Tyrosine (tyr in the pathway-completeness tables) appears in this corpus mainly as one of the amino-acid biosynthesis pathways scored for community completeness in NMDC metagenomes. It is an outlier in two separate analyses of that data 1. See also aromatic amino acid biosynthesis and Community Metabolic Ecology via NMDC × Pangenome Integration.
Black Queen Hypothesis tests
The report tested the Black Queen Hypothesis (BQH) by correlating community pathway completeness with ambient amino-acid metabolite intensity. Under the BQH, that correlation should be negative 1. Tyrosine was the outlier in the opposite (anti-BQH) direction: r = +0.419 with n = 26, a nominal p = 0.033 and q = 0.117. It was therefore not significant after Benjamini–Hochberg FDR correction (false discovery rate), and the report labels it “ns” 1. This positive association conflicts with the predicted direction, and the report treats it as an outlier rather than discarding it 1. By contrast, isoleucine biosynthesis (r = −0.057, n = 18, q = 0.823) could be tested as the 13th pathway but showed no BQH signal at this sample size 1. Related pages: community-metabolic-interdependence and null-results-under-limited-statistical-resolution.
The central discoveries digest gives the same outlier as r = +0.42 (ns) and calls it an anti-BQH outlier 2. The project report gives r = +0.419 for this correlation 1. Each figure is recorded here as its source states it.
Proposed explanation (hypothesis, not tested)
The report says the tyrosine outlier (r = +0.42) “merits caution”. Tyrosine can be made from phenylalanine by non-biosynthetic hydroxylation. Communities with high phenylalanine biosynthesis completeness could therefore still supply tyrosine, and the tyr completeness score does not capture that route. This would decouple biosynthesis from pool size 1. The discoveries digest calls this explanation “likely” 2. The report only says the outlier “may” reflect alternative tyrosine sources, and neither source tests the idea directly 1. It remains a hypothesis: phenylalanine hydroxylation may make the tyrosine completeness score a poor proxy for tyrosine supply 2,1.
Ecosystem-type differentiation
The report ran a separate kruskal-wallis-test on each pathway, corrected with benjamini-hochberg-fdr (BH-FDR). It found that 17 of 18 amino-acid pathways differed significantly in community completeness across ecosystem types (q < 0.05). The largest differences were in the biosynthesis of glycine (H = 92.98, q = 1.2×10⁻¹⁹), asparagine (H = 66.19, q = 3.8×10⁻¹⁴) and cysteine (H = 62.66, q = 1.5×10⁻¹³). Tyrosine was the only pathway without a significant difference (q = 0.71) 1. This makes tyrosine the exception to the habitat structuring described in habitat-structured-community-metabolic-potential 1.