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Journal articles on the topic '"Robust" clade'

Author: Grafiati

Published: 5 June 2025

Last updated: 15 July 2025

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1

Wallach, Van, Rune Midtgaard, and Emma Hsiao. "Revalidation of the Arboreal Asian Snake Genera Gonyophis Boulenger, 1891; Rhynchophis Mocquard, 1897; and Rhadinophis Vogt, 1922, with Description of a New Genus and Tribe (Squamata: Serpentes: Colubridae)." Diversity 16, no. 9 (2024): 576. http://dx.doi.org/10.3390/d16090576.

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Based on the latest molecular phylogenies of Gonyosoma sensu lato, which recovered five clades with robust support, we utilize morphological characters to demonstrate the distinctiveness of each clade, resulting in the resurrection of three genera (Gonyophis Boulenger, 1891; Rhynchophis Mocquard, 1897; and Rhadinophis Vogt, 1922) and a proposal of a new genus and a new tribe. A synopsis of the group, with descriptions and diagnoses, is provided for the five genera and eight species in addition to distribution maps and illustrations of the head of each taxon. An artificial key to the species an

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Hedman, Matthew M. "Constraints on clade ages from fossil outgroups." Paleobiology 36, no. 1 (2010): 16–31. http://dx.doi.org/10.1666/0094-8373-36.1.16.

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This paper presents a method for constraining the age of a clade with the ages of the earliest fossil specimens in that clade's outgroups. Given a sufficiently deep, robust, well-resolved, and stratigraphically consistent cladogram, this method can yield useful age constraints even in the absence of specific information about the fossil preservation and recovery rates of individual taxa. The algorithm is applied to simulated data sets to demonstrate that this method can yield robust constraints of clade ages if there are sufficient fossil outgroups available and if there is a finite chance tha

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Baker, Joanna, Andrew Meade, Mark Pagel, and Chris Venditti. "Nothing Wrong with the Analysis of Clades in Comparative Evolutionary Studies: A Reply to Poe et al." Systematic Biology 70, no. 1 (2020): 197–201. http://dx.doi.org/10.1093/sysbio/syaa067.

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Abstract In a recent paper, Poe et al. assert that scientists should abandon clade-based approaches, particularly those using named taxonomic ranks. Poe et al. attempt to demonstrate that clade selection can have effects on the results of evolutionary analyses but unfortunately fall short of making any robust conclusions. Here, we demonstrate that the assertions made by Poe et al. have two important flaws: (i) an erroneous view of modern phylogenetic comparative methods; and (ii) a lack of statistical rigor in their analyses. We repeat Poe et al.’s analysis but using appropriate phylogenetic c

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Martins, Amely Branquinho, Mônica Mafra Valença-Montenegro, Marcela Guimarães Moreira Lima, et al. "A New Assessment of Robust Capuchin Monkey (Sapajus) Evolutionary History Using Genome-Wide SNP Marker Data and a Bayesian Approach to Species Delimitation." Genes 14, no. 5 (2023): 970. http://dx.doi.org/10.3390/genes14050970.

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Robust capuchin monkeys, Sapajus genus, are among the most phenotypically diverse and widespread groups of primates in South America, with one of the most confusing and often shifting taxonomies. We used a ddRADseq approach to generate genome-wide SNP markers for 171 individuals from all putative extant species of Sapajus to access their evolutionary history. Using maximum likelihood, multispecies coalescent phylogenetic inference, and a Bayes Factor method to test for alternative hypotheses of species delimitation, we inferred the phylogenetic history of the Sapajus radiation, evaluating the

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Matsui, Kumiko, and Takanobu Tsuihiji. "The phylogeny of desmostylians revisited: proposal of new clades based on robust phylogenetic hypotheses." PeerJ 7 (October 17, 2019): e7430. http://dx.doi.org/10.7717/peerj.7430.

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Background Desmostylia is a clade of extinct aquatic mammals with no living members. Today, this clade is considered belonging to either Afrotheria or Perissodactyla. In the currently-accepted taxonomic scheme, Desmostylia includes two families, 10 to 12 genera, and 13–14 species. There have been relatively few phylogenetic analyses published on desmostylian interrelationship compared to other vertebrate taxa, and two main, alternative phylogenetic hypotheses have been proposed in previous studies. One major problem with those previous studies is that the numbers of characters and OTUs were sm

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NADLER, S. A., R. A. CARRENO, H. MEJÍA-MADRID, et al. "Molecular phylogeny of clade III nematodes reveals multiple origins of tissue parasitism." Parasitology 134, no. 10 (2007): 1421–42. http://dx.doi.org/10.1017/s0031182007002880.

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SUMMARYMolecular phylogenetic analyses of 113 taxa representing Ascaridida, Rhigonematida, Spirurida and Oxyurida were used to infer a more comprehensive phylogenetic hypothesis for representatives of ‘clade III’. The posterior probability of multiple alignment sites was used to exclude or weight characters, yielding datasets that were analysed using maximum parsimony, likelihood, and Bayesian inference methods. Phylogenetic results were robust to differences among inference methods for most high-level taxonomic groups, but some clades were sensitive to treatments of characters reflecting diff

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Kadam, Suhas K., Rohit N. Mane, Asif S. Tamboli, Akshay P. Jangam, Yeon-Sik Choo, and Jae Hong Pak. "Molecular phylogenetic and biogeographic evidence of Lepidagathis Willd. (Acanthaceae, Barlerieae) focusing on Indian endemics." PhytoKeys 248 (October 31, 2024): 223–36. http://dx.doi.org/10.3897/phytokeys.248.133776.

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Lepidagathis Willd., a genus belonging to the Acanthaceae family, is primarily distributed in tropical and subtropical regions worldwide, encompassing approximately 153 species. While considerable morphological research has been conducted on Lepidagathis, it has not completely dispelled taxonomic ambiguities and conflicting interpretations. Molecular analysis emerges as a valuable tool for resolving these taxonomic uncertainties, but the availability of nucleotide sequence data for Lepidagathis has been limited thus far. This study delivers a phylogenetic analysis of Lepidagathis species, util

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YUN, CHAN-GYU. "SPINOSAURS AS PHYTOSAUR MIMICS: A CASE OF CONVERGENT EVOLUTION BETWEEN TWO EXTINCT ARCHOSAURIFORM CLADES." Acta Palaeontologica Romaniae, no. 20 (1) (September 9, 2023): 17–29. http://dx.doi.org/10.35463/j.apr.2024.01.02.

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Spinosaurids are a highly morphologically specialized clade of large tetanuran theropod dinosaurs, characterized by their proportionally long, narrow snouts and conical teeth with fluted surfaces. The unusual morphology of spinosaurids has been usually compared with modern crocodilians, but distinct differences between them have been reported as well. Here, numerous craniodental characters that are shared by spinosaurids and large, robust phytosaurs often termed as “brachyrostral” forms are reviewed. Phytosaurs are a clade of carnivorous archosauriforms that resemble crocodilians in overall mo

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Aslanyan, Levon, Hranush Avagyan, and Zaven Karalyan. "Whole-genome-based phylogeny of African swine fever virus." October-2020 13, no. 10 (2020): 2118–25. http://dx.doi.org/10.14202/vetworld.2020.2118-2125.

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Aim: A genome-scale phylogenetic analysis was used to infer the evolutionary dynamics of Asfarviridae – African swine fever virus (ASFV) – and better define its genetic diversity. Materials and Methods: All complete ASFV genomes from NCBI's resource as of March 2020 were used. The phylogenetic analysis used maximum likelihood and neighbor-joining methods. The evolutionary models detection was done with the help of the package of programs MEGA-X. Algorithms were used to build phylogenetic trees for type B DNA polymerases of ASFV (n=34) and HcDNAV (n=2), as an external group. Results: An expedie

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Kadam, Suhas K., Rohit N. Mane, Asif S. Tamboli, Akshay P. Jangam, Yeon-Sik Choo, and Jae Hong Pak. "Molecular phylogenetic and biogeographic evidence of Lepidagathis Willd. (Acanthaceae, Barlerieae) focusing on Indian endemics." PhytoKeys 248 (October 31, 2024): 223–36. https://doi.org/10.3897/phytokeys.248.133776.

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<i>Lepidagathis</i> Willd., a genus belonging to the Acanthaceae family, is primarily distributed in tropical and subtropical regions worldwide, encompassing approximately 153 species. While considerable morphological research has been conducted on <i>Lepidagathis</i>, it has not completely dispelled taxonomic ambiguities and conflicting interpretations. Molecular analysis emerges as a valuable tool for resolving these taxonomic uncertainties, but the availability of nucleotide sequence data for <i>Lepidagathis</i> has been limited thus far. This study delivers a phylogenetic analysis of <i>Le

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Brower, Andrew, Niklas Wahlberg, Thomas Simonsen, and Rienk de Jong. "Morphology, molecules and fritillaries: approaching a stable phylogeny for Argynnini (Lepidoptera: Nymphalidae)." Insect Systematics & Evolution 37, no. 4 (2006): 405–18. http://dx.doi.org/10.1163/187631206788831407.

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AbstractWe examine the phylogenetic relationships among 29 species of Argynnini based on 141 previously published morphological characters and new data from the mitochondrial gene COI and the two nuclear genes EF-1a and wingless. We investigate the stability and robustness of the resulting phylogenetic hypotheses through various combinations of the 4 functionally separate datasets. Increasing the number of datasets in combined analyses led to increased support for clades, sometimes substantially. We find that the tribe Argynnini is a well-supported, robust, monophyletic clade with the followin

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Joshi, Jahnavi, Praveen K. Karanth, and Gregory D. Edgecombe. "The out-of-India hypothesis: evidence from an ancient centipede genus, Rhysida (Chilopoda: Scolopendromorpha) from the Oriental Region, and systematics of Indian species." Zoological Journal of the Linnean Society 189, no. 3 (2019): 828–61. http://dx.doi.org/10.1093/zoolinnean/zlz138.

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Abstract The Oriental Region has been a focus of biogeographical research for more than two centuries. We examined systematics and biogeography of the centipede genus Rhysida in this region. A robust species hypothesis for the Indian subcontinental and Southeast Asian Rhysida clade uses molecular, morphological and distribution data. Twelve species are recognized in two monophyletic species complexes, eight belonging to the Rhysida immarginata and four to the Rhysida longipes species complex. They include Rhysida aspinosa, Rhysida crassispina, R. immarginata, R. longipes and seven new species,

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FREEMAN, BARBIE, LEO G. NICO, MATTHEW OSENTOSKI, HOWARD L. JELKS, and TIMOTHY M. COLLINS. "Molecular systematics of Serrasalmidae: Deciphering the identities of piranha species and unraveling their evolutionary histories." Zootaxa 1484, no. 1 (2007): 1–38. http://dx.doi.org/10.11646/zootaxa.1484.1.1.

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Piranhas and their relatives have proven to be a challenging group from a systematic perspective, with difficulties in identification of species, linking of juveniles to adults, diagnosis of genera, and recognition of higher-level clades. In this study we add new molecular data consisting of three mitochondrial regions for museum vouchered and photo-documented representatives of the Serrasalmidae. These are combined with existing serrasalmid sequences in GenBank to address species and higher-level questions within the piranhas using parsimony and Bayesian methods. We found robust support for t

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Seaman, Michael S., Ling Xu, Kristin Beaudry, et al. "Multiclade Human Immunodeficiency Virus Type 1 Envelope Immunogens Elicit Broad Cellular and Humoral Immunity in Rhesus Monkeys." Journal of Virology 79, no. 5 (2005): 2956–63. http://dx.doi.org/10.1128/jvi.79.5.2956-2963.2005.

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ABSTRACT The development of a human immunodeficiency virus type 1 (HIV-1) vaccine that elicits potent cellular and humoral immune responses recognizing divergent strains of HIV-1 will be critical for combating the global AIDS epidemic. The present studies were initiated to examine the magnitude and breadth of envelope (Env)-specific T-lymphocyte and antibody responses generated by vaccines containing either a single or multiple genetically distant HIV-1 Env immunogens. Rhesus monkeys were immunized with DNA prime-recombinant adenovirus boost vaccines encoding a Gag-Pol-Nef polyprotein in combi

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Jackson, Donavan J., and Joseph A. Cook. "A precarious future for distinctive peripheral populations of meadow voles (Microtus pennsylvanicus)." Journal of Mammalogy 101, no. 1 (2019): 36–51. http://dx.doi.org/10.1093/jmammal/gyz196.

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Abstract Conservation efforts rely on robust taxonomic assessments that should be based on critical assessment of interspecific boundaries, infraspecific variation, and potentially distinctive peripheral populations. The meadow vole (Microtus pennsylvanicus) is widely distributed across North America, including 28 morphologically defined subspecies and numerous isolated populations. Because some subspecies are of high conservation concern, we examined geographic variation across the range of the species to test existing infraspecific taxonomy in terms of local and regional diversification. We

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Bromham, Lindell D., and Bernard M. Degnan. "Hemichordates and deuterostome evolution: robust molecular phylogenetic support for a hemichordate + echinoderm clade." Evolution and Development 1, no. 3 (1999): 166–71. http://dx.doi.org/10.1046/j.1525-142x.1999.99026.x.

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Arredondo, Juan Camilo, Felipe Gobbi Grazziotin, Gustavo Jose Scrocchi Manfrini, Miguel Trefaut Urbano Rodrigues, Sandro Luís Bonatto, and Hussam El Dine Zaher. "Molecular phylogeny of the tribe Philodryadini Cope, 1886 (Dipsadidae: Xenodontinae): Rediscovering the diversity of the South American Racers." Papéis Avulsos de Zoologia 60 (October 20, 2020): e20206053. http://dx.doi.org/10.11606/1807-0205/2020.60.53.

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South American racers of the tribe Philodryadini are a widespread and diverse group of Neotropical snakes with a complex taxonomic and systematic history. Recent studies failed to present a robust phylogenetic hypothesis for the tribe, mainly due to incomplete taxon sampling. Here we provide the most extensive molecular phylogenetic analysis of Philodryadini available so far, including 20 species (83% of the known diversity) from which six were not sampled previously. Our results reveal that Philodryadini is not monophyletic, but instead includes a central Andean clade formed by Philodryas sim

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Brocklehurst, Neil. "Morphological evolution in therocephalians breaks the hypercarnivore ratchet." Proceedings of the Royal Society B: Biological Sciences 286, no. 1900 (2019): 20190590. http://dx.doi.org/10.1098/rspb.2019.0590.

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Large carnivorous mammals have been suggested to show a ratchet-like mode of morphological evolution. A limited number of specializations for hypercarnivory evolve repeatedly in multiple clades, with those lineages evolving such specialities being unable to retreat back along their evolutionary trajectory or jump between adaptive peaks. While it has been hypothesized that such mechanisms should have applied to the evolution of other terrestrial carnivores, the non-mammalian synapsid clade Therocephalia appears to defy this expectation. The earliest, basalmost members of this clade are large ma

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BEAMER, DAVID A., and TRIP LAMB. "Towards rectifying limitations on species delineation in dusky salamanders (Desmognathus: Plethodontidae): An ecoregion-drainage sampling grid reveals additional cryptic clades." Zootaxa 4734, no. 1 (2020): 1–61. http://dx.doi.org/10.11646/zootaxa.4734.1.1.

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Dusky salamanders (Desmognathus) constitute a large, species-rich group within the family Plethodontidae, and though their systematic relationships have been addressed extensively, most studies have centered on particular species complexes and therefore offer only piecemeal phylogenetic perspective on the genus. Recent work has revealed Desmognathus to be far more clade rich—35 reciprocally monophyletic clades versus 22 recognized species—than previously imagined, results that, in turn, provide impetus for additional survey effort within clades and across geographic areas thus far sparsely sam

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Sigwart, Julia D., Isabella Stoeger, Thomas Knebelsberger, and Enrico Schwabe. "Chiton phylogeny (Mollusca : Polyplacophora) and the placement of the enigmatic species Choriplax grayi (H. Adams & Angas)." Invertebrate Systematics 27, no. 6 (2013): 603. http://dx.doi.org/10.1071/is13013.

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Shallow marine chitons (Mollusca : Polyplacophora : Chitonida) are widespread and well described from established morphoanatomical characters, yet key aspects of polyplacophoran phylogeny have remained unresolved. Several species, including Hemiarthrum setulosum Carpenter in Dall, 1876, and especially the rare and enigmatic Choriplax grayi (Adams & Angas, 1864), defy systematic placement. Choriplax is known from only a handful of specimens and its morphology is a mosaic of key taxonomic features from two different clades. Here, new molecular evidence provides robust support for its correct

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SAENGPHAN, NUKUL, BHINYO PANIJPAN, SAENGCHAN SENAPIN, et al. "Morphology and molecular phylogeny of Macrobrachium suphanense sp. nov. (Decapoda: Palaemonidae) from Thailand." Zootaxa 4482, no. 1 (2018): 151. http://dx.doi.org/10.11646/zootaxa.4482.1.7.

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A small freshwater prawn in Thailand has been found to be a new species and is named Macrobrachium suphanense (Decapoda: Palaemonidae). Fully grown male M. suphanense appeared very different from the most closely related male of M. sintangense: size smaller, second pereiopod smaller and less robust, rostrum form different and, in females, fewer eggs. Less closely related, fully grown M. dolatum has sharper distal cutting edge on fixed finger and M. hungi has longer rostrum than M. suphanense. DNA analyses put M. suphanense, M. sintangense and M. nipponense in the same clade with M. nipponense

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GUERATTO, CAIO, AMANDA CRUZ MENDES, and RICARDO PINTO-DA-ROCHA. "Description of two new species of Magnispina and a new hypothesis of phylogenetic relationships for Heteropachylinae (Opiliones: Laniatores: Gonyleptidae)." Zootaxa 4300, no. 2 (2017): 180. http://dx.doi.org/10.11646/zootaxa.4300.2.2.

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Two new species of Heteropachylinae Kury, 1994, are described: Magnispina robusta sp. nov. and Magnispina bahiana sp. nov., both from Serra Bonita Natural Reserve, Camacan, Bahia, Brazil. Magnispina robusta sp. nov. is diagnosed by: free tergites II–III with tubercles on their lateral margins, free tergite III without median armature, dorsal anal operculum with a robust bifurcate median apophysis, femur IV slightly curved (convex side outwards ) in dorsal view and straight in lateral view, with a basal, a robust median and a subapical apophyses on dorsal face. Magnispina bahiana sp. nov. is di

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Noshiro, S., and P. Baas. "Systematic Wood Anatomy of Cornaceae and Allies." IAWA Journal 19, no. 1 (1998): 43–97. http://dx.doi.org/10.1163/22941932-90000652.

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The wood anatomy of Comaceae, Alangiaceae, Garryaceae, and Nyssaceae constituting the Comales in the sense of Cronquist (1981, 1988) is described in great detail and subjected to a cladistic analysis. A microscopic identification key to the woods studied is given. The alliance includes seventeen genera, mostly of trees and shrubs, very rarely herbs. Although wood anatomically fairly homogeneous, variation exists in both qualitative and quantitative characters. Some of the latter show distinct latitudinal trends within individual genera, and character states have only been recognised taking the

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Medina-Ortiz, Abraham J., Teófilo Herrera, Marco A. Vásquez-Dávila, Huzefa A. Raja, and Mario Figueroa. "The genus Podaxis in arid regions of Mexico: preliminary ITS phylogeny and ethnomycological use." MycoKeys 20 (March 6, 2017): 17–36. https://doi.org/10.3897/mycokeys.20.11570.

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Identification of Podaxis species to species-level based on morphology alone is problematic. Thus, species of the genus Podaxis are in dire need of taxonomic and phylogenetic evaluations using molecular data to develop a consensus between morphological taxonomy and more robust molecular analyses. In Mexico, most of the collected specimens of Podaxis have been morphologically identified as Podaxis pistillaris sensu lato and are locally used for its culinary value. In this study, the internal transcribed spacer region of Podaxis specimens from the MEXU fungarium collected between 1948 and 2014 f

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Bello, Sarah, Mohammad Howard-Azzeh, Herb E. Schellhorn, and Radhey S. Gupta. "Phylogenomic Analyses and Molecular Signatures Elucidating the Evolutionary Relationships amongst the Chlorobia and Ignavibacteria Species: Robust Demarcation of Two Family-Level Clades within the Order Chlorobiales and Proposal for the Family Chloroherpetonaceae fam. nov." Microorganisms 10, no. 7 (2022): 1312. http://dx.doi.org/10.3390/microorganisms10071312.

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Evolutionary relationships amongst Chlorobia and Ignavibacteria species/strains were examined using phylogenomic and comparative analyses of genome sequences. In a phylogenomic tree based on 282 conserved proteins, the named Chlorobia species formed a monophyletic clade containing two distinct subclades. One clade, encompassing the genera Chlorobaculum, Chlorobium, Pelodictyon, and Prosthecochloris, corresponds to the family Chlorobiaceae, whereas another clade, harboring Chloroherpeton thalassium, Candidatus Thermochlorobacter aerophilum, Candidatus Thermochlorobacteriaceae bacterium GBChlB,

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Deshpande, Lalitagauri M., Andrew P. Davis, F. Fredrik Dyrkell, Dimitrios Amellos, and Mariana Castanheira. "239. Epidemiologic Analysis of a Worldwide Collection of Escherichia coli ST131 Using the 1928D Core Genome (cg) Multilocus Sequence Type (MLST) Reveals Country Specific and Globally Disseminated Clades." Open Forum Infectious Diseases 6, Supplement_2 (2019): S136. http://dx.doi.org/10.1093/ofid/ofz360.314.

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Abstract Background Increasing antimicrobial resistance (R) among Escherichia coli (EC) isolates can be associated with the expansion of the pandemic sequence type (ST) 131 that harbors virulence factors and causes more severe infections when compared with other antimicrobial-R EC. We evaluated the core genome MLST (cgMLST) profiles and R genes using the bioinformatics tool 1928D to evaluate the epidemiology of a global ST131 EC collection and unrelated STs. Methods A total of 259 EC clinical isolates belonging to ST131 (n = 206), ST131-single loci variant (SLV; n = 25), and 28 non-ST131 isola

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Regassa, Laura B., Kimberly M. Stewart, April C. Murphy, Frank E. French, Tao Lin, and Robert F. Whitcomb. "Differentiation of group VIII Spiroplasma strains with sequences of the 16S–23S rDNA intergenic spacer region." Canadian Journal of Microbiology 50, no. 12 (2004): 1061–67. http://dx.doi.org/10.1139/w04-091.

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Spiroplasma species (Mollicutes: Spiroplasmataceae) are associated with a wide variety of insects, and serology has classified this genus into 34 groups, 3 with subgroups. The 16S rRNA gene has been used for phylogenetic analysis of spiroplasmas, but this approach is uninformative for group VIII because the serologically distinct subgroups generally have similarity coefficients >0.990. Therefore, we investigated the utility of the 16S–23S rRNA spacer region as a means to differentiate closely related subgroups or strains. We generated intergenic sequences and detailed serological profiles f

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Demery, Amelia-Juliette, and Kevin J. Burns. "Widespread convergent morphological evolution within the largest family of songbirds." Evolution 77, no. 3 (2022): 812–22. http://dx.doi.org/10.1093/evolut/qpac069.

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Abstract Although convergence is a common evolutionary phenomenon, few studies have quantified its prevalence across a large, densely sampled clade. Large-scale phylogenies and the advent of novel computational methods facilitate more robust identification of convergent events and their statistical significance. The tanagers (Aves: Thraupidae), the largest family of songbirds, offer an excellent opportunity to study the extent of phenotypic convergence in response to similar ecological pressures on a continental scale. To investigate convergence in the group, we used the largest phylogenetic a

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Gupta, Radhey S., Sudip Patel, Navneet Saini, and Shu Chen. "Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species." International Journal of Systematic and Evolutionary Microbiology 70, no. 11 (2020): 5753–98. http://dx.doi.org/10.1099/ijsem.0.004475.

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To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Sub

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Fragapane, Elena, Roberto Gasparini, Francesco Schioppa, Franco Laghi-Pasini, Emanuele Montomoli, and Angelika Banzhoff. "A Heterologous MF59-Adjuvanted H5N1 Prepandemic Influenza Booster Vaccine Induces a Robust, Cross-Reactive Immune Response in Adults and the Elderly." Clinical and Vaccine Immunology 17, no. 11 (2010): 1817–19. http://dx.doi.org/10.1128/cvi.00461-09.

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ABSTRACT Immunogenicity and safety of a booster dose of an MF59-adjuvanted H5N1 vaccine containing 7.5 μg A/turkey/Turkey/1/2005-like (clade 2.2) H5N1 hemagglutinin, given approximately 18 months after primary vaccination with a heterologous strain, were evaluated. The booster vaccine was well tolerated and induced a robust, cross-reactive immune response.

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Barrett, Paul M., Alistair J. McGowan, and Victoria Page. "Dinosaur diversity and the rock record." Proceedings of the Royal Society B: Biological Sciences 276, no. 1667 (2009): 2667–74. http://dx.doi.org/10.1098/rspb.2009.0352.

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Palaeobiodiversity analysis underpins macroevolutionary investigations, allowing identification of mass extinctions and adaptive radiations. However, recent large-scale studies on marine invertebrates indicate that geological factors play a central role in moulding the shape of diversity curves and imply that many features of such curves represent sampling artefacts, rather than genuine evolutionary events. In order to test whether similar biases affect diversity estimates for terrestrial taxa, we compiled genus-richness estimates for three Mesozoic dinosaur clades (Ornithischia, Sauropodomorp

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CHAI, MAO-LIN, YA-MENG WU, YANG ZHANG, et al. "Sedum xunvense, a new species from Southeast China." Phytotaxa 644, no. 4 (2024): 258–70. http://dx.doi.org/10.11646/phytotaxa.644.4.2.

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In this paper, Sedum xunvense is described as a new species from Zhejiang, Southeast China. Sedum xunvense is morphologically similar to S. formosanum, but the latter differs in clustered and robust stems (vs. solitary, slender), green or slightly red smooth stems and inflorescence rachises (vs. purple-red and ribbed), thick and succulent leaves (vs. thin), yellow anthers (vs. reddish-brown), erect follicles (vs. oblique), and is found in dry habitats in rock crevices (vs. damp ravines, rocks and mossy thickets). A reconstructed ML phylogeny of Sedum, based on nrITS sequence data, strongly sug

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Arrigoni, Roberto, Fabrizio Stefani, Michel Pichon, Paolo Galli, and Francesca Benzoni. "Molecular phylogeny of the Robust clade (Faviidae, Mussidae, Merulinidae, and Pectiniidae): An Indian Ocean perspective." Molecular Phylogenetics and Evolution 65, no. 1 (2012): 183–93. http://dx.doi.org/10.1016/j.ympev.2012.06.001.

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Nieri-Bastos, Fernanda A., Arlei Marcili, Rita De Sousa, Christopher D. Paddock, and Marcelo B. Labruna. "Phylogenetic Evidence for the Existence of Multiple Strains ofRickettsia parkeriin the New World." Applied and Environmental Microbiology 84, no. 8 (2018): e02872-17. http://dx.doi.org/10.1128/aem.02872-17.

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ABSTRACTThe bacteriumRickettsia parkerihas been reported to infect ticks of the “Amblyomma maculatumspecies complex” in the New World, where it causes spotted fever illness in humans. In South America, three additional rickettsial strains, namely, Atlantic rainforest, NOD, and Parvitarsum, have been isolated from the ticksAmblyomma ovale,Amblyomma nodosum, andAmblyomma parvitarsum, respectively. These three strains are phylogenetically closely related toR. parkeri,Rickettsia africae, andRickettsia sibirica. Herein, we performed a robust phylogenetic analysis encompassing 5 genes (gltA,ompA,vir

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Mayrhofer, Josef, Sogue Coulibaly, Annett Hessel, et al. "Nonreplicating Vaccinia Virus Vectors Expressing the H5 Influenza Virus Hemagglutinin Produced in Modified Vero Cells Induce Robust Protection." Journal of Virology 83, no. 10 (2009): 5192–203. http://dx.doi.org/10.1128/jvi.02081-08.

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ABSTRACT The timely development of safe and effective vaccines against avian influenza virus of the H5N1 subtype will be of the utmost importance in the event of a pandemic. Our aim was first to develop a safe live vaccine which induces both humoral and cell-mediated immune responses against human H5N1 influenza viruses and second, since the supply of embryonated eggs for traditional influenza vaccine production may be endangered in a pandemic, an egg-independent production procedure based on a permanent cell line. In the present article, the generation of a complementing Vero cell line suitab

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Worthy, Trevor H., Federico J. Degrange, Warren D. Handley, and Michael S. Y. Lee. "The evolution of giant flightless birds and novel phylogenetic relationships for extinct fowl (Aves, Galloanseres)." Royal Society Open Science 4, no. 10 (2017): 170975. http://dx.doi.org/10.1098/rsos.170975.

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The extinct dromornithids, gastornithids and phorusrhacids are among the most spectacular birds to have ever lived, with some giants exceeding 500 kg. The affinities and evolution of these and other related extinct birds remain contentious, with previous phylogenetic analyses being affected by widespread convergence and limited taxon sampling. We address these problems using both parsimony and tip-dated Bayesian approaches on an expansive taxon set that includes all key extinct flightless and flighted (e.g. Vegavis and lithornithids) forms, an extensive array of extant fowl (Galloanseres), rep

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Shivaji, Sisinthy, and Gundlapally Sathyanarayana Reddy. "Phylogenetic analyses of the genus Glaciecola: emended description of the genus Glaciecola, transfer of Glaciecola mesophila, G. agarilytica, G. aquimarina, G. arctica, G. chathamensis, G. polaris and G. psychrophila to the genus Paraglaciecola gen. nov. as Paraglaciecola mesophila comb. nov., P. agarilytica comb. nov., P. aquimarina comb. nov., P. arctica comb. nov., P. chathamensis comb. nov., P. polaris comb. nov. and P. psychrophila comb. nov., and description of Paraglaciecola oceanifecundans sp. nov., isolated from the Southern Ocean." International Journal of Systematic and Evolutionary Microbiology 64, Pt_9 (2014): 3264–75. http://dx.doi.org/10.1099/ijs.0.065409-0.

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Phylogenetic analyses of the genus Glaciecola were performed using the sequences of the 16S rRNA gene and the GyrB protein to establish its taxonomic status. The results indicated a consistent clustering of the genus Glaciecola into two clades, with significant bootstrap values, with all the phylogenetic methods employed. Clade 1 was represented by seven species, Glaciecola agarilytica , G. aquimarina , G. arctica , G. chathamensis , G. mesophila , G. polaris and G. psychrophila , while clade 2 consisted of only three species, Glaciecola nitratireducens , G. pallidula and G. punicea . Evolutio

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LOWRY, J. K., and A. A. MYERS. "A Phylogeny and Classification of the Senticaudata subord. nov. Crustacea: Amphipoda)." Zootaxa 3610, no. 1 (2013): 1–80. http://dx.doi.org/10.11646/zootaxa.3610.1.1.

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The Amphipoda includes a large clade defined by the presence of a previously unrecognised synapomorphy, apical robust setae on the rami of uropods 1–2. We term this clade the Senticaudata subord. nov. (Latin: sentis = thorn). It includes almost all freshwater species as well as a number of marine benthic taxa, formerly part of the ‘Gammaridea’. The phylogeny of the senticaudates was determined by cladistic analysis of morphological characters and character states. Within the suborder Senticaudata there are six infraorders: Carangoliopsida, Talitrida, Hadziida, Corophiida, Bogidiellida and Gamm

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Zhao, Jing, Xinmao Zhou, Shaoli Fang, et al. "Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae)." Plants 12, no. 12 (2023): 2237. http://dx.doi.org/10.3390/plants12122237.

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Marattiaceae is a phylogenetically isolated family of tropical eusporangiate ferns including six genera with more than one-hundred species. In Marattiaceae, monophyly of genera has been well-supported phylogenetically. However, the phylogenetic relationships among them were elusive and controversial. Here, a dataset of 26 transcriptomes (including 11 newly generated) were used to assess single-copy nuclear genes and to obtain the organelle gene sequences. Through phylotranscriptomic analysis, the phylogeny and hybridization events of Marattiaceae were explored and a robust phylogenomic framewo

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Priest, Shelby J., and Michael C. Lorenz. "Characterization of Virulence-Related Phenotypes in Candida Species of the CUG Clade." Eukaryotic Cell 14, no. 9 (2015): 931–40. http://dx.doi.org/10.1128/ec.00062-15.

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ABSTRACTCandidaspecies cause a variety of mucosal and invasive infections and are, collectively, the most important human fungal pathogens in the developed world. The majority of these infections result from a few related species within the “CUG clade,” so named because they use a nonstandard translation for that codon. Some members of the CUG clade, such asCandida albicans, present significant clinical problems, whereas others, such asCandida(Meyerozyma)guilliermondii, are uncommon in patients. The differences in incidence rates are imperfectly correlated with virulence in animal models of in

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Fulton, James C., B. Sajeewa Amaradasa, Tülin S. Ertek, et al. "Phylogenetic and phenotypic characterization of Fusarium oxysporum f. sp. niveum isolates from Florida-grown watermelon." PLOS ONE 16, no. 3 (2021): e0248364. http://dx.doi.org/10.1371/journal.pone.0248364.

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Fusarium wilt of watermelon (Citrullus lanatus) caused by Fusarium oxysporum f. sp. niveum (Fon), has become an increasing concern of farmers in the southeastern USA, especially in Florida. Management of this disease, most often through the use of resistant cultivars and crop rotation, requires an accurate understanding of an area’s pathogen population structure and phenotypic characteristics. This study improved the understanding of the state’s pathogen population by completing multilocus sequence analysis (MLSA) of two housekeeping genes (BT and TEF) and two loci (ITS and IGS), aggressivenes

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Cui, Xingyong, Kangjia Liu, Enze Li, Zhixiang Zhang, and Wenpan Dong. "Chloroplast Genomes Evolution and Phylogenetic Relationships of Caragana species." International Journal of Molecular Sciences 25, no. 12 (2024): 6786. http://dx.doi.org/10.3390/ijms25126786.

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Caragana sensu lato (s.l.) includes approximately 100 species that are mainly distributed in arid and semi-arid regions. Caragana species are ecologically valuable for their roles in windbreaking and sand fixation. However, the taxonomy and phylogenetic relationships of the genus Caragana are still unclear. In this study, we sequenced and assembled the chloroplast genomes of representative species of Caragana and reconstructed robust phylogenetic relationships at the section level. The Caragana chloroplast genome has lost the inverted repeat region and wascategorized in the inverted repeat los

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Amini, Elham, Shahrokh Kazempour-Osaloo, Ali Maassoumi, and Hassan Zare-Maivan. "Exploring the tempo of species diversification in Astragalus section Incani DC. based on nuclear and plastid DNA sequences." Genetika 54, no. 3 (2022): 1271–84. http://dx.doi.org/10.2298/gensr2203271a.

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This study uses phylogenetic relationships of the species-rich section Astragalus (Incani), to follow up on recent evidence pointing to rapid and recent plant diversification patterns in the west of Iran. Section Incani is introduced for its taxonomic complication resulting from overlapping morphological characters, but few studies have been done on this section; hence, we also lack a robust time-calibrated chronogram to address hypotheses (e.g., biogeography and diversification rates) that have implicit time assumptions. Two loci (rpl32-trnL(UAG) and nrDNA ITS) were amplified and sequenced fo

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Wen, Jun, Ze-Long Nie, Akiko Soejima, and Ying Meng. "Phylogeny of Vitaceae based on the nuclear GAI1 gene sequencesThis article is one of a selection of papers presented at the symposium on Vitis at the XVII International Botanical Congress held in Vienna, Austria, in 2005." Canadian Journal of Botany 85, no. 8 (2007): 731–45. http://dx.doi.org/10.1139/b07-071.

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Phylogenetic analysis of 105 nuclear GAI1 sequences of Vitaceae provided a fairly robust phylogeny, largely congruent with the recently published chloroplast data of the family. In the GAI1 phylogeny, Cayratia Juss., Tetrastigma (Miq.) Planch., and Cyphostemma (Planch.) Alston form a clade. Cyphostemma and Tetrastigma are both monophyletic, and Cayratia is paraphyletic. Ampelopsis Michx is paraphyletic with the African Rhoicissus Planch. and the South American Cissus striata Ruiz & Pav. and its close relatives (e.g., Cissus simsiana Roem. & Schult.) nested within it. The pinnately leav

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McGeoch, Duncan J., Derek Gatherer, and Aidan Dolan. "On phylogenetic relationships among major lineages of the Gammaherpesvirinae." Journal of General Virology 86, no. 2 (2005): 307–16. http://dx.doi.org/10.1099/vir.0.80588-0.

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Phylogenetic relationships within the subfamily Gammaherpesvirinae of the family Herpesviridae were investigated for three species in the genus Lymphocryptovirus (or γ1 group) and nine in the genus Rhadinovirus (or γ2 group). Alignments of amino acid sequences from up to 28 genes were used to derive trees by maximum-likelihood and Bayesian Monte Carlo Markov chain methods. Two problem areas were identified involving an unresolvable multifurcation for a clade within the γ2 group, and a high divergence for Murid herpesvirus 4 (MHV4). A robust final tree was obtained, which was valid for genes fr

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PAN, HENG, YI WANG, GANG TAO, and ZHI-YUAN ZHANG. "Morphological and phylogenetic characterisation of Podospora sichuanensis sp. nov. (Podosporaceae, Sordariales)." Phytotaxa 695, no. 1 (2025): 123–30. https://doi.org/10.11646/phytotaxa.695.1.7.

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This study presents the identification and description of a novel species, Podospora sichuanensis, isolated from horse dung. Phylogenetic analyses of combined ITS, LSU, RPB2, and TUB2 loci indicate that this novel species forms a monophyletic clade with robust support values. In addition, Podospora sichuanensis can be distinguished from other species within the genus based on its longer conidiogenous cells. Descriptions and illustrations of this novel species are provided in this paper.

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Adl, Sina M., David Bass, Christopher E. Lane, et al. "Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes." Journal of Eukaryotic Microbiology 66 (September 26, 2018): 4–199. https://doi.org/10.1111/jeu.12691.

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This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known fro

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ARIYAMA, HIROYUKI. "Species of the Maera-clade collected from Japan. Part 3: genera Maera Leach, 1814, Meximaera Barnard, 1969 and Orientomaera Ariyama, 2018 (addendum), with a key to Japanese species of the clade (Crustacea: Amphipoda: Maeridae)." Zootaxa 4743, no. 4 (2020): 451–79. http://dx.doi.org/10.11646/zootaxa.4743.4.1.

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Two species of Maera Leach, 1814, a species of Meximaera Barnard, 1969 and a species of Orientomaera Ariyama, 2018 included in the Maera clade, are described from Japan. Maera loveni (Bruzelius, 1859) was collected from the Sea of Japan and can be distinguished from its congeners by the very large body size and the gnathopod 2 palm defined by a blunt tooth bearing a strong robust seta. Maera sagamiensis sp. nov. from Sagami Bay is characterized by the presence of small notches on the coxae 1–3. Meximaera mooreana (Myers, 1989) was collected from Wakayama Prefecture and has two distinct charact

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Cornman, Robert S. "Data mining reveals tissue-specific expression and host lineage-associated forms of Apis mellifera filamentous virus." PeerJ 11 (November 14, 2023): e16455. http://dx.doi.org/10.7717/peerj.16455.

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Background Apis mellifera filamentous virus (AmFV) is a large double-stranded DNA virus of uncertain phylogenetic position that infects honey bees (Apis mellifera). Little is known about AmFV evolution or molecular aspects of infection. Accurate annotation of open-reading frames (ORFs) is challenged by weak homology to other known viruses. This study was undertaken to evaluate ORFs (including coding-frame conservation, codon bias, and purifying selection), quantify genetic variation within AmFV, identify host characteristics that covary with infection rate, and examine viral expression pattern

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Gadek, PA, PG Wilson, and CJ Quinn. "Phylogenetic reconstruction in Myrtaceae using matK, with particular reference to the position of Psiloxylon and Heteropyxis." Australian Systematic Botany 9, no. 3 (1996): 283. http://dx.doi.org/10.1071/sb9960283.

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Parsimony analysis of matK sequence data for representatives of Myrtaceae s.1. provides evidence of its potential in phylogenetic inference in this family. Psiloxylon and Heteropyxis comprise a robust clade, basal to representatives of Myrtaceae s. str., and strongly clustered with it. In a limited sample of Myitaceae s. str., several strongly supported groups are identified: the myrtoid genera (excluding Syzygium), representatives of the Chamelaucium alliance, and the Chamelaucium plus Leptospennum alliances.

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