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Phylogenetic Trees

Phylogenetic Trees

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.

What is Variation?

What is Variation?

Apart from the measures of central tendency, distribution, outliers, and the changing characteristics of data with time, an important characteristic of any data set is its variation or spread. In some data sets, the data values are concentrated closely near the mean; in others, the data values are more widely spread out from the mean.
The range, standard deviation, standard error, and variance are the different measures of variation.
Range: The range is the difference between its maximum and...

Conservative Site-specific Recombination and Phase Variation

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...

Systematic Error: Methodological and Sampling Errors

Systematic Error: Methodological and Sampling Errors

In the case of systematic errors, the sources can be identified, and the errors can be subsequently minimized by addressing these sources. According to the source, systematic errors can be divided into sampling, instrumental, methodological, and personal errors.
Sampling errors originate from improper sampling methods or the wrong sample population. These errors can be minimized by refining the sampling strategy. Defective instruments or faulty calibrations are the sources of instrumental...

Fundamental Attribution Error

Fundamental Attribution Error

According to some social psychologists, people tend to overemphasize internal factors as explanations—or attributions—for the behavior of other people. They tend to assume that the behavior of another person is a trait of that person, and to underestimate the power of the situation on the behavior of others. They tend to fail to recognize when the behavior of another is due to situational variables, and thus to the person’s state. This erroneous assumption is...

Variation

Variation

An important characteristic of any set of data is the variation in the data. In some data sets, the data values are concentrated closely near the mean; in other data sets, the data values are more widely spread out from the mean. The most common measure of variation, or spread, is the standard deviation, which is the square root of variance.
When independent and dependent variables are plotted on a scatter plot, the slope of a line is a value that describes the rate of change between the two...

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Updated: Feb 11, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

パンデミック規模の系統学におけるレート変動と再発的配列エラー

Nicola De Maio¹, Myrthe Willemsen^2,3, Samuel Martin²

¹European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridgeshire, UK. demaio@ebi.ac.uk.

|February 9, 2026

まとめ

この要約は機械生成です。

この研究は、数百万の病原体ゲノムの系統推論を強化し、突然変異率の変動と配列エラーを考慮することで精度を向上させます。これにより、SARS-CoV-2のようなウイルスの信頼性の高い進化史が提供されます。

キーワード:

系統発生ゲノム SARS-CoV-2 進化突然変異配列エラー

さらに関連する動画

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

関連する実験動画

Last Updated: Feb 11, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

科学分野:

ゲノミクス
進化的生物学
計算生物学

背景:

病原体ゲノムの系統解析は、特にCOVID-19のようなパンデミック時には、進化と伝播を理解するために不可欠です。
最近の方法により、数百万のゲノムを解析するパンデミック規模の系統推論が可能になっています。
再発的突然変異やエラーによるホモプラジーは、系統再構築における不確実性とバイアスをもたらします。

研究の目的:

パンデミック規模の系統学の計算パフォーマンスと精度を向上させるアルゴリズムとモデルを開発すること。
大規模ゲノムデータにおける突然変異率の変動と再発的配列エラーによってもたらされる課題に対処すること。

主な方法:

系統推論のための新しいアルゴリズムとモデルを開発しました。
突然変異率の変動を特定し、考慮する方法を組み込みました。
再発的配列エラーを検出し、修正するための戦略を実装しました。

主要な成果:

パンデミック規模の系統学における計算パフォーマンスと精度の実質的な向上を達成しました。
信頼性が高く、公開されている配列アラインメントと系統樹を再構築しました。
この解析には、200万以上の重症急性呼吸器症候群コロナウイルス2（SARS-CoV-2）ゲノムが含まれていました。

結論:

開発された方法は、大規模ゲノムデータに対する系統学により正確で計算効率の高いアプローチを提供します。
再構築された系統樹は、2023年2月までのSARS-CoV-2の進化史と世界的な広がりに関する洞察を提供します。
この研究は、世界的な健康危機における病原体の進化を追跡し、理解する能力を高めます。