Related Experiment Video
Updated: Jul 21, 2025
12:00
A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
35.4K
Testing phylogenetic signal with categorical traits and tree uncertainty
Diogo Ribeiro1,2, Rui Borges3, Ana Paula Rocha4,5
1CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Porto, Portugal.
Bioinformatics (Oxford, England)
|July 25, 2023
Summary
This study refines the delta statistic to improve phylogenetic signal assessment by accounting for tree uncertainty. A more accessible implementation is now available for evolutionary research.
Area of Science:
- Evolutionary Biology
- Phylogenetics
- Bioinformatics
Background:
- Phylogenetic signal quantifies trait similarity across species, crucial for understanding evolution.
- The delta statistic measures phylogenetic signal using Shannon entropy.
- Existing methods may be limited by phylogenetic tree uncertainty.
Purpose of the Study:
- To refine the delta statistic for accurate phylogenetic signal assessment.
- To incorporate tree uncertainty into the delta statistic calculation.
- To provide an accessible and efficient implementation for researchers.
Main Methods:
- Developed a refined delta statistic algorithm.
- Incorporated methods to account for phylogenetic tree uncertainty.
- Created a computationally efficient implementation.
Main Results:
- The refined delta statistic provides more accurate assessments of phylogenetic associations.
- The new implementation enhances accessibility and computational efficiency.
- Improved ability to detect evolutionary signatures and gene-phenotype links.
Conclusions:
- The refined delta statistic offers a more robust tool for evolutionary analyses.
- Increased accessibility will promote wider adoption in the scientific community.
- This advancement aids in identifying adaptive evolution and trait associations.
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
5.8K
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...
5.8K
03:21Phylogenetic Trees
45.5K
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.
45.5K
01:19Survival Tree
112
Survival trees are a non-parametric method used in survival analysis to model the relationship between a set of covariates and the time until an event of interest occurs, often referred to as the "time-to-event" or "survival time." This method is particularly useful when dealing with censored data, where the event has not occurred for some individuals by the end of the study period, or when the exact time of the event is unknown.
Building a Survival Tree
Constructing a...
Building a Survival Tree
Constructing a...
112
01:23Phylogeny
44.5K
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.
44.5K
02:05Gene Evolution - Fast or Slow?
7.2K
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...
7.2K
01:20Applications of Molecular Taxonomy
41
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...
41