Related Experiment Video
Updated: Jul 10, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Identifying evolutionary trees and substitution parameters for the general Markov model with invariable sites
Elizabeth S Allman1, John A Rhodes
1Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK 99775, USA. e.allman@uaf.edu
Mathematical Biosciences
|October 30, 2007
Summary
The general Markov plus invariable sites (GM+I) model is identifiable. This means evolutionary tree topology and model parameters can be recovered from sequence data, crucial for phylogenetic analysis.
Area of Science:
- Computational Biology
- Phylogenetics
- Evolutionary Biology
Background:
- The general Markov plus invariable sites (GM+I) model is a two-class model for biological sequence evolution.
- It assumes a proportion of sites are invariable, while others evolve via a Markov process on a phylogenetic tree.
Purpose of the Study:
- To determine the identifiability of the GM+I model.
- To ascertain if tree topology and numerical parameters can be uniquely recovered from sequence data at the leaves.
Main Methods:
- Algebraic analysis using phylogenetic invariants.
- Studying the algebraic variety defined by the GM+I model.
Main Results:
- The study establishes that for generic parameters, both the phylogenetic tree topology and numerical parameter values are recoverable.
- Identifiability issues are limited to 'label swapping', a known ambiguity.
Conclusions:
- The GM+I model is identifiable, enabling robust phylogenetic inference.
- Simple rational formulas derived from determinantal ratios facilitate parameter recovery for invariable sites.
More Related Videos
Related Concept Videos
03:21Phylogenetic 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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
03:21Phylogenetic 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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
01:28Microbial Phylogeny
Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
02:54Evolutionary Relationships through Genome Comparisons
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...
01:19Survival Tree
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.
Building a Survival Tree
Constructing a survival tree begins...
Building a Survival Tree
Constructing a survival tree begins...
02:13Overview of Transposition and Recombination
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...