Related Experiment Video
Updated: Jul 13, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
msBayes: pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian
Michael J Hickerson1, Eli Stahl, Naoki Takebayashi
1Biology Department, Queens College, CUNY, Flushing, NY 11367-1597, USA. michael.hickerson@qc.cuny.edu
BMC Bioinformatics
|July 28, 2007
Summary
This study introduces msBayes, a novel software for testing simultaneous divergence in multiple population pairs. It accurately distinguishes simultaneous isolation from temporal incongruence, even with limited data.
Area of Science:
- Evolutionary Biology
- Population Genetics
- Phylogeography
Background:
- Accurate testing of simultaneous divergence (vicariance) across multiple population pairs is crucial in evolutionary biology.
- Previous methods often conflate gene trees with species trees, leading to inaccurate conclusions about temporal incongruence.
- Existing phylogeographic software lacks the capability to analyze multiple species/population pairs under a hierarchical model.
Purpose of the Study:
- To introduce msBayes, a new software package designed for testing simultaneous divergence (TSD) in multiple co-distributed population pairs.
- To provide a flexible and powerful tool for analyzing complex multi-species biogeographic hypotheses using population genetic data.
Main Methods:
- msBayes utilizes approximate Bayesian computation (ABC) within a hierarchical coalescent model framework.
- It estimates hyper-parameters to quantify variability in divergence times across population pairs.
- The software allows for variation in within-population demographic parameters, accounting for coalescent variance.
Main Results:
- The msBayes method effectively distinguishes simultaneous isolation from temporal incongruence in population pair divergence.
- Accurate results are achievable even with sparse sampling of individuals.
- The decoupled estimation and simulation steps allow for rapid evaluation of ABC conditions and summary statistics.
Conclusions:
- msBayes is a powerful and flexible tool for addressing complex biogeographic questions involving multiple co-distributed species.
- The software pipeline is available as open-source software for Linux, Mac OS-X, and POSIX systems.
- Future implementations will extend capabilities to analyze multi-locus data per species pair.
Related Concept Videos
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...
01:28Microbial 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,...
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...
01:23Phylogeny
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...
02:05Gene Evolution - Fast or Slow?
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...
In contrast, regions which code...