Molecular Ecology最新文献

{"title":"Wind Is a Primary Driver of Fungal Dispersal Across a Mainland-Island System","authors":"D. Naranjo-Orrico,&nbsp;O. Ovaskainen,&nbsp;B. Furneaux,&nbsp;J. Purhonen,&nbsp;P. A. Arancibia,&nbsp;S. Burg,&nbsp;N. Moser,&nbsp;J. Niku,&nbsp;G. Tikhonov,&nbsp;E. Zakharov,&nbsp;N. Monkhouse,&nbsp;N. Abrego","doi":"10.1111/mec.17675","DOIUrl":"10.1111/mec.17675","url":null,"abstract":"<div>\u0000 \u0000 <p>Dispersal is one of the main processes shaping ecological communities. Yet, for species-rich communities in natural systems, the role of dispersal in community assembly remains relatively less studied compared to other processes. This is the case for fungal communities, for which predictable knowledge about where and how the dispersal propagules move across space is largely lacking. We sampled fungal communities at their dispersal stage in a lake mainland-island system in Finland, using a regular grid of 18 × 18 km, including sites on the mainland, islands and over the water. Fungal communities were screened by applying DNA barcoding to air samples. To assess the factors determining fungal dispersal, we modelled aerial fungal communities with a joint species distribution model, including spore traits, weather-related predictors, and spatial predictors. We found that the probability of occurrence of most species (and consequently species richness measured as the number of OTUs per sample) was lower in low-connectivity sites (water and isolated islands) compared to high-connectivity sites (mainland). There was a strong phylogenetic signal in how the fungal species responded to connectivity, indicating that some taxonomic groups are more dispersal limited than others, although such responses were not structured by their trophic guilds. Furthermore, wind speed influenced how species with different spore sizes responded to connectivity: in low-connectivity sites, species with large sexual spores were detected especially when wind was high, whereas, in high-connectivity sites, they were detected especially when wind was low. This study demonstrates that air fungal dispersal might be more predictable than previously considered and contributes to the mechanistic understanding of fungal air dispersal.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 5","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078077","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":"Comparative Genomics Uncovers Molecular Adaptations for Cetacean Deep-Sea Diving.","authors":"Fan Zhang, Tong Zhang, Hao Dong, Jie Jiang, Guang Yang, Inge Seim, Ran Tian","doi":"10.1111/mec.17678","DOIUrl":"https://doi.org/10.1111/mec.17678","url":null,"abstract":"<p><p>Cetaceans show remarkable diversity in diving capability, implying a range of adaptive strategies to hazards such as hydrostatic pressure and oxidative stress, but few studies have considered the evolution of extreme diving. Here, we first examined the relationship between morphological and physiological factors and diving capability and then considered the molecular evolution of candidate deep-sea diving traits in a genomic dataset of cetaceans. Our dataset included six super-divers, sperm whales (families Physeteridae and Kogiidae) and beaked whales (Ziphiidae), species that can dive deeper than 1000 m for about an hour or longer. We found a positive association between diving capability and oxygen-linked globins, and super-diver myoglobin (MB) is under positive selection and harbours a reported functional amino acid change. Blubber thickness was positively associated, likely to provide thermal insulation and hydrostatic pressure resistance. Super-divers have gene changes that may contribute to differences in the composition of outer blubber neutral lipids (triacylglycerols and wax esters), fatty acids and cholesterol. Total lung capacity relative to body mass showed a negative association, ostensibly to limit gas bubbles that can cause decompression sickness. A functional assay suggests that an ATP8B1 amino acid substitution may reduce lung injury in super-divers. Super-diver XDH has two unique amino acids and a decreased ability to produce uric acid under hypoxia when its ROS-generating XO isoform is prevalent, suggesting that it reduces cell damage from oxidative stress and uric acid accumulation in species with prolonged dives. Our study deepens the understanding of how deep-sea diving emerged in the cetacean lineage.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17678"},"PeriodicalIF":4.5,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078066","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":"Adaptive Divergence and Functional Convergence: The Evolution of Pulmonary Gene Expression in Amphibians of the Qingzang Plateau","authors":"Liming Chang,&nbsp;Wei Zhu,&nbsp;Qiheng Chen,&nbsp;Chunlin Zhao,&nbsp;Lulu Sui,&nbsp;Cheng Shen,&nbsp;Qunde Zhang,&nbsp;Bin Wang,&nbsp;Jianping Jiang","doi":"10.1111/mec.17663","DOIUrl":"10.1111/mec.17663","url":null,"abstract":"<div>\u0000 \u0000 <p>The Qingzang Plateau, with its harsh environmental conditions—low oxygen, high ultraviolet radiation and significant temperature fluctuations—demands specialised adaptations for survival. While genetic adaptations have been extensively studied, gene expression's role in amphibian adaptation to high elevations remains understudied. This study analysed pulmonary gene expression in 119 amphibians across the plateau to explore how genetic and environmental factors shape expression evolution. Transcriptomic analyses revealed significant interspecies variation, driven by environmental factors like temperature, oxygen levels, UVB radiation and precipitation. Principal Component and Mantel analyses found no significant correlation between gene expression divergence and genetic distance. Instead, species-specific traits and environmental pressures were pivotal in shaping expression patterns. PERMANOVA analysis showed environmental factors had varying impacts on species. For instance, <i>Bufo gargarizans</i> exhibited a strong gene expression response to multiple environmental factors, while <i>Scutiger boulengeri</i> was less influenced, reflecting diverse adaptive strategies. Functional enrichment analysis highlighted convergence in key biological processes, such as energy metabolism, apoptosis and autophagy, despite species-specific gene expression differences. These processes are critical for surviving the plateau's extremes. The findings suggest that gene expression evolution in amphibians on the Qingzang Plateau is shaped by both genetic diversity and environmental pressures. Although gene expression profiles vary, they converge on essential functions, offering insights into adaptation mechanisms in extreme environments.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 5","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078062","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":"Temporal Changes in Tasmanian Devil Genetic Diversity at Sites With and Without Supplementation.","authors":"Andrea L Schraven, Elspeth A McLennan, Katherine A Farquharson, Andrew V Lee, Katherine Belov, Samantha Fox, Catherine E Grueber, Carolyn J Hogg","doi":"10.1111/mec.17671","DOIUrl":"https://doi.org/10.1111/mec.17671","url":null,"abstract":"<p><p>Management interventions for threatened species are well documented with genetic data now playing a pivotal role in informing their outcomes. However, in situ actions like supplementations (releasing individuals into an existing population) are often restricted to a singular site. Considerable research and management effort have been dedicated to conserving the Tasmanian devil (Sarcophilus harrisii), offering a unique opportunity to investigate the temporal genetic consequences of supplementation at multiple sites, in comparison to outcomes observed in the absence of management interventions. Using 1,778 genome-wide SNPs across 1,546 individuals, we compared four wild-supplemented sites to four monitoring-only sites (not supplemented; control sites) over 9 years (2014-2022). At the study completion, genetic differentiation among supplemented sites had significantly decreased compared to among not-supplemented sites. We found statistically significant variation in genetic change over time between sites using linear mixed-effects modelling with random slopes. Investigating this among-site variation showed that three of the supplemented sites conformed to predictions that supplementations would have a positive impact on the genetic diversity of devils at these sites. We predicted no change over time at our fourth site due to the observed relatively high gene flow, however, this site did not align with predictions, instead showing decreased genetic diversity and increased relatedness. Amongst not supplemented sites, there was no consistent pattern of temporal genetic change, suggesting devil sites across Tasmania are highly heterogeneous, likely reflecting variation in site connectivity and genetic drift. Our study demonstrates that long-term concurrent monitoring of multiple sites, including controls, is necessary to contextualise the influence of management interventions on natural species fluctuations.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17671"},"PeriodicalIF":4.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143072966","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":"Seascape Genomics of Elacatinus punctiulatus (Ginsburg, 1938): Understanding the Historical and Contemporary Drivers of Population Structure in the Gulf of California","authors":"Vladimir Salvador De Jesús-Bonilla,&nbsp;Alejandra Quintero-Grijalva,&nbsp;Pedro Cruz-Hernández,&nbsp;Raúl Octavio Martínez-Rincón,&nbsp;Norma Y. Hernández-Saavedra,&nbsp;Fausto Valenzuela-Quiñonez","doi":"10.1111/mec.17668","DOIUrl":"10.1111/mec.17668","url":null,"abstract":"<div>\u0000 \u0000 <p>The genomic diversity and population structure of marine species represents a complex mosaic shaped by historical and contemporary environmental seascape features that maintain or alter it over time. The Gulf of California (GC) is an interior sea with a dynamic history during its formation and a contemporary environmental and oceanographic complexity; hence, it is a suitable system to test the effect of historical and contemporary factors on genomic diversity in marine species. We investigated the genomic seascape of the redhead goby (<i>Elacatinus puncticulatus</i>; Ginsburg, 1938), a cryptobenthic marine fish, to gain insights into the historical and contemporary drivers shaping its population structure in the GC. A total of 4802 SNPs markers were analysed, with 3775 loci classified as neutral markers and 27 as outlier markers potentially under selection. Both markers demonstrated population structure, with the neutral markers showing two main groups corresponding to northern and southern locatities. The outlier markers identified an additional genetic group emerging in the central area of the sampled localities. Genetic differentiation between the North and South regions and historical demographic simulations was consistent with ancient divergence (1.04 Mya) and secondary contact (0.15 Mya). The genomic environmental association analysis revealed a possible adaptive scenario linked to ocean temperature. The study highlights the importance of historical events, contemporary environmental factors, and oceanographic circulation in shaping the genetic structure of <i>E. puncticulatus</i> populations in the GC.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 5","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062743","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 Footprints of Hybridisation in North Atlantic Eels (Anguilla anguilla and A. rostrata).","authors":"Aja Noersgaard Buur Tengstedt, Shenglin Liu, Magnus W Jacobsen, Gabriela Ulmo-Diaz, Bjarni Jónsson, Jose Martin Pujolar, Michael M Hansen","doi":"10.1111/mec.17664","DOIUrl":"https://doi.org/10.1111/mec.17664","url":null,"abstract":"<p><p>Understanding interspecific introgressive hybridisation and the biological significance of introgressed variation remains an important goal in population genomics. European (Anguilla anguilla) and American eel (A. rostrata) represent a remarkable case of hybridisation. Both are panmictic and spawn in partial sympatry in the Sargasso Sea, occasionally producing viable, fertile hybrids, primarily found in Iceland. We studied introgressive hybridisation from American into European eel using whole-genome sequences of 78 individuals, including European, American and 21 putative hybrid eels. Previous studies using few genetic markers could not resolve whether hybridisation involved simple unidirectional backcrossing or a more complex hybrid swarm scenario. However, local ancestry inference along individual chromosomes revealed that Icelandic hybrids were primarily F1 or first-generation backcrosses towards European eel, with some showing more complex backcrossing. All European eels outside Iceland contained short chromosomal blocks from American eel, indicating a porous genome. We found no evidence for previously hypothesised geographical gradients of introgression in European eel outside Iceland. Several chromosomal regions showed high interspecific divergence, but haplotype blocks introgressed from American eel were identified both within and outside these regions. There was little correspondence between regions of high relative (F_ST) and absolute divergence (d_XY), with the former reflecting selective sweeps within species or reduced recombination rather than barrier loci. A single genomic region showed evidence of repeated introgression from American into European eel under positive selection in both species. The study illustrates that species can maintain genetic integrity despite porous genomes and that standing variation in one species can potentially be available for future adaptive responses in the other species.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17664"},"PeriodicalIF":4.5,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057587","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":"Correction to “Genome-wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses”","authors":"","doi":"10.1111/mec.17674","DOIUrl":"10.1111/mec.17674","url":null,"abstract":"&lt;p&gt;Pan, J., Liu, X., Baca, M., Calvière-Tonasso, L., Schiavinato, S., Chauvey, L., Tressières, G., Perdereau, A., Aury, J.-M., Oliveira, P. H., Wincker, P., Abdykanova, A., Arsuaga, J. L., Bayarsaikhan, J., Belinskiy, A. B., Carbonell, E., Davoudi, H., Lira Garrido, J., Gilbert, A. S., … Orlando, L. (2024). Genome-wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses. &lt;i&gt;Molecular Ecology&lt;/i&gt;, &lt;i&gt;33&lt;/i&gt;, e17527. https://doi.org/10.1111/mec.17527.&lt;/p&gt;&lt;p&gt;In our study, we made use some of previously published genome sequences of &lt;i&gt;Equus&lt;/i&gt; samples. Although we refered to the original work in Supplementary Table 1 by indicating the surname of the leading author followed by ‘et al.’ and the year of publication, we inadvertently failed to report the corresponding articles in the final reference list appearing in the main text. These references are listed below, sorted by alphabetic order:&lt;/p&gt;&lt;p&gt;Bennett et al. (2022): Bennett E. A., J. Weber, W. Bendhafer, et al. 2022. \"The Genetic Identity of the Earliest Human-Made Hybrid Animals, The Kungas of Syro-Mesopotamia\". &lt;i&gt;Science Advances&lt;/i&gt; 8, no. 2: eabm0218. https://doi.org/10.1126/sciadv.abm0218. https://www.science.org/doi/full/10.1126/sciadv.abm0218.&lt;/p&gt;&lt;p&gt;Dong et al. (2022): Dong H., Z. Dong, F. Wang, et al. 2022. \"Whole Genome Sequencing Provides New Insights Into the Genetic Diversity and Coat Color of Asiatic Wild Ass and Its Hybrids\". &lt;i&gt;Frontiers in Genetics&lt;/i&gt; 13: 818420. https://doi.org/10.3389/fgene.2022.818420/full. https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.818420/full.&lt;/p&gt;&lt;p&gt;Han et al. (2022): Han H., B. A. McGivney, L. Allen, et al. 2022. \"Common Protein-Coding Variants Influence the Racing Phenotype in Galloping Racehorse Breeds\". &lt;i&gt;Communications Biology&lt;/i&gt; 5, no. 1: 1320. https://doi.org/10.1038/s42003-022-04206-x. https://www.nature.com/articles/s42003-022-04206-x.&lt;/p&gt;&lt;p&gt;Huang et al. (2015). Huang J., Y. Zhao, D. Bai, et al. 2015. \"Donkey Genome and Insight Into the Imprinting of Fast Karyotype Evolution\". &lt;i&gt;Scientific Reports&lt;/i&gt; 5, no. 1: 14106. https://doi.org/10.1038/srep14106. https://www.nature.com/articles/srep14106.&lt;/p&gt;&lt;p&gt;Librado et al. (2015): Librado P., C. Der Sarkissian, L. Ermini, et al. 2015. \"Tracking the Origins of Yakutian Horses and the Genetic Basis for Their Fast Adaptation to Subarctic Environments\". &lt;i&gt;Proceedings of the National Academy of Sciences of the United States of America&lt;/i&gt; 112, no. 50: E6889–E6897. https://doi.org/10.1073/pnas.1513696112. https://www.pnas.org/doi/10.1073/pnas.1513696112.&lt;/p&gt;&lt;p&gt;Wang et al. (2020): Wang C., H. Li, Y. Guo, et al. 2020. \"Donkey Genomes Provide New Insights Into Domestication and Selection for Coat Color\". &lt;i&gt;Nature Communications&lt;/i&gt; 11, no. 1: 6014. https://doi.org/10.1038/s41467-020-19813-7. https://www.nature.com/articles/s41467-020-19813-7.&lt;/p&gt;&lt;p&gt;Yuan et al. (2019): Yuan J. X., X. D. Hou, A. Barlow, et al. 2019, \"Molecular Identif","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 5","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17674","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062739","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":"Whole-Genome Evaluation of Genetic Rescue: The Case of a Curiously Isolated and Endangered Butterfly","authors":"Zachary G. MacDonald,&nbsp;Julian R. Dupuis,&nbsp;James R. N. Glasier,&nbsp;Robert Sissons,&nbsp;Axel Moehrenschlager,&nbsp;H. Bradley Shaffer,&nbsp;Felix A. H. Sperling","doi":"10.1111/mec.17657","DOIUrl":"10.1111/mec.17657","url":null,"abstract":"<p>Genetic rescue, or the translocation of individuals among populations to augment gene flow, can help ameliorate inbreeding depression and loss of adaptive potential in small and isolated populations. Genetic rescue is currently under consideration for an endangered butterfly in Canada, the Half-moon Hairstreak (<i>Satyrium semiluna</i>). A small, unique population persists in Waterton Lakes National Park, Alberta, isolated from other populations by more than 400 km. However, whether genetic rescue would actually be helpful has not been evaluated. Here, we generate the first chromosome-level genome assembly and whole-genome resequence data for the species. We find that the Alberta population maintains extremely low genetic diversity and is genetically very divergent from the nearest populations in British Columbia and Montana. Runs of homozygosity suggest this is due to a long history of inbreeding, and coalescent analyses show that the population has been small and isolated, yet stable, for up to 40k years. When a population like this maintains its viability despite inbreeding and low genetic diversity, it has likely undergone purging of deleterious recessive alleles and could be threatened by the reintroduction of such alleles via genetic rescue. Ecological niche modelling indicates that the Alberta population also exhibits environmental associations that are atypical of the species. Together, these evolutionary and ecological divergences suggest that population crosses may result in outbreeding depression. We therefore infer that genetic rescue has a relatively unique potential to be harmful rather than helpful for this population at present. However, because of its reduced adaptive potential, the Alberta population may still benefit from future genetic rescue as climate and habitat conditions change. Proactive experimental population crosses should therefore be completed to assess reproductive compatibility and progeny fitness.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 4","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17657","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078082","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":"Dynamic Outlier Slicing Allows Broader Exploration of Adaptive Divergence: A Comparison of Individual Genome and Pool-Seq Data Linked to Humic Adaptation in Perch","authors":"María-Eugenia López,&nbsp;Mikhail Ozerov,&nbsp;Lilian Pukk,&nbsp;Kristina Noreikiene,&nbsp;Riho Gross,&nbsp;Anti Vasemägi","doi":"10.1111/mec.17659","DOIUrl":"10.1111/mec.17659","url":null,"abstract":"<p>How genetic variation contributes to adaptation at different environments is a central focus in evolutionary biology. However, most free-living species still lack a comprehensive understanding of the primary molecular mechanisms of adaptation. Here, we characterised the targets of selection associated with drastically different aquatic environments—humic and clear water—in the common freshwater fish, Eurasian perch (<i>Perca fluviatilis</i>). By using whole-genome sequencing (WGS) on a large population dataset (<i>n</i> = 42 populations) and analysing 873,788 SNPs, our primary aim was to uncover novel and confirm known footprints of selection. We compared individual and pooled WGS, and developed a novel approach, termed dynamic outlier slicing, to assess how the choice of outlier-calling stringency influences functional and Gene Ontology (GO) enrichment. By integrating genome-environment association (GEA) analysis with allele frequency-based approaches, we estimated composite selection signals (CSS) and identified 2679 outlier SNPs distributed across 324 genomic regions, involving 468 genes. Dynamic outlier slicing identified robust enrichment signals in five annotation categories (upstream, downstream, synonymous, 5′UTR and 3′UTR) highlighting the crucial role of regulatory elements in adaptive evolution. Furthermore, GO analyses revealed strong enrichment of molecular functions associated with gated channel activity, transmembrane transporter activity and ion channel activity, emphasising the importance of osmoregulation and ion balance maintenance. Our findings demonstrate that despite substantial random drift and divergence, WGS of high number of population pools enabled the identification of strong selection signals associated with adaptation to both humic and clear water environments, providing robust evidence of widespread adaptation. We anticipate that the dynamic outlier slicing method we developed will enable a more thorough exploration of adaptive divergence across a diverse range of species.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 4","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17659","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021394","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":"Swatting Flies: Biting Insects as Non-Invasive Samplers for Mammalian Population Genomics.","authors":"Anubhab Khan, Ryan Carter, Chengetai D Mpamhanga, Daniel Masiga, Manun Channumsin, Marc Ciosi, Oliva Manangwa, Furaha Mramba, Umer Zeeshan Ijaz, Harriet Auty, Barbara K Mable","doi":"10.1111/mec.17661","DOIUrl":"https://doi.org/10.1111/mec.17661","url":null,"abstract":"<p><p>Advances in next-generation sequencing have allowed the use of DNA obtained from unusual sources for wildlife studies. However, these samples have been used predominantly to sequence mitochondrial DNA for species identification while population genetics analyses have been rare. Since next-generation sequencing allows indiscriminate detection of all DNA fragments in a sample, technically it should be possible to sequence whole genomes of animals from environmental samples. Here we used a blood-feeding insect, tsetse fly, to target whole genome sequences of wild animals. Using pools of flies, we compared the ability to recover genomic data from hosts using the short-read sequencing (Illumina) and adaptive sampling of long-read data generated using Oxford nanopore technology (ONT). We found that most of the short-read data (85%-99%) was dominated by tsetse fly DNA and that adaptive sampling on the ONT platform did not substantially reduce this proportion. However, once tsetse reads were removed, the remaining data for both platforms tended to belong to the dominant host expected in the tsetse fly blood meal. Reads mapping to elephants, warthogs and giraffes were recovered more reliably than for buffalo, and there was high variance in the contribution of DNA by individual flies to the pools, suggesting that there are host specific biases. For elephants, using short-read sequencing we were able to identify over 300,000 unfiltered SNPs, which we used to estimate the allele frequencies and expected heterozygosity for the population. Overall, our results show that at least for certain wild mammals, it is possible to recover genome-wide host data from blood-feeding insects.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17661"},"PeriodicalIF":4.5,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996932","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}