Heredity最新文献_第9页

Dual-trait genomic analysis in highly stratified Arabidopsis thaliana populations using genome-wide association summary statistics 利用全基因组关联汇总统计对高度分层的拟南芥种群进行双性状基因组分析。

IF 3.1 2区生物学

Heredity Pub Date : 2024-05-31 DOI: 10.1038/s41437-024-00688-z

Xiao Feng, Yanjun Zan, Ting Li, Yue Yao, Zheng Ning, Jiabei Li, Hadi Charati, Weilin Xu, Qianhui Wan, Dongyu Zeng, Ziyi Zeng, Yang Liu, Xia Shen

{"title":"Dual-trait genomic analysis in highly stratified Arabidopsis thaliana populations using genome-wide association summary statistics","authors":"Xiao Feng, Yanjun Zan, Ting Li, Yue Yao, Zheng Ning, Jiabei Li, Hadi Charati, Weilin Xu, Qianhui Wan, Dongyu Zeng, Ziyi Zeng, Yang Liu, Xia Shen","doi":"10.1038/s41437-024-00688-z","DOIUrl":"10.1038/s41437-024-00688-z","url":null,"abstract":"Genome-wide association study (GWAS) is a powerful tool to identify genomic loci underlying complex traits. However, the application in natural populations comes with challenges, especially power loss due to population stratification. Here, we introduce a bivariate analysis approach to a GWAS dataset of Arabidopsis thaliana. We demonstrate the efficiency of dual-phenotype analysis to uncover hidden genetic loci masked by population structure via a series of simulations. In real data analysis, a common allele, strongly confounded with population structure, is discovered to be associated with late flowering and slow maturation of the plant. The discovered genetic effect on flowering time is further replicated in independent datasets. Using Mendelian randomization analysis based on summary statistics from our GWAS and expression QTL scans, we predicted and replicated a candidate gene AT1G11560 that potentially causes this association. Further analysis indicates that this locus is co-selected with flowering-time-related genes. The discovered pleiotropic genotype-phenotype map provides new insights into understanding the genetic correlation of complex traits.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 1","pages":"11-20"},"PeriodicalIF":3.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141183290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Simulation of functional additive and non-additive genetic effects using statistical estimates from quantitative genetic models 利用定量遗传模型的统计估算模拟功能加性和非加性遗传效应。

IF 3.1 2区生物学

Heredity Pub Date : 2024-05-31 DOI: 10.1038/s41437-024-00690-5

Thinh Tuan Chu, Peter Skov Kristensen, Just Jensen

{"title":"Simulation of functional additive and non-additive genetic effects using statistical estimates from quantitative genetic models","authors":"Thinh Tuan Chu, Peter Skov Kristensen, Just Jensen","doi":"10.1038/s41437-024-00690-5","DOIUrl":"10.1038/s41437-024-00690-5","url":null,"abstract":"Stochastic simulation software is commonly used to aid breeders designing cost-effective breeding programs and to validate statistical models used in genetic evaluation. An essential feature of the software is the ability to simulate populations with desired genetic and non-genetic parameters. However, this feature often fails when non-additive effects due to dominance or epistasis are modeled, as the desired properties of simulated populations are estimated from classical quantitative genetic statistical models formulated at the population level. The software simulates underlying functional effects for genotypic values at the individual level, which are not necessarily the same as effects from statistical models in which dominance and epistasis are included. This paper provides the theoretical basis and mathematical formulas for the transformation between functional and statistical effects in such simulations. The transformation is demonstrated with two statistical models analyzing individual phenotypes in a single population (common in animal breeding) and plot phenotypes of three-way hybrids involving two inbred populations (observed in some crop breeding programs). We also describe different methods for the simulation of functional effects for additive genetics, dominance, and epistasis to achieve the desired levels of variance components in classical statistical models used in quantitative genetics.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 1","pages":"33-42"},"PeriodicalIF":3.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00690-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141183465","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}

引用次数: 0

Genetic architecture and correlations between the gut microbiome and gut gene transcription in Chinook salmon (Oncorhynchus tshawytscha) 大鳞大麻哈鱼（Oncorhynchus tshawytscha）肠道微生物组与肠道基因转录之间的遗传结构和相关性。

IF 3.1 2区生物学

Heredity Pub Date : 2024-05-31 DOI: 10.1038/s41437-024-00692-3

Javad Sadeghi, Farwa Zaib, Daniel D. Heath

{"title":"Genetic architecture and correlations between the gut microbiome and gut gene transcription in Chinook salmon (Oncorhynchus tshawytscha)","authors":"Javad Sadeghi, Farwa Zaib, Daniel D. Heath","doi":"10.1038/s41437-024-00692-3","DOIUrl":"10.1038/s41437-024-00692-3","url":null,"abstract":"Population divergence through selection can drive local adaptation in natural populations which has implications for the effective restoration of declining and extirpated populations. However, adaptation to local environmental conditions is complicated when both the host and its associated microbiomes must respond via co-evolutionary change. Nevertheless, for adaptation to occur through selection, variation in both host and microbiome traits should include additive genetic effects. Here we focus on host immune function and quantify factors affecting variation in gut immune gene transcription and gut bacterial community composition in early life-stage Chinook salmon (Oncorhynchus tshawytscha). Specifically, we utilized a replicated factorial breeding design to determine the genetic architecture (sire, dam and sire-by-dam interaction) of gut immune gene transcription and microbiome composition. Furthermore, we explored correlations between host gut gene transcription and microbiota composition. Gene transcription was quantified using nanofluidic qPCR arrays (22 target genes) and microbiota composition using 16 S rRNA gene (V5-V6) amplicon sequencing. We discovered limited but significant genetic architecture in gut microbiota composition and transcriptional profiles. We also identified significant correlations between gut gene transcription and microbiota composition, highlighting potential mechanisms for functional interactions between the two. Overall, this study provides support for the co-evolution of host immune function and their gut microbiota in Chinook salmon, a species recognized as locally adapted. Thus, the inclusion of immune gene transcription profile and gut microbiome composition as factors in the development of conservation and commercial rearing practices may provide new and more effective approaches to captive rearing.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 1","pages":"54-66"},"PeriodicalIF":3.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141183365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Island demographics and trait associations in white-tailed deer 白尾鹿的岛屿人口统计学和性状关联。

IF 3.1 2区生物学

Heredity Pub Date : 2024-05-27 DOI: 10.1038/s41437-024-00685-2

Brooklyn S. Cars, Camille Kessler, Eric A. Hoffman, Steeve D. Côté, Daniel Koelsch, Aaron B. A. Shafer

{"title":"Island demographics and trait associations in white-tailed deer","authors":"Brooklyn S. Cars, Camille Kessler, Eric A. Hoffman, Steeve D. Côté, Daniel Koelsch, Aaron B. A. Shafer","doi":"10.1038/s41437-024-00685-2","DOIUrl":"10.1038/s41437-024-00685-2","url":null,"abstract":"When a population is isolated and composed of few individuals, genetic drift is the paramount evolutionary force and results in the loss of genetic diversity. Inbreeding might also occur, resulting in genomic regions that are identical by descent, manifesting as runs of homozygosity (ROHs) and the expression of recessive traits. Likewise, the genes underlying traits of interest can be revealed by comparing fixed SNPs and divergent haplotypes between affected and unaffected individuals. Populations of white-tailed deer (Odocoileus virginianus) on islands of Saint Pierre and Miquelon (SPM, France) have high incidences of leucism and malocclusions, both considered genetic defects; on the Florida Keys islands (USA) deer exhibit smaller body sizes, a polygenic trait. Here we aimed to reconstruct island demography and identify the genes associated with these traits in a pseudo case-control design. The two island populations showed reduced levels of genomic diversity and a build-up of deleterious mutations compared to mainland deer; there was also significant genome-wide divergence in Key deer. Key deer showed higher inbreeding levels, but not longer ROHs, consistent with long-term isolation. We identified multiple trait-related genes in ROHs including LAMTOR2 which has links to pigmentation changes, and NPVF which is linked to craniofacial abnormalities. Our mixed approach of linking ROHs, fixed SNPs and haplotypes matched a high number (~50) of a-priori body size candidate genes in Key deer. This suite of biomarkers and candidate genes should prove useful for population monitoring, noting all three phenotypes show patterns consistent with a complex trait and non-Mendelian inheritance.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 1","pages":"1-10"},"PeriodicalIF":3.1,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141158236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transcriptomics of differences in thermal plasticity associated with selection for an exaggerated male sexual trait 热可塑性差异的转录组学与雄性性状选择有关。

IF 3.1 2区生物学

Heredity Pub Date : 2024-05-27 DOI: 10.1038/s41437-024-00691-4

Agata Plesnar-Bielak, Jonathan M. Parrett, Sebastian Chmielewski, Katarzyna Dudek, Aleksandra Łukasiewicz, Marzena Marszałek, Wiesław Babik, Mateusz Konczal

{"title":"Transcriptomics of differences in thermal plasticity associated with selection for an exaggerated male sexual trait","authors":"Agata Plesnar-Bielak, Jonathan M. Parrett, Sebastian Chmielewski, Katarzyna Dudek, Aleksandra Łukasiewicz, Marzena Marszałek, Wiesław Babik, Mateusz Konczal","doi":"10.1038/s41437-024-00691-4","DOIUrl":"10.1038/s41437-024-00691-4","url":null,"abstract":"The information about the magnitude of differences in thermal plasticity both between and within populations, as well as identification of the underlying molecular mechanisms are key to understanding the evolution of thermal plasticity. In particular, genes underlying variation in the physiological response to temperature can provide raw material for selection acting on plastic traits. Using RNAseq, we investigate the transcriptional response to temperature in males and females from bulb mite populations selected for the increased frequency of one of two discrete male morphs (fighter- and scrambler-selected populations) that differ in relative fitness depending on temperature. We show that different mechanisms underlie the divergence in thermal response between fighter- and scrambler-selected populations at decreased vs. increased temperature. Temperature decrease to 18 °C was associated with higher transcriptomic plasticity of males with more elaborate armaments, as indicated by a significant selection-by-temperature interaction effect on the expression of 40 genes, 38 of which were upregulated in fighter-selected populations in response to temperature decrease. In response to 28 °C, no selection-by-temperature interaction in gene expression was detected. Hence, differences in phenotypic response to temperature increase likely depended on genes associated with their distinct morph-specific thermal tolerance. Selection of males also drove gene expression patterns in females. These patterns could be associated with temperature-dependent fitness differences between females from fighter- vs. scrambler-selected populations reported in previous studies. Our study shows that selection for divergent male sexually selected morphologies and behaviors has a potential to drive divergence in metabolic pathways underlying plastic response to temperature in both sexes.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 1","pages":"43-53"},"PeriodicalIF":3.1,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141158243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ecological divergence despite common mating sites: Genotypes and symbiotypes shed light on cryptic diversity in the black bean aphid species complex 尽管有共同的交配场所，但仍存在生态差异：基因型和共生型揭示了黑豆蚜种群的隐秘多样性。

IF 3.8 2区生物学

Heredity Pub Date : 2024-05-14 DOI: 10.1038/s41437-024-00687-0

Elena Gimmi, Jesper Wallisch, Christoph Vorburger

{"title":"Ecological divergence despite common mating sites: Genotypes and symbiotypes shed light on cryptic diversity in the black bean aphid species complex","authors":"Elena Gimmi, Jesper Wallisch, Christoph Vorburger","doi":"10.1038/s41437-024-00687-0","DOIUrl":"10.1038/s41437-024-00687-0","url":null,"abstract":"Different host plants represent ecologically dissimilar environments for phytophagous insects. The resulting divergent selection can promote the evolution of specialized host races, provided that gene flow is reduced between populations feeding on different plants. In black bean aphids belonging to the Aphis fabae complex, several morphologically cryptic taxa have been described based on their distinct host plant preferences. However, host choice and mate choice are largely decoupled in these insects: they are host-alternating and migrate between specific summer host plants and shared winter hosts, with mating occurring on the shared hosts. This provides a yearly opportunity for gene flow among aphids using different summer hosts, and raises the question if and to what extent the ecologically defined taxa are reproductively isolated. Here, we analyzed a geographically and temporally structured dataset of microsatellite genotypes from A. fabae that were mostly collected from their main winter host Euonymus europaeus, and additionally from another winter host and fourteen summer hosts. The data reveals multiple, strongly differentiated genetic clusters, which differ in their association with different summer and winter hosts. The clusters also differ in the frequency of infection with two heritable, facultative endosymbionts, separately hinting at reproductive isolation and divergent ecological selection. Furthermore, we found evidence for occasional hybridization among genetic clusters, with putative hybrids collected more frequently in spring than in autumn. This suggests that similar to host races in other phytophagous insects, both prezygotic and postzygotic barriers including selection against hybrids maintain genetic differentiation among A. fabae taxa, despite a common mating habitat.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"132 6","pages":"320-330"},"PeriodicalIF":3.8,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00687-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140922135","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}

引用次数: 0

Correction: Meiosis at three loci in autotetraploids: Probabilities of gamete modes and genotypes without and with preferential cross-over formation 更正：自交系三个位点的减数分裂：没有和有优先交叉形成的配子模式和基因型的概率。

IF 3.8 2区生物学

Heredity Pub Date : 2024-05-08 DOI: 10.1038/s41437-024-00686-1

Cortland K. Griswold, Saira Asif

引用次数: 0

Ecotype variation in the endemic tree Callicarpa subpubescens on small oceanic islands: genetic, phenotypic, and environmental insights 海洋小岛上特有树种 Callicarpa subpubescens 的生态型变异：遗传、表型和环境分析。

IF 3.8 2区生物学

Heredity Pub Date : 2024-05-07 DOI: 10.1038/s41437-024-00684-3

Suzuki Setsuko, Kyoko Sugai, Ichiro Tamaki, Kayo Hayama, Hidetoshi Kato

{"title":"Ecotype variation in the endemic tree Callicarpa subpubescens on small oceanic islands: genetic, phenotypic, and environmental insights","authors":"Suzuki Setsuko, Kyoko Sugai, Ichiro Tamaki, Kayo Hayama, Hidetoshi Kato","doi":"10.1038/s41437-024-00684-3","DOIUrl":"10.1038/s41437-024-00684-3","url":null,"abstract":"Callicarpa subpubescens, endemic to the Ogasawara Islands, is suggested to have multiple ecotypes in the Hahajima Islands, specifically in the central part of the Ogasawara Islands. In this study, associations between genetic groups and spatial distribution, habitat, leaf morphology, size structure, and flowering time of each genetic group were investigated on Hahajima and the satellite Imoutojima Islands. Genetic groups were identified using EST-SSR markers, revealing four ecotypes named based on morphological features: Dwarf (D), Glabrescent (G), Tall (T), and Middle (M), with M being a result of the hybridization of G and T. Ecotype D, adapted to dry environments, is characterized by small tree size, dense thick leaves with abundant hairs, and is distributed in dry scrub. Ecotype G, adapted to understory of mesic forests, lacks leaf hairs. Ecotype T, adapted to the canopy of mesic forests, has hairy leaves and is tall in tree height. Ecotype M, adapted to the canopy of mesic scrub or edges of mesic forests, has hairy leaves but with a shorter tree height than ecotype T. Flowering peaks differed among all ecotype pairs except G and M, but the flowering times more or less overlapped among all ecotypes, suggesting that pre-mating isolation among ecotypes is not perfect. Post-mating isolation is considered absent, as there were no differences in the results, germination, and survival rates of one-year seedlings among inter- and intra-ecotype crossings. The existence of such ecotypes provides valuable insights into the ongoing speciation processes adapting to the oceanic island environments.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"132 6","pages":"309-319"},"PeriodicalIF":3.8,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140876345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A historical stepping-stone path for an island-colonizing cactus across a submerged “bridge” archipelago 岛屿殖民仙人掌跨越水下 "桥梁 "群岛的历史性阶梯路径

IF 3.8 2区生物学

Heredity Pub Date : 2024-04-18 DOI: 10.1038/s41437-024-00683-4

Fernando Faria Franco, Danilo Trabuco Amaral, Isabel A. S. Bonatelli, Jared B. Meek, Evandro Marsola Moraes, Daniela Cristina Zappi, Nigel Paul Taylor, Deren A. R. Eaton

{"title":"A historical stepping-stone path for an island-colonizing cactus across a submerged “bridge” archipelago","authors":"Fernando Faria Franco, Danilo Trabuco Amaral, Isabel A. S. Bonatelli, Jared B. Meek, Evandro Marsola Moraes, Daniela Cristina Zappi, Nigel Paul Taylor, Deren A. R. Eaton","doi":"10.1038/s41437-024-00683-4","DOIUrl":"10.1038/s41437-024-00683-4","url":null,"abstract":"Here we use population genomic data (ddRAD-Seq) and ecological niche modeling to test biogeographic hypotheses for the divergence of the island-endemic cactus species Cereus insularis Hemsl. (Cereeae; Cactaceae) from its sister species C. fernambucensis Lem. The Cereus insularis grows in the Fernando de Noronha Islands (FNI), a Neotropical archipelago located 350 km off the Brazilian Atlantic Forest (BAF) coast. Phylogeographic reconstructions support a northward expansion by the common ancestor of C. insularis and C. fernambucensis along the mainland BAF coast, with C. insularis diverging from the widespread mainland taxon C. fernambucensis after colonizing FNI in the late Pleistocene. The morphologically distinct C. insularis is monophyletic and nested within C. fernambucensis, as expected from a progenitor-derivative speciation model. We tested alternative biogeographic and demographic hypotheses for the colonization of the FNI using Approximate Bayesian Computation. We found the greatest support for a stepping-stone path that emerged during periods of decreased sea level (the “bridge” hypothesis), in congruence with historical ecological niche modeling that shows highly suitable habitats on stepping-stone islands during glacial periods. The outlier analyses reveal signatures of selection in C. insularis, suggesting a putative role of adaptation driving rapid anagenic differentiation of this species in FNI.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"132 6","pages":"296-308"},"PeriodicalIF":3.8,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140611196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genetic structure and landscape effects on gene flow in the Neotropical lizard Norops brasiliensis (Squamata: Dactyloidae) 新热带蜥蜴 Norops brasiliensis（Squamata: Dactyloidae）的基因结构和景观对基因流动的影响

IF 3.8 2区生物学

Heredity Pub Date : 2024-04-04 DOI: 10.1038/s41437-024-00682-5

Emanuel M. Fonseca, Nathaniel S. Pope, William E. Peterman, Fernanda P. Werneck, Guarino R. Colli, Bryan C. Carstens

{"title":"Genetic structure and landscape effects on gene flow in the Neotropical lizard Norops brasiliensis (Squamata: Dactyloidae)","authors":"Emanuel M. Fonseca, Nathaniel S. Pope, William E. Peterman, Fernanda P. Werneck, Guarino R. Colli, Bryan C. Carstens","doi":"10.1038/s41437-024-00682-5","DOIUrl":"10.1038/s41437-024-00682-5","url":null,"abstract":"One key research goal of evolutionary biology is to understand the origin and maintenance of genetic variation. In the Cerrado, the South American savanna located primarily in the Central Brazilian Plateau, many hypotheses have been proposed to explain how landscape features (e.g., geographic distance, river barriers, topographic compartmentalization, and historical climatic fluctuations) have promoted genetic structure by mediating gene flow. Here, we asked whether these landscape features have influenced the genetic structure and differentiation in the lizard species Norops brasiliensis (Squamata: Dactyloidae). To achieve our goal, we used a genetic clustering analysis and estimate an effective migration surface to assess genetic structure in the focal species. Optimized isolation-by-resistance models and a simulation-based approach combined with machine learning (convolutional neural network; CNN) were then used to infer current and historical effects on population genetic structure through 12 unique landscape models. We recovered five geographically distributed populations that are separated by regions of lower-than-expected gene flow. The results of the CNN showed that geographic distance is the sole predictor of genetic variation in N. brasiliensis, and that slope, rivers, and historical climate had no discernible influence on gene flow. Our novel CNN approach was accurate (89.5%) in differentiating each landscape model. CNN and other machine learning approaches are still largely unexplored in landscape genetics studies, representing promising avenues for future research with increasingly accessible genomic datasets.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"132 6","pages":"284-295"},"PeriodicalIF":3.8,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00682-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140590920","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}

引用次数: 0