{"id":"https://openalex.org/W4393673906","doi":"https://doi.org/10.5281/zenodo.600659","title":"Signal, Uncertainty, And Conflict In Phylogenomic Data For A Diverse Lineage Of Microbial Eukaryotes (Diatoms, Bacillariophyta)","display_name":"Signal, Uncertainty, And Conflict In Phylogenomic Data For A Diverse Lineage Of Microbial Eukaryotes (Diatoms, Bacillariophyta)","publication_year":2017,"publication_date":"2017-02-28","ids":{"openalex":"https://openalex.org/W4393673906","doi":"https://doi.org/10.5281/zenodo.600659"},"language":"en","primary_location":{"id":"pmh:oai:zenodo.org:344519","doi":null,"is_oa":true,"landing_page_url":"https://zenodo.org/record/344519","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"dataset"},"volume":null,"type":"dataset","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://zenodo.org/record/344519","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102925470","display_name":"Matthew Parks","orcid":"https://orcid.org/0000-0002-9366-7001","observed_orcids":["https://orcid.org/0000-0002-9366-7001"]},"institutions":[{"id":"https://openalex.org/I4387152733","display_name":"Chicago Botanic Garden","ror":"https://ror.org/03js09m24","country_code":"US","type":"archive","lineage":["https://openalex.org/I4387152733"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Parks, Matthew B.","raw_affiliation_strings":["Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL 60022"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL 60022","institution_ids":["https://openalex.org/I4387152733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079387467","display_name":"Norman J. Wickett","orcid":"https://orcid.org/0000-0003-0944-1956","observed_orcids":["https://orcid.org/0000-0003-0944-1956"]},"institutions":[{"id":"https://openalex.org/I4387152733","display_name":"Chicago Botanic Garden","ror":"https://ror.org/03js09m24","country_code":"US","type":"archive","lineage":["https://openalex.org/I4387152733"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wickett, Norman J.","raw_affiliation_strings":["Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL 60022"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL 60022","institution_ids":["https://openalex.org/I4387152733"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054075380","display_name":"Andrew James Alverson","orcid":"https://orcid.org/0000-0003-1241-2654","observed_orcids":["https://orcid.org/0000-0003-1241-2654"]},"institutions":[{"id":"https://openalex.org/I78715868","display_name":"University of Arkansas at Fayetteville","ror":"https://ror.org/05jbt9m15","country_code":"US","type":"education","lineage":["https://openalex.org/I78715868"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alverson, Andrew J.","raw_affiliation_strings":["Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, SCEN 601, Fayetteville, AR 72701"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, SCEN 601, Fayetteville, AR 72701","institution_ids":["https://openalex.org/I78715868"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11879","display_name":"Protist diversity and phylogeny","score":0.9911999702453613,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11879","display_name":"Protist diversity and phylogeny","score":0.9911999702453613,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.007000000216066837,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12012","display_name":"Diatoms and Algae Research","score":0.00039999998989515007,"subfield":{"id":"https://openalex.org/subfields/2502","display_name":"Biomaterials"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/diatoms","display_name":"diatoms","score":0.9980000257492065},{"id":"https://openalex.org/keywords/phylogenomics","display_name":"phylogenomics","score":0.9580000042915344},{"id":"https://openalex.org/keywords/phylogenetic-signal","display_name":"phylogenetic signal","score":0.7689999938011169},{"id":"https://openalex.org/keywords/phylogenetic-conflict","display_name":"phylogenetic conflict","score":0.7839999794960022},{"id":"https://openalex.org/keywords/gene-tree-conflict","display_name":"gene tree conflict","score":0.5389999747276306},{"id":"https://openalex.org/keywords/species-tree","display_name":"species tree","score":0.6790000200271606},{"id":"https://openalex.org/keywords/gene-trees","display_name":"gene trees","score":0.49799999594688416},{"id":"https://openalex.org/keywords/centric-diatoms","display_name":"centric diatoms","score":0.7329999804496765},{"id":"https://openalex.org/keywords/protists","display_name":"protists","score":0.6460000276565552}],"concepts":[{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.6290298700332642},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49096396565437317},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.47953343391418457},{"id":"https://openalex.org/C2778902744","wikidata":"https://www.wikidata.org/wiki/Q162678","display_name":"Diatom","level":2,"score":0.4534684121608734},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.34669074416160583},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.33185309171676636},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10313156247138977},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06206861138343811}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:zenodo.org:344519","doi":null,"is_oa":true,"landing_page_url":"https://zenodo.org/record/344519","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"dataset"},{"id":"doi:10.5281/zenodo.344519","doi":"https://doi.org/10.5281/zenodo.344519","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.344519","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},{"id":"doi:10.5281/zenodo.600659","doi":"https://doi.org/10.5281/zenodo.600659","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.600659","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"}],"best_oa_location":{"id":"pmh:oai:zenodo.org:344519","doi":null,"is_oa":true,"landing_page_url":"https://zenodo.org/record/344519","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"dataset"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4393601407","https://openalex.org/W6892311393","https://openalex.org/W6887860751","https://openalex.org/W4394464621","https://openalex.org/W6925367725","https://openalex.org/W6948660795","https://openalex.org/W7115557134","https://openalex.org/W4394412217","https://openalex.org/W2009664312","https://openalex.org/W7097946654"],"abstract_inverted_index":{"This":[0,235],"data":[1],"depository":[2],"contains":[3,51,102,136,205,237],"analysis":[4],"results":[5],"from":[6,153],"Parks,":[7,227],"Wickett,":[8],"and":[9,14,32,43,54,64,146,150,169,213,229,240,247],"Alverson":[10,230],"2017":[11,231],"(Signal,":[12],"Uncertainty,":[13],"Conflict":[15],"in":[16,113,176],"Phylogenomic":[17],"Data":[18],"for":[19,116,140,209,243],"a":[20,248],"Diverse":[21],"Lineage":[22],"of":[23,160,165,250],"Microbial":[24],"Eukaryotes":[25],"(Diatoms,":[26],"Bacillariophyta)":[27],"(Mol.":[28],"Biol.":[29],"Evol.":[30],"doi:10.1093/molbev/msx268)),":[31],"is":[33],"made":[34],"freely":[35],"available":[36,175],"to":[37,226],"the":[38,154,161,166,170,182],"research":[39],"community.":[40],"The":[41],"file":[42,225,233,236],"subfolders":[44],"here":[45],"are":[46,74,132,173,181],"as":[47],"follows:":[48],"gene_alignments":[49],"-":[50,101,135,179,204,221],"compressed":[52,183],"(tarred":[53],"gzipped)":[55],"folders":[56],"with":[57,126],"all":[58,103,210,244],"gene":[59,80,105],"alignments":[60,81],"at":[61],"0.2,":[62],"0.5":[63],"0.8":[65],"alignment":[66,118,156,214],"column":[67,119,157,215],"occupancy":[68,86,120,158,216],"cutoffs.":[69],"In":[70],"each":[71,117,141],"folder,":[72],"there":[73],"also":[75,174],"text":[76],"files":[77],"listing":[78],"which":[79,84],"fall":[82],"under":[83],"taxon":[85,91,94,97],"subsetting":[87],"strategy":[88],"(i.e.,":[89,191],"10-20%":[90],"occupancy,":[92,95,98],"40-60%":[93],"80-100%":[96],"etc).":[99],"gene_trees":[100],"(compressed)":[104,137,206],"trees":[106,208],"(bootstrapped":[107],"versions,":[108],"100":[109],"bootstrap":[110,130],"pseudo-replicates))":[111],"used":[112],"Astral":[114],"analyses":[115],"cutoff":[121],"(0.2,":[122],"0.5,":[123],"0.8);":[124],"nodes":[125],"less":[127],"than":[128],"33%":[129],"support":[131],"collapsed.":[133],"hmms.mafft_aligned":[134],"hmm":[138,171],"specifications":[139],"major":[142],"diatom":[143],"morphotype":[144],"(radial":[145],"polar":[147],"centrics,":[148],"araphid":[149],"raphid":[151],"pennates)":[152],"0.2":[155],"subset":[159,218],"data.":[162],"A":[163],"summary":[164],"sampling":[167],"scheme":[168],"results/counts":[172],"HMM_sampling.docx.":[177],"mmetsp_nuclear_transcriptome_assemblies":[178],"these":[180],"nuclear":[184],"transcriptome":[185],"assemblies":[186],"that":[187],"were":[188],"done":[189],"in-house":[190],"mostly":[192],"MMETSP":[193],"samples).":[194],"Assemblies":[195],"do":[196],"not":[197],"include":[198],"organellar":[199],"or":[200],"rDNA":[201],"loci.":[202],"species_trees":[203],"species":[207],"phylogenetic":[211],"strategies":[212],"cutoff/data":[217],"strategies.":[219],"Suppl_1.MMETSP_basic_summaries.xlsx":[220],"this":[222],"an":[223],"identical":[224],"Wickett":[228],"supplementary":[232],"1.":[234],"taxon,":[238],"strain":[239],"SRA":[241],"information":[242],"assembled":[245],"taxa,":[246],"variety":[249],"assembly":[251],"metric":[252],"information.":[253]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-10-27T15:51:10.671819","created_date":"2024-04-03T00:00:00"}