DOI: 10.5061/dryad.573n5tbf7
title: 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: 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
 efficiently on genome-scale data and has high accuracy in identifying
 polyploid patterns and assigning homeologs. Using HomeoSorter, the maximum
 pseudo-likelihood model of Phylonet, and genome-scale data, we further
 address the complex origin of Tussilagininae, a speciose group (ca. 45
 genera and 710 species) characterized by having high base chromosome
 numbers (mainly x = 30, 40). In particular, the inferred patterns are
 strongly supported by the chromosomal evidence. Tussilagininae is revealed
 to comprise two large groups with successive allopolyploid origins:
 Tussilagininae s.s. (mainly x = 30) and the Gynoxyoid group (x = 40). Two
 allopolyploidy events first give rise to Tussilagininae s.s., with the
 first event occurring between the ancestor of subtribe Senecioninae (x =
 10) and a lineage (highly probably with x = 10) related to the
 Brachyglottis alliance, and the resulting hybrid lineage crossing with the
 ancestor of Chersodoma (x = 10) and leading to Tussilagininae s.s. Then,
 after early diversification, the Central American group (mainly x = 30) of
 Tussilagininae s.s., is involved in a third allopolyploidy event with,
 again, the Chersodoma lineage and produces the Gynoxyoid group. Our study
 highlights the value of HomeoSorter and the homeolog-sorting approach in
 polyploid phylogenetics. With rich species diversity and clear
 evolutionary patterns, Tussilagininae s.s. and the Gynoxyoid group are
 also excellent models for future investigations of polyploidy.
description: # 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 of the G727_hyb dataset with nodes having support
 lower than 30% collapsed; these trees are used for the ASTRAL analysis]
 │   └── 3_supermatrix_analysis [# Supermatrix analysis of the G727_hyb
 dataset] │   ├── G727_hyb_partition.raxml [# Partition file of the
 concatenated alignment] │   ├── G727_hyb_supermatrix.fasta [# Concatenated
 alignment of the G727_hyb dataset] │   └──
 RAxML_bipartitions.G727_hyb_supermatrix [# The result of the supermatrix
 analysis] ├── 2_G727 [# Phylogenetic analyses based on the 727 genes with
 all potential paralogous sequences retrieved] │   ├──
 1_G727_individual_genes_and_trees [# Individual gene alignments and
 corresponding ML trees, with "xxxxxx" indicating gene codes] │  
 │   ├── [xxxxxx].fas [# Individual alignments ] │   │   ├──
 RAxML_bipartitions.[xxxxxx] [# Maximum likelihood trees] │   └──
 2_rooted_and_collapsing_node_support_less_than_30 [# Rooted individual
 gene trees, with nodes having support lower than 30% collapsed, serving as
 the basis for the following Phylonet and HomeoSorter analyses] │   └──
 4_bs30_rooted │   ├── RAxML_bipartitions.[xxxxxx].bs30.tre.reroot ├──
 3_Phylonet_analyses [# A total of 17 Phylonet analyses based on the G727
 dataset.] │   ├── Phylonet_A[x] │   │   ├── Phylonet_A[x]_1 [# Files for
 Phylonet analyses, including gene trees and settings] │   │   ├──
 Phylonet_A[x]_1.log [# Phylonet results] ├── 4_simulation_tests [# Tests
 of HomeoSorter, AllCoPol, Phylonet, and MPAllopp, using simulated data]
 │   ├── 1_HybridSim_simulations [# Simulation of gene trees using
 HybridSim] │   │   ├── 1_allopolyploidy_parental_contribution_50-50 [#
 Simulation for allopolyploidy with parental contributions of 50 : 50 and
 coalescence rates ranging from 0.1 to 200] │   │   │   ├──
 cr[xx]_input.nex [# Settings for simulation, with "xx"
 indicating the values of coalescence rates] │   │   │   ├──
 cr[xx]_output.txt [# Results of simulation] │   │   ├──
 2_allopolyploidy_parental_contribution_40-60 [# Simulation for
 allopolyploidy with parental contributions of 40 : 60 and coalescence
 rates ranging from 0.1 to 200] │   │   ├──
 3_allopolyploidy_parental_contribution_30-70 [# Simulation for
 allopolyploidy with parental contributions of 30 : 70 and coalescence
 rates ranging from 0.1 to 200] │   │   ├──
 4_allopolyploidy_parental_contribution_20-80 [# Simulation for
 allopolyploidy with parental contributions of 20 : 80 and coalescence
 rates ranging from 0.1 to 200] │   │   ├──
 5_allopolyploidy_parental_contribution_10-90 [# Simulation for
 allopolyploidy with parental contributions of 10 : 90 and coalescence
 rates ranging from 0.1 to 200] │   │   ├── 6_autopolyploidy [# Simulation
 for autopolyploidy with coalescence rates ranging from 0.1 to 200] │   ├──
 2_HomeoSorter_tests [# HomeoSorter analyses based on the simulated data;
 for each scenario 100 replicates of HomeoSorter shuffling analyses are
 run] │   │   ├── 1_allopolyploidy_parental_contribution_50-50 -
 6_autopolyploidy [# Different scenarios for either allopolyploidy or
 autopolyploidy, different parental contributions and coalescence rates]
 │   │   │   ├── cr0.1-cr200 │   │   │   │   ├── r00001-rxxxxx [# Results
 of 100 replicates of HomeoSorter shuffling analyses] │   │   │   │   │  
 ├── final_200_genes.astraltree [# ASTRAL tree suggested by HomeoSorter]
 │   │   │   │   │   └── final_200_genes.taxonmap [# Allele assignments
 suggested by HomeoSorter] │   ├── 3_AllCoPol_tests [# Results of 100
 replicates of AllCoPol analyses] │   │   ├──
 1_allopolyploidy_parental_contribution_50-50 - 6_autopolyploidy [#
 Different scenarios for either allopolyploidy or autopolyploidy, different
 parental contributions and coalescence rates] │   │   │   ├── cr0.1-cr200
 │   │   │   │   ├── r00001-rxxxxx │   │   │   │   │   ├── **.nex │   │  
 │   │   │   ├── **.txt │   ├── 4_Phylonet_tests [# Results of Phylonet
 analyses] │   │   ├── 1_allopolyploidy_parental_contribution_50-50 -
 6_autopolyploidy [# Different scenarios for either allopolyploidy or
 autopolyploidy, different parental contributions and coalescence rates]
 │   │   │   ├── 1_polyploid_not_specified [# Phylonet analyses with the
 polyploid unspecified] │   │   │   ├── 2_polyploid_specified [# Phylonet
 analyses with the polyploid specified] │   └── 5_MPAllopp_tests [# Results
 of MPAllopp analyses] │   │   ├──
 1_allopolyploidy_parental_contribution_50-50 - 6_autopolyploidy [#
 Different scenarios for either allopolyploidy or autopolyploidy, different
 parental contributions and coalescence rates] │   │   │   ├──
 1_polyploid_not_specified [# Phylonet analyses with the polyploid
 unspecified] │   │   │   ├── 2_polyploid_specified [# Phylonet analyses
 with the polyploid specified] ├── 5_HomeoSorter_analyses [# HomeoSorter
 analyses based on the G727 dataset] │   ├── bootstrapping [# Results of 50
 bootstrapping replicates] │   │   ├── majority concensus tree.nexus [#
 Majority concensus tree based on the results of 50 bootstrapping
 replicates] │   │   ├── r[xxxx] [# Results of individual bootstrap
 replicates] │   ├── genetrees.txt [# A list of gene trees for HomeoSorter
 analyses] │   ├── samplelist.txt [# A list of polyploid samples to be
 investigated] │   └── shuffling [# Results of 50 shuffling replicates] │  
 ├── majority concensus tree.nexus [# Majority concensus tree based on the
 results of 50 shuffling replicates] │   ├── r[xxxx] [# Results of
 individual shuffling replicates] ├── 6_Sorted_homeologs [# Phylogenetic
 analyses based on homeologs sorted by HomeoSorter, with and without
 further gene filtration] │   ├── filtered [# Analyses based on sorted and
 filtered homeologs] │   │   ├── 1_individual_genes_and_trees_50_replicates
 [# New gene alignments generated based on the allele assignments suggested
 by HomeoSorter with further gene filtration] │   │   ├── 2_Astral_analysis
 [# ASTRAL analysis based on the sorted and filtered homeologs] │   │   └──
 3_supermatrix_analysis [# Supermatrix analysis based on the sorted and
 filtered homeologs] │   └── unfiltered [# Analyses based on sorted and
 filtered homeologs] │   ├── 1_individual_genes_and_trees_50_replicates [#
 New gene alignments generated based on the allele assignments suggested by
 HomeoSorter without further gene filtration] │   ├── 2_Astral_analysis [#
 ASTRAL analysis based on the sorted and unfiltered homeologs] │   │   ├──
 astral.tre [# ASTRAL result] │   │   └── individual genes.tre [#
 Individual gene trees with nodes having support lower than 30% collapsed]
 │   └── 3_supermatrix_analysis [# Supermatrix analysis based on the sorted
 and unfiltered homeologs] │   ├── r[xxxx] [# Different replicates] │   │  
 ├── RAxML_bipartitions.r[xxxx].unfiltered.tre [# ML tree] │   │   ├──
 r[xxxx].unfiltered.fasta [# Concatenated alignment ] │   │   └──
 r[xxxx].unfiltered.partition.raxml [# Partition file] │   ├── Sample
 codes.xlsx [# A list of samples and corresponding codes] ``` ##
 Supplementary files in Zenodo Supplementary_Table_S1.xls lists the
 information about samples, chromosome numbers, and assembly statistics for
 target nuclear genes and off-target chloroplast genes. Please also see the
 file of Supplementary_Table_S1_notes_and_references.docx for the notes and
 references. Supplementary_Figures.docx contains all the supplementary
 figures supporting the paper.