Phylogenetic studies of a large data set. I. Bambusoideae, Andropogonodae, and Pooideae (Gramineae)
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The Calymperaceae are a large pantropical moss clade. This paper reports the results of a phylogenetic analysis of the Calymperaceae, with an emphasis on the relationships of the large and putatively polyphyletic Syrrhopodon. Two chloroplast genes, rps4 and trnL, part of the nuclear encoded gpd, and morphological characters were analyzed individually and in combination. The total-evidence phylogenetic tree was used to construct a rank-free classification of the Calymperaceae following the guidelines of the current draft of the PhyloCode. The total-evidence cladistic analysis supports the monophyly of Calymperes and Mitthyridium, as well as the “leucobryoid” Calymperaceae, and confirms that Syrrhopodon (s.l.) is polyphyletic. In the context of this phylogeny, the presence of peristome teeth and bordered leaves are derived features within the Calymperaceae. The rank-free system of classification has several advantages over the Linnaean system for dealing with the taxonomic changes implicit in this phylogeny, primarily with regard to preserving the names of well-supported monophyletic groups such as Mitthyridium. However, we question the utility of article 11.7 of the PhyloCode, and offer some practical observations regarding clade names and the use of type specimens as specifiers.
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The analysis of two-stiped dichograptids, largely of baltograptid and expansograptid taxa of the family Didymograptidae from the Floian of northwestern Argentina, provides insight into the evolutionary relationships of this group. The important proximal end characters clearly cluster the baltograptids with the derived genera Didymograptus and Aulograptus. One of the analyses provides the information that the genera Cymatograptus and Expansograptus share a common ancestor but are not closely related to the two-stiped Kiaerograptus and related taxa. Likewise, with the exception of some controversial taxa, the families Tetragraptidae and Didymograptidae can be readily differentiated, supporting previous interpretations that they represent monophyletic clades. Although the present analyses are poorly supported, they provide hypotheses that could be further tested based on new data on isolated dichograptid taxa based on isolated or relief-preserved material.
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One hundred of morphological characters of 69 species (representing 52 genera and all tribes and sub-tribes of the subfamily Chloridoideae of Gramineae) are used to reconstruct the phylogeny for the Chloridoideae. Cladistic analysis show that the monophyly of Chloridoideae and its origination from danthonoid group aresupported. Five clades are found in correlation with traditional classification systems. Clade A comprises 2 genera of Pappophoreae, clade B 5 genera of Eragrostideae, clade C 6 genera of Eragrostideae, clade D 9 genera of Eragrostideae, and clade E comprises 8 genera of Eragrostideae, 9 genera of Chlorideae, and 1 genus of leptureae. The two largest tribes Eragrostideae and Chlorideae turn out to be polyphyletic. The chlorideae affinity of Leptureae is substantiated in the cladistic study. The basal tribe Pappophoreae may provide a link between the chloridoids and the danthonoids. A pattern of segregation of species from Old World to New World is evident in several clades. These results provide a framework for further studies at the supra-generic levels moving toward to a comprehensive systematic treatment of the Chloridoideae.
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Humans are fish according to a cladistic understanding. In the first of a series on technical nomenclature, evolutionary theorist Bret Weinstein distinguishes clade, taxon, and monophyletic group from functional groupings, arguing that taxonomic labels should fully track cladistic relationships.
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The lack of organisation of monophyletic lineages in the phylogeny and taxonomy of the group formerly known as protists has precluded the understanding of the group’s evolutionary history and trait comparison among members of the group. We used a phylogenomic approach to establish phylogenetic hypotheses of this group of organisms. We used an automatic orthologous clustering (OrthoMCL)-based strategy to recover 72 clusters of orthologues from 73 eukaryotic species. A maximum likelihood tree was inferred from the supermatrix. Overall, we obtained consistent inferences with previous published ones, but some unexpected phylogenetic relationships were poorly supported. Despite the large quantity of genes from the Opisthokonta groups, this clade was recovered as polyphyletic. We failed to recover a monophyletic Excavata group, most likely because of longbranch attraction artefacts. A second dataset was constructed after removing the fast-evolving/saturated sites, and a Shimodaira-Hasegawa test was performed to verify whether our data allowed us to reject relationships in previous hypotheses. The results of these tests suggested that the competing tree topologies were not significantly better than our recovered topologies. Novel relationships were shown inside the Opisthokonta, for two species, Thecamonas trahens and Capsaspora owczarzaki. Additionally, some controversial phylogenetic positions among several eukaryotic groups were found. We discuss the relative positions of the Alveolata and Stramenopila groups, the latter being of special interest in our research group. © 2016. Acad. Colomb. Cienc. Ex. Fis. Nat. All rights reserved.
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The family Cleomaceae is in need of taxonomic revision, which begins here with a set of taxa informally recognized as the North American cleomoid clade. This group is evaluated first because molecular-based analyses almost comprehensively sample this lineage. These investigations revealed that the two largest genera, Cleomella and Peritoma, are para- or polyphyletic. Strong support from molecular data necessitates name changes for these taxa. Furthermore, controversy exists on the recognition of the remaining genera, owing to morphological variation and specialization. Three possible classification scenarios are described to accommodate monophyletic lineages based on previously-published evidence. The option to create the single large genus Cleomella is proposed, and as a result one new name, Cleomella oxystyloides, is provided, and 12 new combinations are made: C. arborea, C. arborea var. angustata, C. arborea var. globosa, C. californica, C. jonesii, C. lutea, C. multicaulis, C. palmeri, C. platycarpa, C. refracta, C. serrulata, and C. sparsifolia. Two lectotypes and one isolectotype are designated, and another lectotype is confirmed.
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