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 29 Curated Ortholog Rule Clade Summary source data
16 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_29_curated_ortholog_rule_clade_summary.tsv.
Evidence visualization
Supplementary Data 29 Curated Ortholog Rule Clade Summary source data
16 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_29_curated_ortholog_rule_clade_summary.tsv.
Browse source data · 16 rows
Rows 1–10 of 16
| Ortholog Rule | Clade | Curated Rows N | Rows Total | Curated Fraction |
|---|---|---|---|---|
| exact_symbol_only | Aves | 2254 | 6200 | 0.3635483870967742 |
| exact_symbol_only | Mammalia_Chiroptera | 1377 | 2200 | 0.6259090909090909 |
| exact_symbol_only | Mammalia_nonChiroptera | 2588 | 3600 | 0.7188888888888889 |
| exact_symbol_only | Reptilia | 1126 | 1600 | 0.70375 |
| exact_plus_strict_rescue | Aves | 2319 | 6200 | 0.3740322580645161 |
| exact_plus_strict_rescue | Mammalia_Chiroptera | 1377 | 2200 | 0.6259090909090909 |
| exact_plus_strict_rescue | Mammalia_nonChiroptera | 2588 | 3600 | 0.7188888888888889 |
| exact_plus_strict_rescue | Reptilia | 1126 | 1600 | 0.70375 |
| high_confidence_only | Aves | 203 | 6200 | 0.03274193548387097 |
| high_confidence_only | Mammalia_Chiroptera | 55 | 2200 | 0.025 |
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_29_curated_ortholog_rule_clade_summary.tsv
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Supplementary Data 3 Sequence Evidence Ladder source data
140 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_3_sequence_evidence_ladder.tsv.
Evidence visualization
Supplementary Data 3 Sequence Evidence Ladder source data
140 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_3_sequence_evidence_ladder.tsv.
Browse source data · 140 rows
Rows 1–10 of 140
| Scientific Name | Human Gene Symbol | Clade | Flight Status | Species Taxid | Best Assembly Accession | Maintenance Module | Gene Family Risk | Gff Rescue Call | Gff Rescue Interpretation | Gff Can Count As Annotation Rescue | Matched Id | Matched Gene | Sequence Validation Gff Sequence Decision | Gff Protein Id | Gff Protein Length | Gff Partial | Gff Validation Calls | Gff Reciprocal Best Genes | Gff Max Pident |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Alectura lathami | DNMT1 | Aves | flighted | 81907 | GCA_013399715.1 | transposon_repeat_suppression | module_high_priority | gff_symbol_exact | annotation_presence_supported_pending_sequence | True | gene-ALELAT_R00895 | Dnmt1 | gff_sequence_strict_rescue | NXL95466.1 | 1137 | true | reciprocal_same_gene_supported | DNMT1 | 80.061 |
| Alectura lathami | DNMT3A | Aves | flighted | 81907 | GCA_013399715.1 | transposon_repeat_suppression | module_high_priority | not_found_in_gff | not_found_in_local_gff | False | |||||||||
| Alectura lathami | DNMT3B | Aves | flighted | 81907 | GCA_013399715.1 | transposon_repeat_suppression | module_high_priority | gff_symbol_exact | annotation_presence_supported_pending_sequence | True | gene-ALELAT_R11838 | Dnmt3b | reject_gff_sequence_no_same_gene_reference | NXL89818.1 | 814 | true | no_same_gene_reference_hit | 51.1 | |
| Alectura lathami | HELLS | Aves | flighted | 81907 | GCA_013399715.1 | transposon_repeat_suppression | module_high_priority | gff_symbol_exact | annotation_presence_supported_pending_sequence | True | gene-ALELAT_R07198 | Hells | gff_sequence_strict_rescue | NXL89278.1 | 833 | true | reciprocal_same_gene_supported | HELLS | 81.7 |
| Alectura lathami | MBD2 | Aves | flighted | 81907 | GCA_013399715.1 | transposon_repeat_suppression | module_high_priority | gff_symbol_exact | annotation_presence_supported_pending_sequence | True | gene-ALELAT_R14809 | Mbd2 | gff_sequence_weak_same_gene_not_strict | NXL88475.1 | 103 | true | weak_same_gene_support | MBD2 | 83.5 |
| Alectura lathami | MBD3 | Aves | flighted | 81907 | GCA_013399715.1 | transposon_repeat_suppression | module_high_priority | gff_symbol_exact | annotation_presence_supported_pending_sequence | True | gene-ALELAT_R07785 | Mbd3 | gff_sequence_strict_rescue | NXL94409.1 | 233 | true | reciprocal_same_gene_supported | MBD3 | 95.2 |
| Alectura lathami | MORC3 | Aves | flighted | 81907 | GCA_013399715.1 | transposon_repeat_suppression | high_paralog_family | not_found_in_gff | not_found_in_local_gff | False | |||||||||
| Alectura lathami | SAMHD1 | Aves | flighted | 81907 | GCA_013399715.1 | transposon_repeat_suppression | module_high_priority | gff_symbol_exact | annotation_presence_supported_pending_sequence | True | gene-ALELAT_R12303 | Samhd1 | gff_sequence_strict_rescue | NXL87263.1 | 557 | true | reciprocal_same_gene_supported | SAMHD1 | 64.7 |
| Alectura lathami | SETDB2 | Aves | flighted | 81907 | GCA_013399715.1 | transposon_repeat_suppression | module_high_priority | gff_symbol_exact | annotation_presence_supported_pending_sequence | True | gene-ALELAT_R05240 | Setdb2 | gff_sequence_strict_rescue | NXL92946.1 | 718 | true | reciprocal_same_gene_supported | SETDB2 | 46.332 |
| Alectura lathami | UHRF1 | Aves | flighted | 81907 | GCA_013399715.1 | transposon_repeat_suppression | module_high_priority | gff_symbol_exact | annotation_presence_supported_pending_sequence | True | gene-ALELAT_R03751 | Uhrf1 | gff_sequence_strict_rescue | NXL88609.1 | 743 | true | reciprocal_same_gene_supported | UHRF1 | 69.826 |
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_3_sequence_evidence_ladder.tsv
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Supplementary Data 30 Curated Ortholog Sensitivity Pgls source data
208 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_30_curated_ortholog_sensitivity_pgls.tsv.
Evidence visualization
Supplementary Data 30 Curated Ortholog Sensitivity Pgls source data
208 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_30_curated_ortholog_sensitivity_pgls.tsv.
Browse source data · 208 rows
Rows 1–10 of 208
| Ortholog Rule | Maintenance Module | Scope | Model | Formula | N | Mean Curated Fraction | Lambda | Estimate Per Sd | Se | Conf Low | Conf High | T | P | Error | Q |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| exact_plus_strict_rescue | cancer_surveillance_senescence | all_species | mass_clade_curated_fraction | log10_max_lifespan_years ~ log10_body_mass_g + clade + curated_z | 68 | 0.653886554621849 | 0.57068351420973 | 0.0924624167029927 | 0.0281450720617567 | 0.0372980754619495 | 0.147626757944036 | 3.28520802860653 | 0.00167912747139143 | 0.00336948682372098 | |
| exact_plus_strict_rescue | transposon_suppression | all_species | mass_clade_curated_fraction | log10_max_lifespan_years ~ log10_body_mass_g + clade + curated_z | 68 | 0.544817927170868 | 0.596131751354641 | 0.08526068290332 | 0.0265179888876723 | 0.0332854246834822 | 0.137235941123158 | 3.21520169815577 | 0.00207143734898185 | 0.00336948682372098 | |
| exact_plus_strict_rescue | chromatin_repression_heterochromatin | all_species | mass_clade_curated_fraction | log10_max_lifespan_years ~ log10_body_mass_g + clade + curated_z | 68 | 0.696078431372549 | 0.59927036725405 | 0.0876552659638231 | 0.0273401017596596 | 0.0340686665148903 | 0.141241865412756 | 3.20610606113978 | 0.00212831538920111 | 0.00336948682372098 | |
| exact_plus_strict_rescue | DNA_repair_replication_stress | all_species | mass_clade_curated_fraction | log10_max_lifespan_years ~ log10_body_mass_g + clade + curated_z | 68 | 0.690686274509804 | 0.624441090762294 | 0.0865176110620762 | 0.0272120202472859 | 0.0331820513773959 | 0.139853170746757 | 3.17938948581759 | 0.00230397982545383 | 0.00336948682372098 | |
| exact_plus_strict_rescue | proteostasis_autophagy_mitophagy | all_species | mass_clade_curated_fraction | log10_max_lifespan_years ~ log10_body_mass_g + clade + curated_z | 68 | 0.71524064171123 | 0.601794968676143 | 0.0836778682083431 | 0.0264416054223605 | 0.0318523215805166 | 0.13550341483617 | 3.16462888208673 | 0.00240677630265784 | 0.00336948682372098 | |
| exact_plus_strict_rescue | inflammation_innate_immune_restraint | all_species | mass_clade_curated_fraction | log10_max_lifespan_years ~ log10_body_mass_g + clade + curated_z | 68 | 0.609335038363171 | 0.581485544510827 | 0.0853810173289086 | 0.0278414192783481 | 0.0308118355433463 | 0.139950199114471 | 3.06669054746459 | 0.00320553433601933 | 0.00373979005868922 | |
| exact_plus_strict_rescue | transposon_repeat_suppression | all_species | mass_clade_curated_fraction | log10_max_lifespan_years ~ log10_body_mass_g + clade + curated_z | 68 | 0.786764705882353 | 0.546244715543796 | 0.0581670245994702 | 0.0255622306369557 | 0.00806505255103713 | 0.108268996647903 | 2.2755066029088 | 0.0263428962686807 | 0.0263428962686807 | |
| exact_plus_strict_rescue | DNA_repair | all_species | mass_clade_curated_fraction | log10_max_lifespan_years ~ log10_body_mass_g + clade + curated_z | 68 | 0 | insufficient observations or ortholog-score variation | ||||||||
| exact_plus_strict_rescue | autophagy | all_species | mass_clade_curated_fraction | log10_max_lifespan_years ~ log10_body_mass_g + clade + curated_z | 68 | 0 | insufficient observations or ortholog-score variation | ||||||||
| exact_plus_strict_rescue | cancer_surveillance | all_species | mass_clade_curated_fraction | log10_max_lifespan_years ~ log10_body_mass_g + clade + curated_z | 68 | 0 | insufficient observations or ortholog-score variation |
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_30_curated_ortholog_sensitivity_pgls.tsv
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Supplementary Data 31 Curated Ortholog Module Scores source data
3536 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_31_curated_ortholog_module_scores.tsv.
Evidence visualization
Supplementary Data 31 Curated Ortholog Module Scores source data
3536 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_31_curated_ortholog_module_scores.tsv.
Browse source data · 3,536 rows
Rows 1–10 of 3536
| Ortholog Rule | Scientific Name | Clade | Flight Status | Maintenance Module | Genes Total | Curated Genes N | Curated Fraction | Opentree Tip Label | Genome Analysis Tier | Body Mass G | Log10 Body Mass G | Max Lifespan Years | Pgls Model C Mass Clade Residual |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| exact_symbol_only | Agelaius phoeniceus | Aves | flighted | DNA_repair | 8 | 0 | 0.0 | Agelaius_phoeniceus_ott226605 | tier1_refseq_annotated_chromosome | 56.7 | 1.7535830588929069 | 20.0 | 0.246198779383737 |
| exact_symbol_only | Agelaius phoeniceus | Aves | flighted | DNA_repair_replication_stress | 30 | 27 | 0.9 | Agelaius_phoeniceus_ott226605 | tier1_refseq_annotated_chromosome | 56.7 | 1.7535830588929069 | 20.0 | 0.246198779383737 |
| exact_symbol_only | Agelaius phoeniceus | Aves | flighted | autophagy | 5 | 0 | 0.0 | Agelaius_phoeniceus_ott226605 | tier1_refseq_annotated_chromosome | 56.7 | 1.7535830588929069 | 20.0 | 0.246198779383737 |
| exact_symbol_only | Agelaius phoeniceus | Aves | flighted | cancer_surveillance | 5 | 0 | 0.0 | Agelaius_phoeniceus_ott226605 | tier1_refseq_annotated_chromosome | 56.7 | 1.7535830588929069 | 20.0 | 0.246198779383737 |
| exact_symbol_only | Agelaius phoeniceus | Aves | flighted | cancer_surveillance_senescence | 28 | 22 | 0.7857142857142857 | Agelaius_phoeniceus_ott226605 | tier1_refseq_annotated_chromosome | 56.7 | 1.7535830588929069 | 20.0 | 0.246198779383737 |
| exact_symbol_only | Agelaius phoeniceus | Aves | flighted | chromatin_repression_heterochromatin | 30 | 26 | 0.8666666666666667 | Agelaius_phoeniceus_ott226605 | tier1_refseq_annotated_chromosome | 56.7 | 1.7535830588929069 | 20.0 | 0.246198779383737 |
| exact_symbol_only | Agelaius phoeniceus | Aves | flighted | inflammation_control | 6 | 0 | 0.0 | Agelaius_phoeniceus_ott226605 | tier1_refseq_annotated_chromosome | 56.7 | 1.7535830588929069 | 20.0 | 0.246198779383737 |
| exact_symbol_only | Agelaius phoeniceus | Aves | flighted | inflammation_innate_immune_restraint | 23 | 17 | 0.7391304347826086 | Agelaius_phoeniceus_ott226605 | tier1_refseq_annotated_chromosome | 56.7 | 1.7535830588929069 | 20.0 | 0.246198779383737 |
| exact_symbol_only | Agelaius phoeniceus | Aves | flighted | mitochondrial_quality_control | 6 | 0 | 0.0 | Agelaius_phoeniceus_ott226605 | tier1_refseq_annotated_chromosome | 56.7 | 1.7535830588929069 | 20.0 | 0.246198779383737 |
| exact_symbol_only | Agelaius phoeniceus | Aves | flighted | proteostasis | 6 | 0 | 0.0 | Agelaius_phoeniceus_ott226605 | tier1_refseq_annotated_chromosome | 56.7 | 1.7535830588929069 | 20.0 | 0.246198779383737 |
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_31_curated_ortholog_module_scores.tsv
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Supplementary Data 32 Orthology Evidence Criteria source data
6 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_32_orthology_evidence_criteria.tsv.
Evidence visualization
Supplementary Data 32 Orthology Evidence Criteria source data
6 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_32_orthology_evidence_criteria.tsv.
Browse source data · 6 rows
Loading rows 1–6…
| Evidence Class | Required Evidence | Orthology Risk Handling | Scoring Use |
|---|
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_32_orthology_evidence_criteria.tsv
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Supplementary Data 33 Gene Matrix Summary source data
6 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_33_gene_matrix_summary.tsv.
Evidence visualization
Supplementary Data 33 Gene Matrix Summary source data
6 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_33_gene_matrix_summary.tsv.
Browse source data · 6 rows
Loading rows 1–6…
| 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!/Supplementary_Data/Supplementary_Data_33_gene_matrix_summary.tsv
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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.
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No model is rerun and no missing value is inferred.
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.