Report: Pangenome Openness Analysis

Key Findings

Analysis of pangenome openness vs environment/phylogeny effects revealed no significant relationship:

Metric	Spearman rho	p-value
Openness vs Environment effect	-0.05	0.54
Openness vs Phylogeny effect	0.03	0.73

Pangenome Openness vs Effects

(Notebook: 01_explore_gene_data.ipynb)

Whether a species has an open or closed pangenome does not predict whether environment or phylogeny dominates its gene content. This suggests:

Pangenome structure is independent of eco-phylo dynamics: Open pangenomes don’t necessarily mean environment-driven adaptation
HGT may not track environmental similarity: Gene acquisition might be opportunistic rather than niche-specific
Core/accessory classification may not capture functional adaptation: The genes that vary may not be the ones responding to environment

Tettelin et al. (2005) introduced the open/closed pangenome framework for bacterial genomes. Our null result suggests that the open/closed distinction, while useful for describing gene content variability, does not predict the ecological vs phylogenetic drivers of that variability.
McInerney et al. (2017) argued that pangenome structure reflects a balance of selection, drift, and HGT. Our finding that openness is uncorrelated with environment effects is consistent with HGT being opportunistic rather than ecologically directed.
Parks et al. (2022) provided the GTDB taxonomy and pangenome framework used here, enabling consistent cross-species comparisons of pangenome structure.

Sample size is limited to species with both pangenome statistics and ecotype analysis results
Openness is a single summary metric that may not capture the full complexity of pangenome structure
Environment and phylogeny effects are derived from partial correlations that may not fully disentangle confounded variables
The ecotype analysis upstream may have limited statistical power for some species with few genomes

Stratify by gene function: Do open pangenomes show environment effects specifically in L (mobile) or V (defense) categories?
Test alternative openness metrics: Try auxiliary fraction, Heap’s law alpha, or pangenome fluidity
Lifestyle interaction: Test openness x lifestyle interaction (e.g., open pathogens vs open environmental species)

Dataset	Description	Source
KBase pangenome statistics	Pre-computed openness metrics per species	`pangenome` table via Spark
Ecotype analysis results	Environment and phylogeny effect sizes	`ecotype_analysis` project

File	Description
`data/pangenome_stats.csv`	Pre-computed pangenome statistics for target species
`data/pangenome_ecotype_merged.csv`	Merged pangenome stats with ecotype analysis results
`data/species_selection_stats.csv`	Species selection statistics
`data/target_genomes_expanded.csv`	Expanded target genome information

Parks DH et al. (2022). “GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy.” Nucleic Acids Res 50:D199-D207. PMID: 34520557
Tettelin H et al. (2005). “Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial ‘pan-genome’.” Proc Natl Acad Sci USA 102:13950-13955. PMID: 16172379
McInerney JO et al. (2017). “Why prokaryotes have pangenomes.” Nat Microbiol 2:17040. PMID: 28350002

Notebook	Purpose
`notebooks/01_explore_gene_data.ipynb`	Understand gene table structure and pangenome statistics

Figure	Description
`figures/pangenome_vs_effects.png`	Scatter plots of pangenome openness vs environment and phylogeny effect sizes

v1 (2026-02): Migrated from README.md
v2 (2026-02): Added inline figure, notebook provenance, Data section, Literature Context, Limitations, References, renamed Visualizations to Figures