Suvratha Jayaprasad, Valentina Peona, Simon J Ellerstrand, Roberto Rossini, Ignas Bunikis, Olga V Pettersson, Remi-André Olsen, Carl-Johan Rubin, Elisabet Einarsdottir, Franziska Bonath, Tessa M Bradford, Steven J B Cooper, Bengt Hansson, Alexander Suh, Takeshi Kawakami, Holger Schielzeth, Octavio M Palacios-Gimenez
{"title":"Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes.","authors":"Suvratha Jayaprasad, Valentina Peona, Simon J Ellerstrand, Roberto Rossini, Ignas Bunikis, Olga V Pettersson, Remi-André Olsen, Carl-Johan Rubin, Elisabet Einarsdottir, Franziska Bonath, Tessa M Bradford, Steven J B Cooper, Bengt Hansson, Alexander Suh, Takeshi Kawakami, Holger Schielzeth, Octavio M Palacios-Gimenez","doi":"10.1111/mec.17567","DOIUrl":"https://doi.org/10.1111/mec.17567","url":null,"abstract":"<p><p>The early evolution of sex chromosomes has remained obscure for more than a century. The Vandiemenella viatica species group of morabine grasshoppers is highly suited for studying the early stages of sex chromosome divergence and degeneration of the Y chromosome. This stems from the fact that neo-XY sex chromosomes have independently evolved multiple times by X-autosome fusions with different autosomes. Here, we generated new chromosome-level assemblies for two chromosomal races representing karyotypes with and without neo-sex chromosomes (P24XY and P24X0), and sequence data of a third chromosomal race with a different neo-XY chromosome system (P25XY). Interestingly, these two neo-XY chromosomal races are formed by different X-autosome fusions (involving chr1 and chrB, respectively), and we found that both neo-Y chromosomes have partly ceased to recombine with their neo-X counterpart. We show that the neo-XY chromosomes have diverged through accumulation of SNPs and structural mutations, and that many neo-Y-linked genes have degenerated since recombination ceased. However, the non-recombining regions of neo-Y chromosomes host non-degenerated genes crucial for sex determination, such as sex-lethal and transformer, alongside genes associated with spermatogenesis, fertility, and reproduction, illustrating their integrative role as a masculinizing supergene. Contrary to expectations, the neo-Y chromosomes showed (slightly) lower density of transposable elements (TEs) compared to other genomic regions. The study reveals the unique dynamics of young sex chromosomes, with evolution of recombination suppression and pronounced decay of (some) neo-sex chromosome genes, and provides a compelling case illustrating how chromosomal fusions and post-fusion mutational processes contribute to the evolution of supergenes.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17567"},"PeriodicalIF":4.5,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542397","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}
Xin Sun, Emily Louisa Cavill, Ashot Margaryan, Jianqing Lin, Søren Thingaard, Tamrini A Said, Shyam Gopalakrishnan, M Thomas P Gilbert
{"title":"A Genomic Exploration of the Possible De-Extirpation of the Zanzibar Leopard.","authors":"Xin Sun, Emily Louisa Cavill, Ashot Margaryan, Jianqing Lin, Søren Thingaard, Tamrini A Said, Shyam Gopalakrishnan, M Thomas P Gilbert","doi":"10.1111/mec.17566","DOIUrl":"https://doi.org/10.1111/mec.17566","url":null,"abstract":"<p><p>The recently extirpated Zanzibar leopard was the only known African leopard (Panthera pardus spp.) population restricted exclusively to a major island habitat. Although its demise was driven through habitat change and conflict with humans, given its role as a keystone species for the Zanzibar Archipelago, its successful potential reintroduction might offer a means for helping preserve the natural biodiversity of its former habitat. Whether this is feasible, however, would be contingent on both whether closely related source populations can be identified on mainland Africa, and whether the Zanzibar form exhibited any special adaptations that might need to be considered when choosing such a source. In light of these questions, we genomically profiled two of the six known historic specimens, to explore whether they represent a realistic candidate for de-extirpation through reintroduction. Our analyses indicate that despite its geographical separation, the Zanzibar leopard shared a close genetic relationship with mainland East African individuals. Furthermore, although its uniqueness as an island population was emphasised by genomic signatures of high inbreeding and increased mutation load, the latter similar to the level of the critically endangered Amur leopard (P. p. orientalis), we find no evidence of functionally significant genetic diversity unique to Zanzibar. We therefore conclude that should attempts to restore leopards to Zanzibar be considered, then mainland East African leopards would provide a suitable gene pool.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17566"},"PeriodicalIF":4.5,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542396","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}
Erik E Sotka, A Randall Hughes, Torrance C Hanley, Cynthia G Hays
{"title":"Restricted Dispersal and Phenotypic Response to Water Depth in a Foundation Seagrass.","authors":"Erik E Sotka, A Randall Hughes, Torrance C Hanley, Cynthia G Hays","doi":"10.1111/mec.17565","DOIUrl":"https://doi.org/10.1111/mec.17565","url":null,"abstract":"<p><p>Species conservation and management benefit from precise understanding of natural patterns of dispersal and genetic variation. Using recent advances in indirect genetic methods applied to both adult plants and dispersed seeds, we find that the mean seed dispersal in a threatened marine foundation plant (the eelgrass Zostera marina) is approximately 100-200 m. This distance is surprisingly more similar to that of wind-dispersed terrestrial seeds (~10s to 100s of meters) than the passive dispersal of marine propagules via currents (~10s to 100s of kilometres). Because nearshore marine plants like Zostera are commonly distributed across strong selective gradients driven by bathymetry (depth) even within these restricted spatial scales, seeds are capable of dispersing to novel water depths and experiencing profound shifts in light availability, temperature and wave exposure. We documented strong phenotypic variation and genome-wide differentiation among plants separated by approximately the spatial scale of mean realised dispersal. This result suggests genetic isolation by environment in response to depth-related environmental gradients as one plausible explanation for this pattern. The ratio of effective to census size (or Ne/Nc) approximated 0.1%, indicating that a fraction of existing plants provides the genetic variation to allow adaptation to environmental change. Our results suggest that successful conservation of seagrass meadows that can adapt to microspatial and temporal variation in environmental conditions will be low without direct and persistent intervention using large numbers of individuals or a targeted selection of genotypes.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17565"},"PeriodicalIF":4.5,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542398","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}
Andreas Härer, Ken A Thompson, Dolph Schluter, Diana J Rennison
{"title":"Associations Between Gut Microbiota Diversity and a Host Fitness Proxy in a Naturalistic Experiment Using Threespine Stickleback Fish.","authors":"Andreas Härer, Ken A Thompson, Dolph Schluter, Diana J Rennison","doi":"10.1111/mec.17571","DOIUrl":"https://doi.org/10.1111/mec.17571","url":null,"abstract":"<p><p>The vertebrate gut microbiota is a critical determinant of organismal function, yet whether and how gut microbial communities affect host fitness under natural conditions remains largely unclear. We characterised associations between a fitness proxy-individual growth rate-and bacterial gut microbiota diversity and composition in threespine stickleback fish introduced to large semi-natural ponds. We detected a 63% higher richness of bacterial taxa (α-diversity) in the guts of high-fitness fish compared to low-fitness fish, which might be driven by stronger bacterial dispersal among high-fitness fish according to the fit of a neutral community model. Further, microbial communities of high-fitness fish were more similar to one another (i.e., exhibited lower β-diversity) than those of low-fitness fish. The lower β-diversity found to be associated with higher host fitness is consistent with the Anna Karenina principle-that there are fewer ways to have a functional microbiota than a dysfunctional microbiota. Our study links differences in α- and β-diversity to a fitness-related trait in a vertebrate species reared under naturalistic conditions and our findings provide a basis for functional tests of the fitness consequences of host-microbiota interactions.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17571"},"PeriodicalIF":4.5,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142520550","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}
Marek Šlenker, Adam Kantor, Dušan Senko, Lenka Mártonfiová, Gabriela Šrámková, Veronika Cetlová, Ali A. Dönmez, Sırrı Yüzbaşıoğlu, Judita Zozomová-Lihová
{"title":"Genome-Wide Data Uncover Cryptic Diversity With Multiple Reticulation Events in the Balkan-Anatolian Cardamine (Brassicaceae) Species Complex","authors":"Marek Šlenker, Adam Kantor, Dušan Senko, Lenka Mártonfiová, Gabriela Šrámková, Veronika Cetlová, Ali A. Dönmez, Sırrı Yüzbaşıoğlu, Judita Zozomová-Lihová","doi":"10.1111/mec.17564","DOIUrl":"10.1111/mec.17564","url":null,"abstract":"<div>\u0000 \u0000 <p>Plant species diversity may be considerably underestimated, especially in evolutionarily complex genera and in diversity hotspots that have enabled long-term species persistence and diversification, such as the Balkan Peninsula. Here, we address the topic of underexplored plant diversity and underlying evolutionary and biogeographic processes by investigating the hygrophytic mountain species complex of <i>Cardamine acris</i> s.l. distributed in the Balkans (three subspecies within <i>C. acris</i>) and northwestern Anatolia (<i>C. anatolica</i>). We performed a series of phylogenetic and phylogeographic analyses based on restriction-site associated DNA sequencing (RADseq) and target enrichment (Hyb-Seq) data in combination with habitat suitability modelling. We found <i>C. anatolica</i> as a clade nested within the Balkan <i>C. acris</i>, probably resulting from a founder event, and uncovered three allopatric cryptic lineages within <i>C. acris</i> subsp. <i>acris</i>, allowing us to recognise a total of six entities in this complex. We observed the deepest genetic split within <i>C. acris</i> subsp. <i>acris</i> in the western Balkans, which was at odds with taxonomy and showed no distribution gap. We inferred vicariance as the most likely process for population divergence in the Balkans, accompanied by gene flow between the recognised entities, which was consistent with the modelled habitat suitability dynamics. Furthermore, we discovered several polyploid populations in <i>C. acris</i>, representing both pure intra- and inter-lineage hybrid polyploids, but detected only minor traces of hybridization with related congeners. Overall, our results illustrate that diverse evolutionary processes may influence the history of mountain plant species in the Balkan Peninsula, including vicariance, reticulation, polyploidization and cryptic diversification.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"33 22","pages":""},"PeriodicalIF":4.5,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491745","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":"Contrast and Genomic Characterisation of Ancient and Recent Interspecific Introgression Between Deeply Diverged Moustache Toads (Leptobrachium).","authors":"Jun Li, Qingbo Ai, Siyu Xie, Chunhua Huang, Fuyuan Qiu, Chao Fu, Mian Zhao, Jinzhong Fu, Hua Wu","doi":"10.1111/mec.17569","DOIUrl":"https://doi.org/10.1111/mec.17569","url":null,"abstract":"<p><p>Recent genomic analyses have provided new insights into the process of interspecific introgression and its consequences on species evolution. Most recent studies, however, focused on hybridization between recently radiated species, with few examining the genomic outcomes of ancient hybridization across deeply diverged species. Using whole genome data of moustache toads (Leptobrachium), we identified signals of three hybridization events among nine species that diverged at the Eocene. An ancient introgression from L. leishanense to the ancestral branch (C1) of L. liui introduced adaptive variants. The highly introgressed regions include genes with important functions in odorant detection and immune responses. These genes are preserved in all three descendent populations of L. liui_C1, and these regions likely have been positively selected over a long filtering process. A recent introgression occurred from L. huashen to L. tengchongense, with the introgressed regions being mostly neutral. Furthermore, one F1 hybrid individual was detected between sympatric L. ailaonicum and L. promustache. The signals of introgression largely disappeared after removing the hybrid individual, indicating an occasional hybridization but minimal introgression. Further examination of highly divergent but low introgressed genomic regions revealed both pre-mating isolation and genetic incompatibility as potential mechanisms of resisting introgression and maintaining species boundaries. Additionally, no large X-effect was found in these introgression events. Hybridization between deeply diverged amphibian species may be common, but detectable introgressions are likely less so, with recent introgression being mostly neutral and the rare ancient one potentially adaptive. Our findings complement recent genomic work, and together they provide a better understanding of the genomic characteristics of interspecific introgression and its significance in species adaptation and evolution.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17569"},"PeriodicalIF":4.5,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491743","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}
Callie R Chappell, Pagé C Goddard, Lexi-Ann Golden, Jonathan Hernandez, Daniela Ortiz Chavez, Marziiah Hossine, Sur Herrera Paredes, Ethan VanValkenburg, Lucas A Nell, Tadashi Fukami, Manpreet K Dhami
{"title":"Transcriptional Responses to Priority Effects in Nectar Yeast.","authors":"Callie R Chappell, Pagé C Goddard, Lexi-Ann Golden, Jonathan Hernandez, Daniela Ortiz Chavez, Marziiah Hossine, Sur Herrera Paredes, Ethan VanValkenburg, Lucas A Nell, Tadashi Fukami, Manpreet K Dhami","doi":"10.1111/mec.17553","DOIUrl":"https://doi.org/10.1111/mec.17553","url":null,"abstract":"<p><p>Priority effects, where the order and timing of species arrival influence the assembly of ecological communities, have been observed in a variety of taxa and habitats. However, the genetic and molecular basis of priority effects remains unclear, hindering a better understanding of when priority effects will be strong. We sought to gain such an understanding for the nectar yeast Metschnikowia reukaufii commonly found in the nectar of our study plant, the hummingbird-pollinated Diplacus (Mimulus) aurantiacus. In this plant, M. reukaufii can experience strong priority effects when it reaches flowers after other nectar yeasts, such as M. rancensis. After inoculation into two contrasting types of synthetic nectar simulating early arrival of M. rancensis, we conducted whole-transcriptome sequencing of 108 strains of M. reukaufii. We found that several genes were differentially expressed in M. reukaufii strains when the nectar had been conditioned by growth of M. rancensis. Many of these genes were associated with amino acid metabolism, suggesting that M. reukaufii strains responded molecularly to the reduction in amino acid availability caused by M. rancensis. Furthermore, investigation of expression quantitative trait loci (eQTLs) revealed that genes involved in amino acid transport and resistance to antifungal compounds were enriched in some genetic variants of M. reukaufii. We also found that gene expression was associated with population growth rate, particularly when amino acids were limited. These results suggest that intraspecific genetic variation in the ability of nectar yeasts to respond to nutrient limitation and direct fungal competition underpins priority effects in this microbial system.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17553"},"PeriodicalIF":4.5,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491748","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}
Kim M Parsons, Samuel A May, Zachary Gold, Marilyn Dahlheim, Christine Gabriele, Janice M Straley, John R Moran, Kimberly Goetz, Alexandre N Zerbini, Linda Park, Phillip A Morin
{"title":"Using eDNA to Supplement Population Genetic Analyses for Cryptic Marine Species: Identifying Population Boundaries for Alaska Harbour Porpoises.","authors":"Kim M Parsons, Samuel A May, Zachary Gold, Marilyn Dahlheim, Christine Gabriele, Janice M Straley, John R Moran, Kimberly Goetz, Alexandre N Zerbini, Linda Park, Phillip A Morin","doi":"10.1111/mec.17563","DOIUrl":"https://doi.org/10.1111/mec.17563","url":null,"abstract":"<p><p>Isolation by distance and biogeographical boundaries define patterns of population genetic structure for harbour porpoise along the Pacific coast from California to British Columbia. Until recently, inadequate sample sizes in many regions constrained efforts to characterise population genetic structure throughout the coastal waters of Alaska. Here, tissue samples from beachcast strandings and fisheries bycatch were supplemented with targeted environmental DNA (eDNA) samples in key regions of Alaska coastal and inland waters. Using a geographically explicit, hierarchical approach, we examined the genetic structure of Alaska harbour porpoises, using both mitochondrial DNA (mtDNA) sequence data and multilocus SNP genotypes. Despite a lack of evidence of genetic differentiation from nuclear SNP loci, patterns of relatedness and genetic differentiation from mtDNA suggest natal philopatry at multiple geographic scales, with limited gene flow among sites possibly mediated by male dispersal. A priori clustering of sampled areas at an intermediate scale (eastern and western Bering Sea, Gulf of Alaska and Southeast Alaska) best explained the genetic variance (12.37%) among regions. In addition, mtDNA differentiation between the Gulf of Alaska and eastern Bering Sea, and among regions within the Gulf of Alaska, indicated significant genetic structuring of harbour porpoise populations in Southeast Alaska. The targeted collection of eDNA samples from strata within Southeast Alaska was key for elevating the statistical power of our mtDNA dataset, and findings indicate limited dispersal between neighbouring strata within coastal and inland waters. These results provide evidence supporting a population boundary within the currently recognised Southeast Alaska Stock. Together, these findings will prove useful for ongoing management efforts to reduce fisheries conflict and conserve genetic diversity in this iconic coastal species.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17563"},"PeriodicalIF":4.5,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491749","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}
David Canal, Jacob Roved, Antonio Lara, Carlos Camacho, Jaime Potti, Simone Santoro
{"title":"MHC Class II Supertypes Affect Survival and Lifetime Reproductive Success in a Migratory Songbird","authors":"David Canal, Jacob Roved, Antonio Lara, Carlos Camacho, Jaime Potti, Simone Santoro","doi":"10.1111/mec.17554","DOIUrl":"10.1111/mec.17554","url":null,"abstract":"<p>The major histocompatibility complex (MHC) plays a critical role in the immune response against pathogens. Its high polymorphism is thought to be mainly the consequence of host-pathogen co-evolution, but elucidating the mechanism(s) driving MHC evolution remains challenging for natural populations. We investigated the diversity of MHC class II genes in a wild population of pied flycatchers <i>Ficedula hypoleuca</i> and tested its associations with two key components of individual fitness: lifetime reproductive success and survival. Among 180 breeding adults in our study population, we found 182 unique MHC class II exon 2 alleles. The alleles showed a strong signal of positive selection and grouped into nine functional supertypes based on physicochemical properties at the inferred antigen-binding sites. Three supertypes were found in > 98% of the sampled individuals, indicating that they are nearly fixed in the population. We found no rare supertypes in the population, as all supertypes were present in > 70% of individuals. Three supertypes were related to different components of individual fitness: two were associated with lower offspring production over time, while the third was positively associated with survival. Overall, the substantial allelic and functional diversity and the relationship between specific supertypes and fitness are in accordance with the notion that balancing selection maintains MHC class II diversity in the study population, possibly with fluctuating selection as the underlying mechanism. The absence of rare supertypes in the population suggests that the balancing selection is not driven by rare-allele advantage.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"33 22","pages":""},"PeriodicalIF":4.5,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17554","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491747","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}
Gary C. Longo, Jeremiah J. Minich, Nicholas Allsing, Kelsey James, Ella S. Adams-Herrmann, Wes Larson, Nolan Hartwick, Tiffany Duong, Barbara Muhling, Todd P. Michael, Matthew T. Craig
{"title":"Crossing the Pacific: Genomics Reveals the Presence of Japanese Sardine (Sardinops melanosticta) in the California Current Large Marine Ecosystem","authors":"Gary C. Longo, Jeremiah J. Minich, Nicholas Allsing, Kelsey James, Ella S. Adams-Herrmann, Wes Larson, Nolan Hartwick, Tiffany Duong, Barbara Muhling, Todd P. Michael, Matthew T. Craig","doi":"10.1111/mec.17561","DOIUrl":"10.1111/mec.17561","url":null,"abstract":"<p>Recent increases in frequency and intensity of warm water anomalies and marine heatwaves have led to shifts in species ranges and assemblages. Genomic tools can be instrumental in detecting such shifts. In the early stages of a project assessing population genetic structure in Pacific Sardine (<i>Sardinops sagax</i>), we detected the presence of Japanese Sardine (<i>Sardinops melanosticta</i>) along the west coast of North America for the first time. We assembled a high quality, chromosome-scale reference genome of the Pacific Sardine and generated low coverage, whole genome sequence (lcWGS) data for 345 sardine collected in the California Current Large Marine Ecosystem (CCLME) in 2021 and 2022. Fifty individuals sampled in 2022 were identified as Japanese Sardine based on strong differentiation observed in lcWGS SNP and full mitogenome data. Although we detected a single case of mitochondrial introgression, we did not observe evidence for recent hybridization events. These findings change our understanding of <i>Sardinops</i> spp. distribution and dispersal in the Pacific and highlight the importance of long-term monitoring programs.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"33 22","pages":""},"PeriodicalIF":4.5,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17561","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491744","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}