Datasets for "Dense sampling of taxa and characters improves phylogenetic resolution among deltocephaline leafhoppers (Hemiptera: Cicadellidae: Deltocephalinae)"

The following files were used to reconstruct the phylogeny of the leafhopper subfamily Deltocephalinae, using IQ-TREE v1.6.12 and ASTRAL v 4.10.5. Taxon_sampling.csv: contains the sequencing ids (1st column) and the taxonomic information (2nd column) of each sample. Sequencing ids were used in the alignment files and partition files. concatenated_nt.phy: concatenated nucleotide alignment used for the maximum likelihood analysis of Deltocephalinae by IQ-TREE v1.6.12. The file lists the sequences of 163,365 nucleotide positions from 429 genes in 730 samples. Hyphens are used to represent gaps. concatenated_nt_partition.nex: the partitions for the concatenated nucleotide alignment. The file partitions the 163,365 nucleotide characters into 429 character sets, and defines the best substitution model for each character set. concatenated_aa.phy: concatenated amino acid alignment used for the maximum likelihood analysis of Deltocephalinae by IQ-TREE v1.6.12. The file gives the sequences of 53,969 amino acids from 429 genes in 730 samples. Hyphens are used to represent gaps. concatenated_aa_partition.nex: the partitions for the concatenated amino acid alignment. The file partitions the 53,969 characters into 429 character sets, and defines the best substitution model for each character set. concatenated_nt_106taxa.phy: a reduced concatenated nucleotide alignment representing 107 samples x 86 genes. This alignment is used to estimate the divergence times of Deltocephalinae using MCMCTree in PAML v4.9. The file lists the sequences of 79,239 nucleotide positions from 86 genes in 107 samples. Hyphens are used to represent gaps. concatenated_nt_106taxa_partition.nex: the partitions for the nucleotide alignment concatenated_nt_106taxa.phy. The file partitions the 79,239 nucleotide characters into 86 character sets, and defines the best substitution model for each character set. Individual_gene_alignment.zip: contains 429 FAS files, one for each of the partitioned nucleotide character sets in the concatenated_nt_partition.nex file. Hyphens are used to represent gaps. These files were used to construct gene trees using IQ-TREE v1.6.12, followed by multispecies coalescent analysis using ASTRAL v 4.10.5.

本数据集借助IQ-TREE v1.6.12与ASTRAL v4.10.5两款软件，用于重建叶蝉科角顶叶蝉亚科（Deltocephalinae）的系统发育树。相关文件说明如下：
1. Taxon_sampling.csv：包含每份样本的测序ID（第一列）与分类学信息（第二列），测序ID将被应用于联配文件与分区文件中。
2. concatenated_nt.phy：用于IQ-TREE v1.6.12开展角顶叶蝉亚科最大似然分析的串联核苷酸联配文件。该文件涵盖730份样本中429个基因的163365个核苷酸位点序列，以连字符表示序列空位。
3. concatenated_nt_partition.nex：串联核苷酸联配的分区文件，将163365个核苷酸位点划分为429个特征集，并为每个特征集定义最优替换模型。
4. concatenated_aa.phy：用于IQ-TREE v1.6.12开展角顶叶蝉亚科最大似然分析的串联氨基酸联配文件。该文件涵盖730份样本中429个基因的53969个氨基酸位点序列，以连字符表示序列空位。
5. concatenated_aa_partition.nex：串联氨基酸联配的分区文件，将53969个氨基酸位点划分为429个特征集，并为每个特征集定义最优替换模型。
6. concatenated_nt_106taxa.phy：简化版串联核苷酸联配文件，对应107份样本×86个基因的数据集，用于通过PAML v4.9中的MCMCTree模块估算角顶叶蝉亚科的分化时间。该文件涵盖107份样本中86个基因的79239个核苷酸位点序列，以连字符表示序列空位。
7. concatenated_nt_106taxa_partition.nex：串联核苷酸联配文件concatenated_nt_106taxa.phy的分区文件，将79239个核苷酸位点划分为86个特征集，并为每个特征集定义最优替换模型。
8. Individual_gene_alignment.zip：包含429个FAS格式文件的压缩包，每个文件对应concatenated_nt_partition.nex中的一个分区核苷酸特征集，以连字符表示序列空位。上述文件被用于通过IQ-TREE v1.6.12构建基因树，随后借助ASTRAL v4.10.5开展多物种溯祖分析。