What this entity is
Canonical name: Mantel test. 1
Known aliases: Mantel test; Mantel correlation test. 1
Stable external identifier: None was reported in the source document. 1
The Mantel test assesses the correlation between two distance matrices. 1 In the AMR strain-variation study, it compared average nucleotide identity (ANI) distance matrices with antimicrobial-resistance (AMR) Jaccard distance matrices across species. 1 ANI is a measure of genome-wide nucleotide similarity, while Jaccard distance compares shared and differing gene repertoires. 1
Use in genomic variation and ecology
Mantel tests were conducted for 1,261 species. 1 Of these, 701/1,261 species (55.6%) showed significant phylogenetic signal at FDR < 0.05, where FDR is the false-discovery rate. 1 The median Mantel r for all AMR genes was 0.247, and 87.8% of species showed a positive correlation. 1 These results indicate that closely related strains generally tended to share more AMR genes. 1
In the SSO subsurface ecology study, a Mantel test correlated ecological and geographic distance matrices for 9 wells arranged across approximately 6 m. 2 It detected significant distance-decay of community similarity, with Spearman ρ = 0.323, p = 0.029, using 9,999 permutations. 2 This supports the existing use of Mantel testing to detect structure in distance relationships, while refining its application from genomic similarity to spatial community ecology. 2
The SSO analysis found no significant association with the uphill–downhill direction (Mantel ρ = −0.049, p = 0.580), whereas the east–west association was weaker and non-significant (column Mantel ρ = 0.227, p = 0.092). 2 A second Mantel analysis comparing groundwater community-distance matrices across two dates produced ρ = 0.867, p = 0.001, indicating that well-to-well similarity rankings were nearly unchanged over the 9-day interval. 2 This supports persistent short-term spatial structure but does not establish long-term or seasonal stability. 2
The AMR results support environmental-resistome by showing that lineage structure organizes within-species AMR repertoires. 1 They also contribute to pangenome-integration, which integrates pangenome structure with strain-level AMR variation. 1 The SSO results additionally support ecotype-environment-gene-content by showing that community similarity varies with spatial arrangement, while the proposed contamination-plume explanation remains a hypothesis pending direct geochemistry. 2
Non-core, putatively acquired AMR genes showed a stronger phylogenetic signal than core, intrinsic genes: the median Mantel r was 0.222 for non-core genes versus 0.117 for core genes. 1 A paired t-test comparing these values gave t = -8.35, p = 7.0e-16, and n = 489. 1 This pattern supports the hypothesis that acquired resistance elements can become stably maintained and vertically transmitted within lineages. 1
Interpretation and limitations
The stronger non-core signal may be partly statistical because near-universal core genes have little Jaccard-distance variance, which can suppress Mantel correlations independently of biological processes. 1 ANI extraction for the Mantel analysis was limited to species with <=500 genomes. 1 This limitation excluded mega-species such as Escherichia coli, which had 15,388 genomes, and Klebsiella pneumoniae, which had 14,240 genomes, from phylogenetic-signal analysis. 1
The SSO Mantel associations do not by themselves demonstrate hydrological flow, contamination, or microbial interaction: the plume interpretation is based on community and geographic distances, and direct SSO geochemistry was unavailable. 2 The groundwater temporal result is also limited to 5 wells and a 9-day interval. 2
The study generated 1,259 ANI matrices and 1,261 Mantel results. 1 The report proposes subsampling species with >500 genomes as a future strategy for extending Mantel analysis to larger datasets. 1
Related pages
- Within-Species AMR Strain Variation — source report containing the Mantel-test analysis. 1
- SSO Subsurface Community Ecology — Spatial Structure, Functional Gradients, and Hydrogeological Drivers — source report containing spatial and temporal community Mantel analyses. 2
- average-nucleotide-identity — distance measure used in the phylogenetic comparison. 1
- environmental-resistome — concept addressing lineage and environmental organization of AMR. 1
- pangenome-integration — concept addressing pangenome and strain-level AMR integration. 1
- ecotype-environment-gene-content — concept addressing environment-linked community structure. 2