The Artefactual Branch Effect and Phylogenetic Conflict: Species Delimitation with Gene Flow in Mangrove Pit Vipers (Trimeresurus purpureomaculatus-erythrurus Complex).

This article focuses on the evolutionary history, species boundaries, and gene flow among mangrove pit vipers of the *Trimeresurus purpureomaculatus-erythrurus* complex, the only viper species naturally inhabiting mangrove ecosystems. Using genome-wide single nucleotide polymorphisms (SNPs) and a novel speciation-based delimitation model implemented in the program Delineate, the study identifies three genetically distinct lineages—*T. purpureomaculatus*, *T. erythrurus*, and an unrecognized species referred to as *T. sp.*—despite evidence of gene flow causing phylogenetic conflict. The research demonstrates that gene flow can produce artefactual phylogenetic patterns but that an integrative, hypothesis-driven framework accounting for gene flow and phylogenetic uncertainty can effectively delimit species. These findings clarify the distribution and taxonomy of mangrove pit vipers in Southeast Asia and highlight their potential as a model system for studying hybridization and phenotypic variation.