Gene Tree Species Tree Reconciliation - Usage Guide

Overview

Reconciliation methods compare a gene tree against a species tree under explicit probabilistic models of duplication (D), horizontal transfer (T), and loss (L). The output is a mapping of D/T/L events to species-tree branches, revealing the evolutionary history of each gene family. ALE / GeneRax / AleRax (Szöllősi 2013; Morel 2020/2024) define the modern probabilistic standard; parsimony-based alternatives (RANGER-DTL, NOTUNG) remain useful for screening.

The most consequential decision in reconciliation is how to handle gene-tree uncertainty. Single-ML-tree reconciliation (NOTUNG, RANGER, basic GeneRax) treats input trees as truth and amplifies gene-tree noise as spurious D/T/L events. ALE integrates over a sample of bootstrapped gene trees; AleRax co-estimates everything jointly. For publication-grade DTL inference, ALE or AleRax are required.

Prerequisites

# Probabilistic reconciliation
conda install -c bioconda ale generax
git clone --recursive https://github.com/BenoitMorel/AleRax && cd AleRax && ./install.sh

# Parsimony / alternative methods
# RANGER-DTL: https://compbio.engr.uconn.edu/software/RANGER-DTL/
# NOTUNG: https://www.cs.cmu.edu/~durand/Notung/download

# Bayesian + WGD
julia -e 'using Pkg; Pkg.add("Whale")'

# Tree manipulation
conda install -c bioconda newick_utils iqtree
pip install ete4

Quick Start

Tell the AI agent what to do: - "Reconcile these orthogroup gene trees against the species tree using ALE to identify per-branch D/T/L events" - "Use AleRax to co-estimate gene trees, species tree, and DTL rates from a set of UFBoot bootstrap samples" - "Apply Whale.jl to perform Bayesian DTL inference with explicit WGD nodes for a vertebrate species tree" - "Run RANGER-DTL parsimony sweep across cost weights to identify robust transfer events"

Example Prompts

Bacterial Phylogenomics

"I have UFBoot trees for 5000 orthogroups across 100 bacterial genomes and want to identify horizontal gene transfer events per genome and rates of DTL. Run ALEml_undated on all gene-tree distributions against the rooted species tree, then aggregate the per-branch transfer counts into a summary matrix. Include the optional ALE-rooting (Williams 2017) to validate the species tree root."

Eukaryote Gene Family with WGD

"Analyze ohnolog gene-family history across teleost fish, accounting for the 3R WGD. Use Whale.jl with the WGD node placed at the teleost root; report per-WGD retention probabilities and post-WGD duplication / loss rates per family. Cross-validate the WGD detection by inspecting the per-family Bayes factor for the WGD-vs-non-WGD model."

Refining Gene Trees

"I have orthogroup gene trees from OrthoFinder but they have low bootstrap support. Use GeneRax with --strategy SPR to refine each tree against the species tree under a DL model, producing reconciled gene trees and per-family duplication-loss event histories."

What the Agent Will Do

Validate input format: Check species labels match between species tree and gene tree leaves; verify gene IDs encode species via prefix
Build per-orthogroup gene-tree bootstrap distribution with IQ-TREE2 UFBoot if not provided
Encode gene-tree samples for ALE (ALEobserve produces .ale files)
Run reconciliation with appropriate model:
ALEml_undated for posterior over D/T/L
GeneRax for ML reconciliation with SPR refinement
AleRax for joint co-estimation
Whale.jl for Bayesian DL + WGD
Aggregate per-branch event counts across families
Cross-validate with parsimony (RANGER-DTL, NOTUNG) for screening
Report: per-branch event posteriors, family-level reconciled trees, species-tree refinements
Caveats: explicit ILS vs HGT note; ghost-lineage caveat; WGD if applicable

Tips

ALE undated is the default for bacterial DTL; dated for time-calibrated trees
For gene-tree-error-resistant inference, use ALE with UFBoot bootstrap samples (>= 100 per family)
AleRax (Morel 2024) co-estimates gene tree + species tree + DTL rates; preferred for new publication-grade work
Species labels must match exactly between species tree and gene trees; ALE / GeneRax silently fail on mismatch
Use nw_labels -I (newick utilities) to verify species sets before reconciliation
For HGT-affected clades (bacteria, archaea), transfers >> duplications; opposite for opisthokonts
ILS confounded with HGT at short internal branches; use DLCpar for ILS-aware inference
Multifurcations in species tree break ALE / GeneRax; resolve via ape::multi2di() or randomization
For WGD lineages, use Whale.jl with explicit WGD branch placement
RANGER-DTL parsimony is fine for screening; results sensitive to cost weights; sensitivity sweep required
NOTUNG is duplication-loss only by default; use NOTUNG-HGT extension for HGT-affected; or ALE
Gene-ID separator convention: species|gene_id for ALE / GeneRax; species_gene_id for Whale.jl
AleRax can detect species tree root mis-specification; trust its rooting
GeneRax MPI parallelization requires careful MPI launcher configuration on HPC

comparative-genomics/hgt-detection - HGT inference uses DTL reconciliation comparative-genomics/ortholog-inference - OrthoFinder HOGs feed reconciliation comparative-genomics/gene-family-evolution - CAFE5 birth-death complementary to per-family reconciliation comparative-genomics/whole-genome-duplication - Whale.jl native WGD modeling comparative-genomics/ancestral-reconstruction - DTL informs ancestral gene-content inference phylogenetics/modern-tree-inference - UFBoot bootstrap gene trees phylogenetics/bayesian-inference - MrBayes / RevBayes alternative alignment/multiple-alignment - Quality MSA precedes gene-tree inference