S1 Text. The concatenation and analysis of mitochondrial DNA for the Crotalus viridis complex, with best-supported models of sequence evolution provided.
We created a phylogenetic hypothesis based on 6 concatenated mtDNA regions acquired from GenBank (S2 Table: ATPase 8&6 (ATP8&6: TN+G); cytochrome B (Cyt-b: HKY + G); Displacement Loop (D-loop: HKY+G+I); NADH dehydrogenase subunit 2 (ND2: TIM (Transition Model)+G); and NADH dehydrogenase subunit 4L (ND4L: TN93+G+I). We merged sequences using the concatenation function in Geneious R8  and arrayed them according to their presence in the mitochondrial genome, moving clockwise from D-loop (at 12 o’clock). The final arrangement was: D-loop—Cyt-b—ND4L—ATP8—ATP6—ND2, with sequences aligned using default settings in MUSCLE v 3.8.31  (e.g. Gap Opening Cost = 15, Gap Extending Cost = 7). The model of nucleotide substitution for each mtDNA region was determined using ModelTest v 3.7 , with the concatenated sequences imported and partitioned into Mr. Bayes 3.2.5 [40–42], and the respective model of evolution applied to each partition. The Western Rattlesnake phylogeny was then estimated using the following conditions: heated chains = 4 (temp = 0.2); run simultaneously for 5,100,00 iterations; random seed = 16,288; burn-in = 1,000,000 iterations; subsampling frequency = 5,000 iterations; results = 4,000 trees, [i.e., ((5,100,000–1,000,000) x 4 / 5,000)]; branch lengths = unconstrained. Convergence was achieved within the first 250,000 iterations, autocorrelation was negligible within 1,024 samples, and log-likelihood plot indicated sufficient mixing. The resulting phylogeny was used for analyses requiring a phylogenetic comparative approach.
Citation: Davis MA, Douglas MR, Collyer ML, Douglas ME (2016) Correction: Deconstructing a Species-Complex: Geometric Morphometric and Molecular Analyses Define Species in the Western Rattlesnake (Crotalus viridis). PLoS ONE 11(2): e0149712. https://doi.org/10.1371/journal.pone.0149712
Published: February 12, 2016
Copyright: © 2016 Davis et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.