The new genus Imsharria is proposed for a crustose species found on or near mountain summits on the Falkland Islands. It is separated from other genera of Lecideaceae by a combination of Porpidia-type asci, halonate ascospores, immersed apothecia and a hyaline hypothecium, and forms a distinct branch in the phylogenetic analysis using the markers nrITS and mtSSU. The single species, I. orangei, is characterized by its innate apothecia with a brown disc and a thallus containing norstictic acid and an amyloid (I+ violet) medulla. In addition, Porpidia imshaugii is described for a species from the Falkland Islands resembling P. skottsbergiana but with larger ascospores, and Porpidia navarina is shown to belong in the genus Poeltiaria, with the new combination Poeltiaria navarina being made. A key to the Lecideaceae on the Falkland Islands is provided.

We first sequenced and characterised the complete mitochondrial genome of Toxocara apodeme, then studied the evolutionary relationship of the species within Toxocaridae. The complete mitochondrial genome was amplified using PCR with 14 specific primers. The mitogenome length was 14303 bp in size, including 12 PCGs (encoding 3,423 amino acids), 22 tRNAs, 2 rRNAs, and 2 NCRs, with 68.38% A+T contents. The mt genomes of T. apodemi had relatively compact structures with 11 intergenic spacers and 5 overlaps. Comparative analyses of the nucleotide sequences of complete mt genomes showed that T. apodemi had higher identities with T. canis than other congeners. A sliding window analysis of 12 PCGs among 5 Toxocara species indicated that nad4 had the highest sequence divergence, and cox1 was the least variable gene. Relative synonymous codon usage showed that UUG, ACU, CCU, CGU, and UCU most frequently occurred in the complete genomes of T. apodemi. The Ka/Ks ratio showed that all Toxocara mt genes were subject to purification selection. The largest genetic distance between T. apodemi and the other 4 congeneric species was found in nad2, and the smallest was found in cox2. Phylogenetic analyses based on the concatenated amino acid sequences of 12 PCGs demonstrated that T. apodemi formed a distinct branch and was always a sister taxon to other congeneric species. The present study determined the complete mt genome sequences of T. apodemi, which provide novel genetic markers for further studies of the taxonomy, population genetics, and systematics of the Toxocaridae nematodes.

Squids of the family Gonatidae are key components in oceanic communities. However, issues related to correct species identification, number of species, and their genetic relatedness remain. To address these issues, sequences from three mitochondrial (cytochrome c oxidase subunit I [CO1], 16S rRNA, and 12S rRNA) and two nuclear (18S and 28S) genes were analysed in the Gonatidae. Four of the five sequences (12S rRNA, 16S rRNA, 28S, and CO1) yielded rather similar patterns of genetic relationships among the species. Molecular evidence suggested intra-familial subdivision into two major groups of species having either five or seven longitudinal rows of teeth in the radula. The former group included all species of the genus Gonatus and two sister-species of Gonatopsis s. str. suggesting that all gonatid species with five rows of radular teeth represent a single taxonomic unit of a genus or subfamily level. Species with seven rows of radular teeth formed several ‘species’ clusters. Sequence analysis also addressed species identification issues in the Gonatidae. Two genetically divergent groups were found among squid which conformed to the description of Gonatus berryi. Molecular evidence suggested sister-species relationships between ‘large’ and ‘small’ forms of Boreoteuthis borealis with size-at-maturity as the only reported difference between these two cohorts. Sequence variation was observed within Gonatus pyros. Inclusion of gonatid sequences from the GenBank into the analysis suggested probable species misidentification in several cases. Combined use of several mitochondrial and nuclear sequences served as a valuable tool for species identification and provided a solid background for unravelling molecular genetic and taxonomic relationships in the Gonatidae.

Neocinnamomum plants are evergreen shrubs or small trees belonging to the Neocinnamomeae tribe of the Lauraceae family. Their seeds are rich in fatty acids, and their leaves are often used in traditional Chinese medicine. Presently, only a few studies have been performed on Neocinnamomum plants; therefore, the genome-based phylogeny among Neocinnamomum species has not been determined, which limits the germplasm innovation of this genus. In this study, by the Illumina (next-generation sequencing) and third-generation sequencing technologies, the whole genomes of seven Neocinnamomum species samples were sequenced, their nuclear DNA (nrDNA) sequences were assembled and characterized, and their phylogeny was reconstructed. The results revealed four hypervariable regions (i.e. transcribed spacer regions) in the nrDNA sequences, among which the highest degree of variation was observed in the external transcribed spacer (ETS) region localized behind the 26S gene. A total of 27 insertions/deletions and 184 single-nucleotide polymorphisms, both localized mainly in the ETS and internal transcribed spacer regions, were identified. Phylogenetic trees were constructed based on the nrDNA sequences using the maximum likelihood (ML) and Bayesian inference (BI) methods with Caryodaphnopsis henryi as the outgroup. The ML tree divided the seven Neocinnamomum species into four clades. Clade I consisted of Neocinnamomum caudatum var. macrocarpum and Neocinnamomum caudatum, clade II included Neocinnamomum delavayi and Neocinnamomum mekongense, clade III included Neocinnamomum fargesii and a branch species of N. delavayi and clade IV included Neocinnamomum lecomtei, constituting a monophyletic and basal group. The BI tree shared the same topological structure as the ML tree, and all the support values of the BI tree were one except for that of one Neocinnamomum species (0.98). The results of this study provide new evidence regarding the phylogenetic evolution of the Neocinnamomum plants.

Cephalopod populations have expanded over recent decades, both numerically and geographically. These expansions are particularly noteworthy because cephalopods are a taxon of quickly reproducing, high-metabolic rate predators that can have disproportionate impacts on naïve ecosystems. We report a new occurrence of an octopus species in 11.6 m of water in Burrows Bay, Washington, USA (coastal northeast Pacific Ocean). These newly identified individuals have several characteristics that clearly differentiate them from either of the two known octopus species that occur in shallow water within the area: Octopus rubescens and Enteroctopus dofleini. Instead, specimens superficially resemble Muusoctopus leioderma, a species which is found in the geographic area, but has never been reported at depths less than 70 m. Octopuses were collected for morphological and genetic comparison to known octopus species, focusing on other nominal Muusoctopus species. Genetic comparisons were conducted using three mitochondrial loci (12S ribosomal RNA, cytochrome oxidase subunit III, and cytochrome b) sequenced for the octopus along with two M. leioderma museum specimens, including the species' neotype. Observation of octopus behaviour revealed a unique burrowing behaviour. Morphology of the octopus found in Burrows Bay largely coincides with M. leioderma, with a few notable differences. Phylogenetic analysis revealed that Burrows Bay octopus forms a monophyletic clade with the M. leioderma neotype, but also suggested that M. leioderma is more closely related to Octopus californicus than to the other members of the genus Muusoctopus. These octopuses are thus attributed to M. leioderma but the generic placement of the species should be reviewed.

Plasmodium vivax is the most frequent and widely distributed cause of recurring malaria. It is a public health issue that mostly occurs in Southeast Asia, followed by the Middle East, Latin, and South Americas and sub-Saharan Africa. Although it is commonly known as an etiologic agent of malaria with mild clinical manifestations, it can lead to severe complications. It has been neglected and understudied for a long time, due to its low mortality, culturing infeasibility, and mild clinical manifestations in comparison to P. falciparum. Despite the mild clinical issues commonly rose for P. vivax, the correlation between the clinical manifestations exhibited by patients with severe and non-severe complications and the genetic diversity of parasites responsible for the disease is not clear. An investigation was carried out between 2011 and 2021 on patients referred to Avicenne Hospital for suspected P. vivax infection. Upon arrival, they underwent clinical and biological examinations. The lateral flow test and LAMP-PCR confirmed the presence of malaria parasites, Plasmodium sp‥ Microscopic examination revealed the presence of Plasmodium parasites with a parasitaemia between 0.01 and 0.38%. Conventional PCR amplifications targeting 714 bp DNA fragment of small subunit ribosomal DNA (SSU-rDNA) followed by bidirectional sequencing allowed us to identify the parasites as P. vivax. The neighbor-joining (NJ) phylogenetic tree revealed that P. vivax sequences processed in the present study clustered in two well-differentiated and supported clades. It included a bigger clade including P. vivax specimens of all our patients together with homonymous sequences from Indonesia, India, and El Salvador and the second clade encompassed the sequences from Yemen and India. In addition, the clustering displayed by the median-joining network agreed well with the topology of the phylogenetic tree generated by the neighbor-joining analysis. No correlation between the clinical manifestation of patients with severe and non-severe complications, encompassing diverse geographical origins, and the genetic diversity of parasites was observed since all sequences demonstrated a high homogeneity. These findings can be helpful in getting knowledge about the population genetics of P. vivax and taking proper control management strategies against these parasites.

Rodents and shrews are major reservoirs of various pathogens that are related to zoonotic infectious diseases. The purpose of this study was to investigate co-infections of zoonotic pathogens in rodents and shrews trapped in four provinces of China. We sampled different rodent and shrew communities within and around human settlements in four provinces of China and characterised several important zoonotic viral, bacterial, and parasitic pathogens by PCR methods and phylogenetic analysis. A total of 864 rodents and shrews belonging to 24 and 13 species from RODENTIA and EULIPOTYPHLA orders were captured, respectively. For viral pathogens, two species of hantavirus (Hantaan orthohantavirus and Caobang orthohantavirus) were identified in 3.47% of rodents and shrews. The overall prevalence of Bartonella spp., Anaplasmataceae, Babesia spp., Leptospira spp., Spotted fever group Rickettsiae, Borrelia spp., and Coxiella burnetii were 31.25%, 8.91%, 4.17%, 3.94%, 3.59%, 3.47%, and 0.58%, respectively. Furthermore, the highest co-infection status of three pathogens was observed among Bartonella spp., Leptospira spp., and Anaplasmataceae with a co-infection rate of 0.46%. Our results suggested that species distribution and co-infections of zoonotic pathogens were prevalent in rodents and shrews, highlighting the necessity of active surveillance for zoonotic pathogens in wild mammals in wider regions.

Evolutionary studies on Dengue virus (DENV) in endemic regions are necessary since naturally occurring mutations may lead to genotypic variations or shifts in serotypes, which may lead to future outbreaks. Our study comprehends the evolutionary dynamics of DENV, using phylogenetic, molecular clock, skyline plots, network, selection pressure, and entropy analyses based on partial CprM gene sequences. We have collected 250 samples, 161 in 2017 and 89 in 2018. Details for the 2017 samples were published in our previous article and that of 2018 are presented in this study. Further evolutionary analysis was carried out using 800 sequences, which incorporate the study and global sequences from GenBank: DENV-1 (n = 240), DENV-3 (n = 374), and DENV-4 (n = 186), identified during 1944–2020, 1956–2020, and 1956–2021, respectively. Genotypes V, III, and I were identified as the predominant genotypes of the DENV-1, DENV-3, and DENV-4 serotypes, respectively. The rate of nucleotide substitution was found highest in DENV-3 (7.90 × 10−4 s/s/y), followed by DENV-4 (6.23 × 10−4 s/s/y) and DENV-1 (5.99 × 10−4 s/s/y). The Bayesian skyline plots of the Indian strains revealed dissimilar patterns amongst the population size of the three serotypes. Network analyses showed the presence of different clusters within the prevalent genotypes. The data presented in this study will assist in supplementing the measures for vaccine development against DENV.

Reproductive strategies for specific populations are closely related to environmental factors. Consequently, they are fundamental for conservation plans and the management of threatened habitats like salt marshes. From this viewpoint, germination strategy under different temperatures and salt conditions, voltammetric parameters and molecular analysis were performed and compared in six Halocnemum populations (four of H. cruciatum and two of H. strobilaceum) growing on Mediterranean (Balearic, Tyrrenic and Adriatic) and Red Sea coasts to establish the relation to environmental variables. Significant interpopulation differences were found in all the evaluated parameters. The Mediterranean populations showed a variable opportunistic germination strategy that was directly related to the drought period length at the studied sites. Consequently, potential environmental predictors of seed response were identified. The most noteworthy were bioclimate, soil texture, continentality index, winter temperatures and summer precipitations. Additionally, voltammetric parameters were evidenced as indicators of maternal plant stress levels and, thus, as potential determinants of future seed responses. The phylogenetic analyses showed a split into two species that did not correspond to germination response. The phylogeographic analyses showed interpopulation differences in haplotype composition for H. cruciatum, but not for H. strobilaceum. In conclusion, the tight connection between seed responses and the ecological parameters of natural populations as an adaptation for successful seedling emergence was proved regardless of its phylogenetic relations.

The mitochondrial genome provides important information for phylogenetic analysis and an understanding of evolutionary origin. In this study, the mitochondrial genomes of Ilisha elongata and Setipinna tenuifilis were sequenced, which are typical circular vertebrate mitochondrial genomes composed of 16,770 and 16,805 bp, respectively. The mitogenomes of I. elongata and S. tenuifilis include 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), two ribosomal RNA (rRNA) genes and one control region (CR). Both two species' genome compositions were highly A + T biased and exhibited positive AT-skews and negative GC-skews. The genetic distance and Ka/Ks ratio analyses indicated that 13 PCGs were affected by purifying selection and the selection pressures were different from certain deep-sea fishes, which were most likely due to the difference in their living environment. Results of phylogenetic analysis support close relationships among Chirocentridae, Denticipitidae, Clupeidae, Engraulidae and Pristigasteridae based on the nucleotide and amino acid sequences of 13 PCGs. Within Clupeoidei, I. elongata and S. tenuifilis were most closely related to the family Pristigasteridae and Engraulidae, respectively. These results will help to better understand the evolutionary position of Clupeiformes and provide a reference for further phylogenetic research on Clupeiformes species.

The complete circular mitogenome of Paragonimus skrjabini miyazakii (Platyhelminthes: Paragonimidae) from Japan, obtained by PacBio long-read sequencing, was 17 591 bp and contained 12 protein-coding genes (PCGs), 2 mitoribosomal RNA and 22 transfer RNA genes. The atp8 gene was absent, and there was a 40 bp overlap between nad4L and nad4. The long non-coding region (4.3 kb) included distinct types of long and short repeat units. The pattern of base usage for PCGs and the mtDNA coding region overall in Asian and American Paragonimus species (P. s. miyazakii, P. heterotremus, P. ohirai and P. kellicotti) and the Indian form of P. westermani was T > G > A > C. On the other hand, East-Asian P. westermani used T > G > C > A. Five Asian and American Paragonimus species and P. westermani had TTT/Phe, TTG/Leu and GTT/Val as the most frequently used codons, whereas the least-used codons were different in each species and between regional forms of P. westermani. The phylogenetic tree reconstructed from a concatenated alignment of amino acids of 12 PCGs from 36 strains/26 species/5 families of trematodes confirmed that the Paragonimidae is monophyletic, with 100% nodal support. Paragonimus skrjabini miyazakii was resolved as a sister to P. heterotremus. The P. westermani clade was clearly separate from remaining congeners. The latter clade was comprised of 2 subclades, one of the East-Asian and the other of the Indian Type 1 samples. Additional mitogenomes in the Paragonimidae are needed for genomic characterization and are useful for diagnostics, identification and genetic/ phylogenetic/ epidemiological/ evolutionary studies of the Paragonimidae.

On the basis of the morphological characterization of Chelatrema neilgherriensis Manjula & Janardanan, 2006 recovered from the freshwater fish Barilius gatensis (Valenciennes, 1844) in the Wayanad region of the Western Ghats, the diagnostic features of the genus Chelatrema Gupta & Kumari, 1973 have been modified. Based on the phylogenetic analysis of C. neilgherriensis and comparative morphology studies relative to members of other families of Gorgoderoidea Looss, 1901, this genus is placed in a new family Chelatrematidae n. fam. The studies revealed the molecular and morphological closeness of Chelatrema with Paracreptatrematina limi Amin & Myer, 1982, and the latter is transferred to this new family. Hence the new family Chelatrematidae n. fam. comprises the genera Chelatrema and Paracreptatrematina.

The accurate taxonomic identity for the worldwide-distributed invasive ascidian Botryllus schlosseri has not been resolved. Employing molecular tools, primarily mtDNA, previous studies unveiled five divergent clades (A–E), suggesting a complex of five cryptic species. A recent study allocated clades A and E to different species. Here, worldwide B. schlosseri's COI distribution map has been drawn, based on 2927 specimens, elucidating 160 haplotypes (100 singletons). Clade A emerged as the most abundant and globally widespread, while other clades had more limited distributions (primarily B, C). Inter-clade and intra-clade divergences were similar, with no clear barcoding gaps between the clades, illuminating no more than two putative OTUs. Network analyses for the genetic similarities among the clades' haplotypes identified different groups, depending on threshold values and away from the suggested clades' boundaries. Three additional genetic markers (H3, 18S, 28S) disclosed clade A, segregating from other clades and clades D and E strongly integrating. Allorecognition assays between clades resulted in indifference and rejection outcomes, characteristics of the within-species allorecognition repertoire. The question as to whether Botryllus schlosseri is a single species or a species complex is further discussed, leading to the assertion that while it is a widely variable species, there is not enough evidence for its designation as a species complex.

There was little information regarding the occurrence of canine vector-borne disease (CVBDs) in shelter dogs in Thailand. This work is the first report regarding a molecular method used to determine the occurrence and genetic diversity of three canine tick-borne pathogens (TBPs) (Hepatozoon canis, Anaplasma platys and Ehrlichia canis) in blood samples from 275 shelter dogs in the north and central areas of Thailand. The PCR results based on the 18S rRNA and 16S rRNA genes showed that 71 (25.82%) dogs were positive for at least a TBP. The overall occurrence rates of H. canis, A. platys and E. canis infections were 1.81, 16.36 and 7.64%, respectively. For the phylogenetic analysis, A. platys 16S rRNA gene was genetically diverse, while H. canis 18S rRNA and E. canis 16S rRNA genes were conserved. The haplotype diversity exhibited 12 and 2 haplotypes as well as 78 and 178 polymorphic sites of A. platys and E. canis 16S rRNA genes, respectively. Our findings could be used to improve the understanding of phylogeny and genetic diversity of TBP rRNA genes and used to ameliorate the diagnosis and control programmes for the diseases in Thailand.

Trematode life cycles involve molluscs as first intermediate hosts. The identification of trematodes based on the morphology of cercariae released from molluscs is challenging because the identification relies on adult forms obtained from their definitive hosts. Several studies have recently genetically characterized these larval forms establishing a link with adults sampled from their vertebrate hosts, allowing their identification at species level. In Los Tuxtlas tropical rainforest, in south-eastern Mexico, 57 species of trematodes have been reported from wildlife vertebrates; however, studies evaluating the diversity of trematode cercariae in molluscs are lacking. Here, we studied 11 species of molluscs to assess the diversity of cercariae in two lakes of Los Tuxtlas, Veracruz, Mexico; six of the 11 species were infected. Twelve cercarial morphotypes were collected and characterized morphologically. Sequences of the 28S ribosomal RNA gene were generated to allocate each morphotype into a family using the most recent phylogenetic classification of the Digenea as a framework; molecular work revealed 16 genetic lineages; some cercariae were identified up to genus (Apharyngostrigea, Ascocotyle, Centrocestus, Echinochasmus, Lecithodendrium and Posthodiplostomum), and some to species levels (Gorgoderina rosamondae, Langeronia macrocirra, Oligogonotylus manteri and Phyllodistomum inecoli) based on their phylogenetic position within the tree, and the genetic distance with respect to other sequenced congeners. Therefore, the cercarial morphotypes in the present study represent at least 16 putative species. Our study contributes to a better understanding of the trematode diversity in an area of high vertebrate species diversity, and to the knowledge of trematode life cycles.

In Germany, Eastern regions had a mild first wave of coronavirus disease 2019 (COVID-19) from March to May 2020, but were badly hit by a second wave later in autumn and winter. It is unknown how the second wave was initiated and developed in Eastern Germany where the number of COVID-19 cases was close to zero in June and July 2020. We used genomic epidemiology to investigate the dynamic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage development across the first and second waves in Eastern Germany. With detailed phylogenetic analyses we could show that SARS-CoV-2 lineages prevalent in the first and second waves in Eastern Germany were different, with several new variants including four predominant lineages in the second wave, having been introduced into Eastern Germany between August and October 2020. The results indicate that the major driving force behind the second wave was the introduction of new variants.

Post-mortem examination of a fin whale Balaenoptera physalus stranded in the Mediterranean Sea led to the finding of Bolbosoma balaenae for the first time in this basin. In this work, we describe new structural characteristics of this parasite using light microscopy and scanning electron microscopy approaches. Moreover, the molecular and phylogenetic data as inferred from both ribosomal RNA 18S-28S and the mitochondrial DNA cytochrome oxidase c subunit 1 (cox1) for adult specimens of B. balaenae are also reported for the first time. Details of the surface topography such as proboscis's hooks, trunked trunk spines of the prebulbar foretrunk, ultrastructure of proboscis's hooks and micropores of the tegument are shown. The 18S + 28S rRNA Bayesian tree (BI) as inferred from the phylogenetic analysis showed poorly resolved relationships among the species of Bolbosoma. In contrast, the combined 18S + 28S + mtDNA cox1 BI tree topology showed that the present sequences clustered with the species of Bolbosoma in a well-supported clade. The comparison of cox1 and 18S sequences revealed that the present specimens are conspecific with the cystacanths of B. balaenae previously collected in the euphausiid Nyctiphanes couchii from the North Eastern Atlantic Ocean. This study provided taxonomic, molecular and phylogenetic data that allow for a better characterization of this poor known parasite.

This work introduces new morphological and molecular information on the filaroid nematode Setaria cervi (Rudolphi, 1819) obtained from 13 infected game ungulates out of 96 dissected. The hosts comprised the following: a single moose (Alces alces), ten red deer (Cervus elaphus) and two sika deer (Cervus nippon) originating from the western and northern regions of the Czech Republic. Based on the complete sequences of the gene encoding mitochondrial cytochrome c oxidase subunit 1 (cox1), all 20 females and four males belonged to the species S. cervi. We detected three developmental female stages (adult fertile females, juvenile L5 females and L4 female larvae) differing in size and some morphological traits as the subtle structure of peribuccal crown and shape and features of tail knob. Such differences were described in detail for the first time. The phylogenetic relationships within the family Onchocercidae have been evaluated using new information on the cox1 sequence of S. cervi (maximum likelihood method, GTR + I + G model). In accordance with the latest phylogenetic studies, the present analysis confirmed the ancient separation of the subclass Setariinae from the remaining two onchocercid lineages Dirofilariinae and Onchocerinae.

Kapsulotaenia tidswelli is a proteocephalidean cestode that utilizes varanid lizards as definitive hosts. Fresh specimens of this cestode were observed with endogenous red pigmentation in the neck region that disappeared rapidly if specimens were not preserved in glutaraldehyde. The ultrastructural characteristics of the red pigment, which are described, suggest it is a carotenoid. Phylogenetic analysis confirmed a close relationship between K. tidswelli and other species of Kapsulotaenia for which sequence information is available. There is thus no reason to consider that the red pigmentation is because K. tidswelli is atypical, and it is proposed the carotenoids are likely to be associated with the diet of its varanid host.