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相关概念视频

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Phylogenetic Trees03:21

Phylogenetic Trees

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Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
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Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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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...
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Phylogeny01:23

Phylogeny

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Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
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Synteny and Evolution02:31

Synteny and Evolution

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John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
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Survival Tree01:19

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Survival trees are a non-parametric method used in survival analysis to model the relationship between a set of covariates and the time until an event of interest occurs, often referred to as the "time-to-event" or "survival time." This method is particularly useful when dealing with censored data, where the event has not occurred for some individuals by the end of the study period, or when the exact time of the event is unknown.
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相关实验视频

Updated: Jun 23, 2025

A Practical Guide to Phylogenetics for Nonexperts
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走向一个半监督学习方法,对植物遗传学估计.

Daniele Silvestro1,2, Thibault Latrille3, Nicolas Salamin3

  • 1Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland.

Systematic biology
|June 25, 2024
PubMed
概括

深度学习模型准确地从序列对齐中推断出分子进化参数和进化速率. 这种方法超越了复杂的进化场景的传统方法,提高了家族遗传树的准确性.

关键词:
分子进化是分子进化的过程.遗传学上的推断.经常性的神经网络.模拟器模拟器模拟器模拟器替代率是指替代率的使用率.

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科学领域:

  • 计算生物学 计算生物学
  • 进化生物学 进化生物学
  • 机器学习 机器学习

背景情况:

  • 遗传学树的重建依赖于分子进化模型.
  • 传统模型与复杂的进化场景和大型数据集作斗争,需要简化假设.
  • 最大概率和贝叶斯推理是常见的参数估计方法.

研究的目的:

  • 开发一种深度学习模型,直接从序列数据中推断分子进化参数.
  • 为了估计每个地点的进化速率和差异,而没有预定义的家族遗传树.
  • 提高遗传学推断的准确性和可扩展性,特别是在复杂的进化模型下.

主要方法:

  • 将基因组进化的随机模拟与监督深度学习模型相结合.
  • 对多个序列对齐的直接分析,以估计每个地点的进化速率.
  • 将深度学习衍生率集成到贝叶斯族的基因结构框架中.

主要成果:

  • 深度学习模型的预测与基于概率的推断对简单速率异质性 (马分布) 进行了匹配.
  • 性能明显超过了复杂速率变化的传统方法 (例如,密码子模型).
  • 对大型基因组数据集的可扩展应用证明了2600万个核酸.
  • 深度学习率的整合提高了家族遗传推断的准确性,特别是分支长度.

结论:

  • 深度学习提供了一种强大的,可扩展的方法来推断分子进化参数.
  • 这种方法克服了复杂进化场景中传统模型的局限性.
  • 一种半监督式学习方法,结合了深度学习和概率推理,有望在遗传学中取得未来的进步.