{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T02:51:33Z","timestamp":1791427893098,"version":"4.3.3"},"reference-count":75,"publisher":"Wiley","issue":"9","license":[{"start":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T00:00:00Z","timestamp":1789603200000},"content-version":"vor","delay-in-days":16,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Ecology and Evolution"],"published-print":{"date-parts":[[2026,9]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Isoetes<\/jats:italic>\n                    is one of the most ancient extant vascular plant genera and represents a distinct evolutionary lineage within lycophytes. Its chloroplast genome preserves molecular signatures relevant to early land plant evolution. However, the evolutionary forces shaping codon usage bias (CUB) in\n                    <jats:italic>Isoetes<\/jats:italic>\n                    chloroplast genomes remain poorly characterized. Here, we analyzed the chloroplast genomes of 60\n                    <jats:italic>Isoetes<\/jats:italic>\n                    species to characterize CUB patterns and disentangle the contributions of mutation pressure and natural selection to chloroplast genome evolution in this basal vascular plant lineage. Chloroplast genome structure was highly conserved across species, with genome sizes of 142,880\u2009bp to 145,535\u2009bp and GC contents ranging from 37.56% to 38.18%. Parity rule 2 (PR2) plot analysis revealed a pronounced T\/G bias at the third codon position, whereas neutrality plot analysis revealed no significant correlation between GC3 and GC12. All preferred codons (RSCU &gt;\u20091) terminated in A or U, consistent with an AT\u2010ending preference. Simple sequence repeat (SSR) analysis revealed that SSRs are primarily distributed in intergenic regions, with mononucleotide repeats predominating, suggesting valuable molecular markers for phylogenetic studies. Our findings indicate that\n                    <jats:italic>Isoetes<\/jats:italic>\n                    chloroplast genomes exhibit weak but structured codon usage bias. Mutation pressure appears to be the dominant force establishing the AT\u2010rich compositional background, whereas natural selection acts in a gene\u2010specific manner, mainly through purifying selection and functional constraints on particular chloroplast genes. These results provide new insights into chloroplast genome evolution in basal vascular plants and highlight the combined effects of mutational bias and selective constraints on codon usage evolution. Unlike most previous chloroplast CUB studies focused on angiosperms, this genus\u2010wide analysis of\n                    <jats:italic>Isoetes<\/jats:italic>\n                    provides insight into codon usage evolution in a basal lycophyte lineage and suggests potential associations among CUB patterns, plastome conservation, functional constraints, and gene\u2010level evolutionary dynamics.\n                  <\/jats:p>","DOI":"10.1002\/ece3.74216","type":"journal-article","created":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T01:47:54Z","timestamp":1789696074000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Mutation Pressure and Gene\u2010Specific Selection Shape Codon Usage Bias in the Chloroplast Genomes of\n                    <i>Isoetes<\/i>\n                    , an Ancient Aquatic Vascular Plant Lineage"],"prefix":"10.1002","volume":"16","author":[{"given":"Boxiong","family":"Li","sequence":"first","affiliation":[{"name":"School of Grassland Science Beijing Forestry University  Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Xue","sequence":"additional","affiliation":[{"name":"School of Grassland Science Beijing Forestry University  Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dingqi","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Grassland Science Beijing Forestry University  Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guy","family":"Smagghe","sequence":"additional","affiliation":[{"name":"Department of Biology Vrije Universiteit Brussel (VUB)  Brussels Belgium"},{"name":"Institute of Entomology Guizhou University  Guiyang China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shixiong","family":"Liang","sequence":"additional","affiliation":[{"name":"School of Grassland Science Beijing Forestry University  Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shujing","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Grassland Science Beijing Forestry University  Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuye","family":"Ge","sequence":"additional","affiliation":[{"name":"School of Grassland Science Beijing Forestry University  Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zubaidai","family":"Aimaitijiang","sequence":"additional","affiliation":[{"name":"School of Grassland Science Beijing Forestry University  Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8741-5951","authenticated-orcid":false,"given":"Yunpeng","family":"Gai","sequence":"additional","affiliation":[{"name":"School of Grassland Science Beijing Forestry University  Beijing 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