正向选择对血清果蝇基因组变异的影响:深度学习方法的启示

IF 4.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Yiguan Wang, Scott L. Allen, Adam J. Reddiex, Stephen F. Chenoweth
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引用次数: 0

摘要

本研究通过对110个全基因组序列进行综合分析,探讨了正选择对澳大利亚东部血清果蝇种群遗传组成的影响。利用先进的深度学习算法(partialS/HIC)和一系列推断的人口历史,我们发现约14%的基因组直接受到横扫的影响,其中软横扫(10.6%)比硬横扫(2.1%)更普遍,而部分横扫则不常见(1.3%)。该算法在对完全横扫进行分类时表现出了对人口学假设的稳健性,但在人口学误设的情况下,该算法在区分中性区域与部分横扫和关联区域时面临挑战。研究结果揭示了基因扫面通过连接对近三分之二的基因组产生了间接影响,其中假定有害变体的比例过高,这表明正选择由于搭有益基因座的便车而将有害变体拖向了更高的频率。基因本体富集分析进一步支持了我们对横扫检测准确性的信心,因为在硬横扫中检测到了一些由于进化军备竞赛而预计会受到正选择的性状(如免疫力)。这项研究为了解正选择在塑造自然种群基因组变异中的直接和间接作用提供了宝贵的见解。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach

The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach

This study explores the impact of positive selection on the genetic composition of a Drosophila serrata population in eastern Australia through a comprehensive analysis of 110 whole genome sequences. Utilizing an advanced deep learning algorithm (partialS/HIC) and a range of inferred demographic histories, we identified that approximately 14% of the genome is directly affected by sweeps, with soft sweeps being more prevalent (10.6%) than hard sweeps (2.1%), and partial sweeps being uncommon (1.3%). The algorithm demonstrated robustness to demographic assumptions in classifying complete sweeps but faced challenges in distinguishing neutral regions from partial sweeps and linked regions under demographic misspecification. The findings reveal the indirect influence of sweeps on nearly two-thirds of the genome through linkage, with an over-representation of putatively deleterious variants suggesting that positive selection drags deleterious variants to higher frequency due to hitchhiking with beneficial loci. Gene ontology enrichment analysis further supported our confidence in the accuracy of sweep detection as several traits expected to be under positive selection due to evolutionary arms races (e.g. immunity) were detected in hard sweeps. This study provides valuable insights into the direct and indirect contributions of positive selection in shaping genomic variation in natural populations.

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来源期刊
Molecular Ecology
Molecular Ecology 生物-进化生物学
CiteScore
8.40
自引率
10.20%
发文量
472
审稿时长
1 months
期刊介绍: Molecular Ecology publishes papers that utilize molecular genetic techniques to address consequential questions in ecology, evolution, behaviour and conservation. Studies may employ neutral markers for inference about ecological and evolutionary processes or examine ecologically important genes and their products directly. We discourage papers that are primarily descriptive and are relevant only to the taxon being studied. Papers reporting on molecular marker development, molecular diagnostics, barcoding, or DNA taxonomy, or technical methods should be re-directed to our sister journal, Molecular Ecology Resources. Likewise, papers with a strongly applied focus should be submitted to Evolutionary Applications. Research areas of interest to Molecular Ecology include: * population structure and phylogeography * reproductive strategies * relatedness and kin selection * sex allocation * population genetic theory * analytical methods development * conservation genetics * speciation genetics * microbial biodiversity * evolutionary dynamics of QTLs * ecological interactions * molecular adaptation and environmental genomics * impact of genetically modified organisms
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