Molecular Ecology最新文献

{"title":"Genetic Variation Predominates Over Developmental Temperature-Induced Plasticity in Shaping Migratory Flight Capacity in the Diamondback Moth","authors":"Lei Yue,&nbsp;Jin-Cui Chen,&nbsp;Ya-Ning Zhou,&nbsp;Xiu-Jing Shen,&nbsp;Simon W. Baxter,&nbsp;Mei-Qiong Xie,&nbsp;Ya-Jun Gong,&nbsp;Ary A. Hoffmann,&nbsp;Shu-Jun Wei","doi":"10.1111/mec.70518","DOIUrl":"https://doi.org/10.1111/mec.70518","url":null,"abstract":"<div>\u0000 \u0000 <p>Insects represent the largest group of migratory animals in terms of species and biomass, yet the relative contributions of population-associated genetic differentiation and environmental plasticity to insect migration remain unclear. Here, we integrate population genomics with common garden experiments to infer the geographic origins of immigrant populations and evaluate population- and developmental-temperature-associated variation in migration-related flight traits in the diamondback moth (<i>Plutella xylostella</i>), a major pest of cruciferous crops. Population-genomic analyses indicated that immigrant populations sampled in northern China were genetically most closely associated with southwestern populations, which were therefore considered inferred source populations, whereas southeastern populations showed limited genetic affinity with these immigrants and were treated as non-source reference populations. Genome scans identified 29 genes within outlier regions detected in comparisons of the immigrant and inferred source populations from the non-source reference populations; these genes were enriched for functions related to signal transduction and energy metabolism. Flight-mill assays under common garden conditions revealed that the immigrant and inferred source populations generally exhibited greater migration-associated flight capacity than the non-source reference populations. Individuals developing at lower temperatures also showed greater flight performance. Variance partitioning showed that population origin explained 15%–27% of the variation in flight-performance traits, whereas temperature explained 3%–7%. Genes located in population-genomic outlier regions did not overlap with temperature-responsive genes identified by RNA sequencing across developmental-temperature treatments in the immigrant population examined. Together, these findings show that population-associated differences persisting under common garden conditions accounted for more variation in migration-associated flight capacity than did the developmental-temperature treatments examined here.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 16","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148784422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Over-Representation of Sperm-Associated Deleterious Mutations Across Wild and Ex Situ Cheetah (Acinonyx jubatus) Populations","authors":"Jessica A. Peers,&nbsp;Heather R. Sibley,&nbsp;Ellie E. Armstrong,&nbsp;Adrienne E. Crosier,&nbsp;Will J. Nash,&nbsp;Klaus-Peter Koepfli,&nbsp;Wilfried Haerty","doi":"10.1111/mec.70513","DOIUrl":"10.1111/mec.70513","url":null,"abstract":"<p>As purifying selection becomes less effective and inbreeding increases, small populations frequently develop an increased load of genome-wide deleterious mutations. Reflecting this pattern, deleterious mutations in genes associated with fertility and immunity have previously been identified in the cheetah (<i>Acinonyx jubatus</i>), which has had a low effective population size for at least the last 10,000 years. However, the distribution of deleterious mutations across cheetah populations is currently unknown. Here, we analysed novel whole genome resequencing data from 30 ex situ and 9 wild cheetahs. We investigated variation in genetic diversity, genomic measures of inbreeding, and the distribution of deleterious mutations across cheetah populations. South Sudanese and Tanzanian cheetahs showed higher inbreeding and realised load, while Namibian cheetahs had a higher proportion of population-specific deleterious mutations. Genes containing high- or moderate-impact deleterious mutations were significantly enriched for sperm-related functions, highlighting putative causative loci associated with poor sperm quality in cheetahs. Similar levels of genetic diversity and inbreeding were observed in ex situ cheetahs compared to their wild counterparts, providing empirical evidence of the efficacy of captive breeding programmes in maintaining genetic variation in ex situ populations.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 16","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70513","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148758211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contrasting Oviposition Preference Despite Limited Chemosensory Receptor Gene Differentiation in Two Cryptic Anopheles Species","authors":"Marilene M. Ambadiang,&nbsp;Caroline Fouet,&nbsp;Fred A. Ashu,&nbsp;Desiree E. Rios,&nbsp;Aditi Kulkarni,&nbsp;Sourav Roy,&nbsp;Calmes Bouaka,&nbsp;Véronique Penlap-Beng,&nbsp;Colince Kamdem","doi":"10.1111/mec.70512","DOIUrl":"10.1111/mec.70512","url":null,"abstract":"<div>\u0000 \u0000 <p>Adaptation to novel environments is often associated with behavioural changes, but how decision-making processes and their genetic underpinnings evolve during ecological divergence remains poorly understood. Human-modified environments provide an ideal context in which to investigate how species adjust their behaviours in response to altered ecological conditions. We used oviposition site selection in two incipient mosquito species segregating along gradients of anthropogenic disturbance to investigate how differences in sensory perception modulate behavioural shifts accompanying ecological divergence. Using two-choice assays, we tested oviposition preferences in 1046 gravid female mosquitoes from field and laboratory populations by offering a choice between water collected from natal and foreign natural breeding sites. We found that females of <i>Anopheles gambiae</i>, a species adapted to rural environments, preferentially oviposited in natal water and deposited 89% of their eggs in a single breeding site. In contrast, females of its sibling species, <i>Anopheles coluzzii</i>, which is adapted to urban environments, exhibited weaker natal-water preference and frequently distributed their egg clutches between multiple breeding sites. To assess the extent of chemosensory divergence between these cryptic species, we analyzed amino acid substitutions within odorant, ionotropic and gustatory receptor gene families using whole-genome sequencing data. Despite limited differentiation across the gene families overall, several loci implicated in the detection of carboxylic acids, amines and volatile compounds exhibited elevated genetic divergence between species. Our work suggests that shifts in decision making associated with ecological divergence between emerging species can arise prior to substantial differentiation throughout the genome or across chemosensory receptor gene families.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 16","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148758449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inbreeding in a Fission–Fusion Equid Decreases Following an Increase in the Number and Redistribution of Water Sources","authors":"Noa Yaffa Kan-Lingwood,&nbsp;Alan R. Templeton,&nbsp;Naama Shahar,&nbsp;Daniel I. Rubenstein,&nbsp;Amos Bouskila,&nbsp;Shirli Bar-David","doi":"10.1111/mec.70516","DOIUrl":"https://doi.org/10.1111/mec.70516","url":null,"abstract":"<p>Social structures and habitat configuration influence inbreeding in wild populations. In harem-forming, female-defence polygynous equids, social organization promotes inbreeding avoidance, but this has not been studied in fission–fusion, resource-defence equid species. Because reproduction depends on solitary males establishing territories near resources, shifts in resource distribution are expected to affect mating patterns and inbreeding. We examined inbreeding patterns in the Asiatic wild ass (<i>Equus hemionus</i>) in the Negev Highlands, Israel (2019–2023), by comparing mating-pair relatedness (MPR) to all female–male dyads, within each year, and testing whether these patterns changed following a 2020 water source increase and redistribution by increasing the number of new territorial males. We then examined whether females overall tended to mate with veteran (i.e., mating since 2019) or new (i.e., mating since 2020) reproducing males, and compared female–male genetic relatedness between these two groups. Using 2509 faecal samples (2020–2024) genotyped at 625 SNPs, we assigned parentage to 73 offspring and estimated the MPR. Within years, the MPR was higher than random in 2019 and 2020 but declined after the water source manipulation, in 2021–2023. The MPR was higher near the original water source than near the new water sources. Most females (87.3%) mated with new reproducing males, and in 68.3% of cases, new reproducing males were less related to females than were veteran males. Our study suggests that reduced inbreeding is possible in fission–fusion populations when females have extended mating opportunities with territorial males, which can be achieved by expanding the distribution of resources.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 16","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70516","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148784188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hybridization but Minimal Introgression: Ecologically-Based Divergent Selection Maintains a Steep Hybrid Zone in Parapatric Stickleback Fish","authors":"Olivia Baebler,&nbsp;Quiterie Haenel,&nbsp;Krista Oke,&nbsp;Andrew P. Hendry,&nbsp;Daniel Berner","doi":"10.1111/mec.70510","DOIUrl":"https://doi.org/10.1111/mec.70510","url":null,"abstract":"<p>Steep hybrid zones provide key insights into the mechanisms of speciation by reflecting incomplete reproductive isolation between diverging populations. However, the specific reproductive barriers preventing the fusion of such populations generally remain unclear, particularly the role of ecologically-based divergent selection. To address the latter, we investigate a steep zone of transition between lake and inlet stream ecotypes of threespine stickleback fish inhabiting contiguous habitats within a single watershed. Given the spatial proximity of these habitats and the system's postglacial age, historical allopatry is unlikely to have contributed to the evolution of reproductive isolation. Using individual whole-genome sequencing from clinal sampling sites, we identify ongoing hybridization that is limited to a narrow zone—just a few hundred meters long—around the transition between lake and stream habitat. Individuals in this contact zone exhibit strongly bimodal genome-wide ancestry, with a rapid shift toward the stream ecotype's genomic background across the lowest stream section, consistent with strong divergent selection and asymmetric gene flow. Individual-based simulations tailored to this system demonstrate that divergent ecological selection alone can maintain the sharp cline observed and illustrate sustained antagonism between gene flow and selection near the habitat transition. Our findings underscore the power of ecological divergence to generate and maintain reproductive isolation, even in the absence of historical separation, and motivate further empirical work on the ecological underpinnings of steep hybrid zones.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 16","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70510","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148784186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Transcriptomic Response Along an Urbanization Gradient Is Also Temperature-Dependent in a Freshwater Insect","authors":"Katarzyna Dudek,&nbsp;Guillaume Wos","doi":"10.1111/mec.70511","DOIUrl":"10.1111/mec.70511","url":null,"abstract":"<p>Urbanization has become one of the leading causes of habitat transformation affecting ecosystem functioning. However, the transcriptomic response to urbanization remains poorly understood. Here, we conducted a transcriptomic analysis along an urbanization gradient under different warming temperatures. We further explored the genes underlying phenotypic variation along an urbanization gradient using weighted gene co-expression network analysis (WGCNA). We collected adult females in eight ponds spanning an urbanization gradient (percentage of impervious surface) in Southern Poland and raised their larvae in growth chambers under three temperature treatments: current 22°C, + 3°C, and + 6°C above current temperature. When larvae reached the prefinal instar, they were phenotyped for traits related to development and size, and collected for a gene expression analysis. We found that 24 genes varied in expression along a continuous urbanization gradient and were related to proteolysis, extracellular organization and perception. In addition, some genes showed a significant interaction urbanization × temperature and were associated with detection of chemical stimulus and perception. The WGCNA revealed two gene modules associated with urbanization and some phenotype traits, especially with development time. Genes associated with phenotypic differentiation along the urbanization gradient were part of many different pathways including signal transmission, cell cycle and DNA repair. In conclusion, we demonstrated that the transcriptomic response along an urbanization gradient was context-dependent, here on temperature, suggesting that some genes responding to urbanization also exhibited thermal plasticity. Our work highlights the importance of urbanization in inducing phenotypic and gene expression changes in organisms.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 16","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70511","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148756965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sedimentary DNA and Fossil Archives Reveal Long-Term Phytoplankton Shifts and Their Biogeochemical Influence in a Subtropical Lake","authors":"Yu Zhao,&nbsp;Jianan Zheng,&nbsp;Meifang Zhong,&nbsp;Wenxiu Zheng,&nbsp;Bo Qin,&nbsp;Kexin Zhu,&nbsp;Chenxue Zhang,&nbsp;Yanjie Zhao,&nbsp;Enlou Zhang,&nbsp;Eric Capo,&nbsp;Rong Wang","doi":"10.1111/mec.70509","DOIUrl":"10.1111/mec.70509","url":null,"abstract":"<p>Understanding long-term phytoplankton community dynamics is essential for assessing ecological resilience and informing lake management under global change. However, centennial-scale patterns of phytoplankton dynamics remain poorly resolved due to the limited taxonomic resolution of traditional fossil-based paleoecological approaches. In this study, a combination of sedimentary DNA (sedDNA) and subfossil diatom analysis was used to investigate changes in the phytoplankton community over the past two centuries and associated sedimentary biogeochemical responses in Lake Xiliang, a subtropical lake in the Yangtze River Basin, China. The sedDNA data captured major shifts in both eukaryotic and cyanobacterial communities, revealing distinct ecological phases linked to human activities and regional climate warming. Under near-natural conditions with minimal human disturbance, phytoplankton communities typically exhibit low diversity and are characterized by oligotrophic taxa such as xanthophytes and <i>Gyrosigma</i>. After the 1930s, increases in epiphytic <i>Staurosira</i> and declines in tychoplanktonic <i>Aulacoseira</i> suggest reduced river–lake connectivity and weaker water-column turbulence following the construction of the Jinshui Sluice, likely facilitating macrophyte expansion. In recent decades, intensified anthropogenic pressures combined with regional warming have driven a shift toward more diverse phytoplankton assemblages enriched in cyanobacteria, reflecting elevated nutrient inputs and rising temperatures. The observed associations between phytoplankton community changes and sedimentary geochemical proxies suggest that phytoplankton dynamics may not only have responded to environmental change but also contributed to sedimentary biogeochemical cycling, particularly total organic carbon accumulation and calcium-related processes such as photosynthesis-induced carbonate precipitation. These findings illustrate long-term phytoplankton community dynamics and underscore the value of sedDNA for reconstructing ecological trajectories in lake ecosystems.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 16","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70509","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148756990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic Differences Reveal Early Development of Contrasting Energetic Strategies Between Divergent Migratory Ecotypes in Three-Spined Stickleback","authors":"Megan Barnes,&nbsp;Adam Dowle,&nbsp;Andrew D. C. MacColl,&nbsp;Lisa Chakrabarti","doi":"10.1111/mec.70494","DOIUrl":"10.1111/mec.70494","url":null,"abstract":"<div>\u0000 \u0000 <p>Divergence in migratory behaviour represents a striking and common axis of life-history variation in animals. Plastic changes in adult animals in preparation for migration are well known, but the differences in early development between migratory and non-migratory forms are not well documented. These differences might contribute to reproductive isolation because of the potentially substantial divergence in metabolism and physiology. Here we document substantial differences between migratory ecotypes in sarcomeric development and energetic pathways from immediately after hatching. On North Uist (Scottish Western Isles), migratory and non-migratory (‘resident’) three-spined stickleback (<i>Gasterosteus aculeatus</i>) ecotypes breed in sympatry in brackish lagoons, providing an ideal system for investigating early developmental and energetic strategies associated with migration. Using relative-quantitative proteomics, we compared protein abundance in migratory, resident and reciprocal hybrid crosses of the three-spined stickleback 2 days after hatching. Migratory stickleback exhibited higher abundance of muscle, metabolic and collagen-associated proteins, indicating early investment in growth and preparation for the energetic demands of migration and sustained swimming. In contrast, resident stickleback showed increased abundance of maternal provisioning proteins, delayed hatching and higher hatching success, consistent with a strategy of producing fewer but high-quality offspring. Hybrids generally exhibited intermediate protein abundances, but there was some evidence of negative transgression in proteins related to mitochondrial function which might contribute to reduced fitness through mitonuclear incompatibility. Together, these results reveal early biochemical differences consistent with divergent energy allocation and reproductive strategies between migratory and resident stickleback.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 16","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148756986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental Association Analyses in Plants and the Influence of Methodological Decisions","authors":"James A. Bedford,&nbsp;Mark A. Carine,&nbsp;Mark A. Chapman","doi":"10.1111/mec.70508","DOIUrl":"https://doi.org/10.1111/mec.70508","url":null,"abstract":"<p>Climate change is predicted to impact existing ecological systems, leading to a requirement to improve our understanding of environmental adaptation in plants, particularly for conservation and the development of environmentally tolerant crop varieties. Environmental association analyses (EAAs) are a group of landscape genomic methods for detecting genetic markers or genes associated with environmental factors and therefore provide a top-down approach of studying the genetics of environmental adaptation. Here we review 138 EAA studies in plants, revealing the large diversity of methods at each stage of the analysis, including marker filtering, EAA model selection, the significance criteria used, candidate gene selection and any downstream analyses conducted. Following this, we compared four frequently used EAA models using genetic data from a panel of traditional rice (<i>Oryza sativa</i>) varieties from Vietnam, revealing a greater proportion of significant markers for recent GWAS models (FarmCPU and BLINK) compared to single locus mixed linear models (MLM) and latent factor mixed models (LFMM). Between zero and 22 environmentally associated markers overlapped between models and several genes in proximity to these loci have putative links to abiotic factors. Overall, this highlights the challenges in comparing the results of EAA studies, particularly regarding applying the results to crop breeding for future climates.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 16","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70508","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148710527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic Sampling and Population Structure of Farmer-Maintained Varieties Reveal Previously Uncharacterized Diversity of Theobroma cacao L. in Costa Rica","authors":"Emma M. Herrighty,&nbsp;Chelsea D. Specht,&nbsp;Michael A. Gore,&nbsp;Luis Solano,&nbsp;Joyce Estrada-Gamboa,&nbsp;Carlos Eduardo Hernandez,&nbsp;Hale Ann Tufan,&nbsp;Jacob B. Landis","doi":"10.1111/mec.70506","DOIUrl":"https://doi.org/10.1111/mec.70506","url":null,"abstract":"<div>\u0000 \u0000 <p>Understanding crop genetic diversity is essential for conservation and breeding, yet farmer-maintained germplasm remains largely underrepresented in genomic studies. <i>Theobroma cacao</i> L. has a complex domestication history, extensive global diversity, and is currently cultivated in Central America. Costa Rican cacao has been understudied compared to South American and Mexican cultivars despite cultural and historical importance. In this study, we investigate the genetic diversity of cacao from farmer-managed systems across Costa Rica to search for Criollo germplasm while identifying and characterizing unique local genetic groups. Ninety-four trees were sampled for whole genome resequencing from 17 farms across four regions of the country. Farmer materials were analyzed alongside 166 previously characterized reference accessions representing major cacao genetic groups. Population structure analyses, phylogenetic reconstruction, and network approaches revealed that Costa Rican cacao encompasses multiple known genetic groups, including Criollo-derived lineages while also harbouring locally distinct diversity not represented in current global reference collections. Analyses revealed close kinship between many accessions with no clear geographic patterns corresponding to the observed population differentiation, reflecting the influence of farmers in generating the dominant patterns of gene flow through seed-saving, clonal propagation, and sharing of genotypes among farms. Heterozygosity levels varied substantially among individuals, consistent with a mixture of highly inbred Criollo trees and more heterozygous, admixed genotypes. We find that farmer-managed cacao systems are reservoirs of genetic diversity that can include rare or historically important lineages, underscoring the value of these farming systems for effective conservation and management of genomic resources for cacao resilience and improvement.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"35 16","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148710528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}