scholarly journals VICTOR: Genome-based Phylogeny and Classification of Prokaryotic Viruses

2017 ◽  
Author(s):  
Jan P. Meier-Kolthof ◽  
Markus Göker
Keyword(s):  
Sequence Divergence ◽  
Life Cycles ◽  
Bacterial Strains ◽  
Data Set ◽  
Archaeal Viruses ◽  
Serious Infections ◽  
The Family ◽  
Branch Support ◽  
The Common

AbstractBacterial and archaeal viruses (“phages”) play an enormous role in global life cycles and have recently regained importance as therapeutic agents to fight serious infections by multi-resistant bacterial strains. Nevertheless, taxonomic classification of phages is up to now only insufficiently informed by genome sequencing. Despite thousands of publicly available phage genomes, it still needs to be investigated how this wealth of information can be used for the fast, universal and accurate classification of phages. The Genome BLAST Distance Phylogeny (GBDP) approach is a truly whole-genome method currently used forin silicoDNA: DNA hybridization and phylogenetic inference from prokaryotic genomes. Based on the principles of phylogenetic systematics, we here established GBDP for phage phylogeny and classification, using the common subset of genome-sequenced and officially classified phages. Trees inferred with the best GBDP variants showed only few deviations from the official phage classification, which were uniformly due to incorrectly annotated GenBank entries. Except for low resolution at the family level, the majority of taxa was well supported as monophyletic. Clustering genome sequences with distance thresholds optimized for the agreement with the classification turned out to be phylogenetically reasonable. Accordingly modifying genera and species is taxonomically optional but would yield more uniform sequence divergence as well as stronger branch support. Analysing an expanded data set containing > 4000 phage genomes from public databases allowed for extrapolating regarding the number, composition and host specificity of future phage taxa. The selected methods are implemented in an easy-to-use web service “VICTOR” freely available athttp://ggdc.dsmz.de/victor.php.

A comparison of methodological approaches to the subfamilial classification of the Naididae (Oligochaeta)

1987 ◽  
Vol 65 (3) ◽  
pp. 691-707 ◽  
Author(s):  
A. F. L. Nemec ◽  
R. O. Brinkhurst
Keyword(s):  
Data Matrix ◽  
Jaccard Coefficient ◽  
Data Set ◽  
Parsimony Method ◽  
Fit Statistics ◽  
Reconstruction Methods ◽  
Linkage Methods ◽  
The Family ◽  
First Time

A data matrix of 23 generic or subgeneric taxa versus 24 characters and a shorter matrix of 15 characters were analyzed by means of ordination, cluster analyses, parsimony, and compatibility methods (the last two of which are phylogenetic tree reconstruction methods) and the results were compared inter alia and with traditional methods. Various measures of fit for evaluating the parsimony methods were employed. There were few compatible characters in the data set, and much homoplasy, but most analyses separated a group based on Stylaria from the rest of the family, which could then be separated into four groups, recognized here for the first time as tribes (Naidini, Derini, Pristinini, and Chaetogastrini). There was less consistency of results within these groups. Modern methods produced results that do not conflict with traditional groupings. The Jaccard coefficient minimizes the significance of symplesiomorphy and complete linkage avoids chaining effects and corresponds to actual similarities, unlike single or average linkage methods, respectively. Ordination complements cluster analysis. The Wagner parsimony method was superior to the less flexible Camin–Sokal approach and produced better measure of fit statistics. All of the aforementioned methods contain areas susceptible to subjective decisions but, nevertheless, they lead to a complete disclosure of both the methods used and the assumptions made, and facilitate objective hypothesis testing rather than the presentation of conflicting phylogenies based on the different, undisclosed premises of manual approaches.

A Bayesian approach to the classification of the Turkic languages

2020 ◽  
pp. 114-124
Author(s):  
Alexander Savelyev
Keyword(s):  
Bayesian Approach ◽  
Controversial Issue ◽  
Language Family ◽  
Independent Verification ◽  
Linguistic History ◽  
The Family ◽  
Turkic Languages ◽  
The Common ◽  
Widespread View

Despite more than 150 years of research, the internal structure of the Turkic language family remains a controversial issue. In this study, the Bayesian phylogenetic approach is employed in order to provide an independent verification of the contemporary views on Turkic linguistic history. The data underlying the study are Turkic basic vocabularies, which are resistant to replacement and likely to reflect the genealogical relationships among the Turkic languages. The method tested in the chapter is based on the strict clock model of evolution, which assumes that relevant changes occur at the same rate at every branch of the family. This study supports the widespread view that the binary split between Bulgharic and Common Turkic was the earliest split in the Turkic family. The model further replicates most of the conventional subgroups within the Common Turkic branch. Based on a Bayesian analysis, the time depth of Proto-Turkic is estimated to be around 2,119 years BP, which is in accordance with the traditional estimates of 2,000–2,500 years BP.

Algibacter agarivorans sp. nov. and Algibacter agarilyticus sp. nov., isolated from seawater, reclassification of Marinivirga aestuarii as Algibacter aestuarii comb. nov. and emended description of the genus Algibacter

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3494-3500 ◽  
Author(s):  
Seong Chan Park ◽  
Yeoung Min Hwang ◽  
Ji Hee Lee ◽  
Keun Sik Baik ◽  
Chi Nam Seong
Keyword(s):  
Fatty Acids ◽  
Type Strain ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Emended Description ◽  
The Common ◽  
Gwangyang Bay

Two yellow-pigmented, rod-shaped, non-motile, Gram-reaction-negative and aerobic bacterial strains, designated KYW560T and KYW563T, were isolated from seawater collected from Gwangyang Bay, Republic of Korea. The isolates required sea salts for growth. Flexirubin-type pigments were absent. The common major cellular fatty acids (>5 % of total) of the two strains were C16 : 0, C18 : 0, iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). Strain KYW560T also contained iso-C15 : 0 3-OH and C20 : 1ω9c as major fatty acids. The main polar lipids were phosphatidylethanolamine, an unidentified aminolipid and two unidentified lipids. The predominant isoprenoid quinone was MK-6. The DNA G+C contents of strains KYW560T and KYW563T were 41.0±0.7 and 38.3±0.4 mol% (mean±sd of three determinations), respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates belonged to the family Flavobacteriaceae , and were related to the genus Algibacter . Based on data from this taxonomic study using a polyphasic approach, it is proposed that the isolates represent novel species of the genus Algibacter , for which the names Algibacter agarivorans sp. nov. (type strain, KYW560T = KCTC 23855T = JCM 18285T) and Algibacter agarilyticus sp. nov. (type strain, KYW563T = KCTC 23857T = JCM 18275T) are proposed. Reclassification of Marinivirga aestuarii as Algibacter aestuarii comb. nov. and emended description of the genus Algibacter are also proposed.

scholarly journals Phylogeny and Systematics of Ground Rollers (Brachypteraciidae) of Madagascar

The Auk ◽  
2001 ◽  
Vol 118 (4) ◽  
pp. 849-863 ◽  
Author(s):  
Jeremy J. Kirchman ◽  
Shannon J. Hackett ◽  
Steven M. Goodman ◽  
John M. Bates ◽  
R. Prum
Keyword(s):  
Ribosomal Rna ◽  
Nadh Dehydrogenase ◽  
Sequence Divergence ◽  
Museum Specimens ◽  
Sister Relationship ◽  
Data Set ◽  
Phylogenetic Reconstructions ◽  
The Family ◽  
Two Parameter ◽  
Combined Data

Abstract We studied relationships of five extant members of the endemic Malagasy family Brachypteraciidae, the ground rollers, using several mitochondrial genes (cytochrome-b, NADH dehydrogenase 2, 12S ribosomal RNA, and cytochrome oxidase I). As outgroups, we used other coraciiforms including the Cuckoo Roller (Family Leptosomatidae, Leptosomus discolor), several true rollers (Corcaciidae) and a tody (Todidae). Partial sequences of the Long-tailed Ground Roller (Uratelornis chimaera) were obtained from toe pad samples taken off museum specimens. For a combined data set of all genes, Kimura two-parameter distances between sequences of the five ground roller species were high, averaging 11% divergence. For several species, samples were available from widely separated geographic regions and intraspecific sequence divergence was low (≤0.8%). Unweighted and weighted parsimony and maximum-likelihood analyses consistently recovered monophyly of the family, a sister relationship between Brachypteraciidae and Coraciidae, and monophyly of one of three currently recognized ground roller genera (Atelornis). At the base of the Brachypteraciidae clade, we could not fully resolve relationships between Uratelornis and two species currently placed in Brachypteracias. Because of the uncertainty of basal nodes in our phylogenetic reconstructions, we recommend returning B. squamigera to the monotypic genus Geobiastes. High levels of divergence among ground rollers are similar to levels found in other avian groups endemic to Madagascar. However, we suggest that molecular divergences appear far too low to be consistent with mid-Eocene fossils attributed to the family.

A further revision in the classification of the family Metastrongylidae Leiper [1909] (Phylum Nematoda)

Parasitology ◽  
1951 ◽  
Vol 41 (1-2) ◽  
pp. 91-96 ◽  
Author(s):  
Ellsworth C. Dougherty
Keyword(s):  
Chromosome Number ◽  
Intermediate Host ◽  
Life Cycles ◽  
The Body ◽  
Basic Pattern ◽  
Histological Studies ◽  
Evolutionary Scheme ◽  
The Family ◽  
Marine Littoral

1. Recent studies by Gerichter have demonstrated that I have erred in referring the skrjabingylin lungworms to the family Trichostrongylidae.2. On the basis of his data and a re-evaluation of my theories of metastrongylid evolution it is suggested that the Skrjabingylinae (except Dictyocaulus) are close to the Filaroidinae and that quite possibly the position of the vulva in the former is the consequence of a secondary shift from opening just anterior to the anus to opening in the mid-region of the body; the ‘trichostrongylid’ configuration of the ovejectoral apparatus would thus be convergent.3. The genus Dictyocaulus is removed from the Skrjabingylinae and left in a subfamily Dictyocaulinae in the family Metastrongylidae, although its trichostrongylid affinities are very suggestive. If trichostrongylid, this genus is considered to exhibit convergence with the metastrongylids and not to represent an evolutionary link between the two families.4. The nature of metastrongylid life cycles is discussed, and the compatibility of known data with the evolutionary scheme proposed for the family is pointed out. It is evident that in metastrongylids symbiotizing marine littoral and pelagic hosts (Pinnipedia and Odontoceti) larval development must rely upon new intermediate host groups if the basic pattern has been retained from ancestors in terrestrial hosts.5. The possible importance of histological studies and of investigations on chromosome number and structure for a further understanding of the evolution of the suborder Strongylina is pointed out.6. A revised scheme for the evolution of the Metastrongylidae is presented as Fig. 1. The family Metastrongylidae now includes six subfamilies: Metastrongylinae, Filaroidinae, Skrjabingylinae, Pseudaliinae, Protostrongylinae, and Dictyocaulinae. The basic premises previously expressed (Dougherty, 1949b) on the evolution of the family are retained in the amended scheme.

scholarly journals On the Crossing Numbers of the Join Products of Six Graphs of Order Six with Paths and Cycles

Symmetry ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2441
Author(s):  
Michal Staš
Keyword(s):  
Lower Bounds ◽  
Crossing Number ◽  
Crossing Numbers ◽  
Symmetric Graphs ◽  
The Family ◽  
Minimum Number ◽  
The Common ◽  
First Time ◽  
Edge Crossings

The crossing number of a graph G is the minimum number of edge crossings over all drawings of G in the plane. The main purpose of this paper is to determine the crossing numbers of the join products of six symmetric graphs on six vertices with paths and cycles on n vertices. The idea of configurations is generalized for the first time onto the family of subgraphs whose edges cross the edges of the considered graph at most once, and their lower bounds of necessary numbers of crossings are presented in the common symmetric table. Some proofs of the join products with cycles are done with the help of several well-known auxiliary statements, the idea of which is extended by a suitable classification of subgraphs that do not cross the edges of the examined graphs.

Ontogenesis, morphology and higher classification of archaeococcids (Homoptera: Coccinea: Orthezioidea)

2018 ◽  
pp. 1-260
Author(s):  
I.A. Gavrilov-Zimin
Keyword(s):  
Scale Insect ◽  
Life Cycles ◽  
Individual Development ◽  
Scale Insects ◽  
Original Research ◽  
Traditional Concept ◽  
The Family ◽  
Generic Composition ◽  
Reproduction Pattern

The monograph summarizes original research data and published literature data on reproduction, life cycles, individual development and morphology of scale insects of the superfamily Orthezioidea (archaeococcids). The superfamily system is accepted mainly in its traditional concept, i.e. with four well-defined families: Margarodidae s. l., Ortheziidae, Carayonemidae, and Phenacoleachiidae. The tribe Matsucoccini (Margarodidae s. l.: Xylococcinae s. l.) is considered as a most archaic group of scale insects according to morphological, reproductive and ontogenetic characters. A complicated ontogenesis with an alternation of movable/immovable instars and with arostrate imago of both sexes (as in Matsucoccus Cockerell, 1909 and many other Margarodidae s. l.) is presumed to be initial in scale insect evolution and such ontogenesis is supposed to be an apomorphy of suborder Coccinea. Distribution of different variants of ovoviviparity/viviparity amongst scale insect families is overviewed. It is demonstrated that the evolution of scale insects shows multiple cyclic conversions of oviparous reproduction pattern to ovoviviparous/viviparous ones with the appearance of new and new peculiar adaptations to eggs protection; the most ancient scale insects (Matsucoccini and their ancestor) were probably facultatively ovoviviparous, whereas the origin of the whole neococcid phylogenetic line (Coccoidea s. s.) was probably connected with obligate complete ovoviviparity, which also appeared in some “derived” archaeococcids of the tribe Iceryini (Margarodidae s. l.), in the families Phenacoleachiidae and Carayonemidae. New taxonomic additions and changes in generic composition of some tribes are provided for the family Margarodidae s. l., in its subfamilies Monophlebinae and Callipappinae s. l. The tribe Labioproctini tr. nov. (Monophlebinae) is erected for six genera possessing peculiar quadrilocular wax pores: Aspidoproctus Newstead, 1901, Hemaspidoproctus Morrison, 1927, Labioproctus Green, 1922, Lecaniodrosicha Takahashi, 1930, Misracoccus Rao, 1950, and Walkeriana Signoret, 1876. The presence of quadrilocular pores are considered as a synapomorphic character of the Labioproctini tr. nov. and Ortheziidae. Disputable taxonomic position of Xenococcidae Tang, 1992 is discussed and this family is also placed in Orthezioidea. New genera and species are described and illustrated, based mainly on material collected in the Oriental region: Eremostoma klugei gen. et sp. nov., Crambostoma largecicatricosum gen. et sp. nov. (both in Callipappinae s. l.: Coelostomidiini s. l.), Buchnericoccus reynei sp. nov., Monophlebus neglectus sp. nov. (both in Monophlebinae: Monophlebini), Crypticerya ovivivipara sp. nov., Icerya oculicicatricata sp. nov., I. siamensis sp. nov. (all three in Monophlebinae: Iceryini).

Lafoeina amirantensis (Cnidaria: Hydrozoa, Campanulinoidea), the hydroid stage of the medusa Cirrholovenia tetranema (Cnidaria: Hydrozoa, Lovenelloidea)

Zootaxa ◽  
2005 ◽  
Vol 919 (1) ◽  
pp. 1 ◽  
Author(s):  
ALVARO E. MIGOTTO ◽  
ANDRÉ S. CABRAL
Keyword(s):  
Life History ◽  
Sao Paulo ◽  
Life Cycles ◽  
Important Method ◽  
Constituent Species ◽  
The Family ◽  
Polyp Stage ◽  
The Many ◽  
Species Being

The metagenetic Lafoeina is one of the many leptothecate genera with uncertain affinities, the life cycles of its constituent species being poorly known. The genus has traditionally been recognized as belonging to the polyphyletic superfamily Campanulinoidea, family Campanulinidae, taxa that artificially group together a variety of probably unrelated species. Life-history studies are the most important method to link species that were originally based solely on medusa or polyp stage, as is the case of Lafoeina spp. Findings of Lafoeina amirantensis at the coast of São Sebastião (São Paulo, Brazil) allowed us to study its juvenile medusa and to observe new facts pertinent to the classification of the Order Leptothecata. The hydrotheca of L. amirantensis is similar to those of the genus Cuspidella, except for the absence of nematophores in the latter. The newly released medusa of L. amirantensis is similar in morphology to the young medusae of Cirrholovenia tetranema, a species belonging to the family Cirrholoveniidae (superfamily Lovenelloidea).

Falsirhodobacter halotolerans gen. nov., sp. nov., isolated from dry soils of a solar saltern

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2132-2137 ◽  
Author(s):  
Y. Subhash ◽  
L. Tushar ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Sequence Similarity ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Bacterial Strains ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

Two bacterial strains (JA744T and JA745) were isolated from dry soil samples collected from solar salterns at Humma, Odisha, India. Both strains were Gram-stain-negative, catalase- and oxidase-positive, motile rods. Major fatty acids in both strains included C18 : 1ω7c, C18 : 0 and C16 : 0, while minor amounts of C10 : 0 3-OH, C12 : 0, C12 : 0 3-OH, C14 : 0 and C16 : 0 were also present. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified glycolipid, five unidentified lipids, an unidentified aminolipid and an unidentified phospholipid made up the polar lipids of both strains. Both strains had bacteriohopane derivatives (BHD1,2) and diploptene as major hopanoids. Mean genomic DNA G+C content was 75±1 mol% and the two strains were closely related (mean DNA–DNA hybridization >90 %). Phylogenetic analysis based on the 16S rRNA gene sequence showed that the two strains clustered with species of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria . The highest sequence similarity was observed with Rhodobacter sphaeroides ATH2.4.1T (96 %) and other members of the genera Rhodobacter and Pseudorhodobacter (<96 %). However, the two strains were positioned distinctly outside the group formed by the other genera of the family Rhodobacteraceae . Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of these isolates as representatives of a novel species in a new genus, for which the name Falsirhodobacter halotolerans gen. nov., sp. nov. is proposed. The type strain of Falsirhodobacter halotolerans is JA744T ( = KCTC 32158T  = NBRC 108897T).

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