RNA SEQUENCE DATA IN PHYLOGENETIC RECONSTRUCTION: TESTING THE LIMITS OF ITS RESOLUTION

Area of Science:

• Evolutionary Biology
• Molecular Phylogenetics
• Marine Biology

Background:

• Echinoderm phylogeny is complex, with deep divergences.
• 18S ribosomal RNA (rRNA) gene sequences are commonly used for phylogenetic inference.
• Comparing molecular and morphological phylogenies is crucial for validating evolutionary reconstructions.

Purpose of the Study:

• To investigate phylogenetic relationships among 11 echinoderm species using 18S rRNA sequences.
• To determine the evolutionary distance at which 18S rRNA phylogenies become incongruent with morphological data.
• To assess the reliability of different analytical approaches for 18S rRNA data.

Main Methods:

• Parsimony analysis of 18S rRNA sequences from 11 echinoderms.
• Analysis of three distinct 18S rRNA regions (paired, unpaired, and combined sites).
• Comparison of molecular phylogenies with established morphological phylogenies.

Main Results:

• 18S rRNA parsimony analysis yields reliable results for taxa diverged <100 million years ago (Ma).
• For divergences up to 250 Ma, paired nucleotides in 18S rRNA provided more reliable results than unpaired sites.
• Echinoderm class relationships (diverged 450-550 Ma) remain unresolved using 18S rRNA data.

Conclusions:

• The utility of 18S rRNA sequence data for phylogenetic reconstruction is limited by evolutionary distance.
• For deeper echinoderm divergences, alternative molecular markers or morphological data may be necessary.
• Analytical choices, such as focusing on paired nucleotides, can improve phylogenetic accuracy for intermediate divergence times.