Related Experiment Video
Updated: May 25, 2025
12:00
A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
35.3K
Improved Robustness to Gene Tree Incompleteness, Estimation Errors, and Systematic Homology Errors with Weighted
Yunheng Han1,2, Erin K Molloy1,2
1Department of Computer Science, University of Maryland, College Park, MD 20742, USA.
Systematic Biology
|February 25, 2025
Summary
Weighted TREE-QMC improves species tree reconstruction by incorporating gene tree accuracy. This method is fast, accurate, and robust to missing data, offering an alternative to existing phylogenetic tools.
Area of Science:
- Phylogenetics
- Computational Biology
- Evolutionary Biology
Background:
- Species tree reconstruction methods are vital for understanding evolutionary history.
- Incomplete or erroneous gene trees can reduce the accuracy of phylogenetic analyses.
- Existing methods like ASTRAL face computational challenges with weighted gene tree data.
Purpose of the Study:
- To introduce weighted TREE-QMC, a novel method for species tree reconstruction.
- To evaluate the performance of weighted TREE-QMC against existing weighted methods.
- To assess the robustness of weighted TREE-QMC to gene tree errors and missing data.
Main Methods:
- Leveraging the Quartet Max Cut framework with weighting schemes.
- Implementing weighting by gene tree branch lengths and support values.
- Comparative analysis through simulation studies and avian data set reanalysis.
Main Results:
- Weighted TREE-QMC demonstrates high accuracy and computational efficiency.
- The method is competitive with, and sometimes outperforms, weighted ASTRAL.
- Weighting improves robustness to homology errors and missing taxa.
Conclusions:
- Weighted TREE-QMC offers a robust and accurate approach to species tree reconstruction.
- The method is effective even with challenging data, including large taxon sets and missing data.
- Weighted TREE-QMC shows promise as a reliable supertree method.
Related Concept Videos
03:21Phylogenetic Trees
45.0K
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.
45.0K
02:54Evolutionary Relationships through Genome Comparisons
5.7K
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...
5.7K
01:23Phylogeny
43.5K
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.
43.5K
02:05Gene Evolution - Fast or Slow?
7.0K
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...
7.0K
02:37Gene Duplication and Divergence
6.0K
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...
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...
6.0K
01:10Propagation of Uncertainty from Systematic Error
455
The atomic mass of an element varies due to the relative ratio of its isotopes. A sample's relative proportion of oxygen isotopes influences its average atomic mass. For instance, if we were to measure the atomic mass of oxygen from a sample, the mass would be a weighted average of the isotopic masses of oxygen in that sample. Since a single sample is not likely to perfectly reflect the true atomic mass of oxygen for all the molecules of oxygen on Earth, the mass we obtain from this...
455