Related Experiment Video
Updated: Oct 24, 2025
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
16.1K
Accuracy in Near-Perfect Virus Phylogenies
Joel O Wertheim1, Mike Steel2, Michael J Sanderson3
1Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.
Systematic Biology
|August 16, 2021
Summary
Phylogenetic tree accuracy can be high even with short edges. In near-perfect conditions, the false positive rate for discovering clades is low, especially for viruses like SARS-CoV-2.
Area of Science:
- Phylogenetics
- Computational Biology
- Evolutionary Biology
Background:
- Real-world phylogenetic trees often have short edges, leading to incomplete resolution and reduced accuracy.
- Theoretical models suggest that accurately reconstructing trees requires a number of sites inversely proportional to the square of the shortest edge length.
Purpose of the Study:
- To redefine and assess "accuracy" in phylogenetic inference when short edges are present.
- To analyze the false positive rate of clade discovery in "near-perfect" phylogenetic parameter spaces.
- To compare bootstrap support measures with actual false positive rates.
Main Methods:
- Analytical derivation for maximum parsimony.
- Theoretical analysis and simulations for maximum likelihood.
- Comparison of bootstrap resampling support with false positive rates.
Main Results:
- Accuracy can remain high even with short edges if defined by false split discovery rate.
- In near-perfect parameter spaces, the expected false positive rate is low (less than ξ/3), often below 5%.
- Bootstrap support measures tend to underestimate clade reliability compared to actual false positive rates in near-perfect trees.
Conclusions:
- The "near-perfect" model accurately reflects empirical data from human virus outbreaks (e.g., Ebolavirus, Zika virus, SARS-CoV-2).
- Phylogenetic inference can be reliable in scenarios with low substitution rates relative to high transmission/sampling rates.
- This work provides a more nuanced understanding of phylogenetic accuracy and support measures.
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
6.5K
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...
6.5K
03:21Phylogenetic Trees
48.3K
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.
48.3K
01:23Phylogeny
55.1K
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.
55.1K
00:36Viral Mutations
35.8K
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
35.8K
01:29Viruses with RNA Genomes
256
RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
256
02:05Gene Evolution - Fast or Slow?
7.6K
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...
7.6K