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Evidence for widespread reticulate evolution within human duplicons.

Michael S Jackson1, Karen Oliver, Jane Loveland

  • 1Institute of Human Genetics, University of Newcastle upon Tyne, International Centre for Life, Newcastle upon Tyne, United Kingdom. m.s.jackson@ncl.ac.uk

American Journal of Human Genetics
|October 28, 2005
PubMed
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Reticulate evolution, involving processes like unequal crossing-over, significantly impacts human segmental duplications. These events rapidly disrupt DNA sequences, affecting genome evolution and analysis.

Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Segmental duplications comprise ~5% of the human genome and are implicated in mutations and gene innovation.
  • Reticulate evolutionary processes (e.g., unequal crossing-over, gene conversion) are known but their broad impact on human duplications is unclear.

Purpose of the Study:

  • To investigate the contribution of reticulate evolution to the formation and evolution of human segmental duplications.
  • To quantify the extent of reticulate processes versus nucleotide substitution in duplicated DNA sequences.

Main Methods:

  • Phylogenetic profiling of 24 human duplicon families (>8 Mb DNA).
  • Development and application of a quartet method to differentiate reticulate evolution from nucleotide substitution.
  • Permutation tests to assess sequence identity due to reticulation.

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Main Results:

  • All analyzed duplicon families showed evidence of reticulate evolution, disrupting independent evolutionary trajectories.
  • A significant excess of sites consistent with reticulate evolution was observed, with 15/30 alignments showing >20-fold excess.
  • At least 5% of total sequence exhibits 100% identity due to reticulation, including 74 tracts >2 kb.
  • Reticulation event density can be as high as 1 per 4 kb in some regions.

Conclusions:

  • Reticulate evolution rapidly disrupts phylogenetic relationships in recently duplicated human DNA.
  • These findings have implications for human genome sequencing, comparative analysis of duplicons, and understanding gene-family evolution.