Related Experiment Video
Updated: May 9, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Evolutionary Modeling of Genotype-Phenotype Associations, and Application to Primate Coding and Non-coding mtDNA Rate
Timothy D O'Connor1, Nicholas I Mundy
1Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
Evolutionary Bioinformatics Online
|August 9, 2013
Summary
Evolutionary rate variation in primate mitochondrial DNA is linked to longevity and body mass, particularly at the third codon position. This new method robustly identifies genotype-phenotype associations across multiple categories.
Area of Science:
- Evolutionary Biology
- Genomics
- Molecular Evolution
Background:
- Substitution rate variation across a phylogeny can indicate evolutionary shifts in genomic regions.
- Understanding these signals requires identifying phenotypic correlates of evolutionary rate variation.
Purpose of the Study:
- To extend a likelihood method for detecting evolutionary associations between genotypic evolutionary rate and phenotype over a phylogeny.
- To apply the extended method to primate mitochondrial and nuclear genomes to test hypotheses of rate variation related to life history traits.
Main Methods:
- Extended a previously published likelihood method to detect genotype-phenotype associations.
- Validated the method's performance in simulations with two to four discrete phenotype categories.
- Applied the method to primate mitochondrial and nuclear genomes, categorizing continuous traits like longevity and body mass into discrete groups.
Main Results:
- The extended method demonstrated low false-positive rates and high detection rates in simulations.
- The majority of mitochondrial protein-coding genes showed associations with longevity and body mass, primarily at the third codon position.
- A significant association was found between maximum lifespan and the evolutionary rate of the mtDNA control region.
- Nuclear protein-coding genes did not show consistent associations with generation time, contradicting the hypothesis.
Conclusions:
- The extended method robustly identifies genotype-phenotype associations across at least four phenotypic categories.
- The study provides evidence that longevity and body mass influence evolutionary rates in primate mitochondrial DNA.
- The findings suggest that generation time may not be a primary driver of evolutionary rate variation in nuclear genes within the studied primate sample.
Related Concept Videos
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...
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...
02:05Gene 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...
01:09Mutation, Gene Flow, and Genetic Drift
In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
01:43Incomplete Dominance
Gregor Mendel's work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid cell has two variants called alleles inherited from each parent. He suggested that amongst these two alleles, one allele is dominant in character and the other recessive. The combination of alleles determines the phenotype of a gene in an organism.
02:16Genetics of Speciation
Speciation is the evolutionary process resulting in the formation of new, distinct species—groups of reproductively isolated populations.