通过多核酸替代的进化快捷方式及其对自然选择分析的影响
Alexander G Lucaci1, Jordan D Zehr1, David Enard2
1Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.
Molecular biology and evolution
|July 3, 2023
概括
对多核酸 (MH) 替代和同义速率变化 (SRV) 的计算改善了进化选择分析. 纳入这些因素可以减少对正选择的假阳性,提高进化研究的准确性.
科学领域:
- 进化生物学是进化的生物学.
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 进化过程的统计模型在很大程度上依赖于关于替代模式的假设.
- 建模中的简化,例如忽视多核酸 (MH) 替代或同义速率变化 (SRV),可能会导致参数估计偏差,并导致关于自然选择的不准确结论.
- 之前的研究表明,忽视MH替代和SRV可能会导致虚假阳性,从而使情节性选择多样化.
研究的目的:
- 开发一个综合分析框架和软件工具,同时考虑选择分析中的MH替代和SRV.
- 调查在经验性对齐中MH和SRV的流行率及其对检测积极选择的影响.
- 识别特定的进化场景,如短分支,MH替代在其中显著影响选择检测.
主要方法:
- 开发一个综合分析框架和相关的软件工具.
- 对实证对齐的分析,以评估MH和SRV的无处不在.
- 模拟研究评估新模型的统计性能和功率.
- 详细检查基准对准和对准区域的高分辨率分析,支持积极选择.
主要成果:
- 在实证对齐中,MH替代和SRV广泛存在.
- 纳入MH和SRV将正选择的检测减少了1.4倍,并改变了推断的进化速率分布.
- 模拟研究证实,观察到的效应不是由于使用更复杂的模型而减少的统计能力.
- 在较短的进化分支上的MH替代被确定为选择检测差异的关键因素.
结论:
- 该研究强调了MH替代和SRV对自然选择推断的关键影响.
- 开发的框架提供了一种更准确和更强大的方法来检测正选择,通过考虑这些进化复杂性.
- 建议选择分析经常考虑包括MH替代品以提高可靠性.
- 这些发现挑战了比较基因组学中长期存在的建模假设,并为更准确的进化分析提供了实际解决方案.
更多相关视频
08:46Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms
Published on: December 9, 2015
10.6K
18:10Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
Published on: June 16, 2011
29.6K
相关概念视频
Gene Evolution - Fast or Slow?
7.2K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.2K
Exon Recombination
3.6K
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon...
Exon shuffling follows “splice frame rules.” Each exon...
3.6K
Limits to Natural Selection
31.4K
Organisms that are well-adapted to their environment are more likely to survive and reproduce. However, natural selection does not lead to perfectly adapted organisms. Several factors constrain natural selection.
31.4K
Multi-species Conserved Sequences
4.0K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.0K
Mutations in Microorganisms
33
Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...
33
Single Nucleotide Polymorphisms-SNPs
15.3K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
15.3K
