{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2014:ZSU6Z3PVDJNSGGGIXSL3D3EZNY","short_pith_number":"pith:ZSU6Z3PV","canonical_record":{"source":{"id":"1411.1200","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"stat.AP","submitted_at":"2014-11-05T09:32:04Z","cross_cats_sorted":["q-bio.PE"],"title_canon_sha256":"16ccb6f0deeea1454e1c5f8614d31b1d324a9d4a8caeb345d9c0dc75ea372d1a","abstract_canon_sha256":"1da246aacb136931b63ce9b3edb99b74d96cf0c90e3c9e677808e5a8708620a8"},"schema_version":"1.0"},"canonical_sha256":"cca9ecedf51a5b2318c8bc97b1ec996e22370520982fca95579b4c67cacc3e60","source":{"kind":"arxiv","id":"1411.1200","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1411.1200","created_at":"2026-05-18T01:59:53Z"},{"alias_kind":"arxiv_version","alias_value":"1411.1200v2","created_at":"2026-05-18T01:59:53Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1411.1200","created_at":"2026-05-18T01:59:53Z"},{"alias_kind":"pith_short_12","alias_value":"ZSU6Z3PVDJNS","created_at":"2026-05-18T12:28:59Z"},{"alias_kind":"pith_short_16","alias_value":"ZSU6Z3PVDJNSGGGI","created_at":"2026-05-18T12:28:59Z"},{"alias_kind":"pith_short_8","alias_value":"ZSU6Z3PV","created_at":"2026-05-18T12:28:59Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2014:ZSU6Z3PVDJNSGGGIXSL3D3EZNY","target":"record","payload":{"canonical_record":{"source":{"id":"1411.1200","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"stat.AP","submitted_at":"2014-11-05T09:32:04Z","cross_cats_sorted":["q-bio.PE"],"title_canon_sha256":"16ccb6f0deeea1454e1c5f8614d31b1d324a9d4a8caeb345d9c0dc75ea372d1a","abstract_canon_sha256":"1da246aacb136931b63ce9b3edb99b74d96cf0c90e3c9e677808e5a8708620a8"},"schema_version":"1.0"},"canonical_sha256":"cca9ecedf51a5b2318c8bc97b1ec996e22370520982fca95579b4c67cacc3e60","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T01:59:53.473485Z","signature_b64":"kb8+qkUViH81fEljxmBNtwV4Q/cReyBtzcKmL2SdnoTUXXWhd9brLNEh7Q8xzKzzzc2+A1yQQT9fL6ARpSlRAQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"cca9ecedf51a5b2318c8bc97b1ec996e22370520982fca95579b4c67cacc3e60","last_reissued_at":"2026-05-18T01:59:53.472926Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T01:59:53.472926Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1411.1200","source_version":2,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T01:59:53Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"dEoJGxgl19iqPfiWO/XhuFo/7e5H7gjsXXdC5fCImlQ/Zj242MRxab7vulQpo8oJg6k9ppI1iuYOymtiuyWQDA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-12T08:33:23.269351Z"},"content_sha256":"371b72034b683aef629b2b21b31ddc86a94ef77a905fb20e9c63fff11d339665","schema_version":"1.0","event_id":"sha256:371b72034b683aef629b2b21b31ddc86a94ef77a905fb20e9c63fff11d339665"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2014:ZSU6Z3PVDJNSGGGIXSL3D3EZNY","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["q-bio.PE"],"primary_cat":"stat.AP","authors_text":"Barbara Holland, Nigel French, Patrick Biggs, Paul Fearnhead, Shoukai Yu","submitted_at":"2014-11-05T09:32:04Z","abstract_excerpt":"A number of studies have suggested using comparisons between DNA sequences of closely related bacterial isolates to estimate the relative rate of recombination to mutation for that bacterial species. We consider such an approach which uses single-locus variants: pairs of isolates whose DNA differ at a single gene locus. One way of deriving point estimates for the relative rate of recombination to mutation from such data is to use composite likelihood methods. We extend recent work in this area so as to be able to construct confidence intervals for our estimates, without needing to resort to co"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1411.1200","kind":"arxiv","version":2},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T01:59:53Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"NmxyXwyJvVCBzaIqcPfiAOFj/ZhPKK3b1veS5CvD3EPU/uJ5OG9Mu/hEtJjzVr1R+FNhwA1npSKmdjEhs2wrAw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-12T08:33:23.269728Z"},"content_sha256":"61cd534fd9e916c38b9d7e3bc0951c73673250bb0323385ccb27960eb23e0492","schema_version":"1.0","event_id":"sha256:61cd534fd9e916c38b9d7e3bc0951c73673250bb0323385ccb27960eb23e0492"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/ZSU6Z3PVDJNSGGGIXSL3D3EZNY/bundle.json","state_url":"https://pith.science/pith/ZSU6Z3PVDJNSGGGIXSL3D3EZNY/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/ZSU6Z3PVDJNSGGGIXSL3D3EZNY/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-06-12T08:33:23Z","links":{"resolver":"https://pith.science/pith/ZSU6Z3PVDJNSGGGIXSL3D3EZNY","bundle":"https://pith.science/pith/ZSU6Z3PVDJNSGGGIXSL3D3EZNY/bundle.json","state":"https://pith.science/pith/ZSU6Z3PVDJNSGGGIXSL3D3EZNY/state.json","well_known_bundle":"https://pith.science/.well-known/pith/ZSU6Z3PVDJNSGGGIXSL3D3EZNY/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2014:ZSU6Z3PVDJNSGGGIXSL3D3EZNY","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"1da246aacb136931b63ce9b3edb99b74d96cf0c90e3c9e677808e5a8708620a8","cross_cats_sorted":["q-bio.PE"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"stat.AP","submitted_at":"2014-11-05T09:32:04Z","title_canon_sha256":"16ccb6f0deeea1454e1c5f8614d31b1d324a9d4a8caeb345d9c0dc75ea372d1a"},"schema_version":"1.0","source":{"id":"1411.1200","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1411.1200","created_at":"2026-05-18T01:59:53Z"},{"alias_kind":"arxiv_version","alias_value":"1411.1200v2","created_at":"2026-05-18T01:59:53Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1411.1200","created_at":"2026-05-18T01:59:53Z"},{"alias_kind":"pith_short_12","alias_value":"ZSU6Z3PVDJNS","created_at":"2026-05-18T12:28:59Z"},{"alias_kind":"pith_short_16","alias_value":"ZSU6Z3PVDJNSGGGI","created_at":"2026-05-18T12:28:59Z"},{"alias_kind":"pith_short_8","alias_value":"ZSU6Z3PV","created_at":"2026-05-18T12:28:59Z"}],"graph_snapshots":[{"event_id":"sha256:61cd534fd9e916c38b9d7e3bc0951c73673250bb0323385ccb27960eb23e0492","target":"graph","created_at":"2026-05-18T01:59:53Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"paper":{"abstract_excerpt":"A number of studies have suggested using comparisons between DNA sequences of closely related bacterial isolates to estimate the relative rate of recombination to mutation for that bacterial species. We consider such an approach which uses single-locus variants: pairs of isolates whose DNA differ at a single gene locus. One way of deriving point estimates for the relative rate of recombination to mutation from such data is to use composite likelihood methods. We extend recent work in this area so as to be able to construct confidence intervals for our estimates, without needing to resort to co","authors_text":"Barbara Holland, Nigel French, Patrick Biggs, Paul Fearnhead, Shoukai Yu","cross_cats":["q-bio.PE"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"stat.AP","submitted_at":"2014-11-05T09:32:04Z","title":"Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1411.1200","kind":"arxiv","version":2},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:371b72034b683aef629b2b21b31ddc86a94ef77a905fb20e9c63fff11d339665","target":"record","created_at":"2026-05-18T01:59:53Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"1da246aacb136931b63ce9b3edb99b74d96cf0c90e3c9e677808e5a8708620a8","cross_cats_sorted":["q-bio.PE"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"stat.AP","submitted_at":"2014-11-05T09:32:04Z","title_canon_sha256":"16ccb6f0deeea1454e1c5f8614d31b1d324a9d4a8caeb345d9c0dc75ea372d1a"},"schema_version":"1.0","source":{"id":"1411.1200","kind":"arxiv","version":2}},"canonical_sha256":"cca9ecedf51a5b2318c8bc97b1ec996e22370520982fca95579b4c67cacc3e60","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"cca9ecedf51a5b2318c8bc97b1ec996e22370520982fca95579b4c67cacc3e60","first_computed_at":"2026-05-18T01:59:53.472926Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T01:59:53.472926Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"kb8+qkUViH81fEljxmBNtwV4Q/cReyBtzcKmL2SdnoTUXXWhd9brLNEh7Q8xzKzzzc2+A1yQQT9fL6ARpSlRAQ==","signature_status":"signed_v1","signed_at":"2026-05-18T01:59:53.473485Z","signed_message":"canonical_sha256_bytes"},"source_id":"1411.1200","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:371b72034b683aef629b2b21b31ddc86a94ef77a905fb20e9c63fff11d339665","sha256:61cd534fd9e916c38b9d7e3bc0951c73673250bb0323385ccb27960eb23e0492"],"state_sha256":"f3d147e9b1007ccba301ba072a14dc15f2568c34ba425814cec7adcd0e43c8ee"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"YKytgdonowjQDwqQ80UZhBYWB8HIU5n1D+T5MA1uaN8rHEwkssFvlDbDFoiC3SI4+7e5M9VIKBVAx+vr+9AQDA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-06-12T08:33:23.271888Z","bundle_sha256":"eca8491f670c3918e847863831d8936f1b6c23d229e97e22770c24ab90235c6d"}}