Heredity最新文献_第7页

Long-term climatic stability drives accumulation and maintenance of divergent freshwater fish lineages in a temperate biodiversity hotspot 长期的气候稳定性推动了温带生物多样性热点地区淡水鱼系分化的积累和维持。

IF 3.1 2区生物学

Heredity Pub Date : 2024-06-25 DOI: 10.1038/s41437-024-00700-6

Sean James Buckley, Chris J. Brauer, Peter J. Unmack, Michael P. Hammer, Mark Adams, Stephen J. Beatty, David L. Morgan, Luciano B. Beheregaray

{"title":"Long-term climatic stability drives accumulation and maintenance of divergent freshwater fish lineages in a temperate biodiversity hotspot","authors":"Sean James Buckley, Chris J. Brauer, Peter J. Unmack, Michael P. Hammer, Mark Adams, Stephen J. Beatty, David L. Morgan, Luciano B. Beheregaray","doi":"10.1038/s41437-024-00700-6","DOIUrl":"10.1038/s41437-024-00700-6","url":null,"abstract":"Anthropogenic climate change is forecast to drive regional climate disruption and instability across the globe. These impacts are likely to be exacerbated within biodiversity hotspots, both due to the greater potential for species loss but also to the possibility that endemic lineages might not have experienced significant climatic variation in the past, limiting their evolutionary potential to respond to rapid climate change. We assessed the role of climatic stability on the accumulation and persistence of lineages in an obligate freshwater fish group endemic to the southwest Western Australia (SWWA) biodiversity hotspot. Using 19,426 genomic (ddRAD-seq) markers and species distribution modelling, we explored the phylogeographic history of western (Nannoperca vittata) and little (Nannoperca pygmaea) pygmy perches, assessing population divergence and phylogenetic relationships, delimiting species and estimating changes in species distributions from the Pliocene to 2100. We identified two deep phylogroups comprising three divergent clusters, which showed no historical connectivity since the Pliocene. We conservatively suggest these represent three isolated species with additional intraspecific structure within one widespread species. All lineages showed long-term patterns of isolation and persistence owing to climatic stability but with significant range contractions likely under future climate change. Our results highlighted the role of climatic stability in allowing the persistence of isolated lineages in the SWWA. This biodiversity hotspot is under compounding threat from ongoing climate change and habitat modification, which may further threaten previously undetected cryptic diversity across the region.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 3","pages":"149-159"},"PeriodicalIF":3.1,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00700-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141450367","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 and environmental effects on morphological traits of social phenotypes in wasps 遗传和环境对黄蜂社会表型形态特征的影响。

IF 3.1 2区生物学

Heredity Pub Date : 2024-06-25 DOI: 10.1038/s41437-024-00701-5

Sarah E. Orr, Nicole A. Hedrick, Kayla A. Murray, Abhinav K. Pasupuleti, Jennifer L. Kovacs, Michael A. D. Goodisman

{"title":"Genetic and environmental effects on morphological traits of social phenotypes in wasps","authors":"Sarah E. Orr, Nicole A. Hedrick, Kayla A. Murray, Abhinav K. Pasupuleti, Jennifer L. Kovacs, Michael A. D. Goodisman","doi":"10.1038/s41437-024-00701-5","DOIUrl":"10.1038/s41437-024-00701-5","url":null,"abstract":"Many species exhibit distinct phenotypic classes, such as sexes in dioecious species or castes in social species. The evolution of these classes is affected by the genetic architecture governing traits shared between phenotypes. However, estimates of the genetic and environmental factors contributing to phenotypic variation in distinct classes have rarely been examined. We studied the genetic architecture underlying morphological traits in phenotypic classes in the social wasp Vespula maculifrons. Our data revealed patriline effects on a few traits, indicating weak genetic influences on caste phenotypic variation. Interestingly, traits exhibited higher heritability in queens than workers. This result suggests that genetic variation has a stronger influence on trait variation in the queen caste than the worker caste, which is unexpected because queens typically experience direct selection. Moreover, estimates of heritability for traits were correlated between the castes, indicating that variability in trait size was governed by similar genetic architecture in the two castes. However, we failed to find evidence for a significant relationship between caste dimorphism and caste correlation, as would be expected if trait evolution was constrained by intralocus genetic conflict. Our analyses also uncovered variation in the allometric relationships for traits. These analyses suggested that worker traits were proportionally smaller than queen traits for most traits examined. Overall, our data provide evidence for a strong environmental and moderate genetic basis of trait variation among castes. Moreover, our results suggest that selection previously operated on caste phenotype in this species, and phenotypic variation is now governed primarily by environmental differences.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 2","pages":"126-136"},"PeriodicalIF":3.1,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11286790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141450366","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

Rolling down that mountain: microgeographical adaptive divergence during a fast population expansion along a steep environmental gradient in European beech 滚下那座山：欧洲山毛榉沿陡峭环境梯度快速种群扩张过程中的微地理适应性分化。

IF 3.1 2区生物学

Heredity Pub Date : 2024-06-18 DOI: 10.1038/s41437-024-00696-z

Andrea Modica, Hadrien Lalagüe, Sylvie Muratorio, Ivan Scotti

{"title":"Rolling down that mountain: microgeographical adaptive divergence during a fast population expansion along a steep environmental gradient in European beech","authors":"Andrea Modica, Hadrien Lalagüe, Sylvie Muratorio, Ivan Scotti","doi":"10.1038/s41437-024-00696-z","DOIUrl":"10.1038/s41437-024-00696-z","url":null,"abstract":"Forest tree populations harbour high genetic diversity thanks to large effective population sizes and strong gene flow, allowing them to diversify through adaptation to local environmental pressures within dispersal distance. Many tree populations also experienced historical demographic fluctuations, including spatial population contraction or expansions at various temporal scales, which may constrain their ability to adapt to environmental variations. Our aim is to investigate how recent contraction and expansion events interfere with local adaptation, by studying patterns of adaptive divergence between closely related stands undergoing environmentally contrasted conditions, and having or not recently expanded. To investigate genome-wide signatures of local adaptation while accounting for demography, we analysed divergence in a European beech population by testing pairwise differentiation among four tree stands at ~35k Single Nucleotide Polymorphisms from ~9k genomic regions. We applied three divergence outlier search methods resting on different assumptions and targeting either single SNPs or contiguous genomic regions, while accounting for the effect of population size variations on genetic divergence. We found 27 signals of selective signatures in 19 target regions. Putatively adaptive divergence involved all stand pairs. We retrieved signals both when comparing old-growth stands and recently colonised areas and when comparing stands within the old-growth area. Therefore, adaptive divergence processes have taken place both over short time spans, under strong environmental contrasts, and over short ecological gradients, in populations that have been stable in the long term. This suggests that standing genetic variation supports local, microgeographic divergence processes, which can maintain genetic diversity at the landscape level.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 2","pages":"99-112"},"PeriodicalIF":3.1,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11286953/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141418694","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

Evidence for gene flow and trait reversal during radiation of Mexican Goodeid fish 墨西哥古德鱼辐射过程中基因流动和性状逆转的证据。

IF 3.1 2区生物学

Heredity Pub Date : 2024-06-10 DOI: 10.1038/s41437-024-00694-1

Leeban H. Yusuf, Yolitzi Saldívar Lemus, Peter Thorpe, Constantino Macías Garcia, Michael G. Ritchie

{"title":"Evidence for gene flow and trait reversal during radiation of Mexican Goodeid fish","authors":"Leeban H. Yusuf, Yolitzi Saldívar Lemus, Peter Thorpe, Constantino Macías Garcia, Michael G. Ritchie","doi":"10.1038/s41437-024-00694-1","DOIUrl":"10.1038/s41437-024-00694-1","url":null,"abstract":"Understanding the phylogeographic history of a group and identifying the factors contributing to speciation is an important challenge in evolutionary biology. The Goodeinae are a group of live-bearing fishes endemic to Mexico. Here, we develop genomic resources for species within the Goodeinae and use phylogenomic approaches to characterise their evolutionary history. We sequenced, assembled and annotated the genomes of four Goodeinae species, including Ataeniobius toweri, the only matrotrophic live-bearing fish without a trophotaenia in the group. We estimated timings of species divergence and examined the extent and timing of introgression between the species to assess if this may have occurred during an early radiation, or in more recent episodes of secondary contact. We used branch-site models to detect genome-wide positive selection across Goodeinae, and we specifically asked whether this differs in A. toweri, where loss of placental viviparity has recently occurred. We found evidence of gene flow between geographically isolated species, suggesting vicariant speciation was supplemented by limited post-speciation gene flow, and gene flow may explain previous uncertainties about Goodeid phylogeny. Genes under positive selection in the group are likely to be associated with the switch to live-bearing. Overall, our studies suggest that both volcanism-driven vicariance and changes in reproductive mode influenced radiation in the Goodeinae.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 2","pages":"78-87"},"PeriodicalIF":3.1,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11286751/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300565","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

Why we thrive beneath a northern sky – genomic signals of selection in apple for adaptation to northern Sweden 我们为何在北方的天空下茁壮成长--苹果适应瑞典北部的基因组选择信号。

IF 3.1 2区生物学

Heredity Pub Date : 2024-06-04 DOI: 10.1038/s41437-024-00693-2

J. Skytte af Sätra, L. Garkava-Gustavsson, P. K. Ingvarsson

{"title":"Why we thrive beneath a northern sky – genomic signals of selection in apple for adaptation to northern Sweden","authors":"J. Skytte af Sätra, L. Garkava-Gustavsson, P. K. Ingvarsson","doi":"10.1038/s41437-024-00693-2","DOIUrl":"10.1038/s41437-024-00693-2","url":null,"abstract":"Good understanding of the genomic regions underlying adaptation of apple to boreal climates is needed to facilitate efficient breeding of locally adapted apple cultivars. Proper infrastructure for phenotyping and evaluation is essential for identification of traits responsible for adaptation, and dissection of their genetic composition. However, such infrastructure is costly and currently not available for the boreal zone of northern Sweden. Therefore, we used historical pomological data on climate adaptation of 59 apple cultivars and whole genome sequencing to identify genomic regions that have undergone historical selection among apple cultivars recommended for cultivation in northern Sweden. We found the apple collection to be composed of two ancestral groups that are largely concordant with the grouping into ‘hardy’ and ‘not hardy’ cultivars based on the pomological literature. Using a number of genome-wide scans for signals of selection, we obtained strong evidence of positive selection at a genomic region around 29 MbHFTH1 of chromosome 1 among apple cultivars in the ‘hardy’ group. Using phased genotypic data from the 20 K apple Infinium® SNP array, we identified haplotypes associated with the two cultivar groups and traced transmission of these haplotypes through the pedigrees of some apple cultivars. This demonstrates that historical data from pomological literature can be analyzed by population genomic approaches as a step towards revealing the genomic control of a key property for a horticultural niche market. Such knowledge is needed to facilitate efficient breeding strategies for development of locally adapted apple cultivars in the future. The current study illustrates the response to a very strong selective pressure imposed on tree crops by climatic factors, and the importance of genetic research on this topic and feasibility of breeding efforts in the light of the ongoing climate change.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 2","pages":"67-77"},"PeriodicalIF":3.1,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11286948/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141247246","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

The structure of the TH/INS locus and the parental allele expressed are not conserved between mammals TH/INS基因座的结构和表达的亲本等位基因在哺乳动物之间并不一致。

IF 3.1 2区生物学

Heredity Pub Date : 2024-06-04 DOI: 10.1038/s41437-024-00689-y

Trent Newman, Teruhito Ishihara, Geoff Shaw, Marilyn B. Renfree

{"title":"The structure of the TH/INS locus and the parental allele expressed are not conserved between mammals","authors":"Trent Newman, Teruhito Ishihara, Geoff Shaw, Marilyn B. Renfree","doi":"10.1038/s41437-024-00689-y","DOIUrl":"10.1038/s41437-024-00689-y","url":null,"abstract":"Parent-of-origin-specific expression of imprinted genes is critical for successful mammalian growth and development. Insulin, coded by the INS gene, is an important growth factor expressed from the paternal allele in the yolk sac placenta of therian mammals. The tyrosine hydroxylase gene TH encodes an enzyme involved in dopamine synthesis. TH and INS are closely associated in most vertebrates, but the mouse orthologues, Th and Ins2, are separated by repeated DNA. In mice, Th is expressed from the maternal allele, but the parental origin of expression is not known for any other mammal so it is unclear whether the maternal expression observed in the mouse represents an evolutionary divergence or an ancestral condition. We compared the length of the DNA segment between TH and INS across species and show that separation of these genes occurred in the rodent lineage with an accumulation of repeated DNA. We found that the region containing TH and INS in the tammar wallaby produces at least five distinct RNA transcripts: TH, TH-INS1, TH-INS2, lncINS and INS. Using allele-specific expression analysis, we show that the TH/INS locus is expressed from the paternal allele in pre- and postnatal tammar wallaby tissues. Determining the imprinting pattern of TH/INS in other mammals might clarify if paternal expression is the ancestral condition which has been flipped to maternal expression in rodents by the accumulation of repeat sequences.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 1","pages":"21-32"},"PeriodicalIF":3.1,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00689-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141247245","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

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