Table 1 in Phylogenomics of Phengodidae (Coleoptera: Elateroidea): towards a natural classification of a bioluminescent and paedomorphic beetle lineage, with recognition of a new subfamily
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Table 1. Statistical support for internal branches measured for each phylogenetic reconstruction based on nucleotide (NT) datasets with 45 % completeness. Abbreviations: CPU, unpartitioned analysis; CPP, partitioned analysis. For maximum likelihood (ML) analyses: aBayes, Bayesian-like transformation of aLRT; gCF, gene concordance factor; sCF, site concordance factor; SH-aLRT, Shimodaira – Hasegawa-like approximate likelihood ratio test; UFBoot, ultrafast bootstrap. For Bayesian inference (BI) analyses: PP, posterior probabilities of the clades of the majority-rule consensus tree of the posterior distribution generated via the Markov chain Monte Carlo. For coalescent ASTRAL analysis: Local PP, local posterior probabilities. Grey colour indicates UFBoot> 95 %, PP> 0.95, sCF> 37, or Local PP> 0.95. Dataset / treeSupport(Phengodidae + Rhagophthalmidae)Phengodidae((Mastinocerinae + Cenophenginae) + Phengodinae)(Mastinocerinae + Cenophenginae)CydistinaeMastinocerinaePhengodinaeML- 45 CPU-NTSH-aLRT / aBayes / UFBoot100 / 1 / 100100/ 1 /100100 / 1/ 100100/ 1 /100100 / 1 /100100/ 1 /10099.7/ 1 / 100ML- 45 CPP-NTSH-aLRT / aBayes / UFBoot100 / 1 / 100100/ 1 /100100 / 1/ 100100/ 1 /100100 / 1 /100100/ 1 /10097.1 / 1 / 99ML- 45 CPU-NTgCF /sCF8.39 / 39.74.3/ 32.48 / 32.77.72/ 32.718.3 / 53.39.26 / 29.223.1 / 53ML- 45 CPP-NTgCF /sCF8.39 / 39.84.3 / 38.38 / 38.77.72 / 34.118.3 /56.19.26 / 26.723.1 / 47.8BI- 45 CPU-NTPP1110.99710.9970.997BI- 45CPP-NTPP0.8710.9130.9130.82610.8260.826ASTRAL- 45 CP-NT Local PP0.4430.8910.7540.9940.7970.934
表1. 基于完整度为45%的核苷酸（NT, nucleotide）数据集构建的各系统发育重建的内部分支统计支持度。缩写说明：CPU为非分区分析（unpartitioned analysis），CPP为分区分析（partitioned analysis）。针对最大似然（ML, maximum likelihood）分析：aBayes为类贝叶斯近似似然比变换（Bayesian-like transformation of aLRT）；gCF为基因一致性因子（gene concordance factor）；sCF为位点一致性因子（site concordance factor）；SH-aLRT为类Shimodaira-Hasegawa近似似然比检验（Shimodaira – Hasegawa-like approximate likelihood ratio test）；UFBoot为超快速自展检验（ultrafast bootstrap）。针对贝叶斯推断（BI, Bayesian inference）分析：PP为通过马尔可夫链蒙特卡洛（Markov chain Monte Carlo）生成的后验分布多数规则共识树的分支后验概率（posterior probabilities of the clades of the majority-rule consensus tree of the posterior distribution）。针对溯祖ASTRAL分析：Local PP为局部分支后验概率（local posterior probabilities）。灰色色块代表UFBoot>95%、PP>0.95、sCF>37或Local PP>0.95的分支。 数据集/树支持度 (Phengodidae + Rhagophthalmidae) Phengodidae ((Mastinocerinae + Cenophenginae) + Phengodinae) (Mastinocerinae + Cenophenginae) Cydistinae Mastinocerinae Phengodinae ML-45 CPU-NT SH-aLRT / aBayes / UFBoot 100 / 1 / 100 100 / 1 / 100 100 / 1 / 100 100 / 1 / 100 100 / 1 / 100 100 / 1 / 100 99.7 / 1 / 100 ML-45 CPP-NT SH-aLRT / aBayes / UFBoot 100 / 1 / 100 100 / 1 / 100 100 / 1 / 100 100 / 1 / 100 100 / 1 / 100 100 / 1 / 100 97.1 / 1 / 99 ML-45 CPU-NT gCF / sCF 8.39 / 39.7 4.3 / 32.4 8 / 32.7 7.72 / 32.7 18.3 / 53.3 9.26 / 29.2 23.1 / 53 ML-45 CPP-NT gCF / sCF 8.39 / 39.8 4.3 / 38.3 8 / 38.7 7.72 / 34.1 18.3 / 56.1 9.26 / 26.7 23.1 / 47.8 BI-45 CPU-NT PP 1 1 0.997 1 0.997 0.997 0.997 BI-45 CPP-NT PP 0.87 1 0.913 0.913 0.826 1 0.826 0.826 ASTRAL-45 CP-NT Local PP 0.443 0.891 0.754 0.994 0.797 0.934
