Datasets for Draco lineatus phylogenomics study
Creators: name: McGuire, Jimmy
Publisher: name: Zenodo
Year: 2023
Subjects: Genomics
Introgression
Mitochondria
Phylogeography
Phylogenetics
Population genetics
Reptiles
Indonesia

description: The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of <em>in situ</em> 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 <em>Draco lineatus</em> 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 <em>Draco</em> 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 <em>Draco lineatus</em> 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: 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.Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001<br>Award Number: DEB 0328700Funding provided by: National Geographic Society<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100006363<br>Award Number: Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001<br>Award Number: DEB 0640967Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001<br>Award Number: DEB 1258185Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001<br>Award Number: DEB 1457845Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001<br>Award Number: DEB 1652988
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).