Molecular Ecology最新文献

{"title":"Urbanisation Is Associated With Reduced Genetic Diversity in Marine Fish Populations.","authors":"Eleana Karachaliou, Chloé Schmidt, Evelien de Greef, Margaret F Docker, Colin J Garroway","doi":"10.1111/mec.17711","DOIUrl":"https://doi.org/10.1111/mec.17711","url":null,"abstract":"<p><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":" ","pages":"e17711"},"PeriodicalIF":4.5,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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":"https://doi.org/10.1111/mec.17691","url":null,"abstract":"","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17691"},"PeriodicalIF":4.5,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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, Hannah K Hoff, Timothy J Divoll, Bethan L Littleford-Colquhoun, Heidi Anderson, Mary K Burak, Maria L Kuzmina, Paul M Musili, Haldre Rogers, Alejandra J Troncoso, Rebecca Y Kartzinel","doi":"10.1111/mec.17712","DOIUrl":"https://doi.org/10.1111/mec.17712","url":null,"abstract":"<p><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 >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":" ","pages":"e17712"},"PeriodicalIF":4.5,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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}

{"title":"Overcoming Ploidy Barriers: The Role of Triploid Bridges in the Genetic Introgression of Cardamine amara.","authors":"P Bartolić, A Voltrová, L Macková, G Šrámková, M Šlenker, T Mandáková, N Padilla García, K Marhold, F Kolář","doi":"10.1111/mec.17702","DOIUrl":"https://doi.org/10.1111/mec.17702","url":null,"abstract":"<p><p>Polyploidisation is a significant reproductive barrier, yet genetic evidence indicates that interploidy admixture is more common than previously thought. Theoretical models and controlled crosses support the 'triploid bridge' hypothesis, proposing that hybrids of intermediate ploidy facilitate gene flow. However, comprehensive evidence combining experimental and genetic data from natural mixed-ploidy species is missing. Here, we investigated the rates and directionality of gene flow within a diploid-autotetraploid contact zone of Cardamine amara, a species with abundant natural triploids. We cytotyped over 400 individuals in the field, conducted reciprocal interploidy crosses, and inferred gene flow based on genome-wide sequencing of 84 individuals. Triploids represent a conspicuous entity in mixed-ploidy populations (5%), yet only part of them arose through interploidy hybridisation. Despite being rarely formed, triploid hybrids can backcross with their parental cytotypes, producing viable offspring that are often euploid (in 42% of cases). In correspondence, D-statistics and coalescent simulations documented a significant genome-wide signal of bidirectional gene flow in sympatric but not allopatric populations. Triploids, though rare, thus seem to play a key role in overcoming polyploidy-related reproductive barriers in C. amara. In sum, we present integrative evidence for interploidy gene flow mediated by a triploid bridge in natural populations.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17702"},"PeriodicalIF":4.5,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490315","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 and Host Relatedness Shape Virome Composition in a Widespread, Generalist Carnivore","authors":"Natalie Payne,&nbsp;Desiree Andersen,&nbsp;Cheryl Mollohan,&nbsp;Koenraad Van Doorslaer,&nbsp;Leigh Combrink,&nbsp;Melanie Culver","doi":"10.1111/mec.17681","DOIUrl":"10.1111/mec.17681","url":null,"abstract":"<div>\u0000 \u0000 <p>Urban wildlife species have the potential to serve as links in disease transmission between wildlife, humans and domestic animals at the wildland–urban interface (WUI), contributing to both sustained cross-species transmission of pathogens and the emergence of diseases in susceptible populations. However, the relative roles of host and environmental factors in shaping the composition of pathogen communities in urban wildlife is understudied. In this study, we integrated DNA and RNA virome data with host genomic and GPS datasets to investigate factors shaping virome composition in bobcats (<i>Lynx rufus</i> ) at the WUI in the Tucson Mountains, Arizona, USA. Using a hybrid-capture approach for 31 scats and 17 buccal swabs, we identified multiple viruses that could affect carnivore health at the WUI, including canine parvovirus, feline astrovirus, <i>Felis catus</i> papillomaviruses 2 and 3 and Lyon-IARC polyomavirus. Models of virome composition and distribution of viral taxa indicated contributions of host genetic relatedness and factors relating to urbanisation (such as percentages of urban land cover, road and building densities and distances to roads). Genetic associations with virome compositions were particularly influenced by females. While females exhibit significant isolation by distance, partial Mantel tests revealed a significant correlation between beta diversity and host genetic distance in females only. To our knowledge, this study represents the first assessment of factors shaping virome composition in a wild felid. Our finding of known feline and canine pathogens in bobcats underscores the potential of the WUI to facilitate cross-species transmission between wild and domestic animals.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 6","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481647","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":"Stomach Microbiome Simplification of a Coral Reef Fish at Its Novel Cold-Range Edge Under Climate Change.","authors":"Chloe Hayes, Angus Mitchell, Roger Huerlimann, Jeffrey Jolly, Chengze Li, David J Booth, Timothy Ravasi, Ivan Nagelkerken","doi":"10.1111/mec.17704","DOIUrl":"https://doi.org/10.1111/mec.17704","url":null,"abstract":"<p><p>Climate-driven range extensions of animals into higher latitudes are often facilitated by phenotypic plasticity. Modifications to habitat preference, behaviour and diet can increase the persistence of range-extending species in novel high-latitude ecosystems. These strategies may be influenced by changes in their gut and stomach microbial communities that are critical to host fitness and potentially adaptive plasticity. Yet, it remains unknown if the gut and stomach microbiome of range-extending species is plastic in their novel ranges to help facilitate these modifications. Here, we categorised stomach microbiome communities of a prevalent range-extending coral reef fish along a 2000-km latitudinal gradient in a global warming hotspot, extending from their tropical core range to their temperate cold range edge. At their cold range edge, the coral reef fish's stomach microbiome showed a 59% decrease in bacterial diversity and a 164% increase in the relative abundance of opportunistic bacteria (Vibrio) compared to their core range. Microbiome diversity was unaffected by fish body size, water temperature, physiology (cellular defence and damage) and habitat type (turf, barren, oyster, kelp and coral) across their range. The observed shifts in microbiome composition suggest dysbiosis and low plasticity of tropical range-extending fishes to novel environmental conditions (e.g., temperate prey and lower seawater temperature) at their novel range edges, which may increase their susceptibility to disease in temperate ecosystems. We conclude that fishes extending their ranges to higher latitudes under ocean warming can experience a simplification (i.e., reduced diversity) of their stomach microbiome, which could restrict their current rate of range extensions or establishment in temperate ecosystems.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17704"},"PeriodicalIF":4.5,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476183","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":"Not All Bark Beetles Smell the Same: Population-Level Functional Olfactory Polymorphisms in Ips typographus Pheromone Receptor ItypOR33","authors":"Jibin Johny,&nbsp;Souleymane Diallo,&nbsp;Krystyna Nadachowska-Brzyska,&nbsp;Antonioni Acacio Campos Moliterno,&nbsp;Amit Roy,&nbsp;Blanka Kalinová,&nbsp;Ewald Große-Wilde,&nbsp;Fredrik Schlyter","doi":"10.1111/mec.17693","DOIUrl":"10.1111/mec.17693","url":null,"abstract":"<div>\u0000 \u0000 <p>Eurasian spruce bark beetle <i>Ips typographus</i>, a natural part of forest ecosystems, is a major threat to Norway spruce forests during outbreaks. Olfaction plays a crucial role in the survival and range expansion of these beetles, amid forest disturbances and climate change. As the current management strategies are suboptimal for controlling outbreaks, the reverse chemical ecology approaches based on pheromone receptors offer promising alternatives. While the search for pheromone receptors is in progress, recently found chromosomal inversions indicates signs of adaptation in this species. Our attempts to characterise one of the highly expressed odorant receptors, <i>ItypOR33</i>, located in an inversion, led to the discovery of polymorphic variants distributed with similar frequency across 18 European populations. Deorphanizing <i>ItypOR33</i> and its variant <i>ItypOR33a</i> using the <i>Drosophila</i> empty-neuron system (DeNS) revealed <i>ItypOR33</i> tuned to amitinol, a heterospecific pheromone component in <i>Ips</i> spp., whereas its variant tuned to (<i>S</i>)-(−)-ipsenol, a conspecific pheromone component of <i>I. typographus</i>. The <i>in silico</i> approaches revealed the structural basis of variations by predicting putative ligand-binding sites, tunnels and ligand-receptor interactions. However, no sex-specific differences were found in the <i>ItypOR33</i> expression, and its ligand amitinol elicited behavioural and electrophysiological responses. Reporting population-level functional olfactory polymorphisms for the first time in a non-model organism—bark beetles, provides key evidence for further exploring their survival and adaptation in forests. Additionally, these findings indicate potential long-term complexities of managing bark beetles in forests.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 6","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476182","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}