Molecular Ecology最新文献

{"title":"Independent Genetic Mapping Experiments Identify Diverse Molecular Determinants of Host Adaptation in a Generalist Herbivore.","authors":"Ernesto Villacis-Perez, Femke De Graeve, Berdien De Beer, Seham Ali Alshami, Rick De Jong, Tim De Meyer, Thomas Van Leeuwen","doi":"10.1111/mec.17618","DOIUrl":"https://doi.org/10.1111/mec.17618","url":null,"abstract":"<p><p>Interactions between plants and herbivores promote evolutionary change. Studying the evolution of herbivore mechanisms aimed to cope with different host plant species is a critical intersection between evolutionary biology and sustainable pest management. Generalist herbivores are of particular interest, as hybridization between genetically distinct populations can increase the standing genetic variation and therefore the adaptive potential of the species. Tetranychus urticae is a generalist arthropod known for its adaptive potential, evidenced in its immense host range and ability to develop metabolic resistance to xenobiotics. However, the molecular underpinnings associated with the potential of host adaptation and the consequences of host adaptation in this, and many other pests remain elusive. Here, we use two independent, empirical approaches to identify and map the genetic basis of host plant performance and adaptation in genetically distinct populations of T. urticae. In the first approach, we subject a genetically diverse mite population to tomato selection and map genomic regions linked to the phenotypic evolution of increased reproductive performance. In the second approach, we map genomic regions responsible for performance on tomato by comparing the genomes of pooled individuals from an F2 backcross between populations with high and low reproductive performance. Both approaches revealed specific and shared genomic regions associated with host plant performance and adaptation and key candidate genes were identified. Our findings highlight the power of spider mite genetic approaches to identify the complex genetic basis of host adaptation in generalist herbivores.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17618"},"PeriodicalIF":4.5,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142826824","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":"Recent Origin of a Range-Restricted Species With Subsequent Introgression in its Widespread Congener in the Phyteuma spicatum Group (Campanulaceae).","authors":"Dennis Larsson, Petra Šarhanová, Ovidiu Paun, Gerald M Schneeweiss","doi":"10.1111/mec.17624","DOIUrl":"https://doi.org/10.1111/mec.17624","url":null,"abstract":"<p><p>Understanding the causes of restricted geographic distributions is of major interest to evolutionary and conservation biologists. Inferring historical factors has often relied on ad hoc interpretations of genetic data, and hypothesis testing within a statistical framework under different demographic scenarios remains underutilised. Using coalescent modelling on RAD-sequencing data, we (i) test hypotheses about the origin of Phyteuma gallicum (Campanulaceae), a range-restricted endemic of central France sympatric with its widespread congener Ph. spicatum, and (ii) date its origin, irrespective of its mode of origin, to test the hypothesis that the restricted range is due to a recent time of origin. The best supported model of origin is one of a dichotomous split of Ph. gallicum, confirmed as distinct species, and the Central European Ph. nigrum with subsequent gene flow between Ph. gallicum and Ph. spicatum. The split of Ph. gallicum and Ph. nigrum is estimated at 45-55,000 years ago. Coalescent modelling on genomic data not only clarified the mode of origin (dichotomous speciation instead of a previously hypothesised hybridogenic origin) but also identified recency of speciation as a sufficient, although likely not the sole, factor to explain the restricted distribution range. Coalescent modelling strongly improves our understanding of the evolution of range-restricted species that are frequently of conservation concern, as is the case for Ph. gallicum.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17624"},"PeriodicalIF":4.5,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823659","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":"Leveraging Transcriptional Signatures of Diverse Stressors for Bumble Bee Conservation.","authors":"Gabriela M Quinlan, Heather M Hines, Christina M Grozinger","doi":"10.1111/mec.17626","DOIUrl":"https://doi.org/10.1111/mec.17626","url":null,"abstract":"<p><p>Organisms in nature are subjected to a variety of stressors, often simultaneously. Foremost among stressors of key pollinators are pathogens, poor nutrition and climate change. Landscape transcriptomics can be used to decipher the relative role of stressors, provided there are unique signatures of stress that can be reliably detected in field specimens. In this study, we identify biomarkers of bumble bee (Bombus impatiens) responses to key stressors by first subjecting bees to various short-term stressors (cold, heat, nutrition and pathogen challenge) in a laboratory setting and assessing their transcriptome responses. Using random forest classification on this whole transcriptome data, we were able to discriminate each stressor. Our best model (tissue-specific model trained on a subset of important genes) correctly predicted known stressors with 92% accuracy. We then applied this random forest model to wild-caught bumble bees sampled across a heatwave event at two sites in central Pennsylvania, US, expected to differ in baseline temperature and floral resource availability. Transcriptomes of bees sampled during the heat wave's peak showed signatures of heat stress, while bees collected in the relatively cooler morning periods showed signatures of starvation and cold stress. We failed to pick up on signals of heat stress shortly after the heatwave, suggesting this set of biomarkers is more useful for identifying acute stressors than long-term monitoring of chronic, landscape-level stressors. We highlight future directions to fine-tune landscape transcriptomics towards the development of better stress biomarkers that can be used both for conservation and improving understanding of stressor impacts on bees.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17626"},"PeriodicalIF":4.5,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142816777","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":"Microbiota Composition Associates With Mosquito Productivity Outcomes in Belowground Larval Habitats.","authors":"Serena Y Zhao, Andrew J Sommer, Dan Bartlett, Justin E Harbison, Patrick Irwin, Kerri L Coon","doi":"10.1111/mec.17614","DOIUrl":"https://doi.org/10.1111/mec.17614","url":null,"abstract":"<p><p>Vector mosquitoes are well-adapted to habitats in urban areas, including belowground infrastructure such as stormwater systems. As a major source of larval habitat in population centers, control of larval populations in stormwater catch basins is an important tool for control of vector-borne disease. Larval development and adult phenotypes driving vectorial capacity in mosquitoes are modulated by the larval gut microbiota, which is recruited from the aquatic environment in which larvae develop. Laboratory studies have quantified microbe-mediated impacts on individual mosquito phenotypes, but more work is needed to characterise how microbiota variation shapes population-level outcomes. Here, we evaluated the relationship between habitat microbiota variation and mosquito population dynamics by simultaneously characterising microbiota diversity, water quality, and mosquito productivity in a network of stormwater catch basins in the Chicago metropolitan area. High throughput sequencing of 16S rRNA gene amplicons from water samples collected from 60 basins over an entire mosquito breeding season detected highly diverse bacterial communities that varied with measures of water quality and over time. In situ measurements of mosquito abundance in the same basins further varied by microbiota composition and the relative abundance of specific bacterial taxa. Altogether, these results illustrate the importance of habitat microbiota in shaping ecological processes that affect mosquito populations. They also lay the foundation for future studies to characterise the mechanisms by which specific bacterial taxa impact individual and population-level phenotypes related to mosquito vectorial capacity.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17614"},"PeriodicalIF":4.5,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823623","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":"Pleistocene Glaciation Drove Shared Population Coexpansion in Eastern North American Snakes.","authors":"Sean Harrington, Isaac Overcast, Edward A Myers, Frank T Burbrink","doi":"10.1111/mec.17625","DOIUrl":"https://doi.org/10.1111/mec.17625","url":null,"abstract":"<p><p>Glacial cycles during the Pleistocene had profound impacts on local environments and climatic conditions. In North America, some regions that currently support diverse biomes were entirely covered by ice sheets, while other regions were environmentally unsuitable for the organisms that live there now. Organisms that occupy these regions in the present day must have expanded or dispersed into these regions since the last glacial maximum, leading to the possibility that species with similar geographic distributions may show temporally concordant population size changes associated with these warming trends. We examined 17 lineages from 9 eastern North American snake species and species complexes to test for a signal of temporally concordant coexpansion using a machine learning approach. We found that the majority of lineages show population size increases towards the present, with evidence for coexpansion in five out of fourteen lineages, while expansion in others was idiosyncratic. We also examined relationships between genetic distance and current environmental predictors and showed that genomic responses to environmental predictors are not consistent among species. We, therefore, conclude that Pleistocene warming resulted in population size increases in most eastern North American snake species, but variation in environmental preferences and other species-specific traits results in variance in the exact timing of expansion.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17625"},"PeriodicalIF":4.5,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823658","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":"Defaunation Increases Clustering and Fine-Scale Spatial Genetic Structure in a Small-Seeded Palm Despite Remaining Small-Bodied Frugivores.","authors":"Therese Lamperty, Zoe Diaz-Martin, Varun Swamy, Jordan Karubian, Juanita Choo, Amy E Dunham","doi":"10.1111/mec.17620","DOIUrl":"https://doi.org/10.1111/mec.17620","url":null,"abstract":"<p><p>Anthropogenic pressures such as hunting are increasingly driving the localised functional extinctions of large- and medium-sized wildlife in tropical forests, a phenomenon broadly termed 'defaunation'. Concurrently in these areas, smaller-bodied species benefit from factors such as competitive release and increase in numbers. This transformation of the wildlife community can impact species interactions and ecosystem services such as seed dispersal and seed-mediated geneflow with far-reaching consequences. Evidence for negative genetic effects following defaunation is well-documented in large-seeded plants that require large frugivores for long-distance seed dispersal. However, how defaunation affects plants with small or medium-small seeds (< 1.5 cm), which tend to be consumed and dispersed by frugivorous mutualists of a range of body sizes and responses to anthropogenic threats, is not well understood. To better understand defaunation's impacts on tropical plant communities, we investigated spatial and genetic patterns in a hyperabundant medium-to-small-seeded palm, Euterpe precatoria in three sites with different defaunation levels. Results indicate that defaunation is associated with higher fine-scale spatial genetic structure among seedlings and increased spatial clustering within seedling cohorts and between seedlings and conspecific adults, as well as a reduction in nearest-neighbour distances between seedlings and conspecific adults. There were no clear effects on inbreeding or genetic diversity. However, we caution these trends may indicate that defaunation reduces seed dispersal services for species previously presumed to be robust to deleterious effects of losing large frugivores by virtue of having smaller seeds and broad suites of dispersal agents, and negative downstream effects on genetic diversity could occur.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17620"},"PeriodicalIF":4.5,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142816773","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":"Ancient Hybridisation Fuelled Diversification in Acropora Corals.","authors":"Tianzhen Wu, Alan Ningyuan Xu, Yanli Lei, Haijun Song","doi":"10.1111/mec.17615","DOIUrl":"https://doi.org/10.1111/mec.17615","url":null,"abstract":"<p><p>Introgression is the infiltration or flow of genes from one species to another through hybridisation followed by backcrossing. This may lead to incorrect phylogenetic reconstruction or divergence-time estimation. Acropora is a dominant genus of reef-building corals; however, whether this group has an introgression history before their diversification remains unclear, and previous divergence-time estimates of Acropora have not considered the impact of introgression. In this study, we broke through the limitation of a few genes and a few species and proved the existence of ancient introgression in the evolution of Acropora from whole-genome protein-coding sequences. We inferred 21.9% of all triplet loci (homologous loci from three different species) with a history of introgression and a series of introgression events with a genetic material contribution of up to 30.9% before diversification. Furthermore, 7756 nuclear loci were clustered into three groups using a multidimensional scaling algorithm, the heterogeneity of which resulted in different phylogenetic relationships. The diversification time of Acropora was estimated to be middle to late Miocene when we retained only the gene group with the lowest degree of introgression. The collision of Australia with the Pacific arcs and the Southeast Asian margin in the early Miocene, and a series of cooling events in the middle to late Miocene, may provide geographical and climatic conditions for the diversification of Acropora, respectively. Therefore, our results indicate that at the genome-wide level, ancient introgressive hybridisation may have promoted the radiation evolution of Acropora. Based on our results, the influence of introgression should be taken into account when reconstructing phylogenetic relationships and evaluating divergence time.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17615"},"PeriodicalIF":4.5,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142816769","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":"Parallel Signatures of Diet Adaptation in the Invasive Common Myna Genome.","authors":"Kamolphat Atsawawaranunt, Katarina C Stuart, Annabel Whibley, Kyle M Ewart, Richard E Major, Rebecca N Johnson, Anna W Santure","doi":"10.1111/mec.17607","DOIUrl":"https://doi.org/10.1111/mec.17607","url":null,"abstract":"<p><p>Invasive species offer uniquely replicated model systems to study rapid adaptation. The common myna (Acridotheres tristis) has been introduced to over a dozen countries and is classified as one of the most invasive birds in the world. Their multiple invasions provide an opportunity to identify repeated adaptation, as invasive populations originated from multiple source populations. We compared whole-genome resequencing data from 80 individuals from four native and seven invasive populations, representing two independent introduction pathways. Results from two different selection scan methods were combined and identified a strongly selected region on chromosome 8 that spans two copies of AMY2A, part of the alpha-amylase gene family, a putative ncRNA and an insertion-deletion structural variant (SV) that contains an ERVK transposable element (TE). Outlier SNPs and the SV are polymorphic in native populations, but fixed or close-to-fixed in the two invasive pathways, with the fixation of the same alleles in two independent lineages providing evidence for parallel selection on standing variation. Intriguingly, the second copy of AMY2A has a non-conservative missense mutation at a phylogenetically conserved site. This mutation, alongside variation in the SV, TE and ncRNA, provide possible routes for changes to protein function or expression. AMY2A has been associated with human commensalism in house sparrows, and genes in this family have been linked to adaptation to high-starch diets in humans and dogs. This study illustrates the value of replicated analyses within and across species to understand rapid adaptation at the molecular level.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17607"},"PeriodicalIF":4.5,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142816781","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":"Invasive Buffelgrass, Cenchrus ciliaris, Balances Opportunistic Acquisition of Foliar fungi With Host and Environmental Filtering in Its Introduced Range.","authors":"Elizabeth A Bowman, Christine V Hawkes, Nathan Jones, Robert M Plowes, Dino J Martin, Lawrence E Gilbert","doi":"10.1111/mec.17609","DOIUrl":"https://doi.org/10.1111/mec.17609","url":null,"abstract":"<p><p>Plants host diverse assemblages of fungi on their foliar tissues, both in internal compartments and on exterior surfaces. When plant distributions shift, they can move with their fungal associates (i.e., co-introduction) or acquire new associates present in the novel environment (host-jumping). The fungal communities that plants acquire influence a plant's ability to establish and spread in this new environment. Here, we aimed to assess whether invasive C. ciliaris hosts similar groups of fungi in its native and introduced ranges and to evaluate community overlap of fungi associated with foliar tissue of C. ciliaris and native and non-native plants within the introduced range. In the introduced range, the majority of OTUs associated with C. ciliaris were not found in its native range, although 3.2% of OTUs were common to both ranges. Of these shared OTU, 77.6% were found on co-occurring natives and non-natives in the introduced range, whereas 22.4% were unique to C. ciliaris indicating a possible co-introduction. Fungal communities within the introduced range contained a higher proportion of generalist symbionts and increased heterogeneity of foliar communities than in its native range. Within the introduced range, host phylogenetic distance explained more variation than native status. Our findings provide evidence that non-natives acquire fungi opportunistically from their environment, although host and environmental filtering is present suggesting that successful invasive plants may be able to limit the effect of poor symbionts and select for better ones. Future experimental work will be needed to confirm the occurrence of host selection and identify its mechanisms.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17609"},"PeriodicalIF":4.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811708","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":"Phylosymbiosis and Elevated Cancer Risk in Genetically Depauperate Channel Island Foxes.","authors":"Alexandra L DeCandia, Jasmine Lu, Emily E Hamblen, Lara J Brenner, Julie L King, Calypso N Gagorik, Juliann T Schamel, Stacy S Baker, Francesca J Ferrara, Melissa Booker, Andrew Bridges, Cesar Carrasco, Bridgett M vonHoldt, Klaus-Peter Koepfli, Jesús E Maldonado","doi":"10.1111/mec.17610","DOIUrl":"https://doi.org/10.1111/mec.17610","url":null,"abstract":"<p><p>Examination of the host-associated microbiome in wildlife can provide critical insights into the eco-evolutionary factors driving species diversification and response to disease. This is particularly relevant for isolated populations lacking genomic variation, a phenomenon that is increasingly common as human activities create habitat 'islands' for wildlife. Here, we characterised the gut and otic microbial communities of one such species: Channel Island foxes (Urocyon littoralis). The gut microbiome provided evidence of phylosymbiosis by reflecting the host phylogeny, geographic proximity, history of island colonisation and contemporary ecological differences, whereas the otic microbiome primarily reflected geography and disease. Santa Catalina Island foxes are uniquely predisposed to ceruminous gland tumours following infection with Otodectes cynotis ear mites, while San Clemente and San Nicolas Island foxes exhibit ear mite infections without evidence of tumours. Comparative analyses of otic microbiomes revealed that mite-infected Santa Catalina and San Clemente Island foxes exhibited reduced bacterial diversity, skewed abundance towards the opportunistic pathogen Staphylococcus pseudintermedius and disrupted microbial community networks. However, Santa Catalina Island foxes uniquely harboured Fusobacterium and Prevotella bacteria as potential keystone taxa. These bacteria have previously been associated with colorectal cancer and may predispose Santa Catalina Island foxes to an elevated cancer risk. In contrast, mite-infected San Nicolas Island foxes maintained high bacterial diversity and robust microbial community networks, suggesting that they harbour more resilient microbiomes. Considered together, our results highlight the diverse eco-evolutionary factors influencing commensal microbial communities and their hosts and underscore how the microbiome can contribute to disease outcomes.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17610"},"PeriodicalIF":4.5,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142798795","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}