Molecular Ecology最新文献

{"title":"Museomics and Salvaged Feathers Piece Together the Evolutionary History and Conservation Genomics of the Elusive, Critically Endangered Night Parrot (Pezoporus occidentalis)","authors":"Heng Lin Yeap,&nbsp;Gunjan Pandey,&nbsp;Jeremy J. Austin,&nbsp;John G. Oakeshott,&nbsp;Christopher M. Hardy,&nbsp;Stephen A. Murphy,&nbsp;Nicholas P. Leseberg,&nbsp;Allan H. Burbidge,&nbsp;Kenny J. Travouillon,&nbsp;Leo Joseph,&nbsp;Anna M. Kearns","doi":"10.1111/mec.70055","DOIUrl":"10.1111/mec.70055","url":null,"abstract":"<p>The Night Parrot is a critically endangered nocturnal bird of Australia's arid zone. The species was “lost” for most of the 20th century until its rediscovery in 1990. Extant populations are now known in eastern and western Australia, but the species has been extirpated from much of its historical range. Here we estimate critically needed Essential Biodiversity Variables (EBVs) for the Night Parrot from historical and opportunistically collected contemporary samples. We find little population structure across the species' range and evidence of recent connectivity between extant populations ~2000 km apart. Most eastern individuals show significant kinship with one another, as did two from an extinct population in southern Australia. Heterozygosity is similarly low in all extant populations but ten-fold lower in the extinct population sampled. Coalescent modelling of effective population size (<i>Ne</i>) suggests that Night Parrot numbers were reasonably high until around 90 years ago when <i>Ne</i> crashed from ~10,000 to ~100. Current <i>Ne</i> is now at its lowest in the past several million years. Our findings will help guide the ongoing management of one of Australia's most threatened birds.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 18","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70055","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144726276","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":"Sex-Dependent Influence of Major Histocompatibility Complex Diversity on Fitness in a Social Mammal","authors":"Nadine Schubert,&nbsp;Hazel J. Nichols,&nbsp;Francis Mwanguhya,&nbsp;Robert Businge,&nbsp;Solomon Kyambulima,&nbsp;Kenneth Mwesige,&nbsp;Joseph I. Hoffman,&nbsp;Michael A. Cant,&nbsp;Jamie C. Winternitz","doi":"10.1111/mec.70058","DOIUrl":"10.1111/mec.70058","url":null,"abstract":"<p>Parasite infections affect males and females differently across a wide range of species, often due to differences in immune responses. Generally, females tend to have stronger immune defences and lower parasite loads than males. The major histocompatibility complex (MHC) plays a crucial role in the adaptive immune response, and extensive research has explored how variation in this region influences infection and fitness outcomes. However, studies of sex-specific relationships between MHC variation and infection are scarce, perhaps because MHC genes are located on the autosomes, which are shared by both sexes. Here, we provide evidence of sexually antagonistic selection in a wild, group-living mammal—the banded mongoose. Using genetic and life history data collected from over 300 individuals across 25 years, we found that both MHC class I (MHC-I) and MHC class II (MHC-II) diversity influence lifetime reproductive success differently in males and females. Specifically, higher MHC diversity is linked to increased fitness in males but decreased fitness in females. Furthermore, MHC diversity did not differ between the sexes, indicating an unresolved genetic sexual conflict. Our findings demonstrate that sexually antagonistic selection acts on the MHC and may operate across both MHC classes but differently. This study contributes to the growing body of evidence that sex is a significant factor in shaping host immunity and fitness.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 18","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70058","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717122","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":"Linking DNA Methylation to Localised Genetic Differentiation in Timema cristinae Stick Insects.","authors":"Clarissa F de Carvalho, Nicholas P Planidin, Romain Villoutreix, Víctor Soria-Carrasco, Rüdiger Riesch, Jeffrey L Feder, Jon Slate, Patrik Nosil, Zachariah Gompert","doi":"10.1111/mec.70049","DOIUrl":"https://doi.org/10.1111/mec.70049","url":null,"abstract":"<p><p>Understanding speciation is a fundamental goal in evolutionary biology. Genome scans of genetic differentiation (F_ST) have become a cornerstone of speciation research, helping identify genomic regions likely involved in population divergence and speciation. While such studies have advanced our understanding, the relationship between epigenetic mechanisms and genetic differentiation remains unclear. Here, we present evidence that DNA methylation is associated with regions exhibiting accentuated genetic differentiation between populations of Timema cristinae stick insects. We do so by integrating analyses of differentially methylated regions (DMRs) between individuals from different host-plant species with genomic sequencing. Our results reveal that DMRs often show greater F_ST than expected by chance. Strikingly, the magnitude of this accentuation of F_ST in DMRs increases with the geographical distance between populations. We present results evaluating the contributions of mutation, reduced recombination, gene flow, and selection to these divergence patterns. The overall results are consistent with a role for a balance between selection and gene flow, a finding further supported by a previously published survival field experiment. Nevertheless, details of our results suggest that selection on DMRs might be indirect and not strictly host-related. Our results establish associations between methylation and genetic change, but further work is required to clarify the causes of this association. Nonetheless, our results provide insight into how the interplay of epigenetic and genetic variation may influence population divergence and potentially contribute to speciation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70049"},"PeriodicalIF":4.5,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717121","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 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,&nbsp;Taryn Fuentes-Castillo,&nbsp;María José Román,&nbsp;Ryan A. Folk","doi":"10.1111/mec.70050","DOIUrl":"10.1111/mec.70050","url":null,"abstract":"<div>\u0000 \u0000 <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 <i>Phycella</i> (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 <i>Phycella</i> 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 <i>Phycella</i> 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 <i>Phycella</i> 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 <i>Phycella</i>, and ours is among a few studies on speciation for an endemic element of the Chilean Biodiversity Hotspot.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 17","pages":""},"PeriodicalIF":3.9,"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,&nbsp;Audrey Bras,&nbsp;Michelle F. DiLeo,&nbsp;Marjo Saastamoinen","doi":"10.1111/mec.70037","DOIUrl":"10.1111/mec.70037","url":null,"abstract":"<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":"34 17","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70037","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":"OA","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,&nbsp;Clarisse Lemonnier,&nbsp;Benjamin Alric,&nbsp;Pedro Beja,&nbsp;Lucie Bittner,&nbsp;Jonas Bylemans,&nbsp;Florian Leese,&nbsp;Ramiro Logares,&nbsp;Kristian Meissner,&nbsp;Fabrice Not,&nbsp;Luisa Orsini,&nbsp;Benoit Paix,&nbsp;Naiara Rodríguez-Ezpeleta,&nbsp;Raffaele Siano,&nbsp;Bettina Thalinger,&nbsp;Nicolas Tromas,&nbsp;Valentin Vasselon,&nbsp;Isabelle Domaizon","doi":"10.1111/mec.70041","DOIUrl":"10.1111/mec.70041","url":null,"abstract":"<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":"34 17","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70041","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":"OA","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":"Effective Purging and Conservation of Heterozygous Regions During Independent Evolution to High-Level Inbreeding in Wild Paradise Fishes","authors":"Zhongxing Wang,&nbsp;Dongji Yao,&nbsp;Benchi Zhao,&nbsp;Yi Shao,&nbsp;Fan Li,&nbsp;Ka Yan Ma,&nbsp;Rongfeng Cui","doi":"10.1111/mec.70045","DOIUrl":"10.1111/mec.70045","url":null,"abstract":"<div>\u0000 \u0000 <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, <i>Macropodus hongkongensis</i> and <i>M. opercularis</i>, 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 (<i>F</i>_ROH &gt; 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-<i>F</i>_ROH populations were repeatable, with nearby signals of balancing selection persisting in the polymorphic genomic regions through species divergence.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 17","pages":""},"PeriodicalIF":3.9,"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,&nbsp;Christoph R. Haag,&nbsp;Frida Ben-Ami,&nbsp;Peter D. Fields,&nbsp;Dieter Ebert","doi":"10.1111/mec.70047","DOIUrl":"10.1111/mec.70047","url":null,"abstract":"<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 <i>Hamiltosporidium tvaerminnensis</i> in a dynamic metapopulation of its microcrustacean host <i>Daphnia magna</i>. 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":"34 17","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70047","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}