Molecular Ecology最新文献

{"title":"Reduced Parallel Gene Expression Evolution With Increasing Genetic Divergence—A Hallmark of Polygenic Adaptation","authors":"Dagny A. V. Thorhölludottir,&nbsp;Sheng-Kai Hsu,&nbsp;Neda Barghi,&nbsp;François Mallard,&nbsp;Viola Nolte,&nbsp;Christian Schlötterer","doi":"10.1111/mec.17803","DOIUrl":"10.1111/mec.17803","url":null,"abstract":"<p>Parallel evolution, the repeated evolution of similar traits in independent lineages, is a topic of considerable interest in evolutionary biology. Although previous studies have focused on the parallelism of phenotypic traits and their underlying genetic basis, the extent of parallelism at the level of gene expression across different levels of genetic divergence is not yet fully understood. This study investigates the evolution of gene expression in replicate <i>Drosophila</i> populations exposed to the same novel environment at three divergence levels: within a population, between populations and between species. We show that adaptive gene expression changes are more heterogeneous with increasing genetic divergence between the compared groups. This finding suggests that the adaptive architecture—comprising factors such as allele frequencies and the effect size of contributing loci—becomes more distinct with increasing divergence. As a result, this leads to a reduction in parallel gene expression evolution. This result implies that redundancy is a crucial factor in both genetic selection responses and gene expression evolution. Hence, our findings are consistent with the omnigenic model, which posits that selection acts on higher-order phenotypes. This work contributes to our understanding of phenotypic evolution and the complex interplay between genomic and molecular responses.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 12","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17803","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075082","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":"Using Fitness Surfaces to Better Link Conservation Breeding Programmes With Wild Population Recovery","authors":"Drew Sauve,&nbsp;Hana Thompson,&nbsp;Amy A. Chabot,&nbsp;Denis Réale","doi":"10.1111/mec.17798","DOIUrl":"10.1111/mec.17798","url":null,"abstract":"<p>Fitness surfaces offer a valuable tool for bridging the gap between captive breeding programmes and wild populations. By quantifying the relationship between phenotypes and reproductive success in captive and wild settings, fitness surfaces can help identify the fitness consequences of phenotypic change in either environment. Measuring fitness surfaces in captive and wild populations from the same species would help us to predict the success of reintroduction efforts and help inform the selection of release candidates. Overall, the inclusion of fitness surface estimates into conservation breeding programmes increases the effectiveness of reintroduction efforts and should improve our understanding of evolution at the interface of human-managed and wild populations. Beyond conservation breeding, fitness surfaces may have applications for at-risk species such as predicting outcomes in range expansions, translocation or under changing environmental conditions.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 12","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17798","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075104","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":"Spatiotemporal Dynamics of Non-Ecological Speciation in Rubyspot Damselflies (Hetaerina spp.)","authors":"C. Patterson,&nbsp;A. Brennan,&nbsp;H. Cowling,&nbsp;A. González-Rodríguez,&nbsp;G. F. Grether,&nbsp;L. Mendoza Cuenca,&nbsp;M. Springer,&nbsp;Y. M. Vega-Sánchez,&nbsp;J. Drury","doi":"10.1111/mec.17797","DOIUrl":"10.1111/mec.17797","url":null,"abstract":"<p>Non-ecological speciation is a common mode of speciation, which occurs when allopatric lineages diverge in the absence of pronounced ecological differences. Yet, relative to other speciation mechanisms, non-ecological speciation remains understudied. Numerous damselfly clades are characterised as non-adaptive radiations (the result of several rounds of non-ecological speciation without subsequent divergence), but there are few damselfly lineages for which we have a detailed understanding of the spatiotemporal dynamics of divergence. Recent phylogeographic analyses demonstrate that American rubyspot damselflies (<i>Hetaerina americana</i> sensu lato) actually comprise at least two cryptic lineages that coexist sympatrically across most of Mexico. To broaden our understanding of the dynamics of diversification to other rubyspot lineages, we investigated the phylogeographic history of smoky rubyspot damselflies (<i>Hetaerina titia</i>) using genomic data collected across Central and North America. Unexpectedly, we found evidence of reproductive isolation between the highly genetically differentiated Pacific and Atlantic lineages of <i>H. titia</i> in a narrow secondary contact zone on the Isthmus of Tehuantepec, Mexico. We then fit models of historical demography to both <i>H. americana</i> sensu lato and <i>H. titia</i> to place these comparisons in a temporal context. Our findings indicate that Pacific and Atlantic lineages of <i>H. titia</i> split more recently than the broadly sympatric lineages within <i>H. americana</i> sensu lato, supporting key assumptions of the non-ecological speciation model and demonstrating that these two pairs of sister lineages are at different stages of the speciation cycle.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 12","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17797","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075085","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 Genetics of Host Plant Acceptance in Pea Aphids.","authors":"Isobel Eyres, Hannah Fenton, Jean Christophe Simon, Jean Peccoud, Julia Ferrari, Roger Butlin, Carole M Smadja","doi":"10.1111/mec.17795","DOIUrl":"https://doi.org/10.1111/mec.17795","url":null,"abstract":"<p><p>The evolution of host-associated sympatric populations in phytophagous insects (so called \"host races\") connects adaptive divergence to barriers to gene flow. Pea aphid (Acyrthosiphon pisum) host races specialise on legume species, and because host plant choice leads to assortative mating, the genetic basis of host plant acceptance is key to understanding speciation. Aphids use smell and taste in their host plant selection. While chemosensory genes frequently emerge as \"outliers\" in genome scans, their link to plant acceptance behaviour remains unclear. We examined the genetic basis of host-associated phenotypes using an F2 cross between two pea aphid host-associated races (specialised on alfalfa-Medicago sativa- and pea-Pisum sativum), assaying behaviour on both host plants and conducting QTL and regional heritability analyses based on a high-resolution linkage map. We identified five regions of moderate effect associated with acceptance of alfalfa, two with pea acceptance and two with survival on alfalfa. Two QTLs, one for alfalfa and one for pea acceptance, are located within a large rearranged region on chromosome 1, while other QTLs linked to alfalfa acceptance and survival are in the same region on chromosome 3-linking host plant choice to fitness. These findings highlight the polygenic basis of acceptance behaviour and the role of gene clustering and chromosomal rearrangements in promoting coupling among barrier loci. We identified 60 chemosensory genes within regions connected to acceptance, 24 of which were divergent among pea aphid races in previous genome scan or gene expression analyses. Evidence linking these genes to acceptance phenotypes supports their role in determining host plant specificity and as barrier loci contributing to pea aphid speciation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17795"},"PeriodicalIF":4.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075097","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":"Diet Driven Differences in Host Tolerance Are Linked to Shifts in Global Gene Expression in a Common Avian Host-Pathogen System","authors":"Erin L. Sauer,&nbsp;Carson Stacy,&nbsp;Weston Perrine,&nbsp;Ashley C. Love,&nbsp;Jeffrey A. Lewis,&nbsp;Sarah E. DuRant","doi":"10.1111/mec.17793","DOIUrl":"10.1111/mec.17793","url":null,"abstract":"<p>Wildlife have become increasingly dependent on anthropogenic resources, altering interactions between individuals and subsequently disease transmission. Further, nutritional quantity and quality impact an individual's ability to mitigate damage caused by infectious disease. Thus, understanding how diet affects immune function is critical for predicting disease severity and transmission. Here, we use transcriptomics to explore the previously unstudied molecular mechanisms underpinning diet-driven differences in pathogen tolerance. Using a widespread avian bacterial pathogen, we find significant diet-driven differences in the expression of many genes encoding immune response and translational machinery proteins. Prior to infection, protein-fed birds are more transcriptionally primed for infection than lipid-fed birds, resulting in greater tolerance for protein-fed birds during the recovery period. Given the importance of human supplemented food in wildlife disease systems, the molecular mechanisms by which interactions between diet and infection emerge provide insight into the ecological and immunological consequences of human behaviour on wildlife disease.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 12","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17793","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954044","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":"Hydrological Connectivity Enhances Fish Biodiversity in Amazonian Mining Ponds: Insights From eDNA and Traditional Sampling","authors":"Camila Timana-Mendoza,&nbsp;Alonso Reyes-Calderón,&nbsp;Patrick Venail,&nbsp;Ricardo Britzke,&nbsp;Monica C. Santa-Maria,&nbsp;Julio M. Araújo-Flores,&nbsp;Miles Silman,&nbsp;Luis E. Fernandez","doi":"10.1111/mec.17784","DOIUrl":"10.1111/mec.17784","url":null,"abstract":"<p>Artisanal and small-scale gold mining (ASGM) expansion in the Madre de Dios region of the Peruvian Amazon has transformed primary forests into a novel wetland complex of thousands of abandoned mining ponds. Despite their ecological relevance, post-mining recovery of these systems remains understudied, particularly regarding fish biodiversity and recolonisation. In this study, we evaluate fish community richness and composition in mining ponds of different dimensions, years post abandonment, physicochemical properties and degree of pulse flood connectivity using traditional collection-based methods and environmental DNA (eDNA) with the 12S and COI markers. We compared these two methods of biodiversity inventory and contrasted results from ASGM waterbodies with those obtained from nearby pristine oxbow lakes. Overall, we registered more fish richness at all sites using eDNA versus traditional methods, especially with the 12S marker. We identified 14 and 13 unique genera using traditional methods and eDNA, respectively, with 40 genera detected by both approaches, evidencing their complementarity. Notably, we found that the degree of pulse flooding connectivity was the main predictor of species richness among the abandoned mining ponds (<i>p</i>-value &lt; 0.05). We registered 11–22, 23–71 and 56 morphospecies in non-flooded mining ponds, pulse flooded mining ponds and nearby oxbow lakes, respectively. Furthermore, the fish community composition of mining ponds most influenced by pulse flooding was similar to that of pristine lakes. Our findings highlight the role of hydrological connectivity in ecological recovery within mining-impacted wetlands. Future restoration efforts should enhance aquatic connectivity to accelerate recovery in post-mining environments.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 11","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17784","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952139","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":"Urbanisation Affects Millipede Gut Microbiota Communities by Impeding Host Gene Flow","authors":"Hongyi Liu,&nbsp;Tangjun Xu,&nbsp;Wentao Ye,&nbsp;Yuanyuan Li,&nbsp;Ke He,&nbsp;Ying Zhu,&nbsp;Xiaoming Zou,&nbsp;Honghua Ruan","doi":"10.1111/mec.17792","DOIUrl":"10.1111/mec.17792","url":null,"abstract":"<div>\u0000 \u0000 <p>Urbanisation leads to the alteration of the living environment of soil fauna and isolates them, significantly influencing the evolutionary processes of soil fauna. Faunal gut microbiota serves to bridge hosts with changing environments; thus, they are viable indicators of host adaptation. For this study, we investigated how urbanisation affects the gut microbiota and population genetics of <i>Spirobolus bungii</i>. The results revealed that urbanisation did not affect the genetic diversity of <i>S. bungii</i> populations but acted as a barrier, which hindered its gene flow. Genetic differentiation was associated with the compositional similarity of gut microbiota among populations; however, environmental distinctions had no impact. Our findings highlighted that gene flow between populations was a critical factor, which supported the premise that urbanisation influences the gut microbiota compositions of species. This study contributes to a deeper understanding of the mechanisms that underlie changes in faunal gut microbiota driven by gene flow in the context of urbanisation.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 11","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952141","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":"Multiple Origins or Widespread Gene Flow in Agricultural Fields? Regional Population Genomics of Herbicide Resistance in Bromus tectorum","authors":"Victor H. V. Ribeiro,&nbsp;Joseph Gallagher,&nbsp;Carol Mallory-Smith,&nbsp;Judit Barroso,&nbsp;Caio A. C. G. Brunharo","doi":"10.1111/mec.17791","DOIUrl":"10.1111/mec.17791","url":null,"abstract":"<p>The repeated evolution of herbicide resistance in agriculture provides an unprecedented opportunity to understand how organisms rapidly respond to strong anthropogenic-driven selection pressure. We recently identified agricultural populations of the grass species <i>Bromus tectorum</i> L. with resistance to multiple herbicides. To understand the evolutionary origins and spread of resistance, we investigated the resistance mechanisms to acetolactate synthase (ALS) inhibitors and photosystem II inhibitors, two widely used herbicide modes of action, in 49 <i>B. tectorum</i> populations. We assessed the genetic diversity, structure and relatedness in a subset of 21 populations. Resistance to ALS inhibitors was associated with multiple nonsynonymous mutations in <i>ALS</i>, the target site gene, despite the relatively small geographic region where populations originated, suggesting ALS inhibitor resistance evolution occurred multiple times in the region. We also found evidence that mechanisms not related to the target site evolved and were common in the populations studied. Resistance to photosystem II inhibitors was confirmed in two populations and was conferred by nonsynonymous mutations in the plastid gene <i>psbA</i>. Population genomics analyses suggested that ALS resistance in most populations, at the nucleotide level, spread via gene flow, except for one population where we found evidence that Pro-197-His mutations may have evolved in three separate events. Our results suggest that both gene flow via pollen and/or seed dispersal and multiple local evolutionary events were involved in the spread of herbicide-resistant <i>B. tectorum</i>. Our results provide an empirical example of the rapid repeated evolution of a trait under strong anthropogenic selection and elucidate the evolutionary origins of herbicide resistance in a plant species of agricultural importance.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 11","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17791","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143958505","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":"Putting Structural Variants Into Practice: The Role of Chromosomal Inversions in the Management of Marine Environments.","authors":"Nadja M Schneller, Jan M Strugnell, Matt A Field, Kerstin Johannesson, Ira Cooke","doi":"10.1111/mec.17776","DOIUrl":"https://doi.org/10.1111/mec.17776","url":null,"abstract":"<p><p>Major threats to marine species and ecosystems include overfishing, invasive species, pollution and climate change. The changing climate not only imposes direct threats through the impacts of severe marine heatwaves, cyclones and ocean acidification but also complicates fisheries and invasive species management by driving species range shifts. The dynamic nature of these threats means that the future of our oceans will depend on the ability of species to adapt. This has led to calls for genetic interventions focussed on enhancing species' adaptive capacity, including translocations, restocking and selective breeding. Assessing the benefits and risks of such approaches requires an improved understanding of the genetic architecture of adaptive variation, not only in relation to climate-resilient phenotypes but also locally adapted populations and the fitness of hybrids. Large structural genetic variants such as chromosomal inversions play an important role in local adaptation by linking multiple adaptive loci. Consequently, inversions are likely to be particularly important when managing for adaptive capacity. However, under some circumstances, they also accumulate deleterious mutations, potentially increasing the risk of inbreeding depression. Genetic management that takes account of these dual roles on fitness is likely to be more effective at ensuring population persistence. We summarise evolutionary factors influencing adaptive and deleterious variation of inversions, review inversions found in marine taxa, and provide a framework to predict the consequences of ignoring inversions in key management scenarios. We conclude by describing practical methods to bridge the gap between evolutionary theory and practical application of inversions in conservation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17776"},"PeriodicalIF":4.5,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143953560","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":"Endangered Deep-Snow Mountain Caribou Have a Distinct Winter Diet and Gut Microbiome That May Be Altered by Maternal Penning","authors":"Scott Sugden,&nbsp;Robert Serrouya,&nbsp;Lalenia Neufeld,&nbsp;Helen Schwantje,&nbsp;Colleen Cassady St. Clair,&nbsp;Lisa Stein,&nbsp;Toby Spribille","doi":"10.1111/mec.17783","DOIUrl":"10.1111/mec.17783","url":null,"abstract":"<p>Understanding species- or population-specific dietary specialisation is key to informing habitat conservation needs and successful <i>ex situ</i> recovery programs for many endangered species. One of the most endangered populations in Canada, the behaviourally distinct deep-snow ecotype of the Southern Mountain caribou, is characterised by a winter diet of arboreal rather than terrestrial lichens. We hypothesised that this dietary variation would produce a distinct gut microbiome in deep-snow mountain caribou relative to their shallow-snow counterparts. We additionally hypothesised that the temporary alteration of natural diets for <i>ex situ</i> conservation programs, including the provision of commercial pelleted feed and volunteer-collected lichens during maternity penning of pregnant cows, may alter this specialised microbiome. Here, we use faecal DNA metabarcoding to compare diet and gut microbiome composition among various herds of deep- and shallow-snow caribou, captive deep-snow caribou from the Revelstoke maternity pen, and semi-domesticated reindeer. Our results confirm that free-ranging deep-snow caribou specialise on the arboreal hair lichens <i>Bryoria</i> and <i>Nodobryoria,</i> and we show that this correlates with a microbiome distinct from that of shallow-snow caribou specialising on the terrestrial lichens <i>Cladonia</i> and <i>Stereocaulon</i>. We also show that maternity penning of deep-snow caribou significantly altered forage consumption and microbiome composition: penned caribou consumed more foliose lichens and had a distinct microbiome compared to free-ranging caribou. Our results suggest that managers should carefully consider the preferred forage of caribou populations when designing interventions that require diet modification. We further suggest that faecal samples of caribou and other dietary specialists be routinely monitored for diet and microbiome composition, especially during periods of captivity or diet modification, as an additional component of conservation assessments.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 11","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17783","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952472","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}