Data from: Speciation and historical invasions of the Asian black-spined toad (Duttaphrynus melanostictus)

This data package includes the following datasets analyzed in the corresponding publication: An alignment (fasta format) of 130,792 bp concatenating the RAD tags present in at least 80 of the 88 Duttaphrynus samples considered (Duttaphrynus_ddRADseq_n88p80_131kb.fas). It was used to produce the tree presented in Supplementary Fig. 1. An alignment (fasta format) of 83,652 bp concatenating the RAD tags present in 25 unadmixed Duttaphrynus samples (Duttaphrynus_ddRADseq_n25p25_84kb.fas). It was used in the phylogenetic analyses presented in Fig. 1a and Supplementary Fig. 2. Two alignments (fasta format) of 482,648 bp and 628,293 bp concatenating the RAD tags present in 17 and 52 samples of D. melanostictus s. s. and D. cf. melanostictus, respectively (Duttaphrynus_melanostictus_ss_West_n17p17_483kb.fas and Duttaphrynus_cf_melanostictus_East_n52p52_628kb.fas). These were used in the network analyses presented in Fig. 2b. Three matrices of 851 SNPs, 3364 SNPs and 4782 SNPs, genotyped in 69, 17 and 52 samples of D. melanostictus s. l., D. melanostictus s. s. and D. cf. melanostictus, respectively (Duttaphrynus_melanostictus_sl_n69p69wrs_851SNPs.str, Duttaphrynus_melanostictus_ss_West_n17p17wrs_3364SNPs.str, Duttaphrynus_cf_melanostictus_East_n52p52wrs_4782SNPs.str). These were used in the Bayesian clustering and PCA analyses presented in Fig. 2a and Supplementary Figs. 3-4. An alignement (fasta format) of 383 sequences of the mitochondrial gene 16S (558 bp), including 382 sequences of Duttaphrynus + 1 outgroup (Duttaphrynus_16S.fas). It was used in the network analysis presented in Fig. 3b and the phylogenetic analysis presented in Supplementary Fig. 5. An alignement (fasta format) of 495 sequences of the mitochondrial gene ND3 (469 bp), including 494 sequences of Duttaphrynus + 1 outgroup (Duttaphrynus_ND3.fas). It was used in the network analysis presented in Fig. 3b and the phylogenetic analysis presented in Supplementary Fig. 6. An alignement (fasta format) of 27 full or partial mitogenomes (16,844 bp), including 26 sequences of Duttaphrynus + 1 outgroup (Duttaphrynus_mitogenomes.fas). It was used in the phylogenetic analyses presented in Fig. 1b and Supplementary Fig. 7. The meta-data associated to these datasets are provided in the corresponding publication (Supplementary Data 1 and 4).本数据包包含对应已发表文献中分析所用的如下数据集： 1. 一段长度为130792 bp（碱基对，base pair）的比对序列（FASTA格式），由纳入分析的88份杜蟾属（Duttaphrynus）样本中至少80份样本所携带的RAD标签（RAD tag）拼接而成，文件名为Duttaphrynus_ddRADseq_n88p80_131kb.fas。该数据集用于生成补充图1中的系统发育树。 2. 一段长度为83652 bp（碱基对）的比对序列（FASTA格式），由25份未发生基因混杂的杜蟾属样本所携带的RAD标签拼接而成，文件名为Duttaphrynus_ddRADseq_n25p25_84kb.fas。该数据集用于图1a及补充图2中的系统发育分析。 3. 两段长度分别为482648 bp和628293 bp的比对序列（FASTA格式），分别由17份黑眶蟾蜍指名亚种（Duttaphrynus melanostictus s. s.）样本与52份疑似黑眶蟾蜍（Duttaphrynus cf. melanostictus）样本所携带的RAD标签拼接而成，对应文件名为Duttaphrynus_melanostictus_ss_West_n17p17_483kb.fas及Duttaphrynus_cf_melanostictus_East_n52p52_628kb.fas。上述数据集用于图2b中的种群网状分析。 4. 三组基因型矩阵，分别包含851个、3364个及4782个单核苷酸多态性位点（Single Nucleotide Polymorphism, SNP，复数形式SNPs），分别在69份广义黑眶蟾蜍（Duttaphrynus melanostictus s. l.）、17份黑眶蟾蜍指名亚种及52份疑似黑眶蟾蜍样本中完成基因分型，对应文件名为Duttaphrynus_melanostictus_sl_n69p69wrs_851SNPs.str、Duttaphrynus_melanostictus_ss_West_n17p17wrs_3364SNPs.str及Duttaphrynus_cf_melanostictus_East_n52p52wrs_4782SNPs.str。上述数据集用于图2a及补充图3-4中的贝叶斯聚类与主成分分析（Principal Component Analysis, PCA）。 5. 一段包含383条序列的线粒体16S基因比对序列（FASTA格式），序列总长558 bp（碱基对），其中包含382条杜蟾属序列与1条外类群（outgroup）序列，文件名为Duttaphrynus_16S.fas。该数据集用于图3b中的种群网状分析及补充图5中的系统发育分析。 6. 一段包含495条序列的线粒体ND3基因比对序列（FASTA格式），序列总长469 bp（碱基对），其中包含494条杜蟾属序列与1条外类群序列，文件名为Duttaphrynus_ND3.fas。该数据集用于图3b中的种群网状分析及补充图6中的系统发育分析。 7. 一段包含27条完整或部分线粒体基因组（mitogenome）序列的比对序列（FASTA格式），序列总长16844 bp（碱基对），其中包含26条杜蟾属序列与1条外类群序列，文件名为Duttaphrynus_mitogenomes.fas。该数据集用于图1b及补充图7中的系统发育分析。 上述数据集的关联元数据已在对应已发表文献（补充数据1及4）中提供。