Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28558722", "kind": "science-record", "revision": 4, "content_hash": "sha256:8d92af5c0061283cf819dbe6197188f7cd95da3d1742198a40ba4dac28af22a7", "created_at": "2026-11-01T15:40:26Z", "updated_at": "2026-11-01T21:20:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms.", "doi": "10.1186/s12862-017-0973-4", "pmid": "28558722", "authors": ["Frank E Anderson", "Bronwyn W Williams", "Kevin M Horn", "Christer Erséus", "Kenneth M Halanych", "Scott R Santos", "Samuel W James"], "journal": "BMC evolutionary biology", "year": 2017, "abstract": "BACKGROUND: Earthworms (Crassiclitellata) are a diverse group of annelids of substantial ecological and economic importance. Earthworms are primarily terrestrial infaunal animals, and as such are probably rather poor natural dispersers. Therefore, the near global distribution of earthworms reflects an old and likely complex evolutionary history. Despite a long-standing interest in Crassiclitellata, relationships among and within major clades remain unresolved.\nMETHODS: In this study, we evaluate crassiclitellate phylogenetic relationships using 38 new transcriptomes in combination with publicly available transcriptome data. Our data include representatives of nearly all extant earthworm families and a representative of Moniligastridae, another terrestrial annelid group thought to be closely related to Crassiclitellata. We use a series of differentially filtered data matrices and analyses to examine the effects of data partitioning, missing data, compositional and branch-length heterogeneity, and outgroup inclusion.\nRESULTS AND DISCUSSION: We recover a consistent, strongly supported ingroup topology irrespective of differences in methodology. The topology supports two major earthworm clades, each of which consists of a Northern Hemisphere subclade and a Southern Hemisphere subclade. Divergence time analysis results are concordant with the hypothesis that these north-south splits are the result of the breakup of the supercontinent Pangaea.\nCONCLUSIONS: These results support several recently proposed revisions to the classical understanding of earthworm phylogeny, reveal two major clades that seem to reflect Pangaean distributions, and raise new questions about earthworm evolutionary relationships.", "claims": [{"id": "claim-method", "statement": "both a SOWH test and a Bayesian topology test strongly reject Dichogaster monophyly.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28558722", "locator": "sections[18] \"Crassiclitellata systematics\" paragraph 6", "quote": "both a SOWH test and a Bayesian topology test strongly reject Dichogaster monophyly."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and analyzed in this study, custom scripts used in the phylogenomics pipeline, and phylogenetic trees are available in the Dryad repository (http://datadryad.org/resource/doi:10.5061/dryad.n7n71).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28558722", "locator": "sections[25] \"Availability of data and materials\" paragraph 2", "quote": "The datasets generated during and analyzed in this study, custom scripts used in the phylogenomics pipeline, and phylogenetic trees are available in the Dryad repository (http://datadryad.org/resource/doi:10.5061/dryad.n7n71)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study recovered a consistent, strongly supported earthworm topology irrespective of methodology, using four gene sets and Bayesian CAT-GTR analyses, while its newly generated transcriptomes are available through NCBI’s Sequence Read Archive under BioProject PRJNA362879 and its two public datasets are identified by PRJNA196484 and PRJDB3115.", "kind": "quantitative", "target": {"value": 75.0, "unit": "per cent", "tolerance": null, "source": "Bayesian analyses under the CAT-GTR model were attempted for the unfiltered 25, 50, and 75% data sets and the two filtered “no ?Haplotaxidae sp.” 75% matrices in PhyloBayes"}, "evidence": [{"asset": "source:pmid:28558722", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We recover a consistent, strongly supported ingroup topology irrespective of differences in methodology."}, {"asset": "source:pmid:28558722", "locator": "sections[12] \"Results\" paragraph 2", "quote": "Four gene sets from these transcriptomes were analyzed, reflecting different levels of gene occupancy."}, {"asset": "source:pmid:28558722", "locator": "sections[13] \"Ingroup relationships\" paragraph 4", "quote": "Bayesian analyses under the CAT-GTR model were attempted for the unfiltered 25, 50, and 75% data sets and the two filtered “no ?Haplotaxidae sp.” 75% matrices in PhyloBayes"}, {"asset": "source:pmid:28558722", "locator": "sections[12] \"Results\" paragraph 2", "quote": "Transcriptomes for thirty-one crassiclitellates, one moniligastrid, and six outgroup taxa were generated as part of this study (Table 1; Additional file 1: Figure S1) and are available from the SRA at NCBI under BioProject accession number PRJNA362879."}, {"asset": "source:pmid:28558722", "locator": "sections[12] \"Results\" paragraph 2", "quote": "We added publicly available transcriptome data for two additional crassiclitellates—Hormogaster elisae (PRJNA196484) and Eisenia andrei (PRJDB3115)—for a total of forty transcriptomes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study recovered a consistent, strongly supported earthworm topology irrespective of methodology, using four gene sets and Bayesian CAT-GTR analyses, while its newly generated transcriptomes are available through NCBI’s Sequence Read Archive under BioProject PRJNA362879 and its two public datasets are identified by PRJNA196484 and PRJDB3115.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:28558722"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_unresolved", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PRJDB3115"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PRJDB3115"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_unresolved"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28558722", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12862-017-0973-4", "sha256": "sha256:ef9b00caa6c1999ca4fce179db0279b1ee0ea34d1b045a02366c33ed0f9d9b6f", "bytes": 77517, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12862-017-0973-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5450073", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PRJDB3115", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJDB3115", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJDB3115", "version": null, "note": "The datasets generated during and analyzed in this study, custom scripts used in the phylogenomics pipeline, and phylogenetic trees are available in the Dryad repository (http://datadryad.org/resource/doi:10.5061/dryad.n7n71).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during and analyzed in this study, custom scripts used in the phylogenomics pipeline, and phylogenetic trees are available in the Dryad repository (http://datadryad.org/resource/doi:10.5061/dryad.n7n71).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-10-31T18:35:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PRJNA196484", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA196484", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA196484", "version": null, "note": "The datasets generated during and analyzed in this study, custom scripts used in the phylogenomics pipeline, and phylogenetic trees are available in the Dryad repository (http://datadryad.org/resource/doi:10.5061/dryad.n7n71).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during and analyzed in this study, custom scripts used in the phylogenomics pipeline, and phylogenetic trees are available in the Dryad repository (http://datadryad.org/resource/doi:10.5061/dryad.n7n71).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-10-31T18:35:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PRJNA362879", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA362879", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA362879", "version": null, "note": "The datasets generated during and analyzed in this study, custom scripts used in the phylogenomics pipeline, and phylogenetic trees are available in the Dryad repository (http://datadryad.org/resource/doi:10.5061/dryad.n7n71).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during and analyzed in this study, custom scripts used in the phylogenomics pipeline, and phylogenetic trees are available in the Dryad repository (http://datadryad.org/resource/doi:10.5061/dryad.n7n71).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-10-31T18:35:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:28558722:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bd7477c9a8c556481899a38c58ee37aa2505803ca5098cc7fa8c3ec1d480e78b", "bytes": 6485, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Collection locality, museum location of voucher specimen, museum catalog number, SRA project number, number of Illumina reads, number of Trinity contigs and number of HaMSTr ortholog groups represented for each of the thirty-seven transcriptomes generated in this study", "structure": {"pmcid": "PMC5450073", "section_index": 3, "section_title": "Taxon sampling", "row_count": 42, "column_count": 5}, "table": {"label": "Table 1", "caption": "Collection locality, museum location of voucher specimen, museum catalog number, SRA project number, number of Illumina reads, number of Trinity contigs and number of HaMSTr ortholog groups represented for each of the thirty-seven transcriptomes generated in this study", "rows": [["Taxon", "Locality", "Museum", "# Contigs", "# HaMStR Orthologs"], ["Acanthodrilidae sp.", "Argentina, Tierra del Fuego, Ushuaia (coll. E. Lapied)", "NCSM 27264", "181228", "1140"], ["Alma sp.Almidae", "Gabon, edge of Lac Vembo, Gamba complex, (coll. S James 18 May 2008)", "NCSM 27265", "110015", "558"], ["Avelona ligra Lumbricidae", "France, Jargeau, Loiret Department, (coll. M. Koken)", "MNHN XXXXXX", "182509", "1173"], ["Criodrilus lacuum Criodrilidae", "Hungary (coll. C. Csuzdi)", "NCSM 27266", "119084", "934"], ["Dendrobaena hortensis Lumbricidae", "Sweden, Södermanland, Vingåker, Valltrand, indoor compost, 59.0864 N, 16.0544 E (coll. E. Boräng, 1 Jan 2012)", "SMNH 161291in EtOH CE13942", "179981", "1180"], ["Dichogaster sp. (green tree worm) Benhamiidae", "Brazil, Amazonas, near Manaus, Reserva Campina (coll. S. James, S. Coral, 2 Feb 2012)", "NCSM 27267", "116065", "1140"], ["Dichogaster sp.Benhamiidae", "France, Guadeloupe, Basse Terre (colls. S. James, F. Gamiette Feb 2013)", "NCSM 27268", "106438", "1152"], ["Dichogaster saliens Benhamiidae", "France, Guadeloupe, Chutes Carbet, Basse Terre (colls. S. James, F. Gamiette Feb 2013)", "NCSM 00000", "98665", "999"], ["Drawida sp.Moniligastridae", "USA, Tonganoxie, Kansas (coll. S. James? May 2013)", "NCSM 27269", "159219", "1081"], ["Eisenia andrei Lumbricidae", "Unknown", "---", "137631", "1217"], ["Eisenia andrei Lumbricidae", "Sweden, Södermanland, Vingåker, Valltrand, indoor compost, 59.0864 N, 16.0544 E (coll. E. Boräng, 1 Jan 2012)", "SMNH 161292in EtOH CE13945", "168836", "1191"], ["Eudrilus eugeniae Eudrilidae", "Brazil, Sao Paulo, bait shop (coll. S. James, 7 Nov 2010)", "NCSM 27270", "85990", "1008"], ["Fimoscolex sp.Glossoscolecidae", "Brazil, Assistencia, São Paulo, Fazenda Sta Rosa (coll. S. James, 9 Nov 2012)", "NCSM 27271", "95465", "705"], ["Gatesona chaetophora Lumbricidae", "France, Aveyron, L'Hospitalet du Larzac (coll. S James, 1 Mar 2011)", "NCSM 27272", "104334", "961"], ["Geogenia benhami Microchaetidae", "South Africa, Western Cape, Stellenbosch (colls S. James, D. Plisko, 27 Aug 2011)", "NCSM 27273", "84303", "932"], ["Glossodrilus sp.Glossoscolecidae", "Brazil, Amazonas, near Manaus, Reserva Ducke (colls. S. James, S. Coral 1 Feb 2012)", "NCSM 27274", "122993", "1053"], ["Glossoscolex sp.Glossoscolecidae", "Brazil, Parana, Campina Grande do Sul, Caratuva peak trail (coll. S. James, M. Bartz, 17 Oct 2010)", "NCSM 27275", "58411", "722"], ["Hemigastrodrilus monicae Hormogastridae", "France, Aveyron, L'Hospitalet du Larzac (coll. S James, 1 Mar 2011)", "NCSM 27276", "103338", "1098"], ["Hormogaster elisae Hormogastridae", "SRA PRJNA196484*,Spain, El Molar, 40°44′22.9″N, 3°33′53.1″W", "---", "459282", "1234"], ["Kerriona sp. Graciosa1Ocnerodrilidae", "Brazil, Parana, Graciosa Road (coll. S. James, 4 Nov 2010)", "NCSM 27277", "104982", "1010"], ["Komarekiona eatoni Komarekionidae", "USA, Sideling Hill Wildlife Mgmt. Area, Washington County, Maryland. (colls. S. James, M. Callaham, May 2013)", "NCSM 27278", "83743", "1151"], ["Kynotus pittarelli Kynotidae", "Madagascar, Antsirabe, 19°46'38.60\"S 47°06'41.69\"E", "NCSM 00000", "108836", "1073"], ["Lutodrilus multivesiculatus Lutodrilidae", "USA, Louisiana, Washington Parish (coll S. James, M. Callaham, M. Damoff, C. Erseus, 17 Jan 2011)", "NCSM 00000", "57341", "1049"], ["Maoridrilus wilkini Acanthodrilidae", "New Zealand, Kelly’s Creek (coll. T. Buckley)", "NCSM 27279", "80910", "861"], ["Microchaetidae sp.", "South Africa, Western Cape, Tokai Swamp (colls. S. James and D. Plisko, 29 Aug 2011)", "NCSM 27280", "194638", "1053"], ["Microchaetus sp.Microchaetidae", "South Africa, Northern Cape, Niewwoudtville (colls. S. James, D. Plisko 5 Sep 2011)", "NCSM 27281", "125494", "1093"], ["Parachilota sp.Acanthodrilidae", "South Africa, Western Cape, Table Mountain (coll. James, Meassey, Plisko, 26 Aug 2011)", "NCSM 27282", "102971", "1074"], ["Place Kabary 2 sp.Acanthodrilidae", "Madagascar, Place Kabary, Antsiranana, 12°16'58.27''S 49°17'25.94''E", "NCSM 00000", "146018", "1157"], ["Pontodrilus litoralis Megascolecidae", "USA, Cedar Point, Alabama (colls. S. James, C. Erséus 17 January 2011)", "NCSM 00000", "90268", "1189"], ["Rhinodrilus priollii Rhinodrilidae", "Brazil, Amazonas, Reserve Ducke (colls. S. James, S. Coral, 3 Feb 2012)", "NCSM 00000", "87158", "1102"], ["Scherotheca savignyi Lumbricidae", "France, Midi-Pyrénées, Ariège, Malegoude (coll. S. James, 2 Mar 2011)", "NCSM 27283", "113157", "1041"], ["Sparganophilus sp.Sparganophilidae", "USA, Iowa, Des Moines River, at Douds (coll. S. James 12 May 2012)", "NCSM 27284", "123905", "1199"], ["Urobenus brasiliensis Rhinodrilidae", "Brazil, Rio Grande do Sul, Santo Cristo (coll. G. Steffen 09 Sep 2009)", "NCSM 27285", "55709", "890"], ["Vignysa popi Hormogastridae", "France, Aveyron, Montpellier (colls. S. James, M. Bouche, 1 Mar 2011)", "NCSM 27286", "93260", "779"], ["Outgroups"], ["Delaya leruthi Haplotaxidae", "France, Midi-Pyrénées, Ariège, Cazavet, L'Estelas Cave, in water, 43.000 N, 1.010 E (coll. M.C. des Chatelliers, P. Martin & N. Giani, 24 May 2011) (topotype)", "SMNH 161293in EtOH CE13924", "118020", "1067"], ["Pelodrilus sp.Haplotaxidae", "Western Australia, 25.5 km S of Busselton, Rapids Conservation Park, Margaret River (coll. C. Erséus, 16 Sep 2012)", "WAM V9004", "100864", "1129"], ["Haplotaxis gordioides Haplotaxidae", "Sweden, Västergötland, Göteborg, seeping groundwater at Göteborg Botanical Garden (Vitsippsdalen), 57.6813 N, 11.9562 E (C. Erséus & A. Achurra, 29 Mar 2011)", "SMNH 161294 in EtOH CE11200", "53878", "855"], ["?Haplotaxidae sp.", "Brazil, Amazonas, Reserva Ducke (colls. S. James, S. Coral, 3 Feb 2012) (topotype)", "NCSM 000000 in EtOH CE14372", "93548", "1053"], ["Lumbriculus variegatus Lumbriculidae", "Sweden, Västergötland, Göteborg, Guldheden, spring S of Dr Fries Torg, 57.6827 N, 11.9707 E (coll. M. Svensson, 8 Nov 2011)", "SMNH 161295 slide CE13679", "109949", "985"], ["Propappus volki Propappidae", "Sweden, Blekinge, Ronneby, Väby, Bräkneån River, sand in rapids, 56.1792 N, 15.1052 E (C. Erséus, B. Williams & S. Martinsson, 31 May 2013) (topotype)", "SMNH 161296 slide CE18375", "131574", "1140"]], "row_count": 42, "column_count": 5, "numeric_cells": 153, "header_rows": 1, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:28558722:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:470085a87fd890d0731356f1605c5fb5b1aa3326f70e2d0a07f7cd9d13c79e89", "bytes": 1102, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#Tab2", "version": null, "note": "Characteristics of all data matrices analyzed in this study", "structure": {"pmcid": "PMC5450073", "section_index": 7, "section_title": "Long-branch effects and compositional heterogeneity", "row_count": 17, "column_count": 5}, "table": {"label": "Table 2", "caption": "Characteristics of all data matrices analyzed in this study", "rows": [["Data Set", "# Loci", "# Characters", "# Parsimony-informative Characters", "% Missing"], ["25%"], ["Unpartitioned/partitioned original data", "766", "361,365", "64,892", "77.27"], ["TreSpEx + BaCoCa filtered", "543", "251,614", "40,509", "77.56"], ["Deleted outgroups", "727", "337,650", "59,520", "76.97"], ["50%"], ["Unpartitioned/partitioned original data", "162", "58,085", "18,515", "55.57"], ["TreSpEx + BaCoCa filtered", "131", "46,468", "15,173", "53.29"], ["Deleted outgroups", "206", "78,060", "22,753", "55.34"], ["75%"], ["Unpartitioned/partitioned original data", "58", "16,458", "6596", "35.21"], ["TreSpEx + BaCoCa filtered", "49", "14,075", "5785", "34.99"], ["Deleted outgroups", "92", "28,097", "9844", "35.00"], ["No ?Haplotaxidae sp., all sites", "56", "16,541", "6879", "33.45"], ["No ?Haplotaxidae sp., no gappy sites", "56", "13,168", "6443", "18.62"], ["100%"], ["Unpartitioned/partitioned original data", "7", "1997", "805", "20.21"]], "row_count": 17, "column_count": 5, "numeric_cells": 52, "header_rows": 1, "locator": "section[7]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:28558722:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1a6c5b1e05b963435ceceb63490461842ad10a2b69e6292f644c39f91798179e", "bytes": 5103, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab3", "version": null, "note": "Percent missing data per taxon across all matrices analyzed in this study, calculated using TREE-PUZZLE 5.3", "structure": {"pmcid": "PMC5450073", "section_index": 13, "section_title": "Ingroup relationships", "row_count": 42, "column_count": 13}, "table": {"label": "Table 3", "caption": "Percent missing data per taxon across all matrices analyzed in this study, calculated using TREE-PUZZLE 5.3", "rows": [["", "Matrix"], ["Taxon", "25 U", "25 T", "25D", "50 U", "50 T", "50D", "75 U", "75 T", "75D", "75H", "75HG", "100 U"], ["Acanthodrilidae sp.", "71.28", "70.48", "71.28", "49.23", "48.86", "49.23", "24.94", "48.86", "24.94", "25.32", "8.29", "16.62"], ["Alma sp.", "93.52", "93.39", "93.52", "84.99", "84.61", "84.99", "71.86", "84.61", "71.86", "73.99", "68.13", "44.37"], ["Avelona ligra", "70.46", "67.95", "70.46", "47.68", "42.17", "47.68", "26.91", "42.17", "26.91", "23.52", "6.48", "14.97"], ["Criodrilus lacuum", "84.72", "84.45", "84.72", "62.46", "57.70", "62.46", "44.00", "57.70", "44.00", "44.02", "31.04", "20.93"], ["Delaya leruthi", "78.74", "82.55", "78.74", "52.10", "50.12", "52.10", "28.27", "50.12", "28.27", "29.27", "14.19", "16.88"], ["Dendrobaena hortensis", "70.35", "69.16", "70.35", "44.63", "39.30", "44.63", "23.86", "39.30", "23.86", "18.36", "2.59", "12.52"], ["Dichogaster sp. (green tree worm)", "71.97", "70.21", "71.97", "54.66", "53.56", "54.66", "29.06", "53.56", "29.06", "24.36", "7.03", "17.93"], ["Dichogaster sp.", "69.76", "67.77", "69.76", "50.28", "49.08", "50.28", "27.37", "49.08", "27.37", "24.48", "7.49", "16.07"], ["Dichogaster saliens", "80.45", "78.88", "80.45", "63.13", "62.73", "63.13", "34.41", "62.73", "34.41", "27.56", "11.44", "17.63"], ["Drawida sp.", "78.41", "80.37", "78.41", "57.60", "55.64", "57.60", "39.68", "55.64", "39.68", "39.08", "25.80", "15.82"], ["Eisenia andrei", "62.78", "62.04", "62.78", "39.83", "37.24", "39.83", "25.17", "37.24", "25.17", "23.14", "5.07", "16.07"], ["Eisenia andrei SRA", "69.12", "66.93", "69.12", "43.18", "38.61", "43.18", "25.96", "38.61", "25.96", "21.76", "4.33", "19.93"], ["Eudrilus eugeniae", "79.96", "80.02", "79.96", "58.95", "57.36", "58.95", "31.73", "57.36", "31.73", "31.96", "15.98", "23.99"], ["Fimoscolex sp.", "88.37", "87.75", "88.37", "76.41", "75.80", "76.41", "56.96", "75.80", "56.96", "61.63", "52.16", "31.90"], ["Gatesona chaetophora", "79.32", "78.45", "79.32", "54.76", "49.42", "54.76", "27.69", "49.42", "27.69", "23.66", "7.19", "15.42"], ["Geogenia benhami", "83.35", "84.86", "83.35", "62.53", "57.10", "62.53", "38.68", "57.10", "38.68", "41.06", "27.62", "19.83"], ["Glossodrilus sp.", "76.14", "75.65", "76.14", "54.69", "53.03", "54.69", "33.19", "53.03", "33.19", "31.04", "14.94", "18.13"], ["Glossoscolex sp.", "88.17", "87.55", "88.17", "73.82", "73.67", "73.82", "65.22", "73.67", "65.22", "59.75", "49.91", "33.55"], ["Haplotaxis gordioides", "86.63", "89.16", "86.63", "69.18", "69.65", "69.18", "45.94", "69.65", "45.94", "42.19", "30.48", "21.58"], ["?Haplotaxidae sp.", "81.18", "86.38", "-----", "55.95", "54.58", "-----", "31.37", "54.58", "-----", "22.63", "-----", "-----"], ["Hemigastrodrilus monicae", "74.66", "73.40", "74.66", "47.84", "42.08", "47.84", "28.08", "42.08", "28.08", "22.91", "6.14", "14.72"], ["Hormogaster elisae", "61.55", "61.14", "61.55", "40.13", "35.46", "40.13", "22.07", "35.46", "22.07", "18.66", "1.57", "15.17"], ["Kerriona sp. Graciosa1", "79.62", "77.63", "79.62", "68.83", "69.86", "68.83", "46.30", "69.86", "46.30", "44.66", "32.04", "16.78"], ["Komarekiona eatoni", "75.54", "78.33", "75.54", "49.28", "46.41", "49.28", "30.93", "46.41", "30.93", "29.50", "14.06", "19.33"], ["Kynotus pittarelli", "78.34", "80.98", "78.34", "48.40", "44.51", "48.40", "31.88", "44.51", "31.88", "33.44", "19.32", "20.93"], ["Lumbriculus variegatus", "84.69", "86.95", "-----", "62.91", "63.29", "-----", "44.54", "63.29", "-----", "45.40", "34.07", "33.20"], ["Lutodrilus multivesiculatus", "78.23", "77.77", "78.23", "50.82", "47.41", "50.82", "27.34", "47.41", "27.34", "23.54", "6.18", "18.38"], ["Maoridrilus wilkini", "86.86", "86.10", "86.86", "75.28", "75.10", "75.28", "60.26", "75.10", "60.26", "54.11", "43.85", "35.90"], ["Microchaetidae sp.", "79.37", "80.11", "79.37", "48.98", "43.78", "48.98", "28.13", "43.78", "28.13", "24.11", "7.76", "15.32"], ["Microchaetus sp.", "74.62", "75.20", "74.62", "45.96", "42.02", "45.96", "27.69", "42.02", "27.69", "26.44", "9.31", "14.77"], ["Parachilota sp.", "73.61", "72.09", "73.61", "59.08", "58.99", "59.08", "42.15", "58.99", "42.15", "32.77", "17.19", "25.94"], ["Pelodrilus sp.", "75.31", "79.76", "75.31", "50.98", "50.45", "50.98", "32.80", "50.45", "32.80", "35.99", "21.16", "16.93"], ["Place Kabary 2 sp.", "70.17", "68.40", "70.17", "49.41", "49.91", "49.41", "23.89", "49.91", "23.89", "23.47", "6.43", "18.58"], ["Pontodrilus litoralis", "66.37", "66.34", "66.37", "46.87", "46.53", "46.87", "26.84", "46.53", "26.84", "19.66", "2.16", "15.92"], ["Propappus volki", "77.03", "81.59", "-----", "56.39", "57.47", "-----", "36.90", "57.47", "-----", "36.68", "22.49", "15.02"], ["Rhinodrilus priollii", "75.00", "76.10", "75.00", "45.59", "43.06", "45.59", "24.06", "43.06", "24.06", "26.27", "9.64", "16.17"], ["Scherotheca savignyi", "76.55", "75.20", "76.55", "54.39", "49.26", "54.39", "30.39", "49.26", "30.39", "28.99", "12.94", "14.67"], ["Sparganophilus sp.", "68.43", "71.47", "68.43", "36.25", "32.65", "36.25", "21.49", "32.65", "21.49", "23.05", "7.09", "13.37"], ["Urobenus brasiliensis", "84.07", "85.13", "84.07", "59.66", "56.92", "59.66", "39.04", "56.92", "39.04", "37.79", "23.41", "24.69"], ["Vignysa popi", "86.01", "84.87", "86.01", "69.72", "66.08", "69.72", "50.88", "66.08", "50.88", "51.03", "39.39", "21.53"]], "row_count": 42, "column_count": 13, "numeric_cells": 482, "header_rows": 2, "locator": "section[13]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:28558722:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:45e6e960217f79fbd7b5713c9ccacea162d7d1d758d91a36ce46e12a97704915", "bytes": 903, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#Tab4", "version": null, "note": "PhyloBayes divergence time estimates (mean ± standard error) in millions of years ago for three data matrices for two key nodes in the earthworm radiation—the node separating Kynotus from Sparganophilus + Komarekiona (node 1, Fig. 1) and the node separating the Northern Hemisphere clade comprising Lutodrilus and Lumbricoidea and the clade comprising Southern Hemisphere representatives of several families (node 2, Fig. 1)", "structure": {"pmcid": "PMC5450073", "section_index": 16, "section_title": "Divergence times", "row_count": 4, "column_count": 3}, "table": {"label": "Table 4", "caption": "PhyloBayes divergence time estimates (mean ± standard error) in millions of years ago for three data matrices for two key nodes in the earthworm radiation—the node separating Kynotus from Sparganophilus + Komarekiona (node 1, Fig. 1) and the node separating the Northern Hemisphere clade comprising Lutodrilus and Lumbricoidea and the clade comprising Southern Hemisphere representatives of several families (node 2, Fig. 1)", "rows": [["Data Matrix", "Node 1 (mean ± SE)", "Node 2 (mean ± SE)"], ["75% with ?Haplotaxidae sp., unfiltered", "164.527 ± 22.2868", "161.104 ± 21.0178"], ["no ?Haplotaxidae sp., filtered, all sites", "186.1521 ± 23.2339", "186.0185 ± 22.18"], ["no ?Haplotaxidae sp., filtered, no >50% gaps", "178.1059 ± 21.9198", "177.6679 ± 21.1014"]], "row_count": 4, "column_count": 3, "numeric_cells": 10, "header_rows": 1, "locator": "section[16]/table-wrap[1]#Tab4"}}], "gaps": ["asset:data:geo:PRJDB3115 not downloaded", "asset:data:geo:PRJDB3115 licence not read", "asset:data:geo:PRJNA196484 not downloaded", "asset:data:geo:PRJNA196484 licence not read", "asset:data:geo:PRJNA362879 not downloaded", "asset:data:geo:PRJNA362879 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "SOWH test and Bayesian topology test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "both a SOWH test and a Bayesian topology test strongly reject Dichogaster monophyly."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 75.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (SOWH test and Bayesian topology test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["PRJNA362879", "PRJNA196484", "PRJDB3115"], "resolved_accessions": [], "statements": ["The datasets generated during and analyzed in this study, custom scripts used in the phylogenomics pipeline, and phylogenetic trees are available in the Dryad repository (http://datadryad.org/resource/doi:10.5061/dryad.n7n71)."], "basis": "The paper names PRJNA362879, PRJNA196484, PRJDB3115, but the accession does not resolve in the repository (not_in_ncbi_bioproject, not_in_ncbi_bioproject, not_in_ncbi_bioproject), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:28558722", "data:geo:PRJDB3115", "asset:table:pmid:28558722:1", "asset:table:pmid:28558722:2", "asset:table:pmid:28558722:3", "asset:table:pmid:28558722:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PRJDB3115"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:31:12Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 161864, "completion_tokens": 5787, "cached_tokens": 1824}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:28558722", "type": "paper", "label": "pmid:28558722"}, {"id": "source:pmid:28558722", "type": "manuscript", "label": "PMID 28558722 full text"}, {"id": "data:geo:PRJDB3115", "type": "dataset", "label": "GEO PRJDB3115"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28558722", "type": "paper", "label": "pmid:28558722"}, {"id": "source:pmid:28558722", "type": "manuscript", "label": "PMID 28558722 full text"}, {"id": "data:geo:PRJDB3115", "type": "dataset", "label": "GEO PRJDB3115"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28558722", "type": "extraction", "used": ["source:pmid:28558722"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PRJDB3115", "type": "accession_resolution", "used": ["data:geo:PRJDB3115"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:28558722", "parent_hash": "sha256:e2fb6a9f077d8ea006ce61eebd4877ac2cf899c26404e0a84bb35a83e7faff60", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PRJDB3115 licence not read", "asset:data:geo:PRJDB3115 not downloaded", "asset:data:geo:PRJNA196484 licence not read", "asset:data:geo:PRJNA196484 not downloaded", "asset:data:geo:PRJNA362879 licence not read", "asset:data:geo:PRJNA362879 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_unresolved"]}