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.
Supplementary Data 4 Gene Tree Summary source data
8 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_4_gene_tree_summary.tsv.
Evidence visualization
Supplementary Data 4 Gene Tree Summary source data
8 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_4_gene_tree_summary.tsv.
Browse source data · 8 rows
Loading rows 1–8…
| Family | Tree Variant | Sequences | Genes | Species | Best Model | Convergence Note | Png | Svg | Treefile |
|---|
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_4_gene_tree_summary.tsv
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3210e180…0875dd
Supplementary Data 40 Samhd1 Alignment Sensitivity Pgls source data
12 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_40_samhd1_alignment_sensitivity_pgls.tsv.
Evidence visualization
Supplementary Data 40 Samhd1 Alignment Sensitivity Pgls source data
12 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_40_samhd1_alignment_sensitivity_pgls.tsv.
Browse source data · 12 rows
Rows 1–10 of 12
| Alignment Variant | Scope | Predictor | N | Lambda | Lambda Method | Estimate Per Sd | Se | Conf Low | Conf High | T | P | Fit Note | Error | Q Within Variant Scope |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| original_reference_positions | all_species | domain_identity_coverage_product | 53 | 0.727825239872756 | maximum_likelihood | 0.208395500273607 | 0.0659863548726119 | 0.0790622447232877 | 0.337728755823926 | 3.15816051175912 | 0.00266726201404621 | 0.00266726201404621 | ||
| trim_columns_gap_gt_0.50 | all_species | domain_identity_coverage_product | 53 | 0.727825239872756 | maximum_likelihood | 0.208395500273607 | 0.0659863548726119 | 0.0790622447232877 | 0.337728755823926 | 3.15816051175912 | 0.00266726201404621 | 0.00266726201404621 | ||
| trim_columns_gap_gt_0.70 | all_species | domain_identity_coverage_product | 53 | 0.727825239872756 | maximum_likelihood | 0.208395500273607 | 0.0659863548726119 | 0.0790622447232877 | 0.337728755823926 | 3.15816051175912 | 0.00266726201404621 | 0.00266726201404621 | ||
| original_reference_positions | all_species | domain_minus_nondomain_product | 53 | 1e-06 | maximum_likelihood | 0.127986090503007 | 0.0296504531627903 | 0.0698712023039379 | 0.186100978702076 | 4.31649694526836 | 7.30353793771954e-05 | 0.000146070758754391 | ||
| trim_columns_gap_gt_0.50 | all_species | domain_minus_nondomain_product | 53 | 1e-06 | maximum_likelihood | 0.127969806698772 | 0.0296518357783434 | 0.0698522085732192 | 0.186087404824325 | 4.31574650741309 | 7.32171073289933e-05 | 0.000146434214657987 | ||
| trim_columns_gap_gt_0.70 | all_species | domain_minus_nondomain_product | 53 | 1e-06 | maximum_likelihood | 0.127986090503007 | 0.0296504531627903 | 0.0698712023039379 | 0.186100978702076 | 4.31649694526836 | 7.30353793771954e-05 | 0.000146070758754391 | ||
| original_reference_positions | original_domain_coverage_ge_0.8 | domain_identity_coverage_product | 48 | 0.757028581747695 | maximum_likelihood | 0.157394149499401 | 0.068374926789529 | 0.0233792929919246 | 0.291409006006878 | 2.30192786873309 | 0.0259171219540466 | 0.0259171219540466 | ||
| trim_columns_gap_gt_0.50 | original_domain_coverage_ge_0.8 | domain_identity_coverage_product | 48 | 0.757028581747695 | maximum_likelihood | 0.157394149499401 | 0.068374926789529 | 0.0233792929919246 | 0.291409006006878 | 2.30192786873309 | 0.0259171219540466 | 0.0259171219540466 | ||
| trim_columns_gap_gt_0.70 | original_domain_coverage_ge_0.8 | domain_identity_coverage_product | 48 | 0.757028581747695 | maximum_likelihood | 0.157394149499401 | 0.068374926789529 | 0.0233792929919246 | 0.291409006006878 | 2.30192786873309 | 0.0259171219540466 | 0.0259171219540466 | ||
| original_reference_positions | original_domain_coverage_ge_0.8 | domain_minus_nondomain_product | 48 | 1e-06 | maximum_likelihood | 0.108743004483751 | 0.0294475340620417 | 0.0510258377221493 | 0.166460171245353 | 3.69277115885647 | 0.000587060682182505 | 0.00117412136436501 |
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_40_samhd1_alignment_sensitivity_pgls.tsv
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Supplementary Data 41 Sequence Validation Model Impact source data
10 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_41_sequence_validation_model_impact.tsv.
Evidence visualization
Supplementary Data 41 Sequence Validation Model Impact source data
10 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_41_sequence_validation_model_impact.tsv.
Browse source data · 10 rows
Rows 1–10 of 10
| Comparison Layer | Dataset | Model | Metric | Rank | Estimate | P | Mean Transposon Coverage | Notes |
|---|---|---|---|---|---|---|---|---|
| all_module_pgls | baseline | residual_module | transposon_rank_estimate_p | 4 | 0.317806898196951 | 0.0021253887814418 | 0.7756166982922202 | |
| all_module_pgls | baseline | mass_clade_module | transposon_rank_estimate_p | 4 | 0.31268130201871 | 0.0050434255816211 | 0.7756166982922202 | |
| all_module_pgls | rescued | residual_module | transposon_rank_estimate_p | 4 | 0.323473262943575 | 0.0020420766602127 | 0.7789373814041746 | |
| all_module_pgls | rescued | mass_clade_module | transposon_rank_estimate_p | 4 | 0.322561886870847 | 0.0043364439488367 | 0.7789373814041746 | |
| high_coverage_subset | baseline | all_primary | estimate_p_n_birds | 0.283314517326194 | 0.007530047614829 | n=68;birds=31 | ||
| high_coverage_subset | baseline | transposon_coverage_ge_0_50 | estimate_p_n_birds | 0.615022841056534 | 0.193091471510662 | n=51;birds=17 | ||
| high_coverage_subset | baseline | birds_only_transposon_coverage_ge_0_50 | estimate_p_n_birds | 0.398794503922211 | 0.417129194229116 | n=17;birds=17 | ||
| high_coverage_subset | rescued | all_primary | estimate_p_n_birds | 0.287317251804131 | 0.0075295685457648 | n=68;birds=31 | ||
| high_coverage_subset | rescued | transposon_coverage_ge_0_50 | estimate_p_n_birds | 0.615022841056534 | 0.193091471510662 | n=51;birds=17 | ||
| high_coverage_subset | rescued | birds_only_transposon_coverage_ge_0_50 | estimate_p_n_birds | 0.398794503922211 | 0.417129194229116 | n=17;birds=17 |
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_41_sequence_validation_model_impact.tsv
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Supplementary Data 5 Trimmed Alignment Qc source data
2 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_5_trimmed_alignment_qc.tsv.
Evidence visualization
Supplementary Data 5 Trimmed Alignment Qc source data
2 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_5_trimmed_alignment_qc.tsv.
Browse source data · 2 rows
Loading rows 1–2…
| Family | Input Alignment | Trimmed Alignment | Input Sequences | Trimmed Sequences | Input Columns | Trimmed Columns | Columns Retained Fraction | Dropped Low Information Sequences | Max Column Gap Fraction | Min Non Gap Aa |
|---|
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_5_trimmed_alignment_qc.tsv
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Supplementary Data 6 Branch Length Sensitivity source data
168 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_6_branch_length_sensitivity.tsv.
Evidence visualization
Supplementary Data 6 Branch Length Sensitivity source data
168 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_6_branch_length_sensitivity.tsv.
Browse source data · 168 rows
Rows 1–10 of 168
| Score Variant | Branch Variant | Model | Formula | N | Clade Count | Lambda | LogLik | AIC | Estimate | Se | T | P | Conf Low | Conf High | Error | P Bh By Score Model |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| targeted_domain_sensitivity | datelife_calibrated | clade_residual_score | pgls_model_c_mass_clade_residual ~ transposon_repeat_suppression_score | 68 | 0 | 0.794053834598966 | 9.33048291207433 | -14.6609658241487 | 0.267679232754473 | 0.0900579087009938 | 2.97230122945903 | 0.00412182485017176 | 0.0911657317005248 | 0.444192733808421 | 0.0043720081372971 | |
| targeted_domain_sensitivity | equal_branch_lengths | clade_residual_score | pgls_model_c_mass_clade_residual ~ transposon_repeat_suppression_score | 68 | 0 | 0.828319157681345 | 4.26115684588203 | -4.52231369176405 | 0.329464294130097 | 0.101399577393676 | 3.2491683160668 | 0.00182251216418838 | 0.130721122438491 | 0.528207465821702 | 0.0043720081372971 | |
| targeted_domain_sensitivity | grafen_power_0.5 | clade_residual_score | pgls_model_c_mass_clade_residual ~ transposon_repeat_suppression_score | 68 | 0 | 0.395991305413897 | 9.45728154277284 | -14.9145630855457 | 0.282605879369556 | 0.0931731420066585 | 3.03312599836292 | 0.00345835452692467 | 0.0999865210365056 | 0.465225237702607 | 0.0043720081372971 | |
| targeted_domain_sensitivity | grafen_power_1 | clade_residual_score | pgls_model_c_mass_clade_residual ~ transposon_repeat_suppression_score | 68 | 0 | 0.419170198566128 | 8.93375720012993 | -13.8675144002599 | 0.279920585452455 | 0.0936165723464307 | 2.99007513772883 | 0.00391664851226636 | 0.0964321036534509 | 0.463409067251459 | 0.0043720081372971 | |
| targeted_domain_sensitivity | grafen_power_2 | clade_residual_score | pgls_model_c_mass_clade_residual ~ transposon_repeat_suppression_score | 68 | 0 | 0.616787464848678 | 7.84883220497643 | -11.6976644099529 | 0.277270430263307 | 0.0939356051480621 | 2.95170750032717 | 0.0043720081372971 | 0.0931566441731049 | 0.461384216353508 | 0.0043720081372971 | |
| targeted_domain_sensitivity | grafen_scaled_320Ma | clade_residual_score | pgls_model_c_mass_clade_residual ~ transposon_repeat_suppression_score | 68 | 0 | 0.419170198564023 | 8.93375720012992 | -13.8675144002598 | 0.279920585452368 | 0.0936165723464478 | 2.99007513772736 | 0.00391664851228279 | 0.0964321036533303 | 0.463409067251405 | 0.0043720081372971 | |
| targeted_domain_sensitivity | opentree_original_or_unit | clade_residual_score | pgls_model_c_mass_clade_residual ~ transposon_repeat_suppression_score | 68 | 0 | 0.828319157681345 | 4.26115684588203 | -4.52231369176405 | 0.329464294130097 | 0.101399577393676 | 3.2491683160668 | 0.00182251216418838 | 0.130721122438491 | 0.528207465821702 | 0.0043720081372971 | |
| targeted_domain_sensitivity | datelife_calibrated | mass_clade_score | log10_max_lifespan_years ~ log10_body_mass_g + clade + transposon_repeat_suppression_score | 68 | 4 | 0.63459490607636 | 14.9136312328168 | -17.8272624656337 | 0.313396300367481 | 0.0895857960024431 | 3.49828113777026 | 0.000872444230070268 | 0.137808140202692 | 0.48898446053227 | 0.00228740859535452 | |
| targeted_domain_sensitivity | equal_branch_lengths | mass_clade_score | log10_max_lifespan_years ~ log10_body_mass_g + clade + transposon_repeat_suppression_score | 68 | 4 | 0.74385395069148 | 9.6861173994 | -7.37223479879999 | 0.348575421140693 | 0.100718609696827 | 3.46088396364823 | 0.00098031796943765 | 0.151166946134913 | 0.545983896146474 | 0.00228740859535452 | |
| targeted_domain_sensitivity | grafen_power_0.5 | mass_clade_score | log10_max_lifespan_years ~ log10_body_mass_g + clade + transposon_repeat_suppression_score | 68 | 4 | 1e-06 | 14.8630595391313 | -17.7261190782625 | 0.31039309965157 | 0.098187069108549 | 3.16124213167439 | 0.00243096138639087 | 0.117946444198814 | 0.502839755104326 | 0.00243096410223331 |
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_6_branch_length_sensitivity.tsv
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bf1dc386…646886
Supplementary Data 7 Gene Panel Reconciliation source data
236 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_7_gene_panel_reconciliation.tsv.
Evidence visualization
Supplementary Data 7 Gene Panel Reconciliation source data
236 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_7_gene_panel_reconciliation.tsv.
Browse source data · 236 rows
Rows 1–10 of 236
| Human Gene Symbol | Maintenance Module V2 | Submodule V2 | Seed Status | Symbol Validation Status | Gene Family Risk | V2 Scoring Group | Included In Final 200 | Final Panel Decision | Exclusion Reason | Strict Score Allowed | Sensitivity Score Allowed | Absence Scoring Allowed |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| APEX1 | DNA_repair_replication_stress | end_joining_base_excision_nucleotide_excision | expanded_v2_candidate | validated_exact | standard | standard_mapping_pending | True | included | False | True | False | |
| ATM | DNA_repair_replication_stress | damage_signaling_checkpoint | seed_v0 | validated_exact | standard | strict_ready | True | included | True | True | True | |
| ATR | DNA_repair_replication_stress | damage_signaling_checkpoint | seed_v0 | validated_exact | standard | strict_ready | True | included | True | True | True | |
| BLM | DNA_repair_replication_stress | homologous_recombination_fanconi | expanded_v2_candidate | validated_exact | standard | standard_mapping_pending | True | included | False | True | False | |
| BRCA1 | DNA_repair_replication_stress | homologous_recombination_fanconi | seed_v0 | validated_exact | standard | strict_ready | True | included | True | True | True | |
| BRCA2 | DNA_repair_replication_stress | homologous_recombination_fanconi | seed_v0 | validated_exact | standard | strict_ready | True | included | True | True | True | |
| BRIP1 | DNA_repair_replication_stress | homologous_recombination_fanconi | expanded_v2_candidate | validated_exact | standard | standard_mapping_pending | True | included | False | True | False | |
| CHEK1 | DNA_repair_replication_stress | damage_signaling_checkpoint | expanded_v2_candidate | validated_exact | standard | standard_mapping_pending | True | included | False | True | False | |
| CHEK2 | DNA_repair_replication_stress | damage_signaling_checkpoint | seed_v0 | validated_exact | standard | strict_ready | True | included | True | True | True | |
| ERCC1 | DNA_repair_replication_stress | end_joining_base_excision_nucleotide_excision | expanded_v2_candidate | validated_exact | standard | standard_mapping_pending | True | included | False | True | False |
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_7_gene_panel_reconciliation.tsv
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Deterministic extraction method
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Evidence classified preserved repository files, parsed bounded structured tables, inferred column types, and selected registered components using versioned rules.
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Pinned scientific commit: bf6ac86b961d575f3524b994dcce9fff993637be
Limitations
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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.