Evolutionary Applications最新文献

{"title":"Climate-Induced Genomic Selection: Genetic Structure Variation of Cornus kousa subsp. chinensis and Its Adaptive Reaction to Future Climate Change","authors":"Junru Li,&nbsp;Qian Liu,&nbsp;Xi Gong,&nbsp;Luzhang Ruan,&nbsp;Bicai Guan","doi":"10.1111/eva.70281","DOIUrl":"https://doi.org/10.1111/eva.70281","url":null,"abstract":"<p>Global climate change exerts a far-reaching influence on the geographical distribution, phenological patterns, and genetic diversity of plants, presenting a grave challenge to the survival and evolution of species. Owing to its robust ecological adaptability, restricted dispersal capacity, and abundant intraspecific variation, <i>Cornus kousa</i> subsp. <i>chinensis</i> has emerged as an ideal subject for investigating the responses of woody plants to climate change. Consequently, this study employed the landscape genomics approach to evaluate the survival risks faced by <i>C. kousa</i> under the present and future (2060–2080) climate scenarios (RCP45 and RCP85). A total of 348 leaf samples were gathered from 25 populations of <i>C. kousa</i> spanning diverse regions of China. The research revealed that, under the prevailing climate conditions, the genetic diversity within the populations is remarkably abundant. Nevertheless, the POPs model forecasts that the genetic structure will undergo substantial alterations in future climate scenarios. Notably, 93.6% of the populations will be grouped into a solitary common cluster, and the genetic variation will be conspicuously homogenized. Through BayeScan and Latent Factor Mixed Model (LFMM) analyses, 67 Single Nucleotide Polymorphism (SNP) loci significantly associated with climate factors were identified. Among these loci, 90.3% are closely correlated with the annual mean temperature (Bio 1), suggesting that temperature serves as the primary driving force for adaptive selection at the genomic level. In summary, our findings not only offer valuable perspectives for the conservation of the genetic resources of the <i>C. kousa</i> population but also provide significant reference value for the formulation of subtropical forest conservation strategies.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70281","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148282304","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":"Integrative Advances in Equine Genomics From Reference Assemblies to Evolutionary History and Key Traits","authors":"Ying Lu,&nbsp;Ruoshan Ma,&nbsp;Bo Wang,&nbsp;Jiao Wu,&nbsp;Yuqing Chong,&nbsp;Zhendong Gao,&nbsp;Weidong Deng","doi":"10.1111/eva.70283","DOIUrl":"https://doi.org/10.1111/eva.70283","url":null,"abstract":"<p>Horses are major domestic animals and cultural symbols that have accompanied humans for millennia. They underpin transport, agriculture, warfare and sport, and also provide a model for studying domestication, complex traits and adaptive evolution. Recent work in equine genomics has now generated a much richer picture of how these roles are grounded in the genome. This review brings together advances in several connected areas: the construction and refinement of reference assemblies; genomic reconstructions of origin, domestication and dispersal; global and regional patterns of genetic diversity; and the molecular basis of key traits such as athletic performance, coat colour, body size, environmental adaptation and inherited myopathies. The transition from EquCab1.0/2.0 to EquCab3.0 and a complete Y-chromosome sequence illustrates how long-read and Hi-C/T2T data improve genome completeness and the representation of complex regions. On this foundation, high-coverage resequencing of ancient and modern horses has clarified the geographical core of domestication in the Volga–Don region, the Bronze Age replacement of earlier domestic lineages and the long-term impact of human management on behaviour, conformation and mobility. Comparative analyses of mitochondrial DNA, Y-chromosomal haplotypes and autosomal runs of homozygosity further reveal a combination of diverse maternal lineages, highly constrained paternal lineages and breed-specific inbreeding histories. Against this background, studies of representative traits show how association signals, functional experiments and clinical evidence can be linked to practical tools for breeding and health management, for example through <i>MSTN</i>-guided performance profiling, <i>EPAS1</i>-based altitude adaptation and molecular tests for <i>GYS1</i>, <i>SCN4A</i>, <i>PPIB</i> and <i>MYH1</i>. We conclude by considering how telomere-to-telomere assemblies, pangenome resources, improved structural-variant detection and closer integration between population genomics and functional studies may support conservation, health surveillance and molecular breeding in diverse horse populations.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70283","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148282092","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":"Unlocking the Past to Protect the Future: Forensic DNA and Historical Specimens Reveal the Origins of Smuggled Yellow-Headed Parrots","authors":"Brenda R. Ramirez,&nbsp;Devon A. DeRaad,&nbsp;Allison E. Muhlheim,&nbsp;Pat Latas,&nbsp;Brooke Durham,&nbsp;Nikki Buxton,&nbsp;Marquette J. Mutchler,&nbsp;Eliza J. Kirsch,&nbsp;Whitney L. E. Tsai,&nbsp;Alana K. Pizarro,&nbsp;John E. McCormack","doi":"10.1111/eva.70282","DOIUrl":"10.1111/eva.70282","url":null,"abstract":"<p>Wildlife trafficking poses a major threat to biodiversity, particularly for species like parrots that are targeted in the pet trade. The Yellow-headed Parrot (<i>Amazona oratrix</i>), an endangered species native to Mexico and Central America, is frequently poached from unknown geographic locations, hindering the identification of smuggling sources and repatriation of any confiscated individuals. Here, we used population genomic tools to determine the source of 18 Yellow-headed Parrots confiscated as nestlings during a 2021 U.S.–Mexico border crossing into California. To build a genomic reference map, we extracted and sequenced DNA derived from the toe pads of historical museum specimens from across the range of three out of the four described <i>A. oratrix</i> subspecies. Genomic data revealed that the three sequenced subspecies correspond to unique ancestry groups and revealed a substantial genetic divide between Pacific and Atlantic coastal populations of <i>A. o. oratrix</i>. The smuggled parrots and parrots from the introduced population in southern California both consistently clustered with eastern populations of <i>A. o. oratrix</i> in genomic analyses. Concordantly, the predicted origin of these smuggled birds was eastern Mexico, based on the genomic reference map derived from historical samples. Kinship analysis reveals multiple cases of sibling-level relationships among the smuggled birds, suggesting that wild <i>A. oratrix</i> nests continue to be raided for the pet trade despite the species' endangered status. Overall, this study illustrates the power of using museum genomics to trace wildlife trafficking routes, inform conservation policy, and improve taxonomic resolution in species of conservation concern.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13266085/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148262451","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":"Shade Avoidance Restricts Soybean Breeding Progress and Increases Herbivore Susceptibility","authors":"Lukas Vonmetz,&nbsp;Emanuel B. Kopp,&nbsp;Simon Jäggi,&nbsp;Pascal A. Niklaus,&nbsp;Samuel E. Wuest","doi":"10.1111/eva.70280","DOIUrl":"https://doi.org/10.1111/eva.70280","url":null,"abstract":"<p>High planting densities expose field crops to competition for light, which typically induces shade avoidance responses such as stem elongation. While adaptive in natural environments, these responses can lower yield and increase susceptibility to stress in agricultural systems. We tested whether soybean breeding over the past century has altered shade avoidance and associated trade-offs. Twenty-one Canadian cultivars released between 1922 and 2018 were grown in pots under either control or shade-avoidance-inducing light conditions, achieved by altering reflected light spectrum without reducing photosynthetic radiation. Plants exposed to shade-avoidance-inducing light grew taller and suffered greater thrips damage, consistent with expectations of increased stem elongation and reduced defence. More recent cultivars showed higher susceptibility to thrips than older ones. Breeding progress in seed yield was driven largely by greater biomass allocation to seeds and reduced branching. However, under shade-inducing light, the yield improvements were smaller, pointing to shade avoidance as a limiting factor. Our results indicate that while soybean breeding has improved yield and shifted morphology towards ideotypes suited for high-density stands, persistent shade avoidance responses constrain breeding progress for yield and increase herbivore susceptibility. Breeding strategies that reduce sensitivity to neighbor cues may therefore improve soybean productivity and resilience.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70280","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148237903","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":"Whole Genome Analyses of the Endangered Northern Abalone (Haliotis kamtschatkana) Reveal Population Differentiation and a Genomic Signature of a Dramatic Population Decline","authors":"Anna Tigano,&nbsp;Erin C. Herder,&nbsp;Kayla Long,&nbsp;Janine Supernault,&nbsp;Daniel L. Curtis,&nbsp;S. Christine Hansen,&nbsp;Mackenzie D. Mazur,&nbsp;Eric B. Rondeau,&nbsp;Dominique Bureau","doi":"10.1111/eva.70255","DOIUrl":"https://doi.org/10.1111/eva.70255","url":null,"abstract":"<p>Despite widespread declines of many wildlife species, the effects of population decline on the genome and the recovery potential of affected species are still poorly understood, especially beyond a few charismatic species. The Northern abalone (or Pinto abalone; <i>Haliotis kamtschatkana</i>) is a marine gastropod mollusk of social, cultural and historical economic importance in the Pacific Northwest of North America that experienced a decline in population density due to commercial harvest, and is currently listed as endangered in Canada under the Species at Risk Act. Previous genetic investigations based on microsatellites and reduced-representation approaches concluded that Northern abalone is panmictic throughout its range, from Alaska to California, and identified high levels of genetic variation with no indication of population decline. Using whole genome resequencing data from Northern abalone sampled across the northern part of the species range, we instead identified both: (1) significant differentiation between two genetic groups, albeit concentrated in few genomic regions, and (2) a strong signature of a dramatic population decline, without genomic evidence of genetic inbreeding. Demographic reconstructions showed a modest signal of recent population expansion, supported by an increasing number of juveniles observed during dive surveys. We also found evidence of historical, rather than current, connectivity throughout the area investigated. These results are important for management decisions and highlight the utility of whole genome data in conservation, especially in species with historically large effective population sizes like the Northern abalone.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70255","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148174085","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":"In Search of the Lost Brown Trout (Salmo trutta Complex) Using DNA of Ancient and Modern Samples From the Southern Italian Peninsula","authors":"Tatiana Fioravanti,&nbsp;Andrea Splendiani,&nbsp;Tommaso Righi,&nbsp;Antonio Tagliacozzo,&nbsp;Daniele Albertini,&nbsp;Vincenzo Caputo Barucchi","doi":"10.1111/eva.70270","DOIUrl":"https://doi.org/10.1111/eva.70270","url":null,"abstract":"<p>The current diversity and distribution of species and populations have been shaped by the major climatic oscillations during the Quaternary. The brown trout (<i>Salmo trutta</i>) is a striking example of the strong effect of past climate changes on the evolutionary history of species, in fact, the alternation of glacial/interglacial cycles has led to continuous phenomena of expansion and contraction of its distribution and, consequently, to the evolution of different genetic lineages. This phenomenon was also directly observed by the genetic analysis of <i>S. trutta</i> bones recovered from the archaeological assemblage of a coastal cave named ‘Grotta del Santuario Della Madonna’ (Southern Italy). In this study, additional <i>S. trutta</i> remains were morphologically and genetically analysed, and the genetic results were compared with those of modern samples caught from streams close to the cave locality. The analysis of <i>S. trutta</i> bones confirms that changes in abundance, body size and genetic diversity observed in different stratigraphic sections were determined by environmental changes caused by the Younger Dryas-Holocene transition and by the ability of the species to perform anadromous migration, a behaviour that had disappeared at the end of the Pleistocene in the Mediterranean region. The comparison between ancient and modern samples highlights that extinctions and recolonizations due to past environmental changes affected also the current diversity and distribution of <i>S. trutta</i> in Southern Italian streams. Unfortunately, incorrect management policies related to sport fishing (i.e., stocking with alien brown trout strains) have been eroding millions of years of the trout evolution in just a few centuries.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70270","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148173939","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":"Vulnerable Juniper Populations Show Adaptive Potential in the Face of a Highly Damaging Invasive Tree Pathogen","authors":"Daisy Crowson,&nbsp;Stephen Cavers,&nbsp;Joan E. Cottrell,&nbsp;Richard A. Ennos,&nbsp;Sarah Green","doi":"10.1111/eva.70276","DOIUrl":"https://doi.org/10.1111/eva.70276","url":null,"abstract":"<p>Invasive tree pathogens pose a significant and increasing threat to natural ecosystems. The outcome of these novel host-pathogen interactions depends largely on the presence and nature of resistance in host populations, which will govern the host's potential to respond through natural selection and adaptation to the new threat. This study assessed the adaptive potential of juniper (<i>Juniperus communis</i>) in the face of the invasive tree pathogen <i>Phytophthora austrocedri</i> through two inoculation experiments: an excised-shoot trial using six different <i>P. austrocedri</i> isolates and a progeny-provenance trial that inoculated whole trees with a single highly virulent isolate. We found evidence for both qualitative and quantitative resistance in juniper populations, with lesion length (quantitative resistance) showing moderate to high heritability and lesion development (qualitative resistance) showing very high heritability. There was a significant genotype-by-genotype interaction between pathogen isolate and host genotype, lowering the estimate of heritability to moderate values when calculated across six different isolates. Finally, we found evidence that <i>P. austrocedri</i> is imposing natural selection on juniper populations, with individuals originating from highly exposed populations having a lower predicted probability of developing a lesion. Based on the results of this study, we recommend that the most effective management strategy for vulnerable UK juniper populations is to promote natural regeneration within populations, making use of existing genetic diversity in resistance within natural populations without risking the introduction of new <i>P. austrocedri</i> genotypes through the planting of nursery-grown juniper.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70276","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148174032","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":"Correction to “Environment and Pollen Diversity Differentially Affect the Gut Microbiomes of Introduced Honeybees and Bumblebees”","authors":"","doi":"10.1111/eva.70279","DOIUrl":"https://doi.org/10.1111/eva.70279","url":null,"abstract":"<p>S. Haque, F. Ponton, A. P. Allen, et al. 2026. “Environment and Pollen Diversity Differentially Affect the Gut Microbiomes of Introduced Honeybees and Bumblebees.” <i>Evolutionary Applications</i> 19, no. 4: e70234. https://doi.org/10.1111/eva.70234.</p><p>In the “Data Availability Statement,” the following text was incorrect:</p><p>Tables of ASVs for 16S and ITS2 data; Alpha diversity values for each sample and environmental factors; R scripts for linear mixed effect models are all available on DRYAD at this temporary link for reviewers prior to publishing: http://datadryad.org/share/_uXhFLsTx7hkGquTQgXXbzsPokqhnmEPczCsuWOO074. Raw sequence data can be found here: https://mqoutlook-my.sharepoint.com/:f:/g/personal/rachael_dudaniec_mq_edu_au/IgB7brFOapvgTbjQ2vQ-LnyGAdfA_aKtqi3QmR050G6pAwY?e=JvetOh, and NCBI.</p><p>This has been replaced with:</p><p>Tables of ASVs for 16S and ITS2 data; Alpha diversity values for each sample and environmental factors; R scripts for linear mixed effect models are all available on DRYAD: https://doi.org/10.5061/dryad.ngf1vhj6r. Raw sequencing data for 16S and ITS2 have been deposited in the NCBI Sequence Read Archive (SRA) under BioProject accession number PRJNA1450835 and are accessible through this link: https://www.ncbi.nlm.nih.gov/sra/PRJNA1450835.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70279","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148173918","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":"Predictions From Evolutionary Theory for Urban Environments","authors":"Ailene MacPherson,&nbsp;Aude E. Caizergues,&nbsp;Paul Savary,&nbsp;Kuangyi Xu,&nbsp;Philipp W. Messer,&nbsp;Mia N. Akbar,&nbsp;Marie-Josée Fortin,&nbsp;Robert D. Holt,&nbsp;Amber Gigi Hoi,&nbsp;Nicole Mideo,&nbsp;Rob Ness,&nbsp;Pedro R. Peres-Neto,&nbsp;James S. Santangelo,&nbsp;Marc T. J. Johnson","doi":"10.1111/eva.70275","DOIUrl":"https://doi.org/10.1111/eva.70275","url":null,"abstract":"<p>Urbanization drives rapid and extreme environmental change, profoundly shaping the ecology and evolution of populations. In this Perspective, we call for the integration and development of evolutionary theory and empirical research through collaboration between theoretical and experimental biologists to provide new insights into urban evolutionary ecology. We argue that mathematical models derived from ecological and evolutionary theory can be tailored to provide a powerful framework for generating predictions that can guide empirical research in urban ecology and evolution. At the same time, empirical results can motivate and inform the development and analysis of new theoretical models specific to urban systems. We illustrate how existing evolutionary theory can be harnessed to generate specific predictions of how urbanization can influence evolution. These predictions span the range of urban impacts on all main evolutionary processes, including mutation, gene flow, genetic drift, non-random mating, and selection. We provide a summary of evidence supporting each prediction and outline empirical approaches available to test them. Importantly, these predictions require distinct modeling approaches that can be applied more broadly to better utilize theory for research on urban environments. To facilitate this, we provide an overview of these existing modeling approaches ranging from the application and syntheses of classic model results to the development of novel probabilistic predictions. We advocate for increased integration of theoretical and empirical research through the development of novel models using parameterization specific to urban systems, empirical tests grounded in theoretical models, model-based empirical tests, and model-based data analysis and inference to advance our understanding of evolution in urban environments.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70275","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148173917","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":"Integrative Genomics Identifies Candidate Genes Underlying Trypanotolerance in Hybrid African Cattle","authors":"Gillian P. McHugo,&nbsp;James A. Ward,&nbsp;Said Ismael Ng'ang'a,&nbsp;Laurent A. F. Frantz,&nbsp;John A. Browne,&nbsp;Michael Salter-Townshend,&nbsp;Grace M. O'Gorman,&nbsp;Kieran G. Meade,&nbsp;Emmeline W. Hill,&nbsp;Thomas J. Hall,&nbsp;David E. MacHugh","doi":"10.1111/eva.70274","DOIUrl":"https://doi.org/10.1111/eva.70274","url":null,"abstract":"<p>Integrative genomics combines data from different omics sources to link genotypes and phenotypes with the aim of unravelling biological networks and pathways that undergird complex traits, particularly with respect to disease. In this respect, integrative genomics, leveraging population and functional genomic data, can be employed to understand the evolutionary processes that have shaped adaptation to infectious diseases in domestic cattle. This approach can be particularly informative for African cattle, which exhibit a complex mosaic of genomic ancestry from <i>Bos taurus</i> (taurine) and <i>Bos indicus</i> (indicine) populations. Some African taurine populations have an important evolutionary adaptation known as trypanotolerance, a genetically determined tolerance to infection by trypanosome parasites (<i>Trypanosoma</i> spp.) that cause African animal trypanosomiasis (AAT). AAT is one of the largest constraints to livestock production in sub-Saharan Africa and causes a financial burden of approximately $4.5 billion annually. In this study, we identified putative candidate genes underlying trypanotolerance by integrating local ancestry inference (LAI) from genome-wide SNP data across multiple trypanotolerant and trypanosusceptible hybrid cattle populations with RNA-seq and expression microarray transcriptomic data from multiple tissues collected across time course trypanosome infection experiments. These candidate genes included <i>AGO2</i>, <i>CBL</i>, <i>CNOT1</i>, <i>EDN1</i>, <i>IL1B</i>, <i>NFKB1</i>, <i>RIPK1</i> and <i>TRAF2</i>. Functional analysis of the gene set outputs from this work highlighted GO terms associated with the immune system (including the major histocompatibility complex—MHC) and cell signalling processes. These results signpost future work to elucidate the cellular networks and pathways that drive trypanotolerance.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70274","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148167130","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}