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

本研究使用的45种果蝇科（Drosophilidae）寄主物种的系统发育关系。<br>从GenBank（基因库）中获取了28S、Adh、Amyrel、COI、COII、RpL32及SOD基因的公开序列；各物种对应的基因及登录号的完整明细参见https://doi.org/10.6084/m9.figshare.13079366.v1。<br>使用Geneious v9.1.8（https://www.geneious.com）对基因序列进行多序列比对：采用带自由末端缺口的渐进式成对全局比对算法，搭配70%相似度的IUB代价矩阵；缺口开放罚分、缺口延伸罚分及优化迭代数均采用默认参数。<br>使用BEAST v1.10.4开展系统发育重建：将基因划分为核糖体基因组（28S）、线粒体基因组组（COI、COII）与核基因组组（Adh、Amyrel、RpL32、SOD）三类。线粒体基因组组与核基因组组进一步按密码子第1+2位和第3位进行拆分，并设置不同密码子位点间互不关联的替换速率与碱基频率。每个分组均采用随机起始树与4类别伽马分布HKY替换模型，拟合独立的松弛无相关对数正态分子钟模型。本次BEAST分析共运行两次，以出生-死亡过程作为树形先验，进行10亿次MCMCglmm迭代，每10万代采样一次；使用Tracer v1.7.1评估模型追踪文件的链收敛性、采样情况与自相关性。