Identifying sets of phylogenetically informative markers for Anastrepha (Diptera: Tephritidae).

Phylogenomic analyses have revolutionized our understanding of evolutionary relationships, yet it is complicated by incongruence across the genome. Here, we reanalyzed a genomic dataset comprising 3170 orthologs, and evaluated three methods to identify reduced sets of loci that can accurately resolve evolutionary relationships among Anastrepha fruit flies. Previous phylogenetic analyses consistently revealed well-supported topologies for deeper evolutionary relationships, while more recent divergences, particularly within the A. fraterculus complex, exhibited high levels of phylogenetic incongruence due to gene flow, incomplete lineage sorting, or other evolutionary forces. Here, we explored strategies for selecting reduced subsets: number of informative sites per gene, site concordance factor above 60% for clades consistent to current taxonomy, and tip-to-root variation/bipartition support. Among the strategies tested, subsets based on concordance and evolutionary rate metrics produced topologies consistent with full dataset analyses, with reduced levels of discordance. These subsets maintained robust support for deeper relationships while increasing congruence at shallower nodes. Although genes in reduced subsets exhibited lower evolutionary rates, they had higher internode certainty, treeness, and coalescent times. These findings highlight the potential for carefully selected loci to improve phylogenetic resolution and mitigate conflicting signals. Our study offers practical approaches for refining phylogenomic analyses in systems with complex evolutionary histories.