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Lecture

Constructing Phylogenetic Trees: UPGMA Algorithm

In course

BIO-109: Introduction to life sciences (for IC)

Ce cours présente les principes fondamentaux à l'œuvre dans les organismes vivants. Autant que possible, l'accent est mis sur les contributions de l'Informatique aux progrès des Sciences de la Vie. ...

Description

This lecture introduces the UPGMA algorithm for constructing phylogenetic trees, explaining its simplicity and historical significance. The instructor discusses the importance of choosing relevant genes, aligning sequences, calculating distances, and iteratively building the tree. The lecture also touches on evolutionary concepts, genetic distances, and the implications of molecular clocks. Through practical examples and explanations, students learn how to apply the UPGMA algorithm to analyze genetic relationships and evolutionary divergence.

Instructor

Romain Zufferey

Official source

Related concepts (26)

Molecular phylogenetics

Molecular phylogenetics (məˈlɛkjᵿlər_ˌfaɪloʊdʒəˈnɛtɪks,_mɒ-,_moʊ-) is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to determine the processes by which diversity among species has been achieved. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree.

Molecular clock

The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA, RNA, or amino acid sequences for proteins. The benchmarks for determining the mutation rate are often fossil or archaeological dates. The molecular clock was first tested in 1962 on the hemoglobin protein variants of various animals, and is commonly used in molecular evolution to estimate times of speciation or radiation.

Genetic distance

Genetic distance is a measure of the genetic divergence between species or between populations within a species, whether the distance measures time from common ancestor or degree of differentiation. Populations with many similar alleles have small genetic distances. This indicates that they are closely related and have a recent common ancestor. Genetic distance is useful for reconstructing the history of populations, such as the multiple human expansions out of Africa. It is also used for understanding the origin of biodiversity.

Phylogenetic tree

A phylogenetic tree (also phylogeny or evolutionary tree) is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. All life on Earth is part of a single phylogenetic tree, indicating common ancestry. In a rooted phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants, and the edge lengths in some trees may be interpreted as time estimates.

Phylogenetics

In biology, phylogenetics (ˌfaɪloʊdʒəˈnɛtɪks,_-lə-) is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by phylogenetic inference methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms.

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Exploring Evolution: Molecular Evidence and Mechanisms

Explores molecular evidence and mechanisms of evolution, including phylogenetic trees and protein comparisons.

Exploring Evolution: Molecular Insights and Protein Comparison

Explores evolution through enzymes, DNA models, and protein comparisons, discussing molecular insights and evolutionary mechanisms.

Understanding Generative Models of Protein Sequences

Explores a unified framework for understanding and evaluating generative sequence models of DNA/RNA or Protein, covering topics like coevolution, conservation, and different models such as GREMLIN and BERT.

Phylogenetic Tree Construction

Covers the stages of building a phylogenetic tree using DNA sequences and the UPGMA method.

Spirochetes: Structure and Classification