{"status":"public","file_date_updated":"2025-04-03T11:53:06Z","type":"journal_article","year":"2025","corr_author":"1","page":"367-378","publisher":"Oxford University Press","OA_type":"hybrid","department":[{"_id":"NiBa"}],"doi":"10.1093/jeb/voaf002","article_type":"original","volume":38,"month":"03","title":"Short INDELs and SNPs as markers of evolutionary processes in hybrid zones","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2025-03-23T23:01:25Z","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"ddc":["570"],"oa":1,"publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"has_accepted_license":"1","file":[{"file_size":12826085,"creator":"dernst","success":1,"file_id":"19469","access_level":"open_access","date_created":"2025-04-03T11:53:06Z","content_type":"application/pdf","relation":"main_file","checksum":"01408e626a4131bfec5ffc70b0af9129","date_updated":"2025-04-03T11:53:06Z","file_name":"2025_JourEvolBiology_Perini.pdf"}],"citation":{"apa":"Perini, S., Johannesson, K., Butlin, R. K., &#38; Westram, A. M. (2025). Short INDELs and SNPs as markers of evolutionary processes in hybrid zones. <i>Journal of Evolutionary Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jeb/voaf002\">https://doi.org/10.1093/jeb/voaf002</a>","ama":"Perini S, Johannesson K, Butlin RK, Westram AM. Short INDELs and SNPs as markers of evolutionary processes in hybrid zones. <i>Journal of Evolutionary Biology</i>. 2025;38(3):367-378. doi:<a href=\"https://doi.org/10.1093/jeb/voaf002\">10.1093/jeb/voaf002</a>","mla":"Perini, Samuel, et al. “Short INDELs and SNPs as Markers of Evolutionary Processes in Hybrid Zones.” <i>Journal of Evolutionary Biology</i>, vol. 38, no. 3, Oxford University Press, 2025, pp. 367–78, doi:<a href=\"https://doi.org/10.1093/jeb/voaf002\">10.1093/jeb/voaf002</a>.","ieee":"S. Perini, K. Johannesson, R. K. Butlin, and A. M. Westram, “Short INDELs and SNPs as markers of evolutionary processes in hybrid zones,” <i>Journal of Evolutionary Biology</i>, vol. 38, no. 3. Oxford University Press, pp. 367–378, 2025.","ista":"Perini S, Johannesson K, Butlin RK, Westram AM. 2025. Short INDELs and SNPs as markers of evolutionary processes in hybrid zones. Journal of Evolutionary Biology. 38(3), 367–378.","short":"S. Perini, K. Johannesson, R.K. Butlin, A.M. Westram, Journal of Evolutionary Biology 38 (2025) 367–378.","chicago":"Perini, Samuel, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Short INDELs and SNPs as Markers of Evolutionary Processes in Hybrid Zones.” <i>Journal of Evolutionary Biology</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/jeb/voaf002\">https://doi.org/10.1093/jeb/voaf002</a>."},"license":"https://creativecommons.org/licenses/by-nc/4.0/","abstract":[{"text":"Polymorphic short insertions and deletions (INDELs \r\n 50 bp) are abundant, although less common than single nucleotide polymorphisms (SNPs). Evidence from model organisms shows INDELs to be more strongly influenced by purifying selection than SNPs. Partly for this reason, INDELs are rarely used as markers for demographic processes or to detect divergent selection. Here, we compared INDELs and SNPs in the intertidal snail Littorina saxatilis, focussing on hybrid zones between ecotypes, in order to test the utility of INDELs in the detection of divergent selection. We computed INDEL and SNP site frequency spectra using capture sequencing data. We assessed the impact of divergent selection by analyzing allele frequency clines across habitat boundaries. We also examined the influence of GC-biased gene conversion because it may be confounded with signatures of selection. We show evidence that short INDELs are affected more by purifying selection than SNPs, but part of the observed site frequency spectra difference can be attributed to GC-biased gene conversion. We did not find a difference in the impact of divergent selection between short INDELs and SNPs. Short INDELs and SNPs were similarly distributed across the genome and so are likely to respond to indirect selection in the same way. A few regions likely affected by divergent selection were revealed by INDELs and not by SNPs. Short INDELs can be useful (additional) genetic markers helping to identify genomic regions important for adaptation and population divergence.","lang":"eng"}],"issue":"3","date_published":"2025-03-01T00:00:00Z","publication_status":"published","scopus_import":"1","date_updated":"2025-04-30T13:34:39Z","OA_place":"publisher","day":"01","author":[{"full_name":"Perini, Samuel","last_name":"Perini","first_name":"Samuel"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M"}],"intvolume":"        38","pmid":1,"external_id":{"pmid":["39803902"]},"_id":"19438","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by the Natural Environment Research Council (NE/K014021/1), European Research Council (ERC-2015-AdG-693030- BARRIERS) and Swedish Research Council VR (2018-03695) and we are also very grateful for the support of the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg.\r\nWe thank the Swedish Bioinformatics Advisory Program organized by SciLifeLab for feedback and assistance on the variant calling pipeline and Alan Le Moan for helpful discussions. R.K.B. and A.M.W. contributed equally to this work. We are also very grateful to Tomas Larsson and Marina Panova for their bioinformatic analyses on the genome and the annotation. The bioinformatic analyses were performed on resources at the University of Sheffield’s High Performance Computing cluster, ShARC. We thank two anonymous reviewers for helpful comments on a previous version.","publication":"Journal of Evolutionary Biology","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","quality_controlled":"1"}