Molecular Ecology最新文献

{"title":"Potential Adaptive Introgression From Dogs in Iberian Grey Wolves (Canis lupus).","authors":"Carlos Sarabia, Isabel Salado, Alberto Fernández-Gil, Bridgett M vonHoldt, Michael Hofreiter, Carles Vilà, Jennifer A Leonard","doi":"10.1111/mec.17639","DOIUrl":"https://doi.org/10.1111/mec.17639","url":null,"abstract":"<p><p>Invading species along with increased anthropogenization may lead to hybridization events between wild species and closely related domesticates. As a consequence, wild species may carry introgressed alleles from domestic species, which is generally assumed to yield adverse effects in wild populations. The opposite evolutionary consequence, adaptive introgression, where introgressed genes are positively selected in the wild species, is possible but has rarely been documented. Grey wolves (Canis lupus) are widely distributed across the Holarctic and frequently coexist with their close relative, the domestic dog (C. familiaris). Despite ample opportunity, hybridization rarely occurs in most populations. Here we studied the geographically isolated grey wolves of the Iberian Peninsula, who have coexisted with a large population of loosely controlled dogs for thousands of years in a human-modified landscape. We assessed the extent and impact of dog introgression on the current Iberian grey wolf population by analysing 150 whole genomes of Iberian and other Eurasian grey wolves as well as dogs originating from across Europe and western Siberia. We identified almost no recent introgression and a small (< 5%) overall ancient dog ancestry. Using a combination of single scan statistics and ancestry enrichment estimates, we identified positive selection on six genes (DAPP1, NSMCE4A, MPPED2, PCDH9, MBTPS1, and CDH13) for which wild Iberian wolves carry alleles introgressed from dogs. The genes with introgressed and positively selected alleles include functions in immune response and brain functions, which may explain some of the unique behavioural phenotypes in Iberian wolves such as their reduced dispersal compared to other wolf populations.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17639"},"PeriodicalIF":4.5,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941646","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":"Change Your Diet: How CO₂, Plant Phenology and Genotype Alter Grapevine Quality and Affect Performance and Larval Transcriptome of an Insect Herbivore.","authors":"Christine Becker, Christof B Steingass, Heiko Vogel, Annette Reineke","doi":"10.1111/mec.17636","DOIUrl":"https://doi.org/10.1111/mec.17636","url":null,"abstract":"<p><p>Herbivorous insects need to cope with changing host plant biochemistry caused by abiotic and biotic impacts, to meet their dietary requirements. Larvae of the multivoltine European grapevine moth Lobesia botrana, one of the main insect pests in viticulture, feed on both flowers and berries. The nutritional value and defence compounds of these organs are changing with plant phenology and are affected by climate change which may accordingly alter plant-insect interactions. Here, we assessed the impacts of future elevated atmospheric CO₂ concentrations on the host plant quality of different grapevine organs and the larval performance and the transcriptome of L. botrana. Using the Geisenheim VineyardFACE facility, where 'Riesling' and 'Cabernet Sauvignon' were cultivated in the field under ambient or elevated (ca. + 20%) atmospheric CO₂ concentrations, we found that nutrient (amino acids and sugars) and defence compound (phenolic compounds) concentrations of inflorescences and ripening berries differed strongly due to plant phenology and less due to cultivar and CO₂ concentration. Assessing global gene expression after feeding on the respective organs, we found that larval transcriptomic plasticity largely mirrored the plant biochemical plasticity. Larval relative growth rate differed between treatments in a plant phenology-dependent manner. Grape berries contained higher amino acid concentrations and altered phenolics profiles after larval feeding. In the near future, the grapevine-L. botrana interaction will probably change less because of elevated CO₂ concentrations than it does currently during one season. Changes associated with plant phenology, however, may be relevant for contemporary pest management.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17636"},"PeriodicalIF":4.5,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941989","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":"Evolved and Plastic Gene Expression in Adaptation of a Specialist Fly to a Novel Niche","authors":"Rachel A. Steward,&nbsp;Jesús Ortega Giménez,&nbsp;Shruti Choudhary,&nbsp;Oliver Moss,&nbsp;Yi Su,&nbsp;Olivier Van Aken,&nbsp;Anna Runemark","doi":"10.1111/mec.17653","DOIUrl":"10.1111/mec.17653","url":null,"abstract":"<p>How gene expression evolves to enable divergent ecological adaptation and how changes in gene expression relate to genomic architecture are pressing questions for understanding the mechanisms enabling adaptation and ecological speciation. Furthermore, how plasticity in gene expression can both contribute to and be affected by the process of ecological adaptation is crucial to understanding gene expression evolution, colonisation of novel niches and response to rapid environmental change. Here, we investigate the role of constitutive and plastic gene expression differences between host races, or host-specific ecotypes, of the peacock fly <i>Tephritis conura</i>, a thistle bud specialist. By cross-fostering larvae to new buds of their natal host plant or the alternative, novel host plant, we uncover extensive constitutive differences in gene expression between the host races, especially genes associated with processing of host plant chemicals. However, evidence for expression plasticity was minimal and limited to the ancestral host race. Genes with host race-specific expression are found more often than expected within a large inversion in the <i>T. conura</i> genome, adding to evidence that inversions are important for enabling diversification in the face of gene flow and underscores that altered gene expression may be key to understanding the evolutionary consequences of inversions.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 4","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17653","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941990","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":"Plio-Pleistocene Environmental Changes Drove the Settlement of Aotearoa New Zealand by Australian Open-Habitat Bird Lineages","authors":"Pascale Lubbe,&nbsp;Nicolas J. Rawlence,&nbsp;Nicolas Dussex,&nbsp;Olga Kardialsky,&nbsp;Michael Knapp","doi":"10.1111/mec.17648","DOIUrl":"10.1111/mec.17648","url":null,"abstract":"<div>\u0000 \u0000 <p>In a changing environment, vacant niches can be filled either by adaptation of local taxa or range-expanding invading species. The relative tempo of these patterns is of key interest in the modern age of climate change. Aotearoa New Zealand has been a hotspot of biogeographic research for decades due to its long-term isolation and dramatic geological history. An island with high levels of faunal endemicity, it is a system well suited to studying the relative effects of in situ evolution versus dispersal in determining faunal assemblages, while its turbulent climate and geological history provide valuable insights into the evolutionary impacts of environmental changes. Such investigations are of urgent importance given predicted climate change and human impacts rapidly affecting environments globally. Here, we analyse the divergence dates of nearly all endemic Aotearoa New Zealand bird species from their overseas relatives to assess the role of environmental changes in driving speciation and colonisation, with special regard to cooling climate during the Pliocene and Pleistocene. We uncover a wave of colonisation events by Australian open-habitat adapted species since the Pliocene that peaked at the beginning of the Pleistocene. Furthermore, we highlight an even distribution of divergence dates in forest-adapted taxa through time, consistent with millions of years of extensive forest cover. Finally, we note parallels to the modern-day establishment of new bird populations from Australia and suggest this is largely influenced by anthropogenic land-use patterns. This research contributes to the growing body of work recognising the long-lasting impacts of Pleistocene climate change on Aotearoa New Zealand's avifauna, and reinforces biological invasions as a key evolutionary response to changing environmental conditions.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 4","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941481","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":"The Impact of Administrative Districts and Urban Landscape on the Dispersal of Aedes aegypti via Genetic Differentiation","authors":"Chin-Gi Huang,&nbsp;Yi-Cheng Tseng,&nbsp;Tsung-Han Yu,&nbsp;Hui-Ching Cheng,&nbsp;Tsung-Ju Tsai,&nbsp;Jou-Hsin Ting,&nbsp;Hsin-Yi Ho,&nbsp;Ya-Zhe Lee,&nbsp;Yen-Chieh Chiu,&nbsp;Yu-Ting Huang,&nbsp;Ting-Chun Shih,&nbsp;Hsiang-Yu Hsiao,&nbsp;Yi-Jun Wu,&nbsp;Shi-Ya Li,&nbsp;Yu-Chi Huang,&nbsp;Yung-Cheng Yang,&nbsp;Pei-Qi Chen,&nbsp;Chun-Yi Hsiao,&nbsp;Hurng-Yi Wang","doi":"10.1111/mec.17644","DOIUrl":"10.1111/mec.17644","url":null,"abstract":"<div>\u0000 \u0000 <p>Mosquito-borne diseases affect millions and cause numerous deaths annually. Effective vector control, which hinges on understanding their dispersal, is vital for reducing infection rates. Given the variability in study results, likely due to environmental and human factors, gathering local dispersal data is critical for targeted disease control. To analyse the spread and differentiation of <i>Aedes aegypti</i> in southern Taiwan, we established a dengue vector monitoring network in Southern Taiwan's cities. This network employed GPS-equipped ovitraps to gather eggs that were subsequently hatched in the laboratory and genotyped using genome-wide SNP markers. From 168 individuals, we identified 757,238 SNPs for detailed analysis. The estimated effective dispersal distance was 154 m (95% CI: 126–180 m), consistent with prior mark-release-recapture (MRR) estimates. We discovered that geographic isolation significantly influences genetic differentiation at larger scales, such as between cities, whereas its correlation with genetic distances is considerably weaker at smaller scales, like within cities. This is likely due to the urban landscape in Taiwan, characterised by narrow roads and densely packed buildings, which facilitates extensive dispersal of <i>Ae. aegypti.</i> In evaluating potential barriers to <i>Ae. aegypti</i> dispersal, we found that roads had no significant impact, whereas administrative districts accounted for 4.8% of the population differentiation (<i>p</i> &lt; 10⁻⁴). Surprisingly, this variation aligns with the effects of district-specific mosquito control measures implemented at the municipal level. These findings highlight the complex interplay between urban landscapes, administrative measures and <i>Ae. aegypti</i> dispersal, emphasising the need for implementing targeted control strategies that consider these local dynamics.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 3","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941627","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":"Climate Change Drives Changes in the Size and Composition of Fungal Communities Along the Soil–Seedling Continuum of Schima superba","authors":"Xian Wu,&nbsp;M. Derek MacKenzie,&nbsp;Jiarong Yang,&nbsp;Guoyu Lan,&nbsp;Yu Liu","doi":"10.1111/mec.17652","DOIUrl":"10.1111/mec.17652","url":null,"abstract":"<div>\u0000 \u0000 <p>Plant microbiomes have a major influence on forest structure and functions, as well as tree fitness and evolution. However, a comprehensive understanding of variations in fungi along the soil–plant continuum, particularly within tree seedlings, under global warming is lacking. Here, we investigated the dynamics of fungal communities across different compartments (including bulk soil and rhizosphere soil) and plant organs (including the endosphere of roots, stems and leaves) of <i>Schima superba</i> seedlings exposed to experimental warming and drought using AccuITS absolute quantitative sequencing. Our results revealed that warming and drought significantly reduced the number of specific fungal amplicon sequence variants (ASVs) in the bulk soil and rhizosphere soil, respectively. Variations in fungal communities were mainly explained by compartments and plant organs, with the composition of endophytic fungal communities within leaves (primarily attributed to species gain or loss) being most influenced by climate change. Moreover, warming significantly reduced the migration of Ascomycota, soil saprotrophs, wood saprotrophs and yeasts from the bulk soil to the rhizosphere soil but increased that of plant pathogens from the roots to the stems. Drought significantly decreased the absolute abundances of Chytridiomycota, Glomeromycota and Rozellomycota, as well as the migration of ectomycorrhizal fungi from the bulk soil to the rhizosphere soil but increased that of plant pathogens. Warming could indirectly reduce leaf area by increasing the diversity of leaf pathogens. These findings have potential implications for enhancing the resilience and functioning of natural forest ecosystems under climate change through the manipulation of plant microbiomes, as demonstrated in agroecosystems.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 4","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078080","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":"Molecular Adjustment to a Social Niche: Brain Transcriptomes Reveal Divergent Influence of Social Environment on the Two Queen Morphs of the Ant Temnothorax rugatulus.","authors":"Marah Stoldt, Matteo Antoine Negroni, Barbara Feldmeyer, Susanne Foitzik","doi":"10.1111/mec.17649","DOIUrl":"https://doi.org/10.1111/mec.17649","url":null,"abstract":"<p><p>Social insects form complex societies with division of labour between different female castes. In most species, a single queen heads the colony; in others, several queens share the task of reproduction. These different social organisations are often associated with distinct queen morphologies and life-history strategies and occur in different environments. In the ant Temnothorax rugatulus, queens are dimorphic. Macrogynes and microgynes reside in mono- and polygynous colonies and at lower and higher elevations, respectively. We analysed plastic changes in brain transcriptomes in response to the social environment in these queen morphs and their workers. We manipulated the number of queens over 4 months to investigate whether transcriptional activity is influenced by queen morph, social environment or their interaction. Changes in gene expression in the queens' brains in response to our manipulations were largely influenced by the interaction between social environment and queen morph, rather than independently by these factors. Macrogynes and microgynes thus adjust differently to their social environment. Similarly, worker transcriptomes were influenced by an interaction between behavioural type, that is, nurses or foragers, and queen morph. Nurses differentially regulated genes related to nutrition depending on queen morph, suggesting a link between social environment and metabolic dynamics in ant colonies. Overall, our study sheds light on how the social environment influences the molecular physiology of social insects. Furthermore, we demonstrate that in this ant with two queen morphs, worker physiology depends on queen morph and their role in the colony.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17649"},"PeriodicalIF":4.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941535","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":"DNA Methylation Associates With Sex-Specific Effects of Experimentally Increased Yolk Testosterone in Wild Nestlings","authors":"Bernice Sepers,&nbsp;Suvi Ruuskanen,&nbsp;Tjomme van Mastrigt,&nbsp;A. Christa Mateman,&nbsp;Kees van Oers","doi":"10.1111/mec.17647","DOIUrl":"10.1111/mec.17647","url":null,"abstract":"<p>Maternal hormones can profoundly impact offspring physiology and behaviour in sex-dependent ways. Yet little is known about the molecular mechanisms linking these maternal effects to offspring phenotypes. DNA methylation, an epigenetic mechanism, is suggested to facilitate maternal androgens' effects. To assess whether phenotypic changes induced by maternal androgens associate with DNA methylation changes, we experimentally manipulated yolk testosterone levels in wild great tit eggs (<i>Parus major</i>) and quantified phenotypic and DNA methylation changes in the hatched offspring. While we found no effect on the handing stress response, increased yolk testosterone levels decreased the begging probability, emphasised sex differences in fledging mass, and affected methylation at 763 CpG sites, but always in a sex-specific way. These sites are associated with genes involved in growth, oxidative stress, and reproduction, suggesting sex-specific trade-offs to balance the costs and benefits of exposure to high yolk testosterone levels. Future studies should assess if these effects extend beyond the nestling stage and impact fitness.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 4","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17647","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930078","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":"Runs of Homozygosity and Inferences in Wild Populations","authors":"Aaron B. A. Shafer,&nbsp;Marty Kardos","doi":"10.1111/mec.17641","DOIUrl":"10.1111/mec.17641","url":null,"abstract":"<p>Long homozygous chromosome segments are known as runs of homozygosity (ROH); these reflect patterns of identity by descent and can be used to measure individual inbreeding, map recessive traits, and reconstruct demographic histories. Here, we review some key considerations with ROH detection and the inferences pertaining to inbreeding and demographic analyses in wild populations.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 3","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11754702/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930159","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":"Genomics-Driven Monitoring of Fraxinus latifolia (Oregon Ash) to Inform Conservation and EAB-Resistance Breeding.","authors":"Anthony E Melton, Trevor M Faske, Richard A Sniezko, Tim Thibault, Wyatt Williams, Thomas Parchman, Jill A Hamilton","doi":"10.1111/mec.17640","DOIUrl":"https://doi.org/10.1111/mec.17640","url":null,"abstract":"<p><p>Understanding the evolutionary processes underlying range-wide genomic variation is critical to designing effective conservation and restoration strategies. Evaluating the influence of connectivity, demographic change and environmental adaptation for threatened species can be invaluable to proactive conservation of evolutionary potential. In this study, we assessed genomic variation across the range of Fraxinus latifolia, a foundational riparian tree native to western North America recently exposed to the invasive emerald ash borer (Agrilus planipennis; EAB). Over 1000 individuals from 61 populations were sequenced using reduced representation (ddRAD-seq) across the species' range. Strong population structure was evident along a latitudinal gradient, with population connectivity largely maintained along central valley river systems, and a centre of genetic diversity coinciding with major river systems central to the species' range. Despite evidence of connectivity, estimates of nucleotide diversity and effective population size were low across all populations, suggesting the patchy distribution of F. latifolia populations may impact its long-term evolutionary potential. Range-wide estimates of genomic offset, which indicate genomic change required to adjust to future climate projections, were greatest in the eastern and lowest in the southern portions of the species' range, suggesting the regional distribution of genomic variation may impact evolutionary potential longer-term. To preserve evolutionary capacity across populations needed for the development of breeding and restoration programmes, prioritising conservation of range-wide genomic diversity will provide a foundation for long-term species management.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17640"},"PeriodicalIF":4.5,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930157","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}