In this paper, we explore possible conflict between morphological and molecular interpretations of phylogenetic relationships within the well-known peritrichous genus Zoothamnium. On the basis of morphological evidenc...In this paper, we explore possible conflict between morphological and molecular interpretations of phylogenetic relationships within the well-known peritrichous genus Zoothamnium. On the basis of morphological evidence, for a long time this genus has been believed to be a well-defined monophyletic taxon. Nonetheless, Zoothamnium exhibits higher genetic diversity than the gross morphology of its species. Here, we used all available genetic information for the small subunit of ribosomal RNA （SSU rRNA） and internal transcribed spacer region （ITS1-5.8S-ITS2） for this genus to reconstruct phylogenies for four datasets （SSU rRNA, ITS1, ITS2, and ITS1-5.8S-ITS2） and a combined dataset （SSU rRNA＋ITSI-5.8S- ITS2） using different phylogenetic methods and with consideration of the secondary structure of the genes. Confidence in phylogenetic tree selection was assessed with the approximately unbiased test. The molecular results showed both that Zoothamnium is more likely to be polyphyletic, and morphologically similar genera Zoothamnopsis and Myoschiston were always nested among Zoothamnium species. Accordingly, as with some other groups of ciliates, to understand more fully the correct phylogeny of Zoothamnium there remains a need for additional data from both morphological and molecular studies, covering additional Zoothamnium spp. and members of closely related genera （e.g. Zoothamnopsis, Myoschiston, and Epistylis）.展开更多
Tectariaceae are a pantropical fern family of about 20 genera, among which 8 are distributed in China. The morphological distinctiveness of the family is widely recognized, yet relatively little systematic research ha...Tectariaceae are a pantropical fern family of about 20 genera, among which 8 are distributed in China. The morphological distinctiveness of the family is widely recognized, yet relatively little systematic research has been conducted on members of Tectariaceae. Phylogenetic analyses of chloroplast DNA sequence data (rbcL; atpB) from 15 species representing all 8 genera in China were carried out under parsimony criteria; Bayesian inference. The phylogenetic reconstructions indicated that the fern family Tectariaceae as traditionally circumscribed are polyphyletic. Ctenitis, Dryopsis, Lastreopsis clustered with; should be included within the newly-defined Dryopteridaceae,; Pleocnemia is also tentatively assigned to it. A narrowly monophyletic Tectariaceae is identified, which includes Ctenitopsis, Hemigramma, Pteridrys, Quercifilix,; Tectaria. In the single rbcL analysis, Arthropteris clustered with the above-mentioned monophyletic Tectariaceae. Although further investigations are still needed to identify infrafamilial relationships within the monophyletic Tectariaceae; to redefine several problematic genera, we propose a working concept here that better reflects the inferred evolutionary history of this group.展开更多
Hybridization and introgression have long obscured relationships within Adenophora and its relatives,complicating generic delimitation.Leveraging deep genome skimming(DGS)data,we generated a large dataset,including th...Hybridization and introgression have long obscured relationships within Adenophora and its relatives,complicating generic delimitation.Leveraging deep genome skimming(DGS)data,we generated a large dataset,including thousands of single-copy nuclear(SCN)genes and plastomes,to untangle this reticulate history.Specifically,9.89 terabytes(TB)of DGS data from 165 samples—representing 48 species and 13 subspecies of Adenophora(out of ca.72 species)plus 24 outgroup species—yielded 1506 SCN genes and 77 plastid coding sequences.Tree-like phylogenies inferred with both coalescent-and concatenation-based methods revealed pronounced gene tree heterogeneity.Subsequent analysis showed that incomplete lineage sorting contributed minimally to this discordance;instead,hybridization and introgression were the primary drivers of early diversification.Integrating phylogenomic,morphological,and geographic evidence,we propose a revised generic framework for this group.Adenophora is expanded to include Campanula delavayi and the Korean Peninsula endemic genus Hanabusaya.We also recommend reinstating Hyssaria as a distinct Central Asian genus and introducing two new genera,Boreoasia and Rosomala.展开更多
基金Supported by the National Natural Science Foundation of China(Nos.31071898,31111120437)the Scientific Research Foundation for the Returned Overseas Chinese Scholars,State Education Ministry of China+1 种基金the Key Laboratory of Mariculture(KLM),Ministry of Education,Ocean University of China,the Research Group Project(No.RGP-VPP-083)the King Saud University Deanship of Scientific Research
文摘In this paper, we explore possible conflict between morphological and molecular interpretations of phylogenetic relationships within the well-known peritrichous genus Zoothamnium. On the basis of morphological evidence, for a long time this genus has been believed to be a well-defined monophyletic taxon. Nonetheless, Zoothamnium exhibits higher genetic diversity than the gross morphology of its species. Here, we used all available genetic information for the small subunit of ribosomal RNA （SSU rRNA） and internal transcribed spacer region （ITS1-5.8S-ITS2） for this genus to reconstruct phylogenies for four datasets （SSU rRNA, ITS1, ITS2, and ITS1-5.8S-ITS2） and a combined dataset （SSU rRNA＋ITSI-5.8S- ITS2） using different phylogenetic methods and with consideration of the secondary structure of the genes. Confidence in phylogenetic tree selection was assessed with the approximately unbiased test. The molecular results showed both that Zoothamnium is more likely to be polyphyletic, and morphologically similar genera Zoothamnopsis and Myoschiston were always nested among Zoothamnium species. Accordingly, as with some other groups of ciliates, to understand more fully the correct phylogeny of Zoothamnium there remains a need for additional data from both morphological and molecular studies, covering additional Zoothamnium spp. and members of closely related genera （e.g. Zoothamnopsis, Myoschiston, and Epistylis）.
基金Supported by the National Natural Science Foundation of China (Nos. 30121003 and 30228004)National Basic Research Program of China (973 Program No. 2007CB411600)Wong Kuan Chung Education Foundation of Hong Kong
文摘Tectariaceae are a pantropical fern family of about 20 genera, among which 8 are distributed in China. The morphological distinctiveness of the family is widely recognized, yet relatively little systematic research has been conducted on members of Tectariaceae. Phylogenetic analyses of chloroplast DNA sequence data (rbcL; atpB) from 15 species representing all 8 genera in China were carried out under parsimony criteria; Bayesian inference. The phylogenetic reconstructions indicated that the fern family Tectariaceae as traditionally circumscribed are polyphyletic. Ctenitis, Dryopsis, Lastreopsis clustered with; should be included within the newly-defined Dryopteridaceae,; Pleocnemia is also tentatively assigned to it. A narrowly monophyletic Tectariaceae is identified, which includes Ctenitopsis, Hemigramma, Pteridrys, Quercifilix,; Tectaria. In the single rbcL analysis, Arthropteris clustered with the above-mentioned monophyletic Tectariaceae. Although further investigations are still needed to identify infrafamilial relationships within the monophyletic Tectariaceae; to redefine several problematic genera, we propose a working concept here that better reflects the inferred evolutionary history of this group.
基金supported by the National Natural Science Foundation of China(grant numbers 32270216 and 32000163 to B.B.L.)the Youth Innovation Promotion Association CAS(2023086 to B.B.L.)the Biological Resources Programme,Chinese Academy of Sciences(CAS-TAX-24-013 to B.B.L.).
文摘Hybridization and introgression have long obscured relationships within Adenophora and its relatives,complicating generic delimitation.Leveraging deep genome skimming(DGS)data,we generated a large dataset,including thousands of single-copy nuclear(SCN)genes and plastomes,to untangle this reticulate history.Specifically,9.89 terabytes(TB)of DGS data from 165 samples—representing 48 species and 13 subspecies of Adenophora(out of ca.72 species)plus 24 outgroup species—yielded 1506 SCN genes and 77 plastid coding sequences.Tree-like phylogenies inferred with both coalescent-and concatenation-based methods revealed pronounced gene tree heterogeneity.Subsequent analysis showed that incomplete lineage sorting contributed minimally to this discordance;instead,hybridization and introgression were the primary drivers of early diversification.Integrating phylogenomic,morphological,and geographic evidence,we propose a revised generic framework for this group.Adenophora is expanded to include Campanula delavayi and the Korean Peninsula endemic genus Hanabusaya.We also recommend reinstating Hyssaria as a distinct Central Asian genus and introducing two new genera,Boreoasia and Rosomala.
