DOI: 10.5061/dryad.m0n61
title: Data from: Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards

description: Recent conceptual, technological, and methodological advances in
 phylogenetics have enabled increasingly robust statistical species
 delimitation in studies of biodiversity. As the variety of evidence
 purporting species diversity has increased, so too have the kinds of tools
 and inferential power of methods for delimiting species. Here we showcase
 an organismal system for a data-rich, comparative molecular approach to
 evaluating strategies of species delimitation among monitor lizards of the
 genus Varanus. The water monitors (Varanus salvator Complex), a widespread
 group distributed throughout Southeast Asia and southern India, have been
 the subject of numerous taxonomic treatments, which have drawn recent
 attention due to the possibility of undocumented species diversity. To
 date, studies of this group have relied on purportedly diagnostic
 morphological characters, with no attention given to the genetic
 underpinnings of species diversity. Using a 5-gene dataset, we estimated
 phylogeny and used multilocus genetic networks, analysis of population
 structure, and a Bayesian coalescent approach to infer species boundaries.
 Our results contradict previous systematic hypotheses, reveal surprising
 relationships between island and mainland lineages, and uncover novel,
 cryptic evolutionary lineages (i.e. new putative species). Our study
 contributes to a growing body of literature suggesting that, used in
 concert with other sources of data (e.g., morphology, ecology,
 biogeography), multilocus genetic data can be highly informative to
 systematists and biodiversity specialists when attempting to estimate
 species diversity and identify conservation priorities. We recommend
 holding in abeyance taxonomic decisions until multiple, converging lines
 of evidence are available to best inform taxonomists, evolutionary
 biologists, and conservationists.
description: BPP control
 filecontrol file for one set
 of priors and 1/11 topologies testedvaranus_1.bpp.ctlBPP sequence filephased sequence input file; for specimen IDs please refer to manuscript appendixvaranus1_V1.txtBPP lineage assignmentslineage assignment for each sample in the sequence filevaranus1.Imap.txtSTRUCTURE data fileinput data file for STRUCTURE analysis, with individual coded by haplotype assignment per locusINFILESTRUCTURE control filecontrol file for all parameters run in STRUCTURE analyses, for 1/20 population (K) inferencesmainparams.txtRAxML alignmentconcatenated, 5 locus alignment including all Varanus data and relevant outgroup samplesVaranus_all_concatenated.phyRAxML partitionslocus and codon partitions for phylogenetic analysesVaranus_partitionsDGL-alphaDGL-alpha fasta alignment for *BEAST analysesglor44.fastaL52L52 fasta alignment for *BEAST analysesglor52.fastaL74L74 fasta alignment for *BEAST analysesglor74.fastaPRLRPRLR fasta alignment for *BEAST analysesprlr.fastamtDNAND1, ND2, and flanking tRNAs fasta alignment for *BEAST analysesmt.fasta*BEAST xml 11 of 6 xml files for *BEAST analysisvaranus_sptree_1q_2rr_1strictclock.xml*BEAST xml 22 of 6 xml files for *BEAST analysesvaranus_sptree_1q_2rr_1ucldclock0.05.xml*BEAST xml 33 of 6 xml files for *BEAST analysesvaranus_sptree_2q_0rr_2strictclock.xml*BEAST xml 44 of 6 xml files for *BEAST analysesvaranus_sptree_2q_0rr_2ucldclock0.05.xml*BEAST xml 55 of 6 xml files for *BEAST analysesvaranus_sptree_2q_2rr_1strictclock.xml*BEAST xml 66 of 6 xml files for *BEAST analysesvaranus_sptree_2q_2rr_1ucldclock0.05.xml