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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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Updated: Jul 8, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Do we need many genes for phylogenetic inference?

V V Aleshin1, A V Konstantinova, K V Mikhailov

  • 1Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia. Aleshin@genebee.msu.su

Biochemistry. Biokhimiia
|January 22, 2008
PubMed
Summary

This study supports the close evolutionary relationship between multicellular animals (Metazoa) and choanoflagellates, forming the Holozoa taxon. It also clarifies fungal and gene fusion evolutionary histories.

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Area of Science:

  • * Evolutionary biology
  • * Phylogenomics
  • * Molecular evolution

Background:

  • * Understanding the evolutionary origins of multicellularity and the relationships within Opisthokonta is crucial.
  • * Previous phylogenetic studies have yielded varying hypotheses regarding the placement of Metazoa and Fungi.

Purpose of the Study:

  • * To investigate the interrelationships between Metazoa and other Opisthokonta using phylogenomic analysis.
  • * To examine the evolutionary history of specific genes, such as those coding for ubiquitin-fused ribosomal protein S30.

Main Methods:

  • * Phylogenomic analysis of 56 nuclear protein-coding genes from diverse Opisthokonta representatives.
  • * Statistical support assessment using whole alignment and randomly selected alignment positions.
  • * Comparative analysis of gene fusion events and FUBI orthologs.

Main Results:

  • * Strong support for Metazoa and Choanoflagellata as sister groups within Holozoa.
  • * Chytridiomycota identified as a monophyletic group, distinct from Eumycota.
  • * Multiple independent gene fusion events identified, including in Holozoa and other eukaryotic lineages.

Conclusions:

  • * The Metazoa-Choanoflagellata sister group relationship is robustly supported.
  • * Phylogenetic reconstructions are highly dependent on minimizing reconstruction artifacts, more so than gene number alone.
  • * Gene fusion events provide insights into deep evolutionary history across eukaryotes.