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Heterogeneous genomic differentiation between diverging taxa is commonly documented, with genomic regions of high differentiation interpreted as resulting from differential gene flow, linked selection and reduced recombination rates. Disentangling the roles of each of these non\u2010exclusive processes in shaping genome\u2010wide patterns of divergence is challenging but will enhance our knowledge of the repeatability of genomic landscapes across taxa. Here, we combine whole\u2010genome resequencing and genome feature data to investigate the processes shaping the genomic landscape of differentiation for a sister\u2010species pair of haplodiploid pine sawflies, <jats:italic>Neodiprion lecontei<\/jats:italic> and <jats:italic>Neodiprion pinetum<\/jats:italic>. We find genome\u2010wide correlations between genome features and summary statistics are consistent with pervasive linked selection, with patterns of diversity and divergence more consistently predicted by exon density and recombination rate than the neutral mutation rate (approximated by dS). We also find that both global and local patterns of <jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub>, <jats:italic>d<\/jats:italic><jats:sub>XY<\/jats:sub> and <jats:italic>\u03c0<\/jats:italic> provide strong support for recurrent selection as the primary selective process shaping variation across pine sawfly genomes, with some contribution from balancing selection and lineage\u2010specific linked selection. Because inheritance patterns for haplodiploid genomes are analogous to those of sex chromosomes, we hypothesize that haplodiploids may be especially prone to recurrent selection, even if gene flow occurred throughout divergence. Overall, our study helps fill an important taxonomic gap in the genomic landscape literature and contributes to our understanding of the processes that shape genome\u2010wide patterns of genetic variation.<\/jats:p>","DOI":"10.1111\/mec.17509","type":"journal-article","created":{"date-parts":[[2024,8,21]],"date-time":"2024-08-21T18:52:05Z","timestamp":1724266325000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Recurrent selection shapes the genomic landscape of differentiation between a pair of host\u2010specialized haplodiploids that diverged with gene flow"],"prefix":"10.1111","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1911-0344","authenticated-orcid":false,"given":"Ashleigh N.","family":"Glover","sequence":"first","affiliation":[{"name":"Department of Biology University of Kentucky  Lexington Kentucky USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vitor C.","family":"Sousa","sequence":"additional","affiliation":[{"name":"Department of Animal Biology, CE3C \u2013 Center for Ecology, Evolution and Environmental Changes, Faculdade de Ci\u00eancias da Universidade de Lisboa University of Lisbon, Lisbon  Lisboa Portugal"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ryan D.","family":"Ridenbaugh","sequence":"additional","affiliation":[{"name":"Department of Biology University of Kentucky  Lexington Kentucky USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sheina B.","family":"Sim","sequence":"additional","affiliation":[{"name":"USDA\u2010ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center Tropical Pest Genetics and Molecular Biology Research Unit  Hilo Hawaii USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Scott M.","family":"Geib","sequence":"additional","affiliation":[{"name":"USDA\u2010ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center Tropical Pest Genetics and Molecular Biology Research Unit  Hilo Hawaii USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5715-456X","authenticated-orcid":false,"given":"Catherine R.","family":"Linnen","sequence":"additional","affiliation":[{"name":"Department of Biology University of Kentucky  Lexington Kentucky USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2024,8,20]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1416622112"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1017\/S0016672300026550"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0050310"},{"key":"e_1_2_10_5_1","first-page":"1","article-title":"From genes to species: Ecological speciation with gene flow in Neodiprion pinetum and N.\u2009lecontei","volume":"62","author":"Bendall E. 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