Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus Calandrella, with the description of a range-restricted African relic taxon

This deposition contains the phylogenetic and species delimitation data for the manuscript "Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus <em>Calandrella</em>, with the description of a range-restricted African relic taxon" by Stervander <em>et al</em>. For details of samples/sequences/leaves, please refer to Appendix A of the above manuscript. <strong>Phylogenetic analyses</strong> Fasta sequence alignment of cytochrome b for the lark family and outgroups: Alaudidae_cytb_extended_200316.fa BEAST v. 2.6.1 input file: Alaudidae_cytb_HKYGI_BDrelLN_modOp2003_20M1K.xml BEAST v. 2.6.1 output log file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.log BEAST v. 2.6.1 output (raw) trees file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.trees TreeAnnotator maximum credibility clade tree based on BEAST v. 2.6.1 output, newick format: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K_c40Mbi5.mccmed.nwk <strong>Species delimitation</strong> Input tree, manipulated to remove negative branch lengths (replaced by 0) and tips/leafs that are single representatives of a species, based on current taxonomy (IOC v. 10.2), newick format: Alaudidae_cytb_HKYGI_BDrelLN_c40Mbi5_mccmed_nonNeg_multiSeq_ingroup_remDuplicate.nwk mPTP text output of the multi-rate species delimitation, containing command for run and species delimitation results: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.txt mPTP likelihood log of the multi-rate species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.out.txt mPTP output tree in SVG format, with support values for species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.combined.svg本存档包含Stervander等人发表的论文《百灵科鸟类（Aves: Alaudidae）的分子物种界定及<em>Calandrella</em>属综合分类学研究，并记述一类分布受限的非洲孑遗类群》的系统发育与物种界定数据。有关样本、序列及系统发育树叶节点的详细信息，请详见上述论文的附录A。 <strong>系统发育分析</strong> FASTA序列比对文件（百灵科与外类群细胞色素b）：Alaudidae_cytb_extended_200316.fa BEAST v. 2.6.1 输入文件：Alaudidae_cytb_HKYGI_BDrelLN_modOp2003_20M1K.xml BEAST v. 2.6.1 输出日志文件：Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.log BEAST v. 2.6.1 输出（原始）树文件：Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.trees 基于BEAST v. 2.6.1输出结果构建的TreeAnnotator最大可信支系共识树（Newick格式）：Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K_c40Mbi5.mccmed.nwk <strong>物种界定</strong> 基于当前分类学体系（国际鸟类学委员会v.10.2），经处理以移除负支长（替换为0）并去除仅对应单一物种的末端分支与叶节点的输入树（Newick格式）：Alaudidae_cytb_HKYGI_BDrelLN_c40Mbi5_mccmed_nonNeg_multiSeq_ingroup_remDuplicate.nwk 多速率泊松树过程（mPTP）文本输出文件（含运行命令与物种界定结果）：Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.txt 多速率泊松树过程（mPTP）似然日志文件：Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.out.txt 带有物种界定支持值的SVG格式mPTP输出树：Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.combined.svg