Evolutionary Applications最新文献

{"title":"Reduced Representation and Whole-Genome Sequencing Approaches Highlight Beluga Whale Populations Associated to Eastern Canada Summer Aggregations","authors":"Luca Montana,&nbsp;Trevor T. Bringloe,&nbsp;Audrey Bourret,&nbsp;Caroline Sauvé,&nbsp;Arnaud Mosnier,&nbsp;Steven H. Ferguson,&nbsp;Lianne Postma,&nbsp;Véronique Lesage,&nbsp;Cortney A. Watt,&nbsp;Mike O. Hammill,&nbsp;Geneviève J. Parent","doi":"10.1111/eva.70058","DOIUrl":"https://doi.org/10.1111/eva.70058","url":null,"abstract":"<p>Effective conservation strategies inherently depend on preserving populations, which in turn requires accurate tools for their detection. Beluga whales (<i>Delphinapterus leucas</i>) inhabit the circumpolar Arctic and form discrete summer aggregations. Previous genetic studies using mitochondrial and microsatellite loci have delineated distinct populations associated to summer aggregations but the extent of dispersal and interbreeding among these populations remains largely unknown. Such information is essential for the conservation of populations in Canada as some are endangered and harvested for subsistence by Inuit communities. Here, we used reduced representation and whole-genome sequencing approaches to characterize population structure of beluga whales in eastern Canada and examine admixture between populations. A total of 905 beluga whales sampled between 1989 and 2021 were genotyped. Six main genomic clusters, with potential subclusters, were identified using multiple proxies for population structure. Most of the six main genomic clusters were consistent with previously identified populations, except in southeast Hudson Bay where two clusters were identified. Beluga summer aggregations may consequently be comprised of more than one distinct population. A low number of dispersers were identified between summer aggregations and limited interbreeding was detected between the six genomic clusters. Our work highlights the value of genomic approaches to improve our understanding of population structure and reproductive behavior in beluga whales, offering insights applicable to other cetacean species of conservation concern. An expansion of the geographical scope and increase in number of genotyped individuals will, however, be needed to improve the characterization of the finer scale structure and of the extent of admixture between populations.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 12","pages":"1-20"},"PeriodicalIF":3.5,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70058","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142861469","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":"Comparison of Conservation Strategies for California Channel Island Oak (Quercus tomentella) Using Climate Suitability Predicted From Genomic Data","authors":"Alayna Mead,&nbsp;Sorel Fitz-Gibbon,&nbsp;John Knapp,&nbsp;Victoria L. Sork","doi":"10.1111/eva.70057","DOIUrl":"https://doi.org/10.1111/eva.70057","url":null,"abstract":"<p>Management strategies, such as assisted gene flow, can increase resilience to climate change in tree populations. Knowledge of evolutionary history and genetic structure of species are needed to assess the risks and benefits of different strategies. <i>Quercus tomentella</i>, or Island Oak, is a rare oak restricted to six Channel Islands in California, United States, and Baja California, Mexico. Previous work has shown that Island Oaks on each island are genetically differentiated, but it is unclear whether assisted gene flow could enable populations to tolerate future climates. We performed whole-genome sequencing on Island Oak individuals and <i>Q. chrysolepis</i>, a closely related species that hybridizes with Island Oak (127 total), to characterize genetic structure and introgression across its range and assess the relationship between genomic variation and climate. We introduce and assess three potential management strategies with different trade-offs between conserving historic genetic structure and enabling populations to survive changing climates: the status quo approach; ecosystem preservation approach, which conserves the trees and their associated biodiversity; and species preservation approach, which conserves the species. We compare the impact of these approaches on predicted maladaptation to climate using Gradient Forest. We also introduce a climate suitability index to identify optimal pairs of seed sources and planting sites for approaches involving assisted gene flow. We found one island (Santa Rosa) that could benefit from the ecosystem preservation approach and also serve as a species preservation site. Overall, we find that both the ecosystem and species preservation approaches will do better than the status quo approach. If preserving Island Oak ecosystems is the goal, assisted dispersal into multiple sites could produce adapted populations. If the goal is to preserve a species, the Santa Rosa population would be suitable. This case study both illustrates viable conservation strategies for Island Oak and introduces a framework for tree conservation.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 12","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70057","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142861448","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":"Complications of Estimating Hatchery Introgression in the Face of Rapid Divergence: A Case Study in Brook Trout (Salvelinus fontinalis)","authors":"Bradley Erdman,&nbsp;Wesley Larson,&nbsp;Matthew G. Mitro,&nbsp;Joanna D. T. Griffin,&nbsp;David Rowe,&nbsp;Justin Haglund,&nbsp;Kirk Olson,&nbsp;Michael T. Kinnison","doi":"10.1111/eva.70026","DOIUrl":"10.1111/eva.70026","url":null,"abstract":"<p>Fish stocking has been utilized for over a century to offset extirpations or declines in abundance of many native species. These historical declines and hatchery contributions have led to uncertainty surrounding whether many contemporary populations are native, introgressed with hatchery sources, or entirely of hatchery origin. Such uncertainty is problematic for the conservation of native biodiversity as it hampers management agencies' ability to prioritize the conservation of indigenous locally adapted populations. Fortunately, genetic and genomic tools have allowed researchers to investigate these questions, often through the use of clustering or assignment approaches that are predicated on identifiable and consistent divergence between native populations and hatchery sources. Here, we apply these methods to restriction-site associated DNA (RAD) data from 643 brook trout (<i>Salvelinus fontinalis</i>) originating from 13 wild populations and an exogenous hatchery strain to investigate the extent of historical extirpations, hatchery contributions, and processes affecting population structure in a small area of the previously unglaciated Driftless Area of Wisconsin, USA. The results from these analyses suggest that wild populations in this region are genetically distinct even at small spatial scales, lack strong hydrologically associated population structure, rarely exchange gene flow, and have small effective population sizes. Furthermore, wild populations are substantially diverged from known hatchery strains and show minimal evidence of introgression in clustering analyses. However, we demonstrate through empirically informed simulations that distinct wild populations may potentially be hatchery-founded and have since diverged through rapid genetic drift. Collectively, the apparent lack of hydrological population structure and potential for rapid drift in the Driftless Area suggest that many native populations may have been historically extirpated and refounded by stocking events. If this is the case, then commonly used genomic clustering methods and their associated model selection criteria may result in underestimation of hatchery introgression in the face of rapid drift.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 12","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11648973/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833401","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":"Genetic Signatures of Contrasted Outbreak Histories of “Candidatus Liberibacter asiaticus”, the Bacterium That Causes Citrus Huanglongbing, in Three Outermost Regions of the European Union","authors":"Olivier Pruvost,&nbsp;Karine Boyer,&nbsp;Frédéric Labbé,&nbsp;Marine Weishaar,&nbsp;Anaïs Vynisale,&nbsp;Claire Melot,&nbsp;Cécile Hoareau,&nbsp;Gilles Cellier,&nbsp;Virginie Ravigné","doi":"10.1111/eva.70053","DOIUrl":"10.1111/eva.70053","url":null,"abstract":"<p>In an era of trade globalization and climate change, crop pathogens and pests are a genuine threat to food security. The detailed characterization of emerging pathogen populations is a prerequisite for managing invasive species pathways and designing sustainable disease control strategies. Huanglongbing is the disease that causes the most damage to citrus, a crop that ranks #1 worldwide in terms of fruit production. Huanglongbing can be caused by three species of the phloem-limited alpha-proteobacterium, “<i>Candidatus</i> Liberibacter,” which are transmitted by psyllids. Two of these bacteria are of highest concern, “<i>Ca</i>. Liberibacter asiaticus” and “<i>Ca</i>. Liberibacter africanus,” and have distinct thermal optima. These pathogens are unculturable, which complicates their high-throughput genetic characterization. In the present study, we used several genotyping techniques and an extensive sample collection to characterize <i>Ca</i>. Liberibacter populations associated with the emergence of huanglongbing in three French outermost regions of the European Union (Guadeloupe, Martinique and Réunion). The outbreaks were primarily caused by “<i>Ca</i>. Liberibacter asiaticus,” as “<i>Ca</i>. Liberibacter africanus” was only found at a single location in Réunion. We emphasize the low diversity and high genetic relatedness between samples from Guadeloupe and Martinique, which suggests the putative movement of the pathogen between the two islands and/or the independent introduction of closely related strains. These samples were markedly different from the samples from Réunion, where the higher genetic diversity revealed by tandem-repeat markers suggests that the disease was probably overlooked for years before being officially identified in 2015. We show that “<i>Ca</i>. Liberibacter asiaticus” occurs from sea level to an altitude of 950 m above sea level and lacks spatial structure. This suggests the pathogen's medium- to long-distance movement. We also suggest that backyard trees acted as relays for disease spread. We discuss the implications of population biology data for surveillance and management of this threatful disease.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 12","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11649586/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845398","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":"Concordant Signal of Genetic Variation Across Marker Densities in the Desert Annual Chylismia brevipes Is Linked With Timing of Winter Precipitation","authors":"Daniel F. Shryock,&nbsp;Nila Lê,&nbsp;Lesley A. DeFalco,&nbsp;Todd C. Esque","doi":"10.1111/eva.70046","DOIUrl":"10.1111/eva.70046","url":null,"abstract":"<p>Climate change coupled with large-scale surface disturbances necessitate active restoration strategies to promote resilient and genetically diverse native plant communities. However, scarcity of native plant materials hinders restoration efforts, leading practitioners to choose from potentially viable but nonlocal seed sources. Genome scans for genetic variation linked with selective environmental gradients have become a useful tool in such efforts, allowing rapid delineation of seed transfer zones along with predictions of genomic vulnerability to climate change. When properly applied, genome scans can reduce the risk of maladaptation due to mismatches between seed source and planting site. However, results are rarely replicated among complimentary data sources. Here, we compared RAD-seq datasets with 819 and 2699 SNPs (in 625 and 356 individuals, respectively) from the Mojave Desert winter annual <i>Chylismia brevipes</i>. Overall, we found that the datasets consistently characterized both neutral population structure and genetic–environmental associations. Ancestry analyses indicated consistent spatial genetic structuring into four regional populations. We also detected a marked signal of isolation by resistance (IBR), wherein spatial genetic structure was better explained by habitat resistance than by geographic distance. Potentially adaptive loci identified from genome scans were associated with the same environmental gradients—fall precipitation, winter minimum temperature, and precipitation timing—regardless of dataset. Paired with our finding that habitat resistance best explained genetic divergence, our results suggest that isolation of populations within environmentally similar habitats—and subsequent local adaption along gradients parallel to these habitats—drive genome-wide divergence in this species. Moreover, strong genetic associations with winter precipitation timing, along with forecasted shifts in precipitation regime due to midcentury climate change, could impact future population dynamics, habitat distribution, and genetic connectivity for <i>C. brevipes</i> populations within the Mojave Desert.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 12","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11649585/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845396","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":"Dealing With the Complexity of Effective Population Size in Conservation Practice","authors":"Ancuta Fedorca,&nbsp;Joachim Mergeay,&nbsp;Adejoke O. Akinyele,&nbsp;Tamer Albayrak,&nbsp;Iris Biebach,&nbsp;Alice Brambilla,&nbsp;Pamela A. Burger,&nbsp;Elena Buzan,&nbsp;Ino Curik,&nbsp;Roberta Gargiulo,&nbsp;José A. Godoy,&nbsp;Santiago C. González-Martínez,&nbsp;Christine Grossen,&nbsp;Myriam Heuertz,&nbsp;Sean Hoban,&nbsp;Jo Howard-McCombe,&nbsp;Maria Kachamakova,&nbsp;Peter Klinga,&nbsp;Viktoria Köppä,&nbsp;Elenora Neugebauer,&nbsp;Ivan Paz-Vinas,&nbsp;Peter B. Pearman,&nbsp;Laia Pérez-Sorribes,&nbsp;Baruch Rinkevich,&nbsp;Isa-Rita M. Russo,&nbsp;Adélaïde Theraroz,&nbsp;Nia E. Thomas,&nbsp;Marjana Westergren,&nbsp;Sven Winter,&nbsp;Linda Laikre,&nbsp;Alexander Kopatz","doi":"10.1111/eva.70031","DOIUrl":"10.1111/eva.70031","url":null,"abstract":"<p>Effective population size (<i>Ne</i>) is one of the most important parameters in evolutionary biology, as it is linked to the long-term survival capability of species. Therefore, <i>Ne</i> greatly interests conservation geneticists, but it is also very relevant to policymakers, managers, and conservation practitioners. Molecular methods to estimate <i>Ne</i> rely on various assumptions, including no immigration, panmixia, random sampling, absence of spatial genetic structure, and/or mutation-drift equilibrium. Species are, however, often characterized by fragmented populations under changing environmental conditions and anthropogenic pressure. Therefore, the estimation methods' assumptions are seldom addressed and rarely met, possibly leading to biased and inaccurate <i>Ne</i> estimates. To address the challenges associated with estimating <i>Ne</i> for conservation purposes, the COST Action 18134, Genomic Biodiversity Knowledge for Resilient Ecosystems (G-BiKE), organized an international workshop that met in August 2022 in Brașov, Romania. The overarching goal was to operationalize the current knowledge of <i>Ne</i> estimation methods for conservation practitioners and decision-makers. We set out to identify datasets to evaluate the sensitivity of <i>Ne</i> estimation methods to violations of underlying assumptions and to develop data analysis strategies that addressed pressing issues in biodiversity monitoring and conservation. Referring to a comprehensive body of scientific work on <i>Ne</i>, this meeting report is not intended to be exhaustive but rather to present approaches, workshop findings, and a collection of papers that serve as fruits of those efforts. We aimed to provide insights and opportunities to help bridge the gap between scientific research and conservation practice.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 12","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11645448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827000","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 Effects of Hybridization and Parasite Infection on the Survival and Behaviour of Endangered Landlocked Salmon Subject to Predation—Implications for Genetic Rescue","authors":"Aslak Eronen,&nbsp;Matti Janhunen,&nbsp;Pekka Hyvärinen,&nbsp;Raine Kortet,&nbsp;Anssi Karvonen","doi":"10.1111/eva.70056","DOIUrl":"10.1111/eva.70056","url":null,"abstract":"<p>A prerequisite of genetic rescue in endangered and genetically depauperate populations is to pre-evaluate between possible pros and cons of hybridization for the life history and survival of the target population. We hybridized the critically endangered Saimaa landlocked salmon (<i>Salmo salar</i> m. <i>sebago</i>) with one of its geographically closest relatives, anadromous Baltic salmon from River Kymijoki. In two similar experiments, conducted in semi-natural streams during overwintering (at age 1.5) and in early summer (age 2+), we studied how hybridization and eye parasite infection (<i>Diplostomum pseudospathaceum</i>) affected survival from predation by Northern pike (<i>Esox lucius</i>). Additionally, we recorded movements of the juvenile salmon using passive integrated telemetry to gain insights into the effect of hybridization and infection on antipredatory behaviour (movement activity and habitat use). Among the uninfected groups, we found significantly lower mortality of hybrid salmon (mortality ± S.E. 14.5% ± 5.4%) compared to purebred landlocked salmon (37.2% ± 9.4%), supporting a positive effect of hybridization under predation risk. This benefit, however, was cancelled out by the parasite infection, which impaired vision and increased the susceptibility to predation. The negative effects of infection were particularly pronounced in the anadromous salmon due to lower infection resistance, compared to the landlocked salmon. Hybridization per se did not affect the activity levels of salmon, but overwintering activity correlated positively with eye cataract coverage, and summer activity was highest in anadromous salmon. These results demonstrate that controlled supplementation of a small animal population with genetically more diverse hybrids could entail both positive and negative implications, at least in the first crossbred generation.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 12","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11645445/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142826902","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":"Can Thinning Foster Forest Genetic Adaptation to Drought? A Demo-Genetic Modelling Approach With Disturbance Regimes","authors":"Victor Fririon,&nbsp;Hendrik Davi,&nbsp;Sylvie Oddou-Muratorio,&nbsp;Gauthier Ligot,&nbsp;François Lefèvre","doi":"10.1111/eva.70051","DOIUrl":"10.1111/eva.70051","url":null,"abstract":"<p>In managed populations—whether for production or conservation—management practices can interfere with natural eco-evolutionary processes, providing opportunities to mitigate immediate impacts of disturbances or enhance selection on tolerance traits. Here, we used a modelling approach to explore the interplay and feedback loops among drought regimes, natural selection and tree thinning in naturally regenerated monospecific forests. We conducted a simulation experiment spanning three nonoverlapping generations with the individual-based demo-genetic model Luberon2. Luberon2 integrates forest dynamics processes driving survival and mating success, including tree growth, competition, drought impacts and regeneration, with genetic variation in quantitative traits related to these processes. We focused on two variable traits: individual vigour, determining diameter growth potential without stress as the deviation from average stand growth, and individual sensitivity to drought stress as the slope of the relationship between diameter growth and drought stress level. We simulated simplified thinning scenarios, tailored to even-aged stands. Considering plausible genetic variation and contrasting drought regimes, the predicted evolutionary rates for both traits aligned with documented rates in wild plant and animal populations. Thinning considerably reduced natural selective pressures caused by competition and drought compared to unthinned stands. However, the conventional thinning practice of retaining the larger trees resulted in indirect anthropogenic selection that enhanced genetic gain in vigour and lowered sensitivity by up to 30%. More intensive thinning aimed at reducing drought stress by reducing stand density hampered the selection against sensitivity to drought, potentially hindering long-term adaptation. Conversely, avoiding the early, nonselective thinning step—thereby promoting both natural and anthropogenic selection—ultimately resulted in better stand performance while maintaining long-term evolvability. This study emphasises the potential of evolution-oriented forestry strategies to combine drought stress mitigation with genetic adaptation. It provides general insights into how population management, disturbance regimes and eco-evolutionary responses interfere, aiding sustainable decision-making amid environmental uncertainties.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 12","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11627118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142798901","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":"Recently Delisted Songbird Harbors Extensive Genomic Evidence of Inbreeding, Potentially Complicating Future Recovery","authors":"Anna María Calderón,&nbsp;Andrew W. Wood,&nbsp;Zachary A. Szpiech,&nbsp;David P. L. Toews","doi":"10.1111/eva.70052","DOIUrl":"10.1111/eva.70052","url":null,"abstract":"<p>The Kirtland's warbler (<i>Setophaga kirtlandii</i>) is a rare migratory passerine species and habitat specialist of the North American Jack Pine Forests. Their near extinction in the 1970s classified them as endangered and protected under the Endangered Species Act of 1973. After decades of intense conservation management, their population size recovered, and they were delisted from federal protection in 2019. We explore the genomic consequences of this harsh bottleneck and recovery by comparing the genomic architecture of two closely related species whose population sizes have remained large and stable, Hooded Warblers (<i>Setophaga citrina</i>) and American Redstarts (<i>Setophaga ruticilla</i>). We used whole-genome sequencing to characterize the distribution of runs of homozygosity and deleterious genetic variation. We find evidence that Kirtland's warblers exhibit genetic patterns consistent with recent inbreeding. Our results also show that Kirtland's warblers carry an excess proportion of deleterious variation, which could complicate management for this conservation-reliant species. This analysis provides a genetically informed perspective that should be thoroughly considered when delisting other species from federal protections. Through the increasing accessibility of genome sequencing technology, it will be more feasible to monitor the genetic landscape of recovering populations to ensure their long-term survival independent of conservation intervention.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 12","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11627117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142798902","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":"Simulating Genetic Mixing in Strongly Structured Populations of the Threatened Southern Brown Bandicoot (Isoodon obesulus)","authors":"John G. Black,&nbsp;Steven J. B. Cooper,&nbsp;Thomas L. Schmidt,&nbsp;Andrew R. Weeks","doi":"10.1111/eva.70050","DOIUrl":"10.1111/eva.70050","url":null,"abstract":"<p>Genetic mixing aims to increase the genetic diversity of small or isolated populations, by mitigating genetic drift and inbreeding depression, either by maximally increasing genetic diversity, or minimising the prevalence of recessive, deleterious alleles. However, few studies investigate this beyond a single generation of mixing. Here, we model genetic mixing using captive, low-diversity recipient population of the threatened Southern brown bandicoot (<i>Isoodon obesulus</i>) over 50 generations and compare wild populations across south-eastern Australia as candidate source populations. We first assess genetic differentiation between 12 populations, including the first genomic assessment of three mainland Australian and three Tasmanian populations. We assess genetic diversity in the 12 populations using an individualised autosomal heterozygosity pipeline, using these results to identify a candidate recipient population for genetic mixing simulations. We found that populations fell into four major groups of genetic similarity: Adelaide Hills, western Victoria, eastern Victoria, and Tasmania, but populations within these groups were also distinct, and additional substructure was observed in some populations. Our autosomal heterozygosity pipeline indicated significant variability in mean heterozygosity between populations, identifying one extremely genetically degraded population on Inner Sister Island, Tasmania. Genetic mixing simulations of a low heterozygosity captive population in Victoria suggested the greatest increase in heterozygosity would be reached by using highly differentiated populations as mixing sources. However, when removing populations that may represent taxonomically discrete lineages, neither metrics of differentiation nor heterozygosity was strongly correlated with modelled heterozygosity increase, indicating the value of simulation-based approaches when selecting source populations for population mixing.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 12","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11621039/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142798903","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}