Bio Comparative Genomics Whole Genome Duplication

Version Compatibility

Reference examples tested with: wgd v2.0.31+ (heche-psb/wgd; Chen et al 2024 Bioinformatics 40:btae272), KsRates 1.1.3+ (VIB-PSB/ksrates; Sensalari 2022 Bioinformatics 38:530), DupGen_finder (Qiao 2019 Genome Biol 20:38), MAPS 1.0 (Li 2018), POInT (Conant lab), SLEDGe (bioRxiv 2024.01.17.574559), Whale.jl 2.0+, ksrates pip 1.1+, MCScanX 1.0+, PAML 4.10+ (yn00/codeml for Ks), BLAT 36+, DIAMOND 2.1+, R 4.4+, mclust 6.1+ (for mixture models). Python 3.10+ required for wgd v2.

Before using code patterns, verify installed versions match. If versions differ:

• CLI: wgd --version; ksrates --version; wgd ksd --help
• Python: pip show wgd ksrates
• R: packageVersion('mclust')

If code throws wgd ksd: cannot find PAML output, KsRates: insufficient sister species, MAPS: missing tree, these tools have specific input expectations: wgd needs codon-aware MAFFT/MUSCLE alignment; KsRates needs configured config_ksrates.txt; MAPS needs nucleotide tree. The deprecated arzwa/wgd v1 is replaced by heche-psb/wgd v2.

Whole Genome Duplication Analysis

"Are there WGD events in this lineage and when did they occur?" -> WGD detection combines Ks distributions (synonymous-substitution rates between gene paralog pairs, showing peaks at past polyploidy events) and synteny block analysis (parallel collinear blocks within a genome). Modern best practice uses wgd v2 (Chen et al 2024 Bioinformatics 40:btae272) as an integrated pipeline. KsRates (Sensalari 2022 Bioinformatics 38:530) is mandatory for cross-lineage comparison because substitution rates vary across the tree -- ignoring this places WGDs incorrectly relative to speciation events. The fundamental tradeoff: Ks plot peaks are visually obvious but biologically ambiguous between (1) small-scale tandem duplications, (2) segmental duplications, and (3) true WGD; combining Ks with synteny anchors disambiguates these.

• CLI: wgd dmd and wgd ksd -- paranome construction + Ks distribution
• CLI: wgd syn -- synteny-anchored WGD signal extraction
• CLI: ksrates init then ksrates wgd-paralogs ortho -- substitution-rate-corrected positioning
• CLI: MCScanX -h then dupgen_finder -- duplication-class assignment
• CLI: mapsR -- gene-tree-based WGD phylogenetic placement

Algorithmic Taxonomy

Methodology evolves; verify the current wgd v2 manual and the Chen & Zwaenepoel 2023 review chapter (in Polyploidy: Methods and Protocols) before locking on a single workflow. The 2R vertebrate / 3R teleost / Ss4R salmonid WGDs are well-established; novel WGD claims require concordance across Ks, synteny, and phylogenomic placement.

Decision Tree by Experimental Scenario

Per-Tool Failure Modes

Saturation at Ks > 2

Trigger: Computing Ks for ancient WGD candidates from distantly related taxa.

Mechanism: Synonymous substitutions saturate after Ks ~2; each site has undergone multiple substitutions. Observed Ks underestimates true Ks; the relationship between Ks and time becomes non-monotonic above 1.5. WGD peaks at age 200+ Myr in vertebrates / 100+ Myr in plants are at Ks > 2 and unreliable (Vanneste 2013 MBE 30:177).

Symptom: wgd ksd output shows peak at Ks > 1.5 with broad distribution; KsRates rate-corrected Ks even more uncertain; visual fitting yields ambiguous components.

Fix: Restrict Ks-based WGD inference to Ks < 1.5; for older WGDs, use phylogenomic methods (MAPS, POInT, Whale.jl) which don't rely on Ks alone. Report Ks-based dating with explicit saturation caveat. For 2R vertebrate WGD (~500 Myr), MAPS / Whale.jl is required because Ks is saturated.

Substitution-rate variation across lineages

Trigger: Comparing WGD position in two lineages with different molecular evolutionary rates.

Mechanism: If lineage A evolves twice as fast as lineage B, the same biological time is at twice the Ks in lineage A. A WGD at Ks = 0.5 in lineage A and Ks = 0.25 in lineage B might be the same event biologically.

Symptom: WGD claimed at "different times" in different lineages; speciation-vs-WGD relative timing flips depending on which lineage is the focal species.

Fix: Always use KsRates (Sensalari 2022) when comparing WGDs across lineages. KsRates uses outgroup-species speciation events to calibrate the relative substitution rates, then rescales Ks to a common scale. Single-lineage Ks dating is unreliable for inter-lineage comparison.

Tandem duplication masquerading as WGD peak

Trigger: Ks distribution shows a peak at low Ks (< 0.5); user concludes "recent WGD."

Mechanism: Tandem duplications create paralog pairs with low Ks; these accumulate in clusters (especially in NLR genes in plants, OR genes in mammals). The Ks peak reflects clustered tandem origins, not WGD.

Symptom: "WGD" peak Ks-distribution is dominated by paralogs from tandem clusters; synteny analysis shows few cross-chromosome parallel blocks.

Fix: Use DupGen_finder to classify each paralog pair as tandem / proximal / transposed / dispersed / WGD. The true WGD signal comes from the WGD-classified pairs. Recompute Ks distribution restricted to WGD-classified pairs (or anchor-pair restricted to synteny blocks). wgd v2 integrates this filtering.

Synteny block age inconsistency

Trigger: Different synteny blocks from the same suspected WGD have different Ks distributions.

Mechanism: Real WGD blocks should share a synchronized Ks distribution centered at the WGD age; if blocks have very different ages, the inferred "WGD" was probably a series of segmental duplications.

Symptom: Per-block Ks median varies widely; some blocks show Ks ~ 0.3 and others Ks ~ 1.0; not consistent with single WGD.

Fix: Compute per-block Ks distribution; require synchronization (interquartile range overlapping across blocks). wgd v2 reports per-block age dispersion. If dispersion is high, downgrade to "potentially WGD-like" or attribute to ancient segmental duplication history.

Mixture model under/overfitting components

Trigger: Fitting GMM (gaussian mixture model) or ELMM (exponential-lognormal mixture model) to Ks distribution.

Mechanism: Mixture models with too few components miss real WGD signal; too many components find spurious peaks. BIC-based model selection is standard but sensitive to bin choice in histograms.

Symptom: Different runs with different bin counts give different component numbers; visual peaks don't match component means.

Fix: Use BIC-based component selection with 5-fold cross-validation; report uncertainty in component count. wgd v2 fits both GMM and ELMM and reports BIC for each model up to 5 components. Visually validate against synteny block analysis.

Comparing wgd v1 (deprecated) vs v2 outputs

Trigger: Mixing scripts written for arzwa/wgd v1 with heche-psb/wgd v2.

Mechanism: wgd v1 was deprecated 2023; v2 has different command-line interface, default parameters, and output file structure. Scripts from v1 fail or produce different results in v2.

Symptom: Older scripts using wgd ksd v1 syntax don't work in v2; output paths differ.

Fix: Update all scripts to wgd v2 syntax. The v1 wgd is no longer maintained; v2 is the current standard.

KsRates failing with insufficient species

Trigger: Running KsRates with one focal species and one outgroup.

Mechanism: KsRates calibrates substitution-rate variation via at least two outgroup speciation events; one outgroup species provides only one rate point and cannot resolve rate heterogeneity.

Symptom: KsRates errors or produces unreliable rate-corrected Ks.

Fix: Include >= 2 outgroup species at different phylogenetic distances; for plants, a model angiosperm + gymnosperm pair; for vertebrates, lamprey + invertebrate outgroup. Document outgroup sampling.

Polyploid genome confusion

Trigger: Running wgd v2 on an unassigned-subgenome polyploid (e.g. wheat hexaploid without A/B/D subgenome labels).

Mechanism: WGD signal is muddled when subgenomes are not separated; orthologs across subgenomes appear as paralogs, intermixing tandem / segmental / WGD / homeolog signal.

Symptom: Ks distribution shows multiple overlapping peaks at varying intensities; component fits are unstable.

Fix: Assign subgenomes first using k-mer methods (KMC2 + SubPhaser; Jia 2022 New Phytol 235:801) or synteny-based assignment (GENESPACE; Lovell 2022). Then run wgd v2 on each subgenome separately. Document subgenome assignment.

Confusion of homeologous (WGD) vs orthologous (speciation) pairs

Trigger: Computing Ks across recent WGD species without explicit homeolog labeling.

Mechanism: In recent WGD lineages (e.g. salmonid Ss4R), the "ortholog" between species and the "homeolog within species" can have similar Ks; standard ortholog detection (OrthoFinder) lumps both.

Symptom: wgd v2 reports Ks distributions but doesn't distinguish homeologs from orthologs; downstream dating confused.

Fix: Use synteny-anchored ortholog detection (GENESPACE, ProteinOrtho-synteny) to separate cross-species orthologs from within-species homeologs. Run wgd v2 separately on each class. Report each Ks distribution explicitly.

Quantitative Thresholds

wgd v2 Standard Workflow

Goal: Detect and date WGD events from a focal-species proteome and CDS, with synteny-anchored Ks distribution.

Approach: Build paranome -> compute Ks distribution -> identify synteny anchors -> mixture model fit -> visualize.

# Install (Python 3.10+ required)
pip install wgd

# 1. Build paranome (all-vs-all paralog identification)
wgd dmd cds.fasta -o output/paranome.tsv -t 16

# 2. Compute Ks distribution
# Verify exact flags with `wgd ksd --help` (the wgd v2 CLI evolves; --pairwise / --ks-method spelling differs across versions).
wgd ksd output/paranome.tsv cds.fasta -o output/ksd \
    --aligner mafft --n-threads 16

# 3. Synteny anchors (intra-genome)
wgd syn output/paranome.tsv gff.bed cds.fasta -o output/syn \
    --feature gene --gene-attribute Name --min-block-size 5

# 4. Mixture model on synteny-anchored Ks
wgd mix output/ksd/ks_distributions.tsv -o output/mix \
    --model both --components 1 2 3 4 5

# 5. Visualize
wgd viz output/mix/mix_results.tsv -o output/viz \
    --type histogram --bins 50

'''Parse wgd v2 outputs and identify WGD peak from Ks distribution.'''
import pandas as pd
from scipy import stats


def load_ks_distribution(ksd_file):
    '''Load wgd ksd output: pair  Ks  Ka  ...'''
    df = pd.read_csv(ksd_file, sep='\t')
    # Filter saturated
    df_filt = df[(df['Ks'] > 0) & (df['Ks'] < 2)]
    return df_filt


def fit_mixture(ks_values, n_components=3):
    '''Fit GMM (gaussian mixture model) on Ks via sklearn.'''
    from sklearn.mixture import GaussianMixture
    gmm = GaussianMixture(n_components=n_components, random_state=42)
    gmm.fit(ks_values.reshape(-1, 1))
    return {
        'means': gmm.means_.flatten(),
        'variances': gmm.covariances_.flatten(),
        'weights': gmm.weights_,
        'bic': gmm.bic(ks_values.reshape(-1, 1))
    }


def identify_wgd_peaks(ks_values, min_components=1, max_components=5):
    '''BIC-based model selection.'''
    results = {}
    for n in range(min_components, max_components + 1):
        results[n] = fit_mixture(ks_values, n)
    best_n = min(results.keys(), key=lambda k: results[k]['bic'])
    return best_n, results[best_n]

KsRates Substitution-Rate-Corrected Workflow

Goal: Position a focal-species WGD relative to speciation events with substitution-rate correction.

Approach: Define focal species + 2+ outgroups -> compute orthologous Ks (focal vs outgroup) -> compute paralogous Ks (focal-internal) -> rescale via outgroup calibration.

# KsRates is best driven through its Nextflow pipeline (which orchestrates ortholog Ks,
# paralog Ks, rate correction, and plotting). Subcommand naming differs across releases;
# always verify with `ksrates --help` against the installed version.

# 1. Generate a working config (subcommand spelling varies by release; e.g. `init` in some,
#    `generate-config` in others). Inspect `ksrates --help`.
ksrates init config_ksrates.txt        # OR: ksrates generate-config config_ksrates.txt

# 2. Edit config_ksrates.txt to set focal_species, outgroups, FASTA + GFF paths, tree.

# 3. Run the full pipeline (Nextflow-driven):
ksrates --config config_ksrates.txt --n-threads 16
# Or invoke individual stages (subcommand names: see `ksrates --help`).

The output plot shows the rate-corrected focal-species paralog Ks distribution with vertical lines indicating outgroup-species speciation events; WGD peaks before vs after speciation events can be distinguished.

DupGen_finder for Duplication Class Assignment

Goal: Classify each paralog pair as tandem / proximal / transposed / dispersed / WGD by genomic context.

Approach: MCScanX collinearity + intervening-gene count -> classify each duplicate by class.

# Input: MCScanX collinearity file + GFF
git clone https://github.com/qiao-xin/DupGen_finder
cd DupGen_finder

# Run with intervening-gene count
./DupGen_finder.pl \
    -i input_collinearity_file \
    -t species_name \
    -c gene_count_file \
    -o output

# Output: tandem, proximal, transposed, dispersed, wgd duplicate lists

'''Aggregate DupGen_finder output for downstream Ks distribution per class.'''
def load_dupgen(class_dir):
    classes = {}
    for cls in ('tandem', 'proximal', 'transposed', 'dispersed', 'wgd'):
        path = f'{class_dir}/{cls}.pairs'
        try:
            classes[cls] = pd.read_csv(path, sep='\t', header=None,
                                       names=['gene1', 'gene2'])
        except FileNotFoundError:
            classes[cls] = pd.DataFrame(columns=['gene1', 'gene2'])
    return classes

MAPS Phylogenomic WGD Placement

Goal: Place a WGD event on a species tree using gene-tree-species-tree mapping.

Approach: Build many single-copy ortholog gene trees -> map each tree's topology to the species tree -> identify branches with topology consistent with a WGD event.

MAPS is heavyweight; requires CRG database setup and significant compute. See https://bitbucket.org/barker-lab/maps/src for the current pipeline.

Reconciliation: When Methods Disagree

Operational rule for publication: Concordance across Ks distribution (wgd v2), synteny-anchored block analysis (wgd syn / GENESPACE), KsRates rate-corrected positioning, and at least one phylogenomic method (MAPS / Whale.jl / ALE with WGD node) = publication-grade WGD claim. Single-Ks-peak claims should be downgraded to "Ks evidence for possible WGD."

Cohort Gotchas

• Plant WGD legacy: All angiosperms share at least one ancestral WGD (the epsilon event, 192 Myr); the core-eudicot gamma paleohexaploidy is younger (120 Myr; Jiao 2012 Genome Biol 13:R3), core-eudicot-specific (Soltis 2009 Am J Bot 96:336); confirm consensus against published plant lineages
• Vertebrate 2R: ~500-600 Myr; Ks saturated; use MAPS phylogenomic placement (Dehal & Boore 2005)
• Teleost 3R: ~320 Myr; in addition to 2R; doubles ohnologs in fish
• Salmonid Ss4R: ~80-100 Myr; recent enough that Ks is informative; ohnologs identifiable
• Plant polyploids (wheat, Brassica): recent; subgenomes assignable; subgenome-stratify before wgd v2
• Allopolyploids vs autopolyploids: allopolyploids have higher inter-subgenome divergence (easier to assign subgenomes); autopolyploids have similar subgenomes (chimeric assembly risk)
• Lineage-specific extra duplications post-WGD: make Ks peak broader; differentiate from sequential WGDs

Anticipated Reviewer Pushback

Common Errors

Tool Installation Notes

# wgd v2
pip install wgd
# Or: git clone https://github.com/heche-psb/wgd && cd wgd && pip install .

# KsRates
pip install ksrates

# DupGen_finder (Perl + MCScanX dependency)
git clone https://github.com/qiao-xin/DupGen_finder
# Install MCScanX (Wang 2012): git clone https://github.com/wyp1125/MCScanX && cd MCScanX && make

# MAPS (Python; requires CRG, ete3)
git clone https://bitbucket.org/barker-lab/maps

# Whale.jl (Julia)
julia -e 'using Pkg; Pkg.add("Whale")'

# SLEDGe
git clone https://github.com/SLEDGe-team/SLEDGe

# POInT (C++)
git clone https://github.com/gconant0/PoInT
cd PoInT && make

# PAML for Ks computation (yn00 method)
conda install -c bioconda paml

# DIAMOND / BLAST for paranome
conda install -c bioconda diamond blast

# R packages
install.packages(c('mclust', 'rmixmod'))

For new analyses, default to wgd v2 + KsRates as the primary pipeline; MAPS or Whale.jl for confirmation on phylogenomic placement.

References

• Chen H et al 2024 Bioinformatics 40:btae272 (wgd v2)
• Sensalari C et al 2022 Bioinformatics 38:530 (KsRates)
• Qiao X et al 2019 Genome Biol 20:38 (DupGen_finder)
• Li Z et al 2018 PNAS 115:4713 (MAPS phylogenomic WGD placement)
• Conant GC & Wolfe KH 2008 Genetics 179:1681 (POInT)
• Zwaenepoel A & Van de Peer Y 2019 MBE 36:1384 (Whale.jl)
• Sutherland BL et al 2024 bioRxiv 2024.01.17.574559 (SLEDGe ML classifier)
• Vanneste K et al 2013 MBE 30:177 (Ks saturation)
• Holland PWH et al 1994 Development Suppl:125 (2R hypothesis)
• Dehal P & Boore JL 2005 PLoS Biol 3:e314 (vertebrate 2R confirmation)
• Glasauer SMK & Neuhauss SCF 2014 Mol Genet Genomics 289:1045 (teleost 3R)
• Lien S et al 2016 Nature 533:200 (salmonid Ss4R)
• Soltis DE et al 2009 Am J Bot 96:336 (polyploidy and angiosperm diversification)
• Jiao Y et al 2012 Genome Biol 13:R3 (dates the core-eudicot gamma triplication)
• Birchler JA & Veitia RA 2007 Plant Cell 19:395 (gene balance hypothesis)
• Force A et al 1999 Genetics 151:1531 (subfunctionalization)
• Maere S et al 2005 PNAS 102:5454 (post-WGD retention bias)
• Tang H et al 2008 GR 18:1944 (synteny / MCScan)
• Lovell JT et al 2022 eLife 11:e78526 (GENESPACE)
• Jia K-H et al 2022 New Phytol 235:801 (SubPhaser subgenome assignment)
• Yang Z 2007 PAML manual (yn00 codon Ks)
• Chen H & Zwaenepoel A 2023 Methods Mol Biol 2545:3 (inference of ancient polyploidy from genomic data)

Related Skills

• comparative-genomics/synteny-analysis - Synteny-anchored Ks (wgd syn / GENESPACE)
• comparative-genomics/ortholog-inference - Ortholog detection feeds DupGen / wgd
• comparative-genomics/gene-tree-species-tree-reconciliation - Whale.jl native WGD modeling; ALE with WGD branch
• comparative-genomics/gene-family-evolution - CAFE5 birth-death often shows post-WGD retention bias
• comparative-genomics/positive-selection - Selection on retained ohnologs (post-WGD diversification)
• comparative-genomics/ancestral-reconstruction - Ancestral pre-WGD gene state
• phylogenetics/divergence-dating - Time-calibrated WGD positioning
• alignment/multiple-alignment - Codon-aware MSA for Ks computation
• alignment/pairwise-alignment - Pairwise Ks via PAML yn00 / codeml
• genome-assembly/assembly-qc - BUSCO / Compleasm before WGD analysis