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 23 Targeted Domain Conservation Rows source data
680 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_23_targeted_domain_conservation_rows.tsv.
Evidence visualization
Supplementary Data 23 Targeted Domain Conservation Rows source data
680 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_23_targeted_domain_conservation_rows.tsv.
Browse source data · 680 rows
Rows 1–10 of 680
| Scientific Name | Opentree Tip Label | Clade | Flight Status | Human Gene Symbol | Alignment Record Id | Selected Accession | Sequence Source | Sequence Available | Pfam Domain Instances | Pfam Domain Signatures | Human Domain Reference Residues | Human Nondomain Reference Residues | Domain Reference Coverage | Domain Aligned Identity | Domain Identity Coverage Product | Nondomain Reference Coverage | Nondomain Aligned Identity | Nondomain Identity Coverage Product | Domain Minus Nondomain Identity |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Agelaius phoeniceus | Aves | flighted | DNMT1 | S001 | XP_077048462.1 | ncbi_gene_longest_isoform | True | 6 | 5 | 1015 | 617 | 0.9950738916256158 | 0.8485148514851485 | 0.8443349753694581 | 0.7747163695299838 | 0.6297071129707112 | 0.4878444084278768 | 0.21880773851443724 | |
| Ailuropoda melanoleuca | Mammalia_nonChiroptera | non_flying | DNMT1 | S002 | XP_011225961.3 | ncbi_gene_longest_isoform | True | 6 | 5 | 1015 | 617 | 1.0 | 0.9556650246305419 | 0.9556650246305419 | 0.9692058346839546 | 0.8461538461538461 | 0.820097244732577 | 0.10951117847669578 | |
| Alectura lathami | Aves | flighted | DNMT1 | S003 | NXL95466.1 | strict_gff_sequence | True | 6 | 5 | 1015 | 617 | 0.6591133004926109 | 0.8266068759342302 | 0.5448275862068965 | 0.7228525121555915 | 0.6614349775784754 | 0.47811993517017826 | 0.16517189835575485 | |
| Alligator mississippiensis | Reptilia | non_flying | DNMT1 | S004 | XP_059588198.1 | ncbi_gene_longest_isoform | True | 6 | 5 | 1015 | 617 | 0.9832512315270936 | 0.8406813627254509 | 0.8266009852216749 | 0.7763371150729336 | 0.6388308977035491 | 0.4959481361426256 | 0.20185046502190185 | |
| Alligator sinensis | Reptilia | non_flying | DNMT1 | S005 | XP_025059761.1 | ncbi_gene_longest_isoform | True | 6 | 5 | 1015 | 617 | 0.9980295566502463 | 0.8390918065153011 | 0.8374384236453202 | 0.7844408427876823 | 0.640495867768595 | 0.5024311183144247 | 0.1985959387467061 | |
| Ammodramus caudacutus | Aves | flighted | DNMT1 | S006 | XP_058677345.1 | ncbi_gene_longest_isoform | True | 6 | 5 | 1015 | 617 | 0.9950738916256158 | 0.8504950495049505 | 0.8463054187192118 | 0.7876823338735819 | 0.6069958847736625 | 0.47811993517017826 | 0.24349916473128796 | |
| Anas platyrhynchos | Aves | flighted | DNMT1 | False | 6 | 5 | 1015 | 617 | |||||||||||
| Anolis carolinensis | Reptilia | non_flying | DNMT1 | S008 | XP_008117963.2 | ncbi_gene_longest_isoform | True | 6 | 5 | 1015 | 617 | 0.9950738916256158 | 0.8306930693069307 | 0.8266009852216748 | 0.7747163695299838 | 0.6213389121338913 | 0.4813614262560778 | 0.2093541571730394 | |
| Anseranas semipalmata | Aves | flighted | DNMT1 | S009 | NXI71866.1 | strict_gff_sequence | True | 6 | 5 | 1015 | 617 | 0.6571428571428571 | 0.8320839580209896 | 0.5467980295566502 | 0.7228525121555915 | 0.6614349775784754 | 0.47811993517017826 | 0.1706489804425142 | |
| Antrozous pallidus | Mammalia_Chiroptera | powered_flight | DNMT1 | False | 6 | 5 | 1015 | 617 |
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_23_targeted_domain_conservation_rows.tsv
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Supplementary Data 24 Targeted Domain Conservation Intervals source data
1803 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_24_targeted_domain_conservation_intervals.tsv.
Evidence visualization
Supplementary Data 24 Targeted Domain Conservation Intervals source data
1803 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_24_targeted_domain_conservation_intervals.tsv.
Browse source data · 1,803 rows
Rows 1–10 of 1803
| Scientific Name | Clade | Human Gene Symbol | Selected Accession | Signature Accession | Signature Description | Interpro Accession | Interpro Description | Domain Instance | Human Domain Start | Human Domain End | Human Domain Length | Paired Residues | Domain Reference Coverage | Domain Aligned Identity | Domain Identity Coverage Product |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Agelaius phoeniceus | Aves | DNMT1 | XP_077048462.1 | PF00145 | C-5 cytosine-specific DNA methylase | IPR001525 | C-5 cytosine methyltransferase | 1 | 1156 | 1609 | 454 | 453 | 0.9977973568281938 | 0.9514348785871964 | 0.9493392070484581 |
| Ailuropoda melanoleuca | Mammalia_nonChiroptera | DNMT1 | XP_011225961.3 | PF00145 | C-5 cytosine-specific DNA methylase | IPR001525 | C-5 cytosine methyltransferase | 1 | 1156 | 1609 | 454 | 454 | 1.0 | 0.9713656387665198 | 0.9713656387665198 |
| Alectura lathami | Aves | DNMT1 | NXL95466.1 | PF00145 | C-5 cytosine-specific DNA methylase | IPR001525 | C-5 cytosine methyltransferase | 1 | 1156 | 1609 | 454 | 167 | 0.36784140969163 | 0.9281437125748503 | 0.341409691629956 |
| Alligator mississippiensis | Reptilia | DNMT1 | XP_059588198.1 | PF00145 | C-5 cytosine-specific DNA methylase | IPR001525 | C-5 cytosine methyltransferase | 1 | 1156 | 1609 | 454 | 438 | 0.9647577092511013 | 0.9383561643835616 | 0.9052863436123347 |
| Alligator sinensis | Reptilia | DNMT1 | XP_025059761.1 | PF00145 | C-5 cytosine-specific DNA methylase | IPR001525 | C-5 cytosine methyltransferase | 1 | 1156 | 1609 | 454 | 453 | 0.9977973568281938 | 0.9426048565121413 | 0.9405286343612335 |
| Ammodramus caudacutus | Aves | DNMT1 | XP_058677345.1 | PF00145 | C-5 cytosine-specific DNA methylase | IPR001525 | C-5 cytosine methyltransferase | 1 | 1156 | 1609 | 454 | 453 | 0.9977973568281938 | 0.9536423841059603 | 0.9515418502202643 |
| Anolis carolinensis | Reptilia | DNMT1 | XP_008117963.2 | PF00145 | C-5 cytosine-specific DNA methylase | IPR001525 | C-5 cytosine methyltransferase | 1 | 1156 | 1609 | 454 | 453 | 0.9977973568281938 | 0.9403973509933775 | 0.9383259911894273 |
| Anseranas semipalmata | Aves | DNMT1 | NXI71866.1 | PF00145 | C-5 cytosine-specific DNA methylase | IPR001525 | C-5 cytosine methyltransferase | 1 | 1156 | 1609 | 454 | 165 | 0.3634361233480176 | 0.9333333333333333 | 0.33920704845814975 |
| Artibeus jamaicensis | Mammalia_Chiroptera | DNMT1 | XP_036985019.2 | PF00145 | C-5 cytosine-specific DNA methylase | IPR001525 | C-5 cytosine methyltransferase | 1 | 1156 | 1609 | 454 | 453 | 0.9977973568281938 | 0.9713024282560706 | 0.9691629955947136 |
| Balaenoptera acutorostrata | Mammalia_nonChiroptera | DNMT1 | XP_057396752.1 | PF00145 | C-5 cytosine-specific DNA methylase | IPR001525 | C-5 cytosine methyltransferase | 1 | 1156 | 1609 | 454 | 453 | 0.9977973568281938 | 0.9668874172185431 | 0.9647577092511014 |
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_24_targeted_domain_conservation_intervals.tsv
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Supplementary Data 25 Targeted Domain Conservation Pgls source data
52 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_25_targeted_domain_conservation_pgls.tsv.
Evidence visualization
Supplementary Data 25 Targeted Domain Conservation Pgls source data
52 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_25_targeted_domain_conservation_pgls.tsv.
Browse source data · 52 rows
Rows 1–10 of 52
| Test Family | Scope | Human Gene Symbol | Predictor | N | Lambda | Lambda Method | Estimate Per Sd | Se | Conf Low | Conf High | T | P | Fit Note | Error | Q | Q Gene Scope All Metrics |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| domain_aggregate | all_species_min5 | domain_aggregate | aggregate_domain_contrast_clade_z | 51 | 0.780268999078616 | maximum_likelihood | 0.0602551708719649 | 0.0312318323635522 | -0.000959220560597378 | 0.121469562304527 | 1.92928708666749 | 0.0594967998946472 | 0.0594967998946472 | |||
| domain_aggregate | all_species_min5 | domain_aggregate | aggregate_domain_gene_clade_z | 51 | 0.806534529463264 | maximum_likelihood | 0.0292893603085893 | 0.0313183387407883 | -0.0320945836233558 | 0.0906733042405343 | 0.935214365966465 | 0.35426411504647 | 0.35426411504647 | |||
| domain_aggregate | all_species_min5 | domain_aggregate | aggregate_domain_gene_z | 51 | 0.796461343567351 | maximum_likelihood | 0.0476988179231081 | 0.0523072592096552 | -0.0548234101278162 | 0.150221045974032 | 0.911896716513557 | 0.366287797430306 | 0.366287797430306 | |||
| domain_aggregate | all_species_min8 | domain_aggregate | aggregate_domain_contrast_clade_z | 46 | 0.771079078740101 | maximum_likelihood | 0.0507088637628329 | 0.0354610581587372 | -0.018794810228292 | 0.120212537753958 | 1.42998732682597 | 0.15978359422127 | 0.15978359422127 | |||
| domain_aggregate | all_species_min8 | domain_aggregate | aggregate_domain_gene_clade_z | 46 | 0.77686861061142 | maximum_likelihood | 0.0134046417061485 | 0.0365993495645978 | -0.0583300834404632 | 0.0851393668527601 | 0.366253550011573 | 0.71593114262197 | 0.71593114262197 | |||
| domain_aggregate | all_species_min8 | domain_aggregate | aggregate_domain_gene_z | 46 | 0.773542347362833 | maximum_likelihood | 0.0114562231766759 | 0.0575571967640165 | -0.101355882480796 | 0.124268328834148 | 0.199040672943927 | 0.843147855779109 | 0.843147855779109 | |||
| domain_aggregate | aves_min5 | domain_aggregate | aggregate_domain_contrast_clade_z | 17 | 1e-06 | maximum_likelihood | 0.0786282816678939 | 0.0391018111915651 | 0.00198873173242639 | 0.155267831603361 | 2.0108603481993 | 0.0626706763580909 | 0.0626706763580909 | |||
| domain_aggregate | aves_min5 | domain_aggregate | aggregate_domain_gene_clade_z | 17 | 0.443344782638132 | maximum_likelihood | 0.0533825836092142 | 0.0410878594334545 | -0.0271496208803565 | 0.133914788098785 | 1.2992300972912 | 0.213480615739515 | 0.213480615739515 | |||
| domain_aggregate | aves_min5 | domain_aggregate | aggregate_domain_gene_z | 17 | 0.321230615500601 | maximum_likelihood | 0.0543279772638555 | 0.0406449916332677 | -0.0253362063373492 | 0.13399216086506 | 1.33664628975808 | 0.201259665210062 | 0.201259665210062 | |||
| domain_aggregate | aves_min8 | domain_aggregate | aggregate_domain_contrast_clade_z | 14 | 1e-06 | maximum_likelihood | 0.0355638423141303 | 0.0466290530858499 | -0.0558291017341355 | 0.126956786362396 | 0.76269707318853 | 0.460374492509601 | 0.460374492509601 |
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_25_targeted_domain_conservation_pgls.tsv
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Supplementary Data 26 Samhd1 Domain Robustness source data
36 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_26_samhd1_domain_robustness.tsv.
Evidence visualization
Supplementary Data 26 Samhd1 Domain Robustness source data
36 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_26_samhd1_domain_robustness.tsv.
Browse source data · 36 rows
Rows 1–10 of 36
| Scope | Predictor | N | Predictor Center | Predictor Scale | Lambda | Lambda Method | Estimate Per Sd | Se | Conf Low | Conf High | T | P | Fit Note | Error | Q Within Scope |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| all_species | domain_minus_nondomain_product | 53 | -0.0119165223090969 | 0.0517163812128169 | 1e-06 | maximum_likelihood | 0.127986090503007 | 0.0296504531627903 | 0.0698712023039379 | 0.186100978702076 | 4.31649694526836 | 7.30353793771954e-05 | 0.000292141517508782 | ||
| all_species | domain_identity_coverage_product | 53 | 0.669230769230769 | 0.114195051495553 | 0.727825239872756 | maximum_likelihood | 0.208395500273607 | 0.0659863548726119 | 0.0790622447232877 | 0.337728755823926 | 3.15816051175912 | 0.00266726201404621 | 0.00533452402809242 | ||
| all_species | whole_protein_identity_coverage_product | 53 | 0.678672614383025 | 0.0935758466084188 | 0.800123445303648 | maximum_likelihood | 0.118736696441211 | 0.0832977769510362 | -0.0445269463828205 | 0.282000339265241 | 1.42544856282306 | 0.160119514357124 | 0.213492685809499 | ||
| all_species | nondomain_identity_coverage_product | 53 | 0.681147291539866 | 0.0904932194317602 | 0.752850591156449 | maximum_likelihood | 0.0506855714126685 | 0.0787205937438783 | -0.103606792325333 | 0.20497793515067 | 0.643866731716693 | 0.522546990922319 | 0.522546990922319 | ||
| birds_only | domain_minus_nondomain_product | 20 | -0.0460840570719603 | 0.0505430839828466 | 1e-06 | maximum_likelihood | 0.13245954283179 | 0.0468548797143261 | 0.0406239785917112 | 0.224295107071869 | 2.82701702873629 | 0.0111701911762312 | 0.0341861238179484 | ||
| birds_only | domain_identity_coverage_product | 20 | 0.546153846153846 | 0.0546783579469931 | 1e-06 | maximum_likelihood | 0.125760947658976 | 0.0478693492836662 | 0.0319370230629904 | 0.219584872254962 | 2.62717061211208 | 0.0170930619089742 | 0.0341861238179484 | ||
| birds_only | whole_protein_identity_coverage_product | 20 | 0.582667731629393 | 0.0190136820450344 | 1e-06 | maximum_likelihood | 0.0826671377555787 | 0.0528249244086471 | -0.0208697140853696 | 0.186203989596527 | 1.56492675911992 | 0.135010804222092 | 0.180014405629456 | ||
| birds_only | nondomain_identity_coverage_product | 20 | 0.592237903225806 | 0.0142543091673129 | 1e-06 | maximum_likelihood | 0.0127322381490917 | 0.0562238965250045 | -0.0974665990399171 | 0.1229310753381 | 0.226455989997585 | 0.823398508711525 | 0.823398508711525 | ||
| domain_coverage_ge_0.8 | domain_minus_nondomain_product | 48 | -0.00108237696443343 | 0.0401789877857758 | 1e-06 | maximum_likelihood | 0.108743004483751 | 0.0294475340620417 | 0.0510258377221493 | 0.166460171245353 | 3.69277115885647 | 0.000587060682182505 | 0.00234824272873002 | ||
| domain_coverage_ge_0.8 | domain_identity_coverage_product | 48 | 0.689903846153846 | 0.0984860373827704 | 0.757028581747695 | maximum_likelihood | 0.157394149499401 | 0.068374926789529 | 0.0233792929919246 | 0.291409006006878 | 2.30192786873309 | 0.0259171219540466 | 0.0518342439080932 |
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_26_samhd1_domain_robustness.tsv
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Supplementary Data 27 Samhd1 Leave One Species Out source data
106 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_27_samhd1_leave_one_species_out.tsv.
Evidence visualization
Supplementary Data 27 Samhd1 Leave One Species Out source data
106 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_27_samhd1_leave_one_species_out.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!/Supplementary_Data/Supplementary_Data_27_samhd1_leave_one_species_out.tsv
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Supplementary Data 28 Curated Ortholog Rule Eligibility source data
4 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_28_curated_ortholog_rule_eligibility.tsv.
Evidence visualization
Supplementary Data 28 Curated Ortholog Rule Eligibility source data
4 materialized released rows from submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_28_curated_ortholog_rule_eligibility.tsv.
Browse source data · 4 rows
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| Ortholog Rule | Overall Curated Fraction | Min Clade Fraction | Max Clade Fraction | Max Minus Min Clade Fraction | Species Fraction Sd | Adequate Min Clade Coverage | Balanced Across Clades | Nondegenerate Species Variation | Eligible As Primary Full Matrix Control |
|---|
Source & verification
- File
- submission:submission-0874a5a043ddb0a424e0af00:1/nature-bird-lifespan-data-v1.0.0.zip!/Supplementary_Data/Supplementary_Data_28_curated_ortholog_rule_eligibility.tsv
- Version
released- Integrity
c29d7ad6…90c15a
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.