Two projects report per-metal “deltas” for metal-tolerance genes: the difference between the fraction of fitness-important genes classified as core in the pangenome (the full gene set across a species’ sequenced genomes) and a baseline core fraction. The deltas reported in the metal fitness atlas do not match the pre-correction deltas reported in the counter-ion effects analysis for the same metals. Neither report, as cited here, explains whether different gene sets or baselines account for the gap 1,2. This matters for pangenome-conservation-fitness-decoupling, because the size and sign of these deltas are the evidence for how strongly metal fitness genes concentrate in the core genome.
Evidence Sides
Metal fitness atlas values
The atlas reports cadmium at -0.010 and molybdenum at +0.148 1,2.
Counter-ion effects pre-correction values
Before the counter-ion analysis applies its correction, it reports cadmium at -0.008 and molybdenum at +0.132 1,2.
What is and is not established
The values differ in magnitude for both metals. In the examples cited, they agree in sign: cadmium is negative in both and molybdenum is positive in both 1,2. Neither report, as cited here, says whether different gene sets or baselines explain the difference. The wiki therefore records both values and does not prefer either one 1,2.
Possible Reconciliations
- Hypothesis: different gene sets. The counter-ion analysis may have rebuilt the set of fitness-important genes with a different threshold, organism set or filtering step. That would change which genes enter each metal’s core fraction.
- Hypothesis: different baselines. The two projects may compute the baseline core fraction differently, for example per metal versus pooled across organisms. That would shift every delta even if the gene sets were identical.
- Hypothesis: different data snapshots. The projects may have drawn on different versions of the fitness or pangenome tables in the KBase Data Lakehouse. Small changes in gene-to-cluster mapping would then move the deltas.
Neither report, as cited here, establishes any of these. Each is a candidate explanation only.
Resolving Work
- Gene-level comparison: Join the per-metal gene lists from both projects on gene identifier and compute the set differences. This tests whether the two projects scored the same genes for cadmium and molybdenum.
- Baseline audit: Recompute each metal’s baseline core fraction under both projects’ definitions on one shared organism set. This tests whether the delta gap is entirely due to the baseline.
- Snapshot check: Record the table versions each project queried, rerun the atlas pipeline on the counter-ion project’s snapshot, and compare the outputs. This tests whether data drift accounts for the gap.
- Full-table reconciliation: Line up every metal’s delta from both reports and check whether the gap is systematic (same direction and similar size) or specific to individual metals. This tests whether a single method difference can explain the discrepancy.