Inconsistent performance of multi-type genomic data in phylogenomics of neuropteridan insects, with solutions toward conflicting results
收藏DataONE2025-07-11 更新2025-07-19 收录
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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 repe..., , # 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:**Â It is a folder containing the information of the phylogeny and Divergence time.
```ââ1.phylogeny
â ââMitogenome
â â ââ1.site-homogeneous model [folder]
â â â ââBI [folder, Bayesian inference (BI) under site-homogeneous model was performed using MrBayes v3.1.2]
â â â â ââAA [folder]
â â â â â AA.nex [AA matrix for BI]
â â â â â AA.tre [BI tree using AA matrix]
â â â â â
â â â â ââPCG12 [folder]
â â â â â PCG12.nex [PCG12 matrix for BI]
â â â â â PCG12.tre [BI...,
创建时间：
2025-07-12
