{"id":"https://openalex.org/W7164199515","doi":"https://doi.org/10.64898/2026.06.06.730607","title":"Is level-1 blob reconstruction under the network multispecies coalescent easy?","display_name":"Is level-1 blob reconstruction under the network multispecies coalescent easy?","publication_year":2026,"publication_date":"2026-06-10","ids":{"openalex":"https://openalex.org/W7164199515","doi":"https://doi.org/10.64898/2026.06.06.730607"},"language":"en","primary_location":{"id":"doi:10.64898/2026.06.06.730607","doi":"https://doi.org/10.64898/2026.06.06.730607","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.06.06.730607","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/21/2026.06.06.730607.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":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/21/2026.06.06.730607.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100308559","display_name":"J. P. Dai","orcid":"https://orcid.org/0009-0009-5699-2196","observed_orcids":["https://orcid.org/0009-0009-5699-2196","https://orcid.org/0000-0003-3395-7151"]},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junyan Dai","raw_affiliation_strings":["Department of Computer Science, University of Maryland, College Park, MD 20742, USA"],"raw_orcid":"https://orcid.org/0009-0009-5699-2196","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Maryland, College Park, MD 20742, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045334836","display_name":"Erin K. Molloy","orcid":"https://orcid.org/0000-0001-5553-3312","observed_orcids":["https://orcid.org/0000-0001-5553-3312"]},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Erin K. Molloy","raw_affiliation_strings":["Department of Computer Science, University of Maryland, College Park, MD 20742, USA","University of Maryland Institute for Advanced Computer Studies, College Park, MD 20742, USA"],"raw_orcid":"https://orcid.org/0000-0001-5553-3312","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Maryland, College Park, MD 20742, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"University of Maryland Institute for Advanced Computer Studies, College Park, MD 20742, USA","institution_ids":["https://openalex.org/I66946132"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5045334836"],"corresponding_institution_ids":["https://openalex.org/I66946132"],"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":0.9810000061988831,"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":0.9810000061988831,"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/T10012","display_name":"Genetic diversity and population structure","score":0.0034000000450760126,"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"}},{"id":"https://openalex.org/T10385","display_name":"Plant Diversity and Evolution","score":0.003000000026077032,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/hybridization","display_name":"hybridization","score":0.7799999713897705},{"id":"https://openalex.org/keywords/majority-voting","display_name":"majority voting","score":0.8339999914169312},{"id":"https://openalex.org/keywords/merge-sort","display_name":"merge sort","score":0.9639999866485596},{"id":"https://openalex.org/keywords/hybrid-ancestry","display_name":"hybrid ancestry","score":0.5759999752044678},{"id":"https://openalex.org/keywords/phylogenetic-network-inference","display_name":"phylogenetic network inference","score":0.9020000100135803},{"id":"https://openalex.org/keywords/computational-scalability","display_name":"computational scalability","score":0.6100000143051147}],"concepts":[{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.5706999897956848},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5641999840736389},{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.5415999889373779},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5192000269889832},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.512499988079071},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.45100000500679016},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4471000134944916},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.38679999113082886},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.3813999891281128},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.37549999356269836},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.37549999356269836},{"id":"https://openalex.org/C163797641","wikidata":"https://www.wikidata.org/wiki/Q2067937","display_name":"Tree structure","level":3,"score":0.3589000105857849},{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.3529999852180481},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3474000096321106},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.33149999380111694},{"id":"https://openalex.org/C197855036","wikidata":"https://www.wikidata.org/wiki/Q380172","display_name":"Binary tree","level":2,"score":0.3149000108242035},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.29919999837875366},{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.29760000109672546},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.27549999952316284},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.27000001072883606},{"id":"https://openalex.org/C146599234","wikidata":"https://www.wikidata.org/wiki/Q511093","display_name":"Centroid","level":2,"score":0.25870001316070557},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.2567000091075897},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2565999925136566},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.2547999918460846}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.06.06.730607","doi":"https://doi.org/10.64898/2026.06.06.730607","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.06.06.730607","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/21/2026.06.06.730607.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":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.06.06.730607","doi":"https://doi.org/10.64898/2026.06.06.730607","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.06.06.730607","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/21/2026.06.06.730607.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":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7164199515.pdf","grobid_xml":"https://content.openalex.org/works/W7164199515.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W938539187","https://openalex.org/W1897064680","https://openalex.org/W1979100126","https://openalex.org/W2029991569","https://openalex.org/W2117665706","https://openalex.org/W2141052558","https://openalex.org/W2246743204","https://openalex.org/W2277574918","https://openalex.org/W2608378253","https://openalex.org/W2753562621","https://openalex.org/W2773833981","https://openalex.org/W3005235420","https://openalex.org/W3181359813","https://openalex.org/W4254268221","https://openalex.org/W4302763624","https://openalex.org/W4311577708","https://openalex.org/W4378783481","https://openalex.org/W4387336601","https://openalex.org/W4391988956","https://openalex.org/W4400988409","https://openalex.org/W4403301307","https://openalex.org/W4403854157","https://openalex.org/W4404064679","https://openalex.org/W4408227982","https://openalex.org/W4408655239","https://openalex.org/W4408956274","https://openalex.org/W4410155202","https://openalex.org/W4412483243","https://openalex.org/W4412708182","https://openalex.org/W4413769587","https://openalex.org/W7125039520","https://openalex.org/W7160872922","https://openalex.org/W7162938105","https://openalex.org/W7167632195","https://openalex.org/W7204603796"],"related_works":["https://openalex.org/W7204603796","https://openalex.org/W7208712619","https://openalex.org/W3195891352","https://openalex.org/W7162938105","https://openalex.org/W4404064679","https://openalex.org/W7154909167","https://openalex.org/W4310557608","https://openalex.org/W4395479381","https://openalex.org/W7111871316","https://openalex.org/W4394742879"],"abstract_inverted_index":{"Abstract":[0],"Hybridization":[1],"is":[2,20,88,144,151,255,263,282],"an":[3,59],"important":[4],"evolutionary":[5,15],"process,":[6],"commonly":[7],"modeled":[8],"by":[9],"the":[10,93,111,123,147,174,214,259],"network":[11,272],"multispecies":[12],"coalescent.":[13],"Reconstructing":[14],"histories":[16],"under":[17],"this":[18],"model":[19],"notoriously":[21],"costly,":[22],"even":[23,235],"for":[24,51,270],"level-1":[25,128,141,239,253],"networks":[26,240],"where":[27],"hybridization":[28],"events":[29],"are":[30],"isolated":[31],"from":[32],"each":[33,107,127],"other.":[34],"The":[35],"widely":[36],"used":[37],"methods":[38,208,236],"that":[39,67,237,251,266],"combine":[40],"speed":[41],"with":[42],"statistical":[43],"guarantees":[44],"rely":[45],"on":[46,164],"quartet":[47,179],"concordance":[48,180],"factors":[49],"computed":[50],"all":[52,178],"subsets":[53],"of":[54,74,102,110,126,149,176,196,217,231,261,278],"four":[55],"species,":[56],"resulting":[57],"in":[58,202,223,229,275],"O":[60],"(":[61,76,81],"n":[62,77],"4":[63],"k":[64,82],")":[65,78],"bottleneck":[66,175],"severely":[68],"limits":[69],"scalability":[70],"to":[71,188,227,243],"large":[72],"numbers":[73],"species":[75],"and":[79,120,134,157,170,190,199,265],"genes":[80,201],").":[83],"Among":[84],"quartet-based":[85],"methods,":[86],"NANUQ+":[87,189],"notable":[89],"because":[90],"it":[91],"decomposes":[92],"problem":[94],"into":[95,116],"two":[96,165],"steps:":[97],"first":[98],"reconstructing":[99,122,252],"a":[100,114,117,155,204,267],"tree":[101,148,216,230,260,277],"blobs":[103,150,232,254,262,279],",":[104],"which":[105],"compresses":[106],"non-treelike":[108],"part":[109],"network,":[112],"called":[113,161],"blob,":[115,129],"single":[118],"vertex,":[119],"second":[121],"internal":[124],"structure":[125],"specifically":[130],"its":[131],"circular":[132],"order":[133],"hybrid":[135,246],"vertex.":[136],"Here,":[137],"we":[138],"investigate":[139],"whether":[140],"blob":[142],"reconstruction":[143],"difficult":[145],"once":[146,258],"known.":[152],"We":[153],"present":[154],"fast":[156],"statistically":[158],"consistent":[159],"algorithm,":[160],"NetCS,":[162],"based":[163],"simple":[166],"primitives:":[167],"majority":[168],"voting":[169],"merge":[171],"sort,":[172],"circumventing":[173],"computing":[177],"factors.":[181],"In":[182],"simulations,":[183],"NetCS":[184,281],"achieved":[185],"comparable":[186],"accuracy":[187,211],"was":[191],"dramatically":[192],"faster,":[193],"enabling":[194],"analyses":[195],"200":[197],"taxa":[198],"1000":[200],"only":[203],"few":[205],"minutes.":[206],"Both":[207],"attained":[209],"near-perfect":[210],"when":[212],"given":[213],"true":[215],"blobs;":[218],"however,":[219],"their":[220],"performance":[221],"degraded":[222],"end-to-end":[224],"pipelines":[225],"due":[226],"errors":[228],"reconstruction.":[233,280],"Strikingly,":[234],"reconstruct":[238],"directly":[241],"struggled":[242],"accurately":[244],"predict":[245],"ancestry.":[247],"Our":[248],"results":[249],"suggest":[250],"unexpectedly":[256],"easy":[257],"known,":[264],"major":[268],"challenge":[269],"phylogenetic":[271],"inference":[273],"lies":[274],"accurate":[276],"implemented":[283],"within":[284],"TREE-QMC,":[285],"available":[286],"at":[287],"https://github.com/molloy-lab/TREE-QMC":[288]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-11-05T12:25:35.769452","created_date":"2026-06-11T00:00:00"}