Study
Sequence-audited comparative genomics of genome-maintenance genes in vertebrate lifespan evolution
Processed data and frozen outputs supporting the manuscript “Sequence-audited comparative genomics of genome-maintenance genes in vertebrate lifespan evolution.” The archive includes source data for four main figures, 41 supplementary data tables, a dated species tree, protein alignments, gene-family trees, a reproducibility guide, and SHA-256 checksums.
Abstract
Processed data and frozen outputs supporting the manuscript “Sequence-audited comparative genomics of genome-maintenance genes in vertebrate lifespan evolution.” The archive includes source data for four main figures, 41 supplementary data tables, a dated species tree, protein alignments, gene-family trees, a reproducibility guide, and SHA-256 checksums. Analysis code is available at https://github.com/jackeikee-debug/nature-bird-lifespan, release v1.0.0.
This page presents preserved, source-backed released materials.
Source inventory
Deterministically extracted immutable study materials.
Extracted study record
Authoritative metadata and released result artifacts.
The preserved source contains 50 result tables; 50 have complete deterministic representation coverage.
Manual Life History Supplements source data
3 materialized released rows from config/manual_life_history_supplements.tsv.
Evidence visualization
Manual Life History Supplements source data
3 materialized released rows from config/manual_life_history_supplements.tsv.
Browse source data · 3 rows
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| Scientific Name | Body Mass G | Max Lifespan Years | Sexual Maturity Years | Source Name | Source Url | Source Note | Use In Model | Notes |
|---|
Source & verification
- File
- config/manual_life_history_supplements.tsv
- Version
bf6ac86b- Integrity
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Figure 1 Design Counts source data
6 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Source_Data/Figure_1_design_counts.tsv.
Evidence visualization
Figure 1 Design Counts source data
6 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Source_Data/Figure_1_design_counts.tsv.
Browse source data · 6 rows
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| Module | Expanded Genes | Final Genes | Removed Genes | Domain Required | Exclude From Absence Scoring | Mean Coverage | Estimate | Conf Low | Conf High | P | P Bh By Model |
|---|
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Source_Data/Figure_1_design_counts.tsv
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Figure 2 Module Ranking source data
6 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Source_Data/Figure_2_module_ranking.tsv.
Evidence visualization
Figure 2 Module Ranking source data
6 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Source_Data/Figure_2_module_ranking.tsv.
Browse source data · 6 rows
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| Score Variant | Maintenance Module | Score Col | Model | Formula | N | Lambda | LogLik | AIC | Estimate | Se | T | P | Error | P Bh By Model | Module P Bh All | Genes Total | Mean Coverage | Conf Low | Conf High |
|---|
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Source_Data/Figure_2_module_ranking.tsv
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Figure 3 Evidence By Gene source data
34 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Source_Data/Figure_3_evidence_by_gene.tsv.
Evidence visualization
Figure 3 Evidence By Gene source data
34 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Source_Data/Figure_3_evidence_by_gene.tsv.
Browse source data · 34 rows
Rows 1–10 of 34
| Human Gene Symbol | Sequence Validation Evidence Level | Sequence Validation Scoring Status | Rows | Species |
|---|---|---|---|---|
| DNMT1 | dnmt1_longer_local_isoform_available | not_scoreable_not_absence | 1 | 1 |
| DNMT1 | dnmt1_partial_fragment_not_absence | not_scoreable_not_absence | 7 | 7 |
| DNMT1 | gff_probable_wrong_gene_family | not_scoreable_review | 1 | 1 |
| DNMT1 | local_gff_protein_strict | scoreable_strict | 3 | 3 |
| DNMT1 | not_found_in_local_gff | not_scoreable_unknown | 2 | 2 |
| DNMT3A | external_uniprot_strict | scoreable_sensitivity | 1 | 1 |
| DNMT3A | local_gff_protein_strict | scoreable_strict | 5 | 5 |
| DNMT3A | not_found_in_local_gff | not_scoreable_unknown | 8 | 8 |
| DNMT3B | local_gff_rejected_no_same_gene_reference | not_scoreable_review | 11 | 11 |
| DNMT3B | not_found_in_local_gff | not_scoreable_unknown | 3 | 3 |
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Source_Data/Figure_3_evidence_by_gene.tsv
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Figure 3 Evidence Waterfall source data
9 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Source_Data/Figure_3_evidence_waterfall.tsv.
Evidence visualization
Figure 3 Evidence Waterfall source data
9 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Source_Data/Figure_3_evidence_waterfall.tsv.
Browse source data · 9 rows
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| Waterfall Step | Rows | Interpretation |
|---|
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Source_Data/Figure_3_evidence_waterfall.tsv
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Figure 4 Samhd1 Leave One Species source data
106 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Source_Data/Figure_4_samhd1_leave_one_species.tsv.
Evidence visualization
Figure 4 Samhd1 Leave One Species source data
106 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Source_Data/Figure_4_samhd1_leave_one_species.tsv.
Browse source data · 106 rows
Rows 1–10 of 106
| Scope | Predictor | N | Predictor Center | Predictor Scale | Lambda | Lambda Method | Estimate Per Sd | Se | Conf Low | Conf High | T | P | Fit Note | Error | Omitted Species | Baseline N | Baseline Estimate | Baseline P | Delta Estimate |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| leave_one_species_out | domain_identity_coverage_product | 52 | 0.669230769230769 | 0.114195051495553 | 1e-06 | fixed_near_zero_optimizer_fallback | 0.0800898796432063 | 0.0330474222756986 | 0.015316931982837 | 0.144862827303576 | 2.42348341044742 | 0.0190336802590163 | Problem with optim:52ERROR: ABNORMAL_TERMINATION_IN_LNSRCH | Crocodylus porosus | 53 | 0.208395500273607 | 0.00266726201404621 | -0.128305620630401 | |
| leave_one_species_out | domain_identity_coverage_product | 52 | 0.669230769230769 | 0.114195051495553 | 0.751662950517285 | maximum_likelihood | 0.151939800508425 | 0.0640357201483753 | 0.0264297890176093 | 0.277449811999241 | 2.37273509466856 | 0.0215437588201164 | Pedionomus torquatus | 53 | 0.208395500273607 | 0.00266726201404621 | -0.056455699765182 | ||
| leave_one_species_out | domain_identity_coverage_product | 52 | 0.669230769230769 | 0.114195051495553 | 0.755545319876219 | maximum_likelihood | 0.23422924989893 | 0.0744705628202026 | 0.088266946771333 | 0.380191553026527 | 3.14525956335847 | 0.0027928410986815 | Macaca mulatta | 53 | 0.208395500273607 | 0.00266726201404621 | 0.0258337496253231 | ||
| leave_one_species_out | domain_identity_coverage_product | 52 | 0.669230769230769 | 0.114195051495553 | 0.745688473892174 | maximum_likelihood | 0.232217751536187 | 0.0697167236801248 | 0.0955729731231422 | 0.368862529949231 | 3.33087585414443 | 0.00163305040961692 | Eurypyga helias | 53 | 0.208395500273607 | 0.00266726201404621 | 0.0238222512625798 | ||
| leave_one_species_out | domain_identity_coverage_product | 52 | 0.669230769230769 | 0.114195051495553 | 0.712973267671182 | maximum_likelihood | 0.187257053277302 | 0.0658493293779996 | 0.0581923676964232 | 0.316321738858182 | 2.84371997476812 | 0.0064428284103375 | Heterocephalus glaber | 53 | 0.208395500273607 | 0.00266726201404621 | -0.0211384469963044 | ||
| leave_one_species_out | domain_identity_coverage_product | 52 | 0.669230769230769 | 0.114195051495553 | 0.743274607134113 | maximum_likelihood | 0.229217777683558 | 0.0686250822856524 | 0.0947126164036793 | 0.363722938963437 | 3.34014576083767 | 0.00158920797944484 | Caprimulgus carolinensis | 53 | 0.208395500273607 | 0.00266726201404621 | 0.020822277409951 | ||
| leave_one_species_out | domain_identity_coverage_product | 52 | 0.669230769230769 | 0.114195051495553 | 0.894896984907421 | maximum_likelihood | 0.228929987618066 | 0.0684964083909951 | 0.0946770271717158 | 0.363182948064417 | 3.34221885491098 | 0.00157955704957002 | Chelonia mydas | 53 | 0.208395500273607 | 0.00266726201404621 | 0.0205344873444593 | ||
| leave_one_species_out | domain_identity_coverage_product | 52 | 0.669230769230769 | 0.114195051495553 | 0.711688354264188 | maximum_likelihood | 0.195037233067061 | 0.0663290361686792 | 0.0650323221764501 | 0.325042143957673 | 2.94045028139816 | 0.00495239348362242 | Dromaius novaehollandiae | 53 | 0.208395500273607 | 0.00266726201404621 | -0.0133582672065456 | ||
| leave_one_species_out | domain_identity_coverage_product | 52 | 0.669230769230769 | 0.114195051495553 | 0.610006990227033 | maximum_likelihood | 0.195551621191197 | 0.0637116238662518 | 0.0706768384133438 | 0.320426403969051 | 3.06932407815745 | 0.0034620795242768 | Rhinolophus hipposideros | 53 | 0.208395500273607 | 0.00266726201404621 | -0.0128438790824096 | ||
| leave_one_species_out | domain_identity_coverage_product | 52 | 0.669230769230769 | 0.114195051495553 | 0.649738208380159 | maximum_likelihood | 0.195827505546644 | 0.063819789406717 | 0.0707407183094791 | 0.32091429278381 | 3.0684448721486 | 0.00347064349458437 | Alligator mississippiensis | 53 | 0.208395500273607 | 0.00266726201404621 | -0.0125679947269626 |
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Source_Data/Figure_4_samhd1_leave_one_species.tsv
- Version
released- Integrity
3c0c7096…db58ba
Deterministic extraction method
No generative model selected, summarized, or transformed the results.
Evidence classified preserved repository files, parsed bounded structured tables, inferred column types, and selected registered components using versioned rules.
Data and provenance
Immutable publication and repository sources.
Reuse boundary
Only released and preserved source rows are displayed.
No model is rerun and no missing value is inferred.
Pinned scientific commit: bf6ac86b961d575f3524b994dcce9fff993637be
Limitations
Deterministic coverage boundaries.
Every accepted released table cell is represented by registered Evidence components; unstructured claims are not converted into numerical results.
Citation
Cite the scholarly record and pinned analysis source.
Scholarly publication
Si Li, Yanyan Huang. Sequence-audited comparative genomics of genome-maintenance genes in vertebrate lifespan evolution. 10.5281/zenodo.20798437.
Pinned analysis source
https://github.com/jackeikee-debug/nature-bird-lifespan, commit bf6ac86b961d575f3524b994dcce9fff993637be.