RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds

Area of Science:

• Evolutionary Biology
• Systematic Zoology
• Ornithology

Background:

• The order Charadriiformes, comprising diverse shorebirds, presents phylogenetic challenges due to morphological inconsistencies.
• Previous studies using morphological data and DNA hybridization have yielded conflicting or poorly supported evolutionary trees for shorebirds.
• Uncertainties exist regarding higher-level relationships within Charadriiformes and the placement of certain families like buttonquails.

Purpose of the Study:

• To resolve systematic confusion within the Charadriiformes using molecular phylogenetic analysis.
• To establish a well-supported phylogeny for shorebirds, clarifying inter-familial relationships and the order's limits.
• To investigate the evolutionary origins and divergence times of Charadriiformes.

Main Methods:

• Sequencing of the large RAG-1 nuclear exon (2850 bp) from 36 shorebird species representing 17 families.
• Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood, and Bayesian inference methods.
• Divergence times were estimated using rate-smoothing methods and fossil-based minimum time constraints.

Main Results:

• RAG-1 gene sequences provided a fully resolved phylogeny with high support at basal nodes, confirming its utility for higher-level avian taxonomy.
• The RAG-1 gene tree identified three major subordinal clades: Charadrii, Scolopaci, and Lari, with a basal split between Charadrii and (Scolopaci+Lari).
• The study places Alcidae within Lari and identifies buttonquails as a basal lineage within the Lari clade, contradicting previous hypotheses.

Conclusions:

• The RAG-1 gene provides a robust molecular marker for resolving higher-level avian phylogenies, particularly within the Charadriiformes.
• The revised phylogeny suggests Charadriiformes originated in Gondwanaland, with specific divergence times estimated based on fossil evidence.
• This research clarifies the evolutionary history of shorebirds, resolving long-standing systematic uncertainties and providing a framework for future studies.