A biologist’s guide to Bayesian phylogenetic analysis

Lassa fever is a viral hemorrhagic fever caused by the Lassa virus LASV, which was first isolated in the rodent Mastomys natalensis in 1974 in Kenema, Sierra Leone. As little is known about the abundance and the presence of LASV in rodents living in the Bo area, we carried out a small mammal longitudinal population survey. A standardized trapping session was performed in various habitats and seasons in six villages over two years (2014–2016) and samples collected were tested for arenavirus IgG and LASV. A Bayesian phylogenetic analysis was performed on sequences identified by PCR. A total of 1490 small mammals were collected, and 16 rodent species were identified, with M. natalensis (355, 24%) found to be the most prevalent species. Forty-one (2.8%) samples were IgG positive, and 31 of these were trapped in homes and 10 in surrounding vegetation. Twenty-nine of 41 seropositive rodents were M. natalensis. We detected four LASV by PCR in two villages, all found in M. natalensis. Phylogenetic analysis showed that the sequences were distributed within the Sierra Leonean clade within lineage IV, distinguishing a Bo sub-clade older than a Kenema sub-clade. Compared to other settings, we found a low abundance of M. natalensis and a low circulation of LASV in rodents in villages around Bo district.

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Case of Human Infestation with Dermanyssus gallinae (Poultry Red Mite) from Swallows (Hirundinidae)

Pathogens ◽

10.3390/pathogens10030299 ◽

2021 ◽

Vol 10 (3) ◽

pp. 299

Author(s):

Georgios Sioutas ◽

Styliani Minoudi ◽

Katerina Tiligada ◽

Caterina Chliva ◽

Alexandros Triantafyllidis ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Cytochrome C ◽

Cytochrome C Oxidase ◽

Clinical Symptoms ◽

Skin Lesions ◽

Coi Gene ◽

Dermanyssus Gallinae ◽

Poultry Red Mite ◽

Human Form ◽

Bayesian Phylogenetic Analysis

Dermanyssus gallinae (the poultry red mite, PRM) is an important ectoparasite in the laying hen industry. PRM can also infest humans, causing gamasoidosis, which is manifested as skin lesions characterized by rash and itching. Recently, there has been an increase in the reported number of human infestation cases with D. gallinae, mostly associated with the proliferation of pigeons in cities where they build their nests. The human form of the disease has not been linked to swallows (Hirundinidae) before. In this report, we describe an incident of human gamasoidosis linked to a nest of swallows built on the window ledge of an apartment in the island of Kefalonia, Greece. Mites were identified as D. gallinae using morphological keys and amplifying the Cytochrome C oxidase subunit I (COI) gene by PCR. Bayesian phylogenetic analysis and median-joining network supported the identification of three PRM haplogroups and the haplotype isolated from swallows was identical to three PRM sequences isolated from hens in Portugal. The patient was treated with topical corticosteroids, while the house was sprayed with deltamethrin. After one week, the mites disappeared and clinical symptoms subsided. The current study is the first report of human gamasoidosis from PRM found in swallows’ nest.

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Reassignment of 'Triplophysa' jiarongensis (Cypriniformes: Nemacheilidae) to Oreonectes Günther, 1868

Zootaxa ◽

10.11646/zootaxa.4565.3.6 ◽

2019 ◽

Vol 4565 (3) ◽

pp. 398 ◽

Cited By ~ 1

Author(s):

XUAN LIU ◽

HUAIQING DENG ◽

ZHIJIN LIU ◽

JIANG ZHOU

Keyword(s):

Phylogenetic Analysis ◽

Short Distance ◽

River System ◽

Genetic Distances ◽

Molecular Evidence ◽

Karst Cave ◽

Bayesian Phylogenetic Analysis ◽

As Species ◽

Secondary Sexual Dimorphism ◽

Underground River

Specimens identified as Oreonectes jiarongensis (Cypriniformes: Nemacheilidae) were collected from a karst cave in Jiarong Town and Banzhai Township, Libo County, Guizhou, China. Several lines of morphological and molecular evidence suggested that this species was similar to species of Oreonectes Günther 1868 and not closely related to species of Triplophysa Rendal, 1933. The anterior and posterior nostrils of 'Triplophysa' jiarongensis were separated by a short distance, and there was no secondary sexual dimorphism in male specimens. The Bayesian phylogenetic analysis based on cytochrome b recovered 'T.' jiarongensis in a well-supported clade with Oreonectes daqikongensis, O. shuilongensis, O. furcocaudalis and O. platycephalus, sister to the Triplophysa clade. In addition, the genetic distances between 'T.' jiarongensis and species of Oreonectes were low (O. daqikongensis: 0.114; O. shuilongensis: 0.106; O. platycephalus: 0.180), while distances to species of Triplophysa were higher (T. dorsalis: 0.233; T. yarkandensis: 0.282). Therefore, we reassign 'T.' jiarongensis to Oreonectes. Based on this result, it is now clear that species of both Oreonectes and Triplophysa inhabit the same underground river system in Guizhou. However, as species of Oreonectes are only known from the southern part of Guizhou, it may be that O. jiarongensis inhabits the most northerly part of the range of this genus.

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A66 Multi-drug-resistant Klebsiella pneumoniae strains circulating in hospital setting: Whole-genome sequencing and Bayesian phylogenetic analysis for outbreak investigations

Virus Evolution ◽

10.1093/ve/vey010.065 ◽

2018 ◽

Vol 4 (suppl_1) ◽

Author(s):

E Cella ◽

M Ciccozzi ◽

M Fogolari ◽

T Azarian ◽

M Prosperi ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Hospital Setting ◽

Whole Genome ◽

Drug Resistant ◽

Bayesian Phylogenetic Analysis ◽

Outbreak Investigations

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Taxonomic aspects of Peronosporaceae inferred from Bayesian molecular phylogenetics

Canadian Journal of Botany ◽

10.1139/b03-066 ◽

2003 ◽

Vol 81 (7) ◽

pp. 672-683 ◽

Cited By ~ 61

Author(s):

M Göker ◽

H Voglmayr ◽

A Riethmüller ◽

M Weiß ◽

F Oberwinkler

Keyword(s):

Phylogenetic Analysis ◽

Representative Sample ◽

Molecular Phylogenetics ◽

New Genus ◽

28S Rdna ◽

The Other ◽

Morphological Evidence ◽

Lsu Rdna ◽

Bayesian Phylogenetic Analysis ◽

Downy Mildews

We present the results of a Bayesian phylogenetic analysis of parts of the nuclear 28S rDNA of a representative sample of the Peronosporales. Peronospora s.l. is shown to be paraphyletic. Based on molecular and morphological evidence, several species of the genus Peronospora are transferred to Hyaloperonospora. Plasmopara oplismeni appears to be related only distantly to the other Plasmopara species, and is transferred to the new genus Viennotia based on molecular, morphological, and ecological evidence. The remaining Plasmopara species are likely to be paraphyletic with respect to Bremia, Paraperonospora, and Basidiophora. Phytophthora is shown to be paraphyletic with respect to the obligatory biotrophic genera. Evidence for the assumption that obligatory biotrophism arose independently at least twice in Peronosporales is demonstrated.Key words: LSU rDNA, Straminipila, Peronosporomycetes, Peronosporales, downy mildews, Bayesian phylogenetic analysis.

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The Bayesian phylogenetic analysis of the 18S rRNA sequences from the main lineages of Trichophora (Insecta: Heteroptera: Pentatomomorpha)

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2004.10.015 ◽

2005 ◽

Vol 34 (2) ◽

pp. 448-451 ◽

Cited By ~ 40

Author(s):

Qiang Xie ◽

Wenjun Bu ◽

Leyi Zheng

Keyword(s):

Phylogenetic Analysis ◽

18S Rrna ◽

Bayesian Phylogenetic Analysis ◽

Rrna Sequences

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Molecular Epidemiology of Rabies in Wild Canidae in Tunisia

Viruses ◽

10.3390/v13122473 ◽

2021 ◽

Vol 13 (12) ◽

pp. 2473

Author(s):

Zied Bouslama ◽

Habib Kharmachi ◽

Nourhene Basdouri ◽

Jihen Ben Salem ◽

Samia Ben Maiez ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Wild Animals ◽

Genetic Characteristics ◽

Bayesian Phylogenetic Analysis ◽

Viral Sequencing ◽

Virus Isolates ◽

Virus Strains ◽

Natural Barrier

Rabies is a viral zoonosis that is transmissible to humans via domestic and wild animals. There are two epidemiological cycles for rabies, the urban and the sylvatic cycles. In an attempt to study the epidemiological role of wild canidae in rabies transmission, the present study aimed to analyze the genetic characteristics of virus isolates and confirm prior suggestions that rabies is maintained through a dog reservoir in Tunisia. Virus strains isolated from wild canidae were subject to viral sequencing, and Bayesian phylogenetic analysis was performed using Beast2 software. Essentially, the virus strains isolated from wild canidae belonged to the Africa-1 clade, which clearly diverges from fox-related strains. Our study also demonstrated that genetic characteristics of the virus isolates were not as distinct as could be expected if a wild reservoir had already existed. On the contrary, the geographic landscape is responsible for the genetic diversity of the virus. The landscape itself could have also acted as a natural barrier to the spread of the virus.

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Genotype I hepatitis A virus introduction in Italy: Bayesian phylogenetic analysis to date different epidemics

Journal of Medical Virology ◽

10.1002/jmv.25220 ◽

2018 ◽

Vol 90 (9) ◽

pp. 1493-1502 ◽

Cited By ~ 3

Author(s):

Eleonora Cella ◽

Elisabetta Riva ◽

Silvia Angeletti ◽

Marta Fogolari ◽

Aletheia Blasi ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Hepatitis A ◽

Hepatitis A Virus ◽

Genotype I ◽

Bayesian Phylogenetic Analysis

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A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya

PeerJ ◽

10.7717/peerj.6465 ◽

2019 ◽

Vol 7 ◽

pp. e6465 ◽

Cited By ~ 3

Author(s):

James M. Wainaina ◽

Elijah Ateka ◽

Timothy Makori ◽

Monica A. Kehoe ◽

Laura M. Boykin

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Common Bean ◽

Virus Detection ◽

Primary Source ◽

Amino Acid Sequences ◽

Sub Saharan Africa ◽

Viral Metagenomics ◽

Diagnostic Tools ◽

Bayesian Phylogenetic Analysis

Common bean (Phaseolus vulgaris L.) is the primary source of protein and nutrients in the majority of households in sub-Saharan Africa. However, pests and viral diseases are key drivers in the reduction of bean production. To date, the majority of viruses reported in beans have been RNA viruses. In this study, we carried out a viral metagenomic analysis on virus symptomatic bean plants. Our virus detection pipeline identified three viral fragments of the double-stranded DNA virus Pelargonium vein banding virus (PVBV) (family, Caulimoviridae, genus Badnavirus). This is the first report of the dsDNA virus and specifically PVBV in legumes to our knowledge. In addition two previously reported +ssRNA viruses the bean common mosaic necrosis virus (BCMNVA) (Potyviridae) and aphid lethal paralysis virus (ALPV) (Dicistroviridae) were identified. Bayesian phylogenetic analysis of the Badnavirus (PVBV) using amino acid sequences of the RT/RNA-dependent DNA polymerase region showed the Kenyan sequence (SRF019_MK014483) was closely matched with two Badnavirus viruses: Dracaena mottle virus (DrMV) (YP_610965) and Lucky bamboo bacilliform virus (ABR01170). Phylogenetic analysis of BCMNVA was based on amino acid sequences of the Nib region. The BCMNVA phylogenetic tree resolved two clades identified as clade (I and II). Sequence from this study SRF35_MK014482, clustered within clade I with other Kenyan sequences. Conversely, Bayesian phylogenetic analysis of ALPV was based on nucleotide sequences of the hypothetical protein gene 1 and 2. Three main clades were resolved and identified as clades I–III. The Kenyan sequence from this study (SRF35_MK014481) clustered within clade II, and nested within a sub-clade; comprising of sequences from China and an earlier ALPV sequences from Kenya isolated from maize (MF458892). Our findings support the use of viral metagenomics to reveal the nascent viruses, their viral diversity and evolutionary history of these viruses. The detection of ALPV and PVBV indicate that these viruses have likely been underreported due to the unavailability of diagnostic tools.

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