{"id":"https://openalex.org/W7124809648","doi":"https://doi.org/10.24072/pcjournal.828","title":"Gene tree conflict between genomic and functional partitions impacts phylogenetic inference in Zygophylloideae","display_name":"Gene tree conflict between genomic and functional partitions impacts phylogenetic inference in Zygophylloideae","publication_year":2026,"publication_date":"2026-10-29","ids":{"openalex":"https://openalex.org/W7124809648","doi":"https://doi.org/10.24072/pcjournal.828"},"language":"en","primary_location":{"id":"doi:10.24072/pcjournal.828","doi":"https://doi.org/10.24072/pcjournal.828","is_oa":true,"landing_page_url":"https://doi.org/10.24072/pcjournal.828","pdf_url":"https://peercommunityjournal.org/item/10.24072/pcjournal.828.pdf","source":{"id":"https://openalex.org/S4387278563","display_name":"Peer Community Journal","issn_l":"2804-3871","issn":["2804-3871"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","ddh","doaj","dongbi-d","doyens","jufo-1","ki-jl-1","norway-1"],"host_organization":"https://openalex.org/P4404675295","host_organization_name":"Peer Community in","host_organization_lineage":["https://openalex.org/P4404675295"],"host_organization_lineage_names":["Peer Community in"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Peer Community Journal","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://peercommunityjournal.org/item/10.24072/pcjournal.828.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087667946","display_name":"P. DE WET VAN DER MERWE","orcid":"https://orcid.org/0000-0001-9315-599X","observed_orcids":["https://orcid.org/0000-0001-9315-599X"]},"institutions":[{"id":"https://openalex.org/I26092322","display_name":"Stellenbosch University","ror":"https://ror.org/05bk57929","country_code":"ZA","type":"education","lineage":["https://openalex.org/I26092322"]}],"countries":["ZA"],"is_corresponding":false,"raw_author_name":"Pieter De Wet Van der Merwe","raw_affiliation_strings":["Department of Biochemistry, Stellenbosch University, South Africa"],"raw_orcid":"https://orcid.org/0000-0001-9315-599X","affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Stellenbosch University, South Africa","institution_ids":["https://openalex.org/I26092322"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039467332","display_name":"Michael David Pirie","orcid":"https://orcid.org/0000-0003-0403-4470","observed_orcids":["https://orcid.org/0000-0003-0403-4470"]},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Michael D. Pirie","raw_affiliation_strings":["University Museum, University of Bergen, Postboks 7800, N-5020 Bergen, Norway"],"raw_orcid":"https://orcid.org/0000-0003-0403-4470","affiliations":[{"raw_affiliation_string":"University Museum, University of Bergen, Postboks 7800, N-5020 Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013419514","display_name":"Dirk Uwe Bellstedt","orcid":"https://orcid.org/0000-0002-6376-4855","observed_orcids":["https://orcid.org/0000-0002-6376-4855"]},"institutions":[{"id":"https://openalex.org/I26092322","display_name":"Stellenbosch University","ror":"https://ror.org/05bk57929","country_code":"ZA","type":"education","lineage":["https://openalex.org/I26092322"]}],"countries":["ZA"],"is_corresponding":true,"raw_author_name":"Dirk U. Bellstedt","raw_affiliation_strings":["Department of Biochemistry, Stellenbosch University, South Africa"],"raw_orcid":"https://orcid.org/0000-0002-6376-4855","affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Stellenbosch University, South Africa","institution_ids":["https://openalex.org/I26092322"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5013419514"],"corresponding_institution_ids":["https://openalex.org/I26092322"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0210649,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"6","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10385","display_name":"Plant Diversity and Evolution","score":0.9496999979019165,"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"}},"topics":[{"id":"https://openalex.org/T10385","display_name":"Plant Diversity and Evolution","score":0.9496999979019165,"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/T13168","display_name":"Plant Ecology and Taxonomy Studies","score":0.043800000101327896,"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/T12568","display_name":"Plant Taxonomy and Phylogenetics","score":0.0017000000225380063,"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/zygophyllaceae","display_name":"Zygophyllaceae","score":0.9660000205039978},{"id":"https://openalex.org/keywords/phylogenetic-relationships","display_name":"phylogenetic relationships","score":0.7409999966621399},{"id":"https://openalex.org/keywords/gene-tree-conflict","display_name":"gene tree conflict","score":0.9850000143051147},{"id":"https://openalex.org/keywords/chloroplast-genes","display_name":"chloroplast genes","score":0.7519999742507935},{"id":"https://openalex.org/keywords/nuclear-ribosomal-genes","display_name":"nuclear ribosomal genes","score":0.9240000247955322},{"id":"https://openalex.org/keywords/photosynthesis-genes","display_name":"photosynthesis genes","score":0.7649999856948853},{"id":"https://openalex.org/keywords/internal-transcribed-spacer","display_name":"ITS region","score":0.8149999976158142},{"id":"https://openalex.org/keywords/phylogenetic-incongruence","display_name":"phylogenetic incongruence","score":0.593999981880188},{"id":"https://openalex.org/keywords/introgression","display_name":"introgression","score":0.8510000109672546},{"id":"https://openalex.org/keywords/incomplete-lineage-sorting","display_name":"incomplete lineage sorting","score":1.0},{"id":"https://openalex.org/keywords/zygophyllum","display_name":"Zygophyllum","score":0.7300000190734863},{"id":"https://openalex.org/keywords/tetraena","display_name":"Tetraena","score":0.9729999899864197},{"id":"https://openalex.org/keywords/fagonia","display_name":"Fagonia","score":0.9869999885559082},{"id":"https://openalex.org/keywords/divergence-time-estimation","display_name":"divergence time estimation","score":0.39399999380111694}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7674999833106995},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7335000038146973},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.597000002861023},{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.4936000108718872},{"id":"https://openalex.org/C48050816","wikidata":"https://www.wikidata.org/wiki/Q3182853","display_name":"Chloroplast DNA","level":4,"score":0.4902999997138977},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.4781000018119812},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.47519999742507935},{"id":"https://openalex.org/C20750100","wikidata":"https://www.wikidata.org/wiki/Q7068120","display_name":"Nuclear gene","level":4,"score":0.4706999957561493},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.4480000138282776},{"id":"https://openalex.org/C2778727739","wikidata":"https://www.wikidata.org/wiki/Q18434417","display_name":"Reticulate evolution","level":4,"score":0.43320000171661377},{"id":"https://openalex.org/C155794727","wikidata":"https://www.wikidata.org/wiki/Q2306414","display_name":"Internal transcribed spacer","level":4,"score":0.4097999930381775},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4032999873161316},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.374099999666214},{"id":"https://openalex.org/C50929876","wikidata":"https://www.wikidata.org/wiki/Q164280","display_name":"Subfamily","level":3,"score":0.33149999380111694},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.3292999863624573},{"id":"https://openalex.org/C67905577","wikidata":"https://www.wikidata.org/wiki/Q215980","display_name":"Ribosomal RNA","level":3,"score":0.31220000982284546},{"id":"https://openalex.org/C58677359","wikidata":"https://www.wikidata.org/wiki/Q7201511","display_name":"Plant evolution","level":4,"score":0.29319998621940613},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.29280000925064087},{"id":"https://openalex.org/C166393388","wikidata":"https://www.wikidata.org/wiki/Q856529","display_name":"Molecular evolution","level":4,"score":0.2671000063419342},{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.26460000872612},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2630000114440918},{"id":"https://openalex.org/C195139083","wikidata":"https://www.wikidata.org/wiki/Q3463539","display_name":"Intergenic region","level":4,"score":0.2587999999523163},{"id":"https://openalex.org/C8182607","wikidata":"https://www.wikidata.org/wiki/Q2094405","display_name":"Introgression","level":3,"score":0.2517000138759613},{"id":"https://openalex.org/C141036","wikidata":"https://www.wikidata.org/wiki/Q5158537","display_name":"Concerted evolution","level":4,"score":0.25029999017715454},{"id":"https://openalex.org/C62142553","wikidata":"https://www.wikidata.org/wiki/Q200312","display_name":"Convergent evolution","level":4,"score":0.25029999017715454}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.24072/pcjournal.828","doi":"https://doi.org/10.24072/pcjournal.828","is_oa":true,"landing_page_url":"https://doi.org/10.24072/pcjournal.828","pdf_url":"https://peercommunityjournal.org/item/10.24072/pcjournal.828.pdf","source":{"id":"https://openalex.org/S4387278563","display_name":"Peer Community Journal","issn_l":"2804-3871","issn":["2804-3871"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","ddh","doaj","dongbi-d","doyens","jufo-1","ki-jl-1","norway-1"],"host_organization":"https://openalex.org/P4404675295","host_organization_name":"Peer Community in","host_organization_lineage":["https://openalex.org/P4404675295"],"host_organization_lineage_names":["Peer Community in"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Peer Community Journal","raw_type":"journal-article"},{"id":"doi:10.64898/2026.01.16.699981","doi":"https://doi.org/10.64898/2026.01.16.699981","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.01.16.699981","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/01/17/2026.01.16.699981.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"}],"best_oa_location":{"id":"doi:10.24072/pcjournal.828","doi":"https://doi.org/10.24072/pcjournal.828","is_oa":true,"landing_page_url":"https://doi.org/10.24072/pcjournal.828","pdf_url":"https://peercommunityjournal.org/item/10.24072/pcjournal.828.pdf","source":{"id":"https://openalex.org/S4387278563","display_name":"Peer Community Journal","issn_l":"2804-3871","issn":["2804-3871"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","ddh","doaj","dongbi-d","doyens","jufo-1","ki-jl-1","norway-1"],"host_organization":"https://openalex.org/P4404675295","host_organization_name":"Peer Community in","host_organization_lineage":["https://openalex.org/P4404675295"],"host_organization_lineage_names":["Peer Community in"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Peer Community Journal","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320322007","display_name":"Ministry of Environment","ror":"https://ror.org/04xmt0833"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7124809648.pdf","grobid_xml":"https://content.openalex.org/works/W7124809648.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W143810700","https://openalex.org/W1975879554","https://openalex.org/W1990282786","https://openalex.org/W1994370398","https://openalex.org/W1997588358","https://openalex.org/W1997851081","https://openalex.org/W1999809323","https://openalex.org/W2016661262","https://openalex.org/W2028302194","https://openalex.org/W2028458237","https://openalex.org/W2039446206","https://openalex.org/W2062962705","https://openalex.org/W2083744084","https://openalex.org/W2095646489","https://openalex.org/W2102978689","https://openalex.org/W2115575384","https://openalex.org/W2122766746","https://openalex.org/W2126009362","https://openalex.org/W2131551905","https://openalex.org/W2133514781","https://openalex.org/W2136436332","https://openalex.org/W2141052558","https://openalex.org/W2142260441","https://openalex.org/W2143183702","https://openalex.org/W2143926541","https://openalex.org/W2145581628","https://openalex.org/W2145608399","https://openalex.org/W2152128080","https://openalex.org/W2161444534","https://openalex.org/W2166152751","https://openalex.org/W2169065738","https://openalex.org/W2177605519","https://openalex.org/W2189564092","https://openalex.org/W2235584627","https://openalex.org/W2318157063","https://openalex.org/W2322287152","https://openalex.org/W2342407959","https://openalex.org/W2530618024","https://openalex.org/W2607411230","https://openalex.org/W2895248746","https://openalex.org/W2898357121","https://openalex.org/W2899427385","https://openalex.org/W2899964262","https://openalex.org/W2947934976","https://openalex.org/W2950352437","https://openalex.org/W2956075977","https://openalex.org/W2980373194","https://openalex.org/W2999869862","https://openalex.org/W3075891525","https://openalex.org/W3201978329","https://openalex.org/W3204400973","https://openalex.org/W4245471709","https://openalex.org/W4386156831","https://openalex.org/W4411711488"],"related_works":["https://openalex.org/W6987604930","https://openalex.org/W3204400973","https://openalex.org/W2130311065","https://openalex.org/W793568623","https://openalex.org/W2125726330","https://openalex.org/W7096536661","https://openalex.org/W4210503275","https://openalex.org/W2102978689","https://openalex.org/W2099398736","https://openalex.org/W2775981038"],"abstract_inverted_index":{"Abstract":[0],"The":[1,284],"Zygophyllaceae":[2],"subfamily":[3,125],"Zygophylloideae":[4,33],"includes":[5],"seven":[6],"genera":[7,55],"and":[8,27,67,75,90,95,98,116,121,145,155,158,192,204,254,275,302,327,331],"around":[9],"180":[10],"species":[11,105,281],"distributed":[12],"worldwide":[13],"particularly":[14],"in":[15,37,56,167,184,211,243,298],"arid":[16],"areas":[17],"where":[18],"they":[19,78],"show":[20],"adaptations":[21],"to":[22,49,71,83,223,261],"drought":[23],"including":[24],"C":[25],"4":[26],"CAM":[28],"photosynthesis.":[29,168],"Phylogenetic":[30],"relationships":[31,53,74],"of":[32,65,106,123,176,187,190,286,321],"have":[34,46,79],"been":[35,47],"analysed":[36],"several":[38],"studies":[39,186],"using":[40,142],"Sanger":[41],"sequenced":[42,86],"markers,":[43],"but":[44],"none":[45],"able":[48],"resolve":[50],"all":[51],"deeper":[52],"between":[54],"the":[57,124,171,194,287],"subfamily.":[58],"Here,":[59],"we":[60],"use":[61],"ion":[62],"semi-conductor":[63],"sequencing":[64],"chloroplast":[66,88,136,172,181,220,244,253],"nuclear":[68,91,195,255],"ribosomal":[69,92,196],"regions":[70,182],"analyse":[72],"these":[73,131],"assess":[76],"why":[77],"proved":[80],"so":[81],"challenging":[82],"resolve.":[84],"We":[85,129,169,217],"39":[87],"genes":[89,97,160,247,258,301],"18S,":[93],"5.8S,":[94],"26S":[96],"internal":[99],"transcribed":[100],"spacers":[101],"(ITS)":[102],"for":[103,152,159,214,266],"key":[104],"Zygophyllum":[107,114],"sensu":[108],"stricto,":[109],"Roepera,":[110],"Tetraena,":[111],"Fagonia":[112],",":[113],"stapffii":[115],"monotypic":[117],"Augea":[118],"capensis":[119],";":[120],"Tribulus":[122],"Tribuloideae":[126],"as":[127,248,250],"outgroup.":[128],"aligned":[130],"with":[132,174,198,272,323],"data":[133,173,197,209,229,274],"from":[134],"published":[135],"genomes":[137],"followed":[138],"by":[139,240,251],"phylogenetic":[140,149,234],"analyses":[141],"Maximum":[143],"Likelihood":[144],"Bayesian":[146],"approaches,":[147],"summarising":[148],"results":[150],"separately":[151],"non-coding":[153],"introns":[154],"intergenic":[156],"spacers,":[157],"that":[161,269],"are,":[162],"or":[163],"are":[164],"not,":[165],"involved":[166],"combined":[170],"sequences":[175,203],"three":[177],"highly":[178],"variable":[179],"noncoding":[180],"used":[183,218],"previous":[185],"greater":[188],"numbers":[189],"taxa,":[191],"similarly":[193],"more":[199],"densely":[200],"sampled":[201],"ITS":[202],"assessed":[205],"whether":[206],"adding":[207],"such":[208],"resulted":[210],"improved":[212],"support":[213,265],"consistent":[215,271],"topologies.":[216],"a":[219,225,267,279,318],"sequence":[221],"matrix":[222],"infer":[224],"dated":[226],"phylogeny.":[227],"Adding":[228],"did":[230],"not":[231,259],"always":[232],"improve":[233],"resolution":[235],"which":[236],"was":[237],"apparently":[238],"impacted":[239],"non-informative":[241],"variation":[242],"photosynthesis":[245,262,299],"related":[246,260,300],"well":[249],"conflicting":[252],"signals.":[256],"Chloroplast":[257],"provide":[263],"robust":[264],"topology":[268],"is":[270],"independent":[273],"may":[276],"therefore":[277],"represent":[278],"useful":[280],"tree":[282,289],"hypothesis.":[283],"cause":[285],"gene":[288,334],"conflicts":[290],"remains":[291],"unclear:":[292],"potential":[293],"explanations":[294],"include":[295],"functional":[296],"constraints":[297],"introgressive":[303],"hybridization":[304],"and/or":[305],"incomplete":[306],"lineage":[307],"sorting":[308],"during":[309],"an":[310],"ancient":[311],"rapid":[312],"divergence.":[313],"Further":[314],"testing":[315],"will":[316],"require":[317],"broader":[319],"sampling":[320],"lineages":[322],"different":[324],"photosynthetic":[325],"modes":[326],"multiple":[328],"informative,":[329],"independent,":[330],"selectively":[332],"neutral":[333],"trees.":[335]},"counts_by_year":[],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2026-01-20T00:00:00"}
