The genus Agaricus in the Caribbean. Nine new taxa mostly based on collections from the Dominican Republic

Phytotaxa ◽  
2018 ◽  
Vol 345 (3) ◽  
pp. 219 ◽  
Author(s):  
LUIS A. PARRA ◽  
CLAUDIO ANGELINI ◽  
BEATRIZ ORTIZ-SANTANA ◽  
GERARDO MATA ◽  
CHRISTOPHE BILLETTE ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dominican Republic ◽  
Intraspecific Variability ◽  
Virgin Islands ◽  
Its Sequences ◽  
Phylogenetic Study ◽  
Preliminary Study ◽  
The Caribbean ◽  
Taxonomic System

Field collections of Agaricus were collected in the Dominican Republic from 2009–2016 with the intent to evaluate the diversity in this genus, which was quasi-unknown in this country. In the same period, studies on tropical Agaricus revealed tropical clades that remained unclassified. A new taxonomic system of classification was developed, with the aim, inter alia, to integrate such tropical clades. A recent phylogenetic study, which included some samples from the Dominican Republic, revealed they belonged to three putative new sections. Our objective in this paper is to describe the species of Agaricus collected in this country and to classify them whitin the new taxonomic system, including formal descriptions of the three new sections to which they belong. A preliminary study indicated that the collections of the Dominican Republic belong either to a group of three related subgenera (Flavoagaricus, Minores, and Minoriopsis) or to the unrelated A. subg. Pseudochitonia. For the species of the three related subgenera, a phylogenetic analysis based on ITS sequences data reliably confirmed the classification of the species into five sections including the three new sections, which were well supported. For the collections of A. subg. Pseudochitonia, preliminary studies indicated that they all belonged to species of A. sect. Xanthodermatei without any doubt except for one species. This species was included in a multi-gene (ITS, LSU and tef-1α) phylogenetic analysis which confirmed placement in this section. Consequently, all the samples were included in a phylogenetic analysis based on ITS sequences and focusing on A. sect. Xanthodermatei. We noted an unusually high intraspecific variability in the ITS sequences of five of the 12 studied species. Fifteen taxa are described, among which three sections and six species are new for science: Agaricus sect. Kerrigania, Agaricus sect. Minoriopsis, Agaricus sect. Pantropicales, A. argenteopurpureus, A. candussoi, A. flavidodiscus, A. lodgeae, A. porphyropos and A. tephrolepidus. We report all these taxa from the Dominican Republic but the latter three species are also recorded from Puerto Rico, United States Virgin Islands, and Mexico, respectively.

Cladistic analysis of the Early Cambrian olenelloid trilobites

1998 ◽  
Vol 72 (1) ◽  
pp. 59-78 ◽  
Author(s):  
Bruce S. Lieberman
Keyword(s):  
Phylogenetic Analysis ◽  
Cladistic Analysis ◽  
Intraspecific Variability ◽  
Evolutionary Relationships ◽  
Early Cambrian ◽  
New Genera ◽  
Phylogenetic Structure ◽  
Major Clade ◽  
Lateral Margins

A phylogenetic analysis was used to determine evolutionary relationships within the Early Cambrian superfamily Olenelloidea Walcott, 1890. Phylogenetic patterns within the suborder Olenellina Walcott, 1890, which contains the Olenelloidea and the Fallotaspidoidea Hupé, 1953, are also discussed. The Olenelloidea are monophyletic, and synapomorphies uniting them include the condition of the ocular lobes where they intersect the frontal lobe of the glabella, and the condition of the lateral margins of the glabellar lobes. In contrast, taxa formerly assigned to the Fallotaspidoidea are shown to represent a paraphyletic grade of several genera, some more closely related to the Olenelloidea, and some more closely related to the Redlichiina Richter, 1933. Seventy-nine exoskeletal characters were coded for 26 taxa within the Olenellina. These included 22 ingroup Olenelloidea and four outgroup taxa that have traditionally been assigned to the Fallotaspidoidea. When subjected to parsimony analysis these character data yielded a single most parsimonious cladogram that provides an hypothesis of relationship for the generic clades within the superfamily. Two new genera are recognized herein, Fritzolenellus and Lochmanolenellus. It has been argued that genetic flexibility was so great and trilobite morphology was so plastic in the Early Cambrian that suprageneric classification of Early Cambrian trilobites is precluded. Although levels of intraspecific variability may have been slightly higher in the Early Cambrian relative to the mid Paleozoic, based on the extent of polymorphic character codings, it was not so high as to obviate attempts at recovering phylogenetic structure in a major clade of Early Cambrian taxa. In addition, the consistency index recovered by this analysis is not unduly low for a phylogenetic database of this size. The phylogenetic analysis also has bearing on patterns of allometric heterochrony, which have often been held to be significant in Early Cambrian trilobites. The paedomorphic retention of advanced genal spines into the adult probably evolved at least four times. Three of the episodes can be best described as neoteny, the fourth, as progenesis. Finally, based on the phylogeny, it is likely that rates of speciation in trilobites may have been two to three times higher in the Early Cambrian than in the mid Paleozoic.

The Geology of the British Virgin Islands

1924 ◽  
Vol 61 (8) ◽  
pp. 339-351 ◽  
Author(s):  
K. W. Earle
Keyword(s):  
Dominican Republic ◽  
Volcanic Rocks ◽  
Virgin Islands ◽  
Geological Structure ◽  
Lesser Antilles ◽  
Greater Antilles ◽  
Igneous Intrusion ◽  
British Virgin Islands ◽  
The Caribbean ◽  
Granitoid Intrusions

The geological structure of the British Virgin Islands correlates them indisputably with the Greater and not with the Lesser Antilles. The latter are composed essentially of Tertiary volcanic rocks of andesitic or basaltic type, with or without development of sedimentary strata which, when present, only dip at gentle angles and never show the violent effects of such dynamic forces as have been responsible for the folding and “up-ending” of the strata in the Virgin Islands. The tremendous depth of the channel separating the British Virgin Islands from the Lesser Antilles lias been ascribed to faulting, probably initiated in Pliocene times.The work of Cleve (1), Hill (4), Vaughan (5), and others (6) in the American Virgin Islands, Porto Rico, the Dominican Republic, Cuba, Haiti, and Jamaica, indicates that the British Virgin Islands form geologically only the eastern termination of that main group of islands and have been subjected to the same earth movements as them. The evidence for attributing a Cretaceous age to the sedimentary series has already been referred to.With regard to the age of the folding and igneous intrusion, Vaughan considers that the folding took place between upper Eocene and middle Oligoccne times, and that the intrusion of the diorites took place at approximately the same date. (7)Wythe Cooke considers that the igneous basal complex in the Dominican Republic certainly dates from Cretaceous time, but that part is probably older. He also considers that the stresses that folded and sheared these rocks were probably active during Eocene time or earlier, and that the intrusion of the great masses of dioritic rocks probably occurred before the deposition of the Eocene sediments.According to Hill (4), however, “in mid-Tertiary times granitoid intrusions were pushed upward into the sediments of the Greater Antilles, the Caribbean, Costa Eican, and Panamic regions.” Frazer, on the other hand (8), considered the nuclear axis of Cuba and San Domingo, and possibly of all the Caribbean islands, to be Archaean, a view upheld also by Dr. W. Bergt. (9)There is no doubt that the key to these problems lies in the larger islands of the Greater Antilles, for it is only there that unaltered fossiliferous sediments occur and can be studied in relation to the igneous intrusion and metamorphism. There appears, however, to the writer to be nothing either in the geological or faunal evidence necessarily indicating previous land connexion at any time between the Virgin Islands and the Lesser Antilles, ahd on this matter it is hoped to furnish further evidence at a later date.

scholarly journals Taxonomic Revisiting and Phylogenetic Placement of Two Endangered Plant Species: Silene leucophylla Boiss. and Silene schimperiana Boiss. (Caryophyllaceae)

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 740
Author(s):  
Ahmed EL-Banhawy ◽  
Iman H. Nour ◽  
Carmen Acedo ◽  
Ahmed ElKordy ◽  
Ahmed Faried ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Epidermal Cells ◽  
Phylogenetic Study ◽  
Endangered Plant ◽  
Sinai Peninsula ◽  
Phylogenetic Placement ◽  
Bayesian Phylogenetic Analysis ◽  
Genus Silene ◽  
Sectional Classification

The genus Silene L. is one of the largest genera in Caryophyllaceae, and is distributed in the Northern Hemisphere and South America. The endemic species Silene leucophylla and the near-endemic S. schimperiana are native to the Sinai Peninsula, Egypt. They have reduced population size and are endangered on national and international scales. These two species have typically been disregarded in most studies of the genus Silene. This research integrates the Scanning Electron Microscope (SEM), species micromorphology, and the phylogenetic analysis of four DNA markers: ITS, matK, rbcL and psb-A/trn-H. Trichomes were observed on the stem of Silene leucophylla, while the S. schimperiana has a glabrous stem. Irregular epicuticle platelets with sinuate margin were found in S. schimperiana. Oblong, bone-shaped, and irregularly arranged epidermal cells were present on the leaf of S. leucophylla, while Silene schimperiana leaf has “tetra-, penta-, hexa-, and polygonal” epidermal cells. Silene leucophylla and S. schimperiana have amphistomatic stomata. The Bayesian phylogenetic analysis of each marker individually or in combination represented the first phylogenetic study to reveal the generic and sectional classification of S. leucophylla and S. schimperiana. Two Silene complexes are proposed based on morphological and phylogenetic data. The Leucophylla complex was allied to section Siphonomorpha and the Schimperiana complex was related to section Sclerocalycinae. However, these two complexes need further investigation and more exhaustive sampling to infer their complex phylogenetic relationships.

scholarly journals Phylogenetic systematics of the genera of Thryptocerina Jeannel, 1949 and new species from New Caledonia (Coleoptera, Carabidae, Oodini)

ZooKeys ◽  
2021 ◽  
Vol 1044 ◽  
pp. 375-425 ◽  
Author(s):  
Kipling Will ◽  
Borislav Guéorguiev
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Reproductive Tract ◽  
New Caledonia ◽  
Female Reproductive Tract ◽  
Phylogenetic Systematics ◽  
Adult Morphology ◽  
Australian Species ◽  
Preliminary Study

The Oodini precinctive to New Caledonia are reviewed with nine species recognized, of which seven are newly described in two genera. Five species are described in the genus Coptocarpus Chaudoir: C. micropssp. nov., C. erwinisp. nov., C. amieuensissp. nov., C. magnussp. nov., and C. leschenisp. nov. In the genus Adelopomorpha Heller two species, A. tethyssp. nov. and A. tuberculatasp. nov., are described. In order to place cladistically the newly described species in a genus, a phylogenetic analysis of a matrix of 36 characters of adult morphology was conducted including exemplar species of three putative outgroup genera, six putative ingroup thryptocerine oodine genera, and all oodine species from New Caledonia. Results show support for Thryptocerina and monophyly of Adelopomorpha. Hoplolenus LaFerté-Sénectère is not monophyletic and Hoplolenus cyllodinus Fauvel is newly combined as Coptocarpus cyllodinuscomb. nov. New Caledonian species of Coptocarpus form a clade, but the Australian species of the genus included in the analysis are rendered paraphyletic by African and Malagasy genera. Implications of this preliminary study for the classification of Oodini and trends in the evolution of the female reproductive tract are discussed. A key to the New Caledonian species of Oodini is provided.

scholarly journals Whole-Genome Sequences of SARS-CoV-2 Isolates from the Dominican Republic

2021 ◽  
Vol 10 (47) ◽  
Author(s):  
R. Paulino-Ramirez ◽  
E. Riego ◽  
A. Vallejo-Degaudenzi ◽  
V. V. Calderon ◽  
L. Tapia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Flow ◽  
Severe Acute Respiratory Syndrome ◽  
Dominican Republic ◽  
Molecular Diversity ◽  
Whole Genome ◽  
Genome Sequences ◽  
Starting Point ◽  
Genomic Studies ◽  
The Caribbean

Here, we report the genome sequences of five severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains that were obtained from symptomatic individuals with travel histories during community surveillance in the Dominican Republic in 2020. These sequences provide a starting point for further genomic studies of gene flow and molecular diversity in the Caribbean nation. Phylogenetic analysis suggests that all genomes correspond to the B.1 variant.

Geology and hydrogeology of the Caribbean islands aquifer system of the Commonwealth of Puerto Rico and the U.S. Virgin Islands

2002 ◽  
Author(s):  
Robert A. Renken ◽  
W. C. Ward ◽  
I.P. Gill ◽  
Fernando Gómez-Gómez ◽  
Jesús Rodríguez-Martínez ◽  
...  
Keyword(s):  
Puerto Rico ◽  
Virgin Islands ◽  
Aquifer System ◽  
Caribbean Islands ◽  
The Caribbean ◽  
The U.S

scholarly journals Detection of Rhodococcus fascians, the Causative Agent of Lily Fasciation in South Korea

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 241
Author(s):  
Joon Moh Park ◽  
Jachoon Koo ◽  
Se Won Kang ◽  
Sung Hee Jo ◽  
Jeong Mee Park
Keyword(s):  
Phylogenetic Analysis ◽  
South Korea ◽  
Nicotiana Benthamiana ◽  
Economic Value ◽  
Virulence Gene ◽  
Economic Losses ◽  
Herbaceous Perennials ◽  
Rhodococcus Fascians ◽  
Different Strains

Rhodococcus fascians is an important pathogen that infects various herbaceous perennials and reduces their economic value. In this study, we examined R. fascians isolates carrying a virulence gene from symptomatic lily plants grown in South Korea. Phylogenetic analysis using the nucleotide sequences of 16S rRNA, vicA, and fasD led to the classification of the isolates into four different strains of R. fascians. Inoculation of Nicotiana benthamiana with these isolates slowed root growth and resulted in symptoms of leafy gall. These findings elucidate the diversification of domestic pathogenic R. fascians and may lead to an accurate causal diagnosis to help reduce economic losses in the bulb market.

scholarly journals Diversity of pathogenic Pseudomonas isolated from citrus in Tunisia

AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Maroua Oueslati ◽  
Magdalena Mulet ◽  
Mohamed Zouaoui ◽  
Charlotte Chandeysson ◽  
Jorge Lalucat ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Pseudomonas Syringae ◽  
Ice Nucleation ◽  
Phylogenetic Study ◽  
Future Studies ◽  
Citrus Orchards ◽  
First Time ◽  
New Cultivars

Abstract The damages observed in Tunisian citrus orchards have prompted studies on the Pseudomonas spp. responsible for blast and black pit. Prospective orchards between 2015 and 2017 showed that the diseases rapidly spread geographically and to new cultivars. A screening of Pseudomonas spp. isolated from symptomatic trees revealed their wide diversity according to phylogenetic analysis of their housekeeping rpoD and cts genes. The majority of strains were affiliated to Pseudomonas syringae pv. syringae (Phylogroup PG02b), previously described in Tunisia. However, they exhibited various BOX-PCR fingerprints and were not clonal. This work demonstrated, for the first time in Tunisia, the involvement of Pseudomonas cerasi (PG02a) and Pseudomonas congelans (PG02c). The latter did not show significant pathogenicity on citrus, but was pathogenic on cantaloupe and active for ice nucleation that could play a role in the disease. A comparative phylogenetic study of citrus pathogens from Iran, Montenegro and Tunisia revealed that P. syringae (PG02b) strains are closely related but again not clonal. Interestingly P. cerasi (PG02a) was isolated in two countries and seems to outspread. However, its role in the diseases is not fully understood and it should be monitored in future studies. The diversity of pathogenic Pseudomonas spp. and the extension of the diseases highlight that they have become complex and synergistic. It opens questions about which factors favor diseases and how to fight against them efficiently and with sustainable means.

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

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