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Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates.

David E Northover1, Stephen D Shank1, David A Liberles2,3

  • 1Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.

BMC Evolutionary Biology
|February 13, 2020
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Summary

Chordate genome evolution is shaped by lineage-specific changes, including gene duplication and selection. The Adaptive Evolution Database (TAED) reveals key evolutionary trends in metabolism, immunity, and signaling pathways.

Keywords:
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Area of Science:

  • Comparative genomics
  • Molecular evolution
  • Bioinformatics

Background:

  • Understanding genome content origins is crucial for molecular evolution and comparative genomics.
  • Lineage-specific evolution provides insights into species-specific diversification.
  • The Adaptive Evolution Database (TAED) aids in studying evolutionary events across chordates.

Purpose of the Study:

  • To characterize evolutionary trends in chordate species using TAED.
  • To identify episodes of directional or diversifying selection.
  • To map gene families, functional pathways, and amino acid changes.

Main Methods:

  • Utilized TAED, a phylogenetically indexed gene family database.
  • Assessed lineage-specific estimates of dN/dS ratios.
  • Reconciled gene families to chordate species to identify retained duplicates.
  • Mapped gene families to functional pathways and analyzed amino acid changes on protein structures.

Main Results:

  • Elevated evolutionary rates observed in metabolism, immunity, and cell signaling pathways.
  • Overrepresentation of specific protein folds (e.g., Rossmann, Jelly Roll, TIM barrels) under directional selection.
  • Gene families with increased duplications linked to metabolism, olfactory reception, and signaling.
  • Relaxed constraint in β-sheets and stronger constraint on alpha helices, with substitutions at exposed sites.
  • Lineage-specific evolution in the ornithine decarboxylase gene family in Cetacea.

Conclusions:

  • Lineage-specific evolution, driven by duplication and directional selection, is prevalent in chordates.
  • TAED is a valuable tool for understanding lineage-specific evolutionary processes.
  • Specific pathways and protein structures show distinct evolutionary patterns.