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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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A transcriptome approach to ecdysozoan phylogeny.

Janus Borner1, Peter Rehm1, Ralph O Schill2

  • 1Institute of Zoology and Zoological Museum, University of Hamburg, D-20146 Hamburg, Germany.

Molecular Phylogenetics and Evolution
|August 16, 2014
PubMed
Summary

Phylogenetic analyses confirm Ecdysozoa monophyly and reveal Scalidophora as the earliest branch. Arthropoda are allied with Nematoda and Tardigrada, challenging the Cycloneuralia taxon.

Keywords:
Bayesian analysesEcdysozoaIndelNext generation sequencingPhylogenomics

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Area of Science:

  • Molecular Phylogenetics
  • Evolutionary Biology
  • Invertebrate Zoology

Background:

  • The monophyly of Ecdysozoa (molting phyla) is well-supported, but their internal evolutionary relationships remain debated.
  • Previous studies have presented conflicting hypotheses regarding the placement of key invertebrate groups within Ecdysozoa.

Purpose of the Study:

  • To resolve the internal phylogeny of Ecdysozoa using expressed sequence tags (ESTs) from diverse taxa.
  • To test the monophyly of Cycloneuralia and investigate the evolutionary relationships between major Ecdysozoan lineages.

Main Methods:

  • Generated expressed sequence tags (ESTs) via 454 transcriptome sequencing for priapulids, kinorhynchs, tardigrades, and chelicerates.
  • Assembled a multigene alignment of 24,249 amino acid positions from 63 taxa, optimizing for data density.
  • Conducted phylogenetic analyses using various models (Bayesian, maximum likelihood) and indel pattern analyses.

Main Results:

  • Phylogenetic analyses strongly support the monophyly of Ecdysozoa and recover Scalidophora (Priapulida + Kinorhyncha) as the basalmost clade.
  • The taxon Cycloneuralia is found to be paraphyletic; Arthropoda (including Onychophora) are robustly allied with Nematoda and Tardigrada.
  • Tardigrada and Nematoda form a clade, supported by both gene-based analyses and indel patterns, contradicting some previous findings.

Conclusions:

  • The study refines the Ecdysozoan phylogeny, establishing Scalidophora as the earliest diverging lineage.
  • The results necessitate a revision of the Cycloneuralia concept and highlight a close evolutionary link between Arthropoda, Nematoda, and Tardigrada.
  • The placement of Tardigrada as sister to Arthropoda is rejected in favor of their grouping with Nematoda.