Evolutionary Applications最新文献

{"title":"Genomic Data Characterize Reproductive Ecology Patterns in Michigan Invasive Red Swamp Crayfish (Procambarus clarkii)","authors":"Nicole E. Adams,&nbsp;Jared J. Homola,&nbsp;Nicholas M. Sard,&nbsp;Lucas R. Nathan,&nbsp;Brian M. Roth,&nbsp;John D. Robinson,&nbsp;Kim T. Scribner","doi":"10.1111/eva.70007","DOIUrl":"https://doi.org/10.1111/eva.70007","url":null,"abstract":"<p>The establishment and spread of invasive species are directly related to intersexual interactions as dispersal and reproductive success are related to distribution, effective population size, and population growth. Accordingly, populations established by r-selected species are particularly difficult to suppress or eradicate. One such species, the red swamp crayfish (<i>Procambarus clarkii</i>) is established globally at considerable ecological and financial costs to natural and human communities. Here, we develop a single nucleotide polymorphism (SNP) loci panel for <i>P. clarkii</i> using restriction-associated DNA-sequencing data. We use the SNP panel to successfully genotype 1800 individuals at 930 SNPs in southeastern Michigan, USA. Genotypic data were used to reconstruct pedigrees, which enabled the characterization of <i>P. clarkii's</i> mating system and statistical tests for associations among environmental, demographic, and phenotypic predictors and adult reproductive success estimates. We identified juvenile cohorts using genotype-based pedigrees, body size, and sampling timing, which elucidated the breeding phenology of multiple introduced populations. We report a high prevalence of multiple paternity in each surveyed waterbody, indicating polyandry in this species. We highlight the use of newly developed rapid genomic assessment tools for monitoring population reproductive responses, effective population sizes, and dispersal during ongoing control efforts.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142234921","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":"Weak Local Adaptation to Climate in Seedlings of a Deciduous Conifer Suggests Limited Benefits and Risks of Assisted Gene Flow","authors":"Beth Roskilly,&nbsp;Sally Aitken","doi":"10.1111/eva.70001","DOIUrl":"https://doi.org/10.1111/eva.70001","url":null,"abstract":"<p>Assisted migration provides a potential solution to mitigate the increasing risks of forest maladaptation under climate change. Western larch (<i>Larix occidentalis</i> Nutt.) is a deciduous conifer species undergoing assisted migration beyond its natural range in British Columbia into areas that have become suitable based on climatic niche modelling. We established a seedling common garden experiment in raised beds in a warm location outside the natural range for three growing seasons, with 52 natural populations from across the species range and 28 selectively bred families from British Columbia. Intraspecific genetic variation in growth, phenology and cold hardiness was analyzed to test for signals of local adaptation and the effects of selective breeding to better understand the implications for assisted migration and breeding for future climates. We found weak differentiation among populations in all traits, with the proportion of additive genetic variance (<i>Q</i>_ST) ranging from 0.10 to 0.28. Cold hardiness had the weakest population differentiation and exhibited no clines with geographic or climatic variables. Selective breeding for faster growth has maintained genetic variation in bud flush phenology and cold hardiness despite delaying bud set. The weak signals of local adaptation we found in western larch seedlings highlights that assisted gene flow among populations is likely to have limited benefits and risks for mitigating maladaptation with climate change. Our findings suggest that assisted migration outside of the range and selective breeding may be important management strategies for western larch for future climates.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142234848","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":"DNA Methylation Carries Signatures of Sublethal Effects Under Thermal Stress in Loggerhead Sea Turtles","authors":"Eugenie C. Yen,&nbsp;James D. Gilbert,&nbsp;Alice Balard,&nbsp;Inês O. Afonso,&nbsp;Kirsten Fairweather,&nbsp;Débora Newlands,&nbsp;Artur Lopes,&nbsp;Sandra M. Correia,&nbsp;Albert Taxonera,&nbsp;Stephen J. Rossiter,&nbsp;José M. Martín-Durán,&nbsp;Christophe Eizaguirre","doi":"10.1111/eva.70013","DOIUrl":"https://doi.org/10.1111/eva.70013","url":null,"abstract":"<p>To date, studies of the impacts of climate warming on individuals and populations have mostly focused on mortality and thermal tolerance. In contrast, much less is known about the consequences of sublethal effects, which are more challenging to detect, particularly in wild species with cryptic life histories. This necessitates the development of molecular tools to identify their signatures. In a split-clutch field experiment, we relocated clutches of wild, nesting loggerhead sea turtles (<i>Caretta caretta</i>) to an in situ hatchery. Eggs were then split into two sub-clutches and incubated under shallow or deep conditions, with those in the shallow treatment experiencing significantly higher temperatures in otherwise natural conditions. Although no difference in hatching success was observed between treatments, hatchlings from the shallow, warmer treatment had different length–mass relationships and were weaker at locomotion tests than their siblings incubated in the deep, cooler treatment. To characterise the molecular signatures of these thermal effects, we performed whole genome bisulfite sequencing on blood samples collected upon emergence. We identified 287 differentially methylated sites between hatchlings from different treatments, including on genes with neurodevelopmental, cytoskeletal, and lipid metabolism functions. Taken together, our results show that higher incubation temperatures induce sublethal effects in hatchlings, which are reflected in their DNA methylation status at identified sites. These sites could be used as biomarkers of thermal stress, especially if they are retained across life stages. Overall, this study suggests that global warming reduces hatchling fitness, which has implications for dispersal capacity and ultimately a population's adaptive potential. Conservation efforts for these endangered species and similar climate-threatened taxa will therefore benefit from strategies for monitoring and mitigating exposure to temperatures that induce sublethal effects.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142234750","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 Assumptions and Sampling Bias in the Estimation of Effective Population Size: A Case Study in an Amphibian Population","authors":"Karen Cox,&nbsp;Sabrina Neyrinck,&nbsp;Joachim Mergeay","doi":"10.1111/eva.70015","DOIUrl":"https://doi.org/10.1111/eva.70015","url":null,"abstract":"<p>Accurately estimating effective population size (<i>N</i>_e) is essential for understanding evolutionary processes and guiding conservation efforts. This study investigates <i>N</i>_e estimation methods in spatially structured populations using a population of moor frog (<i>Rana arvalis</i>) as a case study. We assessed the behaviour of <i>N</i>_e estimates derived from the linkage disequilibrium (LD) method as we changed the spatial configuration of samples. Moor frog eggs were sampled from 25 breeding patches (i.e., separate vernal ponds, ditches or parts of larger fens) within a single population, revealing an isolation-by-distance pattern and a local spatial genetic structure. Varying buffer sizes around each patch were used to examine the impact of sampling window size on the estimation of effective number of breeders (<i>N</i>_b). Our results indicate a downward bias in LD <i>N</i>_b estimates with increasing buffer size, suggesting an underestimation of <i>N</i>_b. The observed bias is attributed to LD resulting from including genetically divergent individuals (mixture-LD) confounding LD due to drift. This emphasises the significance of considering even subtle spatial genetic patterns. The implications of these findings are discussed, emphasising the need to account for spatial genetic structure to accurately assess population viability and inform conservation efforts. This study contributes to our understanding of the challenges associated with <i>N</i>_e estimation in spatially structured populations and underscores the importance of refining methodologies to address population-specific spatial dynamics for effective conservation planning and management.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70015","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142230952","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":"Genomic Diversity as a Key Conservation Criterion: Proof-of-Concept From Mammalian Whole-Genome Resequencing Data","authors":"Jong Yoon Jeon,&nbsp;Andrew N. Black,&nbsp;Erangi J. Heenkenda,&nbsp;Andrew J. Mularo,&nbsp;Gina F. Lamka,&nbsp;Safia Janjua,&nbsp;Anna Brüniche-Olsen,&nbsp;John W. Bickham,&nbsp;Janna R. Willoughby,&nbsp;J. Andrew DeWoody","doi":"10.1111/eva.70000","DOIUrl":"https://doi.org/10.1111/eva.70000","url":null,"abstract":"<p>Many international, national, state, and local organizations prioritize the ranking of threatened and endangered species to help direct conservation efforts. For example, the International Union for Conservation of Nature (IUCN) assesses the Green Status of species and publishes the influential Red List of threatened species. Unfortunately, such conservation yardsticks do not explicitly consider genetic or genomic diversity (GD), even though GD is positively associated with contemporary evolutionary fitness, individual viability, and with future evolutionary potential. To test whether populations of genome sequences could help improve conservation assessments, we estimated GD metrics from 82 publicly available mammalian datasets and examined their statistical association with attributes related to conservation. We also considered intrinsic biological factors, including trophic level and body mass, that could impact GD and quantified their relative influences. Our results identify key population GD metrics that are both reflective and predictive of IUCN conservation categories. Specifically, our analyses revealed that Watterson's theta (the population mutation rate) and autozygosity (a product of inbreeding) are associated with the current Red List categorization, likely because demographic declines that lead to “listing” decisions also reduce levels of standing genetic variation. We argue that by virtue of this relationship, conservation organizations like IUCN could leverage emerging genome sequence data to help categorize Red List threat rankings (especially in otherwise data-deficient species) and/or enhance Green Status assessments to establish a baseline for future population monitoring. Thus, our paper (1) outlines the theoretical and empirical justification for a new GD-based assessment criterion, (2) provides a bioinformatic pipeline for estimating GD from population genomic data, and (3) suggests an analytical framework that can be used to measure baseline GD while providing quantitative GD context for consideration by conservation authorities.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70000","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142165487","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":"Demographic History and Inbreeding in Two Declining Sea Duck Species Inferred From Whole-Genome Sequence Data","authors":"María I. Cádiz,&nbsp;Aja Noersgaard Buur Tengstedt,&nbsp;Iben Hove Sørensen,&nbsp;Emma Skindbjerg Pedersen,&nbsp;Anthony David Fox,&nbsp;Michael M. Hansen","doi":"10.1111/eva.70008","DOIUrl":"https://doi.org/10.1111/eva.70008","url":null,"abstract":"<p>Anthropogenic impact has transitioned from threatening already rare species to causing significant declines in once numerous organisms. Long-tailed duck (<i>Clangula hyemalis</i>) and velvet scoter (<i>Melanitta fusca</i>) were once important quarry sea duck species in NW Europe, but recent declines resulted in their reclassification as vulnerable on the IUCN Red List. We sequenced and assembled genomes for both species and resequenced 15 individuals of each. Using analyses based on site frequency spectra and sequential Markovian coalescence, we found <i>C</i>. <i>hyemalis</i> to show more historical demographic stability, whereas <i>M. fusca</i> was affected particularly by the Last (Weichselian) Glaciation. This likely reflects <i>C</i>. <i>hyemalis</i> breeding continuously across the Arctic, with cycles of glaciation primarily shifting breeding areas south or north without major population declines, whereas the more restricted southern range of <i>M. fusca</i> would lead to significant range contraction during glaciations. Both species showed evidence of declines over the past thousands of years, potentially reflecting anthropogenic pressures with the recent decline indicating an accelerated process. Analysis of runs of homozygosity (ROH) showed low but nontrivial inbreeding, with <i>F</i>_ROH from 0.012 to 0.063 in <i>C</i>. <i>hyemalis</i> and ranging from 0 to 0.047 in <i>M. fusca</i>. Lengths of ROH suggested that this was due to ongoing background inbreeding rather than recent declines. Overall, despite demographically important declines, this has not yet led to strong inbreeding and genetic erosion, and the most pressing conservation concern may be the risk of density-dependent (Allee) effects. We recommend monitoring of inbreeding using ROH analysis as a cost-efficient method to track future developments to support effective conservation of these species.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142165486","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":"Creating insect neopolyploid lines to study animal polyploid evolution","authors":"Saminathan Sivaprakasham Murugesan,&nbsp;Leo W. Beukeboom,&nbsp;Eveline C. Verhulst,&nbsp;Kelley Leung","doi":"10.1111/eva.13706","DOIUrl":"https://doi.org/10.1111/eva.13706","url":null,"abstract":"<p>Whole-genome duplication (polyploidy) poses many complications but is an important driver for eukaryotic evolution. To experimentally study how many challenges from the cellular (including gene expression) to the life history levels are overcome in polyploid evolution, a system in which polyploidy can be reliably induced and sustained over generations is crucial. Until now, this has not been possible with animals, as polyploidy notoriously causes first-generation lethality. The parasitoid wasp <i>Nasonia vitripennis</i> emerges as a stunningly well-suited model. Polyploidy can be induced in this haplodiploid system through (1) silencing genes in the sex determination cascade and (2) by colchicine injection to induce meiotic segregation failure. <i>Nasonia</i> polyploids produce many generations in a short time, making them a powerful tool for experimental evolution studies. The strong variation observed in <i>Nasonia</i> polyploid phenotypes aids the identification of polyploid mechanisms that are the difference between evolutionary dead ends and successes. Polyploid evolution research benefits from decades of <i>Nasonia</i> research that produced extensive reference—omics data sets, facilitating the advanced studies of polyploid effects on the genome and transcriptome. It is also possible to create both inbred lines (to control for genetic background effects) and outbred lines (to conduct polyploid selection regimes). The option of interspecific crossing further allows to directly contrast autopolyploidy (intraspecific polyploidy) to allopolyploidy (hybrid polyploidy). <i>Nasonia</i> can also be used to investigate the nascent field of using polyploidy in biological control to improve field performance and lower ecological risk. In short, <i>Nasonia</i> polyploids are an exceptional tool for researching various biological paradigms.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13706","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142165218","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":"Comparative Transcriptomic Reveals Greater Similarities in Response to Temperature Than to Invasive Alien Predator in the Damselfly Ischnura elegans Across Different Geographic Scales","authors":"Guillaume Wos,&nbsp;Gemma Palomar,&nbsp;Marzena Marszałek,&nbsp;Szymon Sniegula","doi":"10.1111/eva.70002","DOIUrl":"10.1111/eva.70002","url":null,"abstract":"<p>The impact of global changes on populations may not be necessarily uniform across a species' range. Here, we aim at comparing the phenotypic and transcriptomic response to warming and an invasive predator cue in populations across different geographic scales in the damselfly <i>Ischnura elegans</i>. We collected adult females in two ponds in southern Poland (central latitude) and two ponds in southern Sweden (high latitude). We raised their larvae in growth chambers and exposed them to combination of temperature and a predator cue released by the crayfish <i>Orconectes limosus</i>. When larvae reached the prefinal larval stage, they were phenotyped for traits related to growth and size and collected for a gene expression analysis. High-latitude populations exhibited greater phenotypic and transcriptomic variation than central-latitude populations. Across latitudes and ponds, temperature generally increased growth rate and the predator cue decreased mass, but the effects of temperature were also pond-specific. Comparison of the transcriptomic profiles revealed a greater overlap in the response to temperature across latitudes and ponds, especially for pathway-related oxidative stress and sugar and lipid metabolism. The transcriptomic response to a predator cue and to the interaction temperature × predator cue was more pond-specific and overlapped only for few genes and pathways related to cuticle, development and signal transduction. We demonstrated that central- and high-latitude populations may partially respond through similar mechanisms to warming and, to a lower extent to a predator cue and to the interaction temperature × predator cue. For the predator cue and the interaction, the large fraction of ponds-specific genes suggests local adaptation. We show that high-latitude populations were generally more plastic at the phenotypic and transcriptomic level and may be more capable to cope with environmental changes than their central-latitude counterparts.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11377989/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142152718","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":"Climate change vulnerability and conservation strategies for tertiary relict tree species: Insights from landscape genomics of Taxus cuspidata","authors":"Yanjun Luo,&nbsp;Wei Qin,&nbsp;Yu Yan,&nbsp;Kangquan Yin,&nbsp;Runguo Zang,&nbsp;Fang K. Du","doi":"10.1111/eva.13686","DOIUrl":"10.1111/eva.13686","url":null,"abstract":"<p>The unprecedented habitat fragmentation or loss has threatened the existence of many species. Therefore, it is essential to understand whether and how these species can pace with the environmental changes. Recent advantages in landscape genomics enabled us to identify molecular signatures of adaptation and predict how populations will respond to changing environments, providing new insights into the conservation of species. Here, we investigated the pattern of neutral and putative adaptive genetic variation and its response to changing environments in a tertiary relict tree species, <i>Taxus cuspidata</i> Sieb. et Zucc, which is distributed in northeast China and adjacent regions. We investigated the pattern of genetic diversity and differentiation using restriction site-associated DNA sequencing (RAD-seq) and seven nuclear microsatellites (nSSRs) datasets. We further explored the endangered mechanism, predicted its vulnerability in the future, and provided guidelines for the conservation and management of this species. RAD-seq identified 16,087 single nucleotide polymorphisms (SNPs) in natural populations. Both the SNPs and nSSRs datasets showed high levels of genetic diversity and low genetic differentiation in <i>T. cuspidata</i>. Outlier detection by <i>F</i>_ST outlier analysis and genotype-environment associations (GEAs) revealed 598 outlier SNPs as putative adaptive SNPs. Linear redundancy analysis (RDA) and nonlinear gradient forest (GF) showed that the contribution of climate to genetic variation was greater than that of geography, and precipitation played an important role in putative adaptive genetic variation. Furthermore, the genetic offset and risk of non-adaptedness (RONA) suggested that the species at the northeast edge may be more vulnerable in the future. These results suggest that although the species has maintained high current genetic diversity in the face of recent habitat loss and fragmentation, future climate change is likely to threaten the survival of the species. Temperature (Bio03) and precipitation (Prec05) variables can be potentially used as predictors of response of <i>T. cuspidata</i> under future climate. Together, this study provides a theoretical framework for conservation and management strategies for wildlife species in the context of future climate change.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11375028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142152717","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":"Deciphering the Genetic Landscape: Insights Into the Genomic Signatures of Changle Goose","authors":"Hao Chen,&nbsp;Yan Wu,&nbsp;Yihao Zhu,&nbsp;Keyi Luo,&nbsp;Sumei Zheng,&nbsp;Hongbo Tang,&nbsp;Rui Xuan,&nbsp;Yuxuan Huang,&nbsp;Jiawei Li,&nbsp;Rui Xiong,&nbsp;Xinyan Fang,&nbsp;Lei Wang,&nbsp;Yujie Gong,&nbsp;Junjie Miao,&nbsp;Jing Zhou,&nbsp;Hongli Tan,&nbsp;Yanan Wang,&nbsp;Liping Wu,&nbsp;Jing Ouyang,&nbsp;Min Huang,&nbsp;Xueming Yan","doi":"10.1111/eva.13768","DOIUrl":"10.1111/eva.13768","url":null,"abstract":"<p>The Changle goose (CLG), a Chinese indigenous breed, is celebrated for its adaptability, rapid growth, and premium meat quality. Despite its agricultural value, the exploration of its genomic attributes has been scant. Our study entailed whole-genome resequencing of 303 geese across CLG and five other Chinese breeds, revealing distinct genetic diversity metrics. We discovered significant migration events from Xingguo gray goose to CLG and minor gene flow between them. We identified genomic regions through selective sweep analysis, correlating with CLG's unique traits. An elevated inbreeding coefficient in CLG, alongside reduced heterozygosity and rare single nucleotide polymorphisms (R_SNPs), suggests a narrowed genetic diversity. Genomic regions related to reproduction, meat quality, and growth were identified, with the <i>GATA3</i> gene showing strong selection signals for meat quality. A non-synonymous mutation in the <i>Sloc2a1</i> gene, which is associated with reproductive traits in the CLG, exhibited significant differences in allelic frequency. The roles of <i>CD82</i>, <i>CDH8</i>, and <i>PRKAB1</i> in growth and development, alongside <i>FABP4</i>, <i>FAF1</i>, <i>ESR1</i>, and <i>AKAP12</i> in reproduction, were highlighted. Additionally, <i>Cdkal1</i> and <i>Mfsd14a</i> may influence meat quality. This comprehensive genetic analysis underpins the unique genetic makeup of CLG, providing a basis for its conservation and informed breeding strategies.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 8","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11340016/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142034662","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}