DOI: 10.5061/dryad.6hdr7srbt
title: Inconsistent performance of multi-type genomic data in phylogenomics of neuropteridan insects, with solutions toward conflicting results

description: Reconstructing the tree of life is facing challenges to infer accurate and
 robust phylogeny based on large data in the genomic era. Currently,
 universal single-copy orthologs (USCOs), ultraconserved elements (UCEs),
 and mitochondrial genomes (mitogenomes) are widely used to reconstruct
 phylogeny. In this study, the higher-level phylogeny of Neuropterida is
 reconstructed based on USCOs, UCEs, and mitogenomes assembled from 42
 newly sequenced low-coverage genomes (above 32.80X), representing all
 orders and almost all families except Rhachiberothidae, under various
 settings in data filtering, model selection, and strategy of tree
 reconstruction. According to cautious evaluation, the topology based on
 amino acids matrices of the USCOs filtered by multifactorial strategies
 under the site heterogeneity model (LG + PMSF (C20)) is demonstrated to be
 the most robust. The average bootstrap support (ABS) values, an important
 criterion in gene filtering, show great variations between different
 repetitions. Applying fossils calibration at deeper nodes close to the
 root of the phylogeny is demonstrated to facilitate accurate estimation of
 evolutionary timescales by comparing three different calibration schemes
 (deeper nodes, shallower nodes and a combination of both). These results
 highlight the complexity of genomic data and offer an integrative solution
 to overcome the systematic error in phylogenomic inference.
description: # Inconsistent performance of multi-type genomic data in phylogenomics of
 neuropteridan insects, with solutions toward conflicting results Dataset
 DOI: [10.5061/dryad.6hdr7srbt](10.5061/dryad.6hdr7srbt) ## Description of
 the data and file structure Supplementary data from: Inconsistent
 performance of multi-type genomic data in phylogenomics of neuropteridan
 insects, with solutions toward conflicting results ### Files and variables
 #### File: Dryad_data.zip **Description:** It is a folder containing the
 information of the phylogeny and Divergence time. ```├─1.phylogeny │
 ├─Mitogenome │ │ ├─1.site-homogeneous model [folder] │ │ │ ├─BI [folder,
 Bayesian inference (BI) under site-homogeneous model was performed using
 MrBayes v3.1.2] │ │ │ │ ├─AA [folder] │ │ │ │ │ AA.nex [AA matrix for BI]
 │ │ │ │ │ AA.tre [BI tree using AA matrix] │ │ │ │ │ │ │ │ │ ├─PCG12
 [folder] │ │ │ │ │ PCG12.nex [PCG12 matrix for BI] │ │ │ │ │ PCG12.tre [BI
 tree using PCG12 matrix] │ │ │ │ │ │ │ │ │ ├─PCG123 │ │ │ │ │ PCG123.nex
 [PCG123 matrix for BI] │ │ │ │ │ PCG123.tre [BI tree using PCG123 matrix]
 │ │ │ │ │ │ │ │ │ ├─PCG123R │ │ │ │ │ PCG123R.nex [PCG123R matrix for BI]
 │ │ │ │ │ PCG123R.tre [BI tree using PCG123R matrix] │ │ │ │ │ │ │ │ │
 └─PCG12R │ │ │ │ PCG12R.nex [PCG12R matrix for BI] │ │ │ │ PCG12R.tre [BI
 tree using PCG12R matrix] │ │ │ │ │ │ │ └─ML [folder, maximum likelihood
 (ML) trees were inferred using IQ-TREE v1.6.10 [88] with the optimization
 model automatically selected for each gene (-m MFP) for all matrices] │ │
 │ ├─AA [folder] │ │ │ │ AA.fas [AA matrix] │ │ │ │ AA.fas.treefile [ML
 tree using AA matrix] │ │ │ │ │ │ │ ├─PCG12 [folder] │ │ │ │ PCG12.fas
 [PCG12 matrix] │ │ │ │ PCG12.fas.treefile [ML tree using PCG12 matrix] │ │
 │ │ │ │ │ ├─PCG123 [folder] │ │ │ │ PCG123.fas [PCG123 matrix] │ │ │ │
 PCG123.fas.treefile [ML tree using PCG123 matrix] │ │ │ │ │ │ │ ├─PCG123R
 [folder] │ │ │ │ PCG123R.fas [PCG123R matrix] │ │ │ │ PCG123R.fas.treefile
 [ML tree using PCG123R matrix] │ │ │ │ │ │ │ └─PCG12R [folder] │ │ │
 PCG12R.fas [PCG12R matrix] │ │ │ PCG12R.fas.treefile [ML tree using PCG12R
 matrix] │ │ │ │ │ └─2.site-heterogeneous model [folder] │ │
 PCG123R_bpcomp.con.tre [BI tree based the PCGR matrix under the
 site-heterogeneous model (CAT-GTR) was also reconstructed with PhyloBayes
 v3.3] │ │ │ └─USCO_UCE [folder] │ ├─0.all [folder, all USCOs and UCEs] │ │
 ├─1.USCO_all [folder, USCO] │ │ │ USCO_all.fas [USCO_all matrix] │ │ │
 USCO_all_astral.tre [coalescent analyses based on USCO_all matrix] │ │ │
 USCO_all_Dayhoff6.fas [Dayhoff6 recoding USCO_all matrix] │ │ │
 USCO_all_Dayhoff6.fas.treefile [concatenated ML analyses using Dayhoff6
 recoding scheme based on USCO_all matrix] │ │ │
 USCO_all_partition.txt.treefile [concatenated partitioning ML analyses
 based on USCO_all matrix] │ │ │ USCO_all_pmsf2.fas.treefile [concatenated
 ML analyses under PMSF model based on USCO_all matrix] │ │ │ │ │
 └─2.UCE_all [folder, UCE] │ │ UCE_all.fas [UCE_all matrix] │ │
 UCE_all_astral.tre [coalescent analyses based on UCE_all matrix] │ │
 UCE_all_partition.txt.treefile [concatenated partitioning ML analyses
 based on UCE_all matrix] │ │ │ ├─1.Strategy I [folder, USCOs and UCEs were
 filtered based on the average bootstrap support (ABS) values of the gene
 trees (ABS≥70, 75, 80 and 85).] │ │ ├─1.USCO_I_abs70 [folder] │ │ │
 USCO_I_abs70.fas [USCO_I_abs70 matrix] │ │ │ USCO_I_abs70_astral.tre
 [coalescent analyses based on USCO_I_abs70 matrix] │ │ │
 USCO_I_abs70_Dayhoff6.fas [Dayhoff6 recoding USCO_I_abs70 matrix] │ │ │
 USCO_I_abs70_Dayhoff6.treefile [concatenated ML analyses using Dayhoff6
 recoding scheme based on USCO_I_abs70 matrix] │ │ │
 USCO_I_abs70_partition.treefile [concatenated partitioning ML analyses
 based on USCO_I_abs70 matrix] │ │ │ USCO_I_abs70_pmsf2.treefile
 [concatenated ML analyses under PMSF model based on USCO_I_abs70 matrix] │
 │ │ │ │ ├─2.USCO_I_abs75 [folder] │ │ │ USCO_I_abs75.fas [USCO_I_abs75
 matrix] │ │ │ USCO_I_abs75_astral.tre [coalescent analyses based on
 USCO_I_abs75 matrix] │ │ │ USCO_I_abs75_Dayhoff6.fas [Dayhoff6 recoding
 USCO_I_abs75 matrix] │ │ │ USCO_I_abs75_Dayhoff6.fas.treefile
 [concatenated ML analyses using Dayhoff6 recoding scheme based on
 USCO_I_abs75 matrix] │ │ │ USCO_I_abs75_partition.txt.treefile
 [concatenated partitioning ML analyses based on USCO_I_abs75 matrix] │ │ │
 USCO_I_abs75_pmsf2.fas.treefile [concatenated ML analyses under PMSF model
 based on USCO_I_abs75 matrix] │ │ │ │ │ ├─3.USCO_I_abs80 [folder] │ │ │
 USCO_I_abs80.fas [USCO_I_abs80 matrix] │ │ │ USCO_I_abs80_astral.tre
 [coalescent analyses based on USCO_I_abs80 matrix] │ │ │
 USCO_I_abs80_Dayhoff6.fas [Dayhoff6 recoding USCO_I_abs80 matrix] │ │ │
 USCO_I_abs80_Dayhoff6.fas.treefile [concatenated ML analyses using
 Dayhoff6 recoding scheme based on USCO_I_abs80 matrix] │ │ │
 USCO_I_abs80_partition.txt.treefile [concatenated partitioning ML analyses
 based on USCO_I_abs80 matrix] │ │ │ USCO_I_abs80_pmsf2.fas.treefile
 [concatenated ML analyses under PMSF model based on USCO_I_abs80 matrix] │
 │ │ │ │ ├─4.USCO_I_abs85 [folder] │ │ │ USCO_I_abs85.fas [USCO_I_abs85
 matrix] │ │ │ USCO_I_abs85_astral.tre [coalescent analyses based on
 USCO_I_abs85 matrix] │ │ │ USCO_I_abs85-Dayhoff6.fas [Dayhoff6 recoding
 USCO_I_abs85 matrix] │ │ │ USCO_I_abs85-Dayhoff6.fas.treefile
 [concatenated ML analyses using Dayhoff6 recoding scheme based on
 USCO_I_abs85 matrix] │ │ │ USCO_I_abs85_partition.txt.treefile
 [concatenated partitioning ML analyses based on USCO_I_abs85 matrix] │ │ │
 USCO_I_abs85_pmsf2.fas.treefile [concatenated ML analyses under PMSF model
 based on USCO_I_abs85 matrix] │ │ │ │ │ ├─5.UCE_I_abs70 [folder] │ │ │
 UCE_I_abs70.fas [UCE_I_abs70 matrix] │ │ │ UCE_I_abs70_astral.tre
 [coalescent analyses based on UCE_I_abs70 matrix] │ │ │
 UCE_I_abs70_partition.txt.treefile [concatenated partitioning ML analyses
 based on UCE_I_abs70 matrix] │ │ │ │ │ ├─6.UCE_I_abs75 [folder] │ │ │
 UCE_I_abs75.fas [UCE_I_abs75 matrix] │ │ │ UCE_I_abs75_astral.tre
 [coalescent analyses based on UCE_I_abs75 matrix] │ │ │
 UCE_I_abs75_partition.txt.treefile [concatenated partitioning ML analyses
 based on UCE_I_abs75 matrix] │ │ │ │ │ ├─7.UCE_I_abs80 [folder] │ │ │
 UCE_I_abs80.fas [UCE_I_abs80 matrix] │ │ │ UCE_I_abs80_astral.tre
 [coalescent analyses based on UCE_I_abs80 matrix] │ │ │
 UCE_I_abs80_partition.txt.treefile [concatenated partitioning ML analyses
 based on UCE_I_abs80 matrix] │ │ │ │ │ └─8.UCE_I_abs85 [folder] │ │
 UCE_I_abs85.fas [UCE_I_abs85 matrix] │ │ UCE_I_abs85.partition.treefile
 [concatenated partitioning ML analyses based on UCE_I_abs85 matrix] │ │
 UCE_I_abs85_astral.tre [coalescent analyses based on UCE_I_abs85 matrix] │
 │ │ ├─2.Strategy II [folder, USCOs and UCEs were filtered based on taxa
 completeness(70%, 75%, 80%, 85% and 90%)] │ │ ├─1.USCO_II_70 [folder] │ │
 │ USCO_II_70-astral.tre [coalescent analyses based on USCO_II_70 matrix] │
 │ │ USCO_II_70.fa [USCO_II_70 matrix] │ │ │ USCO_II_70.partition.treefile
 [concatenated partitioning ML analyses based on USCO_II_70 matrix] │ │ │
 USCO_II_70.pmsf2.fa.treefile [concatenated ML analyses under PMSF model
 based on USCO_II_70 matrix] │ │ │ USCO_II_70_Dayhoff6.fas [Dayhoff6
 recoding USCO_II_70 matrix] │ │ │ USCO_II_70_Dayhoff6.fas.treefile
 [concatenated ML analyses using Dayhoff6 recoding scheme based on
 USCO_II_70 matrix] │ │ │ │ │ ├─10.UCE_II_90 [folder] │ │ │ UCE_II_90.fa
 [UCE_II_90 matrix] │ │ │ UCE_II_90.partition.treefile [concatenated
 partitioning ML analyses based on UCE_II_90 matrix] │ │ │
 UCE_II_90_astral.tre [coalescent analyses based on UCE_II_90 matrix] │ │ │
 │ │ ├─2.USCO_II_75 [folder] │ │ │ USCO_II_75-astral.tre [coalescent
 analyses based on USCO_II_75 matrix] │ │ │ USCO_II_75.fa [USCO_II_75
 matrix] │ │ │ USCO_II_75.partition.treefile [concatenated partitioning ML
 analyses based on USCO_II_75 matrix] │ │ │ USCO_II_75.pmsf2.fa.treefile
 [concatenated ML analyses under PMSF model based on USCO_II_75 matrix] │ │
 │ USCO_II_75_Dayhoff6.fas [Dayhoff6 recoding USCO_II_75 matrix] │ │ │
 USCO_II_75_Dayhoff6.fas.treefile [concatenated ML analyses using Dayhoff6
 recoding scheme based on USCO_II_75 matrix] │ │ │ │ │ ├─3.USCO_II_80
 [folder] │ │ │ USCO_II_80-astral.tre [coalescent analyses based on
 USCO_II_80 matrix] │ │ │ USCO_II_80-partition.treefile [concatenated
 partitioning ML analyses based on USCO_II_80 matrix] │ │ │
 USCO_II_80-pmsf2.fa.treefile [concatenated ML analyses under PMSF model
 based on USCO_II_80 matrix] │ │ │ USCO_II_80.fa [USCO_II_80 matrix] │ │ │
 USCO_II_80_Dayhoff6.fas [Dayhoff6 recoding USCO_II_80 matrix] │ │ │
 USCO_II_80_Dayhoff6.fas.treefile [concatenated ML analyses using Dayhoff6
 recoding scheme based on USCO_II_80 matrix] │ │ │ │ │ ├─4.USCO_II_85
 [folder] │ │ │ USCO_II_85-astral.tre [coalescent analyses based on
 USCO_II_85 matrix] │ │ │ USCO_II_85-Dayhoff6.fas [Dayhoff6 recoding
 USCO_II_85 matrix] │ │ │ USCO_II_85-Dayhoff6.fas.treefile [concatenated ML
 analyses using Dayhoff6 recoding scheme based on USCO_II_85 matrix] │ │ │
 USCO_II_85.fa [USCO_II_85 matrix] │ │ │ USCO_II_85.partition.treefile
 [concatenated partitioning ML analyses based on USCO_II_85 matrix] │ │ │
 USCO_II_85.pmsf2.fa.treefile [concatenated ML analyses under PMSF model
 based on USCO_II_85 matrix] │ │ │ │ │ ├─5.USCO_II_90 [folder] │ │ │
 USCO_II_90-astral.tre [coalescent analyses based on USCO_II_90 matrix] │ │
 │ USCO_II_90-Dayhoff6.fas [Dayhoff6 recoding USCO_II_90 matrix] │ │ │
 USCO_II_90-Dayhoff6.fas.treefile [concatenated ML analyses using Dayhoff6
 recoding scheme based on USCO_II_90 matrix] │ │ │ USCO_II_90.fa
 [USCO_II_90 matrix] │ │ │ USCO_II_90.partition.treefile [concatenated
 partitioning ML analyses based on USCO_II_90 matrix] │ │ │
 USCO_II_90.pmsf2.fa.treefile [concatenated ML analyses under PMSF model
 based on USCO_II_90 matrix] │ │ │ │ │ ├─6.UCE_II_70 [folder] │ │ │
 UCE_II_70.fa [UCE_II_70 matrix] │ │ │ UCE_II_70.partition.treefile
 [concatenated partitioning ML analyses based on UCE_II_70 matrix] │ │ │
 UCE_II_70_astral.tre [coalescent analyses based on UCE_II_70 matrix] │ │ │
 │ │ ├─7.UCE_II_75 [folder] │ │ │ UCE_II_75.fa [UCE_II_75 matrix] │ │ │
 UCE_II_75.partition.treefile [concatenated partitioning ML analyses based
 on UCE_II_75 matrix] │ │ │ UCE_II_75_astral.tre [coalescent analyses based
 on UCE_II_75 matrix] │ │ │ │ │ ├─8.UCE_II_80 [folder] │ │ │ UCE_II_80.fa
 [UCE_II_80 matrix] │ │ │ UCE_II_80.partition.treefile [concatenated
 partitioning ML analyses based on UCE_II_80 matrix] │ │ │
 UCE_II_80_astral.tre [coalescent analyses based on UCE_II_80 matrix] │ │ │
 │ │ └─9.UCE_II_85 [folder] │ │ UCE_II_85.fa [UCE_II_85 matrix] │ │
 UCE_II_85.partition.treefile [concatenated partitioning ML analyses based
 on UCE_II_85 matrix] │ │ UCE_II_85_astral.tre [coalescent analyses based
 on UCE_II_85 matrix] │ │ │ ├─3.Strategy III [folder,matrices were
 generated under the combined filtering conditions of Strategy I and
 Strategy II] │ │ ├─1.USCO_III_70_abs70 [folder] │ │ │
 USCO_III_70_abs70-partition.treefile [concatenated partitioning ML
 analyses based on USCO_III_70_abs70 matrix] │ │ │ USCO_III_70_abs70.fa
 [USCO_III_70_abs70 matrix] │ │ │ USCO_III_70_abs70_astral.tre [coalescent
 analyses based on USCO_III_70_abs70 matrix] │ │ │
 USCO_III_70_abs70_Dayhoff6.fas [Dayhoff6 recoding USCO_III_70_abs70
 matrix] │ │ │ USCO_III_70_abs70_Dayhoff6.fas.treefile [concatenated ML
 analyses using Dayhoff6 recoding scheme based on USCO_III_70_abs70 matrix]
 │ │ │ USCO_III_70_abs70_pmsf2.treefile [concatenated ML analyses under
 PMSF model based on USCO_III_70_abs70 matrix] │ │ │ │ │
 ├─2.USCO_III_75_abs75 [folder] │ │ │ USCO_III_75_abs75-partition.treefile
 [concatenated partitioning ML analyses based on USCO_III_75_abs75 matrix]
 │ │ │ USCO_III_75_abs75-pmsf2.treefile [concatenated ML analyses under
 PMSF model based on USCO_III_75_abs75 matrix] │ │ │ USCO_III_75_abs75.fa
 [USCO_III_75_abs75 matrix] │ │ │ USCO_III_75_abs75_astral.tre [coalescent
 analyses based on USCO_III_75_abs75 matrix] │ │ │
 USCO_III_75_abs75_Dayhoff6.fas [Dayhoff6 recoding USCO_III_75_abs75
 matrix] │ │ │ USCO_III_75_abs75_Dayhoff6.fas.treefile [concatenated ML
 analyses using Dayhoff6 recoding scheme based on USCO_III_75_abs75 matrix]
 │ │ │ │ │ ├─3.USCO_III_80_abs80 [folder] │ │ │
 USCO_III_80_abs80-astral_tree.tre [coalescent analyses based on
 USCO_III_80_abs80 matrix] │ │ │ USCO_III_80_abs80-partition.treefile
 [concatenated partitioning ML analyses based on USCO_III_80_abs80 matrix]
 │ │ │ USCO_III_80_abs80.fa [USCO_III_80_abs80 matrix] │ │ │
 USCO_III_80_abs80_Dayhoff6.fas [Dayhoff6 recoding USCO_III_80_abs80
 matrix] │ │ │ USCO_III_80_abs80_Dayhoff6.fas.treefile [concatenated ML
 analyses using Dayhoff6 recoding scheme based on USCO_III_80_abs80 matrix]
 │ │ │ USCO_III_80_abs80_pmsf2.fa.treefile [concatenated ML analyses under
 PMSF model based on USCO_III_80_abs80 matrix] │ │ │ │ │
 ├─4.USCO_III_85_abs85 [folder] │ │ │ USCO_III_85_abs85-partition.treefile
 [concatenated partitioning ML analyses based on USCO_III_85_abs85 matrix]
 │ │ │ USCO_III_85_abs85.fa [USCO_III_85_abs85 matrix] │ │ │
 USCO_III_85_abs85_astral_tree.tre [coalescent analyses based on
 USCO_III_85_abs85 matrix] │ │ │ USCO_III_85_abs85_Dayhoff6.fas [Dayhoff6
 recoding USCO_III_85_abs85 matrix] │ │ │
 USCO_III_85_abs85_Dayhoff6.fas.treefile [concatenated ML analyses using
 Dayhoff6 recoding scheme based on USCO_III_85_abs85 matrix] │ │ │
 USCO_III_85_abs85_pmsf2.treefile [concatenated ML analyses under PMSF
 model based on USCO_III_85_abs85 matrix] │ │ │ │ │ ├─5.UCE_III_70_abs70
 [folder] │ │ │ UCE_III_70_abs70.fa [UCE_III_70_abs70 matrix] │ │ │
 UCE_III_70_abs70.partition.treefile [concatenated partitioning ML analyses
 based on UCE_III_70_abs70 matrix] │ │ │ UCE_III_70_abs70_astral_tree.tre
 [coalescent analyses based on UCE_III_70_abs70 matrix] │ │ │ │ │
 ├─6.UCE_III_75_abs75 [folder] │ │ │ UCE_III_75_abs75.fa [UCE_III_75_abs75
 matrix] │ │ │ UCE_III_75_abs75.partition.treefile [concatenated
 partitioning ML analyses based on UCE_III_75_abs75 matrix] │ │ │
 UCE_III_75_abs75_astral_tree.tre [coalescent analyses based on
 UCE_III_75_abs75 matrix] │ │ │ │ │ ├─7.UCE_III_80_abs80 [folder] │ │ │
 UCE_III_80_abs80.fa [UCE_III_80_abs80 matrix] │ │ │
 UCE_III_80_abs80.partition.treefile [concatenated partitioning ML analyses
 based on UCE_III_80_abs80 matrix] │ │ │ UCE_III_80_abs80_astral_tree.tre
 [coalescent analyses based on UCE_III_80_abs80 matrix] │ │ │ │ │
 └─8.UCE_III_85_abs85 [folder] │ │ UCE_III_85_abs85.fa [UCE_III_85_abs85
 matrix] │ │ UCE_III_85_abs85.partition.treefile [concatenated partitioning
 ML analyses based on UCE_III_85_abs85 matrix] │ │
 UCE_III_85_abs85_astral_tree.tre [coalescent analyses based on
 UCE_III_85_abs85 matrix] │ │ │ ├─4.Strategy IV [folder, the filtering
 methods were the number of parsimony-informative sites(≥100)，relative
 composition frequency variability (≤0.3),SRH (stationary, reversible, and
 homogeneous)] │ │ ├─1.USCO_IV [folder] │ │ │ USCO_IV-astral.tre
 [coalescent analyses based on USCO_IV matrix] │ │ │ USCO_IV-Dayhoff6.fas
 [Dayhoff6 recoding USCO_IV matrix] │ │ │ USCO_IV-Dayhoff6.fas.treefile
 [concatenated ML analyses using Dayhoff6 recoding scheme based on USCO_IV
 matrix] │ │ │ USCO_IV-pmsf2.fas.treefile [concatenated ML analyses under
 PMSF model based on USCO_IV matrix] │ │ │ USCO_IV.fas [USCO_IV matrix] │ │
 │ USCO_IV_partition.txt.treefile [concatenated partitioning ML analyses
 based on USCO_IV matrix] │ │ │ │ │ └─2.UCE_IV [folder] │ │ UCE_IV.fas
 [UCE_IV matrix] │ │ UCE_IV_astral.tre [coalescent analyses based on UCE_IV
 matrix] │ │ UCE_IV_partition.txt.treefile [concatenated partitioning ML
 analyses based on UCE_IV matrix] │ │ │ └─5.Strategy V [folder, the
 filtering methods based on the gene tree was added to the strategy IV,
 Treeshrink v1.3.7-violation of a molecular clock (DVMC) -treeness] │
 ├─1.USCO_V [folder] │ │ USCO_V-Dayhoff6.fas [Dayhoff6 recoding USCO_V
 matrix] │ │ USCO_V-Dayhoff6.fas.treefile [concatenated ML analyses using
 Dayhoff6 recoding scheme based on USCO_V matrix] │ │ USCO_V-pmsf2.treefile
 [concatenated ML analyses under PMSF model based on USCO_V matrix] │ │
 USCO_V.fas [USCO_V matrix] │ │ USCO_V_astral.tre [coalescent analyses
 based on USCO_V matrix] │ │ USCO_V_partition.txt.treefile [concatenated
 partitioning ML analyses based on USCO_V matrix] │ │ │ └─2.UCE_V [folder]
 │ UCE_V.fas [UCE_V matrix] │ UCE_V_astral.tre [coalescent analyses based
 on UCE_V matrix] │ UCE_V_partition.txt.treefile [concatenated partitioning
 ML analyses based on UCE_V matrix] │ └─2.divergence dating analyses
 ├─1.usco [folder,divergence time estimation under three calibration
 schemes using USCO_V matrix] │ ├─1.calibration scheme 1 [folder,divergence
 time estimation under calibration scheme 1 using USCO_V matrix] │ │
 FigTree.tre [the resulting chronogram tree file] │ │ input.tre [input
 tree] │ │ mcmc.txt [MCMCtree outfile] │ │ mcmctree2.ctl [MCMCtree
 configuration file] │ │ out [MCMCtree outfile] │ │ SeedUsed [Seed] │ │
 USCO_V.fas [USCO_V matrix] │ │ │ ├─2.calibration scheme 2
 [folder,divergence time estimation under calibration scheme 2 using USCO_V
 matrix] │ │ FigTree.tre [the resulting chronogram tree file] │ │ input.tre
 [input tree] │ │ mcmc.txt [MCMCtree outfile] │ │ mcmctree2.ctl [MCMCtree
 configuration file] │ │ out [MCMCtree outfile] │ │ SeedUsed [Seed] │ │
 USCO_V.fas [USCO_V matrix] │ │ │ └─3.calibration scheme 3
 [folder,divergence time estimation under calibration scheme 3 using USCO_V
 matrix] │ FigTree.tre [the resulting chronogram tree file] │ input.tre
 [input tree] │ mcmc.txt [MCMCtree outfile] │ mcmctree2.ctl [MCMCtree
 configuration file] │ out [MCMCtree outfile] │ SeedUsed [Seed] │
 USCO_V.fas [USCO_V matrix] │ ├─2.uce [folder,divergence time estimation
 under three calibration schemes using UCE_V matrix] │ ├─1.calibration
 scheme 1 [folder,divergence time estimation under calibration scheme 1
 using UCE_V matrix] │ │ FigTree.tre [the resulting chronogram tree file] │
 │ input1.tre [input tree] │ │ mcmc.txt [MCMCtree outfile] │ │
 mcmctree2.ctl [MCMCtree configuration file] │ │ out [MCMCtree outfile] │ │
 SeedUsed [Seed] │ │ UCE_V.phy [UCE_V matrix] │ │ │ ├─2.calibration scheme
 2 [folder,divergence time estimation under calibration scheme 2 using
 UCE_V matrix] │ │ FigTree.tre [the resulting chronogram tree file] │ │
 input.tre [input tree] │ │ mcmc.txt [MCMCtree outfile] │ │ mcmctree2.ctl
 [MCMCtree configuration file] │ │ out [MCMCtree outfile] │ │ SeedUsed
 [Seed] │ │ UCE_V.phy [UCE_V matrix] │ │ │ └─3.calibration scheme 3
 [folder,divergence time estimation under calibration scheme 3 using UCE_V
 matrix] │ FigTree.tre [the resulting chronogram tree file] │ input.tre
 [input tree] │ mcmc.txt [MCMCtree outfile] │ mcmctree2.ctl [MCMCtree
 configuration file] │ out [MCMCtree outfile] │ SeedUsed [Seed] │ UCE_V.phy
 [UCE_V matrix] │ └─3.mitogenome [folder,divergence time estimation under
 three calibration schemes using PCGR matrix] ├─1.calibration scheme 1
 [folder,divergence time estimation under calibration scheme 1 using PCGR
 matrix] │ FigTree.tre [the resulting chronogram tree file] │ input.tre
 [input tree] │ mcmc.txt [MCMCtree outfile] │ mcmctree2.ctl [MCMCtree
 configuration file] │ out [MCMCtree outfile] │ PCGR.fas [PCGR matrix] │
 SeedUsed [Seed] │ ├─2.calibration scheme 2 [folder,divergence time
 estimation under calibration scheme 2 using PCGR matrix] │ FigTree.tre
 [the resulting chronogram tree file] │ input.tre [input tree] │ mcmc.txt
 [MCMCtree outfile] │ mcmctree2.ctl [MCMCtree configuration file] │ out
 [MCMCtree outfile] │ PCGR.fas [PCGR matrix] │ SeedUsed [Seed] │
 └─3.calibration scheme 3 [folder,divergence time estimation under
 calibration scheme 3 using PCGR matrix] FigTree.tre [the resulting
 chronogram tree file] input.tre [input tree] mcmc.txt [MCMCtree outfile]
 mcmctree2.ctl [MCMCtree configuration file] out [MCMCtree outfile]
 PCGR.fas [PCGR matrix] SeedUsed [Seed] ```