Standardized nuclear markers improve and homogenize species delimitation in Metazoa

All alignments, including SNP datasets, are in FASTA format and can be opened with standard alignment viewers. In alignments for approaches A1 and A2, ambiguity codes (R, Y, W, S, M, K) stand for positions inferred to be heterozygous. Phylogenetic trees are in NEWICK format, files including multiple named trees are in NEXUS format. Both can be opened in a standard phylogenetic tree viewer such as FigTree. Individual gene trees are unrooted, trees based on whole USCO datasets are rooted. SNP datasets recoded for NMDS analysis are tab-delimited text and numbers have the following meaning: 0: homozygous for more common allele, 1: heterozygous, 2: homozygous for less common allele. Unknown positions are represented by empty cells.

所有序列比对文件（包括单核苷酸多态性（SNP）数据集）均采用FASTA格式，可通过标准序列比对查看器打开。在针对方法A1与A2的序列比对中，歧义碱基编码（R、Y、W、S、M、K）代表被推断为杂合的位点。系统发育树采用NEWICK格式，包含多个命名树的文件则采用NEXUS格式。两类文件均可通过标准系统发育树查看器（如FigTree）打开。单基因树均为无根树，基于完整通用单拷贝同源基因（USCO）数据集构建的系统发育树则为有根树。用于非度量多维尺度（NMDS）分析的重编码SNP数据集为制表符分隔的文本文件，其中各数字的含义如下：0表示携带更常见等位基因的纯合位点，1表示杂合位点，2表示携带较稀有等位基因的纯合位点。未知位点以空单元格表示。