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Comparative and phylogenetic analysis of developmental sequences.

Susanne Schulmeister1, Ward C Wheeler

  • 1Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA. schulmei@amnh.org

Evolution & Development
|April 28, 2004
PubMed
Summary

Event pairing, used for analyzing developmental sequences on phylogenies, contains errors. A new search-based character optimization method directly analyzes developmental sequences, avoiding these issues for accurate phylogenetic analysis.

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Area of Science:

  • Evolutionary developmental biology
  • Phylogenetics
  • Computational biology

Background:

  • Event pairing is a method for optimizing developmental sequences on phylogenetic trees to detect heterochrony.
  • This method has been used to infer evolutionary relationships and developmental changes.

Purpose of the Study:

  • To identify and address critical flaws in the event pairing method for analyzing developmental sequences.
  • To introduce a novel, more accurate method for comparative and phylogenetic analysis of developmental sequences.

Main Methods:

  • Critique of event pairing, highlighting its treatment of dependent features as independent.
  • Development and application of a new method using search-based character optimization.
  • Treating the entire developmental sequence as a single character analyzed with dynamic programming and an edit cost function.

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Main Results:

  • Event pairing leads to the optimization of impossible ancestors and underestimates sequence lengths.
  • Event pairing can propose unsupported synapomorphies and generate phylogenies inconsistent with data.
  • The new method avoids these errors by directly optimizing the developmental sequence on the tree.

Conclusions:

  • The event pairing method is fundamentally flawed for analyzing developmental sequences in phylogenetics.
  • The proposed search-based character optimization method offers a more accurate approach for comparative and phylogenetic analyses.
  • This advancement improves the reliability of inferring evolutionary developmental patterns.