Virus Relatedness Host Tree

Phylogeny of 45 <i>Drosophilidae </i>host species used in this study. <br>Publicly available sequences of the 28S, Adh, Amyrel, COI, COII, RpL32, and SOD genes were collected from Genbank (see https://doi.org/10.6084/m9.figshare.13079366.v1 for a full breakdown of genes and accessions by species). Gene sequences were aligned in Geneious v9.1.8 (https://www.geneious.com) using a progressive pairwise global alignment algorithm with free end gaps and a 70% similarity IUB cost matrix. Gap open penalties, gap extension penalties, and refinement iterations were kept as default. <br>Phylogenetic reconstruction was performed using BEAST v1.10.4 with genes partitioned into separate ribosomal (28S), mitochondrial (COI, COII), and nuclear (Adh, Amyrel, RpL32, SOD) groups. The mitochondrial and nuclear groups were further partitioned into groups for codon position 1+2 and codon position 3, with unlinked substitution rates and base frequencies across codon positions. Each group was fitted to separate relaxed uncorrelated lognormal molecular clock models using random starting trees and 4-category gamma-distributed HKY substitution models. The BEAST analysis was run twice, with 1 billion MCMCglmm generations sampled every 100,000 iterations, using a birth-death process tree-shape prior. Model trace files were evaluated for chain convergence, sampling, and autocorrelation using Tracer v1.7.1