Evolutionary Applications最新文献

{"title":"Thermal Selection Shifts Genetic Diversity and Performance in Blue Mussel Juveniles","authors":"Jennifer C. Nascimento-Schulze,&nbsp;Jahangir Vajedsamiei,&nbsp;Tim P. Bean,&nbsp;Lisa Frankholz,&nbsp;Reid S. Brennan,&nbsp;Frank Melzner,&nbsp;Robert P. Ellis","doi":"10.1111/eva.70118","DOIUrl":"https://doi.org/10.1111/eva.70118","url":null,"abstract":"<p>Exploring evolutionary and physiological responses to environmental stress is crucial for assessing the effects of climate change on wild populations. Mussels, key inhabitants of the benthos with high ecological and economic value, are a particularly vulnerable species that may be pushed to their ecological limits as warming threatens their survival and population stability. Species within the <i>Mytilus edulis</i> complex are commonly found in temperate regions globally; in the Baltic Sea, populations are formed by <i>M. edulis</i> and <i>M. trossulus</i> hybrids with low levels of <i>M. galloprovincialis</i> introgression. This study investigates the mechanisms through which resilience towards global warming may be fast-tracked in Baltic mussels (Kiel, Germany). For this, we studied two cohorts of juvenile mussels (recently settled animals), one exposed to an extreme heat event early in life and one naïve to this stressor. Both cohorts were later exposed to experimental temperatures ranging from 21°C to 26°C, with animal performance measured after 25 days. Impacts of thermal stress on the genetic composition of each cohort was then assessed by genotyping 50 individuals using a blue mussel 60 K SNP-array. We observed a significant increase in <i>M. edulis</i> genotypes together with a decrease in <i>M. trossulus</i> in the challenged cohort, compared to naive juveniles. We also found exposure to high temperature affected performance of mussel cohorts, reducing dry tissue weight of selected individuals. Results from this study provide insights on how selection through thermal stress impacts performance and genetic composition of key globally distributed intertidal species, with important implications for understanding and managing mussel populations under future warming scenarios.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"18 6","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70118","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144314961","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":"Evidence of Fine-Scale Genetic Structure in Tiger Sharks (Galeocerdo cuvier) Highlights the Importance of Stratified Sampling Regimes","authors":"Jessica J. Fish,&nbsp;Christine Dudgeon,&nbsp;Adam Barnett,&nbsp;Paul A. Butcher,&nbsp;Bonnie J. Holmes,&nbsp;Charlie Huveneers,&nbsp;Lauren Meyer,&nbsp;Laurent Vigliola,&nbsp;Craig D. H. Sherman,&nbsp;Adam D. Miller","doi":"10.1111/eva.70117","DOIUrl":"https://doi.org/10.1111/eva.70117","url":null,"abstract":"<p>Understanding the biological connections between populations is essential to wildlife management and conservation. Genetic studies play a central role in characterizing these connections, but typically require stratified sampling regimes to assess the spatial extent and strength of gene flow, and the relative influences of sex and ontogeny on patterns of connectivity. Yet, this can be challenging in some study systems, particularly in large marine species such as sharks, where genetic studies often rely on opportunistic and/or sampling conducted over large spatial scales. We demonstrate the importance of stratified sampling to identify previously undetected genetic structure in tiger sharks (<i>Galeocerdo cuvier</i>) off eastern Australia, where panmixia has been previously reported. We performed population genomic analyses on 414 tiger sharks, representing males and females and both juvenile-subadult and adult-life stages, and 21 locations spanning approximately 3000 km of eastern Australia and the Indo-Pacific region. Similar to previous studies, we demonstrate a lack of overall genetic structure across the sampling area; however, our analysis shows evidence of spatial autocorrelation and local genetic structuring in juvenile-subadult female tiger sharks. These results point to potential influences of sex and ontogeny on patterns of population genetic structure and connectivity in Australian tiger sharks. We discuss these findings in the context of essential habitats supporting tiger shark populations and risks of overstating the strength of biological connections among shark populations in the absence of appropriate sampling regimes.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"18 6","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70117","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144244366","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":"Population Genomics Provides Insights Into Genomic Features of Inbreeding Depression in Arma Chinensis","authors":"Bin Li,&nbsp;Kangkang Song,&nbsp;Zixian Wu,&nbsp;Xiaohua Zhang,&nbsp;Haozhen Li,&nbsp;Long Yang","doi":"10.1111/eva.70107","DOIUrl":"https://doi.org/10.1111/eva.70107","url":null,"abstract":"<p><i>Arma chinensis</i>, a predatory insect renowned for its prey diversity in East Asia, is effective in controlling agricultural and forestry pests. However, after introducing field populations into indoor subcultures, features of inbreeding depression have surfaced within these populations. Clarifying the molecular genetic mechanism of inbreeding depression of <i>A. chinensis</i> is of great significance for its population protection. In this study, phylogenomic analysis revealed that the genus <i>Arma</i> shared a common ancestor with <i>Halyomorpha</i> and <i>Nezara</i> in the Pentatomidae family around 63.62 million years ago. Based on whole-genome resequencing of three consecutive inbred generations of <i>A. chinensis</i>, we investigated the genomic features of inbreeding depression. We observed an accumulation of long runs of homozygosity and extreme variations in nucleotide diversity across generations, collectively affecting 111 genes and multiple biological processes, such as sequence-specific DNA binding, synapse organization, and transcription regulatory region binding. These genomic changes suggest that successive inbreeding may disrupt normal physiological functions, potentially impairing gene expression, neural signaling, and sensory organ development. In conclusion, our study clarifies the evolutionary position of <i>A. chinensis</i>, highlights the genetic consequences of inbreeding, and emphasizes the importance of preserving genetic diversity in natural populations for long-term survival and adaptability.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"18 6","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70107","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144244370","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":"Geographic Range Size Predicts Butterfly Species' Tolerance to Heavy Metals More Than Evolutionary History With Toxic Larval Diets","authors":"Ashley L. Darst,&nbsp;Lindsey R. Kemmerling,&nbsp;Molly Tilsen,&nbsp;J. Alexander Eilts,&nbsp;Emilie C. Snell-Rood","doi":"10.1111/eva.70114","DOIUrl":"https://doi.org/10.1111/eva.70114","url":null,"abstract":"<p>Some organisms appear to thrive in contaminated environments, while others are more sensitive, though the causes of this variation are unclear. The toxin coevolution hypothesis posits that an evolutionary history with natural toxins preadapts species to deal with novel toxins, while the range-size-tolerance hypothesis posits that a larger geographic range selects for broader tolerance to stressors. Butterflies are a prime system to investigate these hypotheses because they are diverse, feed on a range of larval host plants that vary in defensive compounds, and many are found in polluted environments. We ask how these hypotheses explain varying tolerance to heavy metal pollution, measured here as loads of four heavy metals along an urban gradient of metal exposure. We compared 26 butterfly species that vary in their evolutionary history with mutagenic plant defensive chemicals as well as their geographic range size. We built a dataset of plant mutagenicity synthesizing 40 years of standardized mutagenicity screening in plants, including 502 plant species of 103 families within 37 orders. We used this dataset, coupled with butterfly host records, to estimate evolutionary history with mutagens. We found that butterfly species with larger ranges tolerated significantly greater concentrations of lead, arsenic, and cadmium in their tissues. Additionally, species with a history of feeding on relatively more mutagenic host plant families tolerated greater maximum lead concentrations in their thoracic tissue. This research provides additional support for the growing observation that small-ranged species are more vulnerable to environmental change, in this case, metal pollution. In addition, an evolutionary history with mutagenic host plants may provide some additional resilience, although less than geographic range size. In addition, our dataset on comparative plant mutagenicity will facilitate future research on plant-herbivore coevolution, in fields such as chemical, community, and urban ecology.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"18 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70114","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144135624","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":"Vertical Cancer Transmission via Asexual Fragmentation and Associated Cancer Prevalence","authors":"Jibeom Choi","doi":"10.1111/eva.70111","DOIUrl":"https://doi.org/10.1111/eva.70111","url":null,"abstract":"<p>While sexual reproduction is a general feature of animals, fissiparity and budding are relatively uncommon modes of asexual reproduction by which a fragment from a parent becomes an independent organism. Unlike unitary development, tumor cells can be included in the detached fragment destined to become offspring. Although fragmentation facilitates the vertical transmission of parental tumor cells to nascent progeny, this process requires significantly fewer cell replications than development from a zygote. The former is a risk factor for cancer, while the latter reduces oncogenic mutations during replication, indicating that two opposite effects of carcinogenesis are involved in fragmentation. If fragmentation can significantly reduce the number of cell replications for the development and a small portion of parental cancer is transmitted to the offspring during fragmentation, consecutive fragmentation across generations can gradually diminish the cancer risk of offspring, which I term fragmentational purging. On the other hand, consecutive fragmentation may aggravate the cancer risk of the progeny, a process of fragmentational accumulation. The model results imply that fragmentational purging does not necessarily guarantee the evolution of fragmentation, nor does fragmentational accumulation ensure its exclusion. Other relevant factors including juvenile susceptibility of sexual reproduction and loss of genetic diversity stemming from asexual reproduction can influence the selective advantage of fragmentation. Furthermore, owing to the common features of stemness and self-renewal, the existence of pluripotent adult stem cells required for fragmentation could be coupled with elevated cancer risk. The model results across diverse parameters and the associated mathematical analyses highlight multifaceted evolutionary trajectories toward fragmentation. Further investigation of cancer-suppression strategies that fragmentational animals employ could provide insights into regenerative medicine and cancer therapy.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"18 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70111","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144100511","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":"Road Mortality Contributes to the Evolution of an Urban–Rural Cline in Squirrel Coat Color","authors":"Adam F. Parlin,&nbsp;Bradley J. Cosentino,&nbsp;Richard M. Lehtinen,&nbsp;John E. McDonald,&nbsp;Emma C. C. Sinclair,&nbsp;James P. Gibbs","doi":"10.1111/eva.70109","DOIUrl":"https://doi.org/10.1111/eva.70109","url":null,"abstract":"<p>Cities impose unique selection pressures on wildlife and generate clines in phenotypic traits along urban–rural gradients. Roads are a widespread feature of human-dominated landscapes and are known to cause direct wildlife mortality; however, whether they act as a selective force influencing phenotypic trait variation along urban–rural gradients remains unclear. This study tested the hypothesis that roads influence natural selection of coat color in the eastern gray squirrel (<i>Sciurus carolinensis</i>), a species with two distinct coat colors: a gray morph that is common in all areas and a melanic morph more prevalent in urban areas than in rural ones. Vehicular collisions are a significant cause of mortality in eastern gray squirrels, with the melanic morph more visually conspicuous on roads and more easily detected and avoided by drivers than the gray morph. Standardized road cruise surveys along an urbanization gradient in Syracuse, New York, USA, revealed that the prevalence of melanism among living squirrels in Syracuse was negatively related to distance from the city center, whereas there was no urban–rural cline in melanism among road-killed individuals, with the melanic morph underrepresented among road-killed squirrels by up to 30% along the urbanization gradient. An examination of the prevalence of each color morph on and off road surfaces in a range-wide compilation of &gt; 100,000 photographs of <i>S. carolinensis</i> also indicated that the melanic morph was underrepresented among road-killed squirrels imaged. Our study highlights vehicular collisions as an important source of natural selection on phenotypic traits, suggesting a potential role in shaping patterns of urban evolution and contributing to the maintenance of urban–rural clines.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"18 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70109","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144091273","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":"Multiple Stressors in the Anthropocene: Urban Evolutionary History Modifies Sensitivity to the Toxic Effects of Crude Oil Exposure in Killifish","authors":"Jane Park,&nbsp;Charles Brown,&nbsp;Chelsea Hess,&nbsp;Madison Armstrong,&nbsp;David M. Rocke,&nbsp;Fernando Galvez,&nbsp;Andrew Whitehead","doi":"10.1111/eva.70112","DOIUrl":"https://doi.org/10.1111/eva.70112","url":null,"abstract":"<p>Persistence of wild species in human-altered environments is difficult, in part because challenges to fitness are complex when multiple environmental changes occur simultaneously, which is common in the Anthropocene. This complexity is difficult to conceptualize because the nature of environmental change is often highly context specific. A mechanism-guided approach may help to shape intuition and predictions about complexity; fitness challenges posed by co-occurring stressors with similar mechanisms of action may be less severe than for those with different mechanisms of action. We approach these considerations within the context of ecotoxicology because this field is built upon a rich mechanistic foundation. We hypothesized that evolved resistance to one class of common toxicants would afford resilience to the fitness impacts of another class of common toxicants that shares mechanisms of toxicity. <i>Fundulus</i> killifish populations in urban estuaries have repeatedly evolved resistance to persistent organic pollutants including PCBs. Since PCBs and some of the toxicants that constitute crude oil (e.g., high molecular weight PAHs) exert toxicity through perturbation of AHR signaling, we predicted that PCB-resistant populations would also be resilient to crude oil toxicity. Common garden comparative oil exposure experiments, including killifish populations with different exposure histories, showed that most killifish populations were sensitive to fitness impacts (reproduction and development) caused by oil exposure, but that fish from the PCB-resistant population were insensitive. Population differences in toxic outcomes were not compatible with random-neutral expectations. Transcriptomics revealed that the molecular mechanisms that contributed to population variation in PAH resilience were shared with those that contribute to evolved variation in PCB resilience. We conclude that the fitness challenge posed by environmental pollutants is effectively reduced when those chemicals share mechanisms that affect fitness. Mechanistic considerations may help to scale predictions regarding the fitness challenges posed by stressors that may co-occur in human-altered environments.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"18 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70112","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074327","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":"Local Adaptation and Climate Change Vulnerability of the Relict Tree Species Taiwania cryptomerioides Provide Insights Into Its Conservation and Restoration","authors":"Yang Lu,&nbsp;Hao Dong,&nbsp;Saibin Fan,&nbsp;Lu Yuan,&nbsp;Yuhui Wang,&nbsp;Zhuang Zhao,&nbsp;Yong Lai,&nbsp;Shixin Zhu,&nbsp;Jinyong Huang,&nbsp;Caipeng Yue,&nbsp;Yongpeng Ma,&nbsp;Ningning Zhang","doi":"10.1111/eva.70113","DOIUrl":"https://doi.org/10.1111/eva.70113","url":null,"abstract":"<p>Rapid climate change is affecting biodiversity and threatening locally adapted species. Relict species are often confined to relatively narrow, discontinuous geographic ranges and provide excellent opportunities to study local adaptation and extinction. Understanding the adaptive genetic variation and genetic vulnerability of relict species under climate change is essential for their conservation and management efforts. Here, we applied a landscape genomics approach to investigate the population genetic structure and predict adaptive capacity to climatic change for <i>Taiwania cryptomerioides</i> Hayata, a vulnerable Tertiary relict tree species in China. We used restriction site-associated DNA sequencing on 122 individuals across 10 sampling sites. We found three genetic groups across the Chinese range of <i>T. cryptomerioides</i>: the southwest, central-eastern, and Taiwanese groups. We detected significant signals of isolation by environment and isolation by distance, with environment playing a more important role than geography in shaping spatial genetic variation in <i>T. cryptomerioides</i>. Moreover, some outliers were related to defense and stress responses, which could reflect the genomic basis of adaptation. Gradient forest (GF) analysis revealed that precipitation-related variables were important in driving adaptive variation in <i>T. cryptomerioides</i>. Ecological niche modeling and GF analysis revealed that the central-eastern populations were more vulnerable to future climate change than other populations, with range contractions and high genetic offsets, suggesting these populations may be at higher risk of decline or local extinction. These findings deepen our understanding of local adaptation and vulnerability to climate change in relict tree species and will guide conservation and restoration programs for <i>T. cryptomerioides</i> in the future.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"18 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70113","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143950142","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":"A Guide for Developing Demo-Genetic Models to Simulate Genetic Rescue","authors":"Julian E. Beaman,&nbsp;Katie Gates,&nbsp;Frédérik Saltré,&nbsp;Carolyn J. Hogg,&nbsp;Katherine Belov,&nbsp;Kita Ashman,&nbsp;Karen Burke da Silva,&nbsp;Luciano B. Beheregaray,&nbsp;Corey J. A. Bradshaw","doi":"10.1111/eva.70092","DOIUrl":"https://doi.org/10.1111/eva.70092","url":null,"abstract":"<p>Genetic rescue is a conservation management strategy that reduces the negative effects of genetic drift and inbreeding in small and isolated populations. However, such populations might already be vulnerable to random fluctuations in growth rates (demographic stochasticity). Therefore, the success of genetic rescue depends not only on the genetic composition of the source and target populations but also on the emergent outcome of interacting demographic processes and other stochastic events. Developing predictive models that account for feedback between demographic and genetic processes (‘demo-genetic feedback’) is therefore necessary to guide the implementation of genetic rescue to minimize the risk of extinction of threatened populations. Here, we explain how the mutual reinforcement of genetic drift, inbreeding, and demographic stochasticity increases extinction risk in small populations. We then describe how these processes can be modelled by parameterizing underlying mechanisms, including deleterious mutations with partial dominance and demographic rates with variances that increase as abundance declines. We combine our suggestions of model parameterization with a comparison of the relevant capability and flexibility of five open-source programs designed for building genetically explicit, individual-based simulations. Using one of the programs, we provide a heuristic model to demonstrate that simulated genetic rescue can delay extinction of small virtual populations that would otherwise be exposed to greater extinction risk due to demo-genetic feedback. We then use a case study of threatened Australian marsupials to demonstrate that published genetic data can be used in one or all stages of model development and application, including parameterization, calibration, and validation. We highlight that genetic rescue can be simulated with either virtual or empirical sequence variation (or a hybrid approach) and suggest that model-based decision-making should be informed by ranking the sensitivity of predicted probability/time to extinction to variation in model parameters (e.g., translocation size, frequency, source populations) among different genetic-rescue scenarios.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"18 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70092","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143944946","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":"A Multipurpose Microhaplotype Panel for Genetic Analysis of California Chinook Salmon","authors":"Eric C. Anderson,&nbsp;Anthony J. Clemento,&nbsp;Matthew A. Campbell,&nbsp;Devon E. Pearse,&nbsp;Anne K. Beulke,&nbsp;Cassie Columbus,&nbsp;Ellen Campbell,&nbsp;Neil F. Thompson,&nbsp;John Carlos Garza","doi":"10.1111/eva.70110","DOIUrl":"https://doi.org/10.1111/eva.70110","url":null,"abstract":"<p>Genetic methods have become an essential component of ecological investigation and conservation planning for fish and wildlife. Among these methods is the use of genetic marker data to identify individuals to populations, or stocks, of origin. More recently, methods that involve genetic pedigree reconstruction to identify relationships between individuals within populations have also become common. We present here a novel set of multiallelic microhaplotype genetic markers for Chinook salmon, which provide excellent resolution for population discrimination and relationship identification from a rapidly and economically assayed panel of markers. We show how this set of genetic markers assayed by sequencing 204 amplicons, in tandem with a reference dataset of 1636 individual samples from 17 populations, provides definitive power to identify all known lineages of Chinook salmon in California. The inclusion of genetic loci that have known associations with phenotype and that were identified as outliers in examination of whole-genome sequence data allows resolution of stocks that are not highly genetically differentiated but are phenotypically distinct and managed as such. This same set of multiallelic genetic markers has ample variation to accurately identify parent-offspring and full-sibling pairs in all California populations, including the genetically depauperate winter-run lineage. Validation of this marker panel in coastal salmon populations not previously studied with modern genetic methods also reveals novel biological insights, including the presence of a single copy of a haplotype for a phenotype that has not been documented in that part of the species range, and a clear signal of mixed ancestry for a salmon population that is on the geographic margins of the primary evolutionary lineages present in California.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"18 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70110","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143938953","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}