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.
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.
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,...
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 kingdom.
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...
02:37Gene Duplication and Divergence
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
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Updated: May 12, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Anomalous unrooted gene trees.
1Department of Mathematics and Statistics, University of Canterbury, Private Bag 4800, Christchurch, New Zealand. j.degnan@math.canterbury.ac.nz
Systematic Biology
|April 12, 2013
Summary
Gene tree topologies can be misleading when inferring species trees, especially with seven or more taxa. This study characterizes anomalous unrooted gene trees (AUGTs) and their implications for phylogenetic inference.
Area of Science:
- Phylogenetics
- Computational Biology
- Evolutionary Genetics
Background:
- Gene tree topologies are often inferred from molecular sequences, but their direction in time can be ambiguous.
- Ambiguity arises from reversible mutation models, lack of outgroups, and absence of molecular clocks.
- The multispecies coalescent model is a key framework for understanding gene tree-species tree relationships.
Purpose of the Study:
- To investigate the probabilities of unrooted gene-tree topologies under the multispecies coalescent model.
- To identify conditions under which gene trees may not reflect the species tree topology.
- To characterize species trees prone to anomalous unrooted gene trees (AUGTs).
Main Methods:
- Probabilistic analysis of unrooted gene-tree topologies within the multispecies coalescent framework.
- Characterization of species trees exhibiting AUGTs for specific numbers of taxa (five and six).
- Exploration of branch length patterns associated with AUGTs and rooted anomalous gene trees.
Main Results:
- For species trees with seven or more taxa, specific branch lengths can render certain unrooted gene-tree topologies more probable than the species tree's topology.
- Species trees with five and six taxa that exhibit AUGTs are identified and characterized.
- Patterns of branch lengths contributing to anomalous gene trees (both rooted and unrooted) are elucidated.
Conclusions:
- The presence of AUGTs highlights challenges in inferring accurate species trees from gene trees.
- Understanding AUGTs is crucial for interpreting gene tree discordance in phylogenetic studies.
- These findings can inform the design of simulation studies for robust species tree inference.