Gene-wide identification of episodic selection
Ben Murrell1, Steven Weaver1, Martin D Smith2
1Department of Medicine, University of California San Diego.
Molecular Biology and Evolution
|February 22, 2015
Summary
We introduce BUSTED, a novel method for detecting episodic positive selection in genes. This approach identifies periods where the non-synonymous substitution rate exceeds the synonymous rate, offering insights into evolutionary dynamics.
Area of Science:
- Evolutionary biology
- Molecular evolution
- Genomics
Background:
- Detecting positive selection is crucial for understanding adaptation.
- Existing methods may not capture transient or episodic selection events effectively.
- Identifying episodic positive selection across gene-wide phylogenies requires robust statistical approaches.
Purpose of the Study:
- To present BUSTED (Branch-Site Unrestricted Statistical Test for Episodic Diversification), a new method for detecting gene-wide episodic positive selection.
- To provide a flexible tool that can analyze entire phylogenies or specific lineages.
- To develop a computationally efficient metric for identifying sites under episodic positive selection.
Main Methods:
- BUSTED models selection as stochastically varying over branches and sites.
- It employs a computationally inexpensive evidence metric to identify episodic positive selection.
- The method can be applied to all branches of a phylogeny or to a user-defined subset of foreground lineages.
Main Results:
- BUSTED effectively identifies gene-wide evidence of episodic positive selection.
- The method demonstrates comparable or superior performance to existing models on simulated and empirical data.
- An interactive web implementation is available for user-friendly application.
Conclusions:
- BUSTED offers a powerful new approach for detecting episodic positive selection.
- Its flexibility and computational efficiency make it a valuable tool for evolutionary studies.
- The availability of an online implementation facilitates broader adoption and research.
Related Concept Videos
01:11Genome-wide Association Studies-GWAS
17.1K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
17.1K
01:09Epistasis Analysis
6.3K
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
6.3K
01:21Frequency-dependent Selection
24.5K
When the fitness of a trait is influenced by how common it is (i.e., its frequency) relative to different traits within a population, this is referred to as frequency-dependent selection. Frequency-dependent selection may occur between species or within a single species. This type of selection can either be positive—with more common phenotypes having higher fitness—or negative, with rarer phenotypes conferring increased fitness.
24.5K
02:05Gene Evolution - Fast or Slow?
8.4K
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...
8.4K
02:16Genetics of Speciation
23.4K
Speciation is the evolutionary process resulting in the formation of new, distinct species—groups of reproductively isolated populations.
23.4K
03:33Genetic Drift
45.6K
Natural selection—probably the most well-known evolutionary mechanism—increases the prevalence of traits that enhance survival and reproduction. However, evolution does not merely propagate favorable traits, nor does it always benefit populations.
45.6K