Molecular Ecology最新文献

{"title":"Do Snow-Adapted Prey Facilitate Coexistence of the Sierra Nevada Red Fox With Sympatric Carnivores?","authors":"Grace Rosburg-Francot, Catherine B Quinn, Stevi Lee Vanderzwan, Tal Caspi, Pete Figura, Benjamin N Sacks","doi":"10.1111/mec.70087","DOIUrl":"https://doi.org/10.1111/mec.70087","url":null,"abstract":"<p><p>Specialist species in alpine ecosystems may be increasingly threatened by climate-driven habitat loss and encroachment by generalist competitors. Ecological theory predicts that niche differentiation through dietary specialisation can facilitate coexistence with generalist competitors. We quantified dietary overlap between a high-elevation specialist, the Sierra Nevada red fox (SNRF; Vulpes vulpes necator) and a widespread generalist, the coyote (Canis latrans), as well as other sympatric carnivores. We were especially interested in dietary items that were themselves specialised to alpine habitats, as we expected them to be most critical to SNRF. To characterise diet, we used DNA metabarcoding for vertebrate and plant-based food items of 789 carnivore scats collected from the sites of two SNRF populations (Lassen, Sierra Nevada). As expected for potential competitors, SNRFs exhibited substantial dietary overlap with coyotes overall. Dietary niche overlap was lower between SNRF and both bobcats (Lynx rufus) and martens (Martes caurina). Compared to coyotes, however, SNRF more frequently consumed snow-adapted prey, including white-tailed jackrabbits (Lepus townsendii) and American pika (Ochotona princeps) (SIMPER p ≤ 0.005), especially during periods of deep snow. Whitebark pine (Pinus albicaulis; presumably seeds) also appeared more regularly in SNRF winter diets compared to coyotes. These findings support the hypothesis that co-adapted subalpine prey facilitate coexistence between specialist and generalist carnivores by increasing the competitive advantage of specialists under snowier conditions. This environment-mediated shift in competitive dynamics implies that the fates of locally adapted predator and prey may be tightly linked, an important consideration for conservation planning in alpine ecosystems.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70087"},"PeriodicalIF":3.9,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937449","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":"Decoding Past Microbial Communities Shifts Induced by Natural and Anthropogenic Disturbance Events Through Extracellular DNA.","authors":"S Varrella, M Tangherlini, C Corinaldesi, L Musco, A Schirone, G Armiento, R Danovaro, A Dell'Anno","doi":"10.1111/mec.70078","DOIUrl":"https://doi.org/10.1111/mec.70078","url":null,"abstract":"<p><p>Coastal marine ecosystems face escalating threats from multiple anthropogenic stressors, including the release of industrial contaminants. Despite decades of industrial activity impacting marine ecosystems, long-term effects on microbial communities and related key ecological functions remain unclear. Here, we analysed the prokaryotic genetic signatures of extracellular DNA preserved in sediment layers dating from the mid-17th century to the present day collected from two sites of one of the most polluted European coastal areas (i.e., Bagnoli-Coroglio Bay, Tyrrhenian Sea), where industrial activities began in the early 20th century and ended in 1992. Archaeal 16S rDNA copy numbers were higher than bacterial ones, reaching values of 2.3 and 8.8 × 10⁷ copies during pre-industrial volcanic episodes and the intense industrial development period, respectively. Most of the archaeal genetic signatures identified along the sediment vertical profiles belong to Bathyarchaeia. The pre-industrial period showed lower diversity in terms of Amplicon Sequence Variants (ASVs) belonging to 70 prokaryotic families when compared with industrialisation periods (182 families), suggesting prokaryotic ability to respond and change in relation to modified environmental conditions occurring over time. High microbial β-diversity values were observed, with major shifts occurring for more than 50 prokaryotic taxa in both cores, suggesting that chemical contamination and volcanic eruptions fostered microbial succession, selecting certain taxa more adapted to cope with such adverse ecological conditions. Our findings indicate that extracellular DNA pools of marine sediments can hold information on long-term changes in benthic microbial diversity, representing valuable archives for understanding ecosystem dynamics over time.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70078"},"PeriodicalIF":3.9,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937420","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":"Bdh1l Gene Expression Is a Potential Molecular Factor in the Evolution of Carotenoid-Based Colour Diversity of Cichlid Fishes","authors":"Pooja Singh,&nbsp;Angelika Ziegelbecker,&nbsp;Christoph Hahn,&nbsp;Walter Goessler,&nbsp;Ronald A. Glabonjat,&nbsp;Ehsan Pashay Ahi,&nbsp;Kristina M. Sefc","doi":"10.1111/mec.70065","DOIUrl":"10.1111/mec.70065","url":null,"abstract":"<p>Carotenoids contribute substantially to animal body colour pattern diversity. While the ecological and evolutionary drivers of carotenoid coloration are reasonably well understood, the molecular mechanisms facilitating evolutionary transitions between red and yellow hues are less investigated. Here we leverage phylogenetically replicated red-versus-yellow colour contrasts in three pairs of closely related cichlid fishes (<i>Tropheus</i> and <i>Aulonocara</i>; Haplochromini) to investigate biochemical and genetic parallels in carotenoid colour differentiation. Red skin samples contained the ketocarotenoids rhodoxanthin, canthaxanthin, and astacene, the latter as likely saponification product of astaxanthin. A re-analysis of existing RNA-seq data using an improved bioinformatics pipeline identified consistent red-versus-yellow gene expression differences. Notably, transcripts of a gene coding for a 3-hydroxybutyrate dehydrogenase type 1 enzyme (<i>bdh1l</i>) and further known carotenoid genes (<i>scarb1</i>, <i>bco2</i>, <i>ttc39b</i>) were significantly more abundant in red than in yellow skin tissue in all taxon pairs. Homologues of Bdh1l have recently been discovered to mediate C4-ketocarotenoid biosynthesis in birds and fish, but only in the presence of a cytochrome P450 enzyme. We found no consistent differences in cytochrome P450 gene expression. Our results suggest that <i>bdh1l</i> expression regulation might operate as a molecular switch for C4-ketocarotenoid biosynthesis and colour pattern differentiation in different radiations of cichlid fish, apparently in the presence of a stably expressed and therefore inconspicuous P450 cytochrome enzyme. The divergent chemical structure of rhodoxanthin requires a different biosynthesis pathway than the C4-ketocarotenoids astaxanthin and canthaxanthin. Differential expression of <i>hsd3b</i>, encoding a dehydrogenase with a corresponding function in the steroid pathway, suggests a new candidate for rhodoxanthin biosynthesis.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 18","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70065","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144881800","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":"Biochemical and Genomic Underpinnings of Carotenoid Colour Variation Across a Hybrid Zone Between South Asian Flameback Woodpeckers","authors":"Rashika W. Ranasinghe,&nbsp;Jocelyn Hudon,&nbsp;Sampath S. Seneviratne,&nbsp;Darren Irwin","doi":"10.1111/mec.70084","DOIUrl":"10.1111/mec.70084","url":null,"abstract":"<p>Colouration and patterning have been implicated in lineage diversification across various taxa, as colour traits are heavily influenced by sexual and natural selection. Investigating the biochemical and genomic foundations of these traits therefore provides deeper insights into the interplay between genetics, ecology and social interactions in shaping the diversity of life. In this study, we assessed the pigment chemistries and genomic underpinnings of carotenoid colour variation in naturally hybridising <i>Dinopium</i> flamebacks in tropical South Asia. We employed reflectance spectrometric analysis to quantify species-specific plumage colouration, High-Performance Liquid Chromatography (HPLC) to elucidate the feather carotenoids of flamebacks across the hybrid zone, and Genome-Wide Association Study (GWAS) using next-generation sequencing data to uncover the genetic factors underlying carotenoid colour variation in flamebacks. Our analysis revealed that the red mantle feathers of <i>D. psarodes</i> primarily contained astaxanthin, with small amounts of other 4-keto-carotenoids. In contrast, the yellow mantle feathers of <i>D. benghalense</i> predominantly contained lutein and 3′-dehydro-lutein, alongside minor amounts of zeaxanthin, β-cryptoxanthin and canary-xanthophylls A and B. Hybrids with an intermediate, orange colouration deposited all of these pigments in their mantle feathers, with notably higher concentrations of carotenoids with ε-end rings. The GWAS analysis identified the <i>CYP2J2</i> gene, which plays a role in carotenoid ketolation, as associated with the expression of carotenoid colouration. Read depth data suggested variation in copy number of this gene in flamebacks. These findings contribute to the growing knowledge of avian carotenoid metabolism and highlight how genomic architecture can influence phenotypic diversity.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 19","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70084","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870568","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":"Combined Evidence Reveals the Origin of a Rapid Range Expansion Despite Retained Genetic Diversity and a Weak Founder Effect","authors":"Nora M. Bergman,&nbsp;Petteri Lehikoinen,&nbsp;Edward Kluen,&nbsp;Staffan Bensch,&nbsp;Camilla Lo Cascio Sætre,&nbsp;Fabrice Eroukhmanoff,&nbsp;Frode Fossøy,&nbsp;Petr Procházka,&nbsp;William J. Smith,&nbsp;Bård G. Stokke,&nbsp;Craig R. Primmer,&nbsp;Rose Thorogood,&nbsp;Katja Rönkä","doi":"10.1111/mec.70077","DOIUrl":"10.1111/mec.70077","url":null,"abstract":"<p>Many species are currently experiencing range shifts in response to changing environmental conditions with potentially serious genetic consequences. Repeated founder events and strong genetic drift are expected to erode genetic variation at the range front, reducing adaptive potential and slowing or even halting the expansion. However, the severity of these consequences for common and highly mobile species undergoing environment-driven range shifts (c.f. invasions) is less clear. Here, we combined historical observations and contemporary movement data of the common reed warbler (<i>Acrocephalus scirpaceus</i>) with genomic evidence from across its European breeding range to (1) infer the origin and (2) quantify the genetic consequences of a recent and rapid northward range expansion. Although there were no reductions in levels of nucleotide diversity or allelic richness, nor a signal of founder effect in the directionality index (<i>ψ</i>), our combined dataset approach was able to infer an expansion origin from the southwest. Furthermore, we found that private allelic richness retained a slight but significant linear decline along the colonisation route. These results suggest that high dispersal capabilities can allow even philopatric species to avoid the loss of genetic diversity during rapid range expansions. Nevertheless, if multiple lines of evidence enable identification of an expansion pathway, we may still detect genetic signals of expansion.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 19","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70077","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870569","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":"Geographical, Ecological, and Genetic Drivers of Gut Microbial Diversity in Native and Invasive Minnows (Leuciscidae: Cyprinella)","authors":"William Hanson-Regan,&nbsp;Francesca Leasi,&nbsp;Fernando Alda","doi":"10.1111/mec.70011","DOIUrl":"10.1111/mec.70011","url":null,"abstract":"<div>\u0000 \u0000 <p>The gut microbiome is important for many physiological processes that are critical in the adaptation of an animal to its environment. Conversely, abrupt ecological changes, as in the colonisation of a new territory, may also influence the microbiome. Therefore, anthropogenic introductions of invasive species offer a natural model in which to study these relationships. We compared the gut microbiomes (16S rRNA gene) of four freshwater fish species of the genus <i>Cyprinella</i>, including both native and introduced populations of the prolific invader <i>C. lutrensis</i>, to investigate if differences in their diversity and structure are determined by their host or depend more on the ecology and geographical location where they occur. Our results suggest that at this taxonomic level, the external environment of the fish is the strongest corollary of microbial diversity and community composition of the gut, followed to a lesser extent by species identity and genetic factors. Our findings emphasise the dynamic nature of the minnow gut microbiome, with high individual variation and rapid changes over time. We also found that new invasions may reduce the invader's gut microbiome alpha diversity while not conferring any clear distinction compared with cohabiting native species. This research addresses the perennial question of whether nature or nurture plays a greater role in shaping the gut microbiome, revealing the intricate interplay of factors and scales involved.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 18","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870585","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":"Genomic Insights Into Local Adaptation Across Heterogeneous Understory Habitats and Climate Change Vulnerability","authors":"Nan Lin,&nbsp;Yakun Wang,&nbsp;Xiankun Wang,&nbsp;Yuxuan He,&nbsp;Xianhan Huang,&nbsp;Qun Liu,&nbsp;Hengchang Wang,&nbsp;Tao Deng","doi":"10.1111/mec.70068","DOIUrl":"10.1111/mec.70068","url":null,"abstract":"<p>Understanding adaptive evolution and survival risks in understory herbs is crucial for the effective conservation of biodiversity. How environmental gradients shape species local adaptation patterns is not well understood, nor is how populations of understory herbs respond to a changing climate. In this study, we conducted population genomic analyses of <i>Adenocaulon himalaicum</i> (Asteraceae) with a pan-East Asian distribution, representing a good model for dominant understory herbs to elucidate adaptation mechanisms in heterogeneous forest ecosystems. Based on 34,398 putatively neutral single nucleotide polymorphisms (SNPs) across 27 populations, we identified three genetic lineages accompanied by high levels of genetic differentiation between populations. Our isolation by environment results (IBE) indicated a significant effect of environmental gradients on genomic variation of <i>A. himalaicum</i> (<i>r</i> = 0.18, <i>p</i> = 0.03). To decompose the relative contributions of climate, geography and population structure in explaining genetic variance, our partial RDA found that the prominent contribution of environmental effects (climatic and soil variables) explained 29% and 36% of the neutral and adaptive genetic variation, respectively. Using two genotype–environment association (GEA) methods, we identified 13 SNPs as candidates for core climate-related adaptation loci, with two of these loci further validated by qRT-PCR experiments. Projections of spatiotemporal genomic vulnerability under different future climate scenarios revealed that populations in the southeastern edge of the Himalayas, near the Sichuan Basin, the southernmost region of Northeast China and the northern Korean Peninsula, as well as northern Japan, were identified as the most vulnerable and should be prioritised for conservation. Therefore, our current study provides the genomic foundations for conservation and management strategies to elucidate how these understory herbs cope with future climate changes.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 19","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70068","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870570","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":"History and Dynamics of an Extensive Plant Hybrid Zone on the Great Plains of North America","authors":"Victor Andreev,&nbsp;Joshua Puzey,&nbsp;Elizabeth Davies,&nbsp;Carrie Olson-Manning,&nbsp;Sydney Kreutzmann,&nbsp;Mark Fishbein","doi":"10.1111/mec.70048","DOIUrl":"10.1111/mec.70048","url":null,"abstract":"<div>\u0000 \u0000 <p>Hybridisation affects the spatial and temporal patterns of morphological and genetic variation, shaping species evolution. <i>Asclepias speciosa</i> and <i>A. syriaca</i> provide an excellent system for uncovering how these patterns are generated. The ranges of <i>A. speciosa</i> and <i>A. syriaca</i> overlap on the North American Great Plains, and multiple intermediates are observed in this contact zone, consistent with hybridisation. However, other processes, such as preservation of ancestral polymorphism or selective pressure imposed by environmental clines, could explain the presence of morphological intermediates. In this study, we characterised patterns of variation within and between <i>A. speciosa</i> and <i>A. syriaca</i> using morphological and genetic data to validate the hybrid origin of intermediates, evaluate the impact of hybridisation on the parental species and reconstruct the demographic history of hybridisation events. In addition, we explored species-specific associations of genetic variation with climatic variables. We demonstrated that hybridisation best explains the occurrence of large numbers of morphologically intermediate individuals in the contact zone and documented bidirectional and asymmetric genetic introgression. We found a strong relationship between precipitation patterns and genetic variation in <i>A. speciosa</i> and <i>A. syriaca,</i> which suggests that the hybrid zone is maintained by differences in annual precipitation. We discovered that the timing of secondary contact is relatively recent, coinciding with rapid range shifts during the Pleistocene. Our findings provide new insights into the dynamics of hybridisation on the North American Great Plains, the setting for numerous contact zones between taxa affiliated with eastern and western biotas.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 18","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870586","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":"Arid Soil Bacterial Legacies Improve Drought Resilience of the Keystone Grass, Themeda triandra","authors":"Riley J. Hodgson,&nbsp;Christian Cando-Dumancela,&nbsp;Tarryn Davies,&nbsp;Victoria Drysdale,&nbsp;Nicole W. Fickling,&nbsp;Craig Liddicoat,&nbsp;Shawn D. Peddle,&nbsp;Sunita A. Ramesh,&nbsp;Declan Spoor,&nbsp;Alex Taylor,&nbsp;Carl Watson,&nbsp;Martin F. Breed","doi":"10.1111/mec.70062","DOIUrl":"10.1111/mec.70062","url":null,"abstract":"<p>Plant–microbe interactions are critical to ecosystem functioning and impact soil legacies, where plants exert a lasting influence on the microbial and physicochemical conditions of the soils in which they grow. These soil legacies can affect subsequent plant growth and fitness. Specifically, biotic soil legacies can influence microbially associated plant fitness through the movement of soil microbiota in a two-step selection process: Microbes are recruited from bulk soil into the rhizosphere (the space around roots) and then into the endosphere (within plant roots). Furthermore, these endosphere root microbiota can also influence plant behaviour, shaping bulk soil communities over time. However, the potential of these soil legacies to provide host plant drought tolerance remains poorly understood. In a drought stress greenhouse trial, we show that arid soil legacies increased the biomass of the keystone grass <i>Themeda triandra</i> under both drought and control conditions. We report strong positive associations between <i>T. triandra</i> biomass and bacterial alpha diversity across soils, rhizospheres and endospheres. These findings show that bacterial soil legacies have an important but underappreciated role in grassland species resilience to drought and could be better harnessed to support resilient grassland restoration efforts.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 18","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70062","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870567","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":"Gene Expression Divergence Between Locally Adapted Inland Annual and Coastal Perennial Ecotypes of Mimulus guttatus Across Developmental Stages.","authors":"Jason D Olsen, Billie A Gould, Yani Chen, David B Lowry","doi":"10.1111/mec.70080","DOIUrl":"https://doi.org/10.1111/mec.70080","url":null,"abstract":"<p><p>The action of natural selection across heterogeneous natural landscapes drives local adaptation and the formation of plant ecotypes, the precursors to new species. Plant ecotypes typically differ significantly in morphology, physiology, and development, yet our understanding of their underlying genetic basis remains limited. Despite their importance, studies of the molecular underpinnings of ecotypic divergence through developmental stages are rare. Here, we compared gene expression at different developmental time points between ecologically reproductively isolated coastal perennial and inland annual ecotypes of the yellow monkeyflower, Mimulus guttatus. We took two major approaches to understand differences in gene regulation between the ecotypes at the level of gene networks. First, we evaluated expression variation between the ecotypes in candidate molecular pathways. Next, we conducted gene co-expression network analyses to identify new candidate mechanisms driving ecotypic divergence. Overall, we found significant differences in global expression between the ecotypes and across developmental stages. Among the candidate pathways we evaluated, genes in the jasmonic acid pathway were the most significantly enriched for divergent gene expression. This includes the most differentially expressed gene in our analyses, which is a key gene (cytochrome P450 CYP94B1) involved in the degradation of bioactive jasmonic acid. Our gene co-expression network analysis revealed different but complementary insights into the differential regulation of genes between the ecotypes, especially at a more microscopic level of these organisms. Overall, our research further supports the hypothesis that plant hormone pathways play a crucial role in the evolution of plant ecotypes and, consequently, the emergence of new species.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70080"},"PeriodicalIF":3.9,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144843897","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}