Related Experiment Video
Updated: Nov 26, 2025
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
16.2K
Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny
Lenore Pipes1, Hongru Wang1, John P Huelsenbeck1
1Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.
Molecular Biology and Evolution
|December 9, 2020
Summary
Determining the SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) root is complex. Phylogenetic methods yield conflicting results, suggesting limited evidence for pinpointing the virus origin or early spread.
Area of Science:
- Virology
- Phylogenetics
- Molecular Evolution
Background:
- Understanding the origin and early transmission of SARS-CoV-2 is crucial.
- Previous phylogenetic analyses of SARS-CoV-2 have employed inconsistent rooting strategies.
- Discrepancies in rooting methods hinder definitive conclusions about viral origins.
Purpose of the Study:
- To investigate various rooting strategies for the SARS-CoV-2 phylogenetic tree.
- To assess the statistical uncertainty associated with different rooting methods.
- To evaluate the reliability of phylogenetic evidence in determining SARS-CoV-2 origins.
Main Methods:
- Application of multiple distinct phylogenetic rooting strategies.
- Utilized molecular clock-based methods for root placement.
- Employed outgroup rooting techniques for comparative analysis.
Main Results:
- Molecular clock methods suggested rooting within the B clade.
- Outgroup rooting methods indicated rooting within the A clade.
- Statistical incompatibility observed between the two main approaches, potentially due to molecular clock deviations or excess back-mutations.
- No method provided strong statistical support for any specific root placement.
Conclusions:
- Phylogenetic evidence alone is insufficient to definitively identify the origin of SARS-CoV-2.
- Caution is advised against making strong inferences about early viral spread based solely on current phylogenetic data.
- Further research may be needed to reconcile conflicting rooting results and improve understanding of SARS-CoV-2 evolution.
Related Concept Videos
03:21Phylogenetic Trees
48.8K
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.
48.8K
01:23Phylogeny
56.0K
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.
56.0K
02:54Evolutionary Relationships through Genome Comparisons
6.6K
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...
6.6K
01:29Modern Molecular Taxonomy
395
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
395
01:20Applications of Molecular Taxonomy
320
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
320
02:05Gene Evolution - Fast or Slow?
7.7K
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...
7.7K