DOI: 10.5061/dryad.crjdfn38p
title: Supplementary information for: The artefactual branch effect and phylogenetic conflict: Species delimitation with gene flow in mangrove pit vipers (Trimeresurus purpureomaculatus-erythrurus complex)

description: 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.
description: This package includes phylogenetic trees, RADseq data sequencing
 report, and supplementary tables and figures.
description: # Supplementary Information for Systematic Biology: manuscript ID
 USYB-2023-054 --- 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) based on the
 Fast-Greedy and Infomap algorithms **Fig. S2.** NetView plots of K=1–19.
 **Fig. S3.** Preserved specimen of *Trimeresurus erythrurus* CAS239502
 (sequenced in this study) from Ayeyarwady region, Pathein district.