Related Experiment Video
Updated: Jul 17, 2026
04:52
Following the Dynamics of Structural Variants in Experimentally Evolved Populations
Published on: February 3, 2023
Using variable rate models to identify genes under selection in sequence pairs: their validity and limitations for
Sheri A Church1, Kevin Livingstone, Zhao Lai
1Department of Biology, Indiana University, Bloomington, IN 47405, USA. schurch@gwu.edu
Journal of Molecular Evolution
|January 4, 2007
Summary
Researchers identified 56 genes under positive selection in sunflower and lettuce using advanced models. Many of these genes, crucial for domestication traits, were missed by simpler methods, highlighting the power of variable rate models in evolutionary studies.
Area of Science:
- Evolutionary Biology
- Genomics
- Molecular Evolution
Background:
- Detecting positive selection is key to understanding adaptation.
- Variable rate models are challenging for sequence pair comparisons.
- Likelihood ratio tests (LRT) are reliable for detecting positive selection, even with limited data.
Purpose of the Study:
- To identify genes under positive selection in sunflower and lettuce lineages.
- To compare the efficacy of variable rate models versus simpler models for detecting selection.
- To investigate the role of selected genes in sunflower domestication.
Main Methods:
- Analyzed 523 EST sequence pairs from sunflower and lettuce using likelihood-based variable selection models.
- Employed the likelihood ratio test (LRT) to detect signatures of positive selection.
- Mapped positively selected genes to quantitative trait loci (QTLs) in sunflower.
Main Results:
- Identified 56 genes showing a signature of positive selection.
- 75% of these selected genes were not detected by simpler, codon-averaging models.
- Four out of five identified positively selected genes in sunflower mapped to domestication QTLs.
Conclusions:
- Variable rate models are effective for detecting positive selection in sequence pair comparisons, despite limitations.
- Advanced models identify genes missed by simpler methods, offering deeper evolutionary insights.
- Positively selected genes identified are linked to important domestication traits in sunflower.
Related Concept Videos
02:05Gene Evolution - Fast or Slow?
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...
02:54Evolutionary Relationships through Genome Comparisons
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...
01:21Frequency-dependent Selection
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.Positive Frequency-Dependent SelectionIn positive...
02:51Multi-species Conserved Sequences
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
02:46Genetic Screens
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...