Molecular Ecology最新文献

{"title":"Introgression—Friend or Foe?","authors":"M. Hindrikson, E. Tammeleht","doi":"10.1111/mec.17810","DOIUrl":"10.1111/mec.17810","url":null,"abstract":"<p>In this issue of Molecular Ecology, Sarabia et al. (<span>2025</span>), findings on potential adaptive introgression from dogs (Canis familiaris) into Iberian grey wolves (Canis lupus) present several fascinating and intriguing aspects. The study highlights a rare case of adaptive introgression, where genes from domestic dogs that were incorporated into the genome of Iberian grey wolves may have provided beneficial effects rather than deleterious ones. This challenges the common assumption that hybridization between wild species and domestic relatives primarily leads to negative outcomes. Six genes linked to immune response mechanisms and brain functions were found to carry alleles introgressed from dogs under positive selection in wild Iberian wolves, suggesting that the introgressed genes may help explain unique behavioural phenotypes observed in Iberian wolves (Figure 1), particularly their reduced dispersal compared to other wolf populations in Europe. Despite evidence for ancient gene flow between dogs and wolves over thousands of years, current study reports minimal recent hybridization events among contemporary Iberian wolf population (averaging around 0.6% recent dog ancestry). Understanding how adaptive traits could be introduced through introgression is vital for conservation efforts aimed at preserving genetic diversity within endangered species populations like the Iberian wolf.</p><p>Natural hybridization in the form of the interbreeding of two distinct taxa is a positive evolutionary force for introducing beneficial adaptive genetic variation into the genomic structure of species or populations Figure 1. The remarkable influence of hybridization and gene flow among canids in shaping phylogenetic relationships and population structures (Figure 2) underscores the potential significance of wolf-dog hybridization on existing grey wolf populations, particularly as wolves, being one of the most studied carnivore species with an abundance of ancient and modern genomes available, provide an excellent model for examining the effects of hybridization and introgression. Indeed, in Sarabia et al. (<span>2025</span>) recent availability of entire genomes of both wolves and domestic dogs has been put to use for the benefit of the current Iberian wolf population: 150 whole genomes of Iberian and other Eurasian grey wolves as well as dogs originating from across Europe were analysed to assess the extent and impact of dog introgression.</p><p>Hybridization between domesticated forms and their wild ancestors—anthropogenic hybridization—is mostly considered a threat to biodiversity, for example due to waste of reproductive effort of wild parental taxa. Wolf and dog, like all the other species in genus <i>Canis</i>, can interbreed and their fertile hybrids can backcross with both parental populations, leading to the introgression of domesticated genes into the wolf gene pool (Vilà and Wayne <span>1999</span>). Hybridization between wolves and dogs h","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 12","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17810","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":"OA","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,&nbsp;Jason T. Weir","doi":"10.1111/mec.17802","DOIUrl":"10.1111/mec.17802","url":null,"abstract":"<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 <i>Pipra</i> 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 <i>Pipra</i> 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 <i>Pipra</i> 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":"34 12","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17802","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":"OA","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,&nbsp;Isabella L. Moya,&nbsp;Kenneth L. Chiou,&nbsp;Alice Baniel,&nbsp;Abebaw Azanaw Haile,&nbsp;Fanuel Kebede,&nbsp;Belayneh Abebe,&nbsp;Amy Lu,&nbsp;Thore J. Bergman,&nbsp;Noah Snyder-Mackler,&nbsp;Arvind Varsani","doi":"10.1111/mec.17801","DOIUrl":"10.1111/mec.17801","url":null,"abstract":"<div>\u0000 \u0000 <p>Intestivirids (order Crassvirales, family <i>Intestiviridae</i>), 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 (<i>Carjivirus communis</i>) 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, <i>Theropithecus gelada</i>) 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 <i>Intestiviridae</i>). Eight intestivirid genomes were identified based on terminal redundancy representing six unique variants (&lt; 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>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 12","pages":""},"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":"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":"Speciation in the Peninsular Indian Flying Lizard (Draco dussumieri) Follows Climatic Transition and Not Physical Barriers","authors":"Ramamoorthi Chaitanya,&nbsp;Aranya Dhibar,&nbsp;Akshay Khandekar,&nbsp;Channakesava Murthy,&nbsp;Shai Meiri,&nbsp;Praveen Karanth","doi":"10.1111/mec.17800","DOIUrl":"10.1111/mec.17800","url":null,"abstract":"<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 (<i>Draco dussumieri</i>). We found strong evidence for two independently evolving, geographically distinct, northern and southern lineages within <i>D. dussumieri</i> 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":"34 12","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17800","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":"OA","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}

{"title":"Constitutive Differences in Immune Gene Expression Are Correlated With Wood Frog Populations From Contrasting Winter Environments","authors":"Grace J. Vaziri,&nbsp;Noah M. Reid,&nbsp;Tracy A. G. Rittenhouse,&nbsp;Daniel I. Bolnick","doi":"10.1111/mec.17804","DOIUrl":"10.1111/mec.17804","url":null,"abstract":"<p>Many terrestrial ectotherms have gone to great evolutionary lengths to adapt to long cold winters; some have even evolved the ability to tolerate the freezing of most of the extracellular fluid in the body. Now, however, high-elevation and high-latitude winters are experiencing an accelerated period of warming. Specialised winter adaptations that promoted fitness in a seasonally frozen environment may soon be superfluous or even maladaptive. We ask whether winter adaptations include changes in immune functions, and whether changing winter conditions could exert disparate effects on populations of a wide-ranging terrestrial ectotherm, the wood frog (<i>Lithobates sylvaticus</i>). By rearing wood frogs from ancestral winter environments that vary in length and temperature in a common garden, and reciprocally exposing post-metamorphic frogs to unfrozen and frozen artificial winter conditions in the lab, we were able to decompose transcriptomic differences in ventral skin gene expression into those that were environmentally induced (responsive to temperature) and genetically determined and those that varied as an interaction between the genotype and environment. We found that frogs from harsh ancestral winter environments constitutively upregulated immune processes, including cellular immunity, inflammatory processes and adaptive immune processes, as compared to frogs from mild ancestral winter environments. Further, we saw that the expression of several genes varied in an interaction between the genotype and artificial winter. We suggest that just as winter climates likely served as the selective force resulting in remarkable winter adaptations such as freeze tolerance, they may have also induced constitutive changes in immune gene expression.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 12","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17804","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092449","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}