HOST SWITCHING IN DICYEMIDS (PHYLUM DICYEMIDA)

Dicyemids (phylum Dicyemida) are the most common and most characteristic endosymbionts in the renal sacs of benthic cephalopod molluscs: octopuses and cuttlefishes. Typically, 2 or 3 dicyemid species are found in a single specimen of the host, and most dicyemids have high host specificity. Host-specific parasites are restricted to a limited range of host species by ecological barriers that impede dispersal and successful establishment; therefore, phylogenies of interacting groups are often congruent due to repeated co-speciation. Most frequently, however, host and parasite phylogenies are not congruent, which can be explained by processes such as host switching and other macro-evolutionary events. Here, the history of dicyemids and their host cephalopod associations were studied by comparing their phylogenies. Dicyemid species were collected from 8 decapodiform species and 12 octopodiform species in Japanese waters. Using whole mitochondrial cytochrome c oxidase subunit 1 (COI) sequences, a phylogeny of 37 dicyemid species, including 4 genera representing the family Dicyemidae, was reconstructed. Phylogenetic trees derived from analyses of COI genes consistently suggested that dicyemid species should be separated into 3 major clades and that the most common genera, Dicyema and Dicyemennea, are not monophyletic. Thus, morphological classification does not reflect the phylogenetic relationships of these 2 genera. Divergence (speciation) of dicyemid species seems to have occurred within a single host species. Possible host-switching events may have occurred between the Octopodiformes and Decapodiformes or within the Octopodiformes or the Decapodiformes. Therefore, the mechanism of dicyemid speciation may be a mixture of host switching and intra-host speciation. This is the first study in which the process of dicyemid diversification involving cephalopod hosts has been evaluated with a large number of dicyemid species and genera.

Gene expression plasticity facilitates different host feeding in Ips sexdentatus (Coleoptera: Curculionidae: Scolytinae)

Host shift is ecologically advantageous and a crucial driver for herbivore insect speciation. Insects on the non-native host obtain enemy-free space and confront reduced competition, but they must adapt to survive. Such signatures of adaptations can often be detected at the gene expression level. It is astonishing how bark beetles cope with distinct chemical environments while feeding on various conifers. Hence, we aim to disentangle the six-toothed bark beetle (Ips sexdentatus) response against two different conifer defences upon host shift (Scots pine to Norway spruce). We conducted bioassay and metabolomic analysis followed by RNA-seq experiments to comprehend the beetle's ability to surpass two different terpene-based conifer defence systems. Beetle growth rate and fecundity were increased when reared exclusively on spruce logs (alternative host) compared to pine logs (native host). Comparative gene expression analysis identified differentially expressed genes (DEGs) related to digestion, detoxification, transporter activity, growth, signalling, and stress response in the spruce-feeding beetle gut. Transporter genes were highly abundant during spruce feeding, suggesting they could play a role in pumping a wide variety of endogenous and xenobiotic compounds or allelochemicals out. Trehalose transporter (TRET) is also up-regulated in the spruce-fed beetle gut to maintain homeostasis and stress tolerance. RT-qPCR and enzymatic assays further corroborated some of our findings. Taken together, the transcriptional plasticity of key physiological genes plays a crucial role after the host shift and provides vital clues for the adaptive potential of bark beetles on different conifer hosts.

Mobilome characterization of the beetle Euchroma gigantea (Buprestidae) uncovers multiple long range Tc1-Mariner horizontal transfer events

Transposable elements (TEs) are mobile repetitive DNA sequences that can transfer horizontally between species. Due to their mutagenic characteristics, TEs are associated with different evolutionary events, including chromosomal rearrangements that are abundant in the beetle Euchroma gigantea. In order to understand more in depth the impact of TEs on the genomic evolution of E. gigantea, we characterized the E. gigantea mobilome and evaluated the horizontal transfer of Tc1-Mariner elements. Genomic sequencing data was generated on the Illumina Hiseq plataform, from a specimen (Northeast lineage) collected in Recife, Pernambuco - Brazil. The TEs were characterized by two independent approaches based on the clustering and assembly of highly repetitive sequences, the RepeatExplorer and dnaPipeTE. The sequences obtained were further characterized using ORFfinder and CD-Search, to obtain the TEs' potential coding proteins and verify the presence and integrity of known TE domains. Evidence for horizontal transfer was evaluated by nucleotide and protein genetic distance between TEs from E. gigantea and other species and phylogenetic incongruences detected between TEs and hosts phylogenetic trees. The mobilome of E. gigantea represents about 21 to 26% of its genome. This mobilome is composed of TEs from 31 superfamilies, belonging to different classes and most known orders of TEs. Several types of TEs with intact domains were observed with emphasis on Tc1-Mariner suggesting the presence of potentially autonomous elements. This superfamily also stands out for having the greatest abundance and diversity, with TEs being classified into four families. When compared to TEs deposited in databases, Mariner TEs stood out as having the highest nucleotide identity (above 90%) with TEs from phylogenetically distant species, such as ants and bees. Altogether these results suggest that E. gigantea Mariner TEs underwent multiple horizontal transfer events to other insect species.

Fragmented mitochondrial genomes of seal lice (family Echinophthiriidae) and gorilla louse (family Pthiridae): frequent minichromosomal splits and a host switch of lice between seals

Background

The mitochondrial (mt) genomes of 15 species of sucking lice from seven families have been studied to date. These louse species have highly dynamic, fragmented mt genomes that differ in the number of minichromosomes, the gene content, and gene order in a minichromosome between families and even between species of the same genus.

Results

In the present study, we analyzed the publicly available data to understand mt genome fragmentation in seal lice (family Echinophthiriidae) and gorilla louse, Pthirus gorillae (family Pthiridae), in particular the role of minichromosome split and minichromosome merger in the evolution of fragmented mt genomes. We show that 1) at least three ancestral mt minichromosomes of sucking lice have split in the lineage leading to seal lice, 2) one minichromosome ancestral to primate lice has split in the lineage to the gorilla louse, and 3) two ancestral minichromosomes of seal lice have merged in the lineage to the northern fur seal louse. Minichromosome split occurred 15-16 times in total in the lineages leading to species in six families of sucking lice investigated. In contrast, minichromosome merger occurred only four times in the lineages leading to species in three families of sucking lice. Further, three ancestral mt minichromosomes of sucking lice have split multiple times independently in different lineages of sucking lice. Our analyses of mt karyotypes and gene sequences also indicate the possibility of a host switch of crabeater seal louse to Weddell seals.

Conclusions

We conclude that: 1) minichromosome split contributes more than minichromosome merger in mt genome fragmentation of sucking lice, and 2) mt karyotype comparison helps understand the phylogenetic relationships between sucking louse species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08530-8.

Gastropod first intermediate hosts for two species of Monorchiidae Odhner, 1911 (Trematoda): I can't believe it's not bivalves!

The trematode superfamily Monorchioidea comprises three families of teleost parasites: the Monorchiidae Odhner, 1911, Lissorchiidae Magath, 1917, and Deropristidae Cable & Hunninen, 1942. All presently known lissorchiid and deropristid life cycles have gastropods as first intermediate hosts, whereas those of monorchiids involve bivalves. Here, we report an unexpected intermediate host for monorchiids; two species of Hurleytrematoides Yamaguti, 1954 use gastropods as first intermediate hosts. Sporocysts and cercariae were found infecting two species of the family Vermetidae, highly specialised sessile gastropods that form calcareous tubes, from two locations off the coast of Queensland, Australia. These intramolluscan infections broadly corresponded morphologically to those of known monorchiids in that the cercariae have a spinous tegument, oral and ventral suckers, a simple tail and distinct eye-spots. Given the simplified morphology of intramolluscan infections, genetic data provided a definitive identification. ITS2 rDNA and cox1 mtDNA sequence data from the gastropod infections were identical to two species of Hurleytrematoides, parasites of butterflyfishes (Chaetodontidae); Hurleytrematoides loi McNamara & Cribb, 2011 from Moreton Bay (south-eastern Queensland) and Heron Island (southern Great Barrier Reef) and Hurleytrematoides morandi McNamara & Cribb, 2011 from Heron Island. Notably, species of Hurleytrematoides are positioned relatively basal in the phylogeny of the Monorchiidae and are a sister lineage to that of species known to infect bivalves. Thus, the most parsimonious evolutionary hypothesis to explain infection of gastropods by these monorchiids is that basal monorchiids (in our analyses, species of Cableia Sogandares-Bernal, 1959, Helicometroides Yamaguti, 1934 and Hurleytrematoides) will all prove to infect gastropods, suggesting a single host switching event into bivalves for more derived monorchiids (17 other genera in our phylogenetic analyses). A less parsimonious hypothesis is that the infection of vermetids will prove to be restricted to species of Hurleytrematoides, as an isolated secondary recolonisation of gastropods from a bivalve-infecting lineage. Regardless of how their use arose, vermetids represent a dramatic host jump relative to the rest of the Monorchiidae, one potentially enabled by their specialised feeding biology.

Plasmodium-a brief introduction to the parasites causing human malaria and their basic biology

Malaria is one of the most devastating infectious diseases of humans. It is problematic clinically and economically as it prevails in poorer countries and regions, strongly hindering socioeconomic development. The causative agents of malaria are unicellular protozoan parasites belonging to the genus Plasmodium. These parasites infect not only humans but also other vertebrates, from reptiles and birds to mammals. To date, over 200 species of Plasmodium have been formally described, and each species infects a certain range of hosts. Plasmodium species that naturally infect humans and cause malaria in large areas of the world are limited to five—P. falciparum, P. vivax, P. malariae, P. ovale and P. knowlesi. The first four are specific for humans, while P. knowlesi is naturally maintained in macaque monkeys and causes zoonotic malaria widely in South East Asia. Transmission of Plasmodium species between vertebrate hosts depends on an insect vector, which is usually the mosquito. The vector is not just a carrier but the definitive host, where sexual reproduction of Plasmodium species occurs, and the parasite’s development in the insect is essential for transmission to the next vertebrate host. The range of insect species that can support the critical development of Plasmodium depends on the individual parasite species, but all five Plasmodium species causing malaria in humans are transmitted exclusively by anopheline mosquitoes. Plasmodium species have remarkable genetic flexibility which lets them adapt to alterations in the environment, giving them the potential to quickly develop resistance to therapeutics such as antimalarials and to change host specificity. In this article, selected topics involving the Plasmodium species that cause malaria in humans are reviewed.

First adult cyclophyllidean tapeworm (Cestoda) from teleost fishes: host switching beyond tetrapods in Africa

Tapeworms (Cestoda) of the order Cyclophyllidea include over 3,000 species of intestinal parasites of tetrapods, especially birds and mammals including humans. However, adults of cyclophyllideans have never been found in bony fishes, even though hundreds of thousands of these hosts have been examined for parasites globally over more than 250 years. In the present paper, we report on a unique example of host switching of a tapeworm from birds to teleost fish in Africa. A new genus, Ichthyolepis (Cyclophyllidea: Dilepididae), is erected to accommodate Ichthyolepis africana n. sp., which is the first cyclophyllidean tapeworm that sexually matures in teleost fishes. The new species parasitises several freshwater elephantfishes (Mormyriformes: Mormyridae) including Marcusenius macrolepidotus (type host) in South Africa, Marcusenius senegalensis in Senegal, Mormyrus caschive, M. niloticus and Pollimyrus isodori in the Sudan, and Mormyrus kannume in Egypt. Ichthyolepis n. gen. is typified by a large musculo-glandular apical apparatus with rostellar pouch and a rostellum armed with robust hooks similar in size, but different in shape, deep, sandglass-shaped genital atrium, vaginal atrium and cirrus armed with tiny spines, thick-walled, subspherical cirrus sac, large, lobulated ovary occupying a large part of the median pre-equatorial field of mature proglottids, numerous testes filling almost entirely the postequatorial median field of proglottids, long and narrow, sleeve-like lateral uterine diverticula, and spindle-shaped eggs. Molecular phylogenetics considers Ichthyolepis as a member of the lineage consisting of dilepidids from swifts (Apodidae) in Africa. All fish hosts of the new tapeworm are bottom feeders, live in muddy biotopes and are insectivorous, which indicates that its intermediate hosts may be insect larvae.

Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses

The recent pandemic caused by the novel human coronavirus, referrred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), not only is having a great impact on the health care systems and economies in all continents but it is also causing radical changes of common habits and life styles. The novel coronavirus (CoV) recognises, with high probability, a zoonotic origin but the role of animals in the SARS-CoV-2 epidemiology is still largely unknown. However, CoVs have been known in animals since several decades, so that veterinary coronavirologists have a great expertise on how to face CoV infections in animals, which could represent a model for SARS-CoV-2 infection in humans. In the present paper, we provide an up-to-date review of the literature currently available on animal CoVs, focusing on the molecular mechanisms that are responsible for the emergence of novel CoV strains with different antigenic, biologic and/or pathogenetic features. A full comprehension of the mechanisms driving the evolution of animal CoVs will help better understand the emergence, spreading, and evolution of SARS-CoV-2.

Characterization of swine-origin H1N1 canine influenza viruses

Host switch events of influenza A viruses (IAVs) continuously pose a zoonotic threat to humans. In 2013, swine-origin H1N1 IAVs emerged in dogs soon after they were detected in swine in the Guangxi province of China. This host switch was followed by multiple reassortment events between these H1N1 and previously circulating H3N2 canine IAVs (IAVs-C) in dogs. To evaluate the phenotype of these newly identified viruses, we characterized three swine-origin H1N1 IAVs-C and one reassortant H1N1 IAV-C. We found that H1N1 IAVs-C predominantly bound to human-type receptors, efficiently transmitted via direct contact in guinea pigs and replicated in human lung cells. Moreover, the swine-origin H1N1 IAVs-C were lethal in mice and were transmissible by respiratory droplets in guinea pigs. Importantly, sporadic human infections with these viruses have been detected, and preexisting immunity in humans might not be sufficient to prevent infections with these new viruses. Our results show the potential of H1N1 IAVs-C to infect and transmit in humans, suggesting that these viruses should be closely monitored in the future.

Mode and tempo of human hepatitis virus evolution

Human viral hepatitis, a major cause of morbidity and mortality worldwide, is caused by highly diverse viruses with different genetic, ecological, and pathogenetic features. Technological advances that allow throughput sequencing of viral genomes, as well as the development of computational tools to analyze such genome data, have largely expanded our knowledge on the host range and evolutionary history of human hepatitis viruses. Thus, with the exclusion of hepatitis D virus, close or distant relatives of these human pathogens were identified in a number of domestic and wild mammals. Also, sequences of human viral strains isolated from different geographic locations and over different time-spans have allowed the application of phylogeographic and molecular dating approaches to large viral phylogenies. In this review, we summarize the most recent insights into our understanding of the evolutionary events and ecological contexts that determined the origin and spread of human hepatitis viruses.

Geographical structure of bat SARS-related coronaviruses

Bats are the natural reservoirs of severe acute respiratory syndrome coronavirus (SARS-CoV) which caused the outbreak of human SARS in 2002-2003. We introduce the genetic diversity of SARS-related coronaviruses (SARSr-CoVs) discovered in bats and provide insights on the bat origin of human SARS. We also analyze the viral geographical structure that may improve our understanding of the evolution of bat SARSr-CoVs.

Two's company, three's a crowd: co-occurring pollinators and parasite species in Breynia oblongifolia (Phyllanthaceae)

BACKGROUND

Obligate pollination mutualisms (OPMs) are specialized interactions in which female pollinators transport pollen between the male and female flowers of a single plant species and then lay eggs into those same flowers. The pollinator offspring hatch and feed upon some or all of the developing ovules pollinated by their mothers. Strong trait matching between plants and their pollinators in OPMs is expected to result in reciprocal partner specificity i.e., a single pollinator species using a single plant species and vice versa, and strict co-speciation. These issues have been studied extensively in figs and fig wasps, but little in the more recently discovered co-diversification of Epicephala moths and their Phyllanthaceae hosts. OPMs involving Epicephala moths are believed occur in approximately 500 species of Phyllanthaceae, making it the second largest OPM group after the Ficus radiation (> 750 species). In this study, we used a mixture of DNA barcoding, genital morphology and behavioral observations to determine the number of Epicephala moth species inhabiting the fruits of Breynia oblongifolia, their geographic distribution, pollinating behavior and phylogenetic relationships.

RESULTS

We found that B. oblongifolia hosts two species of pollinator that co-occurred at all study sites, violating the assumption of reciprocal specificity. Male and female genital morphologies both differed considerably between the two moth species. In particular, females differed in the shape of their ovipositors, eggs and oviposition sites. Phylogenetic analyses indicated that the two Epicephala spp. on B. oblongifolia likely co-exist due to a host switch. In addition, we discovered that Breynia fruits are also often inhabited by a third moth, an undescribed species of Herpystis, which is a non-pollinating seed parasite.

CONCLUSIONS

Our study reveals new complexity in interactions between Phyllantheae and Epicephala pollinators and highlights that host switching, co-speciation and non-pollinating seed parasites can shape species interactions in OPMs. Our finding that co-occurring Epicephala species have contrasting oviposition modes parallels other studies and suggests that such traits are important in Epicephala species coexistence.

Geography but not alternative host species explain the spread of raccoon rabies virus in Vermont

In North America, the raccoon-associated variant of rabies virus (RRV) is of special concern, given its relatively rapid spread throughout the eastern USA and its potential public health impact due to high raccoon host densities in urban areas. Northward expansion of this epizootic included an outbreak in the Canadian province of Quebec in 2006-2009 due to trans-border spread from the State of Vermont. To inform a more proactive approach to future control efforts, this study uses phylogenetic analyses to explore the role of geography and alternative carnivore hosts in the dynamics of RRV spread within Vermont. Specifically, we sought to examine whether striped skunks, a species frequently infected by RRV, could be part of the maintenance host community. Whole genome sequencing of 160 RRV samples from Vermont and neighbouring US states were used for fine-scale phylogeographic analyses. Results, together with the complete surveillance record of raccoon rabies since its entry into Vermont in 1994, document incursions by two distinct viral lineages and identify topographical features of the landscape which have significantly influenced viral spread, resulting in a complex distribution pattern of viral variants throughout the state. Results of phylogenetic cluster analysis and discrete state reconstruction contained some evidence of skunk-to-skunk and skunk-to-raccoon transmission but overall failed to support a role for skunks as alternative maintenance hosts.

Are humans the initial source of canine mange?

Background

Scabies, or mange as it is called in animals, is an ectoparasitic contagious infestation caused by the mite Sarcoptes scabiei. Sarcoptic mange is an important veterinary disease leading to significant morbidity and mortality in wild and domestic animals. A widely accepted hypothesis, though never substantiated by factual data, suggests that humans were the initial source of the animal contamination. In this study we performed phylogenetic analyses of populations of S. scabiei from humans and from canids to validate or not the hypothesis of a human origin of the mites infecting domestic dogs.

Methods

Mites from dogs and foxes were obtained from three French sites and from other countries. A part of cytochrome c oxidase subunit 1 (cox1) gene was amplified and directly sequenced. Other sequences corresponding to mites from humans, raccoon dogs, foxes, jackal and dogs from various geographical areas were retrieved from GenBank. Phylogenetic analyses were performed using the Otodectes cynotis cox1 sequence as outgroup. Maximum Likelihood and Bayesian Inference analysis approaches were used. To visualize the relationship between the haplotypes, a median joining haplotype network was constructed using Network v4.6 according to host.

Results

Twenty-one haplotypes were observed among mites collected from five different host species, including humans and canids from nine geographical areas. The phylogenetic trees based on Maximum Likelihood and Bayesian Inference analyses showed similar topologies with few differences in node support values. The results were not consistent with a human origin of S. scabiei mites in dogs and, on the contrary, did not exclude the opposite hypothesis of a host switch from dogs to humans.

Conclusions

Phylogenetic relatedness may have an impact in terms of epidemiological control strategy. Our results and other recent studies suggest to re-evaluate the level of transmission between domestic dogs and humans.

The Schistosoma indicum species group in Nepal: presence of a new lineage of schistosome and use of the Indoplanorbis exustus species complex of snail hosts

From 2007-2014, 19,360 freshwater snails from the Terai and Hilly regions of Nepal were screened for cercariae of mammalian schistosomes. Based on analysis of mitochondrial cytochrome oxidase I, 12S, 16S and 28S sequences (3,675bp) of the cercariae recovered, we provide, to our knowledge, the first report of the Schistosoma indicum species group in Nepal. Five samples of Schistosoma nasale, nine of Schistosoma spindale and 17 of Schistosoma sp. were recovered, all from the snail Indoplanorbis exustus. The last-mentioned lineage failed to group in any of our analyses with S. nasale, S. spindale or S. indicum. It diverged in cox1 sequence from them by 16%, 13% and 13%, respectively, levels of difference comparable to well-studied species pairs of Schistosoma. Analysis of cox1, 16S and internal transcribed spacer 1 sequences (1,874bp) for Nepalese specimens of I. exustus was also surprising in revealing the presence of four genetically distinct clades. They diverged from one another at levels comparable to those noted for species pairs in the sister genus Bulinus. There was no obvious pattern of use by Nepalese Schistosoma of the Indoplanorbis clades. We found high support for a close relationship between S. indicum and Schistosoma haematobium groups, but failed to retrieve support for a clean separation of the two, with a tendency for S. nasale to fall as the most basal representative. If this pattern holds, hypotheses for the origin of the Asian Indoplanorbis-transmitted S. indicum group from the Bulinus-transmitted S. haematobium group may require modification, including consideration of more contemporaneous origins of the two groups. The Indian subcontinent is under-studied with respect to schistosome diversity and our current knowledge of the S. indicum and I. exustus species groups is inadequate. Further study is warranted given the ability of indicum group species to cause veterinary problems and cercarial dermatitis, with a worrisome potential in the future to establish infections in humans.