Supplementary information for: The artefactual branch effect and phylogenetic conflict: Species delimitation with gene flow in mangrove pit vipers (Trimeresurus purpureomaculatus-erythrurus complex)

Mangrove pit vipers of the Trimeresurus purpureomaculatus-erythrurus
complex are the only species of viper known to naturally inhabit
mangroves. Despite serving integral ecological functions in mangrove
ecosystems, the evolutionary history, distribution, and species boundaries
of mangrove pit vipers remain poorly understood, partly due to overlapping
distributions, confusing phenotypic variations, and the lack of focused
studies. Here, we present the first genomic study on mangrove pit vipers
and introduce a robust hypothesis-driven species delimitation framework
that considers gene flow and phylogenetic uncertainty in conjunction with
a novel application of a new class of speciation-based delimitation model
implemented through the program Delineate. Our results showed that gene
flow produced phylogenetic conflict in our focal species and substantiated
the artefactual branch effect where highly admixed populations appear as
divergent nonmonophyletic lineages arranged in a stepwise manner at the
basal position of clades. Despite the confounding effects of gene flow, we
were able to obtain unequivocal support for the recognition of a new
species based on the intersection and congruence of multiple lines of
evidence. This study demonstrates that an integrative hypothesis-driven
approach predicated on the consideration of multiple plausible
evolutionary histories, population structure/ differentiation, gene flow,
and the implementation of a speciation-based delimitation model can
effectively delimit species in the presence of gene flow and phylogenetic
conflict.