{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T12:59:17Z","timestamp":1791377957770,"version":"4.3.2"},"reference-count":104,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T00:00:00Z","timestamp":1785196800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100020414","name":"NSF","doi-asserted-by":"publisher","award":["2224885"],"award-info":[{"award-number":["2224885"]}],"id":[{"id":"10.13039\/501100020414","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000854","name":"HFSP","doi-asserted-by":"publisher","award":["RGP0001\/2019"],"award-info":[{"award-number":["RGP0001\/2019"]}],"id":[{"id":"10.13039\/501100000854","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"NIEHS","doi-asserted-by":"publisher","award":["R01ES029930"],"award-info":[{"award-number":["R01ES029930"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"NIEHS","doi-asserted-by":"publisher","award":["R50ES037948"],"award-info":[{"award-number":["R50ES037948"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004794","name":"Centre National de la Recherche Scientifique","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004794","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007175","name":"CNRS","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007175","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001677","name":"Institut national de la sant\u00e9 et de la recherche m\u00e9dicale","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001677","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100013371","name":"Universit\u00e9 C\u00f4te d\u2019Azur","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013371","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012264","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012264","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35 GM141906"],"award-info":[{"award-number":["R35 GM141906"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Biodiversity Research Center"},{"DOI":"10.13039\/501100001869","name":"Academia Sinica, Taiwan","doi-asserted-by":"publisher","award":["103-CDA-L01"],"award-info":[{"award-number":["103-CDA-L01"]}],"id":[{"id":"10.13039\/501100001869","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100020950","name":"National Science and Technology Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100020950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017492","name":"NSC","doi-asserted-by":"publisher","award":["100-2311-B-001-015-MY3"],"award-info":[{"award-number":["100-2311-B-001-015-MY3"]}],"id":[{"id":"10.13039\/501100017492","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Self-fertilization reduces genetic diversity compared to outcrossing and hypothetically decreases the ability to adapt to diverse environments. Among Caenorhabditis nematodes, self-fertilization evolved three times independently in Caenorhabditis elegans, Caenorhabditis briggsae, and the more recently discovered Caenorhabditis tropicalis. To survey C. tropicalis genetic relatedness, the influence of geography and niche on species-wide variation, and the signatures of selection, we collected 785 wild strains, sequenced their genomes, and identified 622 distinct genotypes (isotypes). In contrast to C. elegans and C. briggsae, C. tropicalis relatedness shows substantial association with geography and no transcontinental selective sweeps or broadly sampled isotypes. Populations from the Hawaiian Islands or Taiwan harbor more genetic variation than populations from the Caribbean or Americas, suggesting a Pacific species origin similar to other members of the Elegans subclade. Punctuated genomic regions of extreme genetic variation pervade the genome. These hyper-divergent regions (HDRs) comprise less than 6% of the reference genome despite harboring 73% of all variant sites on average and are enriched for genes likely involved in environmental adaptation. HDRs represent a shared genomic feature of self-fertilizing Caenorhabditis nematodes despite their independent evolutionary origins and suggest a mechanism to explain worldwide distributions despite low species-wide levels of genetic variation.<\/jats:p>","DOI":"10.1093\/genetics\/iyag196","type":"journal-article","created":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T04:53:31Z","timestamp":1785214411000},"source":"Crossref","is-referenced-by-count":0,"title":["Global genomic diversity of the selfing nematode\n                    <i>Caenorhabditis tropicalis<\/i>\n                    correlates with geography"],"prefix":"10.1093","volume":"234","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5794-2144","authenticated-orcid":false,"given":"Bowen","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Biology, Johns Hopkins University , Baltimore, MD 21218 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas D","family":"Moya","sequence":"additional","affiliation":[{"name":"Department of Biology, Johns Hopkins University , Baltimore, MD 21218 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robyn E","family":"Tanny","sequence":"additional","affiliation":[{"name":"Department of Biology, Johns Hopkins University , Baltimore, MD 21218 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael E G","family":"Sauria","sequence":"additional","affiliation":[{"name":"Department of Biology, Johns Hopkins University , Baltimore, MD 21218 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-1373-183X","authenticated-orcid":false,"given":"Lance M","family":"O\u2019Connor","sequence":"additional","affiliation":[{"name":"Department of Biology, Johns Hopkins University , Baltimore, MD 21218 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayeh","family":"Khorshidian","sequence":"additional","affiliation":[{"name":"Department of Biology, Johns Hopkins University , Baltimore, MD 21218 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan","family":"McKeown","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, Northwestern University , Evanston, IL 60208 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lewis","family":"Stevens","sequence":"additional","affiliation":[{"name":"Tree of Life, Wellcome Sanger Institute , Hinxton CB10 1RQ ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire","family":"Buchanan","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, Northwestern University , Evanston, IL 60208 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5645-4154","authenticated-orcid":false,"given":"Timothy A","family":"Crombie","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, Northwestern University , Evanston, IL 60208 ,","place":["United States"]},{"name":"Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology , Melbourne, FL 32901 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clayton","family":"Dilks","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, Northwestern University , Evanston, IL 60208 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn S","family":"Evans","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, Northwestern University , Evanston, IL 60208 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3347-562X","authenticated-orcid":false,"given":"Daniel E","family":"Cook","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, Northwestern University , Evanston, IL 60208 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gaotian","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, Northwestern University , Evanston, IL 60208 ,","place":["United States"]},{"name":"Institut de Biologie de l'Ecole Normale Sup\u00e9rieure, CNRS, Inserm , Paris 75005 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Loraina A","family":"Stinson","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, Northwestern University , Evanston, IL 60208 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole M","family":"Roberto","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, Northwestern University , Evanston, IL 60208 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0546-8484","authenticated-orcid":false,"given":"Daehan","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, Northwestern University , Evanston, IL 60208 ,","place":["United States"]},{"name":"Department of Biological Sciences, Sungkyunkwan University , Suwon 16419 ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Zdraljevic","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, Northwestern University , Evanston, IL 60208 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlie","family":"Gosse","sequence":"additional","affiliation":[{"name":"Institut de Biologie de l'Ecole Normale Sup\u00e9rieure, CNRS, Inserm , Paris 75005 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clotilde","family":"Gimond","sequence":"additional","affiliation":[{"name":"Universit\u00e9 C\u00f4te d\u2019Azur, CNRS, Inserm, IBV Institut de Biologie Valrose, , Nice 06108 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mu-En","family":"Chen","sequence":"additional","affiliation":[{"name":"Biodiversity Program, Taiwan International Graduate Program, Academia Sinica , Taipei 115201 ,","place":["Taiwan"]},{"name":"Department of Life Science, National Taiwan Normal University , Taipei 116059 ,","place":["Taiwan"]},{"name":"Biodiversity Research Center, Academia Sinica , Taipei 115201 ,","place":["Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3462-9419","authenticated-orcid":false,"given":"Viet Dai","family":"Dang","sequence":"additional","affiliation":[{"name":"Institute of Advanced Technology, Vietnam Academy of Science and Technology , Hanoi ,","place":["Vietnam"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6179-775X","authenticated-orcid":false,"given":"John","family":"Wang","sequence":"additional","affiliation":[{"name":"Biodiversity Research Center, Academia Sinica , Taipei 115201 ,","place":["Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7141-0013","authenticated-orcid":false,"given":"Asher D","family":"Cutter","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, University of Toronto , Toronto, Ontario M5S3B2 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew V","family":"Rockman","sequence":"additional","affiliation":[{"name":"Department of Biology and Center for Genomics & Systems Biology, New York University , New York, NY 10003 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie-Anne","family":"F\u00e9lix","sequence":"additional","affiliation":[{"name":"Institut de Biologie de l'Ecole Normale Sup\u00e9rieure, CNRS, Inserm , Paris 75005 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Braendle","sequence":"additional","affiliation":[{"name":"Universit\u00e9 C\u00f4te d\u2019Azur, CNRS, Inserm, IBV Institut de Biologie Valrose, , Nice 06108 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik C","family":"Andersen","sequence":"additional","affiliation":[{"name":"Department of Biology, Johns Hopkins University , Baltimore, MD 21218 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,7,28]]},"reference":[{"key":"2026100708022988100_iyag196-B1","doi-asserted-by":"publisher","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Res"},{"key":"2026100708022988100_iyag196-B2","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1038\/ng.1050","article-title":"Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity","volume":"44","author":"Andersen","year":"2012","journal-title":"Nat Genet"},{"key":"2026100708022988100_iyag196-B3","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004156","article-title":"A variant in the neuropeptide receptor npr-1 is a major determinant of Caenorhabditis elegans growth and physiology","volume":"10","author":"Andersen","year":"2014","journal-title":"PLoS Genet"},{"key":"2026100708022988100_iyag196-B4","doi-asserted-by":"publisher","first-page":"990","DOI":"10.1016\/j.cub.2020.12.013","article-title":"Ubiquitous selfish toxin-antidote elements in Caenorhabditis Species","volume":"31","author":"Ben-David","year":"2021","journal-title":"Curr Biol"},{"key":"2026100708022988100_iyag196-B5","doi-asserted-by":"publisher","first-page":"1051","DOI":"10.1126\/science.aan0621","article-title":"A maternal-effect selfish genetic element in Caenorhabditis elegans","volume":"356","author":"Ben-David","year":"2017","journal-title":"Science"},{"key":"2026100708022988100_iyag196-B6","doi-asserted-by":"publisher","first-page":"1699","DOI":"10.1093\/bioinformatics\/btq268","article-title":"Gap5--editing the billion fragment sequence assembly","volume":"26","author":"Bonfield","year":"2010","journal-title":"Bioinformatics"},{"key":"2026100708022988100_iyag196-B7","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive protein alignments at tree-of-life scale using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nat Methods"},{"key":"2026100708022988100_iyag196-B8","doi-asserted-by":"publisher","first-page":"1361","DOI":"10.1534\/g3.119.400908","article-title":"BlobToolKit - interactive quality assessment of genome assemblies","volume":"10","author":"Challis","year":"2020","journal-title":"G3 (Bethesda)"},{"key":"2026100708022988100_iyag196-B9","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"Gigascience"},{"key":"2026100708022988100_iyag196-B10","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1016\/S0959-437X(00)00254-9","article-title":"Breeding systems and genome evolution","volume":"11","author":"Charlesworth","year":"2001","journal-title":"Curr Opin Genet Dev"},{"key":"2026100708022988100_iyag196-B11","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.107","article-title":"Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp","volume":"2","author":"Chen","year":"2023","journal-title":"Imeta"},{"key":"2026100708022988100_iyag196-B12","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","article-title":"Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm","volume":"18","author":"Cheng","year":"2021","journal-title":"Nat Methods"},{"key":"2026100708022988100_iyag196-B13","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1093\/jeb\/voaf009","article-title":"Perspectives on mating-system evolution: comparing concepts in plants and animals","volume":"38","author":"Clo","year":"2025","journal-title":"J Evol Biol"},{"key":"2026100708022988100_iyag196-B14","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1534\/genetics.116.191148","article-title":"The genetic basis of natural variation in Caenorhabditis elegans telomere length","volume":"204","author":"Cook","year":"2016","journal-title":"Genetics"},{"key":"2026100708022988100_iyag196-B15","author":"Cook","year":"2020"},{"key":"2026100708022988100_iyag196-B16","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1038\/nature14450","article-title":"Condensin-driven remodelling of X chromosome topology during dosage compensation","volume":"523","author":"Crane","year":"2015","journal-title":"Nature"},{"key":"2026100708022988100_iyag196-B17","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.50465","article-title":"Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations","volume":"8","author":"Crombie","year":"2019","journal-title":"Elife"},{"key":"2026100708022988100_iyag196-B18","doi-asserted-by":"publisher","first-page":"2327","DOI":"10.1111\/mec.16400","article-title":"Local adaptation and spatiotemporal patterns of genetic diversity revealed by repeated sampling of Caenorhabditis elegans across the Hawaiian Islands","volume":"31","author":"Crombie","year":"2022","journal-title":"Mol Ecol"},{"key":"2026100708022988100_iyag196-B19","doi-asserted-by":"publisher","first-page":"D850","DOI":"10.1093\/nar\/gkad887","article-title":"CaeNDR, the Caenorhabditis natural diversity resource","volume":"52","author":"Crombie","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026100708022988100_iyag196-B20","doi-asserted-by":"publisher","first-page":"1080","DOI":"10.1111\/nph.16075","article-title":"Reproductive transitions in plants and animals: selfing syndrome, sexual selection and speciation","volume":"224","author":"Cutter","year":"2019","journal-title":"New Phytol"},{"key":"2026100708022988100_iyag196-B21","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1038\/nrg3425","article-title":"Genomic signatures of selection at linked sites: unifying the disparity among species","volume":"14","author":"Cutter","year":"2013","journal-title":"Nat Rev Genet"},{"key":"2026100708022988100_iyag196-B22","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"2026100708022988100_iyag196-B23","doi-asserted-by":"publisher","first-page":"Unit 10.3","DOI":"10.1002\/0471250953.bi1003s00","article-title":"Using MUMmer to identify similar regions in large sequence sets","volume":"Chapter 10","author":"Delcher","year":"2003","journal-title":"Curr Protoc Bioinformatics"},{"key":"2026100708022988100_iyag196-B24","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2026100708022988100_iyag196-B25","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1126\/science.aal3327","article-title":"De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds","volume":"356","author":"Dudchenko","year":"2017","journal-title":"Science"},{"key":"2026100708022988100_iyag196-B26","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","article-title":"Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst"},{"key":"2026100708022988100_iyag196-B27","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1002\/mrd.22668","article-title":"\u201cThe persistence of memory\u201d-hermaphroditism in nematodes","volume":"84","author":"Ellis","year":"2017","journal-title":"Mol Reprod Dev"},{"key":"2026100708022988100_iyag196-B28","doi-asserted-by":"publisher","author":"Emms","year":"2026","DOI":"10.1038\/s41592-026-03126-6"},{"key":"2026100708022988100_iyag196-B29","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1534\/g3.116.035162","article-title":"Correlations of genotype with climate parameters suggest Caenorhabditis elegans niche adaptations","volume":"7","author":"Evans","year":"2017","journal-title":"G3 (Bethesda)"},{"key":"2026100708022988100_iyag196-B30","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/1471-2148-13-10","article-title":"Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest","volume":"13","author":"F\u00e9lix","year":"2013","journal-title":"BMC Evol Biol"},{"key":"2026100708022988100_iyag196-B31","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0094723","article-title":"A streamlined system for species diagnosis in Caenorhabditis (Nematoda: Rhabditidae) with name designations for 15 distinct biological species","volume":"9","author":"F\u00e9lix","year":"2014","journal-title":"PLoS One"},{"key":"2026100708022988100_iyag196-B32","unstructured":"Felsenstein \u00a0J\n          . 1993. PHYLIP (phylogeny inference package), version 3.5 c. Joseph Felsenstein. https:\/\/csbf.stanford.edu\/phylip\/"},{"key":"2026100708022988100_iyag196-B33","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12898-017-0150-z","article-title":"Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes","volume":"17","author":"Ferrari","year":"2017","journal-title":"BMC Ecol"},{"key":"2026100708022988100_iyag196-B34","doi-asserted-by":"publisher","first-page":"1459","DOI":"10.1002\/joc.4437","article-title":"Comparison of geostatistical approaches to spatially interpolate month-year rainfall for the Hawaiian Islands","volume":"36","author":"Frazier","year":"2016","journal-title":"Int J Climatol"},{"key":"2026100708022988100_iyag196-B35","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.05849","article-title":"C. elegans outside the Petri dish","volume":"4","author":"Fr\u00e9zal","year":"2015","journal-title":"Elife"},{"key":"2026100708022988100_iyag196-B36","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1101\/gr.278090.123","article-title":"BRAKER3: fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA","volume":"34","author":"Gabriel","year":"2023","journal-title":"Genome Res"},{"key":"2026100708022988100_iyag196-B37","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1175\/BAMS-D-11-00228.1","article-title":"Online rainfall atlas of Hawai\u2018i","volume":"94","author":"Giambelluca","year":"2013","journal-title":"Bull Am Meteorol Soc"},{"key":"2026100708022988100_iyag196-B38","doi-asserted-by":"publisher","first-page":"3087","DOI":"10.1111\/evo.12203","article-title":"Outbreeding depression with low genetic variation in selfing Caenorhabditis nematodes","volume":"67","author":"Gimond","year":"2013","journal-title":"Evolution"},{"key":"2026100708022988100_iyag196-B39","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1126\/science.1194513","article-title":"Species selection maintains self-incompatibility","volume":"330","author":"Goldberg","year":"2010","journal-title":"Science"},{"key":"2026100708022988100_iyag196-B40","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.43","article-title":"Complex heatmap visualization","volume":"1","author":"Gu","year":"2022","journal-title":"Imeta"},{"key":"2026100708022988100_iyag196-B41","doi-asserted-by":"publisher","first-page":"420","DOI":"10.1016\/j.tig.2017.04.002","article-title":"The evolutionary interplay between adaptation and self-fertilization","volume":"33","author":"Hartfield","year":"2017","journal-title":"Trends Genet"},{"key":"2026100708022988100_iyag196-B42","doi-asserted-by":"publisher","first-page":"17758","DOI":"10.1073\/pnas.1212380109","article-title":"The great human expansion","volume":"109","author":"Henn","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026100708022988100_iyag196-B43","author":"Hijmans","year":"2024"},{"key":"2026100708022988100_iyag196-B44","author":"Hijmans","year":"2025"},{"key":"2026100708022988100_iyag196-B45","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1007\/978-1-4939-9173-0_5","article-title":"Whole-genome annotation with BRAKER","volume":"1962","author":"Hoff","year":"2019","journal-title":"Methods Mol Biol"},{"key":"2026100708022988100_iyag196-B46","unstructured":"Ortiz EM . 2019. vcf2phylip v2.0: convert a VCF matrix into several matrix formats for phylogenetic analysis. Zenodo. 10.5281\/ZENODO.1257057"},{"key":"2026100708022988100_iyag196-B47","unstructured":"Dainat J \u00a0et al \u00a02024. NBISweden\/AGAT: AGAT-v1.4.1. Zenodo. 10.5281\/ZENODO.13799920"},{"key":"2026100708022988100_iyag196-B48","unstructured":"Wan-Jyun C, Chi-Chun L, Fu-An T, An-Yu C. 2020. Using open data to establish a multi-temporal and terrestrial environmental dataset of Taiwan. Taiwan Journal of Biodiversity. [updated 2025 November 12]. https:\/\/github.com\/WanJyunChen\/Taiwan_environmental_dataset"},{"key":"2026100708022988100_iyag196-B49","doi-asserted-by":"publisher","first-page":"1773","DOI":"10.1038\/s41592-024-02406-3","article-title":"The SplitsTree app: interactive analysis and visualization using phylogenetic trees and networks","volume":"21","author":"Huson","year":"2024","journal-title":"Nat Methods"},{"key":"2026100708022988100_iyag196-B50","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1111\/nph.12182","article-title":"Is self-fertilization an evolutionary dead end?","volume":"198","author":"Igic","year":"2013","journal-title":"New Phytol"},{"key":"2026100708022988100_iyag196-B51","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"2026100708022988100_iyag196-B52","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1038\/nature01278","article-title":"Systematic functional analysis of the Caenorhabditis elegans genome using RNAi","volume":"421","author":"Kamath","year":"2003","journal-title":"Nature"},{"key":"2026100708022988100_iyag196-B53","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1186\/1471-2148-11-339","article-title":"A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits","volume":"11","author":"Kiontke","year":"2011","journal-title":"BMC Evol Biol"},{"key":"2026100708022988100_iyag196-B54","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2026100708022988100_iyag196-B55","doi-asserted-by":"publisher","first-page":"1359","DOI":"10.1111\/1755-0998.13326","article-title":"Pixy: unbiased estimation of nucleotide diversity and divergence in the presence of missing data","volume":"21","author":"Korunes","year":"2021","journal-title":"Mol Ecol Resour"},{"key":"2026100708022988100_iyag196-B56","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1186\/s13059-019-1910-1","article-title":"Transcriptome assembly from long-read RNA-seq alignments with StringTie2","volume":"20","author":"Kovaka","year":"2019","journal-title":"Genome Biol"},{"key":"2026100708022988100_iyag196-B57","doi-asserted-by":"publisher","first-page":"794","DOI":"10.1038\/s41559-021-01435-x","article-title":"Balancing selection maintains hyper-divergent haplotypes in Caenorhabditis elegans","volume":"5","author":"Lee","year":"2021","journal-title":"Nat Ecol Evol"},{"key":"2026100708022988100_iyag196-B58","author":"Li","year":"2013"},{"key":"2026100708022988100_iyag196-B59","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2026100708022988100_iyag196-B60","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2026100708022988100_iyag196-B61","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.0020166","article-title":"Inferring the demographic history and rate of adaptive substitution in Drosophila","volume":"2","author":"Li","year":"2006","journal-title":"PLoS Genet"},{"key":"2026100708022988100_iyag196-B62","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005944","article-title":"MUMmer4: a fast and versatile genome alignment system","volume":"14","author":"Mar\u00e7ais","year":"2018","journal-title":"PLoS Comput Biol"},{"key":"2026100708022988100_iyag196-B63","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2026100708022988100_iyag196-B64","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msad270","article-title":"A fast, reproducible, high-throughput variant calling workflow for population genomics","volume":"41","author":"Mirchandani","year":"2024","journal-title":"Mol Biol Evol"},{"key":"2026100708022988100_iyag196-B65","doi-asserted-by":"publisher","author":"Moya","year":"2025","DOI":"10.64898\/2025.12.08.693002"},{"key":"2026100708022988100_iyag196-B66","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1016\/j.tig.2024.11.005","article-title":"The long and short of hyperdivergent regions","volume":"41","author":"Moya","year":"2025","journal-title":"Trends Genet"},{"key":"2026100708022988100_iyag196-B67","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1038\/nature21347","article-title":"Tracing the peopling of the world through genomics","volume":"541","author":"Nielsen","year":"2017","journal-title":"Nature"},{"key":"2026100708022988100_iyag196-B68","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.62587","article-title":"Selfing is the safest sex for Caenorhabditis tropicalis","volume":"10","author":"Noble","year":"2021","journal-title":"Elife"},{"key":"2026100708022988100_iyag196-B69","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.0020190","article-title":"Population structure and eigenanalysis","volume":"2","author":"Patterson","year":"2006","journal-title":"PLoS Genet"},{"key":"2026100708022988100_iyag196-B70","doi-asserted-by":"publisher","first-page":"439","DOI":"10.32614\/RJ-2018-009","article-title":"Simple features for R: standardized support for spatial vector data","volume":"10","author":"Pebesma","year":"2018","journal-title":"R J"},{"key":"2026100708022988100_iyag196-B71","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1093\/bioinformatics\/btx699","article-title":"Mosdepth: quick coverage calculation for genomes and exomes","volume":"34","author":"Pedersen","year":"2018","journal-title":"Bioinformatics"},{"key":"2026100708022988100_iyag196-B72","doi-asserted-by":"publisher","first-page":"304","DOI":"10.12688\/f1000research.23297.1","article-title":"GFF utilities: gffRead and GffCompare","volume":"9","author":"Pertea","year":"2020","journal-title":"F1000Res"},{"key":"2026100708022988100_iyag196-B73","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1038\/s41586-018-0030-5","article-title":"Genome evolution across 1,011 Saccharomyces cerevisiae isolates","volume":"556","author":"Peter","year":"2018","journal-title":"Nature"},{"key":"2026100708022988100_iyag196-B74","author":"Picard Toolkit","year":"2019"},{"key":"2026100708022988100_iyag196-B75","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1093\/genetics\/117.2.353","article-title":"On the theory of partially inbreeding finite populations. I. Partial selfing","volume":"117","author":"Pollak","year":"1987","journal-title":"Genetics"},{"key":"2026100708022988100_iyag196-B76","doi-asserted-by":"publisher","author":"Poplin","year":"2018","DOI":"10.1101\/201178"},{"key":"2026100708022988100_iyag196-B77","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1111\/ede.12170","article-title":"Evolutionarily divergent thermal sensitivity of germline development and fertility in hermaphroditic Caenorhabditis nematodes","volume":"17","author":"Poullet","year":"2015","journal-title":"Evol Dev"},{"key":"2026100708022988100_iyag196-B78","doi-asserted-by":"publisher","first-page":"904","DOI":"10.1038\/ng1847","article-title":"Principal components analysis corrects for stratification in genome-wide association studies","volume":"38","author":"Price","year":"2006","journal-title":"Nat Genet"},{"key":"2026100708022988100_iyag196-B79","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am J Hum Genet"},{"key":"2026100708022988100_iyag196-B80","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2026100708022988100_iyag196-B81","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1186\/s13059-020-02134-9","article-title":"Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies","volume":"21","author":"Rhie","year":"2020","journal-title":"Genome Biol"},{"key":"2026100708022988100_iyag196-B82","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/genetics\/iyae175","article-title":"Parental-effect gene-drive elements under partial selfing, or why do Caenorhabditis genomes have hyperdivergent regions?","volume":"229","author":"Rockman","year":"2025","journal-title":"Genetics"},{"key":"2026100708022988100_iyag196-B83","doi-asserted-by":"publisher","first-page":"1013","DOI":"10.1093\/evolut\/qpag031","article-title":"Caenorhabditis diversity on Pohnpei, Micronesia, provides evidence that the Elegans supergroup has its roots in the Americas and diversified in the Pacific en route to Asia","volume":"80","author":"Rockman","year":"2026","journal-title":"Evolution"},{"key":"2026100708022988100_iyag196-B84","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1126\/science.1151107","article-title":"Widespread genetic incompatibility in C. elegans maintained by balancing selection","volume":"319","author":"Seidel","year":"2008","journal-title":"Science"},{"key":"2026100708022988100_iyag196-B85","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"key":"2026100708022988100_iyag196-B86","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.9124","article-title":"Caenorhabditis nematodes colonize ephemeral resource patches in neotropical forests","volume":"12","author":"Sloat","year":"2022","journal-title":"Ecol Evol"},{"key":"2026100708022988100_iyag196-B87","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evac042","article-title":"Chromosome-level reference genomes for two strains of Caenorhabditis briggsae: an improved platform for comparative genomics","volume":"14","author":"Stevens","year":"2022","journal-title":"Genome Biol Evol"},{"key":"2026100708022988100_iyag196-B88","doi-asserted-by":"publisher","first-page":"1143","DOI":"10.2307\/3558325","article-title":"Is self-fertilization an evolutionary dead end? Revisiting an old hypothesis with genetic theories and a macroevolutionary approach","volume":"88","author":"Takebayashi","year":"2001","journal-title":"Am J Bot"},{"key":"2026100708022988100_iyag196-B89","doi-asserted-by":"publisher","first-page":"2032","DOI":"10.1093\/bioinformatics\/btv098","article-title":"Sambamba: fast processing of NGS alignment formats","volume":"31","author":"Tarasov","year":"2015","journal-title":"Bioinformatics"},{"key":"2026100708022988100_iyag196-B90","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1010879","article-title":"Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes","volume":"19","author":"Teterina","year":"2023","journal-title":"PLoS Genet"},{"key":"2026100708022988100_iyag196-B91","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1101\/gr.187237.114","article-title":"Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis","volume":"25","author":"Thomas","year":"2015","journal-title":"Genome Res"},{"key":"2026100708022988100_iyag196-B92","doi-asserted-by":"publisher","first-page":"2374","DOI":"10.1038\/s41559-025-02894-2","article-title":"Recurrent evolution of selfishness from an essential tRNA synthetase in Caenorhabditis tropicalis","volume":"9","author":"Tikanova","year":"2025","journal-title":"Nat Ecol Evol"},{"key":"2026100708022988100_iyag196-B93","doi-asserted-by":"publisher","first-page":"D609","DOI":"10.1093\/nar\/gkae1010","article-title":"UniProt: the universal protein knowledgebase in 2025","volume":"53","author":"UniProt Consortium","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026100708022988100_iyag196-B94","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1101\/gr.214270.116","article-title":"Fast and accurate de novo genome assembly from long uncorrected reads","volume":"27","author":"Vaser","year":"2017","journal-title":"Genome Res"},{"key":"2026100708022988100_iyag196-B95","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0272843","article-title":"Genetic architecture and temporal analysis of Caenorhabditis briggsae hybrid developmental delay","volume":"17","author":"Velazco-Cruz","year":"2022","journal-title":"PLoS One"},{"key":"2026100708022988100_iyag196-B96","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PLoS One"},{"key":"2026100708022988100_iyag196-B97","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1038\/hdy.2016.43","article-title":"Prediction and estimation of effective population size","volume":"117","author":"Wang","year":"2016","journal-title":"Heredity (Edinb)."},{"key":"2026100708022988100_iyag196-B98","doi-asserted-by":"publisher","DOI":"10.1126\/science.ade0705","article-title":"Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities","volume":"380","author":"Widen","year":"2023","journal-title":"Science"},{"key":"2026100708022988100_iyag196-B99","doi-asserted-by":"publisher","DOI":"10.1016\/j.xinn.2021.100141","article-title":"clusterProfiler 4.0: a universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation (Camb)"},{"key":"2026100708022988100_iyag196-B100","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2603772123","article-title":"Sequential evolution of antidote and toxin links genetic incompatibility with immune responses","volume":"123","author":"Xie","year":"2026","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026100708022988100_iyag196-B101","doi-asserted-by":"publisher","first-page":"3292","DOI":"10.1038\/s41596-024-01020-z","article-title":"Using clusterProfiler to characterize multiomics data","volume":"19","author":"Xu","year":"2024","journal-title":"Nat Protoc"},{"key":"2026100708022988100_iyag196-B102","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1126\/science.aao0827","article-title":"Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins","volume":"359","author":"Yin","year":"2018","journal-title":"Science"},{"key":"2026100708022988100_iyag196-B103","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"Ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"Yu","year":"2017","journal-title":"Methods Ecol Evol"},{"key":"2026100708022988100_iyag196-B104","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"}],"container-title":["GENETICS"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/genetics\/advance-article-pdf\/doi\/10.1093\/genetics\/iyag196\/70230135\/iyag196.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/genetics\/article-pdf\/234\/2\/iyag196\/70230135\/iyag196.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/genetics\/article-pdf\/234\/2\/iyag196\/70230135\/iyag196.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T12:02:44Z","timestamp":1791374564000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/genetics\/article\/doi\/10.1093\/genetics\/iyag196\/8743783"}},"subtitle":[],"editor":[{"given":"A","family":"Sweigart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,7,28]]},"references-count":104,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,7,28]]},"published-print":{"date-parts":[[2026,10,7]]}},"URL":"https:\/\/doi.org\/10.1093\/genetics\/iyag196","relation":{},"ISSN":["1943-2631"],"issn-type":[{"value":"1943-2631","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,10]]},"published":{"date-parts":[[2026,7,28]]},"article-number":"iyag196"}}