West Nile Virus Lineage 1 in Italy: Newly Introduced or a Re-Occurrence of a Previously Circulating Strain?

In Italy, West Nile virus (WNV) appeared for the first time in the Tuscany region in 1998. After 10 years of absence, it re-appeared in the areas surrounding the Po River delta, affecting eight provinces in three regions. Thereafter, WNV epidemics caused by genetically divergent isolates have been documented every year in the country. Since 2018, only WNV Lineage 2 has been reported in the Italian territory. In October 2020, WNV Lineage 1 (WNV-L1) re-emerged in Italy, in the Campania region. This is the first occurrence of WNV-L1 detection in the Italian territory since 2017. WNV was detected in the internal organs of a goshawk (Accipiter gentilis) and a kestrel (Falco tinnunculus). The RNA extracted in the goshawk tissue samples was sequenced, and a Bayesian phylogenetic analysis was performed by a maximum-likelihood tree. Genome analysis, conducted on the goshawk WNV complete genome sequence, indicates that the strain belongs to the WNV-L1 Western-Mediterranean (WMed) cluster. Moreover, a close phylogenetic similarity is observed between the goshawk strain, the 2008–2011 group of Italian sequences, and European strains belonging to the Wmed cluster. Our results evidence the possibility of both a new re-introduction or unnoticed silent circulation in Italy, and the strong importance of keeping the WNV surveillance system in the Italian territory active.

Molecular Epidemiology of Rabies in Wild Canidae in Tunisia

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.

Real-time and remote MCMC trace inspection with Beastiary

Bayesian phylogenetic methods have gained substantial popularity in the last decade, due to their ability to incorporate independent information and fit complex models. Most Bayesian implementations rely on Markov chain Monte Carlo (MCMC), which in turn requires careful interpretation of the output to assess the statistical validity of any resulting inferences. Here we describe Beastiary, a package for real-time and remote inspection of log flies generated by MCMC analysis commonly utilised in Bayesian phylogenetic analysis. Beastiary is an easily deployed web-sever that can be used to summarise and visualise the output of many popular software packages including BEAST, BEAST2, RevBayes, and MrBayes. We describe the overall design and implementation of Beastiary and some typical use cases, with a particular focus on the capability of monitoring analyses from remote servers.

Out of Xanthopygus (Coleoptera: Staphylinidae): escape from polyphyly

Xanthopygus as currently defined is the largest genus in the subtribe Xanthopygina (Coleoptera: Staphylinidae: Staphylininae) with 40 described species. However, the genus is poorly defined, morphologically heterogeneous and previous studies have questioned whether it is a natural group. A morphological (51 characters) Bayesian phylogenetic analysis was performed to test whether Xanthopygus is a monophyletic group. The analysis indicated that Xanthopygus was polyphyletic, and therefore species were split into four different genera. Xanthopygus nigricornis Scheerpeltz was transferred to Oligotergus as Oligotergus nigricorniscomb. nov. and Xanthopygus skalitzkyi (Bernhauer) was transferred to Styngetus as Styngetus skalitzkyicomb. nov. A new genus, Photinopygusgen. nov. was erected to accommodate the majority of the species previously in Xanthopygus and Xanthopygus sensu novo is used in a new restricted sense to accommodate the remaining species. Diagnostic features are provided to distinguish species in the genera Photinopygus and Xanthopygus from each other and all other Xanthopygina genera.

Bayesian phylogenetic analysis of linguistic data using BEAST

Bayesian phylogenetic methods provide a set of tools to efficiently evaluate large linguistic datasets by reconstructing phylogenies—family trees—that represent the history of language families. These methods provide a powerful way to test hypotheses about prehistory, regarding the subgrouping, origins, expansion, and timing of the languages and their speakers. Through phylogenetics, we gain insights into the process of language evolution in general and into how fast individual features change in particular. This article introduces Bayesian phylogenetics as applied to languages. We describe substitution models for cognate evolution, molecular clock models for the evolutionary rate along the branches of a tree, and tree generating processes suitable for linguistic data. We explain how to find the best-suited model using path sampling or nested sampling. The theoretical background of these models is supplemented by a practical tutorial describing how to set up a Bayesian phylogenetic analysis using the software tool BEAST2.

The Hyalella species flock of Lake Titicaca (Crustacea: Amphipoda): perspectives and drawbacks of dna-based identification

Lake Titicaca, in the High Andes of Perú and Bolivia, harbours the world’s third most speciose ancient-lake amphipod radiation on record. A minimum of nineteen species of Hyalella derived from at least five independent colonization episodes concentrate in this high altitude water body, although the actual species number present has not yet been established and could be much higher. Herein, we take advantage of the description of three new species (H. krolli, H. gonzalezi, and H. hirsuta) and the re-description of other two (H. solida and H. nefrens) to assess the feasibility of adopting a dna-based identification approach to resolve the magnitude of this highly speciose amphipod assemblage. A Bayesian phylogenetic analysis of the evolutionary relationships among South American Hyalella cox1 haplotypes, including those of four out of the five species dealt with herein, shows a great disagreement between taxonomic units delimited under morphological and genetic data, hampering species identification exclusively based on cox1 dna barcode sequences.

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

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.

Revision and phylogeny of the genus Andocaeculus (Acari: Caeculidae) I: the A. weyrauchi species group

Two new caeculid mite species, Andocaeculus beatrizrosso sp. nov. and Andocaeculus burmeisteri sp. nov., are described and A. weyrauchi (Franz, 1964) is redescribed based on material collected at the type locality. All post-larval stages are described for A. weyrauchi and Andocaeculus beatrizrosso sp. nov. and stochastic variation in the idiosomal and appendages chaetotaxy is considered. A clade of Andocaeculus containing the three species (the A. weyrauchi group) is established based on morphological characters, and confirmed with a Bayesian phylogenetic analysis of sequences from the CO1 marker. As result of the same analysis, the absence of the (st) pair of setae on leg II is proposed as a derived condition for the genus Andocaeculus, and the presence of the φ solenidion on leg IV is a derived condition for some Andocaeculus species of the A. weyrauchi species group.

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

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.