bio-comparative-genomics-whole-genome-duplication

What it does

Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using multiple tools (wgd v2, KsRates, DupGen_finder, MAPS, POInT, SLEDGe, Whale.jl) and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

How it works

The skill instructs the agent to run a sequence of CLI tools and analyses that together identify WGD signals and place them in an evolutionary context. Concrete steps include:

• Use CLI: wgd dmd and wgd ksd to construct paranome data and compute Ks distributions; then wgd syn to extract synteny-anchored WGD signals.
• Run ksrates init followed by ksrates wgd-paralogs ortho to obtain substitution-rate-corrected ages for focal paralogs vs orthologs.
• Execute MCScanX -h then dupgen_finder to classify paralogs into tandem, proximal, dispersed, segmental, or WGD categories.
• Run mapsR for gene-tree-based WGD phylogenetic placement.
• Refer to table-driven guidance on the integration of these outputs, including mixture-model fits (GMM/ELMM) and per-block Ks analyses, to support dating and placement decisions.
• Consider scenarios like vertebrate 2R/3R WGDs, or salmonid Ss4R, where specific tool choices (e.g., Whale.jl) may be preferred.

When to use it

Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

What it can touch

The skill lists the following tools and inputs: wgd, KsRates, DupGen_finder, MAPS, POInT, SLEDGe, Whale.jl, MCScanX, dupgen_finder, mapsR. It requires command-line interaction with these tools and alignment/orthology inputs as described in the workflow steps.

Caveats

Includes notes on Ks saturation (Ks < 1.5 for reliable inference; >= 2 is saturated), substitution-rate variation across lineages (KsRates necessary for cross-lineage comparisons), and per-block Ks synchronization checks. Also covers failure modes and recommended mitigations, such as distinguishing WGD from tandem clusters using DupGen_finder, and subgenome separation for polyploid genomes. The workflow references deprecated v1 outputs and emphasizes using wgd v2 as the current standard.