Molecular Ecology最新文献

{"title":"Spatial Replication Is Important for Developing Landscape Genetic Inferences for a Wetland Salamander.","authors":"Bryce S Wade, Todd W Pierson, Benjamin M Fitzpatrick, Evin T Carter","doi":"10.1111/mec.17808","DOIUrl":"https://doi.org/10.1111/mec.17808","url":null,"abstract":"<p><p>Habitat fragmentation is a pressing threat to wildlife populations, and maintenance of gene flow between populations is an essential goal of conservation. Resistance surfaces have emerged as an important tool for modelling connectivity and developing management strategies to mitigate effects of habitat fragmentation. However, recent studies have noted inconsistencies in the factors most strongly associated with connectivity across different landscapes. Thus, replication of genetic-based resistance surface optimisation across landscapes may be necessary for making robust conclusions about the influence of environmental variables. Accordingly, replication represents a substantive challenge and opportunity in the field of landscape genetics. In this study, we conducted replicated landscape genetic analyses across five landscapes in Tennessee and Kentucky for a threatened wetland amphibian, the four-toed salamander (Hemidactylium scutatum). We tested multiple hypotheses of how different landscape features that could directly affect small, desiccation-intolerant amphibians (e.g., canopy cover) influenced gene flow and assessed the appropriate scale at which to model different features. We found some concordance in the landscape features that influenced gene flow (e.g., a common importance of forest cover and topography), but also some differences-potentially owing to the difference in variability of predictors across landscapes. We also found discordance in the scale of effect of different features across landscapes. Our work emphasises that flat areas of moist forest not bisected by roads may be important for H. scutatum conservation, and our replicated design allows us to identify relationships that would have been missed if only using one study site.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17808"},"PeriodicalIF":4.5,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144155436","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":"Introgression-Friend or Foe?","authors":"M Hindrikson, E Tammeleht","doi":"10.1111/mec.17810","DOIUrl":"https://doi.org/10.1111/mec.17810","url":null,"abstract":"","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17810"},"PeriodicalIF":4.5,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144155435","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 Analysis Suggests That Mitonuclear Coevolution Proceeds Over Rapid Timescales in the Amazonian Pipra Manakin Complex.","authors":"Ellen Nikelski, Jason T Weir","doi":"10.1111/mec.17802","DOIUrl":"https://doi.org/10.1111/mec.17802","url":null,"abstract":"<p><p>Mitonuclear coevolution is defined as reciprocal selection between the nuclear and mitochondrial genomes and is necessary to maintain compatibility between nuclear- and mitochondrially-encoded products that interact during mitochondrial processes including mitochondrial genome replication, transcription and translation and oxidative phosphorylation. Theory predicts that mitonuclear coevolution may play a crucial role in the early phases of speciation by generating strong genetic incompatibilities between recently diverged taxa that have evolved unique mitochondrial-mitonuclear haplotypes. However, the timescale over which mitonuclear coevolution proceeds remains unclear, making it difficult to definitively link this process with early speciation. Here, we test for expected genomic signals of mitonuclear coevolution across the Amazonian Pipra manakin complex, which includes recently and more deeply diverged avian lineages. Using dN/dS ratio analyses, we compared signals of positive selection in mitonuclear gene categories and functionally equivalent nuclear gene categories that do not participate in mitonuclear coevolution for each pair of Pipra lineages separately and for all the lineages simultaneously. For the ribosomal protein and aminoacyl tRNA synthetase (AARS) gene categories, we identified genomic patterns consistent with stronger positive selection in mitonuclear versus nuclear genes, which is suggestive of mitonuclear coevolution having occurred across the Pipra complex. Significantly, we determined that expected genomic signals of mitonuclear coevolution could be identified between lineages that diverged as recently as 0.35-0.4 MYA. This time span is in keeping with the initial stages of avian speciation and suggests that mitonuclear coevolution may operate on a timescale that would allow it to play an important role during early speciation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17802"},"PeriodicalIF":4.5,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144140951","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":"Land Use Interacts With Climate to Influence Microbial Diversity-To-Biomass Ratios Across Europe via Soil Organic Carbon and Nitrogen.","authors":"José A Siles, Alfonso Vera, Maëva Labouyrie, Johan van den Hoogen, Thomas W Crowther, Ferran Romero, Leho Tedersoo, Carlos García, Arwyn Jones, Panos Panagos, Marcel G A van der Heijden, Alberto Orgiazzi, Felipe Bastida","doi":"10.1111/mec.17806","DOIUrl":"https://doi.org/10.1111/mec.17806","url":null,"abstract":"<p><p>Ecosystem functioning is potentially dependent on the relationships between soil microbial diversity and biomass. Yet, it remains unclear how land use and climate influence these relationships. Here, we (i) analysed relationships and ratios between richness and biomass of bacteria and fungi in ~500 soils across Europe, including three land-use types (woodlands, grasslands and croplands) and climates (cold, temperate and arid) and (ii) identified the driving factors of changes in richness:biomass (R:B) ratios. Richness and biomass of soil bacteria and fungi followed a unimodal pattern, with a peak in mid-levels of biomass. This pattern was more evident in bacteria and more clearly exerted by land use than by climate. Bacterial R:B ratios decreased with land use in the following order: croplands > woodlands > grasslands. Fungal R:B ratios decreased as follows: grasslands > croplands > woodlands. Climate was found to interact with land use. In this way, arid climate tended to increase bacterial R:B ratios in the different land uses; however, the agricultural practices associated with croplands seem to buffer this effect. In fungi, the interactive effect of land use and climate was less straightforward than for bacteria. According to our models, soil organic carbon (SOC) and total nitrogen (N) in bacteria and SOC in fungi were identified as the primary predictors of R:B ratios. Therefore, factors related to climate and land-use change with impact on SOC and N contents are potential disruptors of soil microbial R:B ratios. This study clarifies the diversity:biomass relationships across different land uses and climates.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17806"},"PeriodicalIF":4.5,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126159","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":"Intestivirid Acquisition Increases Across Infancy in a Wild Primate Population.","authors":"India A Schneider-Crease, Isabella L Moya, Kenneth L Chiou, Alice Baniel, Abebaw Azanaw Haile, Fanuel Kebede, Belayneh Abebe, Amy Lu, Thore J Bergman, Noah Snyder-Mackler, Arvind Varsani","doi":"10.1111/mec.17801","DOIUrl":"https://doi.org/10.1111/mec.17801","url":null,"abstract":"<p><p>Intestivirids (order Crassvirales, family Intestiviridae), viruses that infect Bacteroidales bacteria in the mammalian gastrointestinal tract, have been identified as a highly abundant component of the healthy human virome that may shape patterns of human health and disease through direct action on the microbiome. While double-stranded DNA bacteriophages called crAssphages (Carjivirus communis) that infect bacteria in the Bacteroidales order have been identified in humans within the first month of life, the enormous variation in post-parturition infant environments and diets has inhibited a robust understanding of the physiological and environmental factors that govern acquisition patterns. We turned to a wild population of graminivorous nonhuman primates (geladas, Theropithecus gelada) under long-term study in the Simien Mountains National Park, Ethiopia, analysing faecal samples from infants and mothers in this population across the infancy period for richness and presence of crAssphage-like viruses (family Intestiviridae). Eight intestivirid genomes were identified based on terminal redundancy representing six unique variants (< 98% intergenomic similarity) closely related to the human crAssphage. The prevalence of intestivirids in gelada faecal samples begins to rise at about 10 months of age, peaks in the months surrounding weaning (~18 months), and somewhat decreases but maintains high levels into adulthood. We found a strong association between cumulative rainfall and intestivirid detection, with a higher likelihood accompanying wetter seasons with higher grass availability. In this population, the months prior to weaning have been found to be accompanied by a shift in the microbiome characterised by a decrease in glycan degrader Bacteroidales taxa and an increase in fermentative Bacteroidales taxa, and wetter seasons when the vast majority of the gelada diet comprises grasses are associated with an increase in fermentative Bacteroidales taxa. In the context of these microbiome shifts, our results suggest that the intestivirid-bacterial host relationship may interact with major developmental and seasonal dietary shifts in the mammalian host.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17801"},"PeriodicalIF":4.5,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118473","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":"A Female-Biased Gene Expression Signature of Dominance in Cooperatively Breeding Meerkats.","authors":"","doi":"10.1111/mec.17767","DOIUrl":"https://doi.org/10.1111/mec.17767","url":null,"abstract":"","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17767"},"PeriodicalIF":4.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101282","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":"Speciation in the Peninsular Indian Flying Lizard (Draco dussumieri) Follows Climatic Transition and Not Physical Barriers.","authors":"Ramamoorthi Chaitanya, Aranya Dhibar, Akshay Khandekar, Channakesava Murthy, Shai Meiri, Praveen Karanth","doi":"10.1111/mec.17800","DOIUrl":"https://doi.org/10.1111/mec.17800","url":null,"abstract":"<p><p>Marked with high levels of endemism and in situ radiations, the Western Ghats mountains make for a compelling backdrop to examine processes that lead to the formation and maintenance of species. Regional geographic barriers and paleoclimatic fluctuations have been implicated as drivers of speciation, but their roles have not been explicitly tested in a phylogenomic framework. We integrated mitochondrial DNA, genome-wide SNPs and climatic data to examine the influence of geographic barriers and climatic transitions in shaping phylogeography and potential speciation in the Peninsular Indian Flying lizard (Draco dussumieri). We found strong evidence for two independently evolving, geographically distinct, northern and southern lineages within D. dussumieri that diverged during the early Pleistocene, and a gradient of admixed populations across a broad hybrid zone in the Central Western Ghats. Migrations after initial divergence were continuous, but gene flow remained consistently below thresholds required to homogenise lineages. We found more support for isolation by environment (especially rainfall regimes) than by distance. The range-break between lineages occurs at a transition zone in the Central Western Ghats that separates dissimilar rainfall regimes with no physical barriers. This limit is potentially an ecological barrier, which nevertheless was permeable during glacial maxima. We hypothesise that similar phylogeographic patterns will emerge in other widespread, wet-adapted species in the Western Ghats that presumably endured the same climatic processes.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17800"},"PeriodicalIF":4.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101284","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":"Wildfire-Driven Changes in Terrestrial Subsidies Shift Freshwater Microbial and Zooplankton Communities to New Compositional States.","authors":"Margaret Y Demmel, Christopher B Wall, Cody J Spiegel, Natalia Erazo, Evelyn M Diaz, Madeline G Perreault, Elisabet Perez-Coronel, Sara L Jackrel, Jeff S Bowman, Jonathan B Shurin","doi":"10.1111/mec.17794","DOIUrl":"https://doi.org/10.1111/mec.17794","url":null,"abstract":"<p><p>Wildfire frequency and intensity are increasing globally, impacting terrestrial and aquatic ecosystems. Deposition of burned materials into aquatic environments can affect biotic communities and nutrient cycling. We investigated how post-fire terrestrial deposition shapes microbial and zooplankton community composition and function across time by manipulating plant material amount (loading; 0-400 g) and chemical composition (burned vs. unburned) in 400 L experimental mesocosms over four months. Burning treatment had minimal effects (1.4%), while loading (6.6%) and time (19.2%) contributed significantly to free-living microbial community variation. Dramatic changes in environmental conditions and microbiome composition occurred at a 50-100 g loading threshold within 30 days. High-loading mesocosms showed hypoxia, increased dissolved organic carbon and aromaticity, elevated bacterial density, and shifts in bacterial community function relating to enhanced carbon degradation, suggesting efficient microbial use of carbon resources despite low oxygen and increased water colour. Zooplankton communities were primarily influenced by time (24.9%), with loading (10.3%) and burning (2.3%) having weaker effects. Zooplankton community composition shifted at a 100 g-150 g threshold that persisted over time, with crustaceans declining and mosquito larvae dominating at higher loading levels. Zooplankton- and plant detritus-associated microbiomes were distinct but showed minimal treatment effects after four months, indicating greater environmental filtering for these microhabitats relative to horizontal transmission from treatment-altered water microbiomes. In contrast, free-living microbiomes maintained loading-driven compositional differences, while predicted genome traits and functions converged across treatments. These results suggest that post-wildfire deposition drives zooplankton and microbial communities into distinct compositional states punctuated by abrupt transitions, but microbiomes may recover community-level functionality over time.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17794"},"PeriodicalIF":4.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101285","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":"Immune Gene Regulation Is Associated With Age and Environmental Adversity in a Nonhuman Primate.","authors":"","doi":"10.1111/mec.17768","DOIUrl":"https://doi.org/10.1111/mec.17768","url":null,"abstract":"","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17768"},"PeriodicalIF":4.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101283","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":"Selection for Tameness in Red Junglefowl Recapitulates Genetic Loci Associated With Domestication-Related Brain Composition.","authors":"Carlos Guerrero-Bosagna, Fábio Pértille, Zahra Moradinour, Rebecca Katajama, Maria Luisa Martin Cerezo, Rie Henriksen, Per Jensen, Dominic Wright","doi":"10.1111/mec.17788","DOIUrl":"https://doi.org/10.1111/mec.17788","url":null,"abstract":"<p><p>Domestication involves huge phenotypic shifts via strong directional selection. The resulting changes, often termed the Domestication Syndrome, typically encompass numerous traits; however, the most universal of these are changes in reduced fear of humans (tameness) and brain composition. To assess how early domestication selection may have focused on tameness and its interaction with brain composition, a Red Junglefowl (Gallus gallus) population (the wild progenitor of the domestic chicken) was used to create two lines bidirectionally selected for fear of humans over eight generations of selection. These selection lines were then used to make an intercross population. Using a combination of genome-wide mapping in the intercross and between-line analysis of the selection lines, we show that the genetic loci for tameness co-localise with genetic loci for brain composition and anxiety behaviour. Furthermore, the detected loci for brain composition also co-localise with brain composition loci identified in a separate wild × domestic intercross. These results indicate that tameness and brain composition are either pleiotropic or genetically linked, and that tameness selection appears to recapitulate the same loci that have been selected by domestication itself. Therefore, selection for increased tameness could be the initial selection pressure driving the core of the domestication syndrome.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17788"},"PeriodicalIF":4.5,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092451","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}