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 manne..., , This package includes phylogenetic trees, RADseq data sequencing report, and supplementary tables and figures., # Supplementary Information for Systematic Biology: manuscript ID USYB-2023-054

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This package contains phylogenetic trees (\"trees.zip\"), ddRADseq sequencing report (\"RADseq Report.pdf\"), supplementary tables and figures (\"Supplementary Information.docx\").

**Table S1.** List of samples used in this study and associated metadata including SRA accession numbers. Sample ID = museum voucher number. See Materials and Methods for an explanation of museum abbreviations.

**Table S2.** Summary statistics of raw reads

**Table S3.** Assembled datasets analyzed in this study

**Table S4.** Results of the Dtrios analysis using the program Dsuite. First three columns represent ingroup populations 1, 2, and 3 followed by the calculated D-statistic, Z-score, p-values, and f4-ratio statistic obtained from the Dtrios analysis. The last three columns represent the number of sites corresponding to the BBAA, ABBA, and BABA site patterns.

**Fig. S1.** The mutual *k*-nearest neighbors’ graph (mkNNG) ...