biostudies-literatureCui YShanghai Municipal Science and Technology Major ProjectKey Research Program of the Chinese Academy of SciencesMedical Research CouncilNational Natural Science Foundation of ChinaNational Key Program for Infectious Diseases of ChinaSanming Project of Medicine in ShenzhenNational Key Research and Development Program of Chinae54136https://www.ebi.ac.uk/biostudies/studies/S-EPMC7101233biostudies-literatureUnknown9Investigating fitness interactions in natural populations remains a considerable challenge. We take advantage of the unique population structure of <i>Vibrio parahaemolyticus</i>, a bacterial pathogen of humans and shrimp, to perform a genome-wide screen for coadapted genetic elements. We identified 90 interaction groups (IGs) involving 1,560 coding genes. 82 IGs are between accessory genes, many of which have functions related to carbohydrate transport and metabolism. Only 8 involve both core and accessory genomes. The largest includes 1,540 SNPs in 82 genes and 338 accessory genome elements, many involved in lateral flagella and cell wall biogenesis. The interactions have a complex hierarchical structure encoding at least four distinct ecological strategies. One strategy involves a divergent profile in multiple genome regions, while the others involve fewer genes and are more plastic. Our results imply that most genetic alliances are ephemeral but that increasingly complex strategies can evolve and eventually cause speciation.eLifeThe landscape of coadaptation in &lt;i&gt;Vibrio parahaemolyticus&lt;/i&gt;.PMC71012332018ZX10714-0022017YFC1601503ZDRW-ZS-2017-1SZSM2018110712018YFC160390231770001MR/M501608/12019SHZDZX022018ZX10101003Qiu HCui YYang RWang HYang CFalush DfalseThe landscape of coadaptation in &lt;i&gt;Vibrio parahaemolyticus&lt;/i&gt;.Investigating fitness interactions in natural populations remains a considerable challenge. We take advantage of the unique population structure of <i>Vibrio parahaemolyticus</i>, a bacterial pathogen of humans and shrimp, to perform a genome-wide screen for coadapted genetic elements. We identified 90 interaction groups (IGs) involving 1,560 coding genes. 82 IGs are between accessory genes, many of which have functions related to carbohydrate transport and metabolism. Only 8 involve both core and accessory genomes. The largest includes 1,540 SNPs in 82 genes and 338 accessory genome elements, many involved in lateral flagella and cell wall biogenesis. The interactions have a complex hierarchical structure encoding at least four distinct ecological strategies. One strategy involves a divergent profile in multiple genome regions, while the others involve fewer genes and are more plastic. Our results imply that most genetic alliances are ephemeral but that increasingly complex strategies can evolve and eventually cause speciation.2020-01-01T00:00:00Z2020 Mar2026-05-04T03:36:31.507Z2025-05-29T19:04:45.327ZS-EPMC71012333219566310.7554/eLife.54136