18S ribosomal RNA and tetrapod phylogeny

Area of Science:

• Molecular biology
• Evolutionary biology
• Phylogenetics

Background:

• Phylogenetic analyses of tetrapod 18S ribosomal RNA (rRNA) sequences have yielded conflicting results regarding avian evolutionary relationships.
• Some studies group birds with mammals based on 18S rRNA, while other molecular, morphological, and paleontological data support a bird-crocodile grouping.
• This discrepancy led to 18S rRNA being considered anomalous in phylogenetic inference for higher organisms.

Purpose of the Study:

• To resolve the conflicting phylogenetic signals from tetrapod 18S rRNA sequences.
• To investigate the causes of previous discrepancies between 18S rRNA phylogenies and other data sources.
• To re-evaluate the phylogenetic position of birds using corrected 18S rRNA data.

Main Methods:

• Re-alignment of tetrapod 18S rRNA sequences utilizing the molecule's secondary structure.
• Appropriate estimation of frequency parameters, considering all sites or variable domains.
• Assessment of sequence quality to minimize noise in phylogenetic reconstruction.

Main Results:

• The primary causes for previous phylogenetic discrepancies were identified as sequence misalignment, inappropriate frequency parameter usage, and poor sequence quality.
• Corrected sequence alignment and parameter estimation resolved the anomalous phylogenetic signal from 18S rRNA.
• Under these improved conditions, 18S rRNA sequences no longer support the grouping of avian species with mammalian species.

Conclusions:

• The perceived anomaly of the 18S rRNA gene in tetrapod phylogenetics is an artifact of methodological issues, not an inherent property of the gene.
• When analyzed with appropriate methods, 18S rRNA data is consistent with other evidence, supporting the grouping of birds with crocodiles.
• This study highlights the importance of rigorous sequence alignment and parameter selection in molecular phylogenetics.