repository (reference transcriptome, annotation report, SNP data of bank voles: https://doi.org/10.5061/dryad.jm63xsjg0) and at NCBI (raw RNA sequence data of bank vole: BioProject ID PRJNA930868).

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Acknowledgements

This study was financed by the Foundation for Polish Science, project POMOST/2010-2/11 to M.N. (in the frames of the Program Innovative Economy, one of six national programs under the National Strategy Reference Framework, which was co-financed from the European Regional Development Fund of the EU) and (to E.T.) the National Science Centre – UMO-2014/13/N/NZ8/02472. M.K. was supported by the National Science Centre – grant no 2019/34/A/NZ8/00231. Computations were performed at the Poznan Supercomputing and Networking Center. We thank Kamila Plis for her help in preparing Fig. S2 and Steve Jones for the revision of the English language.

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MN, BJ and WB conceived the ideas, MN applied for financial support, ET collected the samples, performed the laboratory work and statistically analysed the RAD-tag and mtDNA data sets, MK conducted the transcriptome analyses, TC and KG designed and supervised RAD-tag library preparation, sequencing and initial SNP filtering, ET and MK prepared the tables and figures, MN wrote the main manuscript, and all authors reviewed it.

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Correspondence to Magdalena Niedziałkowska.

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Niedziałkowska, M., Tarnowska, E., Babik, W. et al. Different waves of postglacial recolonisation and genomic structure of bank vole populations in NE Poland. Heredity 130, 269–277 (2023). https://doi.org/10.1038/s41437-023-00600-1

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