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Gene Evolution - Fast or Slow?02:05

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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.
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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...
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Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
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The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
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Evolution shapes the features of organisms over time, ensuring that they are suited for the environments in which they live. Sometimes, selection pressure leads to the rise of similar but unrelated adaptations in organisms with no recent common ancestors, a process known as convergent evolution.
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Updated: Jun 13, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Reticulate evolution: Detection and utility in the phylogenomics era.

Saelin Bjornson1, Heroen Verbruggen2, Nathan S Upham3

  • 1School of BioSciences, University of Melbourne, Victoria, Australia.

Molecular Phylogenetics and Evolution
|September 13, 2024
PubMed
Summary

Phylogenomics reveals complex evolutionary histories beyond simple trees. New methods help distinguish reticulate evolution, like hybridization and gene transfer, from other patterns to better understand life's history.

Keywords:
Divergence time estimationGene-tree-species-tree discordanceHorizontal gene transferHybridizationIntrogressionLateral gene transferPhylogenetic incongruencePhylogenetics

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Area of Science:

  • Evolutionary Biology
  • Genomics
  • Phylogenetics

Background:

  • The Tree of Life is increasingly understood to exhibit network-like structures due to reticulate evolution.
  • Hybridization/introgression and horizontal gene transfer are key non-vertical evolutionary processes.
  • Reticulate patterns can be mistaken for incomplete lineage sorting or recombination, causing ambiguity.

Purpose of the Study:

  • To provide an overview of phylogenomic workflows for inferring organismal histories.
  • To compare methods for distinguishing different modes of reticulate evolution.
  • To highlight the importance of embracing reticulate patterns for a clearer view of evolutionary history.

Main Methods:

  • Overview of phylogenomic workflows.
  • Comparison of methods for distinguishing reticulate evolution.
  • Analysis of coalescent event timing to differentiate introgression from incomplete lineage sorting.
  • Utilizing horizontal gene transfer events to determine relative speciation timing.

Main Results:

  • Timing of coalescent events can disentangle introgression from incomplete lineage sorting.
  • Horizontal gene transfer aids in determining relative speciation event timing.
  • Identified pitfalls in current methods for inferring reticulate evolution.

Conclusions:

  • Embracing reticulate evolutionary patterns is crucial for accurately understanding the timing and rates of evolutionary events.
  • Extended utility of methods across the Tree of Life is discussed.
  • A clearer view of life's history is achievable by accounting for reticulate evolution.