{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2014:2MK5SVKY5MY5MG4P64FIWYRB6W","short_pith_number":"pith:2MK5SVKY","canonical_record":{"source":{"id":"1405.6546","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2014-05-26T11:37:34Z","cross_cats_sorted":[],"title_canon_sha256":"0e4c8751072afc94b69efab17202506762c62d6c72498f5ad64de596ba0ae258","abstract_canon_sha256":"818f2b99605323ffcda1608fa61aee7ee7cdea9f2ac75b26dae34ad1724de722"},"schema_version":"1.0"},"canonical_sha256":"d315d95558eb31d61b8ff70a8b6221f59f4e61dd10f36c11b3d614058a0259bd","source":{"kind":"arxiv","id":"1405.6546","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1405.6546","created_at":"2026-05-18T02:39:23Z"},{"alias_kind":"arxiv_version","alias_value":"1405.6546v2","created_at":"2026-05-18T02:39:23Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1405.6546","created_at":"2026-05-18T02:39:23Z"},{"alias_kind":"pith_short_12","alias_value":"2MK5SVKY5MY5","created_at":"2026-05-18T12:28:11Z"},{"alias_kind":"pith_short_16","alias_value":"2MK5SVKY5MY5MG4P","created_at":"2026-05-18T12:28:11Z"},{"alias_kind":"pith_short_8","alias_value":"2MK5SVKY","created_at":"2026-05-18T12:28:11Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2014:2MK5SVKY5MY5MG4P64FIWYRB6W","target":"record","payload":{"canonical_record":{"source":{"id":"1405.6546","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2014-05-26T11:37:34Z","cross_cats_sorted":[],"title_canon_sha256":"0e4c8751072afc94b69efab17202506762c62d6c72498f5ad64de596ba0ae258","abstract_canon_sha256":"818f2b99605323ffcda1608fa61aee7ee7cdea9f2ac75b26dae34ad1724de722"},"schema_version":"1.0"},"canonical_sha256":"d315d95558eb31d61b8ff70a8b6221f59f4e61dd10f36c11b3d614058a0259bd","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T02:39:23.678563Z","signature_b64":"u3DvchhHrH5Z7Tp9T5ZP8DwyPfvCxJPFiIRJyCc6WAc+KU9ysOkbo/S0wH9eJbbhhz1GnEmHuBln83d5o3uABA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"d315d95558eb31d61b8ff70a8b6221f59f4e61dd10f36c11b3d614058a0259bd","last_reissued_at":"2026-05-18T02:39:23.678212Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T02:39:23.678212Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1405.6546","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":"2026-05-18T02:39:23Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"N3CEwsSwJIKCO8DCJsyHhjYeSn202vsfCUhZKRqFcLZ7Dr8J3Zw6M9FAivsVU/0Qli70wb9+bSl8M6b0iu+3BQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-26T21:41:18.401277Z"},"content_sha256":"3c493df7ef28197941f8b4debd51ae7df77f3ef8c3052d51c8716621e2bb3289","schema_version":"1.0","event_id":"sha256:3c493df7ef28197941f8b4debd51ae7df77f3ef8c3052d51c8716621e2bb3289"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2014:2MK5SVKY5MY5MG4P64FIWYRB6W","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Invariant versus classical quartet inference when evolution is heterogeneous across sites and lineages","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.PE","authors_text":"Jes\\'us Fern\\'andez-S\\'anchez, Marta Casanellas","submitted_at":"2014-05-26T11:37:34Z","abstract_excerpt":"One reason why classical phylogenetic reconstruction methods fail to correctly infer the underlying topology is because they assume oversimplified models. In this paper we propose a topology reconstruction method consistent with the most general Markov model of nucleotide substitution, which can also deal with data coming from mixtures on the same topology. It is based on an idea of Eriksson on using phylogenetic invariants and provides a system of weights that can be used as input of quartet-based methods. We study its performance on real data and on a wide range of simulated 4-taxon data (bo"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1405.6546","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":"2026-05-18T02:39:23Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"ydG4f6neVMXi+Nf8pvraXDOmgw5zK5otrRrvMxFJeOQ5ydADVMzHZz1up8dvmBfEZbeo0xAQ45GxG9nisZ+6BA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-26T21:41:18.401650Z"},"content_sha256":"bba6045684a0cc572c756e2d903bf4333955747b83c61b77e6347950311d3a69","schema_version":"1.0","event_id":"sha256:bba6045684a0cc572c756e2d903bf4333955747b83c61b77e6347950311d3a69"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/2MK5SVKY5MY5MG4P64FIWYRB6W/bundle.json","state_url":"https://pith.science/pith/2MK5SVKY5MY5MG4P64FIWYRB6W/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/2MK5SVKY5MY5MG4P64FIWYRB6W/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":"2026-05-26T21:41:18Z","links":{"resolver":"https://pith.science/pith/2MK5SVKY5MY5MG4P64FIWYRB6W","bundle":"https://pith.science/pith/2MK5SVKY5MY5MG4P64FIWYRB6W/bundle.json","state":"https://pith.science/pith/2MK5SVKY5MY5MG4P64FIWYRB6W/state.json","well_known_bundle":"https://pith.science/.well-known/pith/2MK5SVKY5MY5MG4P64FIWYRB6W/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2014:2MK5SVKY5MY5MG4P64FIWYRB6W","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":"818f2b99605323ffcda1608fa61aee7ee7cdea9f2ac75b26dae34ad1724de722","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2014-05-26T11:37:34Z","title_canon_sha256":"0e4c8751072afc94b69efab17202506762c62d6c72498f5ad64de596ba0ae258"},"schema_version":"1.0","source":{"id":"1405.6546","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1405.6546","created_at":"2026-05-18T02:39:23Z"},{"alias_kind":"arxiv_version","alias_value":"1405.6546v2","created_at":"2026-05-18T02:39:23Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1405.6546","created_at":"2026-05-18T02:39:23Z"},{"alias_kind":"pith_short_12","alias_value":"2MK5SVKY5MY5","created_at":"2026-05-18T12:28:11Z"},{"alias_kind":"pith_short_16","alias_value":"2MK5SVKY5MY5MG4P","created_at":"2026-05-18T12:28:11Z"},{"alias_kind":"pith_short_8","alias_value":"2MK5SVKY","created_at":"2026-05-18T12:28:11Z"}],"graph_snapshots":[{"event_id":"sha256:bba6045684a0cc572c756e2d903bf4333955747b83c61b77e6347950311d3a69","target":"graph","created_at":"2026-05-18T02:39:23Z","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":"One reason why classical phylogenetic reconstruction methods fail to correctly infer the underlying topology is because they assume oversimplified models. In this paper we propose a topology reconstruction method consistent with the most general Markov model of nucleotide substitution, which can also deal with data coming from mixtures on the same topology. It is based on an idea of Eriksson on using phylogenetic invariants and provides a system of weights that can be used as input of quartet-based methods. We study its performance on real data and on a wide range of simulated 4-taxon data (bo","authors_text":"Jes\\'us Fern\\'andez-S\\'anchez, Marta Casanellas","cross_cats":[],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2014-05-26T11:37:34Z","title":"Invariant versus classical quartet inference when evolution is heterogeneous across sites and lineages"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1405.6546","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":"sha256:3c493df7ef28197941f8b4debd51ae7df77f3ef8c3052d51c8716621e2bb3289","target":"record","created_at":"2026-05-18T02:39:23Z","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":"818f2b99605323ffcda1608fa61aee7ee7cdea9f2ac75b26dae34ad1724de722","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2014-05-26T11:37:34Z","title_canon_sha256":"0e4c8751072afc94b69efab17202506762c62d6c72498f5ad64de596ba0ae258"},"schema_version":"1.0","source":{"id":"1405.6546","kind":"arxiv","version":2}},"canonical_sha256":"d315d95558eb31d61b8ff70a8b6221f59f4e61dd10f36c11b3d614058a0259bd","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"d315d95558eb31d61b8ff70a8b6221f59f4e61dd10f36c11b3d614058a0259bd","first_computed_at":"2026-05-18T02:39:23.678212Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T02:39:23.678212Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"u3DvchhHrH5Z7Tp9T5ZP8DwyPfvCxJPFiIRJyCc6WAc+KU9ysOkbo/S0wH9eJbbhhz1GnEmHuBln83d5o3uABA==","signature_status":"signed_v1","signed_at":"2026-05-18T02:39:23.678563Z","signed_message":"canonical_sha256_bytes"},"source_id":"1405.6546","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:3c493df7ef28197941f8b4debd51ae7df77f3ef8c3052d51c8716621e2bb3289","sha256:bba6045684a0cc572c756e2d903bf4333955747b83c61b77e6347950311d3a69"],"state_sha256":"5c92a02ce807600b0a62221e42785423a7ce386ab6b417bbc3d61bd2fb7482ad"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"0n2UbR82dFYAJDc5jqr1v/NGe3R/FiWj+MUX8iuvWf2ZSLojNi3WQeNaMxOgJrUrxEK63vMeW6TSLLlFCagsBQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-26T21:41:18.403888Z","bundle_sha256":"0a341d7b0a6fc8a50caa15269920903748d83c1d58b3c421a9814293e39b9fa3"}}