DOI: 10.6078/d1s99x
title: Datasets for Draco lineatus phylogenomics study

description: The biota of Sulawesi is noted for its high degree of endemism and for its
 substantial levels of in situ biological diversification. While the
 island’s long period of isolation and dynamic tectonic history have been
 implicated as drivers of regional diversification, this has rarely been
 tested in the context of an explicit geological framework. Here we provide
 a tectonically-informed biogeographical framework that we use to explore
 the diversification history of Sulawesi flying lizards (the Draco lineatus
 Group), a radiation that is endemic to Sulawesi and its surrounding
 islands. We employ a framework for inferring cryptic speciation that
 involves phylogeographic and genetic clustering analyses as a means of
 identifying potential species followed by population demographic
 assessment of divergence-timing and rates of bi-directional migration as
 means of confirming lineage independence (and thus species status). Using
 this approach, phylogenetic and population genetic analyses of
 mitochondrial sequence data obtained for 613 samples, a 50-SNP data set
 for 370 samples, and a 1249-locus exon-capture data set for 106 samples
 indicate that the current taxonomy substantially understates the true
 number of Sulawesi Draco species, that both cryptic and arrested
 speciation have taken place, and that ancient hybridization confounds
 phylogenetic analyses that do not explicitly account for reticulation. The
 Draco lineatus Group appears to comprise 15 species – nine on Sulawesi
 proper and six on peripheral islands. The common ancestor of this group
 colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two
 ancestral islands, and began to radiate ~6 Ma as new islands formed and
 were colonized via overwater dispersal. The enlargement and amalgamation
 of many of these proto-islands into modern Sulawesi, especially during the
 past 3 Ma, set in motion dynamic species interactions as once-isolated
 lineages came into secondary contact, some of which resulted in lineage
 merger, and others surviving to the present.
                                 
description: We generated a mitochondrial sequence data
 set for 593 individuals representing the nine currently-recognized species
 in the <em>Draco lineatus</em> Group (McGuire et al. 2007)
 plus 20 additional individuals representing this clade’s sister taxon,
 <em>Draco bimaculatus,</em> from the Philippines (see McGuire
 and Alcala 2000). This sampling regime allowed for many individuals to be
 screened for each species with particularly dense coverage of Sulawesi
 proper. The mitochondrial data
 set was subjected to partitioned Bayesian phylogenetic analysis using
 MrBayes 3.2.7 (Ronquist et al. 2012), with 5 <em style="color:#1f1f1f;font-family:'Times New Roman' , serif;font-size:12pt;text-indent:0.5in;">a
 priori</em> designated partitions
 (ND2 codon positions 1, 2, and 3, 12S rRNA+ND2 flanking tRNAs, and 16S
 rRNA). The most appropriate nucleotide substitution model for each
 partition was selected using likelihood ratio-tests implemented in
 MrModelTest (Nylander 2004). Four separate analyses were undertaken, each
 with Metropolis-coupling (four chains), and 50 million generations.
 Convergence was assessed by confirming that all four analyses settled on
 the same tree topology and parameter estimates and that all model
 parameters had ESS values over 200 using Tracer v1.7.2 (Rambaut et al.
 2018). The tree was rooted using the outgroup<em>
 </em><em style="color:#1f1f1f;font-family:'Times New Roman' , serif;font-size:12pt;text-indent:0.5in;">Draco
 bimaculatus</em>.
 We also
 obtained a more comprehensive multi-locus data set comprising 1249
 sequence loci for 106 individual <em>Draco</em>
 <em>lineatus</em> Group samples using an exon-capture approach
 plus two <em>D. bimaculatus</em> that serve as the outgroup.
 These data were analyzed using RAxML and IQTree, ASTRAL-III, StarBEAST,
 and BPP v. 4.3.8 with a number of combinations of the full set of 108
 samples included. For example, the full data set was too large for
 StarBEAST, so subsets of samples for each mitochondrial lineage were
 included (35, 38, or 41 samples).
  
description: The data files can be opened with any text editor, such as BBEdit
 and can be analyzed using programs compatible with the nexus and phylip
 file formats.