{"title":"SLRfinder:利用连锁不平衡聚类检测候选性连锁区域的方法。","authors":"Xueling Yi, Petri Kemppainen, Juha Merilä","doi":"10.1111/1755-0998.13985","DOIUrl":null,"url":null,"abstract":"<p>Despite their critical roles in genetic sex determination, sex chromosomes remain unknown in many non-model organisms, especially those having recently evolved sex-linked regions (SLRs). These evolutionarily young and labile sex chromosomes are important for understanding early sex chromosome evolution but are difficult to identify due to the lack of Y/W degeneration and SLRs limited to small genomic regions. Here, we present SLRfinder, a method to identify candidate SLRs using linkage disequilibrium (LD) clustering, heterozygosity and genetic divergence. SLRfinder does not rely on specific sequencing methods or a specific type of reference genome (e.g., from the homomorphic sex). In addition, the input of SLRfinder does not require phenotypic sexes, which may be unknown from population sampling, but sex information can be incorporated and is necessary to validate candidate SLRs. We tested SLRfinder using various published datasets and compared it to the local principal component analysis (PCA) method and the depth-based method Sex Assignment Through Coverage (SATC). As expected, the local PCA method could not be used to identify unknown SLRs. SATC works better on conserved sex chromosomes, whereas SLRfinder outperforms SATC in analysing labile sex chromosomes, especially when SLRs harbour inversions. Power analyses showed that SLRfinder worked better when sampling more populations that share the same SLR. If analysing one population, a relatively larger sample size (around 50) is needed for sufficient statistical power to detect significant SLR candidates, although true SLRs are likely always top-ranked. SLRfinder provides a novel and complementary approach for identifying SLRs and uncovering additional sex chromosome diversity in nature.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":null,"pages":null},"PeriodicalIF":5.5000,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13985","citationCount":"0","resultStr":"{\"title\":\"SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering\",\"authors\":\"Xueling Yi, Petri Kemppainen, Juha Merilä\",\"doi\":\"10.1111/1755-0998.13985\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>Despite their critical roles in genetic sex determination, sex chromosomes remain unknown in many non-model organisms, especially those having recently evolved sex-linked regions (SLRs). These evolutionarily young and labile sex chromosomes are important for understanding early sex chromosome evolution but are difficult to identify due to the lack of Y/W degeneration and SLRs limited to small genomic regions. Here, we present SLRfinder, a method to identify candidate SLRs using linkage disequilibrium (LD) clustering, heterozygosity and genetic divergence. SLRfinder does not rely on specific sequencing methods or a specific type of reference genome (e.g., from the homomorphic sex). In addition, the input of SLRfinder does not require phenotypic sexes, which may be unknown from population sampling, but sex information can be incorporated and is necessary to validate candidate SLRs. We tested SLRfinder using various published datasets and compared it to the local principal component analysis (PCA) method and the depth-based method Sex Assignment Through Coverage (SATC). As expected, the local PCA method could not be used to identify unknown SLRs. SATC works better on conserved sex chromosomes, whereas SLRfinder outperforms SATC in analysing labile sex chromosomes, especially when SLRs harbour inversions. Power analyses showed that SLRfinder worked better when sampling more populations that share the same SLR. If analysing one population, a relatively larger sample size (around 50) is needed for sufficient statistical power to detect significant SLR candidates, although true SLRs are likely always top-ranked. SLRfinder provides a novel and complementary approach for identifying SLRs and uncovering additional sex chromosome diversity in nature.</p>\",\"PeriodicalId\":211,\"journal\":{\"name\":\"Molecular Ecology Resources\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":5.5000,\"publicationDate\":\"2024-06-08\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13985\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Molecular Ecology Resources\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13985\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Ecology Resources","FirstCategoryId":"99","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13985","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering
Despite their critical roles in genetic sex determination, sex chromosomes remain unknown in many non-model organisms, especially those having recently evolved sex-linked regions (SLRs). These evolutionarily young and labile sex chromosomes are important for understanding early sex chromosome evolution but are difficult to identify due to the lack of Y/W degeneration and SLRs limited to small genomic regions. Here, we present SLRfinder, a method to identify candidate SLRs using linkage disequilibrium (LD) clustering, heterozygosity and genetic divergence. SLRfinder does not rely on specific sequencing methods or a specific type of reference genome (e.g., from the homomorphic sex). In addition, the input of SLRfinder does not require phenotypic sexes, which may be unknown from population sampling, but sex information can be incorporated and is necessary to validate candidate SLRs. We tested SLRfinder using various published datasets and compared it to the local principal component analysis (PCA) method and the depth-based method Sex Assignment Through Coverage (SATC). As expected, the local PCA method could not be used to identify unknown SLRs. SATC works better on conserved sex chromosomes, whereas SLRfinder outperforms SATC in analysing labile sex chromosomes, especially when SLRs harbour inversions. Power analyses showed that SLRfinder worked better when sampling more populations that share the same SLR. If analysing one population, a relatively larger sample size (around 50) is needed for sufficient statistical power to detect significant SLR candidates, although true SLRs are likely always top-ranked. SLRfinder provides a novel and complementary approach for identifying SLRs and uncovering additional sex chromosome diversity in nature.
期刊介绍:
Molecular Ecology Resources promotes the creation of comprehensive resources for the scientific community, encompassing computer programs, statistical and molecular advancements, and a diverse array of molecular tools. Serving as a conduit for disseminating these resources, the journal targets a broad audience of researchers in the fields of evolution, ecology, and conservation. Articles in Molecular Ecology Resources are crafted to support investigations tackling significant questions within these disciplines.
In addition to original resource articles, Molecular Ecology Resources features Reviews, Opinions, and Comments relevant to the field. The journal also periodically releases Special Issues focusing on resource development within specific areas.