Evolutionary Applications最新文献

{"title":"Farmed Escapees Threaten MHC Diversity in Wild Atlantic Salmon","authors":"Morten Lukacs,&nbsp;Åse Helen Garseth,&nbsp;Sten Karlsson,&nbsp;Kyrre Kausrud,&nbsp;Ottavia Benedicenti,&nbsp;Arvind Y. M. Sundaram,&nbsp;Lars Austbø,&nbsp;Cathrine Arnason Bøe,&nbsp;Håvard Lo,&nbsp;Unni Grimholt","doi":"10.1111/eva.70278","DOIUrl":"https://doi.org/10.1111/eva.70278","url":null,"abstract":"<p>Wild Atlantic salmon populations in Norway and elsewhere are experiencing long-term declines driven by reduced marine survival, climate change, impacts from aquaculture, introduction of alien species, and environmental degradation. Understanding how immune diversity is affected by these declines, and thus the ability of Atlantic salmon to combat current and future invading pathogens, is essential for the success of conservation programs such as gene banks. Major histocompatibility complex (MHC) genes, some of the most polymorphic genes known to date, are essential in the host immune defense against invading pathogens. Here we investigate MHC class I and class II diversity in escaped farmed salmon and in eight wild Atlantic salmon populations defined as being at risk. The study demonstrates that rare alleles can be found in single closely related wild populations within a fjord, and collectively, the populations hold a large immune diversity. Moreover, our study found that a broad spatial and temporal collection of escaped farmed salmon had an MHC-diversity at the same level as individual wild salmon populations, while escaped farmed salmon from single escape events had lower diversity. Overall, the wild salmon had considerably higher MHC diversity than escaped farmed salmon. Accumulated genetic introgression of escaped farmed salmon is therefore a major threat as it can compromise the MHC diversity within and among the wild populations. Conservation of MHC diversity in the ongoing gene bank program for Norwegian Atlantic salmon is important, and our observation emphasizes that a large number of founders to the gene bank are needed to conserve the many rare MHC alleles and that genotyping of potential founders may be useful in broodfish selection.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70278","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148097054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Blood Relatives: Linking Evolutionary History and Conservation of Medicinal Leeches (Hirudo spp.)","authors":"Gianluca Lombardo,&nbsp;Alessandro Alvaro,&nbsp;Andrea De Benedictis,&nbsp;Marta Cavallini,&nbsp;Milo Manica,&nbsp;Edward C. Netherlands,&nbsp;Laura Pulze,&nbsp;Nicolò Baranzini,&nbsp;Annalisa Grimaldi,&nbsp;Francesco Acquati,&nbsp;Giorgio Binelli","doi":"10.1111/eva.70273","DOIUrl":"https://doi.org/10.1111/eva.70273","url":null,"abstract":"<p>Medicinal leeches of the genus <i>Hirudo</i> are both historically important in medicine and increasingly studied as models in ecology and biomedicine. However, the taxonomy, population structure and evolutionary history of this genus remain partially unresolved. Here, we present the most comprehensive phylogenetic analysis of the <i>Hirudo</i> complex to date, incorporating 350 <i>COX1</i> sequences (103 newly generated) and 247 complete mitogenomes from across the distribution range. In <i>Hirudo verbana</i>, three major clades corresponding to Iberian (A), Western (B) and Eastern (C) haplogroups were found, with sub-haplogroups reflecting glacial refugia and Pleistocene expansions. Diversity was highest in Eastern populations, consistent with Anatolia and the Black Sea basin acting as long-term refugia. Bayesian divergence dating indicates that the genus originated in the mid-Miocene (~15 Mya), with an early split of <i>H. nipponia</i> in East Asia. Subsequent radiations shaped the Western Eurasian clade, with <i>H. sulukii</i> diverging ~9.9 Mya, <i>H. orientalis</i> splitting from European lineages ~6.4 Mya and differentiating ~440 kya, and recent radiations of <i>H. verbana</i>, <i>H. medicinalis</i> and <i>H. troctina</i> occurring during the late Pleistocene. Notably, nucleotide diversity within <i>H. nipponia</i> (~8.8%) and deep divergence among its haplogroups suggest the presence of multiple cryptic species, with <i>H. tianjinensis</i> clustering within these lineages. We also molecularly identified several Italian specimens as <i>Haemopis sanguisuga</i> or a potential new <i>Dina</i> species. These findings emphasise the importance of taxonomic clarity and genetic monitoring to guide conservation and prevent overexploitation of <i>Hirudo</i> leeches, ensuring the long-term sustainability and biomedical utility of these ecologically significant annelids.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70273","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148095487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Genetically Homogeneous Population Structure of Evynnis cardinalis Along the Chinese Coast Revealed by Whole Genome Sequencing","authors":"Sailan Liu,&nbsp;Yan Gao,&nbsp;Xingboyu Zhang,&nbsp;Xinrui Long,&nbsp;Qilin Gutang,&nbsp;Hancheng Zhao,&nbsp;Jianqing Lin,&nbsp;Wenhua Liu","doi":"10.1111/eva.70272","DOIUrl":"https://doi.org/10.1111/eva.70272","url":null,"abstract":"<p><i>Evynnis cardinalis</i> is a warm-water demersal fish inhabiting the northwestern Pacific coastal waters. Previous studies based on limited molecular markers and morphological traits have yielded inconsistent conclusions regarding its phylogenetic position and population differentiation. To address these uncertainties, we assembled a high-quality chromosome-level genome using PacBio HiFi and Hi-C technologies, and then clarified its close phylogenetic relationship with <i>Pagrus major</i>. At the population genomic level, genome-wide single nucleotide polymorphism (SNP) analysis detected 8,643,907 high-quality SNPs from three geographically distinct populations (Shantou, Zhuhai, and Hainan). The results revealed weak population structure and extremely low genetic differentiation among the three geographic populations, a pattern consistent with high genetic connectivity in the ocean. However, subsequent analysis showed that chromosome 8 had the most candidate genes for genomic variation among populations, involved in cell structure, energy metabolism, and DNA repair. It suggests that certain genomic regions may provide potential targets for future studies on environmental responses in complex nearshore benthic environments despite the overall population genetic homogeneity. Our study not only provides the first chromosome-level genome assembly but also clarifies the taxonomic status and single population genetic structure of <i>E. cardinalis</i> in Chinese coastal waters at genome-wide level. These findings are expected to facilitate the biodiversity conservation and sustainable management of this commercially important species.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 5","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70272","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148174774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Genetically Homogeneous Population Structure of Evynnis cardinalis Along the Chinese Coast Revealed by Whole Genome Sequencing","authors":"Sailan Liu,&nbsp;Yan Gao,&nbsp;Xingboyu Zhang,&nbsp;Xinrui Long,&nbsp;Qilin Gutang,&nbsp;Hancheng Zhao,&nbsp;Jianqing Lin,&nbsp;Wenhua Liu","doi":"10.1111/eva.70272","DOIUrl":"https://doi.org/10.1111/eva.70272","url":null,"abstract":"<p><i>Evynnis cardinalis</i> is a warm-water demersal fish inhabiting the northwestern Pacific coastal waters. Previous studies based on limited molecular markers and morphological traits have yielded inconsistent conclusions regarding its phylogenetic position and population differentiation. To address these uncertainties, we assembled a high-quality chromosome-level genome using PacBio HiFi and Hi-C technologies, and then clarified its close phylogenetic relationship with <i>Pagrus major</i>. At the population genomic level, genome-wide single nucleotide polymorphism (SNP) analysis detected 8,643,907 high-quality SNPs from three geographically distinct populations (Shantou, Zhuhai, and Hainan). The results revealed weak population structure and extremely low genetic differentiation among the three geographic populations, a pattern consistent with high genetic connectivity in the ocean. However, subsequent analysis showed that chromosome 8 had the most candidate genes for genomic variation among populations, involved in cell structure, energy metabolism, and DNA repair. It suggests that certain genomic regions may provide potential targets for future studies on environmental responses in complex nearshore benthic environments despite the overall population genetic homogeneity. Our study not only provides the first chromosome-level genome assembly but also clarifies the taxonomic status and single population genetic structure of <i>E. cardinalis</i> in Chinese coastal waters at genome-wide level. These findings are expected to facilitate the biodiversity conservation and sustainable management of this commercially important species.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 5","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70272","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148174775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-Wide Population Structure of Lake Whitefish (Coregonus clupeaformis) in a Subarctic Great Lake","authors":"Philippe Hénault,&nbsp;Raphaël Bouchard,&nbsp;David A. Boguski,&nbsp;Brendan K. Malley,&nbsp;Eric Normandeau,&nbsp;Charles Babin,&nbsp;Xavier Dallaire,&nbsp;Louis Bernatchez,&nbsp;Xinhua Zhu,&nbsp;Jean-Sébastien Moore","doi":"10.1111/eva.70268","DOIUrl":"https://doi.org/10.1111/eva.70268","url":null,"abstract":"<p>Advances in genomics have facilitated the delineation of fisheries management units, which can be challenging in systems such as large lakes, in which high gene flow tends to limit genetic structure. In Great Slave Lake, Lake Whitefish populations have supported an important commercial fishery since the mid-1940s. The genetic structure of Lake Whitefish, however, has never been assessed, preventing the implementation of population-specific monitoring. Using low-coverage whole-genome resequencing of 305 samples from 10 sampling locations, we identified eight genetically differentiated populations of Lake Whitefish in Great Slave Lake and its main tributary, the Slave River. In the lake, we observed elevated levels of genetic differentiation among putative spawning locations in environmentally heterogeneous sections of the Main Basin despite small geographic distances among sites. In contrast, we observed weak genetic structure between populations in the comparatively homogeneous East Arm despite large geographic distances. Our observations suggest that mechanisms such as spawning site fidelity, adfluvial migratory behaviour, or local adaptation might shape population structure in this system. Using genome-wide scans, we found multiple genomic regions of elevated differentiation, with some displaying patterns coherent with chromosomal inversions. These results highlight the potential role of chromosomal rearrangements in maintaining local adaptation in the face of gene flow in environmentally heterogeneous lakes. Overall, our study provides novel insights into the genetic structure of fish populations in vast, recently deglaciated lakes. Furthermore, our results highlight the power of genomic data for population delineation in systems with high gene flow. Lastly, our precise assessment of genetic structure will provide a baseline for the genetic monitoring of culturally and socio-economically important Lake Whitefish commercial fisheries in this subarctic Great Lake.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70268","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148095484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 5","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148121745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 5","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148091993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 5","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148121744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple Genetic Origins of Non-Native, Self-Sustaining Rainbow Trout <i>Oncorhynchus mykiss</i> in Streams in Baden-Württemberg, Germany.","authors":"J Peter Koene, Arne Jacobs, Patrick Bartolin, Jan Baer, David Frei, Pascal Vonlanthen, Alexander Brinker","doi":"10.1111/eva.70271","DOIUrl":"10.1111/eva.70271","url":null,"abstract":"<p><p>Introduced in the late 19th Century, <i>Oncorhynchus mykiss</i> (rainbow trout) has been stocked historically in streams throughout Baden-Württemberg, Germany, and some populations have become self-sustaining with unclear impact on native salmonid populations. We sampled 223 rainbow trout from 14 streams and 3 hatcheries, each with different levels of domestication, from which the streams are known to have been stocked. We conducted genomic analyses to uncover evidence confirming self-sustaining populations, to deduce potential sources of these populations, to compare the genetic diversity of hatchery versus stream populations and to discover genetic differences between stream and hatchery populations. We found genetic population structuring amongst the stream populations, consistent with natural reproduction over several generations, and we inferred multiple genetic origins, potentially including source populations beyond the three hatcheries considered, indicating that naturalisation occurs independently of domestication level and that all lineages pose similar likelihoods of establishing in the wild. We found no significant difference in genetic diversity between stream and hatchery populations, but there were nine loci across four genomic regions associated with naturalisation within or adjacent to immunity, growth and development genes. Whether such genes are under selection in wild stream environments needs still to be determined to inform fisheries and conservation management.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 5","pages":"e70271"},"PeriodicalIF":3.2,"publicationDate":"2026-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13239981/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148196414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 5","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148091992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}