Complex but clear allopolyploid pattern of subtribe Tussilagininae (Asteraceae: Senecioneae) revealed by robust phylogenomic evidence, with development of a novel homeolog-sorting pipeline

Polyploidy is a significant mechanism in eukaryotic evolution and is particularly prevalent in the plant kingdom. However, our knowledge about this phenomenon and its effects on evolution remains limited. A major obstacle to the study of polyploidy is the great difficulty in untangling the origins of allopolyploids. Due to the drastic genome changes and the erosion of allopolyploidy signals caused by the combined effects of hybridization and complex post-polyploid diploidization processes, resolving the origins of allopolyploids has long been a challenging task. Here we revisit this issue with the interesting case of subtribe Tussilagininae (Asteraceae: Senecioneae) and by developing HomeoSorter, a new pipeline for network inferences by phasing homeologs to parental subgenomes. The pipeline is based on the basic idea of a previous study but with major changes to address the scaling problem and implement some new functions. With simulated data, we demonstrate that HomeoSorter works effic..., , , # Data from: Complex but clear allopolyploid pattern of subtribe Tussilagininae (Asteraceae: Senecioneae) revealed by robust phylogenomic evidence, with development of a novel homeolog-sorting pipeline

## Description of files

The `data_matrices_and_results.zip` contains all the data matrices used in this study as well as the corresponding results. The organization of the data is illustrated below:

```
├── 1_G727_hyb [# Phylogenetic analyses based on the HybPiper-selected sequences of 727 genes]
│   ├── 1_G727_hyb_individual_genes_and_trees [# Individual alignments of 727 genes and the corresponding maximum likelihood trees, with \"xxxxxx\" indicating gene codes]
│   │   ├── [xxxxxx].maincopy [# Individual alignments ]
│   │   ├── RAxML_bipartitions.[xxxxxx] [# Maximum likelihood trees]
│   ├── 2_astral_analysis [# ASTRAL analysis based on the G727_hyb dataset]
│   │   ├── astral.tre [# ASTRAL result]
│   │   └── individual_genes.tre [# Individual gene trees ...