{"id":"https://openalex.org/W7208712619","doi":"https://doi.org/10.64898/2026.08.31.748319","title":"BROOQS: Quartet-based Resolution of Level-1 Hybridization Cycles without Tests of Symmetry","display_name":"BROOQS: Quartet-based Resolution of Level-1 Hybridization Cycles without Tests of Symmetry","publication_year":2026,"publication_date":"2026-09-04","ids":{"openalex":"https://openalex.org/W7208712619","doi":"https://doi.org/10.64898/2026.08.31.748319","pmid":"https://pubmed.ncbi.nlm.nih.gov/42818219","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13622453"},"language":"en","primary_location":{"id":"doi:10.64898/2026.08.31.748319","doi":"https://doi.org/10.64898/2026.08.31.748319","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.31.748319","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/04/2026.08.31.748319.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/04/2026.08.31.748319.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5093277856","display_name":"Shayesteh Arasti","orcid":"https://orcid.org/0009-0005-1607-5300","observed_orcids":["https://orcid.org/0009-0005-1607-5300"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shayesteh Arasti","raw_affiliation_strings":["Department of Computer Science and Engineering, UC San Diego, 9500 Gilman Dr., 92093, CA, USA"],"raw_orcid":"https://orcid.org/0009-0005-1607-5300","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, UC San Diego, 9500 Gilman Dr., 92093, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087959579","display_name":"Siavash Mirarab","orcid":"https://orcid.org/0000-0001-5410-1518","observed_orcids":["https://orcid.org/0000-0001-5410-1518"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Siavash Mirarab","raw_affiliation_strings":["Department of Electrical and Computer Engineering, UC San Diego, 9500 Gilman Dr., 92093, CA, USA"],"raw_orcid":"https://orcid.org/0000-0001-5410-1518","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, UC San Diego, 9500 Gilman Dr., 92093, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5087959579"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9854000210762024,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9854000210762024,"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/T10385","display_name":"Plant Diversity and Evolution","score":0.002300000051036477,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.00139999995008111,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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"}}],"keywords":[{"id":"https://openalex.org/keywords/spectral-algorithms","display_name":"spectral algorithms","score":0.47099998593330383},{"id":"https://openalex.org/keywords/pq-trees","display_name":"PQ-trees","score":0.6690000295639038},{"id":"https://openalex.org/keywords/phylogenomics","display_name":"phylogenomics","score":0.5860000252723694},{"id":"https://openalex.org/keywords/reticulate-evolution","display_name":"reticulate evolution","score":0.8519999980926514}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6624000072479248},{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.6284000277519226},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5674999952316284},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5360999703407288},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.524399995803833},{"id":"https://openalex.org/C2778727739","wikidata":"https://www.wikidata.org/wiki/Q18434417","display_name":"Reticulate evolution","level":4,"score":0.5242999792098999},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.48240000009536743},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.47269999980926514},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.4564000070095062},{"id":"https://openalex.org/C55919133","wikidata":"https://www.wikidata.org/wiki/Q7644297","display_name":"Supertree","level":4,"score":0.45590001344680786},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4447000026702881},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4429999887943268},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4404999911785126},{"id":"https://openalex.org/C2779886137","wikidata":"https://www.wikidata.org/wiki/Q21030012","display_name":"Symmetry (geometry)","level":2,"score":0.4162999987602234},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4081999957561493},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4074000120162964},{"id":"https://openalex.org/C38976095","wikidata":"https://www.wikidata.org/wiki/Q752641","display_name":"Asymmetry","level":2,"score":0.37599998712539673},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.349700003862381},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.334199994802475},{"id":"https://openalex.org/C2780432395","wikidata":"https://www.wikidata.org/wiki/Q21149008","display_name":"Reticulate","level":2,"score":0.32910001277923584},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.31380000710487366},{"id":"https://openalex.org/C64543145","wikidata":"https://www.wikidata.org/wiki/Q162942","display_name":"Intersection (aeronautics)","level":2,"score":0.29319998621940613},{"id":"https://openalex.org/C123439655","wikidata":"https://www.wikidata.org/wiki/Q3977978","display_name":"Supermatrix","level":5,"score":0.2897999882698059},{"id":"https://openalex.org/C163797641","wikidata":"https://www.wikidata.org/wiki/Q2067937","display_name":"Tree structure","level":3,"score":0.2750000059604645},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.26660001277923584},{"id":"https://openalex.org/C2779304628","wikidata":"https://www.wikidata.org/wiki/Q3503480","display_name":"Face (sociological concept)","level":2,"score":0.25929999351501465},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.2574000060558319},{"id":"https://openalex.org/C111696304","wikidata":"https://www.wikidata.org/wiki/Q2303697","display_name":"Sorting","level":2,"score":0.257099986076355},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2556000053882599},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.2529999911785126}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.64898/2026.08.31.748319","doi":"https://doi.org/10.64898/2026.08.31.748319","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.31.748319","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/04/2026.08.31.748319.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:42818219","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42818219","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13622453","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13622453/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.64898/2026.08.31.748319","doi":"https://doi.org/10.64898/2026.08.31.748319","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.31.748319","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/04/2026.08.31.748319.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1260914621","display_name":"Biology-aware machine learning methods for characterizing microbiome genotype and phenotype","funder_award_id":"1r35gm142725-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7208712619.pdf","grobid_xml":"https://content.openalex.org/works/W7208712619.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W7164199515","https://openalex.org/W7204603796","https://openalex.org/W7167632195","https://openalex.org/W4412708182","https://openalex.org/W4415474926","https://openalex.org/W7162938105","https://openalex.org/W7111871316","https://openalex.org/W4404064679","https://openalex.org/W1967944500","https://openalex.org/W4310557608"],"abstract_inverted_index":{"Modern":[0],"phylogenomic":[1],"analyses":[2],"often":[3,66],"seek":[4],"to":[5,59,70,82,134,245,261,288,304,309],"reconstruct":[6],"both":[7,158],"vertical":[8],"and":[9,27,143,160,202,284,294,301,307],"reticulate":[10],"evolutionary":[11],"histories.":[12],"While":[13],"the":[14,31,155,212,216,227,230,250],"prevalence":[15],"of":[16,33,53,99,182,258,311],"non-vertical":[17],"evolution":[18],"is":[19,133,275],"increasingly":[20],"appreciated,":[21],"inferring":[22],"networks":[23,132],"remains":[24],"conceptually":[25,159],"challenging":[26],"computationally":[28],"demanding.":[29],"Following":[30],"success":[32],"quartet-based":[34,45,55,177],"methods":[35,48,56,110,306],"for":[36,72,91,130,179,256],"species":[37,88],"tree":[38,42,89,139],"inference":[39,47,90],"despite":[40],"gene":[41],"discordance,":[43],"several":[44],"network":[46,251],"have":[49,77,94,272],"been":[50,80],"developed.":[51],"Most":[52],"these":[54,75],"boil":[57],"down":[58],"detecting":[60],"asymmetry":[61],"in":[62,87,199,277],"minor":[63],"quartet":[64,222],"frequencies,":[65],"using":[67],"statistical":[68,247],"tests":[69],"control":[71],"noise.":[73],"However,":[74,162],"approaches":[76],"not":[78,273],"yet":[79],"amenable":[81],"dynamic":[83],"programming":[84],"algorithms":[85],"used":[86],"search,":[92,124],"nor":[93],"they":[95],"allowed":[96],"efficient":[97],"calculation":[98],"statistics":[100],"across":[101],"all":[102,106,113,194],"quartets":[103,169,195],"without":[104,218],"listing":[105],"quartets.":[107],"Instead,":[108],"existing":[109,239,305],"either":[111,167],"enumerate":[112],"quartets,":[114],"losing":[115,121],"some":[116],"scalability,":[117],"or":[118,170],"subsample":[119],"them,":[120],"information.":[122],"For":[123],"an":[125,238],"effective":[126],"recently":[127],"developed":[128],"strategy":[129],"level-1":[131,186],"first":[135],"build":[136],"a":[137,141,149,176,185,197,204,265],"multifurcating":[138],"called":[140],"tree-of-blobs":[142],"then":[144],"resolve":[145],"each":[146],"polytomy":[147],"into":[148,184],"cycle.":[150],"This":[151],"two-step":[152],"approach":[153],"makes":[154],"problem":[156],"easier":[157],"computationally.":[161],"resolving":[163,180],"blobs":[164,183,257],"still":[165],"requires":[166],"subsampling":[168],"sacrificing":[171],"scalability.":[172],"We":[173],"introduce":[174],"BROOQS,":[175],"method":[178],"trees":[181],"phylogenetic":[187],"network.":[188],"BROOQS":[189],"efficiently":[190],"aggregates":[191],"information":[192],"from":[193,229],"around":[196,215],"blob":[198,217],"quadratic":[200],"time":[201],"builds":[203],"pairwise":[205],"similarity":[206],"matrix":[207],"that":[208],"we":[209,232,269],"prove":[210,246],"encodes":[211],"cyclic":[213],"ordering":[214],"relying":[219],"on":[220,281],"individual":[221],"symmetry":[223],"tests.":[224],"To":[225],"recover":[226],"order":[228],"matrix,":[231],"use":[233],"two":[234],"approaches.":[235],"BROOQS-PQtree":[236],"uses":[237,264],"combinatorial":[240],"method,":[241],"which":[242,268],"allows":[243],"us":[244],"consistency":[248],"under":[249],"multi-species":[252],"coalescent":[253],"(NMSC)":[254],"model":[255],"size":[259],"5":[260],"15.":[262],"BROOQS-Spectral":[263,297],"spectral":[266],"algorithm,":[267],"conjecture":[270],"(but":[271],"proved)":[274],"consistent":[276],"similar":[278],"conditions":[279],"based":[280],"our":[282],"simulations,":[283],"shows":[285],"better":[286],"robustness":[287],"noise":[289],"than":[290],"BROOQS-PQtree.":[291],"Across":[292],"simulated":[293],"empirical":[295],"datasets,":[296],"consistently":[298],"improves":[299],"accuracy":[300],"scalability":[302],"compared":[303],"extends":[308],"thousands":[310],"taxa.":[312]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-09-05T00:00:00"}