A fine-scale phylogenetic assessment of digenean trematodes in central Alberta reveals we have yet to uncover their total diversity.
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ABSTRACT:
SUBMITTER: Gordy MA
PROVIDER: S-EPMC6434566 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Occurrence of metacercariae of potentially zoonotic trematodes (Platyhelminthes: Digenea) in the musculature of common carp (Cyprinus carpio L. 1758) was monitored in four Hungarian aquacultures. Four geographically distinct fish farms (located in the Northwestern, Southwestern, Northeastern and Southeastern parts of Hungary) were selected for the investigation. From each farm, a total of 258 one-summer-old fingerlings were sampled and examined in the years 2016 and 2017. In addition, in 2017, we examined 60 market size specimens (30 two-summers and 30 three-summers) sampled from the most infected aquaculture in the Northeastern part of Hungary. The fish were euthanized and decapitated whereafter their musculature (fillets) was digested in a pepsin solution to isolate metacercariae from the tissue whereafter morphological and molecular analyses (PCR and sequencing of ITS region) were performed. Opisthorchiid metacercariae were not recovered but in one of the farms numerous metacercariae were detected in the musculature of carp. They were identified as cyathocotylid trematodes based on their morphological characteristics and by sequencing the ITS region. The infection levels proved to be remarkably different among the four fish farms. Carps from the Northeastern farm were infected by large numbers of cyathocotylid metacercariae, while 8 Posthodiplostomum cuticola metacercariae were detected in the Northwestern aquaculture. In the other two farms (Southwestern and Southeastern) no infection was recorded. The infected farm is located close to a protected natural wetland habitat populated by a rich fauna of aquatic birds (potential final hosts) and snails (first intermediate host) which may create a higher risk of infection in the neighbouring fish farms.
| S-EPMC7750318 | biostudies-literature
Project description:The classification and description of digenean trematodes are commonly accomplished by using morphological features, especially in adult stages. The aim of this study was to provide an analysis of the genetic composition of larval digenean trematodes using polymerase chain reaction (PCR) and sequence analysis. Deoxyribonucleic acid (DNA) was extracted from clinostomatid metacercaria, 27-spined echinostomatid redia, avian schistosome cercaria and strigeid metacercaria from various dams in the proximity of Tshwane metropolitan, South Africa. Polymerase chain reaction was performed using the extracted DNA with primers targeting various regions within the larval digenean trematodes' genomes. Agarose gel electrophoresis technique was used to visualise the PCR products. The PCR products were sequenced on an Applied Bioinformatics (ABI) genetic analyser platform. Genetic information obtained from this study had a higher degree of discrimination than the morphological characteristics of seemingly similar organisms.
| S-EPMC6779965 | biostudies-literature
Project description:BackgroundNeorickettsia are a group of intracellular α proteobacteria transmitted by digeneans (Platyhelminthes, Trematoda). These endobacteria can also infect vertebrate hosts of the helminths and cause serious diseases in animals and humans. Neorickettsia have been isolated from infected animals and maintained in cell cultures, and their morphology in mammalian cells has been described. However, limited information is available on the morphology and localization of Neorickettsia in the trematode host.MethodsWe used a Neorickettsia-infected strain of the model trematode Plagiorchis elegans to infect Syrian Golden hamsters to produce adult worms. Ultrastructure of Neorickettsia was assessed by transmission electron microscopy of high pressure freezing/freeze substitution fixed specimens. A Neorickettsia surface protein from P. elegans (PeNsp-3) was cloned and antibodies against the recombinant protein were used to localize Neorickettsia by immunohistochemistry.ResultsUltrastructural analysis revealed moderate numbers of pleomorphic endobacteria with a median size of 600 × 400 nm and characteristic double membranes in various tissue types. Endobacteria showed tubular membrane invaginations and secretion of polymorphic vesicles. Endobacteria were unevenly localized as single cells, or less frequently as small morula-like clusters in the ovary, Mehlis' gland, vitelline follicles, uterus, intrauterine eggs, testis, cirrus-sac, tegument, intestine and the oral and ventral sucker. Examination of hamster small intestine infected with P. elegans showed many endobacteria at the host-parasite interface such as the oral and ventral sucker, the tegument and the excretory pore.ConclusionsWe conclude that adult P. elegans trematodes carry Neorickettsia endobacteria in varying numbers in many tissue types that support vertical transmission, trematode to trematode transmission via seminal fluid, and possibly horizontal transmission from trematodes to vertebrate hosts. These means appear to be novel mechanisms of pathogen transmission by endoparasitic worms.
| S-EPMC5390476 | biostudies-literature
Project description:'Cryptic' species are an emerging biological problem that is broadly discussed in the present study. Recently, a cryptic species definition was suggested for those species which manifest low morphological, but considerable genetic, disparity. As a case study we present unique material from a charismatic group of nudibranch molluscs of the genus Trinchesia from European waters to reveal three new species and demonstrate that they show a dual nature: on one hand, they can be considered a 'cryptic' species complex due to their overall similarity, but on the other hand, stable morphological differences as well as molecular differences are demonstrated for every species in that complex. Thus, this species complex can equally be named 'cryptic', 'pseudocryptic' or 'non-cryptic'. We also present evidence for an extremely rapid speciation rate in this species complex and link the species problem with epigenetics. Available metazoan-wide data, which are broadly discussed in the present study, show the unsuitability of a 'cryptic' species concept because the degree of crypticity represents a continuum when a finer multilevel morphological and molecular scale is applied to uncover more narrowly defined species making the 'cryptic' addition to 'species' redundant. Morphological and molecular methods should be applied in concordance to form a fine-scale multilevel taxonomic framework, and not necessarily implying only an a posteriori transformation of exclusively molecular-based 'cryptic' species into morphologically-defined 'pseudocryptic' ones. Implications of the present study have importance for many fields, including conservation biology and fine-scale biodiversity assessments.
| S-EPMC6494890 | biostudies-other
Project description:Population genetic theory predicts discordance in the true phylogeny of different genomic regions when studying recently diverged species. Despite this expectation, genome-wide discordance in young species groups has rarely been statistically quantified. The house mouse subspecies group provides a model system for examining phylogenetic discordance. House mouse subspecies are recently derived, suggesting that even if there has been a simple tree-like population history, gene trees could disagree with the population history due to incomplete lineage sorting. Subspecies of house mice also hybridize in nature, raising the possibility that recent introgression might lead to additional phylogenetic discordance. Single-locus approaches have revealed support for conflicting topologies, resulting in a subspecies tree often summarized as a polytomy. To analyze phylogenetic histories on a genomic scale, we applied a recently developed method, Bayesian concordance analysis, to dense SNP data from three closely related subspecies of house mice: Mus musculus musculus, M. m. castaneus, and M. m. domesticus. We documented substantial variation in phylogenetic history across the genome. Although each of the three possible topologies was strongly supported by a large number of loci, there was statistical evidence for a primary phylogenetic history in which M. m. musculus and M. m. castaneus are sister subspecies. These results underscore the importance of measuring phylogenetic discordance in other recently diverged groups using methods such as Bayesian concordance analysis, which are designed for this purpose.
| S-EPMC2770633 | biostudies-literature
Project description:Although some parasitological efforts have focused on the frigate tuna Auxis thazard (Lacepède) (Scombriformes, Scombridae) in Brazil, its digenean fauna remains poorly known. Combining morphological and molecular methods, we investigated the diversity of digenean trematodes of A. thazard collected from the coastal waters off the state of Rio de Janeiro, Brazil in 2021. Six species belonging to four families were recorded: the bucephalid Rhipidocotyle cf. angusticolle Chandler, 1941, the didymozoid Didymocystis sp. 6 sensu Louvard et al. (2022), the fellodistomid Tergestia sp., and three hemiurids, Dinurus euthynni Yamaguti, 1934, Lecithochirium floridense (Manter, 1934), and L. synodi Manter, 1931. The current study brings the total number of digenean trematode species parasitising A. thazard in Brazil up to eight, with hemiuroid trematodes being most diverse. Auxis thazard is a new host record for L. floridense, L. synodi and potentially for R. angusticolle. The geographic distribution of several species found in our study appeared to be wider than previously known. Our study is the first to apply a DNA-based approach to digenean diversity in marine fishes in Brazil and we believe that both morphological descriptions and molecular sequence data provided in our study will aid future research assessing the diversity of digenean trematodes of A. thazard and other marine fishes in Brazil.
| S-EPMC9541523 | biostudies-literature
Project description:BACKGROUND:Many species of snakes exhibit epidermal surface nanostructures that form complex motifs conferring self-cleaning properties, and sometimes structural iridescence, to their skin. RESULTS:Using confocal microscopy, we show that these specialised cells can be greatly elongated along their left-right axis and that different types of nanostructures are generated by cell borders and cell surface. To characterise the complexity and diversity of these surface gratings, we analysed scanning electron microscopy images of skin sheds from 353 species spanning 19 of the 26 families of snakes and characterised the observed nanostructures with four characters. The full character matrix, as well as one representative SEM image of each of the corresponding species, is available as a MySQL relational database at https://snake-nanogratings.lanevol.org . We then performed continuous-time Markov phylogenetic mapping on the snake phylogeny, providing an evolutionary dynamical estimate for the different types of nanostructures. These analyses suggest that the presence of cell border digitations is the ancestral state for snake skin nanostructures which was subsequently and independently lost in multiple lineages. Our analyses also indicate that cell shape and cell border shape are co-dependent characters whereas we did not find correlation between a simple life habit classification and any specific nanomorphological character. CONCLUSIONS:These results, compatible with the fact that multiple types of nanostructures can generate hydrophobicity, suggest that the diversity and complexity of snake skin surface nano-morphology are dominated by phylogenetic rather than habitat-specific functional constraints. The present descriptive study opens the perspective of investigating the cellular self-organisational cytoskeletal processes controlling the patterning of different skin surface nanostructures in snakes and lizards.
| S-EPMC6469093 | biostudies-literature
Project description:The most familiar icy environments, seasonal lake and stream ice, have received little microbiological study. Bacteria and Eukarya dominated the microbial assemblage within the seasonal ice of Miquelon Lake, a shallow saline lake in Alberta, Canada. The bacterial assemblages were moderately diverse and did not vary with either ice depth or time. The closest relatives of the bacterial sequences from the ice included Actinobacteria, Bacteroidetes, Proteobacteria, Verrucomicrobia, and Cyanobacteria. The eukaryotic assemblages were less conserved and had very low diversity. Green algae relatives dominated the eukaryotic gene sequences; however, a copepod and cercozoan were also identified, possibly indicating the presence of complete microbial loop. The persistence of a chlorophyll a peak at 25-30 cm below the ice surface, despite ice migration and brine flushing, indicated possible biological activity within the ice. This is the first study of the composition, diversity, and stability of seasonal lake ice.
| S-EPMC3960880 | biostudies-literature
Project description:Predator diets are largely influenced by prey availability and abundance. Yet, in heterogenous marine environments, identifying the prey species consumed by diving mammals remains a fundamental challenge. For rorqual whales, the energetic constraints of prey engulfment require that the whales seek areas of high prey abundance and execute discrete lunge feeding events on patches of high-density prey. Prey occurrences in feces should therefore provide meaningful insight into the dominant taxa in food patches selected by the animal. We investigated the prey consumed by humpback whales in three regions in southern British Columbia (BC), Canada, using opportunistic fecal sampling, microscopy, and DNA metabarcoding of 14 fecal samples. Fish including Pacific herring (Clupea pallasii), hake (Merluccius productus), and eulachon (Thaleichthys pacificus) were the most common fish species potentially targeted by humpback whales in two regions. The krill Euphausia pacifica was the most prevalent invertebrate DNA detected in all three regions, while sergestid and mysid shrimp may also be important. High DNA read abundances from walleye pollock (Gadus chalcogrammus) and sablefish (Anoplopoma fimbria) were also recovered in one sample each, suggesting that juveniles of these semi-pelagic species may occasionally be targeted. In general, we observed heavily digested fecal material that drove substantial dissimilarities in taxonomic resolution between polymerase chain reaction-based and morphological analyses of the feces. Pacific herring and walleye pollock were the only prey species confirmed by both methods. Our results highlight that molecular and visual analyses of fecal samples provide a complementary approach to diet analysis, with each method providing unique insight into prey diversity.
| S-EPMC9797768 | biostudies-literature
Project description:BackgroundRed clover (Trifolium pratense L.) is a diploid perennial temperate legume with 14 chromosomes (2n = 14) native to Europe and West Asia, with high nutritional and economic value. It is a very important forage grass and is widely grown in marine climates, such as the United States and Sweden. Genetic research and molecular breeding are limited by the lack of high-quality reference genomes. In this study, we used Illumina, PacBio HiFi, and Hi-C to obtain a high-quality chromosome-scale red clover genome and used genome annotation results to analyze evolutionary relationships among related species.ResultsThe red clover genome obtained by PacBio HiFi assembly sequencing was 423 M. The assembly quality was the highest among legume genome assemblies published to date. The contig N50 was 13 Mb, scaffold N50 was 55 Mb, and BUSCO completeness was 97.9%, accounting for 92.8% of the predicted genome. Genome annotation revealed 44,588 gene models with high confidence and 52.81% repetitive elements in red clover genome. Based on a comparison of genome annotation results, red clover was closely related to Trifolium medium and distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum among legumes. Analyses of gene family expansions and contractions and forward gene selection revealed gene families and genes related to environmental stress resistance and energy metabolism.ConclusionsWe report a high-quality de novo genome assembly for the red clover at the chromosome level, with a substantial improvement in assembly quality over those of previously published red clover genomes. These annotated gene models can provide an important resource for molecular genetic breeding and legume evolution studies. Furthermore, we analyzed the evolutionary relationships among red clover and closely related species, providing a basis for evolutionary studies of clover leaf and legumes, genomics analyses of forage grass, the improvement of agronomic traits.
| S-EPMC9277957 | biostudies-literature