{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2012:XSNEI4O3VSSGJMSV234OXFEWG7","short_pith_number":"pith:XSNEI4O3","canonical_record":{"source":{"id":"1212.5239","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2012-12-20T20:44:06Z","cross_cats_sorted":[],"title_canon_sha256":"d39b728e71887bc66518bcf2e2ed96cd886515f5f43b5813c8e104d994c06e25","abstract_canon_sha256":"00dd90efdf2abee295f983936e2daac5f3c1f54bc4b8a1885f23088b29afa589"},"schema_version":"1.0"},"canonical_sha256":"bc9a4471dbaca464b255d6f8eb949637c6a74ab1067c857fe1351cb19a31aa5e","source":{"kind":"arxiv","id":"1212.5239","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1212.5239","created_at":"2026-05-18T03:14:17Z"},{"alias_kind":"arxiv_version","alias_value":"1212.5239v1","created_at":"2026-05-18T03:14:17Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1212.5239","created_at":"2026-05-18T03:14:17Z"},{"alias_kind":"pith_short_12","alias_value":"XSNEI4O3VSSG","created_at":"2026-05-18T12:27:27Z"},{"alias_kind":"pith_short_16","alias_value":"XSNEI4O3VSSGJMSV","created_at":"2026-05-18T12:27:27Z"},{"alias_kind":"pith_short_8","alias_value":"XSNEI4O3","created_at":"2026-05-18T12:27:27Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2012:XSNEI4O3VSSGJMSV234OXFEWG7","target":"record","payload":{"canonical_record":{"source":{"id":"1212.5239","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2012-12-20T20:44:06Z","cross_cats_sorted":[],"title_canon_sha256":"d39b728e71887bc66518bcf2e2ed96cd886515f5f43b5813c8e104d994c06e25","abstract_canon_sha256":"00dd90efdf2abee295f983936e2daac5f3c1f54bc4b8a1885f23088b29afa589"},"schema_version":"1.0"},"canonical_sha256":"bc9a4471dbaca464b255d6f8eb949637c6a74ab1067c857fe1351cb19a31aa5e","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T03:14:17.422380Z","signature_b64":"lLwFkBb5OjQmJBwMwYAmpb7JVmXDfpJvsNc7iXLvDhAFobmgo9isyAXessUj9mvtYA+m+LMZrMc8e2HxkSJsCg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"bc9a4471dbaca464b255d6f8eb949637c6a74ab1067c857fe1351cb19a31aa5e","last_reissued_at":"2026-05-18T03:14:17.421693Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T03:14:17.421693Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1212.5239","source_version":1,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T03:14:17Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"NGe5X5EzzkTL/G67aH57yHyq/c1RmGuxVXqEifOdI/IjCluZz1BsNNNv3QD+i0xFJGTlL8DNuO65DZD3umSYAw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-27T15:50:19.134138Z"},"content_sha256":"b2450fa412276a467bc15e85c079f68890f6da48a093f13640e67ad34f7ccda6","schema_version":"1.0","event_id":"sha256:b2450fa412276a467bc15e85c079f68890f6da48a093f13640e67ad34f7ccda6"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2012:XSNEI4O3VSSGJMSV234OXFEWG7","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Epistasis not needed to explain low dN/dS","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.PE","authors_text":"David M. McCandlish, Etienne Rajon, Joshua B. Plotkin, Premal Shah, Yang Ding","submitted_at":"2012-12-20T20:44:06Z","abstract_excerpt":"An important question in molecular evolution is whether an amino acid that occurs at a given position makes an independent contribution to fitness, or whether its effect depends on the state of other loci in the organism's genome, a phenomenon known as epistasis. In a recent letter to Nature, Breen et al. (2012) argued that epistasis must be \"pervasive throughout protein evolution\" because the observed ratio between the per-site rates of non-synonymous and synonymous substitutions (dN/dS) is much lower than would be expected in the absence of epistasis. However, when calculating the expected d"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1212.5239","kind":"arxiv","version":1},"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":"2026-05-18T03:14:17Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"C8P9vcabEdy1d5O1t4KAoSNyo8YGFHV+GOHm5HaU4MAgmhhP4cRUgZw93FMH9MpMmGsAIbVC5FbHdKHQ8rXwDA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-27T15:50:19.134821Z"},"content_sha256":"914b10bf52f4ea52c82af4b1cd4eba262fecaad37c33781903a10a0f1c223d22","schema_version":"1.0","event_id":"sha256:914b10bf52f4ea52c82af4b1cd4eba262fecaad37c33781903a10a0f1c223d22"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/XSNEI4O3VSSGJMSV234OXFEWG7/bundle.json","state_url":"https://pith.science/pith/XSNEI4O3VSSGJMSV234OXFEWG7/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/XSNEI4O3VSSGJMSV234OXFEWG7/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":"2026-05-27T15:50:19Z","links":{"resolver":"https://pith.science/pith/XSNEI4O3VSSGJMSV234OXFEWG7","bundle":"https://pith.science/pith/XSNEI4O3VSSGJMSV234OXFEWG7/bundle.json","state":"https://pith.science/pith/XSNEI4O3VSSGJMSV234OXFEWG7/state.json","well_known_bundle":"https://pith.science/.well-known/pith/XSNEI4O3VSSGJMSV234OXFEWG7/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2012:XSNEI4O3VSSGJMSV234OXFEWG7","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":"00dd90efdf2abee295f983936e2daac5f3c1f54bc4b8a1885f23088b29afa589","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2012-12-20T20:44:06Z","title_canon_sha256":"d39b728e71887bc66518bcf2e2ed96cd886515f5f43b5813c8e104d994c06e25"},"schema_version":"1.0","source":{"id":"1212.5239","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1212.5239","created_at":"2026-05-18T03:14:17Z"},{"alias_kind":"arxiv_version","alias_value":"1212.5239v1","created_at":"2026-05-18T03:14:17Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1212.5239","created_at":"2026-05-18T03:14:17Z"},{"alias_kind":"pith_short_12","alias_value":"XSNEI4O3VSSG","created_at":"2026-05-18T12:27:27Z"},{"alias_kind":"pith_short_16","alias_value":"XSNEI4O3VSSGJMSV","created_at":"2026-05-18T12:27:27Z"},{"alias_kind":"pith_short_8","alias_value":"XSNEI4O3","created_at":"2026-05-18T12:27:27Z"}],"graph_snapshots":[{"event_id":"sha256:914b10bf52f4ea52c82af4b1cd4eba262fecaad37c33781903a10a0f1c223d22","target":"graph","created_at":"2026-05-18T03:14:17Z","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":"An important question in molecular evolution is whether an amino acid that occurs at a given position makes an independent contribution to fitness, or whether its effect depends on the state of other loci in the organism's genome, a phenomenon known as epistasis. In a recent letter to Nature, Breen et al. (2012) argued that epistasis must be \"pervasive throughout protein evolution\" because the observed ratio between the per-site rates of non-synonymous and synonymous substitutions (dN/dS) is much lower than would be expected in the absence of epistasis. However, when calculating the expected d","authors_text":"David M. McCandlish, Etienne Rajon, Joshua B. Plotkin, Premal Shah, Yang Ding","cross_cats":[],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2012-12-20T20:44:06Z","title":"Epistasis not needed to explain low dN/dS"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1212.5239","kind":"arxiv","version":1},"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:b2450fa412276a467bc15e85c079f68890f6da48a093f13640e67ad34f7ccda6","target":"record","created_at":"2026-05-18T03:14:17Z","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":"00dd90efdf2abee295f983936e2daac5f3c1f54bc4b8a1885f23088b29afa589","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2012-12-20T20:44:06Z","title_canon_sha256":"d39b728e71887bc66518bcf2e2ed96cd886515f5f43b5813c8e104d994c06e25"},"schema_version":"1.0","source":{"id":"1212.5239","kind":"arxiv","version":1}},"canonical_sha256":"bc9a4471dbaca464b255d6f8eb949637c6a74ab1067c857fe1351cb19a31aa5e","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"bc9a4471dbaca464b255d6f8eb949637c6a74ab1067c857fe1351cb19a31aa5e","first_computed_at":"2026-05-18T03:14:17.421693Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T03:14:17.421693Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"lLwFkBb5OjQmJBwMwYAmpb7JVmXDfpJvsNc7iXLvDhAFobmgo9isyAXessUj9mvtYA+m+LMZrMc8e2HxkSJsCg==","signature_status":"signed_v1","signed_at":"2026-05-18T03:14:17.422380Z","signed_message":"canonical_sha256_bytes"},"source_id":"1212.5239","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:b2450fa412276a467bc15e85c079f68890f6da48a093f13640e67ad34f7ccda6","sha256:914b10bf52f4ea52c82af4b1cd4eba262fecaad37c33781903a10a0f1c223d22"],"state_sha256":"21134c624da0b9cb8eb2c12189aaca1a64d7a6d308c3a45e480275dff574dfdb"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"eJLr1kkSt6PIgdtzhKHTY8tVHWR7G2sZGAY+WdTlNQo0Yv/WsFvSFy9Yse5EA0Ch4PBuVId/G4Y7YxN5rtq6BQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-27T15:50:19.138226Z","bundle_sha256":"85a9e363a6812b6690ad73f1490c154585f6785a2d544955fc8fe736a9edd3fa"}}