{ "dataset": { "archive": "dryad", "id": "tdz08kq5d", "label": "DRYAD:tdz08kq5d" }, "page": "datasets/dryad/tdz08kq5d/", "generated": "2026-11-05T07:41:23+00:00", "caution": "A failure to reproduce is not a finding that the paper is wrong. It may be a failure of the attempt.", "outcome_counts": { "reproduced": 24, "partially_reproduced": 4, "not_reproduced": 1, "blocked": 3 }, "outcome_counts_with_outside_data": { "reproduced": 0, "partially_reproduced": 0, "not_reproduced": 0, "blocked": 0 }, "outcome_counts_elsewhere": { "reproduced": 0, "partially_reproduced": 0, "not_reproduced": 0, "blocked": 0 }, "outcome_counts_links": { "reproduced": 0, "partially_reproduced": 0, "not_reproduced": 0, "blocked": 0 }, "attempts": [ { "id": "dryad-tdz08kq5d-wang-2024-01", "dataset": { "archive": "dryad", "id": "tdz08kq5d", "version": "263142", "doi": "10.5061/dryad.tdz08kq5d" }, "key": "dryad:tdz08kq5d", "label": "DRYAD:tdz08kq5d", "dataset_version": "263142", "paper": "10.1093/evlett/qrad056", "paper_title": null, "date": "2026-10-27", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code", "model": "claude-opus-5-5", "protocol": "pilot-10" }, "runner": { "platform": "GitHub Actions", "url": "https://github.com/catalystneuro/encore/actions/runs/40514288746" }, "tier": "agent_verified", "deprecated": "", "deprecated_on": null, "entry": "dryad-tdz08kq5d-wang-2024", "entry_title": "Phage selection and resistance-virulence trade-offs in Ralstonia solanacearum (Wang et al. 2024)", "description": "Tests the findings of Wang, Wang, Yang, Lu, Fields, Xu, Shen, Wei and Friman (2024) on Dryad dataset tdz08kq5d, one workbook with the data behind each figure of the paper. It covers the selection experiment (bacterial and phage densities, colony types), the phage resistance, growth, twitching, biofilm and virulence of evolved clones, the variant calls of 28 sequenced clones, the phage adsorption assay and the transcriptome tables. The growth curves, per-clone variant calls, genome reads and the pilB and pilM data of Table S6 are not in the dataset.", "notebooks": [ { "path": "reproduce_wang_2024.ipynb", "title": "Reproducing Wang et al. (2024) from Dryad dataset tdz08kq5d", "executed": "notebooks/dryad-tdz08kq5d-wang-2024/reproduce_wang_2024.html" } ], "outcomes": [ { "claim": "fig1b-temperature-density", "statement": "R. solanacearum reached higher population densities at 35 degrees C than at 25 degrees C during the selection experiment.", "source": "Results, Ralstonia solanacearum and phage population density dynamics, paragraph 1; Figure 1B; Supplementary Table S1a", "quote": "In general, R. solanacearum reached higher population densities at 35 \u00b0C than at 25 \u00b0C (temperature, F1,36 = 73.989, p < .001", "statistics": [ { "test": "three-way repeated-measures ANOVA, temperature effect", "statistic": "F(1, 36) = 73.989", "p": 0.001, "p_relation": "<", "n": "40 populations (10 per treatment), six time points" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "Days 2 to 12, as the criterion now names them, temperature F(1, 36) = 73.989, p = 2.96e-10, as in Table S1a; mean OD600 0.5627 at 35 C against 0.2550 at 25 C. Variants, days 0 to 10 F = 70.911 and all seven days F = 74.019, both p < 1e-9, with 35 C higher. The first run asked which six of the data's seven time points enter the ANOVA; the reader's answer put days 2 to 12 in the criterion, the reading this claim had been decided on, so the outcome is unchanged and days 0 to 10 and all seven days are now variants only.", "deviations": [ "ANOVA computed in Python (statsmodels, strata as R's aov with Error(ID)) where the paper used R 3.6.3." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig1b-phage-reduces-density", "statement": "Phage presence reduced R. solanacearum densities at both temperatures.", "source": "Results, Ralstonia solanacearum and phage population density dynamics, paragraph 1; Figure 1B; Supplementary Table S1a", "quote": "While the presence of phage significantly reduced R. solanacearum densities at both temperatures (phage: F1,36 = 48.80, p < .001", "statistics": [ { "test": "three-way repeated-measures ANOVA, phage effect", "statistic": "F(1, 36) = 48.80", "p": 0.001, "p_relation": "<", "n": "40 populations (10 per treatment), six time points" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "Days 2 to 12, phage F(1, 36) = 48.800, p = 3.43e-08; mean OD600 lower with phage by 68.4% at 25 C (0.1225 against 0.3876) and by 34.5% at 35 C (0.4454 against 0.6801). Variants, days 0 to 10 F = 57.811 and all seven days F = 48.881, with the same direction. The first run asked which six of the data's seven time points enter the ANOVA; the reader's answer put days 2 to 12 in the criterion, the reading this claim had been decided on, so the outcome is unchanged and days 0 to 10 and all seven days are now variants only.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig1b-phage-effect-diminishes", "statement": "The reduction of bacterial density by phage diminished over time, with a significant temperature by phage by time interaction.", "source": "Results, Ralstonia solanacearum and phage population density dynamics, paragraph 1; Figure 1B; Supplementary Table S1a", "quote": "the phage effect on bacteria gradually diminished over time, likely due to the emergence of phage-resistant mutants (temperature \u00d7 phage \u00d7 time: F5,180 = 3.870, p < .01", "statistics": [ { "test": "three-way repeated-measures ANOVA, temperature by phage by time interaction", "statistic": "F(5, 180) = 3.870", "p": 0.01, "p_relation": "<", "n": "40 populations, six time points" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "Days 2 to 12, as the criterion now names them, temperature x phage x time F(5, 180) = 3.870, p = 0.0024, as in Table S1a; the -P minus +P difference at day 12 (0.3219 at 25 C, -0.0080 at 35 C) is below its largest earlier value (0.4362, 0.5046, day 2). With days 0 to 10 the interaction is F = 1.464, p = 0.2039 (not significant), while the differences still decline; with all seven days p = 0.0025. The first run asked which six time points enter the ANOVA and decided this claim on days 2 to 12, noting that days 0 to 10 would make it partially reproduced. The reader's answer put days 2 to 12 in the criterion and ruled out days 0 to 10, so the outcome stands on the criterion's own time points and the other two sets are variants that decide nothing. The criterion compares only the last day with the largest earlier value; at 25 C the difference is not a steady decline, falling to 0.049 on day 8 and rising to 0.322 on day 12.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "auc-phage-reduction-by-temperature", "statement": "Over the whole experiment, phages reduced bacterial density (area under the density curve) more at 25 degrees C (66.8%) than at 35 degrees C (37.18%), with a significant phage effect at each temperature.", "source": "Results, Ralstonia solanacearum and phage population density dynamics, paragraph 1", "quote": "We found that phages reduced the bacterial growth more clearly at 25 \u00b0C compared with 35 \u00b0C temperature treatment (66.8% vs. 37.18% density reductions; 25 \u00b0C... p < .001, 35 \u00b0C... p < .001, respectively)", "statistics": [ { "about": "phage effect on area under the density curve at 25 degrees C", "test": "ANOVA", "statistic": "F(1, 19) = 88.78", "p": 0.001, "p_relation": "<", "n": "10 +P and 10 -P populations" }, { "about": "phage effect on area under the density curve at 35 degrees C", "test": "ANOVA", "statistic": "F(1, 19) = 15.66", "p": 0.001, "p_relation": "<", "n": "10 +P and 10 -P populations" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "Reading (a), trapezoid over days 2 to 12, 64.55% and 33.73% (F = 63.16 and 11.26 at df (1, 18)). Reading (b), trapezoid over days 0 to 12, 66.80% and 37.18%, with the paper's F of 88.77 and 15.66 at df (1, 18) (the paper prints (1, 19)). Reading (c), sum over days 2 to 12, 68.40% and 34.50%. All within tolerance, 25 C larger, every p < 0.004. The first run had to map the criterion's 'all time points' and 'after inoculation' onto the data's seven days and asked; the answer names the readings by day, which drops the earlier reading (c), sum over days 0 to 12 (66.58% and 34.00%, now a variant) and adds the sum over days 2 to 12, which was a variant before. Under the new readings the outcome is unchanged. The variants over days 0 to 10 give 70.03% and 43.02% (trapezoid, 35 C outside tolerance) and 64.90% and 40.29% (sum, within); they decide nothing.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig1c-phage-density-temperature", "statement": "Phage densities were higher at 25 than at 35 degrees C, and at both temperatures rose rapidly at first and then declined over time.", "source": "Results, Ralstonia solanacearum and phage population density dynamics, paragraph 1; Figure 1C; Supplementary Table S1b", "quote": "relatively higher phage densities were found at 25 \u00b0C than 35 \u00b0C treatment, while phage density dynamics showed similar patterns by rapidly increasing at the beginning of the experiment before reducing over time (temperature: F1,18 = 32.75, p < .001; time: F1,18 = 84.88, p < .001", "statistics": [ { "about": "temperature effect", "test": "two-way repeated-measures ANOVA", "statistic": "F(1, 18) = 32.75", "p": 0.001, "p_relation": "<", "n": "20 +P populations (10 per temperature)" }, { "about": "time effect; the text prints F1,18 = 84.88, while Table S1b gives df 2 and 36, sum of squares 84.88, F = 86.963, p = 1.65E-14", "test": "two-way repeated-measures ANOVA", "statistic": "F(2, 36) = 86.963 (Table S1b)", "p": 0.001, "p_relation": "<", "n": "20 +P populations" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "Repeated-measures ANOVA as Table S1b: temperature F(1, 18) = 32.746, time F(2, 36) = 86.963. Mean log10 PFU/ml 8.756 at 25 C, 7.375 at 35 C. Highest on day 4 (10.511 and 8.947, from 4.0 at inoculation), lower on day 12 (8.037, 6.859); the lowest is day 8 at both temperatures. The paper's text prints the time effect as F1,18 = 84.88, which is its sum of squares.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig1d-mucoid-lost-with-phage", "statement": "At day 12, ancestral mucoid colonies were lost in the presence of phage at both temperatures and replaced by small colony variants (SCVs), except in one phage replicate at 25 degrees C.", "source": "Results, Ralstonia solanacearum and phage population density dynamics, paragraph 2; Figure 1D", "quote": "We found that ancestral mucoid (M) colony types were lost in the presence of phage at both temperature treatments and replaced by small non-mucoid colony variants (SCV), except for one phage treatment replicates at 25 \u00b0C (Figure 1D; hardly visible in the mean plot due to low frequency of SCVs: 0.24% of all colonies within this treatment)", "statistics": [], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "35 C +P, 0 of 4 replicates with mucoid colonies; 25 C +P, 1 of 4 (replicate 2, 700 of 71700 CFU/ml), the other three 100% SCV. Mucoid share of the 25 C +P treatment, mean of replicate frequencies, 0.244%, within 0.24 +- 0.024 (reading a1). From pooled counts (reading a2) it is 0.561%; reading (b), SCV share of the exceptional replicate, 99.02%. The paper calls the 0.24% the frequency of SCVs; in the data it is that of mucoid colonies. The first run asked whether reading (a) is a mean of replicate frequencies or a pooled share; the answer says the paper does not fix it and names both as readings (a1) and (a2) under the criterion's rule that one matching reading is enough. The outcome is unchanged, and the open choice is now a reading of the criterion, not a deviation.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig1d-phage-raises-scv-frequency", "statement": "SCVs also increased without phage, but around 20% (25 degrees C) and 55% (35 degrees C) of colonies stayed mucoid in the -P treatments, and phage presence raised the SCV frequency.", "source": "Results, Ralstonia solanacearum and phage population density dynamics, paragraph 2; Figure 1D; Supplementary Table S2", "quote": "While the frequency of SCVs also considerably increased in the absence of phage, around 20% and 55% colonies still had mucoid colony morphology at low- and high-temperature treatments, respectively (phage: F1,12 = 7.016, p < .05", "statistics": [ { "test": "two-way ANOVA, phage effect on colony type frequency", "statistic": "F(1, 12) = 7.016", "p": 0.05, "p_relation": "<", "n": "16 replicate populations, four per treatment" } ], "kind": "finding", "inferred": "", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "Two-way ANOVA as Table S2, phage F(1, 12) = 7.016, p = 0.0212; mean SCV share 99.88% with phage against 64.83% without. Mucoid share without phage, mean of replicates, 15.34% at 25 C (outside 20 +- 2) and 55.00% at 35 C (within); pooled, 15.64% and 23.78%, both outside. The phage effect and the 55% hold; the 20% does not.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2a-phage-exposed-more-resistant", "statement": "Clones previously exposed to phage were more phage-resistant than clones from the no-phage treatments, at both temperatures.", "source": "Results, SCVs have relatively higher phage resistance, paragraph 1; Figure 2A; Supplementary Table S3a", "quote": "clones that had previously been exposed to phages showed higher levels of phage resistance compared to no-phage control treatments in both temperature treatments (phage: F1,15 = 280.752, p < .001", "statistics": [ { "test": "ANOVA (Table S3a), phage effect", "statistic": "F(1, 15) = 280.752", "p": 0.001, "p_relation": "<", "n": "128 clones from 16 replicate populations" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "On unit means, phage F(1, 15) = 280.75 with sequential sums of squares (the paper's value; unit means with sequential sums of squares reproduce Tables S3a to S3c term by term) and 30.50 with type II, both p < 1e-4; the clone variant gives 973.58 and 51.76. Mean R +P against -P, 0.9481 against 0.5980 at 25 C and 1.0381 against 0.5566 at 35 C. The first run treated unit means and clones as readings; the answer fixes the unit as the mean of the clones of each colony type within each replicate population and makes clones a variant. All readings agreed before, so the outcome is unchanged.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2a-temperature-resistance", "statement": "Clones from the 35 degrees C treatments had higher phage resistance than clones from 25 degrees C.", "source": "Results, SCVs have relatively higher phage resistance, paragraph 1; Figure 2A; Supplementary Table S3a", "quote": "We found that prior exposure to high temperature was linked to higher phage resistance (temperature: F1,15 = 6.459, p < .05", "statistics": [ { "test": "ANOVA (Table S3a), temperature effect", "statistic": "F(1, 15) = 6.459", "p": 0.05, "p_relation": "<", "n": "128 clones from 16 replicate populations" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "On unit means, temperature p = 0.0226 (sequential, F(1, 15) = 6.459 as Table S3a) and 0.0092 (type II), mean R 0.7902 at 35 C against 0.7314 at 25 C. Clone variant, p = 0.0708 (sequential, F(1, 121) = 3.32) and 6e-6 (type II), mean R 0.7973 against 0.7730. The first run treated unit means and clones as readings; the answer fixes the unit as the mean of the clones of each colony type within each replicate population and makes clones a variant. The first run blocked the claim as methods_underspecified because the clone reading with sequential sums of squares gave p = 0.0708; with clones a variant, both readings of the criterion give p < 0.05, and the outcome moves from blocked to reproduced. Within colony type mucoid clones have higher R at 25 C (0.378 against 0.295); the effect over all clones comes in part from the colony types each treatment yielded.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2a-no-temperature-phage-interaction", "statement": "The increase in phage resistance after phage exposure did not differ between the two temperatures (no phage by temperature interaction).", "source": "Results, SCVs have relatively higher phage resistance, paragraph 1; Figure 2A; Supplementary Table S3a", "quote": "phage \u00d7 temperature: F1,15 = 2.099, p = .168", "statistics": [ { "test": "ANOVA (Table S3a), phage by temperature interaction", "statistic": "F(1, 15) = 2.099", "p": 0.168, "n": "128 clones from 16 replicate populations" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "On unit means, phage x temperature p = 0.168 (sequential, F = 2.099 as Table S3a) and 0.489 (type II); clone variant 0.609 and 0.237. Increase in mean R with phage 0.3502 at 25 C and 0.4815 at 35 C. The first run treated unit means and clones as readings; the answer fixes the unit as the mean of the clones of each colony type within each replicate population and makes clones a variant. All readings agreed before, so the outcome is unchanged.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2a-scv-more-resistant", "statement": "SCVs were much more phage-resistant than mucoid clones, whether or not they had been exposed to phage during selection, with a significant colony type by phage interaction.", "source": "Results, SCVs have relatively higher phage resistance, paragraph 1; Figure 2A; Supplementary Table S3a", "quote": "Interestingly, SCVs were much more resistant to phages compared to mucoid colonies (colony morphology: F1,15 = 445.207, p < .001 Supplementary, Table S3a, Figure 2A) regardless of if they had been exposed to phages during the selection experiment (colony type \u00d7 phage: F1,15 = 86.063, p < .001", "statistics": [ { "about": "colony type effect", "test": "ANOVA (Table S3a)", "statistic": "F(1, 15) = 445.207", "p": 0.001, "p_relation": "<", "n": "128 clones from 16 replicate populations" }, { "about": "colony type by phage interaction", "test": "ANOVA (Table S3a)", "statistic": "F(1, 15) = 86.063", "p": 0.001, "p_relation": "<", "n": "128 clones from 16 replicate populations" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "On unit means, colony type F(1, 15) = 445.21 and colony type x phage F = 86.06 (sequential, as Table S3a), p < 1e-6 under both sums of squares and in the clone variant. Mean R of SCVs against mucoid, 0.9683 against 0.2731 among -P clones and 0.9989 against 0.9055 among +P clones. The first run treated unit means and clones as readings; the answer fixes the unit as the mean of the clones of each colony type within each replicate population and makes clones a variant. All readings agreed before, so the outcome is unchanged.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2a-mucoid-25p-replicate-resistant", "statement": "Mucoid clones from one 25 degrees C phage replicate were the exception, showing increased phage resistance.", "source": "Results, SCVs have relatively higher phage resistance, paragraph 1; Figure 2A", "quote": "The only exception was mucoid colonies isolated from one treatment replicate at 25 \u00b0C in the presence of phage that also showed an increase in phage resistance (phage: F1,18 = 174.5, p < .001)", "statistics": [ { "test": "ANOVA, phage effect", "statistic": "F(1, 18) = 174.5", "p": 0.001, "p_relation": "<" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "The four 25 C +P mucoid clones (all from tube 2) have mean R 0.9055. Reading (a), against the 16 mucoid clones of 25 C -P (0.2459), F(1, 18) = 174.50, p = 1.1e-10, the paper's F and df. Reading (b), against the 36 mucoid clones of both -P treatments (0.2731), F(1, 38) = 88.09, p = 1.9e-11.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2b-scv-higher-growth-rate", "statement": "SCVs had a higher maximum growth rate than mucoid clones, regardless of prior phage or temperature exposure.", "source": "Results, SCVs show increased growth rate but reduced carrying capacity, paragraph 1; Figure 2B; Supplementary Table S3b", "quote": "We found that SCVs had higher growth rate compared to mucoid colonies (colony type: F1,15 = 29.393, p < .001, Supplementary Table S3b, Figure 2B) regardless of the prior phage exposure (phage \u00d7 colony type: F1,15 = 2.898, p = .109, Supplementary Table S3b, Figure 2B) or temperature exposure (temperature \u00d7 colony type: F1,15 = 0.002, p = .967", "statistics": [ { "about": "colony type effect", "test": "ANOVA (Table S3b)", "statistic": "F(1, 15) = 29.393", "p": 0.001, "p_relation": "<", "n": "128 clones from 16 replicate populations" }, { "about": "phage by colony type interaction", "test": "ANOVA (Table S3b)", "statistic": "F(1, 15) = 2.898", "p": 0.109 }, { "about": "temperature by colony type interaction", "test": "ANOVA (Table S3b)", "statistic": "F(1, 15) = 0.002", "p": 0.967 } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "On unit means, colony type p = 7e-5 (sequential, F(1, 15) = 29.39, as Table S3b) and 4e-5 (type II), SCVs higher (0.05235 against 0.04585 per clone); phage x colony type p = 0.109 under both and temperature x colony type p = 0.967 (sequential) and 0.559 (type II). Clone variant, phage x colony type p = 0.065, temperature x colony type 0.931 and 0.428. The first run treated unit means and clones as readings; the answer fixes the unit as the mean of the clones of each colony type within each replicate population and makes clones a variant. All readings agreed before, so the outcome is unchanged.", "deviations": [ "The dataset holds one fitted value per clone and no growth curves, so the grofit fits (logistic, or the code's best of four) were not repeated and the deposited values are tested; which fit produced them is not stated. Their ANOVA reproduces Tables S3b and S3c." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2c-scv-lower-carrying-capacity", "statement": "SCVs had a lower carrying capacity than mucoid clones, not affected by prior temperature or phage exposure.", "source": "Results, SCVs show increased growth rate but reduced carrying capacity, paragraph 1; Figure 2C; Supplementary Table S3c", "quote": "non-mucoid SCVs showed a clear reduction in their carrying capacity (colony type: F1,15 = 87.965, p < .001, Supplementary Table S3c, Figure 2C), which was not affected by prior temperature (temperature \u00d7 colony type: F1,15 = 3.222, p = .093, Supplementary Table S3c, Figure 2C) and phage exposure treatments (phage \u00d7 colony type: F1,15 = 2.900, p = .109", "statistics": [ { "about": "colony type effect", "test": "ANOVA (Table S3c)", "statistic": "F(1, 15) = 87.965", "p": 0.001, "p_relation": "<", "n": "128 clones from 16 replicate populations" }, { "about": "temperature by colony type interaction", "test": "ANOVA (Table S3c)", "statistic": "F(1, 15) = 3.222", "p": 0.093 }, { "about": "phage by colony type interaction", "test": "ANOVA (Table S3c)", "statistic": "F(1, 15) = 2.900", "p": 0.109 } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "On unit means, colony type p < 1e-6 under both sums of squares (F(1, 15) = 87.97 sequential, as Table S3c), SCVs lower (1.1335 against 1.3568 per clone); temperature x colony type p = 0.093 (sequential) and 0.273 (type II), phage x colony type p = 0.109 under both. Clone variant, phage x colony type p = 0.0199 under both sums of squares and temperature x colony type p = 0.0027 (sequential) and 0.057 (type II). The first run treated unit means and clones as readings; the answer fixes the unit as the mean of the clones of each colony type within each replicate population and makes clones a variant. The first run blocked the claim as methods_underspecified because the clone reading made the interactions significant; with clones a variant, both readings of the criterion give non-significant interactions, and the outcome moves from blocked to reproduced.", "deviations": [ "The dataset holds one fitted value per clone and no growth curves, so the grofit fits (logistic, or the code's best of four) were not repeated and the deposited values are tested; which fit produced them is not stated. Their ANOVA reproduces Tables S3b and S3c." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2d-scv-twitching-no-exposure-effect", "statement": "Prior temperature or phage exposure had no effect on the twitching motility of SCVs.", "source": "Results, Phage resistance and loss of mucoidy leads to reduced R. solanacearum virulence, paragraph 1; Figure 2D; Supplementary Table S3d", "quote": "While prior temperature or phage exposure had no effect on the twitching motility of SCVs (all p > .05, Supplementary Table S3d)", "statistics": [ { "about": "temperature effect", "test": "ANOVA (Table S3d)", "statistic": "F(1, 21) = 2.264", "p": 0.147, "n": "28 evolved clones" }, { "about": "phage effect", "test": "ANOVA (Table S3d)", "statistic": "F(1, 21) = 0.123", "p": 0.729, "n": "28 evolved clones" }, { "about": "temperature by phage interaction", "test": "ANOVA (Table S3d)", "statistic": "F(1, 21) = 0.355", "p": 0.558, "n": "28 evolved clones" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "Temperature, phage and temperature x phage p = 0.190, 0.438, 0.844 (sequential) and 0.673, 0.201, 0.058 (type II) under the design reading; 0.196, 0.445, 0.345 by strain name (a rank-deficient fit); 0.766, 0.281, 0.092 on SCVs alone. The deposited values do not reproduce Table S3d: residual sum of squares 28.32 against 35.78, temperature 2.48 against 3.857; only colony type x phage (27.04) and temperature x colony type (0.081) agree. The total sum of squares is 72.28 against 82.08 summed from Table S3d, and a total does not depend on the colony types, so no assignment of colony types reproduces Table S3d if its sums of squares are sequential and add up to the total. The table does not say so; it is likely, since Tables S3a to S3c, S3e and S3f match with sequential sums of squares and the F ratios of S3d are its sums of squares over its residual mean square.", "deviations": [ "The twitching sheet has no morphotype column and its strain names do not identify the clones; colony types are read from the design (the second block of 25_0 rows as the SCVs, the 35_1 rows as the 35_1 SCVs), and the reading by strain name is shown as a variant." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2d-mucoid-25p-reduced-twitching", "statement": "Phage-resistant mucoid clones from the 25 degrees C phage treatment showed clearly reduced twitching motility.", "source": "Results, Phage resistance and loss of mucoidy leads to reduced R. solanacearum virulence, paragraph 1; Figure 2D", "quote": "phage-resistant mucoid colony types from the treatment at 25 \u00b0C in the presence of phage showed a clear reduction in twitching motility (F1,6 = 27.22, p < .01, Figure 2D)", "statistics": [ { "test": "one-way ANOVA", "statistic": "F(1, 6) = 27.22", "p": 0.01, "p_relation": "<", "n": "8 clones" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "25 C +P mucoid mean 6.242 mm. Reading (a), against 25 C -P mucoid (9.558 mm), F(1, 6) = 27.22, p = 0.0020, the paper's F; reading (b), against 35 C -P mucoid (8.562 mm), F(1, 6) = 14.66, p = 0.0087. Ancestor 9.383 mm. With all eight 25_0 rows as mucoid (strain-name reading) F(1, 10) = 20.62, p = 0.0011.", "deviations": [ "The twitching sheet has no morphotype column and its strain names do not identify the clones; colony types are read from the design (the second block of 25_0 rows as the SCVs, the 35_1 rows as the 35_1 SCVs), and the reading by strain name is shown as a variant. The four 25 C +P mucoid rows are named and placed consistently with the other sheets.", "The claims file gives the ancestor's diameter as 9.38 cm; the data's unit is mm." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2e-mucoid-biofilm-increased", "statement": "Mucoid clones formed more biofilm than the ancestor, while SCVs kept ancestral-level biofilm formation.", "source": "Results, Phage resistance and loss of mucoidy leads to reduced R. solanacearum virulence, paragraph 1; Figure 2E; Supplementary Table S3e", "quote": "overall, mucoid colonies showed increased biofilm formation relative to ancestral strain, while SCVs retained ancestral-level biofilm formation (colony type: F1,21 = 42.370, p < .001", "statistics": [ { "test": "ANOVA (Table S3e), colony type effect", "statistic": "F(1, 21) = 42.370", "p": 0.001, "p_relation": "<", "n": "28 evolved clones" } ], "kind": "finding", "inferred": "", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "Colony type F(1, 21) = 42.37, p < 1e-4, mucoid higher, as Table S3e. The ancestor (0.4887 OD570) lies below the mucoid interquartile range (from 1.4914) and median (1.8157), but below every SCV clone too (16 of 16; SCV range 0.5763 to 0.9507, mean 0.7204, 47% above the ancestor), so it is within neither the SCV interquartile range (reading a) nor the SCV range (reading b). The mucoid part holds; SCVs do not keep ancestral-level biofilm. The criterion defines no partial outcome. The first record gave not reproduced; after verification round 1 it is partially reproduced, as the colony type effect and the mucoid half hold and the SCV half fails, which is a claim that holds in part. The ancestor value is the sheet's one ancestor row (printed in the data check).", "deviations": [], "assumed": false, "disagreed": true, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2e-biofilm-no-exposure-effect", "statement": "Prior temperature or phage exposure had no significant effect on biofilm formation.", "source": "Results, Phage resistance and loss of mucoidy leads to reduced R. solanacearum virulence, paragraph 1; Supplementary Table S3e", "quote": "Prior temperature or phage exposure had no significant effects on biofilm formation (all p > .05, Supplementary Table S3e)", "statistics": [ { "about": "temperature effect", "test": "ANOVA (Table S3e)", "statistic": "F(1, 21) = 1.806", "p": 0.193, "n": "28 evolved clones" }, { "about": "phage effect", "test": "ANOVA (Table S3e)", "statistic": "F(1, 21) = 0.000", "p": 0.993, "n": "28 evolved clones" }, { "about": "temperature by phage interaction", "test": "ANOVA (Table S3e)", "statistic": "F(1, 21) = 0.264", "p": 0.613, "n": "28 evolved clones" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "Temperature, phage and temperature x phage p = 0.193, 0.993, 0.613 (sequential, the F values of Table S3e) and 0.748, 0.186, 0.657 (type II). Table S3e prints the temperature sum of squares as 0.346 where its F of 1.806 and the data give 0.3646.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2f-phage-exposure-reduces-virulence", "statement": "Prior exposure to phage reduced virulence in tomato, irrespective of the temperature at which the bacteria evolved; the main effect of temperature was not significant.", "source": "Results, Phage resistance and loss of mucoidy leads to reduced R. solanacearum virulence, paragraph 1; Figure 2F; Supplementary Table S3f", "quote": "We found that prior exposure to the phage resulted in reduced virulence, irrespective of the temperature environment in which the bacteria had evolved (phage: F1,21 = 20.310, p < .001, Supplementary Table S3f, Figure 2F; the main effect of temperature was nonsignificant)", "statistics": [ { "about": "phage effect", "test": "ANOVA (Table S3f)", "statistic": "F(1, 21) = 20.310", "p": 0.001, "p_relation": "<", "n": "28 evolved clones" }, { "about": "temperature effect", "test": "ANOVA (Table S3f)", "statistic": "F(1, 21) = 1.987", "p": 0.173, "n": "28 evolved clones" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "As Table S3f, phage F(1, 21) = 20.310, p = 0.0002 (type II p = 0.0174); mean incidence 0 in +P clones against 0.1806 in -P clones; temperature p = 0.173 (type II 0.508).", "deviations": [ "The dataset holds one incidence per clone, the share of wilted plants over its three blocks (each value times 18 is a whole number), not the three block values; the mean over blocks equals that share." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2f-scv-avirulent", "statement": "All SCVs showed complete loss of virulence regardless of prior phage exposure.", "source": "Results, Phage resistance and loss of mucoidy leads to reduced R. solanacearum virulence, paragraph 1; Figure 2F; Supplementary Table S3f", "quote": "Moreover, all SCVs showed complete loss of virulence regardless of if they had previously been exposed to phage (colony type: F1,21 = 33.413, p < .001", "statistics": [ { "test": "ANOVA (Table S3f), colony type effect", "statistic": "F(1, 21) = 33.413", "p": 0.001, "p_relation": "<", "n": "28 evolved clones" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "All 16 SCV clones have incidence 0, so no plant wilted in any block; colony type F(1, 21) = 33.41, p = 9.7e-06, SCVs lower (0 against 0.2408).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2f-mucoid-25p-avirulent", "statement": "The phage-resistant mucoid clones from the 25 degrees C phage treatment lost their virulence.", "source": "Results, Phage resistance and loss of mucoidy leads to reduced R. solanacearum virulence, paragraph 1; Figure 2F; Supplementary Table S3f", "quote": "Interestingly, the phage-resistant mucoid colonies isolated from 25 \u00b0C-phage treatment lost their virulence (colony type \u00d7 phage: F1,21 = 9.992, p < .01", "statistics": [ { "test": "ANOVA (Table S3f), colony type by phage interaction", "statistic": "F(1, 21) = 9.992", "p": 0.01, "p_relation": "<", "n": "28 evolved clones" } ], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "Colony type x phage F(1, 21) = 9.992, p = 0.0047. The four 25 C +P mucoid clones each have incidence 0, below 25 C -P mucoid (0.3194), 35 C -P mucoid (0.4028) and the ancestor (0.7222).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "sequencing-mutation-count", "statement": "Sequenced clones carried on average 8.5 nonsynonymous mutations, and the number did not depend on colony morphology.", "source": "Results, Genetic changes associated with SCVs and phage resistance, paragraph 1; Supplementary Table S4", "quote": "Sequenced clones had an average of 8.5 nonsynonymous mutations each... The average number of detected mutations was not affected by the colony morphology.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "The variant table gives 282 protein-changing variants (frameshifts, in-frame insertions and deletions, missense) summed over the clones carrying them, 10.07 per clone over 28 clones, outside 8.5 +- 0.85. Mucoid clones carry 10.17 and SCVs 10.00 on average. The ANOVA on per-clone counts cannot be run, as the table does not say which clone carries which variant; the mean alone decides the outcome. Counting every variant gives 16.96 per clone. The claims file marked this claim data elsewhere (NCBI SRA) and the first run tested it on the dataset's processed table anyway; the answer makes it data dataset, as the Data availability statement puts the study's generated data in Dryad, so the claim now counts with the dataset. The outcome is unchanged.", "deviations": [ "Tested on the dataset's processed table, the authors' output of the pipeline the criterion names, which was not re-run (the tools are not installable in a locked Python environment, and the genome reads are not public).", "The mean assumes four clones per group, as the Methods and Table 1 give; the largest carrier count in each group is 4." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "table1-phcs-in-scvs", "statement": "SCVs carried mutations in the quorum-sensing histidine kinase gene phcS (13 of 16 SCV clones), while no mucoid clone did.", "source": "Results, Genetic changes associated with SCVs and phage resistance, paragraph 2; Table 1", "quote": "Interestingly, SCVs were also associated with mutations in phcS quorum sensor histidine kinase gene (Table 1 and Figure 3)", "statistics": [], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "phcS (RS-N_03191, PROKKA name sasA_8) variants in SCV groups only: 25 C +P 4, 25 C -P 3, 35 C +P 2, and in 35 C -P two variants carried by 1 and 3 clones. That is 13 SCV clones if those two are in different clones and 12 if not, both within 13 +- 1.3; 0 mucoid clones. The claims file marked this claim data elsewhere (NCBI SRA) and the first run tested it on the dataset's processed table anyway; the answer makes it data dataset, as the Data availability statement puts the study's generated data in Dryad, so the claim now counts with the dataset. The outcome is unchanged.", "deviations": [ "Tested on the dataset's processed table, the authors' output of the pipeline the criterion names, which was not re-run (the tools are not installable in a locked Python environment, and the genome reads are not public)." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "table1-pild-in-25p-mucoid", "statement": "Two of the four mucoid phage-resistant clones from 25 degrees C with phage had mutations in pilD, which no other clone carried.", "source": "Results, Genetic changes associated with SCVs and phage resistance, paragraph 2; Table 1", "quote": "Interestingly, two of four mucoid phage-resistant clones that had evolved at 25 \u00b0C temperature treatment in the presence of phage had mutations in pilD gene (Table 1 and Figure 3)", "statistics": [], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "One pilD (RS-N_03289, PROKKA name outO) in-frame insertion, carried by 2 of the 4 mucoid clones of 25 C +P and by no clone of another group. The claims file marked this claim data elsewhere (NCBI SRA) and the first run tested it on the dataset's processed table anyway; the answer makes it data dataset, as the Data availability statement puts the study's generated data in Dryad, so the claim now counts with the dataset. The outcome is unchanged.", "deviations": [ "Tested on the dataset's processed table, the authors' output of the pipeline the criterion names, which was not re-run (the tools are not installable in a locked Python environment, and the genome reads are not public)." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "table1-t2ss-in-35p-scv", "statement": "Three of four SCVs from 35 degrees C with phage had mutations in the type II secretion genes gspE or gspF.", "source": "Results, Genetic changes associated with SCVs and phage resistance, paragraph 3; Table 1", "quote": "Finally, three of four sequenced small colony types that had evolved at 35 \u00b0C in the presence of phage had mutations in T2SS genes gspF and gspE (Table 1 and Figure 3)", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "metadata_insufficient", "notebook": "reproduce_wang_2024.ipynb", "notes": "In the 35 C +P SCV group, 2 clones carry a gspE missense variant and 1 a gspF frameshift, as Table 1; no other group carries either. The table does not say whether the gspF clone is one of the gspE clones, so the count is 3 or 2, and with a tolerance of 0 the claim cannot be decided. The claims file marked this claim data elsewhere (NCBI SRA) and the first run tested it on the dataset's processed table anyway; the answer makes it data dataset, as the Data availability statement puts the study's generated data in Dryad, so the claim now counts with the dataset. The outcome is unchanged.", "deviations": [ "Tested on the dataset's processed table, the authors' output of the pipeline the criterion names, which was not re-run (the tools are not installable in a locked Python environment, and the genome reads are not public)." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "tables6-pil-mutants-resistant", "statement": "The pilM and pilB mutants were fully resistant to phage NNP42, unlike their wild types.", "source": "Results, Genetic changes associated with SCVs and phage resistance, paragraph 2; Supplementary Table S6", "quote": "we used previously constructed pilM and pilB mutant strains for phage infections and found that both mutants were fully resistant to phage NNP42 relative to the wildtype strains (Supplementary Table S6)", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_wang_2024.ipynb", "notes": "No sheet of the workbook names the pilB or pilM mutants or their wild types OE1-1 and QL-Rs1115 (checked in the notebook), and the README lists no such data; the paper gives only the means of Table S6 and names no other deposit.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "figs3-adsorption", "statement": "pilD mutants showed reduced phage adsorption, while the phcS and the T2SS (gspE, gspF) mutants showed no reduction.", "source": "Results, Genetic changes associated with SCVs and phage resistance, paragraphs 2 and 3; Supplementary Figure S3", "quote": "However, either of the T2SS mutants or any of the tested phcS mutants showed no reduction in phage adsorption (Supplementary Figure S3), which suggests that these mutations were not associated with phage binding.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "One-way ANOVA across 13 strains, F(12, 26) = 19.75, p = 4.6e-10. Tukey against the ancestor (0.773): both pilD mutants lower (0.283 and 0.412, adjusted p < 0.001); none of the eight phcS mutants, the gspE or the gspF mutant lower (smallest adjusted p 0.736, gspF, 0.663).", "deviations": [ "The sheet holds proportions where Figure S3 speaks of percentages; the scale does not change the test." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "rnaseq-differential-expression-count", "statement": "After 6 h of phage exposure, 1477 R. solanacearum genes were differentially expressed, 707 up and 770 down.", "source": "Results, Activation of restriction modification and abortive infection phage defense systems..., paragraph 1; Figure 4A", "quote": "We found that a total 1477 of R. solanacearum genes were differentially expressed after phage exposure (|log2foldchange| > 1, FDR < 0.05, Figure 4A). Of these, around half (707) were upregulated, and another half (770) downregulated in the presence of phage.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "In the dataset's DESeq2 table, 1477 genes have padj < 0.05 and |log2FC| > 1, 707 up and 770 down. 32 genes have no padj and are left out by the thresholds. The claims file marked this claim data elsewhere (NCBI SRA) and the first run tested it on the dataset's processed table anyway; the answer makes it data dataset, as the Data availability statement puts the study's generated data in Dryad, so the claim now counts with the dataset. The outcome is unchanged.", "deviations": [ "Tested on the dataset's processed table, the authors' output of the pipeline the criterion names, which was not re-run (the tools are not installable in a locked Python environment). The RNA-seq reads are public (PRJNA1032726, ten runs, 9.1 GB)." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "rnaseq-kegg-enrichment", "statement": "Five KEGG pathways were enriched in the phage compared to the control treatment, namely propanoate metabolism, RNA degradation, synthesis and degradation of ketone bodies, bacterial secretion system and valine, leucine and isoleucine degradation.", "source": "Results, Activation of restriction modification and abortive infection phage defense systems..., paragraph 1; Supplementary Figure S5", "quote": "Based on KEGG pathway enrichment analysis, a total of five metabolic pathways were significantly enriched in phage compared to control treatment (p < .05, Supplementary Figure S5).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "methods_underspecified", "notebook": "reproduce_wang_2024.ipynb", "notes": "In the dataset's KEGG (KOBAS) table exactly the five named pathways have uncorrected p < 0.05 (0.0024 to 0.0464); none has FDR < 0.05 (smallest 0.1958). The criterion's two readings give different outcomes. The match of the five with uncorrected p suggests the paper used uncorrected p; a question asks the reader to settle it. The claims file marked this claim data elsewhere (NCBI SRA) and the first run tested it on the dataset's processed table anyway; the answer makes it data dataset, as the Data availability statement puts the study's generated data in Dryad, so the claim now counts with the dataset. The outcome is unchanged.", "deviations": [ "Tested on the dataset's processed table, the authors' output of the pipeline the criterion names, which was not re-run (the tools are not installable in a locked Python environment)." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "rnaseq-mutated-genes-expression", "statement": "Under phage exposure phcR and phcS were upregulated and pilD and other pilus and fimbrial genes downregulated; seven of the 13 genes mutated under phage selection were differentially expressed.", "source": "Results, Activation of restriction modification and abortive infection phage defense systems..., paragraph 1; Figure 4B and 4C", "quote": "For example, phcR and phcS virulence-associated genes that were significantly upregulated, while pilD and other pilus biogenesis and adherence (fimbriae) associated genes were significantly downregulated in the presence of phage (Figure 4B and C). Of 13 mutated genes that were selected for in the presence of phage, seven showed differential gene expression", "statistics": [], "kind": "finding", "inferred": "", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "phcR up (log2FC 1.835, padj 8e-28), pilD down (-1.349, padj 7e-36), and the pilus and fimbrial genes of the Figure 4C list down (-2.10 to -5.94). phcS has padj 0.003 but log2FC 0.411, below the threshold of 1. Of the 11 genes of the dataset's Figure 4B list (numbered 0 to 12 without 8 and 9), 3 meet both thresholds and 6 meet padj < 0.05 alone; at most 5 of 13 could meet both. Among the 18 genes with a variant in a +P group of the variant table, 5 meet both. phcR up and pilD and the other pilus and fimbrial genes down hold; phcS up and seven of 13 fail. The criterion defines no partial outcome. The first record gave not reproduced; after verification round 1 it is partially reproduced, as the claim holds in part. The claims file marked this claim data elsewhere (NCBI SRA) and the first run tested it on the dataset's processed table anyway; the answer makes it data dataset, as the Data availability statement puts the study's generated data in Dryad, so the claim now counts with the dataset. The outcome is unchanged.", "deviations": [ "Tested on the dataset's processed table, the authors' output of the pipeline the criterion names, which was not re-run (the tools are not installable in a locked Python environment).", "The dataset's Figure 4B list holds 11 of the 13 genes; the two missing ones cannot change the outcome." ], "assumed": false, "disagreed": true, "data": "dataset", "where": null, "proposed": null }, { "claim": "rnaseq-defense-systems", "statement": "Phage exposure upregulated type I restriction-modification genes (MTases, REases) and CBASS genes (SMODS cyclase, Gros effector) and downregulated the Wadjet gene JetC.", "source": "Results, Activation of restriction modification and abortive infection phage defense systems..., paragraph 1; Figure 4C", "quote": "Specifically, JetC gene belonging to Wadjet system, was downregulated, while genes linked to MTases and Reases belonging to Restriction-Modification type I system, and SMODS (cyclase) and Gros (effector) genes belonging to CBASS abortive infection system, were upregulated (Figure 4C).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "JetC (RS-N004717) log2FC -4.21; type I MTase (RS-N000213) 2.30, REase (RS-N000215) 2.60, SMODS cyclase (RS-N000217) 2.64 and the CBASS effector (RS-N000216) 2.32, all padj < 1e-25. The dataset labels the effector Effector_1TM_DUF1043, not Gros; it is the locus beside the SMODS cyclase. The claims file marked this claim data elsewhere (NCBI SRA) and the first run tested it on the dataset's processed table anyway; the answer makes it data dataset, as the Data availability statement puts the study's generated data in Dryad, so the claim now counts with the dataset. The outcome is unchanged.", "deviations": [ "Tested on the dataset's processed table, the authors' output of the pipeline the criterion names, which was not re-run (the tools are not installable in a locked Python environment).", "The loci are those the dataset's Figure 4C list names for each system; the RS-N annotation was not read." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "rnaseq-virulence-genes-down", "statement": "Phage exposure downregulated motility genes and type II (e.g. gspG, rcpA, tadC) and type III secretion system genes (several hrp and hrc genes).", "source": "Results, Activation of restriction modification and abortive infection phage defense systems..., paragraph 1; Figure 4C", "quote": "We also found that phage exposure led to downregulation of several virulence genes associated with motility and type II and III secretions systems (Figure 4C).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_wang_2024.ipynb", "notes": "rcpA (RS-N003916, log2FC -4.41) and tadC (-4.27) down; six hrp or hrc genes (hrpB2, hrpB1, hrcS, hrcV, hrcR, hrcQ) down at log2FC -2.00 to -2.49, all padj < 1e-4. gspG (RS-N004330) is up, log2FC 2.04, padj 0.0015, and labelled UP in the dataset's Figure 4C list, against the text's downregulation. The criterion's condition that none is up fails for gspG; the rest holds. The claims file marked this claim data elsewhere (NCBI SRA) and the first run tested it on the dataset's processed table anyway; the answer makes it data dataset, as the Data availability statement puts the study's generated data in Dryad, so the claim now counts with the dataset. The outcome is unchanged.", "deviations": [ "Tested on the dataset's processed table, the authors' output of the pipeline the criterion names, which was not re-run (the tools are not installable in a locked Python environment)." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null } ], "findings": [ { "kind": "metadata_error", "statement": "The twitching sheet (Figure 2D) does not identify its clones. It has no morphotype column; its four 35_1 rows carry the names of four 35_0 SCV clones (6b6s1, 6b6s2, 6b8s1, 6b8s2) with different values, where the biofilm and disease sheets name the 35_1 clones 6b1s1, 6b1s2, 6b2s3 and 6b2s4; and in 25_0 the four mucoid names 6d5a2 to 6d8a2 appear twice with different values, where the other sheets have four SCVs.", "found": null, "status": null }, { "kind": "other", "statement": "The deposited twitching values do not reproduce Table S3d: with the colony types of the design, the residual sum of squares is 28.32 against 35.78 and the temperature sum of squares 2.48 against 3.857; only colony type x phage (27.04) and temperature x colony type (0.081) agree. The total sum of squares of the data is 72.28 against 82.08 summed from Table S3d, so no assignment of colony types reproduces it if its sums of squares are sequential, which the table does not state. Every other ANOVA the paper prints (Tables S1a, S1b, S2, S3a to S3c, S3e, S3f) is reproduced from the deposited data.", "found": null, "status": null }, { "kind": "metadata_insufficient", "statement": "The variant table (snp_indel) gives, per variant and group of four sequenced clones, the number of clones that carry it, not which clones. Per-clone mutation counts and co-occurrence (for example whether the gspE and gspF mutations of 35 C +P SCVs are in different clones) cannot be read, and the genome reads are not public.", "found": null, "status": null }, { "kind": "data_missing", "statement": "BioProject PRJNA1028400, named in the paper for the genomes of the evolved clones, has 28 BioSamples and 14 assemblies and no sequencing runs, so the reads the variant calls come from are not public. The RNA-seq reads are public in PRJNA1032726 (ten runs), though the Methods say they are shared on request.", "found": null, "status": null }, { "kind": "data_missing", "statement": "The growth curves the maximum growth rates and carrying capacities were fitted to are not deposited, only one fitted value per clone, so the fits cannot be repeated and the model behind them (logistic, as the Methods say, or the code's best of four by AIC) cannot be checked. The pilB and pilM data of Table S6 are not deposited either.", "found": null, "status": null }, { "kind": "paper_inconsistency", "statement": "The data disagree with statements of the text: SCVs form more biofilm than the ancestor in every clone (0.58 to 0.95 against 0.49 OD570), where the text says they retained ancestral-level biofilm; gspG is upregulated (log2FC 2.04) in the deposited DESeq2 table and Figure 4C list, where the text lists it as downregulated; phcS has log2FC 0.41, below the threshold under which the text calls it significantly upregulated; mucoid colonies are 15.3% at 25 C without phage, where the text says around 20%; and the 0.24% the text gives as an SCV frequency is the mucoid frequency of the 25 C +P treatment.", "found": null, "status": null }, { "kind": "paper_inconsistency", "statement": "Small misprints in the paper's statistics, against the data: the area-under-curve ANOVAs are printed with df (1, 19) for 20 populations (the data give the printed F at df (1, 18)); the phage density time effect is printed in the text as F1,18 = 84.88, which is its sum of squares (F(2, 36) = 86.963 in Table S1b); Table S3e prints the temperature sum of squares as 0.346 for 0.3646; Table 1 places the RSc3091 deletion at C-432461, the variant table at 431461.", "found": null, "status": null }, { "kind": "metadata_insufficient", "statement": "The OD600 values of Figure 1B include day 0 and negative values (eight, down to -0.029, at 25 C with phage), so they are blank-corrected and include the inoculation, neither of which the README or Methods says; the paper's ANOVA uses days 2 to 12. The README does not give units for the growth rate (headed maxgrowthrate(OD600)) or say that adsorption is a proportion.", "found": null, "status": null }, { "kind": "metadata_error", "statement": "In the carrying capacity sheet the ancestor's value (1.4355) is headed maxgrowthrate(OD600). The variant table's GENE column holds PROKKA names that differ from the paper's (phcS is sasA_8, pilD outO, gspE hxcR, gspF epsF_1); the gene_blast sheet gives the paper's names by locus tag. The Figure 4B list holds 11 genes where the paper speaks of 13.", "found": null, "status": null } ], "reconciliation": null, "verifications": [ { "date": "2026-10-27", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1: the executed notebook of the author-answers run (commit 87e0a97) with the conclusion cells and the summary removed, the helper module and the claims file, with the paper. The verifier listed the version's files through the Dryad API, ran synthetic checks of rm_anova, and checked parse_strain, unit_means and clone_table. Report transcripts/dryad-tdz08kq5d/verifier-1-report.md.", "agreed": 30, "of": 32, "disagreements": [ { "claim": "fig2e-mucoid-biofilm-increased", "outcome": "partially_reproduced", "reason": "Colony type F=42.37 with mucoid higher, and the ancestor (0.489) is below the mucoid IQR. But the ancestor lies below the SCV minimum (0.576): all 16 SCVs are above it and their mean is 47% higher. Both readings agree that SCVs within ancestral level fails (cell 54). The ancestor value is taken without checking how many anc rows exist; the outcome turns on it (B3)." }, { "claim": "rnaseq-mutated-genes-expression", "outcome": "partially_reproduced", "reason": "phcR is up (log2FC 1.83) and pilD down (-1.35), and the other pilus and fimbrial genes are down. phcS is up but only by log2FC 0.41, below the threshold. Only 3 of the 11 listed Figure 4B genes meet both thresholds (at most 5 of 13) against the claimed 7 (cell 80)." } ] }, { "date": "2026-10-27", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2: the full executed notebook of the author-revise-1 run (commit 63faa18), the helper module, the claims file, the attempt record and the entry README, with the paper. Report transcripts/dryad-tdz08kq5d/verifier-2-report.md. The verifier agreed with all 32 outcomes and listed six statements the printed numbers did not support; each is recorded under the claim it bears on most closely (the R range under fig2a-phage-exposed-more-resistant, the RSc3091 position under table1-pild-in-25p-mucoid, the 25_0 strain names under fig2d-mucoid-25p-reduced-twitching, the Table S4 clause under sequencing-mutation-count).", "agreed": 32, "of": 32, "disagreements": [] } ] } ], "entries": [ { "name": "dryad-tdz08kq5d-wang-2024", "type": "reproduction", "title": "Phage selection and resistance-virulence trade-offs in Ralstonia solanacearum (Wang et al. 2024)", "description": "Tests the findings of Wang, Wang, Yang, Lu, Fields, Xu, Shen, Wei and Friman (2024) on Dryad dataset tdz08kq5d, one workbook with the data behind each figure of the paper. It covers the selection experiment (bacterial and phage densities, colony types), the phage resistance, growth, twitching, biofilm and virulence of evolved clones, the variant calls of 28 sequenced clones, the phage adsorption assay and the transcriptome tables. The growth curves, per-clone variant calls, genome reads and the pilB and pilM data of Table S6 are not in the dataset.", "datasets": [ "dryad:tdz08kq5d" ], "papers": [ "10.1093/evlett/qrad056" ], "derived_from": [], "notebooks": [ { "path": "reproduce_wang_2024.ipynb", "title": "Reproducing Wang et al. (2024) from Dryad dataset tdz08kq5d", "executed": "notebooks/dryad-tdz08kq5d-wang-2024/reproduce_wang_2024.html" } ] } ] }