NEXUS file for Phylogeny and Biogeography of the Sharpshooters (Hemiptera: Cicadellidae: Cicadellinae)

The text file contains the original aligned DNA nucleotide sequence data used in the phylogenetic analyses of Feng et al. (in review), comprising the 3 protein-coding genes (histone H3, cytochrome oxidase I and 2) and 2 ribosomal genes (28S D8 and 16S). The text file is marked up according to the standard NEXUS format commonly used by various phylogenetic analysis software packages. The file will be parsed automatically by a variety of programs that recognize NEXUS as a standard bioinformatics file format. The first six lines of the file identify the file as NEXUS, indicate that the file contains data for 257 taxa (species) and 2995 characters (nucleotide positions), indicate that the characters are DNA sequence, that gaps inserted into the DNA sequence alignment are indicated by a dash, and that missing data are indicated by a question mark. The remainder of the file contains the aligned nucleotide sequence data for the five genes. Data partitions, representing the individual genes and different codon positions of the protein-coding genes, are indicated by the lines beginning "charset" near the end of the file. Two supplementary tables in the provided PDF file provide additional information on the species in the dataset, including the GenBank accession numbers for the sequence data (Table S1) and the DNA substitution models used for each of the data partitions used for analyses in the phylogenetic analysis program IQ-Tree (version 1.6.8) (Table S3), as described in the Methods section of the paper. The supplemental tables will also be linked to the article upon publication at the journal website.

该文本文件包含用于 Feng 等人（待审稿）的进化分析的原版对齐 DNA 核苷酸序列数据，包括 3 个蛋白质编码基因（组蛋白 H3、细胞色素氧化酶 I 和 II）以及 2 个核糖体基因（28S D8 和 16S）。文本文件按照标准 NEXUS 格式进行标注，该格式为多种进化分析软件包所普遍采用。该文件将被多种识别 NEXUS 作为标准生物信息学文件格式的程序自动解析。文件的前六行标识该文件为 NEXUS，表明文件包含 257 个分类单元（物种）和 2995 个字符（核苷酸位置）的数据，指出字符代表 DNA 序列，DNA 序列对齐中插入的间隙由破折号表示，缺失数据由问号表示。文件的其余部分包含五个基因的对齐核苷酸序列数据。数据分区，代表单个基因和蛋白质编码基因的不同密码子位置，由文件末尾附近的“charset”行指示。提供的 PDF 文件中的两个补充表格提供了数据集中物种的额外信息，包括序列数据的 GenBank 访问号（表 S1）以及用于在 IQ-Tree（版本 1.6.8）进化分析程序中进行分析的每个数据分区所采用的 DNA 替换模型（表 S3），如论文方法部分所述。补充表格也将与期刊网站上的文章一同发布。