Molecular Ecology最新文献

{"title":"Reproductive Barriers and Genomic Hotspots of Adaptation During Allopatric Species Divergence.","authors":"Riddhi Deshmukh, Saurav Baral, Muktai Kuwalekar, Athulya Girish Kizhakke, Krushnamegh Kunte","doi":"10.1111/mec.17703","DOIUrl":"https://doi.org/10.1111/mec.17703","url":null,"abstract":"<p><p>Theory predicts that in allopatric populations, genomic divergence and reproductive barriers may be driven by random genetic drift and thereby evolve slowly in large populations. However, local adaptation and divergence under selection may also play important roles, which remain poorly characterised. Here, we address three key questions in young allopatric species: (a) How widespread are genomic signatures of adaptive divergence?, (b) What is the functional space along which young sister species show divergence at the genomic level? and (c) How quickly might prezygotic and postzygotic reproductive barriers evolve? Analysis of 82 re-sequenced genomes of the Oriental Papilio polytes species group revealed surprisingly widespread hotspots of intense selection and selective sweeps at hundreds of genes, spanning all chromosomes, rather than divergence only in a few genomic islands. These genes are involved in diverse ecologically important adaptive functions such as wing development, colour patterning, courtship behaviour, mimicry, pheromone synthesis and olfaction, and host plant use and digestion of secondary metabolites, that could contribute to local adaptation and subsequent reproductive isolation. Divergence at such functional genes appeared to have evolved in conjunction with reproductive consequences: behavioural and hybridisation experiments revealed strong assortative mate preference (prezygotic barriers) as well as postzygotic barriers to hybridisation in timespans as short as 1.5 my, indicating that speciation was already complete rather than incipient. Our study thus demonstrates an underappreciated role of intense selection and potential local adaptation in creating genome-wide hotspots of rapid molecular evolution and divergence during differentiation and speciation in young allopatric species.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17703"},"PeriodicalIF":4.5,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143539732","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":"Climate Change Drives Long-Term Spatiotemporal Shifts in Red Noctiluca scintillans Blooms Along China's Coast","authors":"Xiangyuan Lin,&nbsp;Wenjia Hu,&nbsp;Kieng Soon Hii,&nbsp;Wupeng Xiao,&nbsp;Hongjian Tan,&nbsp;Lingqi Ma,&nbsp;Hala F. Mohamed,&nbsp;Rongsuo Cai,&nbsp;Jianhua Kang,&nbsp;Zhaohe Luo","doi":"10.1111/mec.17709","DOIUrl":"10.1111/mec.17709","url":null,"abstract":"<div>\u0000 \u0000 <p>Climate change has significantly altered the spatiotemporal distribution and phenology of marine organisms, yet the long-term trends and mechanisms driving these changes remain insufficiently understood. In this study, we analysed historical <i>Noctiluca scintillans</i> bloom data from coastal China (1933, 1952, 1981–2023), sea surface temperature (SST) records from the past 40 years, and 509 field samples using Single Molecule Real-Time (SMRT) sequencing (2019–2024). Our results indicate that SST is the primary driver of <i>N. scintillans</i> blooms, exhibiting a nonlinear unimodal correlation. Long-term SST warming has caused a northward shift in bloom locations, aligning with the 21.9°C–22.7°C isotherms, as reflected by the increasing average latitudes of bloom occurrences. Over the past 4 decades, bloom frequency and duration have followed an overall increasing trend, displaying an approximate 10-year cyclical pattern. Ocean warming has also contributed to earlier bloom initiation, extended peak bloom periods and delayed bloom termination, shaping the long-term dynamics of <i>N. scintillans</i> blooms. SMRT sequencing confirmed that local <i>N. scintillans</i> populations persist year-round, serving as latent seed sources that can rapidly bloom when environmental conditions become favourable. These findings provide critical insights into the dynamics of harmful algal blooms in the context of climate change and lay a foundation for future ecological and environmental research.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143539728","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":"Fifty Years of Conservation Genetics: A Personal Perspective.","authors":"Fred W Allendorf","doi":"10.1111/mec.17705","DOIUrl":"https://doi.org/10.1111/mec.17705","url":null,"abstract":"<p><p>I provide my personal account of the application of genetics to conservation. I began graduate school shortly after the first description of genetic variation in natural populations. The use of allozymes uncovered an unexpected amount of genetic variation in a wide variety of species. During this same period, Motoo Kimura proposed the Neutral Theory of Evolution. Understanding the adaptive significance of allozyme variation became the major focus of population genetics. The utility of population genetic data for conservation and management was questioned because if the observed patterns were determined primarily by selection, then they could not be used to estimate gene flow or genetic drift. The study of mitochondrial DNA next provided a different view of genetic variation by allowing the overlaying of genealogical information on the locations of sampled individuals (phylogeography). The introduction of microsatellites allowed the study of a large number of nuclear markers. The many loci and large number of alleles at microsatellites were valuable for detecting bottlenecks and identifying relationships of individuals. The use of single nucleotide polymorphisms (SNPs) next opened the door to genomic analysis that allowed sampling a mapped genome to detect forces affecting particular genomic regions instead of using a representative sample of loci. For example, using runs of homozygosity has revolutionised our understanding of the effects of inbreeding and the detection of inbreeding depression. Current techniques provide unprecedented power to study genetic variation in natural populations. Nevertheless, the application of this information requires a sound understanding of population genetics theory.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17705"},"PeriodicalIF":4.5,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536149","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":"Species Delimitation Using Genomic Data: Options and Limitations.","authors":"Bernhard Hausdorf","doi":"10.1111/mec.17717","DOIUrl":"https://doi.org/10.1111/mec.17717","url":null,"abstract":"<p><p>The most effective approaches for species discovery and species validation with genomic data remain underexplored. This study evaluates the merits and limitations of phylogenetic approaches based on the multispecies coalescent model and population genetic approaches for species discovery, i.e., species delimitation in the absence of prior knowledge, using genomic datasets from four well-known radiations. Furthermore, it demonstrates how geographic data can be integrated with the genomic data for species validation, i.e., for testing primary species hypotheses. The multispecies coalescent model-based approaches tr2 and soda resulted in high over-splitting of species, low percentages of species delimited according to the current classification, and low percentages of individuals assigned to the same species as in the current classification across all four species complexes studied. Conversely, the species numbers were slightly underestimated based on the structure results. Although the proportion of species delimited according to the current classification and the proportion of individuals assigned to the same species as in the current classification in the classifications based on the structure results is approximately twice that of the classifications proposed by the multispecies coalescent model-based approaches, it remains unsatisfactory. A slight over-splitting of species into population groups can be corrected by species validation with isolation-by-distance tests if a sufficient number of populations have been sampled for each species. Sampling design is an essential step in any taxonomic study, as it has a significant impact on the delimitation of the species and the possibility of their validation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17717"},"PeriodicalIF":4.5,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143539400","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":"Urbanisation Is Associated With Reduced Genetic Diversity in Marine Fish Populations","authors":"Eleana Karachaliou,&nbsp;Chloé Schmidt,&nbsp;Evelien de Greef,&nbsp;Margaret F. Docker,&nbsp;Colin J. Garroway","doi":"10.1111/mec.17711","DOIUrl":"10.1111/mec.17711","url":null,"abstract":"<p>The benefits to humans of living by the ocean have led many coastal settlements to grow into large, densely populated cities. Large coastal cities have had considerable environmental effects on marine ecosystems through resource extraction, waste disposal, coastal development, and trade and travel routes. While our understanding of the ecological and evolutionary consequences of urbanisation for wildlife in terrestrial systems has received considerable recent attention, the consequences of urbanisation in marine systems are not well known. Using microsatellite datasets associated with published research on marine fish population genetics, we built a global database of genotypic data spanning 75,361 individuals sampled from 73 species at 1085 sample sites throughout the world's oceans. We found that genetic diversity and effective population sizes were significantly lower at marine fish sample sites associated with denser human populations, regardless of species and locality. The loss of genetic diversity near denser human populations indicates habitats near human settlements are less able to support large populations. Small effective population sizes, in turn, dampen the efficiency of natural selection near dense urban settlements. The loss of genetic diversity near cities is concerning for maintaining functioning marine ecosystems and sustainable fisheries. Our work highlights the need to mitigate environmental threats from human activities and focus efforts on sustainable urban planning and resource use to conserve marine biodiversity and sustain coastal fisheries and ecosystems.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17711","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536152","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":"Correction to “The Opposed Forces of Differentiation and Admixture Across Glacial Cycles in the Butterfly Aglais urticae”","authors":"","doi":"10.1111/mec.17691","DOIUrl":"10.1111/mec.17691","url":null,"abstract":"<p>Marques, V., Hinojosa, J. C., Dapporto, L., Talavera, G., Stefanescu, C., Gutiérrez, D., &amp; Vila, R. (2024). The opposed forces of differentiation and admixture across glacial cycles in the butterfly Aglais urticae. Molecular Ecology, 33, e17304. https://doi.org/10.1111/mec.17304</p><p>This manuscript (MEC-23-0570) contains an incorrect citation of a work by M. E. Ateş.</p><p>The article currently cites the work as follows:</p><p>Mustafa, A. (2021). Pioneers of the ice age models: A brief history from Agassiz to Milankovitch. https://doi.org/10.5194/hgss-2021-1</p><p>The correct citation is as follows:</p><p>Ateş, M. E. (2022). Pioneers of the Ice Age Models: A Brief History from Agassiz to Milankovitch. History of Geo- and Space Sciences, 13(1), 23–37. https://doi.org/10.5194/hgss-13-23-2022</p><p>In Paragraph 9 of the Discussion, under “The opposed forces of differentiation by isolation and admixture by gene flow,” it is cited as “Mustafa, 2021” and it should be “Ateş, 2022.”</p><p>We apologise for this error.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17691","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522279","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":"Admixture Increases Genetic Diversity and Adaptive Potential in Australasian Killer Whales.","authors":"Isabella M Reeves, John A Totterdell, Jonathan Sandoval-Castillo, Emma L Betty, Karen A Stockin, Ramari Oliphant Stewart, Muriel Johnstone, Andrew D Foote","doi":"10.1111/mec.17689","DOIUrl":"https://doi.org/10.1111/mec.17689","url":null,"abstract":"<p><p>Admixture is the exchange of genetic variation between differentiated demes, resulting in ancestry within a population coalescing in multiple ancestral source populations. Low-latitude killer whales (Orcinus orca) populations typically have higher genetic diversity than those in more densely populated, high productivity and high-latitude regions. This has been hypothesized to be due to episodic admixture between populations with distinct genetic backgrounds. We test this hypothesis by estimating variation in local ancestry of whole genome sequences from three genetically differentiated, low-latitude killer whale populations and comparing them to global genetic variation. We find 'Antarctic-like' ancestry tracts in the genomes of southwestern Australia (SWA) population including recent (within the last 2-4 generations) admixture. Admixed individuals had, on average, shorter and fewer runs of homozygosity than unadmixed individuals and increased effective population size (N_e). Thus, connectivity between demes results in the maintenance of N_e of relatively small demes at a level comparable to the sum of N_e across demes. A subset of the admixed regions was inferred to be evolving under selection in the SWA population, suggesting that this admixed variation may be contributing to the population's adaptive potential. This study provides important and rare empirical evidence that small populations can maintain genetic diversity due to sporadic admixture between different genetic backgrounds and that admixed ancestry can promote the long-term stability of N_e.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17689"},"PeriodicalIF":4.5,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522276","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":"Global Availability of Plant DNA Barcodes as Genomic Resources to Support Basic and Policy-Relevant Biodiversity Research","authors":"Tyler R. Kartzinel,&nbsp;Hannah K. Hoff,&nbsp;Timothy J. Divoll,&nbsp;Bethan L. Littleford-Colquhoun,&nbsp;Heidi Anderson,&nbsp;Mary K. Burak,&nbsp;Maria L. Kuzmina,&nbsp;Paul M. Musili,&nbsp;Haldre Rogers,&nbsp;Alejandra J. Troncoso,&nbsp;Rebecca Y. Kartzinel","doi":"10.1111/mec.17712","DOIUrl":"10.1111/mec.17712","url":null,"abstract":"<p>Genetic technologies such as DNA barcoding make it easier and less expensive to monitor biodiversity and its associated ecosystem services, particularly in biodiversity hotspots where traditional assessments are challenging. Successful use of these data-driven technologies, however, requires access to appropriate reference data. We reviewed the &gt;373,584 reference plant DNA barcodes in public repositories and found that they cumulatively cover a remarkable quarter of the ~435,000 extant land plant species (Embryophyta). Nevertheless, coverage gaps in tropical biodiversity hotspots reflect well-documented biases in biodiversity science – most reference specimens originated in the Global North. Currently, at least 17% of plant families lack any reference barcode data whatsoever, affecting tropical and temperate regions alike. Investigators often emphasise the importance of marker choice and the need to ensure protocols are technically capable of detecting and identifying a broad range of taxa. Yet persistent geographic and taxonomic gaps in the reference datasets show that these protocols rely upon risk undermining all downstream applications of the strategy, ranging from basic biodiversity monitoring to policy-relevant objectives – such as the forensic authentication of materials in illegal trade. Future networks of investigators could work strategically to improve data coverage, which will be essential in global efforts to conserve biodiversity while advancing more fair and equitable access to benefits arising from genetic resources.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17712","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522363","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":"High Quality Diet Enhances Immune Response and Affects Gene Expression During Viral Infection in an Insect Herbivore.","authors":"Su'ad A Yoon, Kevin So, Joshua G Harrison, Vivaswat Shastry, Katherine Urie, Zach Gompert, Pedro Miura, Angela M Smilanich, Matthew L Forister, Samridhi Chaturvedi","doi":"10.1111/mec.17694","DOIUrl":"https://doi.org/10.1111/mec.17694","url":null,"abstract":"<p><p>Herbivorous insects tolerate chemical and metabolic variation in their host plant diet by modulating physiological traits. Insect immune response is one such trait that plays a crucial role in maintaining fitness but can be heavily influenced by variation in host plant quality. An important question is how the use of different host plants affects the ability of herbivorous insects to resist viral pathogens. Furthermore, the transcriptional changes associated with this interaction of diet and viral pathogens remain understudied. The Melissa blue butterfly (Lycaeides melissa) has colonised the exotic legume Medicago sativa as a larval host within the past 200 years. We used this system to study the interplay between the effects of host plant variation and viral infection on physiological responses and global gene expression. We measured immune strength in response to infection by the Junonia coenia densovirus (JcDV) in two ways: (1) direct measurement of phenoloxidase activity and melanisation, and (2) transcriptional sequencing of individuals exposed to different viral and host plant treatments. Our results demonstrate that viral infection caused total phenoloxidase (total PO) to increase and viral infection and host plant interactively affected total PO such that for infected larvae, total PO was significantly higher for larvae consuming the native host plant. Additionally, L. melissa larvae differentially expressed several hundred genes in response to host plant treatment, but with minimal changes in gene expression in response to viral infection. Not only immune genes, but several detoxification, transporter, and oxidase genes were differentially expressed in response to host plant treatments. These results demonstrate that in herbivorous insects, consumption of a novel host plant can alter both physiological and transcriptional responses relevant to viral infection, emphasising the importance of considering immune and detoxification mechanisms into models of evolution of host range in herbivorous insects.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17694"},"PeriodicalIF":4.5,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497732","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":"Genomics-Enabled Mixed-Stock Analysis Uncovers Intraspecific Migratory Complexity and Detects Unsampled Populations in a Harvested Fish.","authors":"Julie Gibelli, Hari Won, Sozos Michaelides, Hyung-Bae Jeon, Dylan J Fraser","doi":"10.1111/mec.17707","DOIUrl":"https://doi.org/10.1111/mec.17707","url":null,"abstract":"<p><p>The contributions of distinct populations to annual harvests provide key insights to conservation, especially in migratory species that return to specific reproductive areas. In this context, genetic stock identification (GSI) requires reference samples from source populations to assign harvested individuals, yet sampling might be challenging as reproductive areas could be remote and/or unknown. To investigate intraspecific variation in walleye (Sander vitreus) populations harvested in two large lakes in northern Quebec, we used genotyping-by-sequencing data to develop a panel of 303 filtered single-nucleotide polymorphisms. We then genotyped 1465 fish and assessed individual migration distances from GPS coordinates of capture locations. Samples were assigned to a source population using two methods, one requiring allele frequencies of known populations (RUBIAS) and the other without prior knowledge (STRUCTURE). Individual assignments to a known population reached 93% consistency between both methods in the main lake where we identified all five major source populations. However, the analyses also revealed up to three small unsampled populations. Furthermore, populations were characterised by large differences in average migration distance. In contrast, assignment consistency reached 99% in the neighbouring lake and walleye were assigned with high confidence to two populations having a similar distribution throughout the lake. The complex population structure and migration patterns in the main lake suggest a more heterogeneous habitat and thus, greater potential for local adaptation. This study highlights how combining analytical approaches can inform the robustness of GSI results in a given system and detect intraspecific diversity and complexity relevant for conservation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17707"},"PeriodicalIF":4.5,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490313","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}