• We conducted maximum likelihood (ML), maximum parsimony (MP) and Bayesian (B) analyses on partial RNA polymerase largest (RPB1) and second largest subunit (RPB2) nucleotide sequences of 93 fusaria to infer the first comprehensive and well-supported phylogenetic hypothesis of evolutionary relationships within the genus and 20 of its near relatives. (usda.gov)
  • One of the basic questions in evolutionary analyses [ 1 ] is whether parasites (e.g., lice or Papillomaviruses) or mutualists have co-speciated with their respective hosts (e.g., mammals). (biomedcentral.com)
  • The uniparental inheritance and non-recombinant nature of cp genomes make them potentially useful tools for inferring evolutionary and ancient phylogenetic relationships. (plos.org)
  • Multiple analyses of these genomic data suggest that hybridization events have occurred throughout Ficus evolutionary history. (nature.com)
  • The mitochondrial (mt) genome has drawn increased attention during the genomic and now post-genomic eras owing to its maternal pattern of inheritance and unique evolutionary features, and is often used for the phylogenetic study of plants (Gualberto et al. (springeropen.com)
  • In recent years, significant progress has been made in the field of bioregionalisation by incorporating evolutionary information from phylogenetic trees, instead of solely emphasising the importance of endemic taxa or using taxonomic dissimilarity. (journalofbiogeographynews.org)
  • Toward a new synthesis: Major evolutionary trends in the angiosperm fossil record. (wikipedia.org)
  • Molecular phylogenetic analysis shows Buglossoporus be closely related to Neolentiporus. (wikipedia.org)
  • Our results reveal that similarities between the cuticular biochemical signatures of major plant groups (extant and fossil) are mostly consistent with recent phylogenetic hypotheses based on molecular and morphological data. (nature.com)
  • The introduction of molecular analysis of the relationships between these major groups, in the form of DNA sequence data, has revolutionised the subject in the last twenty years. (nmmra.org)
  • 1994) and the first combined molecular/morphological analysis (Albert et al. (cornell.edu)
  • 2000) and the combined molecular/morphological analysis of Archaefructus (Sun et al. (cornell.edu)
  • My role in these collaborative studies has been to apply my knowledge of angiosperm diversity and identification (see teaching section) in preliminary fossil identifications, followed by intensive cladistic analysis of morphological or combined morphological/molecular datasets to accurately and reproducibly identify fossils. (cornell.edu)
  • Molecular docking analysis demonstrated strong binding affinity between key bioactive components cyclamic acid, perfluoroalkyl carboxylic acid, perfluorosulfonic acid, alpha-linolenic acid, adenosine receptor antagonist (CGS 15943), and Prodigiosin and TOP2A and CDK1. (bvsalud.org)
  • In addition, phylogenetic analyses of a nuclear rDNA 28S D1-D2 domains (28S) dataset and analyses of a second dataset consisting of three genetic markers - nuc rDNA 28S D1-D2 domains (28S), nuc rDNA ITS1-5.8S-ITS2 ( ITS ), and translation elongation factor 1-alpha ( TEF1 ) - are performed to complement our morphological observations and place the newly described species in a molecular phylogenetic framework. (pensoft.net)
  • Molecular phylogenetic data (Soltis et al. (swbiodiversity.org)
  • Our studies of Cretaceous fossil flowers remain the most extensive, and I believe the most completely analyzed, of any angiosperm fossil flower sites, and provide the best view of the Late Cretaceous diversification of angiosperms into modern taxonomic groups. (cornell.edu)
  • In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. (frontiersin.org)
  • Taxonomic classification of the family Fagaceae and Betulaceae from Angiosperm Phylogenetic System Classification (APG II System) was successfully performed using supervised pattern recognition techniques. (lincoln.ac.uk)
  • As outlined by the case-study on smut fungi on page 6 these accelerated programs allow for more thorough large-scale co-phylogenetic analyses and extend the applicability of the approach by 1-2 orders of magnitude, thus closing the aforementioned performance gap concerning current phylogenetic meta-analysis tools. (biomedcentral.com)
  • The relationships recovered by these trees strongly support the current phylogenetic classification of palms. (morphobank.org)
  • In that context their approach was admitted to be overly optimistic in modelling how well a hypothetical student of extant groups would analyse characters. (nmmra.org)
  • My role in this paper was to develop the morphological matrix for extant seed plants, combine this with a selected three-gene data set, and analyze with our tools for large data set analysis. (cornell.edu)
  • Based on well-preserved fossil specimens and previously published data the phylogenetic relationships of extant and extinct lineages of Ommatidae were analyzed for the first time cladistically. (biomedcentral.com)
  • These attractive fossils provide a very good opportunity to study morphological transformations within the family, such as changes of body size and modifications of the antennae, prothorax and elytra, and induced us to carry out the phylogenetic investigation of extant and extinct groups of this ancestral group of beetles. (biomedcentral.com)
  • de Queiroz, K. and S. Poe (2001) Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration. (berkeley.edu)
  • The large amount of genomic data now available and statistical tools to analyze them provide unprecedented power for phylogenetic inference. (frontiersin.org)
  • Efficiency of algorithms for maximum likelihood phylogenetic inference. (arizona.edu)
  • Bias and variance in phylogenetic inference. (arizona.edu)
  • Here we show that geothermally resistant fossil cuticles of seed-bearing plants, analysed with Fourier transform infrared (FTIR) spectroscopy and hierarchical cluster analysis (HCA), retain biomolecular suites that consistently distinguish major taxa even after experiencing different diagenetic histories. (nature.com)
  • The highly efficient AxPcoords and AxParafit programs allow for large-scale co-phylogenetic analyses on several thousands of taxa for the first time. (biomedcentral.com)
  • However, most common co-phylogenetic tools or methods such as BPA, TreeMap or TreeFitter (see review in [ 13 ]) are not able to handle datasets with a large number of taxa or have not been tested in this regard with respect to their statistical properties. (biomedcentral.com)
  • 2000). I plan to continue these large-scale analyses, combining new approaches for the analysis of large data sets (e.g., the parsimony ratchet and Goloboff tree search methods) with new morphological data sets over large numbers of taxa. (cornell.edu)
  • Important findings We found that (1) leaf habit, be either EBL or DBL, was phylogenetically conserved in the 788 study angiosperm taxa. (plant-ecology.com)
  • Since the phylogenetic relationships of the taxa in Aleurodiscus s.l., as well as in the Stereaceae at large, are not resolved, we adopt a broad and inclusive generic concept of Aleurodiscus for the new taxa presented in this study. (pensoft.net)
  • This grant project is aimed to test several hypotheses explaining the controversy in the worldwide distribution pattern of angiosperm genome sizes. (muni.cz)
  • Furthermore, phylogenetic trees reconstructed under alternative hypotheses placed the putative whole-genome duplication event after the divergence of the S. cerevisiae and K. waltii lineages, but in the lineage leading to K. waltii . (biomedcentral.com)
  • Alternative phylogenetic hypotheses are highlighted for groups with uncertain position. (lu.se)
  • To test this hypothesis for campo rupestre vegetation, we analyzed phylogenetic diversity and community structure of angiosperm communities at two study sites within the Itacolomi State Park, Minas Gerais, Brazil. (scielo.br)
  • Plots representing more favorable habitats, such as those with a higher percentage of rocky outcrops that might permit the tapping of deeper water and nutrient resources as well as higher contents of clay and loam thereby increasing water and nutrient availability, show higher phylogenetic diversity and therefore lower phylogenetic clustering than plots with more sever habitats. (scielo.br)
  • 2009. Phylogenetic Resolution and Quantifying the Phylogenetic Diversity and Dispersion of Communities. (scielo.br)
  • 2. Phylogenetic relationships and diversity of higher seed plants and angiosperm groups. (cornell.edu)
  • We assessed changes in phylogenetic diversity of angiosperm flora on six oceanic islands located in the southeastern Pacific Ocean, by comparing flora from two periods: the pre-European colonization of islands and current times. (pucv.cl)
  • We hypothesize that, in the time between these periods, extinction of local plant species and addition of exotic plants modified phylogenetic-α-diversity at different levels (deeper and terminal phylogeny) and increased phylo-β-diversity among islands. (pucv.cl)
  • Despite extinction of 18 native angiosperm species, an increase in species richness and phylo-α-diversity was observed for all islands studied, attributed to introduction of exotic plants (between 6 to 477 species per island). (pucv.cl)
  • We did not observe significant variation of mean phylogenetic distance (MPD), a measure of the 'deeper' phylogenetic diversity of assemblages (e.g., orders, families), suggesting that neither extinctions nor introductions altered phylogenetic structure of the angiosperms of these islands. (pucv.cl)
  • In regard to phylo-β-diversity, we detected temporal turnover (variation in phylogenetic composition) between periods to flora (0.38 ± 0.11). (pucv.cl)
  • These results indicate that introduction of exotic angiosperms has contributed more notably than extinctions to the configuration of plant assemblages and phylogenetic diversity on the studied islands. (pucv.cl)
  • Because phylogenetic diversity is closely related to functional diversity (species trait variations and roles performed by organisms), our results suggests that the introduction of exotic plants to these islands could have detrimental impacts for ecosystem functions and ecosystem services that islands provide (e.g. productivity). (pucv.cl)
  • Castro, Sergio A. / Invasions but not extinctions change phylogenetic diversity of angiosperm assemblage on southeastern Pacific Oceanic islands . (pucv.cl)
  • Beyond morphoclines and trends: the elements of diversity and the phylogenetic patterning of morphology. (arizona.edu)
  • 1997 ). The comparative analysis of plant mt genomes enhances our understanding of genome rearrangement and DNA transfer mechanisms, and of phylogenetic diversity. (springeropen.com)
  • Wiley, E. O. (1981) Phylogenetics: The Theory and Practice of Phylogenetic Systematics. (berkeley.edu)
  • 2004. Morphological evolution and systematics of Synthyris and Besseya (Veroniceae): A phylogenetic analysis. (arizona.edu)
  • Homology and Systematics: Coding Characters for Phylogenetic Analysis. (arizona.edu)
  • We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition. (biomedcentral.com)
  • Thus, although plastome nucleotide composition shows "A+T richness", an A+T bias is not apparent upon more in-depth analysis, at least in these aspects. (biomedcentral.com)
  • similarly, between plots, DBLs were less diverse in phylogenetic composition, but more diverse in ecological behaviors, than EBLs. (plant-ecology.com)
  • On the other hand, divergence in phylogenetic composition of DBLs between plots increased with difference in mean annual temperature ( MAT ). (plant-ecology.com)
  • 2003. The major clades of Loasaceae: phylogenetic analysis using the plastid matK and trnL-trnF regions. (arizona.edu)
  • Phylogenetic analyses using Bayesian methods recovered a monophyletic grouping of all Dendrobium species (D. nobile, D. huoshanense, D. officinale, D. pendulum, D. strongylanthum and D. chrysotoxum). (plos.org)
  • However, more comprehensive studies including tests for phylogenetic signal of ecological niches are necessary before generalizations for larger regions may be carried out. (scielo.br)
  • Fig. 2 Phylogenetic (A) and ecological behavior dispersions (B) of evergreen and deciduous plants of the eight plots. (plant-ecology.com)
  • Fig. 3 Phylogenetic (A) and ecological behavior compositional differences (B) of evergreen and deciduous woody angiosperms of the eight plots. (plant-ecology.com)
  • Analysis of morphological characters in Commelinaceae indicate Geogenanthus is closely related to Dichoriscantieae and Siderasis, but Geogenanthus is placed as the sister to Dichoriscantieae and Siderasis in the cladogram from the combined morphology and sequence analysis, with high bootstrap value supporting the placement. (wikipedia.org)
  • I have been involved in several large analyses of seed plant/angiosperm relationships, beginning with a morphological analysis (Nixon et al. (cornell.edu)
  • We assembled a supermatrix consisting of 16 partitions, comprising DNA sequence data, plastid restriction fragment length polymorphism data, and morphological data for all genera, from which a highly resolved and well-supported phylogenetic tree was built despite abundant missing data. (morphobank.org)
  • Our analysis revealed that Cylindrocarpon formed a basal monophyletic sister to a 'terminal Fusarium clade' (TFC, sensu Gräfenhan et al. (usda.gov)
  • A phylogenetic analysis of land plant GSKs indicated that TaSK1 and TaSK2 belong to clade II of plant GSKs, the Arabidopsis members of which are all involved in Brassinosteroid signaling. (biomedcentral.com)
  • We test the ability of two targeted sequencing kits to resolve relationships in the C4 Cyperus clade, the universal Angiosperms-353 kit and a Cyperaceae-specific kit. (frontiersin.org)
  • Phylogenetic analysis of deduced protein sequences has shown that PcLFY belongs to the LFY-like clade. (embrapa.br)
  • Phylogenetic relationships and floral evolution in the papilionoid legume clade Amorpheae. (arizona.edu)
  • Phylogenetic analysis indicated a highly dynamic evolution of all three lipid-modifying enzymes in land plants, with many clade-specific duplications or losses and massive diversification of the C2-PLD family. (frontiersin.org)
  • A phylogenetic tree of 23 representative terrestrial plants strongly supports S. purpurea inclusion in the Malpighiales clade. (springeropen.com)
  • Phylogenetic relationships in the Commelinaceae: I. A cladistic analysis of rbcL sequences and morphology. (wikipedia.org)
  • A cladistic analysis of rbcL sequences and morphology. (wikipedia.org)
  • Therefore morphology as a basis for the construction of phylogenetic trees is a very low resolution and highly contestable method. (nmmra.org)
  • 2009. Complete Generic-Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches. (morphobank.org)
  • To construct supertrees, we used variants of matrix representation with parsimony (MRP) analysis based on input trees generated directly from subsamples of the supermatrix. (morphobank.org)
  • This study demonstrates that supertree and supermatrix methods can provide effective, explicit, and complimentary mechanisms for synthesizing disjointed phylogenetic evidence while emphasizing the need for further refinement of supertree methods. (morphobank.org)
  • 2006. Phylogenetic supermatrix analysis of GenBank sequences from 2228 Papilionoid legumes. (arizona.edu)
  • Phylogenetic relationships in the Commelinaceae: II. (wikipedia.org)
  • The capability to analyze large datasets is important to infer "deep co-phylogenetic" relationships which could otherwise not be assessed [ 14 ]. (biomedcentral.com)
  • The relationships between land plants, particularly the lower levels of the Bryophytes and the origins of the Angiosperms, has been a highly contested debate throughout the history of plant sciences. (nmmra.org)
  • Gilly, Charles Louis 1950 Phylogenetic development of the inflorescence and generic relationships in the Kobresiaceae Retrospective Theses and Dissertations 13679. (climb.com.tw)
  • Phylogenetic relationships of these four new species were inferred from analyses of a combined dataset consisting of three genetic markers, viz. (pensoft.net)
  • In the species studied FTIR in combination with multivariate analysis highlighted significant chemical differences in hemicelluloses, cellulose and guaiacyl (lignin) and shows promise as a suitable approach for wood sample classification. (lincoln.ac.uk)
  • A phylogenetic analysis determined F3'5'H first appeared in the Streptophyta and is present in only 41% of Angiosperm reference genomes. (usda.gov)
  • An analysis of DNA sequences indicate Geogenanthus is closely related to the genus Plowmanianthus followed by Cochliostema. (wikipedia.org)
  • Current tools for Co-phylogenetic analyses are not able to cope with the continuous accumulation of phylogenetic data. (biomedcentral.com)
  • The funders had no role in the study design, the data collection and analysis, the decision to publish, or the preparation of the manuscript. (plos.org)
  • My background in this area includes several papers focusing on various theoretical issues in phylogenetic analysis, and software implementations of "user-friendly" programs for data visualization and analysis. (cornell.edu)
  • Davis, Nixon, and Little 2004), the original analysis of the "3-gene" angiosperm data set (Soltis et al. (cornell.edu)
  • Our results demonstrate that data generated with a family-specific kit do not necessarily have more power than those obtained with a universal kit, but that data generated with different targeted sequencing kits can often be merged for downstream analyses. (frontiersin.org)
  • Survival curve and receiver operating characteristic (ROC) analyses were conducted using alcoholic HCC-related data from TCGA and GEO to determine the diagnostic value of the identified DEGs. (bvsalud.org)
  • Based on floristic studies, we assembled a phylogenetic tree from occurrence data that includes 921 species, of which 165 and 756 were native or exotic in origin, respectively. (pucv.cl)
  • Inferring angiosperm phylogeny from EST data with widespread gene duplication. (arizona.edu)
  • Fragmentation of large data sets in phylogenetic analyses. (arizona.edu)
  • We compiled distribution data and elevation ranges of angiosperms in the Sino-Himalaya and adjacent areas and reconstructed a species-level phylogenetic tree of 19,313 angiosperm species. (journalofbiogeographynews.org)
  • In this study, we built a regionalisation scheme of the Sino-Himalayan flora by combining phylogenetic and elevation data. (journalofbiogeographynews.org)
  • Doyle and Donoghue [1] whilst studying the role the Gnetales play in macroevolution stated that with slightly different characters, the relative parsimony of the two arrangements (referring to the nesting of Gnetales near the Angiosperms or the Coniferopsids) could of easily been reversed. (nmmra.org)
  • 2023. The phylogenetic reconstruction of the Neotropical cycad genus Ceratozamia (Zamiaceae) reveals disparate patterns of niche evolution. (montgomerybotanical.org)
  • Our analysis contributes toward understanding the organization and evolution of organelle genomes in Salicaceae species. (springeropen.com)
  • By comparative phylogenetic analysis we showed that CYP71P1 gene family emerged early in angiosperm evolution but has been recurrently lost in some lineages including Arabidopsis thaliana (L.) Heynh. (unibo.it)
  • Here, we report the identification and structural characterization of two GSK homologs named TaSK1 and TaSK2 in the hexaploid wheat genome as well as a widespread phylogenetic analysis of land plant GSKs. (biomedcentral.com)
  • In this paper we report the complete chloroplast genome sequences of the angiosperms Nuphar advena (Nymphaeaceae) and Ranunculus macranthus (Ranunculaceae). (biomedcentral.com)
  • In the majority of angiosperm chloroplast genomes two copies of a large inverted repeat (IR) of about 25 kb separate the remainder of the genome into two regions of unique DNA, the large (about 90 kb) and small (about 20 kb) single copy regions (LSC and SSC, respectively). (biomedcentral.com)
  • Genome-wide identification and expression analysis of the bZIP transcription factor family genes in response to abiotic stress in Nicotiana tabacum L. (biomedcentral.com)
  • Phylogenetic studies in the Commelinaceae subfamily Commelinoideae inferred from nuclear ribosomal and chloroplast DNA sequences. (wikipedia.org)
  • This array of sequences presents new opportunities to perform comparative analyses. (biomedcentral.com)
  • 2005. A phylogenetic analysis of Loasaceae subfamily Loasoideae based on plastid DNA sequences. (arizona.edu)
  • Angiosperm Phylogeny Group 1998, 2003) reveal that genera of Saxifragaceae in the broad sense are allied with at least ten separate, often distantly related families of flowering plants. (swbiodiversity.org)
  • Penthorum , the only genus in Penthoroideae of Saxifragaceae (H. G. A. Engler 1930), is morphologically anomalous in the Saxifragaceae and has often been included in Crassulaceae or, as treated here, its own family, Penthoraceae (Angiosperm Phylogeny Group 1998). (swbiodiversity.org)
  • Finally, our results also reveal that the extinct putative araucariacean, Allocladus , when analysed through HCA, is grouped closer to Ginkgoales than to conifers. (nature.com)
  • Robust and unequivocal interactions have been identified confirming the phylogenetic tree, although it's intricacies and temporal detail is still far from complete. (nmmra.org)
  • and (v) bivalve interactions with other FS were typically more positive at higher temperatures, but angiosperm‐seaweed interactions were not moderated by temperature.Synthesis: Despite variations in experimental and spatiotemporal conditions, the stronger positive interactions at higher temperatures suggest that facilitation, particularly involving bivalves, may become more important in a future warmer world. (bionomia.net)
  • 2010. " Assembling the Angiosperm Tree of Life: Progress and Future Prospects . (wikipedia.org)
  • 2014. From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. (nih.gov)
  • Based on a single ancestral gene in the last common ancestor of all land plants, paralogs were acquired and retained through paleopolyploidization events, resulting in six to eight genes in angiosperms. (biomedcentral.com)
  • TOP2A and CDK1 genes were identified as advantageous for diagnosing alcoholic HCC using univariate Cox regression, RF, survival curve, and ROC analysis. (bvsalud.org)
  • In angiosperms, flower formation is controlled by meristem identity genes, one of which, FLORICAULA (FLO)/LEAFY (LFY), plays a central role. (embrapa.br)
  • In contrast to angiosperms, conifers have two divergent genes resembling LFY. (embrapa.br)
  • The sophisticated statistical test for host-parasite co-phylogenetic analyses implemented in Parafit does not allow it to handle large datasets in reasonable times. (biomedcentral.com)
  • Parafit [ 15 ] implements statistical tests for both overall phylogenetic congruence as well as for the significance of individual associations. (biomedcentral.com)
  • This project will namely revise formerly observed patterns taking in to the account phylogenetic dependence of observed characters in the design and statistical analyses of experiments, and will test possible limitation of polyploids and larger genomes in phosphorus deficient environments hypothesized recently by Leitch & Leitch (2008) in Science. (muni.cz)
  • Thus, large-scale co-phylogenetic studies have also potentially become feasible. (biomedcentral.com)
  • I have a long standing research program in fossil angiosperms, beginning with a review of Tertiary fossil oaks in my Ph.D. thesis, continuing with papers on the earliest fossil evidence of Fagaceae in the Tertiary, and continuing with studies of Cretaceous fossil flowers in collaboration with Crepet and Gandolfo (see publication list). (cornell.edu)
  • Aims Evergreen (EBL) and deciduous broad-leaved (DBL) woody angiosperms are two major plant groups in the subtropical broad-leaved forests of eastern Asia. (plant-ecology.com)
  • I especially enjoy examining these suites in a phylogenetic context and view that such analyses can give us enhanced insight into interspecific differences. (phylodiversity.net)
  • However, when analyses were performed only considering native plants, we did not observe significant temporal turnover between periods (0.07 ± 0.06). (pucv.cl)
  • Abstract The aquatic Lemnaceae family, commonly called duckweed, comprises some of the smallest and fastest growing angiosperms known on Earth. (osti.gov)
  • 3. Fossil history of angiosperms. (cornell.edu)
  • I also was invited to collaborate on an analysis of what may be the oldest angiosperm fossil flower, Archaefructus. (cornell.edu)
  • Lastly, our results provide a robust framework and a useful guide for future analyses of this agriculturally and medically important genus. (usda.gov)
  • A candidate gene was selected based on flavonoid analysis and confirmed by recombinational mapping. (usda.gov)
  • The evolutionarily related flavonoid pathway gene flavonoid 3' hydroxylase (F3'H) is found nearly universally in all Angiosperms. (usda.gov)
  • We recently developed a pipeline involving homologous gene dotplotting and characterizing event-related gene collinearity to help the analysis of complex genomes. (biomedcentral.com)
  • This gene has a large C-terminal region of high similarity to angiosperm FLO/LFY orthologs and shorter regions of local similarity. (embrapa.br)
  • This has had grave implications on the creation of phylogenetic trees. (nmmra.org)
  • Here, we employed both methods to construct phylogenetic trees of all genera of palms (Arecaceae/Palmae), an iconic angiosperm family of great economic importance. (morphobank.org)
  • To the best of our knowledge, this study represents the largest co-phylogenetic analysis to date. (biomedcentral.com)
  • O'Keefe, F. R. and P. M. Sander (1999) Paleontological paradigms and inferences of phylogenetic pattern: a case study. (berkeley.edu)