Phylum Nematoda: a classification, catalogue and index of valid genera, with a census of valid species

A classification of the entire Phylum Nematoda is presented, based on current molecular, developmental and morphological evidence. The classification reflects the evolutionary relationships within the phylum, as well as significant areas of uncertainty, particularly related to the early evolution of nematodes.   It includes 3 classes, 8 subclasses, 12 superorders, 32 orders, 53 suborders, 101 superfamilies, 276 families, 511 subfamilies, 3030 genera, and 28537 species.   All valid species named from the time of publication of the previous classification and census (2010) to the end of 2019 are listed, along with the number of valid species in each genus.   Taxonomic authorities are provided for taxon names of all ranks.   The habitats where the species in each genus are found are listed, and an alphabetic index of genus names is provided.   The systematics of nematodes is reviewed, along with a history of nematode classification; evolutionary affinities and origins of nematodes; and the current diagnosis of the group.   Short overviews of the general biology, ecology, scientific and economic importance of the group are presented.  

Selective nematocidal effects of essential oils from two cultivated Artemisia absinthium populations

Essential oils (EOs) obtained from two crops and populations of thujone-free cultivated Artemisia absinthium were tested against two nematode models, the mammalian parasite Trichinella spiralis, and the plant parasitic root knot nematode Meloidogyne javanica. The EOs were characterized by the presence of (Z)-epoxyocimene and chrysanthenol as major components and showed time and population dependent quantitative and qualitative variations in composition. The EOs showed a strong ex vivo activity against the L1 larvae of the nematode Trichinella spiralis with a reduction of infectivity between 72 and 100% at a dose range of 0.5-1 mg/ml in absence of cytotoxicity against mammalian cells. Moreover, the in vivo activity of the EO against T. spiralis showed a 66% reduction of intestinal adults. However, these oils were not effective against M. javanica.

An evolutionary perspective on gastrointestinal nematodes of sheep

The purpose of this paper was to discuss from an evolutionary perspective the interaction between domestic sheep (Ovis aries) and their gastrointestinal nematodes. Although evolution is the central theme of biology, there has been little attempt to consider how evolutionary forces have shaped and continue to shape the relationships between domestic animals and their parasite community. Mathematical modelling of the host-parasite relationship indicated that the system is remarkably robust to perturbations in its parameters. This robustness may be a consequence of the long coevolution of host and parasites. Although nematodes can potentially evolve faster than the host, coevolution is not dominated by the parasite and there are several examples where breeds of cattle or sheep have evolved high levels of resistance to disease. Coevolution is a more equal partnership between host and nematode than is commonly assumed. Coevolution between parasites and the host immune system is often described as an arms race where both host immune response genes and parasite proteins evolve rapidly in response to each other. However, initial results indicate that nematode antigens are not evolving rapidly; the arms race between the immune system and nematodes, if it exists, is happening very slowly. Fisher's fundamental theorem of natural selection states that genes with positive effects on fitness will be fixed by natural selection. Consequently, heritable variation in fitness traits is expected to be low. Contrary to this argument, there is considerable genetic variation in resistance to nematode infection. In particular, the heritabilities of nematode-specific IgA and IgE activity are moderate to high. The reasons for this apparent violation of the fundamental theorem of natural selection are not clear but several possible explanations are explored. Faecal nematode egg counts increase at the beginning of the grazing season - a phenomenon known as the periparturient rise. This increase benefits host and parasite and appears to be a consequence of coevolution. In conclusion, an evolutionary perspective can shed light on many aspects of the host-parasite relationship in domestic animals.

Characterization of immunosuppressive surface coat proteins from Steinernema glaseri that selectively kill blood cells in susceptible hosts

Surface coat proteins (SCPs) of entomopathogenic nematodes are implicated in the suppression/evasion of host immune responses, which is required for successful host colonization. Steinernema glaseri NC strain SCPs suppressed immune responses in oriental beetle larvae (Exomala orientalis), a susceptible host for S. glaseri, in a dosage-dependent manner, thus protecting Heterorhabditis bacteriophora from being killed in the same host. Melanization of H. bacteriophora decreased from 92+/-5% in the untreated check to 1+/-3% when protected by injection of 230ng of S. glaseri SCPs. As the SCPs dosage increased, freely moving H. bacteriophora increased from 3+/-4% in the untreated group to 57+/-15% with an SCPs dose of 940ng. At 2h and in the absence of SCPs, 8% and 11% of hemocytes of E. orientalis were stained by propidium iodide and Hoechst, respectively. When exposed to 300ng/microl SCPs, 70% and 96% were stained, respectively. At 6h, propidium iodide stained 37% and 92% of the hemocytes without and with SCPs, respectively. In contrast, more than 90% of the cells were stained by Hoechst with or without SCPs. As native proteins, two isolated S. glaseri SCPs had an immunosuppressive effect; they were each composed of 38kDa (PI=4.6) and 56kDa (PI=3.6) subunits. SCP peptides were sequenced using LC-MS/MS and the mass fingerprints obtained with MALDI-TOF-MS; there were no significant matches found in peptide databases, which suggests that the SCPs studied are novel proteins. Twelve cDNA sequences were derived based on short peptides and 7 of them had no significant match against the Caenorhabditis elegans protein database. One of the cDNA matched an unknown C. elegans protein and the remaining 4 cDNAs matched proteins of C. elegans and Brugia malayi.

Nematode small subunit phylogeny correlates with alignment parameters

The number of nuclear small subunit (SSU) ribosomal RNA (rRNA) sequences for Nematoda has increased dramatically in recent years, and although their use in constructing phylogenies has also increased, relatively little attention has been given to their alignment. Here we examined the sensitivity of the nematode SSU data set to different alignment parameters and to the removal of alignment ambiguous regions. Ten alignments were created with CLUSTAL W using different sets of alignment parameters (10 full alignments), and each alignment was examined by eye and alignment ambiguous regions were removed (creating 10 reduced alignments). These alignment ambiguous regions were analyzed as a third type of data set, culled alignments. Maximum parsimony, neighbor-joining, and parsimony bootstrap analyses were performed. The resulting phylogenies were compared to each other by the symmetric difference distance tree comparison metric (SymD). The correlation of the phylogenies with the alignment parameters was tested by comparing matrices from SymD with corresponding matrices of Manhattan distances representing the alignment parameters. Differences among individual parsimony trees from the full alignments were frequently correlated with the differences among alignment parameters (580/1000 tests), as were trees from the culled alignments (403/1000 tests). Differences among individual parsimony trees from the reduced alignments were less frequently correlated with the differences among alignment parameters (230/1000 tests). Differences among majority-rule consensus trees (50%) from the parsimony analysis of the full alignments were significantly correlated with the differences among alignment parameters, whereas consensus trees from the reduced and culled analyses were not correlated with the alignment parameters. These patterns of correlation confirm that choice of alignment parameters has the potential to bias the resultant phylogenies for the nematode SSU data set, and suggest that the removal of alignment ambiguous regions reduces this effect. Finally, we discuss the implications of conservative phylogenetic hypotheses for Nematoda produced by exploring alignment space and removing alignment ambiguous regions for SSU rDNA.

An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa

Phylogenetic reconstructions of relations within the phylum Nematoda are inherently difficult but have been advanced with the introduction of large-scale molecular-based techniques. However, the most recent revisions were heavily biased towards terrestrial and parasitic species and greater representation of clades containing marine species (e.g. Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, Enoplida, and Monhysterida) is needed for accurate coverage of known taxonomic diversity. We now add small subunit ribosomal DNA (SSU rDNA) sequences for 100 previously un-sequenced species of nematodes, including 46 marine taxa. SSU rDNA sequences for >200 taxa have been analysed based on Bayesian inference and LogDet-transformed distances. The resulting phylogenies provide support for (i) the re-classification of the Secernentea as the order Rhabditida that derived from a common ancestor of chromadorean orders Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, and Monhysterida and (ii) the position of Bunonema close to the Diplogasteroidea in the Rhabditina. Other, previously controversial relationships can now be resolved more clearly: (a) Alaimus, Campydora, and Trischistoma belong in the Enoplida, (b) Isolaimium is placed basally to a big clade containing the Axonolaimidae, Plectidae, and Rhabditida, (c) Xyzzors belongs in the Desmodoridae, (d) Comesomatidae and Cyartonema belongs in the Monhysterida, (e) Globodera belongs in the Hoplolaimidae and (f) Paratylenchus dianeae belongs in the Criconematoidea. However, the SSU gene did not provide significant support for the class Chromadoria or clear evidence for the relationship between the three classes, Enoplia, Dorylaimia, and Chromadoria. Furthermore, across the whole phylum, the phylogenetically informative characters of the SSU gene are not informative in a parsimony analysis, highlighting the short-comings of the parsimony method for large-scale phylogenetic modelling.

Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward crown Clades

Inference of evolutionary relationships between nematodes is severely hampered by their conserved morphology, the high frequency of homoplasy, and the scarcity of phylum-wide molecular data. To study the origin of nematode radiation and to unravel the phylogenetic relationships between distantly related species, 339 nearly full-length small-subunit rDNA sequences were analyzed from a diverse range of nematodes. Bayesian inference revealed a backbone comprising 12 consecutive dichotomies that subdivided the phylum Nematoda into 12 clades. The most basal clade is dominated by the subclass Enoplia, and members of the order Triplonchida occupy positions most close to the common ancestor of the nematodes. Crown Clades 8-12, a group formerly indicated as "Secernentea" that includes Caenorhabditis elegans and virtually all major plant and animal parasites, show significantly higher nucleotide substitution rates than the more basal Clades 1-7. Accelerated substitution rates are associated with parasitic lifestyles (Clades 8 and 12) or short generation times (Clades 9-11). The relatively high substitution rates in the distal clades resulted in numerous autapomorphies that allow in most cases DNA barcode-based species identification. Teratocephalus, a genus comprising terrestrial bacterivores, was shown to be most close to the starting point of Secernentean radiation. Notably, fungal feeding nematodes were exclusively found basal to or as sister taxon next to the 3 groups of plant parasitic nematodes, namely, Trichodoridae, Longidoridae, and Tylenchomorpha. The exclusive common presence of fungivorous and plant parasitic nematodes supports a long-standing hypothesis that states that plant parasitic nematodes arose from fungivorous ancestors.

The evolutionary origins of nematodes within the order Strongylida are related to predilection sites within hosts

The evolutionary relationships of the different groups of nematodes within the order Strongylida based on morphological data have been speculative and the subject of conjecture. In this paper, we present a multigene phylogenetic analysis, using sequence data of the 18S and 28S ribosomal RNA genes from representatives of all four suborders and seven superfamilies of the Strongylida, to test existing hypotheses proposed for the relationships of the suborders based on morphological data sets. The results obtained demonstrated that the Strongylida is a monophyletic assemblage, with only the Metastrongylina (but not the other suborders) forming a distinct monophyletic clade. We show that, in contrast to all previous hypotheses, one major lineage comprises taxa which occur exclusively in the pulmonary, circulatory or nervous systems of marsupial and eutherian mammals, whereas a second lineage comprises species occurring in the gastrointestinal tracts or perirenal tissues of vertebrates, or in the lungs of birds. The findings suggest that the predilection site of adult nematodes and host type reflect the evolutionary origin of the different taxonomic groups within the Strongylida.

Molecular characterization of Thelastomatoidea (Nematoda: Oxyurida) from cockroaches in Australia

A molecular approach was used to genetically characterize 5 species (Aoruroides queenslandensis, Blattophila sphaerolaima, Cordonicola gibsoni, Desmicola ornata and Leidynemella fusiformis) belonging to the superfamily Thelastomatoidea (Nematoda: Oxyurida), a group of pinworms that parasitizes terrestrial arthropods. The D3 domain of the large subunit of nuclear ribosomal RNA (LSU) was sequenced for individual specimens, and the analysis of the sequence data allowed the genetic relationships of the 5 species to be studied. The sequence variation in the D3 domain within individual species (0-1.8%) was significantly less than the differences among species (4.3-12.4%). Phylogenetic analyses, using maximum parsimony, maximum likelihood, and neighbour-joining, tree-building methods, established relationships among the 5 species of Thelastomatoidea and Oxyuris equi (a species of the order Oxyurida). The molecular approach employed provides the prospect for developing DNA tools for the specific identification of the Thelastomatoidea, irrespective of developmental stage and sex, as a basis for systematic, ecological and/or population genetic investigations of members within this superfamily.

Insect-parasitic nematodes: From lab curiosities to model organisms

Interest in studying insect-parasitic nematodes was originally focused on their potential as biological control agents of insects and other arthropod pests. Now, after 30 years of intense basic and applied research, realization of the practical use of insect-parasitic nematodes, particularly of entomopathogenic nematodes and their symbiotic bacteria, has spurred developments across a far broader scientific front. We are now entering a new era of discovery in which tools of molecular genetics are being increasingly used to address a range of biological questions. The knowledge gained from these efforts will directly benefit the practical application of insect-parasitic nematodes as more effective biopesticides. Moreover, these studies will advance these nematodes as unique and intrinsically interesting biological model systems not only for basic research but also in applied fields such as plant health, human medicine, pharmaceutical bioprospecting, and genetic engineering. In this review, the past and current state of insect-parasitic nematode research is summarized. Future research priorities and goals are identified and discussed.

Evolution of plant parasitism among nematodes

Despite extraordinary diversity of free-living species, a comparatively small fraction of nematodes are parasites of plants. These parasites represent at least three disparate clades in the nematode tree of life, as inferred from rRNA sequences. Plant parasites share functional similarities regarding feeding, but many similarities in feeding structures result from convergent evolution and have fundamentally different developmental origins. Although Tylenchida rRNA phylogenies are not fully resolved, they strongly support convergent evolution of sedentary endoparasitism and plant nurse cells in cyst and root-knot nematodes. This result has critical implications for using model systems and genomics to identify and characterize parasitism genes for representatives of this clade. Phylogenetic studies reveal that plant parasites have rich and complex evolutionary histories that involve multiple transitions to plant parasitism and the possible use of genes obtained by horizontal transfer from prokaryotes. Developing a fuller understanding of plant parasitism will require integrating more comprehensive and resolved phylogenies with appropriate choices of model organisms and comparative evolutionary methods.

Molecular phylogenetic analysis of the genus Strongyloides and related nematodes

Strongyloides spp., parasitic nematodes of humans and many other terrestrial vertebrates, display an unusual heterogonic lifecycle involving alternating parasitic and free-living adult reproductive stages. A number of other genera have similar lifecycles, but their relationships to Strongyloides have not been clarified. We have inferred a phylogeny of 12 species of Strongyloides, Parastrongyloides, Rhabdias and Rhabditophanes using small subunit ribosomal RNA gene (SSU rDNA) sequences. The lineage leading to Strongyloides appears to have arisen within parasites of terrestrial invertebrates. Inferred lifecycle evolution was particularly dynamic within these nematodes. Importantly, the free-living Rhabditophanes sp. KR3021 is placed within a clade of parasitic taxa, suggesting that this species may represent a reversion to a non-parasitic lifecycle. Species within the genus Strongyloides are very closely related, despite the disparity of host species parasitised. The highly pathogenic human parasite Strongyloides fuelleborni kelleyi is not supported as a subspecies of the primate parasite S. fuelleborni fuelleborni, but is most likely derived from a local zoonotic source.

Caenorhabditis elegans: how good a model for veterinary parasites?

The organism about which most is known on a molecular level is a nematode, the free-living organism Caenorhabditis elegans. This organism has served as a reasonable model for the discovery of anthelmintic drugs and for research on the mechanism of action of anthelmintics. Useful information on mechanisms of anthelmintic resistance has also been obtained from studies on C. elegans. Unfortunately, there has not been a large-scale extension of genetic techniques developed in C. elegans to research on parasitic species of veterinary (or human) parasites. Much can be learned about the essentials of nematode biology by studying C. elegans, but discovering the basic biology of nematode parasitism can only be gained through comparative studies on multiple parasitic species.

Phylogeny of Steinernema travassos, 1927 (Cephalobina: Steinernematidae) inferred from ribosomal DNA sequences and morphological characters

Entomopathogenic nematodes in Steinernema, together with their symbiont bacteria Xenorhabdus, are obligate and lethal parasites of insects that can provide effective biological control of some important lepidopteran, dipteran, and coleopteran pests of commercial crops. Phylogenetic relationships among 21 Steinernema species were estimated using 28S ribosomal DNA (rDNA) sequences and morphological characters. Sequences of the rDNA internal transcribed spacers were obtained to provide additional molecular characters to resolve relationships among Steinernema carpocapsae, Steinernema scapterisci, Steinernema siamkavai, and Steinernema monticolum. Four equally parsimonious trees resulted from combined analysis of 28S sequences and 22 morphological characters. Clades inferred from analyses of molecular sequences and combined datasets were primarily reliably supported as assessed by bootstrap resampling, whereas those inferred from morphological data alone were not. Although partially consistent with some traditional expectations and previous phylogenetic studies, the hypotheses inferred from molecular evidence, and those from combined analysis of morphological and molecular data, provide a new and comprehensive framework for evaluating character evolution of steinernematids. Interpretation of morphological character evolution on 6 trees inferred from sequence data and combined evidence suggests that many structural features of these nematodes are highly homoplastic, and that some structures previously used to hypothesize relationships represent ancestral character states.

Evolutionary relationships of trichostrongyloid nematodes (Strongylida) inferred from ribosomal DNA sequence data

The evolutionary relationships of 21 species of trichostrongyloid nematodes were determined by use of sequence data of the second internal transcribed spacer of the ribosomal DNA aligned according to secondary structure information. Irrespective of the method of analysis used, the topologies of the phylogenetic trees derived from the molecular data differed with respect to all four hypotheses proposed previously for the evolutionary relationships of the different subfamilies within the Trichostrongylidae based on morphological data. Thus, the molecular data set did not resolve the conflict between the four previous proposals for the subfamilial relationships. Nonetheless, all trees derived from the molecular data showed strong support for the exclusion of the genera Filarinema and Amidostomum from the clade containing the species within the family Trichostrongylidae. This represents a major difference from the most recent proposal of the systematics of the Trichostrongyloidea in which these two genera were included within the Trichostrongylidae. Therefore, the molecular data support an earlier systematic framework in which Filarinema and Amidostomum were considered to be sister groups of the Trichostrongyloidea.