Discovery of the parasite Marteilia cocosarum sp. nov. In common cockle (Cerastoderma edule) fisheries in Wales, UK and its comparison with Marteilia cochillia.

Diseases of bivalve molluscs caused by paramyxid parasites of the genus Marteilia have been linked to mass mortalities and the collapse of commercially important shellfish populations. Until recently, no Marteilia spp. have been detected in common cockle (Cerastoderma edule) populations in the British Isles. Molecular screening of cockles from ten sites on the Welsh coast indicates that a Marteilia parasite is widespread in Welsh C. edule populations, including major fisheries. Phylogenetic analysis of ribosomal DNA (rDNA) gene sequences from this parasite indicates that it is a closely related but different species to Marteilia cochillia, a parasite linked to mass mortality of C. edule fisheries in Spain, and that both are related to Marteilia octospora, for which we provide new rDNA sequence data. Preliminary light and transmission electron microscope (TEM) observations support this conclusion, indicating that the parasite from Wales is located primarily within areas of inflammation in the gills and the connective tissue of the digestive gland, whereas M. cochillia is found mainly within the epithelium of the digestive gland. The impact of infection by the new species, here described as Marteilia cocosarum n. sp., upon Welsh fisheries is currently unknown.

High prevalence of Paramarteilia canceri infecting velvet swimming crabs Necora puber in Ireland.

The velvet swimming crab Necora puber has been fished in Ireland since the early 1980s and contributes significant income to smaller fishing vessels. From 2016 onwards, reduced landings have been reported. We undertook a full pathological investigation of crabs from fishing grounds at 3 sites on the west (Galway), southwest (Castletownbere) and east (Howth) coasts of Ireland. Histopathology, transmission electron microscopy and molecular taxonomic and phylogenetic analyses showed high prevalence and infection level of Paramarteilia canceri, previously only reported from the edible crab Cancer pagurus. This study provides the first molecular data for P. canceri, and shows its phylogenetic position in the order Paramyxida (Rhizaria). Other parasites and symbionts detected in the crabs were also noted, including widespread but low co-infection with Hematodinium sp. and a microsporidian consistent with the Ameson and Nadelspora genera. This is the first histological record of Hematodinium sp. in velvet crabs from Ireland. Four N. puber individuals across 2 sites were co-infected by P. canceri and Hematodinium sp. At one site, 3 velvet crabs infected with P. canceri were co-infected with the first microsporidian recorded from this host; the microsporidian 18S sequence was almost identical to Ameson pulvis, known to infect European shore crabs Carcinus maenas. The study provides a comprehensive phylogenetic analysis of this and all other available Ameson and Nadelspora 18S sequences. Together, these findings provide a baseline for further investigations of N. puber populations along the coast of Ireland.

Eco-epidemiological screening of multi-host wild rodent communities in the UK reveals pathogen strains of zoonotic interest.

Wild rodent communities represent ideal systems to study pathogens and parasites shared among sympatric species. Such studies are useful in the investigation of eco-epidemiological dynamics, improving disease management strategies and reducing zoonotic risk. The aim of this study was to investigate pathogen and parasites shared among rodent species (multi-host community) in West Wales in an area where human/wildlife disease risk was not previously assessed. West Wales is predominantly rural, with human settlements located alongside to grazing areas and semi-natural landscapes, creating a critical human-livestock-wildlife interface. Ground-dwelling wild rodent communities in Wales were live-trapped and biological samples - faeces and ectoparasites - collected and screened for a suite of pathogens and parasites that differ in types of transmission and ecology. Faecal samples were examined to detect Herpesvirus, Escherichia coli, and Mycobacterium microti. Ticks and fleas were collected, identified to species based on morphology and genetic barcodes, and then screened for Anaplasma phagocytophilum, Babesia microti, Borrelia burgdorferi sensu lato, and Bartonella sp. All the pathogens and parasites screened pose a characteristic epidemiological challenge, such as variable level of generalism, unknown zoonotic potential, and lack of data. The results showed that the bank vole Myodes glareolus had the highest prevalence of all pathogens and parasites. Higher flea species diversity was detected than in previous studies, and at least two Bartonella species were found circulating, one of which has not previously been detected in the UK. These key findings offer new insights into the distribution of selected pathogen and parasites and subsequent zoonotic risk, and provide new baselines and perspectives for further eco-epidemiological research.

Fine-scale seascape genomics of an exploited marine species, the common cockle Cerastoderma edule, using a multimodelling approach.

Population dynamics of marine species that are sessile as adults are driven by oceanographic dispersal of larvae from spawning to nursery grounds. This is mediated by life-history traits such as the timing and frequency of spawning, larval behaviour and duration, and settlement success. Here, we use 1725 single nucleotide polymorphisms (SNPs) to study the fine-scale spatial genetic structure in the commercially important cockle species Cerastoderma edule and compare it to environmental variables and current-mediated larval dispersal within a modelling framework. Hydrodynamic modelling employing the NEMO Atlantic Margin Model (AMM15) was used to simulate larval transport and estimate connectivity between populations during spawning months (April-September), factoring in larval duration and interannual variability of ocean currents. Results at neutral loci reveal the existence of three separate genetic clusters (mean F ST = 0.021) within a relatively fine spatial scale in the north-west Atlantic. Environmental association analysis indicates that oceanographic currents and geographic proximity explain over 20% of the variance observed at neutral loci, while genetic variance (71%) at outlier loci was explained by sea surface temperature extremes. These results fill an important knowledge gap in the management of a commercially important and overexploited species, bringing us closer to understanding the role of larval dispersal in connecting populations at a fine geographic scale.

Accumulation and exchange of parasites during adaptive radiation in an ancient lake.

In the ancient Lake Baikal, Russia, amphipod crustaceans have undergone a spectacular adaptive radiation, resulting in a diverse community of species. A survey of microsporidian parasites inhabiting endemic and non-endemic amphipod host species at the margins of Lake Baikal indicates that the endemic amphipods harbour many microsporidian parasite groups associated with amphipods elsewhere in Eurasia. While these parasites may have undergone a degree of adaptive radiation within the lake, there is little evidence of host specificity. Furthermore, a lack of reciprocal monophyly indicates that exchanges of microsporidia between Baikalian and non-Baikalian hosts have occurred frequently in the past and may be ongoing. Conversely, limitations to parasite exchange between Baikalian and non-Baikalian host populations at the margins of the lake are implied by differences in parasite prevalence and lack of shared microsporidian haplotypes between the two host communities. While amphipod hosts have speciated sympatrically within Lake Baikal, the parasites appear instead to have accumulated, moving into the lake from external amphipod populations on multiple occasions to exploit the large and diverse community of endemic amphipods in Lake Baikal.

Should sex-ratio distorting parasites abandon horizontal transmission?

BACKGROUND: Sex-ratio distorting parasites are of interest due to their effects upon host population dynamics and their potential to influence the evolution of host sex determination systems. In theory, the ability to distort host sex-ratios allows a parasite with efficient vertical (hereditary) transmission to dispense completely with horizontal (infectious) transmission. However, recent empirical studies indicate that some sex-ratio distorting parasites have retained the capability for horizontal transmission. RESULTS: Numerical simulations using biologically realistic parameters suggest that a feminising parasite is only likely to lose the capability for horizontal transmission if its host occurs at low density and/or has a male-biased primary sex ratio. It is also demonstrated that even a small amount of horizontal transmission can allow multiple feminising parasites to coexist within a single host population. Finally it is shown that, by boosting its host's rate of population growth, a feminising parasite can increase its own horizontal transmission and allow the invasion of other, more virulent parasites. CONCLUSIONS: The prediction that sex-ratio distorting parasites are likely to retain a degree of horizontal transmission has important implications for the epidemiology and host-parasite interactions of these organisms. It may also explain the frequent co-occurrence of several sex-ratio distorting parasite species in nature.

Genetic diversity of the feminising microsporidian parasite Dictyocoela: new insights into host-specificity, sex and phylogeography.

Microsporidia of the genus Dictyocoela are parasites of gammarid amphipod Crustacea. They typically exhibit low virulence and efficient vertical transmission and at least some strains are capable of feminising their hosts. Sequencing of a region of the 16S rDNA of Dictyocoela spp. from various gammarid host species and localities in Europe and northern Asia indicates that Dictyocoela is genetically diverse and that different strains predominate in different host species. However, the presence of intermediate sequences casts doubt upon previous attempts to describe Dictyocoela spp. on the basis of rDNA divergence alone. Phylogenetic analysis provides little support for coevolution between gammarids and Dictyocoela. Furthermore, observations of heavily infected individuals, together with genetic evidence of recombination, suggest that some strains of Dictyocoela may be horizontally transmitted and are sexually reproducing. These findings suggest that Dictyocoela may be phenotypically, as well as genotypically, diverse, with the potential to exhibit a range of different interactions with its host populations.

No amicable divorce? Challenging the notion that sexual antagonism drives sex chromosome evolution.

Although sexual antagonism may have played a role in forming some sex chromosome systems, there appears to be little empirical or theoretical justification in assuming that it is the driving force in all cases of sex chromosome evolution. In many species, sex chromosomes have diverged in size and shape through the accumulation of mutations in regions of suppressed recombination. It is commonly assumed that recombination is suppressed in sex chromosomes due to selection to resolve sexually antagonistic pleiotropy. However, the requirement for a sex chromosome-specific mechanism for suppressing recombination is questionable, since more general models of recombination suppression on autosomes also appear to be applicable to sex chromosomes. Direct tests of the predictions of the sexual antagonism hypothesis offer only limited support in specific sex chromosome systems and circumstantial evidence remains open to interpretation.

Distribution and host range of the microsporidian Pleistophora mulleri.

Microsporidia of the genus Pleistophora are important parasites of fish and crustacea. Pleistophora mulleri has been described previously as a parasite of the gammarid amphipod crustacean Gammarus duebeni celticus in Irish freshwater habitats. Through a survey of European G. duebeni populations, P. mulleri was found to be widely distributed in the western British Isles (Wales, Scotland, and the Isle of Man), and populations of the subspecies Gammarus duebeni duebeni as well as G. d. celticus were infected. Pleistophora infections were also detected in G. d. duebeni sampled from the Bay of Gdansk on Poland's Baltic coast, indicating a wide distribution of Pleistophora in European G. duebeni. Sequencing and phylogenetic analysis of the 16S rRNA, 18S rRNA, and Rpb1 genes of P. mulleri suggest that this species may be synonymous with P. typicalis, a parasite of fish. These findings suggest that amphipod crustaceans may act as intermediate or reservoir hosts for microsporidian parasites of fish.

A higher-level phylogenetic classification of the Fungi.

A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotina. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella.

Multiple losses of sex within a single genus of Microsporidia.

BACKGROUND: Most asexual eukaryotic lineages have arisen recently from sexual ancestors and contain few ecologically distinct species, providing evidence for long-term advantages of sex. Ancient asexual lineages provide rare exceptions to this rule and so can yield valuable information relating to the evolutionary forces underlying the maintenance of sex. Microsporidia are parasitic, unicellular fungi. They include many asexual species which have traditionally been grouped together into large, presumably ancient taxonomic groups. However, these putative ancient asexual lineages have been identified on the basis of morphology, life cycles and small subunit ribosomal RNA (16S rRNA) gene sequences, all of which hold questionable value in accurately inferring phylogenetic relationships among microsporidia. RESULTS: The hypothesis of a single, ancient loss of sex within the Nosema/Vairimorpha group of microsporidia was tested using phylogenetic analyses based on alignments of rRNA and RPB1 gene sequences from sexual and asexual species. Neither set of gene trees supported ancient asexuality, instead indicating at least two, recent losses of sex. CONCLUSION: Sex has been lost on multiple, independent occasions within the Nosema/Vairimorpha group of microsporidia and there is no evidence for ancient asexual lineages. It appears therefore that sex confers important long-term advantages even upon highly simplified eukaryotes such as microsporidia. The rapid evolution of microsporidian life cycles indicated by this study also suggests that even closely related microsporidia cannot be assumed to have similar life cycles and the life cycle of each newly discovered species must therefore be completely described. These findings are relevant to the use of microsporidia as biological control agents, since several species under consideration as potential agents have life cycles that have been incompletely described.

Extreme population structure and high interspecific divergence of the Silene Y chromosome.

Previous studies have demonstrated that the diversity of Y-linked genes is substantially lower than that of their X-linked homologs in the plant Silene latifolia. This difference has been attributed to selective sweeps, Muller's ratchet, and background selection, processes that are predicted to severely affect the evolution of the nonrecombining Y chromosome. We studied the DNA diversity of a noncoding region of the homologous genes DD44Y and DD44X, sampling S. latifolia populations from a wide geographical area and also including the closely related species S. dioica, S. diclinis, and S. heuffelii. On the Y chromosome of S. latifolia, we found substantial DNA diversity. Geographical population structure was far higher than on the X chromosome and differentiation between the species was also higher for the Y than for the X chromosome. Our findings indicate that the loss of genetic diversity on the Y chromosome in Silene occurs within local populations rather than within entire species. These results are compatible with background selection, Muller's ratchet, and local selective sweeps, but not with species-wide selective sweeps. The higher interspecific divergence of DD44Y, compared to DD44X, supports the hypothesis that Y chromosome differentiation between incipient species precedes reproductive isolation of the entire genome, forming an early stage in the process of speciation.

Widespread vertical transmission and associated host sex-ratio distortion within the eukaryotic phylum Microspora.

Vertical transmission (VT) and associated manipulation of host reproduction are widely reported among prokaryotic endosymbionts. Here, we present evidence for widespread use of VT and associated sex-ratio distortion in a eukaryotic phylum. The Microspora are an unusual and diverse group of eukaryotic parasites that infect all animal phyla. Following our initial description of a microsporidian that feminizes its crustacean host, we survey the diversity and distribution of VT within the Microspora. We find that vertically transmitted microsporidia are ubiquitous in the amphipod hosts sampled and that they are also diverse, with 11 species of microsporidia detected within 16 host species. We found that infections were more common in females than males, suggesting that host sex-ratio distortion occurs in five out of eight parasite species tested. Phylogenetic reconstruction demonstrates that VT occurs in all major lineages of the phylum Microspora and that sex-ratio distorters are found on multiple branches of the phylogenetic tree. We propose that VT is either an ancestral trait or evolves with peculiar frequency in this phylum. If the association observed here between VT and host sex-ratio distortion holds true across other host taxa, these eukaryotic parasites may join the bacterial endosymbionts in their importance as sex-ratio distorters.