{"refrec":{"BRefID":355099,"RR":"<b>Fang, L.; Leliaert, F.; Novis, P.M.; Zhang, Z.; Zhu, H.; Liu, G.; Penny, D.; Zhong, B.</b> (2018). Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models. <i>Mol. Phylogenet. Evol. 127</i>: 248-255. <a href=\"https://dx.doi.org/10.1016/j.ympev.2018.06.006\" target=\"_blank\">https://dx.doi.org/10.1016/j.ympev.2018.06.006</a>","BEntID":352812,"PublicFlag":1,"CheckedFlag":0,"wosflag":1,"vabbflag":1,"RefStringPartII":". <i>Mol. Phylogenet. Evol. 127</i>: 248-255. <a href=\"https://dx.doi.org/10.1016/j.ympev.2018.06.006\" target=\"_blank\">https://dx.doi.org/10.1016/j.ympev.2018.06.006</a>","DocTypID":8,"DocType":"Journal article","MarineFlag":0,"FreshFlag":0,"BrackishFlag":0,"TerrestrialFlag":0,"Authorstring":"Fang, L.; Leliaert, F.; Novis, P.M.; Zhang, Z.; Zhu, H.; Liu, G.; Penny, D.; Zhong, B.","OrigTitleTranslFlag":0,"Authorstringtrunc":"Fang, L. <i>et al.</i>","Englishabstract":"Phylogenetic relationships within the green algal phylum Chlorophyta have proven difficult to resolve. The core Chlorophyta include Chlorophyceae, Ulvophyceae, Trebouxiophyceae, Pedinophyceae and Chlorodendrophyceae, but the relationships among these classes remain unresolved and the monophyly of Ulvophyceae and Trebouxiophyceae are highly controversial. We analyzed a dataset of 101 green algal species and 73 protein-coding genes sampled from complete and partial chloroplast genomes, including six newly sequenced ulvophyte genomes (<em>Blidingia minima</em> NIES-1837, <em>Ulothrix zonata</em>, <em>Halochlorococcum</em> sp. NIES-1838, <em>Scotinosphaera</em> sp. NIES-154, <em>Caulerpa brownii</em> and <em>Cephaleuros</em> sp. HZ-2017). We applied the Tree Certainty (TC) score to quantify the level of incongruence between phylogenetic trees in chloroplast genomic datasets, and show that the conflicting phylogenetic trees of core Chlorophyta stem from the most GC-heterogeneous sites. With removing the most GC-heterogeneous sites, our chloroplast phylogenomic analyses using heterogeneous models consistently support monophyly of the Chlorophyceae and of the Trebouxiophyceae, but the Ulvophyceae was resolved as polyphyletic. Our analytical framework provides an efficient approach to reconstruct the optimal phylogenetic relationships by minimizing conflicting signals.","AbstractOtherLang":null,"BibLvlCode":"AS","StandardTitle":"Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models","OrigTitleLangCode":"en","OrigTitleLangCodeExtended":"eng","OrigTitleLangID":15,"DateLastModified":{"date":"2026-04-17 01:32:45.932350","timezone_type":1,"timezone":"+02:00"},"UserAccessRight":null,"UserAccID":null,"AuthorKeywords":"Green algae; Phylogenomics; GC-heterogeneous sites; Heterogeneous models; Phylogenetic signals","OtherDescriptors":null,"Notes":null,"AnaPub":2018,"MonPub":null,"DateUpdate":"2022-08-23","DateCreate":"2022-08-23","SecASFANote":null,"ConfID":null,"PeerRev":1,"VlizCoreFlag":1,"WoScode":"WOS:000446021300021","VABBcode":null,"OpenAcc":0,"DOI":"10.1016/j.ympev.2018.06.006"},"refs":null,"anarec":{"AnaID":355099,"PubliDate":2018,"Pagination":"248-255","XtraPublOfAnaID":null,"ISBN":null,"Volume":"127","Issue":null,"BRefMon":null,"BRefMonRR":null,"BRefXtra":null,"BRefXtraRR":null,"SerBRefID":45071,"SerRR":"Molecular Phylogenetics and Evolution. 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