Evolutionary Applications最新文献

{"title":"Adaptive Genomic Variation Across Sub-Alpine Climates in a Keystone Forest Tree: Implications for Seed Sourcing for Restoration in a Changing Climate","authors":"John W. Whale,&nbsp;Katarina C. Stuart,&nbsp;Jessica Bruce,&nbsp;Melinda Pickup,&nbsp;David L. Field","doi":"10.1111/eva.70339","DOIUrl":"https://doi.org/10.1111/eva.70339","url":null,"abstract":"<p>A major challenge for ecological restoration is seed sourcing decisions that ensure that restored populations have the adaptive variation for current and future environments. This is increasingly important for alpine and sub-alpine communities where climate change is predicted to be rapid and drive shifts in selective pressures. Selecting source populations representing future climates is an evolutionary-based strategy for increasing adaptive capacity, but requires an understanding of population genetic structure, identification of putatively adaptive genomic variation and an assessment of how these change across the landscape. Using 3978 single-nucleotide polymorphism (SNP) markers we assessed the population structure and diversity of 33 sampled populations of <i>Eucalyptus delegatensis</i> from across its distribution, including 22 populations from the mainland (<i>E. delegatensis</i> subsp. <i>delegatensis</i>) and 11 from Tasmania (<i>E. delegatensis</i> subsp. <i>tasmaniensis</i>). Genotype-environment association (GEA) analysis identified strong genetic associations with seasonal climate variables, particularly minimum temperature of the coldest month, and revealed a parallel cline at one outlier locus across the mainland and Tasmanian range, consistent with independent sorting of standing variation along environmental gradients in both subspecies. By projecting genetic offset under future climate change scenarios, we identify regions of the species' range most vulnerable to projected change; despite this, seed-sourcing projections suggest that suitable future climate matches may be available for most of the range. Together, these findings demonstrate the value of comparative GEA approaches in validating outlier loci, and show that even in regions of projected dramatic environmental shifts, such as Australian alpine environments, landscape genomic analyses can help identify potential suitable seed sources for climate-resilient ecological restoration.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 11","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70339","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149356705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Eco-Evolutionary Dynamics of Anadromous Alewife Restoration in a Whole-Ecosystem Experiment","authors":"Kerry Reid,&nbsp;Katherine A. Littrell,&nbsp;Andrew D. MacDonald,&nbsp;Kevin Job,&nbsp;Stephen R. Gephard,&nbsp;John Carlos Garza,&nbsp;David M. Post,&nbsp;Eric P. Palkovacs","doi":"10.1111/eva.70350","DOIUrl":"https://doi.org/10.1111/eva.70350","url":null,"abstract":"<p>Restoration efforts can serve as opportunities to conduct ecological and evolutionary experiments at the whole-ecosystem scale. We evaluated the eco-evolutionary dynamics of restoring anadromous alewives (<i>Alosa pseudoharengus</i>) to a lake occupied by a well-established landlocked population isolated ca. 350 years ago. The restoration of Rogers Lake involved the construction of fishways on all downstream dams and the annual stocking of anadromous adults. Throughout the restoration project, we quantified juvenile recruitment, abundance, and growth, as well as hybridization and introgression with the landlocked population. Restoration led to the annual production of anadromous juveniles and the natural return of anadromous adults. During the decade of restoration, &gt; 27,000 anadromous adults ascended the fishway, with ~78% identified as offspring of stocked parents. Juvenile anadromous abundance fluctuated annually but never exceeded 8% of the total juvenile composition. Anadromous juveniles in Rogers Lake grew faster than those in nearby Bride Lake, the source of the stocked anadromous adults, and matched landlocked and hybrid growth rates. Parentage analyses revealed that stocking date influenced reproductive success, age-of-return, and day-of return. Hybrid juveniles appeared early in the restoration and increased in abundance. Hybrids exhibited both life histories, with the majority remaining in the lake as freshwater residents, but several returning as mature anadromous adults. Landlocked juvenile abundance declined, suggesting ongoing demographic shifts through the restoration. Overall, restoration efforts reestablished the anadromous life history in the lake but also led to hybridization between forms. These results provide an example of how evolutionary processes can shape the outcome of restoration efforts.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 11","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70350","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149356706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modelling Resistance Management Benefits of Incomplete Cross-Resistance Within a Fungicide Mode of Action Group","authors":"Isabel Corkley,&nbsp;Neil D. Paveley,&nbsp;Bart A. Fraaije,&nbsp;Joseph Helps,&nbsp;Michael W. Shaw,&nbsp;Alice E. Milne,&nbsp;Nichola J. Hawkins,&nbsp;Frank van den Bosch","doi":"10.1111/eva.70346","DOIUrl":"10.1111/eva.70346","url":null,"abstract":"&lt;p&gt;Mixing fungicides with different modes of action (MoA) is a well-established resistance management tactic which relies on the general absence of cross-resistance between MoAs. Mixtures of fungicides with the same MoA and complete cross-resistance are not expected to contribute to resistance management. However, in some cases cross-resistance is only partial within a MoA, for example azole fungicides in the demethylation inhibitor (DMI) group. We developed and used a mathematical population genetic model to explore possible resistance management benefits of mixtures of fungicides with the same MoA with incomplete cross-resistance. An important example in agriculture is the deployment of DMIs against the wheat pathogen &lt;i&gt;Zymoseptoria tritici&lt;/i&gt;. We modelled selection for known &lt;i&gt;Z. tritici&lt;/i&gt; CYP51 haplotypes following application of solo azoles or two, three or four-way mixtures of epoxiconazole, prothioconazole, prochloraz and tebuconazole. The resulting rate of resistance development was measured as the rate of change in the pathogen population growth rate, &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mo&gt;∆&lt;/mo&gt;\u0000 &lt;mover&gt;\u0000 &lt;mi&gt;r&lt;/mi&gt;\u0000 &lt;mo&gt;¯&lt;/mo&gt;\u0000 &lt;/mover&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ Delta overline{r} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;: this indicates how fast the level of disease severity will increase as resistance develops. We focused on within-MoA programmes to investigate resistance management benefits of within-MoA active substance diversity; in practice azoles should be used in combination with other MoA wherever possible. Our results show that mixtures of fungicides with incomplete cross-resistance within a MoA can contribute to resistance management, achieving greater stability of disease control. Increasing the number of azole active substances available to mix in various combinations reduced &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mo&gt;∆&lt;/mo&gt;\u0000 &lt;mover&gt;\u0000 &lt;mi&gt;r&lt;/mi&gt;\u0000 &lt;mo&gt;¯&lt;/mo&gt;\u0000 &lt;/mover&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ Delta overline{r} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; on average, but with diminishing returns. A generalised linear model fitted to the population genetic model results showed that &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mo&gt;∆&lt;/mo&gt;\u0000 &lt;mover&gt;\u0000 &lt;mi&gt;r&lt;/mi&gt;\u0000 &lt;mo&gt;¯&lt;/mo&gt;\u0000 &lt;/mover&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ Delta overline{r} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; increased with the average level of disease control and with the maximum variance in haplotype sensitivity to an individual az","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 11","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13736046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149340001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Climate-Associated Genetic Variation in Native and Introduced Populations of Eustenopus villosus, a Biological Control Agent for Yellow Starthistle","authors":"Brittany S. Barker,&nbsp;Jessie A. Pelosi,&nbsp;Osman Sert,&nbsp;Katrina M. Dlugosch","doi":"10.1111/eva.70341","DOIUrl":"10.1111/eva.70341","url":null,"abstract":"<p>Contemporary evolution in biological control systems is rarely studied, though biological agents are repeatedly exposed to novel environmental conditions upon introduction. Their ability to adapt to new conditions could influence management efficacy and reveal important aspects of environmental selection. Using a ddRADseq dataset, we tested for genomic evidence of adaptation to climate in populations of <i>Eustenopus villosus</i> (Boheman, Coleoptera: Curculionidae), the “hairy weevil”, which is used in classical biological control for yellow starthistle (<i>Centaurea solstitialis</i> L., Asteraceae) in the western United States. We first estimated population structure in <i>E. villosus</i> across our samples of the native and introduced ranges and then used six complementary genotype-environment association analyses to identify single nucleotide polymorphisms (SNPs) associated with climate in both native and introduced populations. Additionally, we used historical release records to categorize sampling sites according to their serial founding history and test for impacts of this history on total and putatively adaptive genomic variation in the introductions. We also tested whether candidate loci associated with climate in the native range exhibit similar associations in the introductions, or if new associations have evolved. We identified many candidate loci in both native and introduced populations and found little evidence of a decline in genomic variation, which suggests that serial founding events did not prevent climatic adaptation. Candidate loci differed between native and introduced populations, indicating that local adaptation has occurred in different regions of the genome after introduction of <i>E. villosus</i>. Our findings suggest an important role for novel contemporary adaptation in this biological control system and provide insight into how genetic variation can persist in biological control agents through introduction and serial founding events.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 11","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13736000/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149340000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New Genomic Resources for an Invasive Mite Pest Expand the Known Diversity of Pesticide Resistance Mechanisms and Guide Development of KASP Diagnostic Markers","authors":"Joshua A. Thia,&nbsp;Kelly Richardson,&nbsp;Courtney Brown,&nbsp;Aston Arthur,&nbsp;Svetlana Micic,&nbsp;Alan Lord,&nbsp;Neil D. Young,&nbsp;Sunita B. Sumanam,&nbsp;Jia Chang,&nbsp;Bill C. H. Chang,&nbsp;Shujun Wei,&nbsp;Robin B. Gasser,&nbsp;Thomas L. Schmidt,&nbsp;Paul A. Umina,&nbsp;Ary A. Hoffmann","doi":"10.1111/eva.70344","DOIUrl":"https://doi.org/10.1111/eva.70344","url":null,"abstract":"<p>The redlegged earth mite, <i>Halotydeus destructor</i>, is an invasive pest of grain and pasture crops in Australia. Australian populations are increasingly developing resistance to broad-spectrum pesticides. Here, we assembled a chromosome-level genome for <i>H. destructor</i>, comprising nine chromosomes and totalling approximately 46 Mb. We also generated a genomic dataset from 190 populations collected across thousands of kilometres of its invasive Australian range and across 4 years (2018, 2021, 2022 and 2023), and used this dataset to develop KASP (Kompetitive allele-specific PCR) markers for identifying resistance mutations. We combined pooled whole-genome sequencing with resistance testing for organophosphate pesticides, chlorpyrifos and omethoate, and the pyrethroid pesticide, bifenthrin. Target-site resistance to chlorpyrifos was strongly associated with the common <i>ace</i> G119S mutation. A second mutation, <i>ace</i> A201S, was also common, although its association with chlorpyrifos or omethoate resistance was less clear. Target-site resistance to bifenthrin was strongly associated with the common para L1024F mutation. We also detected several rare target-site mutations that likely contribute to resistance in specific populations, including F331Y in <i>ace</i>, and M918T, M918V, L925I, F1020S and F1538I in <i>para</i>. Copy number variation in <i>ace</i> showed mixed associations with resistance, potentially reflecting the co-occurrence of variable gene copies and target-site mutations segregating within and among populations. Finally, we observed putative compositional and structural differences in genomic regions containing carboxylesterases with high <i>ace</i>-like homology, a group of genes that might be involved in organophosphate metabolism. This study advances the genomic and molecular resources available for <i>H. destructor</i>, and represents the most comprehensive investigation to date of resistance mechanisms and their spatiotemporal distribution in this invasive pest. Our data showed that pesticide resistance in <i>H. destructor</i> likely involves many genes. Nevertheless, target-site mutations are likely to remain key markers for rapid resistance diagnostics, for which our KASP markers will provide valuable tools.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 11","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70344","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149310839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing the Potential for Genetic Rescue in Critically Endangered Saimaa Salmon: Early Viability and Genomic Outcomes via First Backcrossing","authors":"Matti Janhunen,&nbsp;Miika Tapio,&nbsp;Aslak Eronen,&nbsp;Raine Kortet,&nbsp;Antti Kause","doi":"10.1111/eva.70349","DOIUrl":"https://doi.org/10.1111/eva.70349","url":null,"abstract":"<p>Small, threatened populations often suffer from a limited gene pool, which increases inbreeding and reduces their adaptability. We investigated the phenotypic and genomic effects of hybridization (resulting from backcrossing) on the critically endangered Lake Saimaa landlocked salmon, <i>Salmo salar</i> m. <i>sebago</i>, focusing on a particularly sensitive alevin-fry life stage. The Saimaa salmon has undergone severe genetic bottlenecks and relies exclusively on a hatchery-based conservation program. Since 2017, crossings with geographically proximate anadromous Baltic Sea salmon populations (Neva and Tornio) have been conducted as a possible means to restore genetic diversity. Here, we used a maternal half-sib design to compare early viability of purebred Saimaa salmon with their first-generation Neva and Tornio backcrosses in semi-natural conditions. The backcrossed fry survived better than purebreds, showing a 9–12 percentage-point increase in viability, whereas no significant cross differences were found in body mass. Quantitative genetic analysis further showed that hybrid sires conferred higher genetic merit for survival. Genomic analyses using a high-density SNP array (47,901 loci) confirmed clear differentiation between pure and backcross groups, validating admixture. Pure Saimaa salmon had heterozygosity (<i>H</i>_S) of 0.13 (over 50% of loci monomorphic), while backcrosses possessed <i>H</i>_S of 0.25 and substantially more polymorphism (96%–97% of loci). Analysis of homozygous genomic segments showed that the inbreeding of Saimaa salmon has predominantly accumulated prior to the conservation program. Widespread reductions in autozygosity were found in both cross types, though introgression varied across the genome and also showed substantial donor- and family-specificity. Overall, the results suggest that hybridization improved early survival through additive and potential dominance effects (reduced genetic load, heterozygote advantage), and expanded genomic variation without immediate indication of outbreeding depression. However, sequential backcrossing across multiple generations is necessary to ensure the preservation of Saimaa salmon's unique genetic identity while enhancing its resilience through the life cycle.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 11","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70349","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149311125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"EXPRESSION OF CONCERN: Calibrating Epigenetic Clocks with Training Data Error","authors":"","doi":"10.1111/eva.70343","DOIUrl":"https://doi.org/10.1111/eva.70343","url":null,"abstract":"<p>\u0000 <b>EXPRESSION OF CONCERN</b>: <span>B. Mayne</span>, <span>O. Berry</span> and <span>S. Jarman</span>, “ <span>Calibrating Epigenetic Clocks with Training Data Error</span>,” <i>Evolutionary Applications</i> <span>16</span>, no. <span>8</span> (<span>2023</span>): <span>1496</span>–<span>1502</span>, https://doi.org/10.1111/eva.13582.\u0000 </p><p>This Expression of Concern is for the above article, published online on 26 July 2023 in Wiley Online Library (wileyonlinelibrary.com), and has been issued by agreement between the journal Editor-in-Chief, Maren Wellenreuther; and John Wiley &amp; Sons Ltd. The Expression of Concern has been agreed since there are currently difficulties in replicating the relevant data. Therefore, the journal has decided to issue an Expression of Concern to alert readers to these concerns while this matter remains under investigation.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 11","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70343","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149312664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Variation in Disease Susceptibility Is Associated With Immunogenetics in a Threatened Amphibian","authors":"Rebecca A. Clemons,&nbsp;Anat M. Belasen,&nbsp;Bennett M. Hardy,&nbsp;Erin Muths,&nbsp;Larissa L. Bailey,&nbsp;W. Chris Funk,&nbsp;Kelly R. Zamudio","doi":"10.1111/eva.70348","DOIUrl":"10.1111/eva.70348","url":null,"abstract":"<p>Emerging infectious diseases affect wildlife populations around the world, making effective conservation strategies essential to the long-term persistence of threatened species. Understanding the drivers of protective host responses to pathogens can help guide conservation efforts. Species that vary intraspecifically in their susceptibility to pathogens are often best for identifying significant drivers, as this reduces potentially confounding effects of highly divergent genetic and adaptive backgrounds. Boreal toads (<i>Anaxyrus boreas boreas</i>) exhibit such intraspecific variation in disease susceptibility. This species ranges across western North America and declines due to the fungal pathogen <i>Batrachochytrium dendrobatidis</i> (Bd) have varied in severity across populations. Previous experimental work shows that some populations of boreal toads are better able to tolerate Bd than others, though the mechanisms are currently unclear. We sequenced the immune locus MHC IIβ exon 2 across tolerant and susceptible populations of boreal toads to determine if host genetics is correlated with Bd susceptibility in this system. We found that tolerant populations differ from susceptible populations at this locus. Specifically, tolerant populations had several distinct MHC alleles, higher observed heterozygosity, and a higher proportion of alleles belonging to one of two functional supertypes. Using these data, we predicted the Bd response of additional boreal toad populations with unknown susceptibility. Boreal toad conservation efforts will benefit from the ability to identify at-risk populations and individuals with genetic signatures of Bd tolerance for use in captive breeding and reintroduction efforts.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 11","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13717072/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149293529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Legacy of Recurrent Gene Flow and Evidence of Independent Evolution of ALS Resistance Mutations in Weedy Rice","authors":"Guilherme Menegol Turra,&nbsp;Paula Sinigaglia Angonese,&nbsp;Eduardo Carlos Rudell,&nbsp;Vinícius Ferrari Tasca,&nbsp;Catarine Markus,&nbsp;Aldo Merotto Junior","doi":"10.1111/eva.70342","DOIUrl":"10.1111/eva.70342","url":null,"abstract":"<p>Weedy rice (<i>Oryza</i> spp.) provides a unique model for studying adaptive evolution because herbicide resistance can arise through both crop-to-weed gene flow and independent mutational events. In Brazil, nearly two decades of cultivation of imidazolinone (IMI)-resistant rice have imposed intense selection for acetolactate synthase (ALS) inhibitors resistance. This study investigated how historical gene flow and independent evolution have shaped the contemporary landscape of ALS resistance mutations in Brazilian weedy rice. Specifically, we characterized the diversity and distribution of ALS resistance mutations and developed rapid allele-specific molecular markers for major resistance alleles. A total of 200 weedy rice accessions collected from the major rice-growing region of Brazil were screened for IMI resistance and genotyped using newly developed SNAP (single nucleotide amplified polymorphism) qPCR markers targeting the IMI rice-derived mutations Ala122Thr, Ser653Asn, and Gly654Glu. Samples negative for these mutations were sequenced, and dose-response assays were conducted with imazethapyr, penoxsulam, nicosulfuron, and cloransulam-methyl. Ninety-three percent of the accessions were resistant to IMI herbicides. The ALS mutation Gly654Glu, present in rice cultivars used until 2006, was found in 15.5% of weedy rice resistant accessions, Ala122Thr became the dominant mutation (54.5%), whereas Ser653Asn occurred at an intermediate frequency (16.0%), indicating a temporal shift in the genetic basis of ALS resistance. Sequencing further identified the ALS substitutions Ala205Val, Trp574Leu, and Ser653Thr, which were not associated with commercial IMI-resistant rice cultivars, indicating ongoing independent evolution of target-site resistance. Trp574Leu conferred broad cross-resistance to all ALS-inhibiting herbicides evaluated, whereas the remaining mutations displayed mutation-specific resistance spectra. The SNAP markers showed high specificity and sensitivity, enabling reliable high-throughput detection of resistance alleles. Together, our findings demonstrate that the contemporary ALS resistance landscape in Brazilian weedy rice has been shaped mainly by repeated crop-to-weed gene flow, but also ongoing independent mutational events that continue to diversify resistance under herbicide selection.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 11","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13714446/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149293542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cancer Evolvability Determines Therapy Outcomes","authors":"Ranjini Bhattacharya,&nbsp;Anuraag Bukkuri,&nbsp;Robert A. Gatenby,&nbsp;Joel S. Brown","doi":"10.1111/eva.70320","DOIUrl":"https://doi.org/10.1111/eva.70320","url":null,"abstract":"<p>Cancer progression following treatment failure is an evolutionary process in which therapy acts as a selection pressure driving Darwinian selection on heritable variation to favor resistant clones. Heritable variation is a key determinant of how rapidly tumors can adapt to therapy. Heritable variation arises through various mechanisms such as genetic mutations, epigenetics, chromosomal rearrangements, and copy number variations, resulting in a lack of replicative fidelity. We consider evolvability as a property or trait of the cancer cells that influences the rate at which fitness-relevant heritable variation is generated. Using this as our definition, we present an evolutionary game-theoretic model to evaluate how evolvability shapes resistance dynamics under two treatment modalities: targeted therapy and chemotherapy. We first compare cancer populations with fixed evolvabilities: low or high. Targeted therapy imposes a steep selection gradient, enabling rapid resistance evolution, while chemotherapy imposes a flatter selection gradient but drives tumors toward more extreme resistance strategies. We show that targeted therapy works better in cancers with low evolvability, whereas chemotherapy better controls cancers with high evolvability. We then extend the model to incorporate “plastic evolvability,” in which cancer cells can adjust their evolvability in response to therapy-induced stress. In this case, cells fine-tune the trade-off between acquiring higher resistance and limiting the costs of resistance and evolvability. Plastic evolvability sustains a higher tumor burden than fixed-evolvability. To address the challenge of plastic evolvability, we develop and simulate an evolutionary double bind using sequential cycles of chemotherapy and targeted therapy. With an appropriate sequence and timing, the double bind can drive cancers with plastic evolvability to extinction. Our results highlight the importance of evolvability in shaping treatment response and underscore the need to incorporate evolutionary principles into therapy design.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 10","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70320","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149258946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}