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Updated: May 11, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
A population genetics-phylogenetics approach to inferring natural selection in coding sequences.
Daniel J Wilson1, Ryan D Hernandez, Peter Andolfatto
1Department of Human Genetics and Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA. daniel.wilson@ndm.ox.ac.uk
Plos Genetics
|December 7, 2011
Summary
We developed a new method to analyze how selection pressures vary across genomes and over evolutionary time. This approach helps understand genetic adaptation and evolutionary changes in species like Drosophila.
Area of Science:
- Evolutionary Biology
- Population Genetics
- Genomics
Background:
- Understanding the distribution of selective effects of mutations is crucial for deciphering genome evolution.
- Changes in fitness landscapes over time and the genetic basis of adaptations are key areas of research.
- Existing methods may not fully capture the spatial and temporal dynamics of selection pressures.
Purpose of the Study:
- To introduce a novel method for analyzing variation in selection pressures within and between species.
- To spatially map selection along the genome and temporally track changes between lineages.
- To infer ancestral states and utilize allele frequency information for robust evolutionary modeling.
Main Methods:
- Developed a joint population genetics-phylogenetics approach to model codon evolution.
- Constructed multiallelic models incorporating mutation, selection, and genetic drift.
- Employed a Bayesian sliding window model to analyze intragenic variation in selection coefficients, capturing spatial clustering.
Main Results:
- The novel method allows direct inference on coding sequences and probabilistic ancestral state reconstruction.
- The approach generalizes to multiple species and effectively utilizes allele frequency data.
- Selective pressures in Drosophila melanogaster and D. simulans were inferred for 100 X-linked coding regions.
Conclusions:
- The developed method provides a powerful tool for dissecting the complex patterns of selection in genomes.
- This approach enhances our ability to study adaptation, genome evolution, and lineage-specific changes.
- The findings offer insights into the dynamic nature of selection pressures across evolutionary timescales.
Related Concept Videos
01:25What is Population Genetics?
A population is composed of members of the same species that simultaneously live and interact in the same area. When individuals in a population breed, they pass down their genes to their offspring. Many of these genes are polymorphic, meaning that they occur in multiple variants. Such variations of a gene are referred to as alleles. The collective set of all the alleles within a population is known as the gene pool.
01:49Hardy-Weinberg Principle
Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.
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).
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...
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...