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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.
45.2K
Phylogeny01:23

Phylogeny

43.7K
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.
43.7K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.7K
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...
5.7K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

7.0K
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...
7.0K
Synteny and Evolution02:31

Synteny and Evolution

3.2K
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.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
3.2K
Pedigree Analysis01:35

Pedigree Analysis

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Overview
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相关实验视频

Updated: Jun 6, 2025

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

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通过系统地扩展指向的非循环图,找到高后密度的族系.

Chris Jennings-Shaffer1, David H Rich1, Matthew Macaulay2

  • 1Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

ArXiv
|November 28, 2024
PubMed
概括

本研究引入了分拆定向非循环图 (sDAG),以改进贝叶斯系遗传分析. 将树木聚合到sDAG中更快,并且比以前的方法识别了更多可能的树木.

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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相关实验视频

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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
  • 统计方法 统计方法

背景情况:

  • 贝叶斯系遗传学通常使用马尔科夫链蒙特卡洛 (MCMC) 进行后部分布估计.
  • MCMC 方法通过使用局部重新排列的随机步行来探索树木空间.
  • 以前的系统搜索尝试受到大量可能的树木的阻碍.

研究的目的:

  • 开发新的方法,以有效地探索贝叶斯系遗传学中的树木空间.
  • 为了利用分拆定向非循环图 (sDAG) 来同时表示多个树.
  • 为了更有效地识别具有高后密度的树木集合.

主要方法:

  • 使用分拆定向非循环图 (sDAG) 来表示一组树.
  • 在SDAG上开发引入,排序和选择本地重组的方法.
  • 将基于sDAG的新型系统搜索与传统的MCMC随机步行进行比较.

主要成果:

  • 一种拟议的方法成功地在各种数据集中恢复了高后密度树.
  • 一个更简单的策略是将树集成到sDAG中,这在计算上被证明是更快的.
  • sDAG聚合方法产生了更高比例的可能树.

结论:

  • sDAG提供了一个强大的框架,用于增强贝叶斯的遗传学推理.
  • 将树集成为一个sDAG是一个计算效率高的策略.
  • 这种方法改善了在植物遗传学分析中识别可能的树木.