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Panagrolaimid nematode species display different modes of reproduction. Sexual reproduction with distinct males and females, asexual reproduction through parthenogenesis in the genus <jats:italic>Panagrolaimus<\/jats:italic>, and hermaphroditism in <jats:italic>Propanagrolaimus<\/jats:italic>. Here, we compared genomic features of free\u2010living nematodes in populations and species isolated from geographically distant regions to study diversity, and genome\u2010wide differentiation under different modes of reproduction. We firstly estimated genome\u2010wide spontaneous mutation rates in a triploid parthenogenetic <jats:italic>Panagrolaimus<\/jats:italic>, and a diploid hermaphroditic <jats:italic>Propanagrolaimus<\/jats:italic> via long\u2010term mutation accumulation lines. Secondly, we calculated population genetic parameters including nucleotide diversity, and fixation index (<jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub>) between populations of asexually and sexually reproducing nematodes. Thirdly, we used phylogenetic network methods on sexually and asexually reproducing <jats:italic>Panagrolaimus<\/jats:italic> populations to understand evolutionary relationships between them. The estimated mutation rate was slightly lower for the asexual population, as expected for taxa with this reproductive mode. Natural polyploid asexual populations revealed higher nucleotide diversity. Despite their common ancestor, a gene network revealed a high level of genetic differentiation among asexual populations. The elevated heterozygosity found in the triploid parthenogens could be explained by the third genome copy. Given their tendentially lower mutation rates it can be hypothesized that this is part of the mechanism to evade Muller's ratchet. Our findings in parthenogenetic triploid nematode populations seem to challenge common expectations of evolution under asexuality.<\/jats:p>","DOI":"10.1002\/ece3.10831","type":"journal-article","created":{"date-parts":[[2024,1,8]],"date-time":"2024-01-08T02:45:40Z","timestamp":1704681940000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Parthenogenomics: Insights on mutation rates and nucleotide diversity in parthenogenetic <i>Panagrolaimus<\/i> nematodes"],"prefix":"10.1002","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0906-8373","authenticated-orcid":false,"given":"Laura I.","family":"Villegas","sequence":"first","affiliation":[{"name":"Institute of Zoology University of Cologne  K\u00f6ln Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Ferretti","sequence":"additional","affiliation":[{"name":"Big Data Institute University of Oxford  Oxford UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Wiehe","sequence":"additional","affiliation":[{"name":"Institute for Genetics University of Cologne  K\u00f6ln Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ann\u2010Marie","family":"Waldvogel","sequence":"additional","affiliation":[{"name":"Institute of Zoology University of Cologne  K\u00f6ln Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philipp H.","family":"Schiffer","sequence":"additional","affiliation":[{"name":"Institute of Zoology University of Cologne  K\u00f6ln Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,1,7]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.4102\/ajlm.v9i1.1340"},{"key":"e_1_2_9_3_1","unstructured":"Andrews S.(2010).Fastqc.https:\/\/qubeshub.org\/resources\/fastqc."},{"key":"e_1_2_9_4_1","volume-title":"Genomics in the cloud: Using Docker, GATK, and WDL in Terra","author":"Auwera G. V. D.","year":"2020"},{"key":"e_1_2_9_5_1","unstructured":"B\u00e5\u00e5th R.(2014).Bayesian first aid: A package that implements Bayesian alternatives to the classical *.test functions in r. 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Misra S. Li H. &Aluru S.(2019).Efficient architecture\u2010aware acceleration of BWA\u2010MEM for multicore systems. In 2019 IEEE International Parallel And Distributed Processing Symposium (IPDPS) (pp. 314\u2013324). Rio de Janeiro Brazil: IEEE.https:\/\/ieeexplore.ieee.org\/document\/8820962\/(Backup Publisher: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS))https:\/\/doi.org\/10.1109\/IPDPS.2019.00041","DOI":"10.1109\/IPDPS.2019.00041"},{"key":"e_1_2_9_80_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-24277-4"},{"key":"e_1_2_9_81_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty165"},{"key":"e_1_2_9_82_1","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/16.2.97"},{"key":"e_1_2_9_83_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt593"},{"key":"e_1_2_9_84_1","doi-asserted-by":"publisher","DOI":"10.1186\/1756\u20103305\u20106\u2010233"}],"container-title":["Ecology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/ece3.10831","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,30]],"date-time":"2024-01-30T01:50:25Z","timestamp":1706579425000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/ece3.10831"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1]]},"references-count":83,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,1]]}},"alternative-id":["10.1002\/ece3.10831"],"URL":"https:\/\/doi.org\/10.1002\/ece3.10831","archive":["Portico"],"relation":{},"ISSN":["2045-7758","2045-7758"],"issn-type":[{"value":"2045-7758","type":"print"},{"value":"2045-7758","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,1]]},"assertion":[{"value":"2023-09-20","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-12-13","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-01-07","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e10831"}}