Data from: Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss
Data files
Dec 16, 2025 version files 12.41 GB
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ASTRALIII_SU.tar.xz
287.63 MB
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biological.tar.xz
126.44 MB
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GDL_SU.tar.xz
6.97 GB
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HGT_SU.tar.xz
5.02 GB
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README.md
18.53 KB
Abstract
Phylogenetic branch lengths are essential for many analyses, such as estimating divergence times, analyzing rate changes, and studying adaptation. However, true gene tree heterogeneity due to incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer can complicate the estimation of species tree branch lengths. While several tools exist for estimating the topology of a species tree addressing various causes of gene tree discordance, much less attention has been paid to branch length estimation on multi-locus datasets. For single-copy gene trees, some methods are available that summarize gene tree branch lengths onto a species tree, including coalescent-based methods that account for heterogeneity due to incomplete lineage sorting. However, no such branch length estimation method exists for multi-copy gene family trees that have evolved with gene duplication and loss. To address this gap, we introduce the CASTLES-Pro algorithm for estimating species tree branch lengths while accounting for both gene duplication and loss and incomplete lineage sorting. CASTLES-Pro improves on the existing coalescent-based branch length estimation method CASTLES by increasing its accuracy for single-copy gene trees and extending it to handle multi-copy ones. Our simulation studies show that CASTLES-Pro is generally more accurate than alternatives, eliminating the systematic bias toward overestimating terminal branch lengths often observed when using concatenation. Moreover, while not theoretically designed for horizontal gene transfer, we show that CASTLES-Pro is relatively robust to random horizontal gene transfer, though its accuracy can degrade at the highest levels of horizontal gene transfer.
CASTLES-Pro Datasets
This repository contains the datasets and scripts used in the following paper:
- Y. Tabatabaee, C. Zhang, S. Arasti, S. Mirarab (2025). Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss. Genome Biology and Evolution. Volume 17, Issue 11. https://academic.oup.com/gbe/article/17/11/evaf200/8343050
For experiments in this study, we analyzed three sets of simulated datasets and nine biological datasets with different sources of gene tree discordance. In all simulated datasets, the true species trees have branch lengths in substitution-units.
We provide a description of the relevant files included in each dataset below. Note that some log and intermediate files generated during the analyses are also included with the datasets for completeness, but are not listed here.
Simulated datasets
ILS-only simulations
For the ILS simulations, we reused the 100-taxon ILS-only dataset from Tabatabaee et. al. (2023) available at https://github.com/ytabatabaee/CASTLES-paper/. This dataset has four model conditions with varying sequence lengths (1600bp, 800bp, 400bp, 200bp) corresponding to different levels of gene tree estimation error (23%, 31%, 42%, and 55%), each with 50 replicates. Results and intermediate data from the experiments in the paper are available in ASTRALIII_SU.tar.xz.
Below is a description of files in each directory.
s_tree.trees: true species tree in substitution unitss_tree.ralpha: mutation rates for species tree branches in pre-order traversalg_trees_ralpha.txt: mutation rates for gene tree branches in pre-order traversaltruegenetrees: true gene trees in substitution unitsfasttree_genetrees_[seq-len]_non: gene trees estimated using FastTree2 from alignments with length [seq-len]bperable_patristic_all_fasttree_genetrees_[seq-len]_non_s_tree.trees.derooted.length.nwk: true species tree furnished with ERaBLE SU branch lengths on gene trees estimated from alignments with length [seq-len]bppatristic_[MODE]_fasttree_genetrees_[seq-len]_non.mat: patristic distance matrix calculated using minimum (min), average (avg) or all (all) pairwise distances for gene trees estimated from alignments with length [seq-len]bpconcat_for_fasttree_[seq-len].fastaorall-genes_for_fasttree.phylip: concatenation of all gene alignments with length [seq-len]bpRAxML_result.concat_for_fasttree_[seq-len]_s_tree.trees: true species tree furnished with RAxML SU branch lengths from concatenation of alignments with length [seq-len]bpcastles_fasttree_genetrees_[seq-len]_non_s_tree.trees: true species tree furnished with CASTLES SU branch lengths run on gene trees estimated from alignments with length [seq-len]bpcastles2_fasttree_genetrees_[seq-len]_non_s_tree.trees: true species tree furnished with CASTLES-Pro (with Taylor approximation) SU branch lengths run on gene trees estimated from alignments with length [seq-len]bpcastles2_lambert_fasttree_genetrees_[seq-len]_non_s_tree.trees: true species tree furnished with CASTLES-Pro (with Lambert approximation) SU branch lengths run on gene trees estimated from alignments with length [seq-len]bpcastles2_lamberts1_fasttree_genetrees_[seq-len]_non_s_tree.trees: true species tree furnished with CASTLES-Pro (with Lambert approximation and psuedocountof 1/s) SU branch lengths run on gene trees estimated from alignments with length [seq-len]bpcastles2_lamberts_fasttree_genetrees_[seq-len]_non_s_tree.trees: true species tree furnished with CASTLES-Pro (with Lambert approximation and psuedocountof 1/2s) SU branch lengths run on gene trees estimated from alignments with length [seq-len]bpcastlespro_fasttree_genetrees_[seq-len]_non_s_tree.trees: true species tree furnished with CASTLES-Pro SU branch lengths run on gene trees estimated from alignments with length [seq-len]bpfastme_BalLS_patristic_[MODE]_fasttree_genetrees_[seq-len]_non_s_tree.trees.derooted: true species tree furnished with FastME SU branch lengths with minimum or average distances run on gene trees estimated from alignments with length [seq-len]bpTCMM_castlespro_fasttree_genetrees_[seq-len]_non_s_tree_lam_0.trees: true species tree furnished with TCMM SU branch lengths on gene trees estimated from alignments with length [seq-len]bpTCMM_castlespro_fasttree_genetrees_[seq-len]_non_s_tree_lam_best.trees: true species tree furnished with TCMM+CASTLES-Pro SU branch lengths on gene trees estimated from alignments with length [seq-len]bp
HGT+ILS simulations
We generated a new 50-taxon HGT+ILS dataset based on the parameters from Davidson et. al. (2015) study. This dataset has six model conditions named as model.50.2000000.0.000001.[HGT-rate] with different levels of HGT, each with 50 replicates. The average number of HGT events per gene for the six model conditions are 0, 0.08, 0.2, 0.8, 8 and 20, corresponding to HGT rates of 10^−9x(0, 2, 5, 20, 200, and 500). The original dataset is available at https://databank.illinois.edu/datasets/IDB-6670066. Our new dataset, as well as the intermediate data and output of methods are available in HGT_SU.tar.xz.
Below is a description of files in each directory.
s_tree.trees: true species tree in substitution unitss_tree.ralpha: mutation rates for species tree branches in pre-order traversalg_trees_ralpha.txt: mutation rates for gene tree branches in pre-order traversaltruegenetrees: true gene trees in substitution unitsestimatedgenetre: estimated gene treeserable_patristic_all_estimatedgenetre_s_tree.trees.derooted.length.nwk: true species tree furnished with ERaBLE SU branch lengths on estimated gene treespatristic_[MODE]_estimatedgenetre.mat: patristic distance matrix calculated using minimum (min), average (avg) or all (all) pairwise distances for estimated gene treesall-genes.phylip: concatenation of all gene alignmentsRAxML_result.concat_s_tree.trees: true species tree furnished with RAxML SU branch lengthscastles_estimatedgenetre_s_tree.trees: true species tree furnished with CASTLES SU branch lengths run on estimated gene treescastlespro_estimatedgenetre_s_tree.trees: true species tree furnished with CASTLES-Pro SU branch lengths run on estimated gene treesfastme_BalLS_patristic_[MODE]_estimatedgenetre_s_tree.trees.derooted: true species tree furnished with FastME SU branch lengths with minimum or average distances (specified with MODE) run on estimated gene treesTCMM_castlespro_estimatedgenetre_lam_0.trees: true species tree furnished with TCMM SU branch lengths run on estimated gene treesTCMM_castlespro_estimatedgenetre_lam_best.trees: true species tree furnished with TCMM+CASTLES-Pro SU branch lengths run on estimated gene trees
GDL+ILS simulations
We updated the GDL+ILS dataset from Willson et. al. (2022, 2023) to produce species trees with substitution-unit branch lengths. The model conditions of this dataset are represented as [num-taxa]_gdl_[GDL-rate]_[dup/loss-ratio]_[high/low-ILS]. The default model condition has 100 taxa, GDL rate of 10^-10 with equal loss rate. The number of genes varies between 50-1000, with the exception of the model condition gtrees_10000_l1 that has up to 10,000 genes. The number of species varies between 20 to 1000 (for the species_1000 model condition). The original datasets (including the sequence alignments) are available at https://databank.illinois.edu/datasets/IDB-4050038 and https://databank.illinois.edu/datasets/IDB-5748609. Results and intermediate data from the experiments in the paper are available in GDL_SU.tar.xz.
Below is a description of files in each directory.
s_tree.trees: true species tree in substitution unitss_tree.ralpha: mutation rates for species tree branches in pre-order traversalg_trees_ralpha.txt: mutation rates for gene tree branches in pre-order traversaltruegenetrees: true gene trees in substitution unitsg_[seq-len].trees.[num-genes]:num-genesgene family trees estimated fromseq-lensequence alignmentserable_patristic_all_disco_g_[seq-len].trees.[num-genes]_s_tree.trees.derooted.length.nwk: true species tree furnished with ERaBLE SU branch lengths on DISCO decomposed gene treespatristic_[MODE]_disco_g_[seq-len].trees.[num-genes].mat: patristic distance matrix calculated using average (avg) or all (all) pairwise distances for DISCO decomposed estimated gene treesconcat_g_[seq-len].[num-genes]: concatenation ofnum-genesgene sequence alignments with lengthseq-lendisco_g_[seq-len].trees.[num-genes]: single-copy DISCO decomposed gene trees estimated fromg_[seq-len].trees.[num-genes]gene family treesRAxML_result.concat_g_[seq-len].[num-genes]_s_tree.trees: true species tree furnished with CA-DISCO (with RAxML) SU branch lengthscastles-original_disco_g_[seq-len].trees_s_tree.trees: true species tree furnished with CASTLES-DISCO SU branch lengths run on gene trees estimated fromseq-lensequence alignmentscastlespro_g_[seq-len].trees.[num-genes]_s_tree.trees: true species tree furnished with CASTLES-Pro SU branch lengths run on gene trees estimated fromseq-lensequence alignmentsfastme_BalLS_patristic_avg_disco_g_[seq-len].trees.[num-genes]_s_tree.trees.derooted: true species tree furnished with FastME SU branch lengths with average distances run on DISCO decomposed estimated gene trees
Biological datasets
We analyzed three biological datasets where ILS is the primary source of gene tree discordance, three datasets with GDL, and three bacterial datasets with high rates of HGT. The results of all experiments are provided in biological.tar.xz.
The following files appear in all subdirectories, where [DATASET-NAME] indicates the name of the dataset.
draw_rtt.R: script for drawing the Root-to-tip (RTT) distance distribution plots and branch length correlation plots.caml_rtt.csv: Root-to-tip (RTT) distance values for CAML.castles_pro_rtt.csv: Root-to-tip (RTT) distance values for CASTLES-Pro.rtt_[DATASET-NAME].pdf: Root-to-tip (RTT) distance plot for CAML and CASTLES-Pro.[DATASET-NAME]_corr.csv: Correlation between CAML and CASTLES-Pro branch lengths.[DATASET-NAME]_corr_r.pdf: Plot showing correlation between CAML and CASTLES-Pro branch lengths.[DATASET-NAME]_caml.pdf: Plot showing the CAML tree.[DATASET-NAME]_castles_pro.pdf: Plot showing the CASTLES-Pro tree.
Below is a description of other files in each directory.
ILS datasets
- Brids: 363-taxon dataset from Stiller et al. (2024) with 63,430 single-copy genes.
- Original dataset: https://erda.ku.dk/archives/341f72708302f1d0c461ad616e783b86/published-archive.html
stiller_concat.rooted.tre: ASTRAL species tree with SU branch lengths estimated using concatenation.stiller_castles_pro.rooted.tre: ASTRAL species tree with SU branch lengths estimated using CASTLES-Pro.stiller.nexus: Comparison between CASTLES-Pro and CAML branch lengths.astral_63K.tre: ASTRAL tree estimated from the 63K gene trees.
- Bees: 32-taxon dataset from Bossert et al. (2021) with 853 single-copy genes.
- Original dataset: https://datadryad.org/stash/dataset/doi:10.5061/dryad.z08kprrb6
genetrees.tre: Gene trees with SU branch lengths.genetrees_remove_305.tre: SU gene trees with gene 305 removed.treeshrink_bees.tre: TreeShrink gene trees with SU branch lengths.bees.nexusandbee_caml_astral.pdf: Comparison between CASTLES-Pro and CAML branch lengths.caml_no_outgroup.tre: ASTRAL species tree with SU branch lengths estimated using concatenation.castles_pro_no_outgroup.tre: ASTRAL species tree with SU branch lengths estimated using CASTLES-Pro.castles_pro_remove_305_no_outgroup.tre: ASTRAL species tree with SU branch lengths estimated using CASTLES-Pro on gene trees with gene 305 removed.castles_pro_treeshrink_no_outgroup.tre: ASTRAL species tree with SU branch lengths estimated using CASTLES-Pro on TreeShrink gene trees.
- Mammals: 37-taxon dataset from Song et al. (2012) with 424 single-copy genes.
- Original dataset: https://erda.ku.dk/archives/341f72708302f1d0c461ad616e783b86/published-archive.html
genetrees.tre: Gene trees with SU branch lengths.treeshrink_mammals.tre: TreeShrink gene trees.astral4_no_outgroup.tre: Species tree estimated using ASTRAL.mammals.nexus: Comparison between CASTLES-Pro and CAML branch lengths.caml_no_outgroup.tre: ASTRAL species tree with SU branch lengths estimated using concatenation.castles_pro_no_outgroup.tre: ASTRAL species tree with SU branch lengths estimated using CASTLES-Pro.castles_pro_treeshrink_no_outgroup.tre: CASTLES-Pro tree estimated from TreeShrink gene trees.
GDL datasets
- Fungi: 16-taxon dataset from Butler et al. (2009) with 706 single-copy genes and 7,180 multi-copy genes.
- Original dataset: https://compbio.mit.edu/candida/
mrbayes.tre: MrBayes species tree with SU branch lengths.castles_pro_pep.ml.renamed.trees: ASTRAL-Pro species tree with SU branch lengths estimated using CASTLES-Pro.apro_pep.ml.renamed.trees: ASTRAL-Pro species tree.pep.ml.renamed.trees: Multi-copy gene trees with SU branch lengths.fungi.nexus: Comparison between CASTLES-Pro and MrBayes branch lengths.
- Plants (
1KP): 80-taxon dataset from Wickett et al. (2014) with 424 single-copy genes and 9,610 multi-copy genes.- Original dataset: https://datacommons.cyverse.org/browse/iplant/home/shared/onekp_pilot
caml.tre.induced: Concatenation species tree with SU branch lengths.1kp.nexus: Comparison between CASTLES-Pro and concatenation branch lengths.castlespro_mul.tre.induced: ASTRAL species tree with SU branch lengths estimated using CASTLES-Pro.mul.trees.renamed: Multi-copy gene trees with SU branch lengths.
- Eudicots (
buxus): 40-taxon dataset from Chanderbali et al. (2022) with 345 single-copy genes and 2,573 multi-copy genes.- Original dataset: https://datadryad.org/dataset/doi:10.5061/dryad.cjsxksn6d
caml_353_no_outgroup.tre: Main concatenation species tree with SU branch lengths.castles_pro_mul_2573_no_outgroup.tre: ASTRAL-Pro species tree with SU branch lengths estimated using CASTLES-Pro.castles_pro_353_no_outgroup.tre: ASTRAL-Pro species tree with SU branch lengths estimated using CASTLES-Pro using 353 single-copy gene trees.castles_pro_busco_no_outgroup.tre: ASTRAL-Pro species tree with SU branch lengths estimated using CASTLES-Pro using BUSCO gene trees.orthogroups_2573_clean.trees: Multi-copy gene trees with SU branch lengths.sc_353.trees: Single-copy gene trees with SU branch lengths.Busco_1246.trees: BUSCO gene trees.buxus.nexus: Comparison between CASTLES-Pro and concatenation branch lengths.
HGT datasets
- Bacterial (core genes): 72-taxon dataset from Williams et al. (2020) with 49 single-copy genes.
- Original dataset: https://doi.org/10.6084/m9.figshare.13395470
astral_core_genes.tre: ASTRAL species tree estimated using the core gene trees.caml_core_genes.tre: ASTRAL species tree with SU branch lengths estimated using concatenation.castles_pro_core_genes.tre: ASTRAL species tree with SU branch lengths estimated using CASTLES-Pro.core_genes.tre: Gene trees with SU branch lengths.core.nexus: Comparison between CASTLES-Pro and concatenation branch lengths.
- Bacterial (non-ribosomal genes): 108-taxon dataset from Petitjean et al. (2015) with 38 single-copy genes.
- Original dataset: https://doi.org/10.6084/m9.figshare.13395470
astral_non_ribosomal_genes.tre: ASTRAL species tree estimated on non-ribosomal gene trees.caml_non_ribosomal_genes.tre: ASTRAL species tree with SU branch lengths estimated using concatenation.castles_pro_non_ribosomal.tre: ASTRAL species tree with SU branch lengths estimated using CASTLES-Pro.non_ribosomal_genes.tre: Gene trees with SU branch lengths.non_ribosomal.nexus: Comparison between CASTLES-Pro and concatenation branch lengths.
- Bacterial (WoL): 10,575-taxon dataset from Zhu et al. (2019) with 381 single-copy genes.
- Original dataset: https://biocore.github.io/wol/
astral.rand.lpp.nwk: ASTRAL species trees with SU branch lengths estimated using concatenation.castles_pro_wol.tre: ASTRAL species tree with SU branch lengths estimated using CASTLES-Pro.wol_genestrees.tre.zip: WoL gene trees.wol.nexus: Comparison between CASTLES-Pro and concatenation branch lengths.aster_v1.13.2.4_wol.annotated.nwk: ASTER annotation of ASTRAL species tree for branch length estimation.castles_pro_wol_treeshrink.tre: ASTRAL species tree with SU branch lengths estimated using CASTLES-Pro using TreeShrink gene trees.