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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary 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...
Gene Evolution - Fast or Slow?02:05

Gene 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...
Gene Evolution - Fast or Slow?02:05

Gene 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...
Synteny and Evolution02:31

Synteny and Evolution

John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral chromosome underwent...
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.

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Related Experiment Video

Updated: May 9, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models.

Nicola De Maio1, Christian Schlötterer, Carolin Kosiol

  • 1Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria.

Molecular Biology and Evolution
|August 3, 2013
PubMed
Summary

This study introduces a new model to estimate mutation rates and fixation biases in great ape genomes, accounting for complex evolutionary patterns like incomplete lineage sorting. The findings reveal variations in these forces across species and GC content, offering insights into evolutionary history.

Keywords:
biased gene conversioncoding sequence evolutionmutation ratesphylogenetics-population genetics modelprimates evolutionrate heterogeneity

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Population Genetics

Background:

  • Great ape genomes offer insights into evolutionary history but present challenges like incomplete lineage sorting and ancestral shared polymorphisms.
  • Existing genome-scale analysis methods are limited by the number of individuals analyzed or their inability to separate mutation rates from fixation biases.

Purpose of the Study:

  • To develop a novel model for estimating mutation rates and fixation biases from genetic variation within and between species.
  • To account for shared ancestral polymorphisms and incomplete lineage sorting in evolutionary analyses.
  • To analyze genome-wide synonymous site alignments across multiple individuals from human, chimpanzee, and orangutan species.

Main Methods:

  • Developed a new model that relaxes the assumption of instantaneous substitutions, modeling them as gradual fixation events.
  • Analyzed genome-wide synonymous site alignments from multiple individuals of humans, chimpanzees, and two orangutan species.
  • Estimated mutation rates and GC-biased gene conversion intensity.

Main Results:

  • Mutation rates and GC-biased gene conversion intensity were found to vary with GC content.
  • Lineage-specific differences were observed, with orangutan species exhibiting weaker fixation biases, suggesting a reduced historical effective population size.
  • Results support the action of directional selection on coding sequences, particularly in relation to exonic splicing enhancers.

Conclusions:

  • The new model effectively estimates mutation rates and fixation biases, improving our understanding of evolutionary forces in great apes.
  • Variations in mutation and fixation biases across species and GC content provide insights into lineage-specific evolutionary histories.
  • Evidence for directional selection acting on coding sequences, linked to exonic splicing enhancers, was identified.