通过分析适应度效应的充分分布来检测驯化信号。

Peer community journal Pub Date : 2025-01-01 Epub Date: 2025-03-27 DOI:10.24072/pcjournal.540
David Castellano, Ioanna-Theoni Vourlaki, Ryan N Gutenkunst, Sebastian E Ramos-Onsins
{"title":"通过分析适应度效应的充分分布来检测驯化信号。","authors":"David Castellano, Ioanna-Theoni Vourlaki, Ryan N Gutenkunst, Sebastian E Ramos-Onsins","doi":"10.24072/pcjournal.540","DOIUrl":null,"url":null,"abstract":"<p><p>Domestication is a process marked by complex interactions between demographic changes and selective pressures, which together shape genetic diversity. While the phenotypic outcomes of domestication are well documented, its genetic basis-particularly the dynamics of selection-remain less well understood. To investigate these dynamics, we performed simulations designed to approximate the demographic history of large domestic mammals. These simulations used selection coefficients as a modeling tool to represent changes in selection pressures, recognizing that such coefficients are abstractions rather than direct representations of biological reality. Specifically, we analyzed site frequency spectra (SFS) under varying distributions of fitness effects (DFE) and proportions of mutations with divergent selective pressures. Our results show that the discretized deleterious DFE can be reliably inferred from the SFS of a single population, but reconstructing the beneficial DFE and demographic history remains challenging, even when using the joint SFS of both populations. We further developed a novel joint DFE inference model to estimate the proportion of mutations with divergent selection coefficients (<i>p</i> <sub>c</sub>), although we found that signals of classic hard sweeps can mimic increases in <i>p</i> <sub>c</sub>, complicating interpretation. These findings underscore both the utility and limitations of DFE inference and highlight the need for caution when interpreting demographic histories in domesticated populations based on such modeling assumptions.</p>","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"5 ","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12007895/pdf/","citationCount":"0","resultStr":"{\"title\":\"Detection of domestication signals through the analysis of the full distribution of fitness effects.\",\"authors\":\"David Castellano, Ioanna-Theoni Vourlaki, Ryan N Gutenkunst, Sebastian E Ramos-Onsins\",\"doi\":\"10.24072/pcjournal.540\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Domestication is a process marked by complex interactions between demographic changes and selective pressures, which together shape genetic diversity. While the phenotypic outcomes of domestication are well documented, its genetic basis-particularly the dynamics of selection-remain less well understood. To investigate these dynamics, we performed simulations designed to approximate the demographic history of large domestic mammals. These simulations used selection coefficients as a modeling tool to represent changes in selection pressures, recognizing that such coefficients are abstractions rather than direct representations of biological reality. Specifically, we analyzed site frequency spectra (SFS) under varying distributions of fitness effects (DFE) and proportions of mutations with divergent selective pressures. Our results show that the discretized deleterious DFE can be reliably inferred from the SFS of a single population, but reconstructing the beneficial DFE and demographic history remains challenging, even when using the joint SFS of both populations. We further developed a novel joint DFE inference model to estimate the proportion of mutations with divergent selection coefficients (<i>p</i> <sub>c</sub>), although we found that signals of classic hard sweeps can mimic increases in <i>p</i> <sub>c</sub>, complicating interpretation. These findings underscore both the utility and limitations of DFE inference and highlight the need for caution when interpreting demographic histories in domesticated populations based on such modeling assumptions.</p>\",\"PeriodicalId\":74413,\"journal\":{\"name\":\"Peer community journal\",\"volume\":\"5 \",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2025-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12007895/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Peer community journal\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.24072/pcjournal.540\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/3/27 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Peer community journal","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.24072/pcjournal.540","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/3/27 0:00:00","PubModel":"Epub","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0

摘要

驯化是一个以人口变化和选择压力之间复杂的相互作用为特征的过程,它们共同形成了遗传多样性。虽然驯化的表型结果有很好的文献记载,但其遗传基础——特别是选择的动力学——仍然不太清楚。为了研究这些动态,我们进行了模拟,以近似大型家养哺乳动物的人口历史。这些模拟使用选择系数作为建模工具来表示选择压力的变化,认识到这些系数是抽象的,而不是生物现实的直接表示。具体来说,我们分析了不同适应度效应(DFE)分布和不同选择压力下突变比例下的位点频谱(SFS)。我们的研究结果表明,离散化的有害DFE可以从单个种群的SFS中可靠地推断出来,但即使使用两个种群的联合SFS,重建有益DFE和人口历史仍然具有挑战性。我们进一步开发了一种新的联合DFE推理模型来估计具有发散选择系数(p c)的突变的比例,尽管我们发现经典硬扫描的信号可以模拟p c的增加,使解释复杂化。这些发现强调了DFE推断的效用和局限性,并强调了在基于这种建模假设解释驯化种群的人口历史时需要谨慎。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Detection of domestication signals through the analysis of the full distribution of fitness effects.

Domestication is a process marked by complex interactions between demographic changes and selective pressures, which together shape genetic diversity. While the phenotypic outcomes of domestication are well documented, its genetic basis-particularly the dynamics of selection-remain less well understood. To investigate these dynamics, we performed simulations designed to approximate the demographic history of large domestic mammals. These simulations used selection coefficients as a modeling tool to represent changes in selection pressures, recognizing that such coefficients are abstractions rather than direct representations of biological reality. Specifically, we analyzed site frequency spectra (SFS) under varying distributions of fitness effects (DFE) and proportions of mutations with divergent selective pressures. Our results show that the discretized deleterious DFE can be reliably inferred from the SFS of a single population, but reconstructing the beneficial DFE and demographic history remains challenging, even when using the joint SFS of both populations. We further developed a novel joint DFE inference model to estimate the proportion of mutations with divergent selection coefficients (p c), although we found that signals of classic hard sweeps can mimic increases in p c, complicating interpretation. These findings underscore both the utility and limitations of DFE inference and highlight the need for caution when interpreting demographic histories in domesticated populations based on such modeling assumptions.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
自引率
0.00%
发文量
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信