Phylogeography of Hypomasticus copelandii Reveals Distinct Genetic Lineages along Atlantic Coastal Drainages of Eastern Brazil (Teleostei, Anostomidae)

Hypomasticus copelandii is a Neotropical freshwater fish widely distributed across coastal drainages of southeastern Brazil, a highly impacted region of South America. The interspecific phylogenetic relationships within the genus and the taxonomic status of the species remain uncertain. Using two mitochondrial and one nuclear locus, we performed a phylogenetic, species delimitation, and time-calibrated analyses to test the hypothesis that H. copelandii is a species complex currently delimited by different Atlantic coastal systems. Results indicate that H. copelandii presents two well-delimited genetic lineages: one in the northern drainages of the Jucuruçu, Mucuri and Doce rivers, and the other in the southern region represented by the Paraíba do Sul River Basin. The time-calibrated phylogeny indicated a split between the two genetic lineages at around 2.8 million years ago (Ma), which might be related to headwater capture events during the Plio-Pleistocene. The discovery of a distinct genetic lineage for H. copelandii suggests distinct management plans for the northern and southern drainages. Such hidden diversity within the H. copelandii provides useful information for taxonomy and conservation across a severely impacted region of Brazil.

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Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level

Pathogens ◽

10.3390/pathogens10030302 ◽

2021 ◽

Vol 10 (3) ◽

pp. 302

Author(s):

Malik Sallam ◽

Azmi Mahafzah

Keyword(s):

Amino Acid ◽

Amino Acid Substitution ◽

Rapid Evolution ◽

Molecular Signature ◽

Special Focus ◽

Genetic Lineage ◽

Synonymous Mutation ◽

Spike Gene ◽

Genetic Lineages ◽

The Uk

The rapid evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is manifested by the emergence of an ever-growing pool of genetic lineages. The aim of this study was to analyze the genetic variability of SARS-CoV-2 in Jordan, with a special focus on the UK variant of concern. A total of 579 SARS-CoV-2 sequences collected in Jordan were subjected to maximum likelihood and Bayesian phylogenetic analysis. Genetic lineage assignment was undertaken using the Pango system. Amino acid substitutions were investigated using the Protein Variation Effect Analyzer (PROVEAN) tool. A total of 19 different SARS-CoV-2 genetic lineages were detected, with the most frequent being the first Jordan lineage (B.1.1.312), first detected in August 2020 (n = 424, 73.2%). This was followed by the second Jordan lineage (B.1.36.10), first detected in September 2020 (n = 62, 10.7%), and the UK variant of concern (B.1.1.7; n = 36, 6.2%). In the spike gene region, the molecular signature for B.1.1.312 was the non-synonymous mutation A24432T resulting in a deleterious amino acid substitution (Q957L), while the molecular signature for B.1.36.10 was the synonymous mutation C22444T. Bayesian analysis revealed that the UK variant of concern (B.1.1.7) was introduced into Jordan in late November 2020 (mean estimate); four weeks earlier than its official reporting in the country. In Jordan, an exponential increase in COVID-19 cases due to B.1.1.7 lineage coincided with the new year 2021. The highest proportion of phylogenetic clustering was detected for the B.1.1.7 lineage. The amino acid substitution D614G in the spike glycoprotein was exclusively present in the country from July 2020 onwards. Two Jordanian lineages dominated infections in the country, with continuous introduction/emergence of new lineages. In Jordan, the rapid spread of the UK variant of concern should be monitored closely. The spread of SARS-CoV-2 mutants appeared to be related to the founder effect; nevertheless, the biological impact of certain mutations should be further investigated.

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Helicometrina nimia Linton, 1910 (Digenea: Opecoelidae) in dusky grouper Epinephelus marginatus (Lowe, 1834) (Teleostei: Serranidae) from southeastern Brazil

Brazilian Journal of Biology ◽

10.1590/1519-6984.12612 ◽

2014 ◽

Vol 74 (2) ◽

pp. 472-479 ◽

Cited By ~ 3

Author(s):

K. Roumbedakis ◽

NC. Marchiori ◽

P. Garcia ◽

J Pereira Junior ◽

LAS. Castro ◽

...

Keyword(s):

Taxonomic Status ◽

Wide Distribution ◽

Sao Paulo ◽

Diagnostic Character ◽

Southeastern Brazil ◽

Diagnostic Features ◽

New Host ◽

Paulo State ◽

Dusky Grouper ◽

São Paulo State

Helicometrina nimia (Opecoelidae) is a digenean with wide distribution. Fish families most commonly used as hosts for H. nimia are Serranidae, Pomodasydae, Scorpaenidae and Clinidae. In the present study, a new host and a new host locality are presented for the species. A description of the studied specimens, besides comments concerning its taxonomic status and biometrically compared tables of H. nimia reports are given. The taxonomic status of members of Helicometrina has been questionable. The greatest controversy for the genus seems to be related to the validity of diagnostic features, especially in regard to the number of testes. In the present study, all studied specimens presented a permanent and steady number of testes (n=9) and therefore its use as a diagnostic character is supported by the present authors. Epinephelus marginatus is considered a new host for Helicometrina nimia, and São Paulo state, southeastern Brazil, a new locality for the species.

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Taxonomic implications of morphological variation in three species of Trinomys (Rodentia: Echimyidae) from eastern Brazil

Zootaxa ◽

10.11646/zootaxa.3919.1.3 ◽

2015 ◽

Vol 3919 (1) ◽

pp. 61 ◽

Cited By ~ 2

Author(s):

JERONYMO DALAPICOLLA ◽

YURI L. R. LEITE

Keyword(s):

Morphological Variation ◽

Taxonomic Status ◽

The State ◽

Geographic Ranges ◽

Espírito Santo ◽

Eastern Brazil ◽

North Bank ◽

Taxonomic Implications ◽

The Right ◽

Espirito Santo

Trinomys is a genus of terrestrial spiny rats from the Atlantic Forest, and three species occur in the state of Espírito Santo, eastern Brazil: T. gratiosus, T. paratus, and T. setosus. The levels of morphological variation within and among these species are virtually unknown, and their geographic ranges have not been properly assessed. These three species are externally very similar, hampering their identification in surveys and ecological studies that are not based on voucher specimens. We evaluated 162 specimens of Trinomys spp. from eastern Brazil, especially from the state of Espírito Santo, and used data from skulls, skins, and bacula to examine morphological variation and its taxonomic implications. We found extensive morphological variation in the skins and skulls even when diagnostic characters were examined, such as the number of dental lophs and bones contributing to the postorbital process. We also found variation in bacular shape among and within species, including polymorphism among individuals from the same population. The geographic range of each species in Espírito Santo was well defined: T. setosus occurred on the left (north) bank of the Doce River, and the other two species, T. gratiosus and T. paratus, occurred on the right (south) bank of this river; however, T. gratiosus was found at altitudes above 500 m, whereas T. paratus occurred below 580 m. Despite difficulties in species identification, the results of morphological and morphometric analyses are compatible with the current classification of these three species. In addition, the level of morphological variation found in specimens identified as T. g. panema—including types—falls within the range of T. g. gratiosus, confirming the taxonomic status of the former as a junior synonym of the latter.

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The protected tree Dimorphandra wilsonii (Fabaceae) is a population of inter-specific hybrids: recommendations for conservation in the Brazilian Cerrado/Atlantic Forest ecotone

Annals of Botany ◽

10.1093/aob/mcaa066 ◽

2020 ◽

Vol 126 (1) ◽

pp. 191-203

Author(s):

André Carneiro Muniz ◽

José Pires Lemos-Filho ◽

Helena Augusta Souza ◽

Rafaela Cabral Marinho ◽

Renata Santiago Buzatti ◽

...

Keyword(s):

Atlantic Forest ◽

Cytogenetic Analysis ◽

Taxonomic Status ◽

Conservation Strategies ◽

F1 Hybrids ◽

Individual Level ◽

Intermediate Phenotypes ◽

Eastern Brazil ◽

Heterozygosity Excess ◽

The Individual

Abstract Backgrounds and Aims Dimorphandra wilsonii Rizzini, a critically endangered and protected tree, has a restricted distribution in the ecotone between the Cerrado and the Atlantic Forest in south-eastern Brazil. In this area, it co-occurs with D. mollis Benth., a common tree from the Cerrado, and D. exaltata Schott., a rare tree from the Atlantic Forest. Previous studies of D. wilsonii indicated heterozygosity excess at the individual level. Field observation of some intermediate phenotypes between D. wilsonii and both congeners suggests hybridization of D. wilsonii with D. mollis and/or D. exaltata. Here, we tested the hypothesis that D. wilsonii may have originated from hybridization between D. exaltata and D. mollis. We also performed cytogenetic analysis to examine if the heterozygosity excess could be explained by polyploidy in D. wilsonii. Methods We evaluated the genetic diversity and population structure of D. wilsonii using 11 nuclear simple sequence repeats (SSRs) genotyped in 152 individuals sampled across the taxon’s range. We performed comparative genetic analyses using overlapping SSR markers between D. wilsonii and previously published SSR data in D. mollis and D. exaltata to subsequently perform a series of allelic comparisons, multivariate and Bayesian analysis. Key Results Our results suggest that D. wilsonii individuals are most likely to correspond to F1 hybrids between D. exaltata and D. mollis. Cytogenetic analysis indicated that D. wilsonii is diploid with the same chromosome number as D. mollis (2n = 2x = 28). Conclusions Our study raises questions about the taxonomic status and the evolutionary future of D. wilsonii. We suggest that the conservation and management strategy for D. wilsonii should be revised and that it should take into account both parental Dimorphandra species in the ecotone, with special emphasis on the threatened D. exaltata. Finally, this study highlights the value of genetic information for the design of conservation strategies.

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1235. Transmission of Genetically Related, Multidrug Resistant, and Invasive Vancomycin-Resistant Enterococci (VRE) Between Patients and Rooms on the Stem Cell Transplant (SCT) and Leukemia (LKM) Units

Open Forum Infectious Diseases ◽

10.1093/ofid/ofy210.1068 ◽

2018 ◽

Vol 5 (suppl_1) ◽

pp. S375-S375

Author(s):

Lynn El Haddad ◽

Blake Hanson ◽

Cesar Arias ◽

Glen Otero ◽

Cynthia Harb ◽

...

Keyword(s):

Stem Cell ◽

Stem Cell Transplant ◽

Phylogenetic Analyses ◽

Hospital Setting ◽

Multidrug Resistant ◽

Genetic Lineage ◽

Cell Transplant ◽

Research Support ◽

Genetic Lineages ◽

Sequence Types

Abstract Background VRE are a major cause of morbidity and mortality in immunocompromised patients. Tracking the dissemination of VRE strains is crucial to understand the dynamics of infections, emergence, and spread of VRE in the hospital setting. Methods Whole-genome sequencing (WGS) and phylogenetic analyses were performed to identify dominant VRE strains and potential transmission networks between patients and their rooms on the leukemia (LKM) and the stem cell transplant (SCT) units, located on two consecutive floors. We included 35 VRE-positive rectal swabs from SCT and LKM patients, and 55 environmental swabs from the patients’ main rooms and bathrooms. Sequence types, drug resistance genes, virulence genes, and patients’ outcomes were also determined. Results We identified VRE strains with newly described sequence types (ST) such as ST736, ST494, and ST772 which were isolated from both floors. One VRE genetic lineage belonged to ST494 (only previously isolated in Peru and was the only VanB-type strain). All other strains harbored the vanA gene. We observed highly genetically related strains transmitted between distinct rooms, floors, and time periods within the hospital in a period of 1 month (figure). Of five VRE bacteremia events, three strains were lacking the pili operon fms14-17-13 (ST203) and the remaining two were resistant to daptomycin (ST736, ST664) (figure). Of 10 patients harboring daptomycin-resistant strains, only 3 (30%) were exposed to daptomycin within 18 months before strain recovery. Conclusion Our findings confirmed horizontal transfer of highly related genetic lineages of multidrug resistant and invasive VRE strains between SCT and LKM patients and their room environment. New STs were identified and some correlated with bacteremia events. The use of a routine real-time WGS can characterize VRE strains and identify potential reservoirs of transmission in the healthcare setting in order to design interventions to prevent and control the spread of opportunistic and highly resistant organisms. Disclosures C. Arias, Merck & Co., Inc.: Grant Investigator, Research support. MeMed: Grant Investigator, Research support. Allergan: Grant Investigator, Research support. M. Stibich, Xenex Services: Employee, Salary. R. F. Chemaly, Xenex Services: Consultant and Grant Investigator, Research grant.

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Surveys for natural enemies of the tomato red spider mite Tetranychus evansi (Acari: Tetranychidae) in northeastern and southeastern Brazil

Zootaxa ◽

10.11646/zootaxa.1395.1.2 ◽

2007 ◽

Vol 1395 (1) ◽

pp. 33-58 ◽

Cited By ~ 3

Author(s):

KOMI K.M. FIABOE ◽

MANOEL G.C. GONDIM JR ◽

GILBERTO J. DE MORAES ◽

CALLISTUS K.P.O. OGOL ◽

MARKUS KNAPP

Keyword(s):

Natural Enemies ◽

Spider Mite ◽

Predatory Mites ◽

Southeastern Brazil ◽

Tetranychus Evansi ◽

Eastern Brazil ◽

Three Samples ◽

Red Spider Mite ◽

Solanum Americanum ◽

Solanaceous Plants

Surveys for predators of the tomato red spider mite Tetranychus evansi Baker & Pritchard on solanaceous plants were carried out in north-eastern and south-eastern Brazil to determine prospective species for the control of the pest in Africa. Surveys were carried out in areas identified as climatically similar to regions in Africa where T. evansi has been reported as a pest and where prospective natural enemies may be introduced. A total of 56,445 mites and insects were found in 330 samples collected from 20 different species of solanaceous plants. Tetranychus evansi was found in only three samples, on Solanum americanum Mill. and Lycopersicon esculentum Mill.. A total of 5,023 specimens of predatory mites, of at least 44 species, and 494 specimens of acarophagous insects, of at least three species were collected. The predominant predatory mites were (in decreasing order): Phytoseius guianensis DeLeon, Pronematus ubiquitus (McGregor), Asca sp., Paraphytoseius orientalis (Narayanan, Kaur & Ghai), Phytoseius woodburyii DeLeon, Amblyseius compositus Denmark & Muma, Homeopronematus anconai (Baker), Neoparaphytoseius sooretamus (El-Banhawy), Cunaxoides sp., Typhlodromus paraevectus Moraes & McMurtry, Typhlodromalus peregrinus (Muma) and Phytoseius cismontanus DeLeon. However, no predatory mites were found in association with T. evansi. Among the insects, although not the most abundant, Stethorus tridens Gordon seemed to be most promising, as it was found associated with T. evansi in all samples in which the latter was found. Feltiella sp. was the most abundant acarophagous insect found, but it was never found associated with the pest.

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Yellow fever in Brazil: thoughts and hypotheses on the emergence in previously free areas

Revista de Saúde Pública ◽

10.1590/s0034-89102010005000046 ◽

2010 ◽

Vol 44 (6) ◽

pp. 1144-1149 ◽

Cited By ~ 63

Author(s):

Pedro Fernando da Costa Vasconcelos

Keyword(s):

Yellow Fever ◽

Human Population ◽

Transmission Dynamics ◽

Southeastern Brazil ◽

Surveillance Program ◽

Genetic Lineage ◽

Rio Grande Do Sul ◽

Climate Conditions ◽

Factors Associated ◽

High Prevalence

This article describes and discusses factors associated to the reemergence of yellow fever and its transmission dynamics in the states of São Paulo (Southeastern Brazil) and Rio Grande do Sul (Southern) during 2008 and 2009. The following factors have played a pivotal role for the reemergence of yellow fever in these areas: large susceptible human population; high prevalence of vectors and primary hosts (non-human primates); favorable climate conditions, especially increased rainfall; emergence of a new genetic lineage; and circulation of people and/or monkeys infected by virus. There is a need for an effective surveillance program to prevent the reemergence of yellow fever in other Brazilian states.

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Low courtship song variation in South and Southeastern Brazilian populations of Drosophila meridionalis (Diptera, Drosophilidae)

Revista Brasileira de Biologia ◽

10.1590/s0034-71082000000100008 ◽

2000 ◽

Vol 60 (1) ◽

pp. 53-61 ◽

Cited By ~ 2

Author(s):

C. T. A. COSTA ◽

G. C. S. KUHN ◽

F. M. SENE

Keyword(s):

South America ◽

Taxonomic Status ◽

Wide Distribution ◽

Courtship Song ◽

Southeastern Brazil ◽

Metaphase Chromosomes ◽

Song Variation ◽

Chromosomal Variability ◽

Karyotypic Variation ◽

Brazilian Populations

Drosophila meridionalis is a cactus-breeding species with a wide distribution in South America. Most populations of this species are geographically isolated, what provides a promising scenario for studying evolution. Former studies of this species revealed a remarkable karyotypic variation among its populations. Up to six distinct metaphase chromosomes were described, showing that this species is polymorphic at least at the chromosomal level. In order to elucidate the taxonomic status of populations showing different metaphase chromosomes, we analyzed the courtship song of five populations of D. meridionalis in South and Southeastern Brazil. In addition, we analyzed the metaphase chromossomes of each population. Our results show that, despite the two karyotype observed, most courtship song parameters did not vary among the populations. Altogether, our results suggest that D. meridionalis from South and Southeastern Brazil represents one species with an inter-population chromosomal variability.

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