Molecular Ecology最新文献

{"title":"The Devil Is in the Details: Assessing Temporal Changes in Genetic Diversity Across Managed and Unmanaged Sites.","authors":"Jana R Wold, Tammy E Steeves","doi":"10.1111/mec.70020","DOIUrl":"https://doi.org/10.1111/mec.70020","url":null,"abstract":"","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70020"},"PeriodicalIF":4.5,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717123","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":"Revealing Speciation Mechanisms Across Endemic Southern Andean Lilies (Phycella, Hippeastreae, Amaryllidaceae) in the Chilean Biodiversity Hotspot.","authors":"Nicolás García, Taryn Fuentes-Castillo, María José Román, Ryan A Folk","doi":"10.1111/mec.70050","DOIUrl":"https://doi.org/10.1111/mec.70050","url":null,"abstract":"<p><p>Cryptic speciation, an endemic problem in biodiversity hotspots, arises as a result of an uncoupling among three processes: lineage splitting, morphological diversification, and ecological divergence during rapid speciation. We studied speciation processes in Phycella (Amaryllidaceae), a clade mostly restricted to the Chilean Biodiversity Hotspot, aiming to differentiate the relative roles of geographic and ecological speciation as well as the role of secondary gene flow in this radiation. We sampled a total of 137 individuals from 47 populations, including all described taxa throughout the geographic range of the group. Using 884 nuclear genes (1125 exons) and near-complete plastomes through hybrid capture, we resolved the phylogeny of Phycella with high support and demonstrated substantial phylogenetic resolution at the population level. Analyses of niche overlap among species and nuclear clades suggest that the diversification of Phycella was associated with niche divergence, supporting a predominantly geographic mode of speciation in the group, likely driven by the mountainous landscape characteristic of the central area of the Chilean Biodiversity Hotspot. Phylogenetic network and modelling approaches identified major cytonuclear discord, attributable to proximity-based secondary gene flow among species, largely restricted to cytoplasmic DNA. Finally, we present a major integrative taxonomic proposal that divides Phycella into 18 species on the basis of molecular, morphological, and ecological data. Overall, our results highlight the relevance of the mountainous landscape of central Chile to promote diversification in Phycella, and ours is among a few studies on speciation for an endemic element of the Chilean Biodiversity Hotspot.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70050"},"PeriodicalIF":4.5,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144705899","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":"Relative Effects of Habitat Amount and Fragmentation Per Se on Genetic Diversity of the Glanville Fritillary Butterfly.","authors":"Lola Fernández Multigner, Audrey Bras, Michelle F DiLeo, Marjo Saastamoinen","doi":"10.1111/mec.70037","DOIUrl":"https://doi.org/10.1111/mec.70037","url":null,"abstract":"<p><p>Habitat loss and fragmentation are considered key drivers of biodiversity loss. Understanding their relative roles is difficult as habitat loss and fragmentation tend to co-occur. It has been proposed that the total habitat amount available in the local landscape mainly drives species richness, while fragmentation per se-the breaking apart of habitat independent of habitat amount-has a negligible or even a positive effect on biodiversity. Several studies support this at the species richness level. Yet, the potential effects of fragmentation per se on genetic diversity at the landscape scale are understudied. Using the Glanville fritillary butterfly metapopulation in the Åland islands, we tested the effects of fragmentation on genetic diversity using a landscape-based approach and 2610 individuals genotyped at 40 neutral SNP markers. We assessed the independent effect of habitat amount and fragmentation (i.e., number of patches, habitat aggregation) within the local landscape on focal patch genetic diversity. The amount of habitat in the local landscape had a positive effect on genetic diversity. Fragmentation measured as the number of patches within the landscape had a negligible impact on genetic diversity, whereas habitat aggregation had a negative effect on genetic diversity when the available amount of habitat in the landscape was low. Focal patch size increased genetic diversity, whereas focal patch structural connectivity had no impact. Our results highlight that all fragments are important to contribute to the total amount of habitat available, and that the impact of habitat fragmentation matters more when the total amount of habitat available is low.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70037"},"PeriodicalIF":4.5,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144705898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple Origins of Sex Chromosomes in Nothobranchius Killifishes.","authors":"Monika Hospodářská, Pablo Mora, Anna Chung Voleníková, Ahmed Al-Rikabi, Marie Altmanová, Sergey A Simanovsky, Nikolas Tolar, Tomáš Pavlica, Karolína Janečková, Jana Štundlová, Kseniya Bobryshava, Marek Jankásek, Matyáš Hiřman, Thomas Liehr, Martin Reichard, Eugene Yu Krysanov, Petr Ráb, Christoph Englert, Petr Nguyen, Alexandr Sember","doi":"10.1111/mec.70029","DOIUrl":"https://doi.org/10.1111/mec.70029","url":null,"abstract":"<p><p>Sex chromosomes have evolved repeatedly across eukaryotes. The emergence of a sex-determining (SD) locus is expected to progressively restrict recombination, driving convergent molecular differentiation. However, evidence from taxa like teleost fishes, representing over half of vertebrate species with unmatched diversity in SD systems, challenges this model. Teleost sex chromosomes are often difficult to detect as they experience frequent turnovers, resetting the differentiation process. Nothobranchius killifishes, which include the XY system shared by N. furzeri and N. kadleci and X₁X₂Y systems in six other species, offer a valuable model to study sex chromosome turnovers. We characterised X₁X₂Y systems in five killifish species and found that sex chromosomes evolved at least four times independently. Sex-determining regions resided near centromeres or predicted chromosome rearrangement breakpoints in N. brieni and N. guentheri, suggesting recombination cold spots may facilitate sex chromosome evolution. Chromosomes representing the XY system in N. furzeri/N. kadleci were sex-linked also in the outgroup Fundulosoma thierryi, with several genes, including gdf6, residing in the region of differentiation. Although the X₁X₂Y systems of N. guentheri, N. lourensi (both Coastal clade), and N. brieni (Kalahari clade) involved different chromosomes, they shared a potential SD region. We uncovered two sex-linked evolutionary strata of distinct age in N. guentheri. However, its potential SD gene amhr2 was located in the younger stratum and is hence unlikely to be the ancestral SD gene in this lineage. Our findings suggest recombination landscapes shape sex chromosome turnover and that certain synteny blocks are repeatedly co-opted as sex chromosomes in killifishes.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70029"},"PeriodicalIF":4.5,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697220","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":"Omics to Study and Manage Aquatic Environments: A Snapshot From the AquaEcOmics Meeting (Evian-les-Bains, 2025).","authors":"Frédéric Rimet, Clarisse Lemonnier, Benjamin Alric, Pedro Beja, Lucie Bittner, Jonas Bylemans, Florian Leese, Ramiro Logares, Kristian Meissner, Fabrice Not, Luisa Orsini, Benoit Paix, Naiara Rodríguez-Ezpeleta, Raffaele Siano, Bettina Thalinger, Nicolas Tromas, Valentin Vasselon, Isabelle Domaizon","doi":"10.1111/mec.70041","DOIUrl":"https://doi.org/10.1111/mec.70041","url":null,"abstract":"<p><p>The AquaEcOmics meeting brought together 280 scientists applying omics tools to aquatic research in March 2025 (Evian-les-Bains, France). We synthesised here the main outcomes from the 167 presentations which were given. A similar number of presentations were about micro- and macroorganisms. While studies on macroorganisms mostly focused on stakeholder-driven research and methodology development, studies on microorganisms tended to focus on fundamental scientific questions. These questions mostly contributed to community ecology studies using metabarcoding; functional ecology studies using metagenomics, metatranscriptomics and metabolomics; and to a lesser degree population genomics studies using metabarcoding and RADseq, ddRADseq. Stakeholder-driven research presentations could be clustered in two groups: those using omics to replace existing standardised monitoring methods-also termed 'retrofitting'-to meet regulatory frameworks (e.g., fish biomonitoring), and those investigating anthropogenic pressures by harnessing the full power of omics, for instance by sequencing the entire microbial diversity or by detecting resistance genes to antibiotics and metals in rivers. The carbon footprint and applicability of omics were also questioned, sparking animated debates among attendees. Finally, some presentations focused on methodological developments and encompassed sampling strategies and devices, issues related to reference libraries (completeness, curation), comparison of short reads versus long reads, and in situ detection and quantification of organisms (dPCR, models). The use of omics to study aquatic ecosystems is a fast-evolving field. Meeting attendees agreed to maintain the generated momentum to promote omics as tools to improve the monitoring and protection of our environment.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70041"},"PeriodicalIF":4.5,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144688486","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":"Recurrent Hybridisations During Diversification of One Rhododendron Species Complex.","authors":"Ji Wang, Xingxing Mao, Bao Liu, Zefu Wang, Yazhen Ma, Qin Li, Jianquan Liu","doi":"10.1111/mec.70046","DOIUrl":"https://doi.org/10.1111/mec.70046","url":null,"abstract":"<p><p>Hybridisation plays a significant role in plant diversification, yet successive hybrid speciation within species-rich groups remains undocumented. We focused on a monophyletic species complex comprising one subsection, which belongs to the highly diverse genus of Rhododendron centred in the mountains of southwest China. By assembling the genome of one individual and resequencing all populations found, we uncovered four well-delimitated lineages within this subsection. Further structure analyses and allele frequency spectrum tests revealed nearly stable genetic admixture and hybrid origin of two lineages. Coalescent modelling results tentatively suggested that hybridisation between the two early diverged lineages likely gave rise to the third lineage, potentially facilitating a shift in habitat preference from rocky substrates to trees. Subsequently, further hybridisation between this hybrid and one parental lineage gave rise to the fourth lineage. The alternating inheritance of parental alleles may have strengthened reproductive isolation between each hybrid lineage and their respective parent lineages during two potential successive hybrid speciation events. We further found that the second hybrid lineage exhibited similar phenotypes and habitat adaptations to the first, and most of the positively selected genes related to reproductive isolation in the second hybridisation event were derived from the first. Although we could not exclude other hybridisation-triggered scenarios during the diversification of this species complex, our findings highlight the crucial and recurrent hybridisations in promoting rhododendron species diversity across varied mountain niches.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70046"},"PeriodicalIF":4.5,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144688487","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":"Naturally Occurring Epialleles and Their Roles in Response to Climate Change in Birch.","authors":"Bowei Chen, Tianxu Zhang, Yile Guo, Lesheng Cao, Xu Zhang, Shahid Ali, Renyi Ma, Linan Xie, Jiang Wang, Gaurav Zinta, Shanwen Sun, Guifeng Liu, Qingzhu Zhang","doi":"10.1111/mec.70031","DOIUrl":"https://doi.org/10.1111/mec.70031","url":null,"abstract":"<p><p>Epigenetics has been proposed to be an important mechanism that enables plant species to respond and adapt to environmental and climatic fluctuations and is sometimes entirely uncoupled from genetic variation. Nevertheless, the extent of this uncoupling and the contribution of epigenetics to plant responses to global climate change have not been well studied, particularly in forest trees. Here, we generated a high-quality genome assembly for Betula platyphylla, a key pioneer species in temperate and boreal forest ecosystems, one of the most sensitive areas to global warming. Extensive multi-omics sequencing of naturally white birch across the 48 provenances captured their full scope of temperate/boreal forests in Northeast China. Using a genome-wide association study (GWAS), it was shown that over 55% of differentially methylated regions (DMRs) were spontaneous, independent of genetic factors. More than 30% of the spontaneous DMRs were significantly associated with gene expression, that is, potential epialleles, which are primarily involved in metabolism and responses to abiotic stresses; and 1819 of these epialleles were significantly associated with bio-climatic variables (i.e., climatic epialleles, cEpialleles). Integrating these cEpialleles into a gradient modelling framework revealed that the natural populations of Asian white birch at high altitude/latitude might be most vulnerable to future climates. Our findings highlight the importance of integrating epigenomic and climatic data sets to forecast the adaptive capacity of a key forest species to rapid climate change.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70031"},"PeriodicalIF":4.5,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673541","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":"Effective Purging and Conservation of Heterozygous Regions During Independent Evolution to High-Level Inbreeding in Wild Paradise Fishes.","authors":"Zhongxing Wang, Dongji Yao, Benchi Zhao, Yi Shao, Fan Li, Ka Yan Ma, Rongfeng Cui","doi":"10.1111/mec.70045","DOIUrl":"https://doi.org/10.1111/mec.70045","url":null,"abstract":"<p><p>Inbreeding may initially lower population fitness by converting masked genetic load into realised load. As deleterious variants become increasingly homozygous, purifying selection acts more effectively to purge load. Nevertheless, not all populations can survive the initial fitness decline, and it would be interesting to examine scenarios that facilitate their survival. Herein, we assembled chromosome-level reference genomes of two paradise fishes, Macropodus hongkongensis and M. opercularis, and resequenced 109 wild individuals of 15 populations to infer the history of runs of homozygosity (ROH) formation, effectiveness of purging in ROH, and the role of balancing selection in maintaining lingering polymorphisms in independently evolved small populations. While the two species diverged in genes potentially adaptive to their local niches, there were large variations in inbreeding coefficients and the amount of genetic load within species. Three populations became highly inbred (F_ROH > 0.50) from independent origins. Simulations showed that the ROH segment size distribution can be best explained by living in a small population for hundreds, if not thousands, of generations. The genetic load negatively correlated with summed ROH length. This was driven by more effective purging in ROH. The non-ROH regions between individuals from different high-F_ROH populations were repeatable, with nearby signals of balancing selection persisting in the polymorphic genomic regions through species divergence.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70045"},"PeriodicalIF":4.5,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673540","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":"Strong Bottlenecks Constrain Adaptive Coevolution in a Host-Parasite Metapopulation.","authors":"Pascal Angst, Christoph R Haag, Frida Ben-Ami, Peter D Fields, Dieter Ebert","doi":"10.1111/mec.70047","DOIUrl":"https://doi.org/10.1111/mec.70047","url":null,"abstract":"<p><p>Although parasites are well-known for adaptively evolving in order to exploit their hosts, they may experience strong genetic drift during transmission bottlenecks when infecting a new host. Host population structure and host population bottlenecks can also lead to genetic drift effects in parasite populations, constraining their adaptive evolution further. Here, we investigate the role of host population structure on the evolution of the microsporidian parasite Hamiltosporidium tvaerminnensis in a dynamic metapopulation of its microcrustacean host Daphnia magna. In following whole-genome allele frequencies of 59 host and parasite subpopulations for up to 10 years, we found that both antagonists showed patterns of co-dispersal and isolation-by-distance, but allele frequencies were much more dynamic in the host, where we found signatures of recurrent genetic bottlenecks. In the parasite, we observed high levels of shared heterozygosity among subpopulations but also subpopulation-specific runs of homozygosity (ROHs). We hypothesise that deleterious ROHs, which originate from loss of heterozygosity events during asexual recombination, are fixed in subpopulations following host-mediated parasite population bottlenecks when host and parasite co-disperse into a habitat patch where the parasite is not yet present. Thus, host population structure and metapopulation dynamics leave a clearly traceable genomic signature in the coevolving parasite. Contrary to the prevailing assumption that parasites evolve at higher rates than their hosts, our study not only suggests that parasites can evolve more slowly than their host, but also that host dynamics can accelerate drift processes in the parasite.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70047"},"PeriodicalIF":4.5,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673542","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 Spatial Spread and the Persistence of Gene Drives Are Affected by Demographic Feedbacks, Density Dependence and Allee Effects.","authors":"Léna Kläy, Léo Girardin, Vincent Calvez, Florence Débarre","doi":"10.1111/mec.70028","DOIUrl":"https://doi.org/10.1111/mec.70028","url":null,"abstract":"<p><p>Homing gene drive alleles bias their own transmission by converting wild-type alleles into drive alleles. If introduced in a natural population, they might fix within a relatively small number of generations, even if they are deleterious. No engineered homing gene drive organisms have been released in the wild so far, and modelling is essential to develop a clear understanding of the potential outcomes of such releases. We use deterministic models to investigate how different demographic features affect the spatial spread of a gene drive. Building on previous work, we first consider the effect of the intrinsic population growth rate on drive spread. We confirm that including demographic dynamics can change outcomes compared to a model ignoring changes in population sizes because changes in population density can oppose the spatial spread of a drive. Secondly, we study the consequences of including an Allee effect and find that it makes a population more prone to eradication following drive spread. Finally, we investigate the effects of the fitness component on which density dependence operates (fecundity or survival) and find that it affects the speed of drive invasion in space and can accentuate the consequences of an Allee effect. These results confirm the importance of checking the robustness of model outcomes to changes in the underlying assumptions, especially if models are to be used for gene drive risk assessment.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70028"},"PeriodicalIF":4.5,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144666659","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}