Phylogeny of Cephalobina (Nematoda): Molecular evidence for recurrent evolution of probolae and incongruence with traditional classifications

The Caenorhabditis elegans cuticle and precuticle: a model for studying dynamic apical extracellular matrices in vivo

Apical extracellular matrices (aECMs) coat the exposed surfaces of animal bodies to shape tissues, influence social interactions, and protect against pathogens and other environmental challenges. In the nematode Caenorhabditis elegans, collagenous cuticle and zona pellucida protein-rich precuticle aECMs alternately coat external epithelia across the molt cycle and play many important roles in the worm's development, behavior, and physiology. Both these types of aECMs contain many matrix proteins related to those in vertebrates, as well as some that are nematode-specific. Extensive differences observed among tissues and life stages demonstrate that aECMs are a major feature of epithelial cell identity. In addition to forming discrete layers, some cuticle components assemble into complex substructures such as ridges, furrows, and nanoscale pillars. The epidermis and cuticle are mechanically linked, allowing the epidermis to sense cuticle damage and induce protective innate immune and stress responses. The C. elegans model, with its optical transparency, facilitates the study of aECM cell biology and structure/function relationships and all the myriad ways by which aECM can influence an organism.

Exploiting fly ash as an ecofriendly pesticide/nematicide on Abesmoschus esculuntus: Insights into soil amendment-induced antioxidant fight against nematode mediated ROS

Conventional pest control measures, such as chemical pesticides and nematicides, have limited efficacy and raise environmental concerns, necessitating sustainable and eco-friendly alternatives for pest management. Therefore, to find a complementary eco-friendly pesticide/nematicide, this study investigated the role of fly ash (FA) in managing a notorious pest, Meloidogyne javanica and its impact on the growth and physiology of Abelmoschus esculentus. Molecular characterization using SSU and LSU rDNA gene markers confirmed the identity of Indian M. javanica as belonging to the same species. Biotic stress induced by nematode infection was significantly alleviated (P < 0.05) by FA application at a 20% w/v, regulating of ROS accumulation (44.1% reduction in superoxide anions and 39.7% reduction in hydrogen peroxide content) in the host plant. Moreover, FA enhanced antioxidant defence enzymes like superoxide dismutase (46.6%) and catalase (112%) to combat nematode induced ROS. Furthermore, the application of FA at a 20% concentration significantly improved the biomass and biochemical attributes of okra. Fly ash also upregulated the activity of the important osmo-protectant proline (11.5 μmol/g FW) to mitigate nematode stress in host cells. Suppression of disease indices like gall index and reproduction factor, combined with in-vitro experiments, revealed that FA exhibits strong nematode mortality capacity and thus can be used as a sustainable and eco-friendly control agent against root-knot nematodes.

Morphological and molecular characterizations of Pratylenchus coffeae infecting Ming aralia and coffee in Vietnam

Pratylenchus coffeae, belonging to the root-lesion nematode group, is a highly prevalent and destructive plant-parasitic nematode that is able to infest a wide range of host plants. Although this species' devastating impacts on coffee plantations across the world are widely known on other host plants, its association with Ming aralia has never been reported. Our study characterized two popu lations of P. coffeae (associated with Ming aralia and coffee) and compared them with other popu lations from previous studies in Vietnam and other countries in the world. The identification of P. coffeae in our study was confirmed by the comprehensive analysis encompassing morphological examination, morphometric data, and molecular characterizations of the COI mtDNA and D2D3 of 28S rRNA regions. The cluster and MDS analyses revealed that the two populations of P. coffeae from Vietnam are closely related to those from Japan and Indonesia. The D2-D3 sequences of 28S rRNA and COI mtDNA regions exhibited high similarity among these populations, indicating a stable genetic profile. Our research contributes to a better understanding of the distribution and genetic characterizations of P. coffeae by offering new morphological and molecular insights into the presence of this nematode in Vietnam. Additionally, this nematode species was found to be associated with host plant's symptoms such as chlorotic leaves, stunted growth and root lesion in both hosts. Given the economic significance of both Ming aralia and coffee crops in Vietnam, as well as the damaging potential of P. coffeae, this study emphasizes the need of proactive nematode management measures to control this destructive pest.

Morphological and molecular profiling of an entomopathogenic nematode Steinernema feltiae: Unlocking its biocontrol potential against vegetable insect pests

A population of entomopathogenic nematodes, belonging to the Feltiae-clade and labelled J13, was discovered in the agricultural soils of the hilly regions of the Union territory of Jammu and Kashmir, India. Based on morphological, morphometric, and molecular analyses, the nematodes were identified as Steinernema feltiae. The J13 nematode isolate was tested in a laboratory assay for its pathogenicity against six major pests of vegetable crops: Pieris brassicae, Plutella xylostella, Helicoverpa armigera, Agrotis iplison, Trichoplusia ni, and Exelastis atomosa. The morphology of the isolated nematode closely matched the original description, except for the adult females, which had prominent epiptygmata instead of the weakly developed, double-flapped epiptygmata described in the original report. Analysis of the internal transcribed spacer and large subunit rRNA data from the J13 nematodes showed 100% similarity to sequences of the type population, indicating that they are conspecific. The virulence assays revealed that the nematode caused 100% mortality in the tested insect pests within 4872 hours, even at the lowest concentration of 50 infective juveniles per insect. The calculated median lethal concentration varied among the pests, with the lowest number of infective juveniles needed to achieve 50% larval killing being 117 for P. xylostella, 181.74 for P. brassicae, 226.35 for H. armigera, and 202.07 for T. ni at 24 hours post-inoculation. These findings suggest that S. feltiae isolated during the present investigation, may be a viable option for the biocontrol of these insect pests in Kashmir valley, India.

Characterization of Hoplolaimus seinhorsti and Hoplolaimus pararobustus (Tylenchina: Hoplolaimidae) from banana, with phylogeny and species delineation in the genus Hoplolaimus

The morphological and molecular characterisations of two lance nematode species isolated from the rhizosphere of banana, Hoplolaimus seinhorsti and H. pararobustus, are provided based on an integrative study that includes light and scanning electron microscopy, phylogenetic analysis and two tree-based molecular species delimitation methods (GMYC and bPTP). Nineteen new sequences were obtained, including 5 partial 18S rRNA, 6 D2-D3 of 28S rRNA, 1 ITS rRNA and 7 COI mtDNA (the first COI sequences of H. seinhorsti and H. pararobustus), and an updated morphological character comparison of 37 Hoplolaimus species is presented. The tree-based molecular species-delimitation approaches employed gave markedly differing results, and also showed remarkable discrepancies among the investigated genes, although the bPTP output was found to agree well with established morphological species delimitations. Both species-delimitation approaches did, however, provide the same output for the COI mtDNA sequences, and the COI mtDNA gene sequence was also found to correspond better to established morphological species. It is therefore recommended by this paper as representing the most suitable barcode marker for Hoplolaimus species identification. This integrative study also resulted in the corrective reassignment of 17 gene sequences that were previously unidentified or incorrectly classified, as well as concluding that H. pararobustus consists of two cryptic species.

Comparative morphological and molecular analyses of Acrobeloides bodenheimeri and A. tricornis Cobb, 1924 (Rhabditida, Cephalobidae) from Tunisia

Four populations of Acrobeloides nematodes were isolated from Tunisian soils. Based on morphological and morphometric data, two populations, TC9 and HWO, were identified as A. tricornis and the other two, TC7 and K18g, as A. bodenheimeri. Acrobeloides tricornis is distinguished from its closely related species by its high labial probolae with arcuate termini, inconspicuous post-uterine sac, and five lateral incisures, while A. bodenheimeri is distinguished from other acrobeloids by having a low and rounded labial probolae, distinct post-uterine sac, five lateral incisures, and vulva frequently with vaginal plug. The A. tricornis and A. bodenheimeri reported in this study are distinguished by the shape of labial probolae (high with acute distal part vs low and rounded), post-uterine sac (inconspicuous vs distinct), position of the reproductive system with respect to the intestine (sinistral vs dextral), vulva with vaginal plug (present vs absent) and some morphometric characters (such as body length). Further, these species were also molecularly characterised using the sequences of the D2-D3 region of the 28S rRNA gene, the 18S rRNA gene, the ITS rRNA gene, and of the mitochondrial cytochrome c oxidase subunit I (mtCO1) gene. Phylogenetic trees using ribosomal RNA gene sequences clearly separate species of the ‘Maximus’ group, but these sequences appear to be identical in several other Acrobeloides species, and thus are unlikely to be useful as molecular markers for species-level molecular identification in the genus Acrobeloides. The mtCO1 gene sequences of two A. tricornis populations differ in 58 and 64 nucleotide bases from A. varius and A. nanus, respectively, indicating that the mtCO1 gene sequences have greater phylogenetic resolving power than nuclear rRNA gene sequences, and that this gene marker can differentiate closely related species in the genus Acrobeloides.

PHYLOGENETIC ANALYSIS OF THE LUNGWORMS (NEMATODA: METASTRONGYLOIDEA) INFERRED USING NUCLEAR RIBOSOMAL AND MITOCHONDRIAL DNA SEQUENCES

Phylogenetic relationships among the mammal-parasitic lungworms (Metastrongyloidea) were inferred using small- and large-subunit ribosomal DNA sequences together with 12S ribosomal mtDNA sequences. Maximum parsimony and Bayesian inference methods were used from optimal alignments and those filtered for alignment ambiguity. Analysis of 30 ingroup sequences using ribosomal DNA sequences yielded a single most parsimonious tree. Monophyly of the Metastrongyloidea was supported, but there was no support for monophyly of any of the 7 families as they have been traditionally defined. Parafilaroides decorus, an abursate lungworm of pinnipeds currently classified in the Filaroididae, was nested within a clade containing members of the Pseudaliidae, parasites of cetaceans. The tree also shows clades somewhat resembling the traditional familial divisions of the Metastrongyloidea, but in all groups, paraphyletic relationships were recovered. In a combined analysis of nuclear rDNA and 12S mtDNA, maximum parsimony and Bayesian analyses showed similar patterns to those observed with only nuclear rDNA sequences. Based on the phylogeny, the respiratory tract was inferred to be the ancestral predilection site for Metastrongyloidea, with multiple evolutionary invasions of extrapulmonary sites such as sinuses, circulatory system, and meninges. Similarly, the ancestral host was inferred to be a carnivore with subsequent colonization events into marsupial, rodent, artiodactyl, pinniped, and cetacean hosts.

Description of Ruehmaphelenchus americanum n. sp. (Nematoda: Aphelenchoididae) found in Loblolly pine from the USA

Ruehmaphelenchus americanum n. sp., isolated from southern yellow pine (Pinus taedae L.) from the USA is described and figured. It is characterised by a relatively stout body (a = 30 for females and males), three lines in the lateral field, both oocytes and spermatocytes arranged in two rows, male spicules relatively small (14-18 μm) with weakly developed condylus and rostrum, short tail with a bluntly pointed tip, seven papilliform genital papillae present, female vulva positioned at ca 82% of body length, vulval lips slightly protruding, post-uterine branch extending two-thirds of vulva to anus distance, tail cylindrical, ca two anal body diam. long, terminus forming a spike-like projection or mucron, 7.6-12.2 μm long, with pointed tip. The new species can be separated from 11 known species (except R. thailandae) by male genital papillae arrangement (the second and third pair adjacent vs separated). Detailed phylogenetic analysis based on 18S and 28S D2-D3 region ribosomal RNA (rRNA) sequences has confirmed the status of this nematode as a new species.

Detection and identification of Ektaphelenchoides diversislocis sp. n. isolated from Pinus woodlands of China and Japan

Understanding the occurrence and distribution of parasitic nematodes is crucial – some are economic pests, and some are important predators of their insect associates. In our recent nematode inventory survey, two populations of an ektaphelechid nematode were detected in the branches of Pinus trees; later the same nematode population was detected in plant quarantine examinations of wood packaging material imported from Japan. The species was processed and identified as Ektaphelenchoides diversislocis sp. n. The new species can be characterised by having three lateral lines, stylet long and tripartite, excretory pore at the level of nerve ring, comparatively longer post-vulval uterine sac, indistinct rectum and anus. Female posterior body region conical, gradually narrowing, like a mucron or filiform. Male spicule with well-developed condylus, triangular rostrum, and cucullus absent. The species is morphologically and molecularly close to E. compsi. The new species was characterised with near full-length 18S, 28S D2-D3 regions, and internal transcribed spacer (ITS) rRNA genes and mitochondrial cytochrome oxidase I (COI) gene sequences. The species within the Ektaphelenchoides genus are considered to have predatory roles against insect associates; therefore, the discovery of E. diversislocis sp. n. from local and foreign woodlands warrants increased sampling and research attention.

Redescription of Diastolaimus grossus (Truskova & Eroshenko, 1977) Andrássy, 1984 (Rhabditida, Chambersiellidae) from Europe and comments on its phylogenetic position

Two populations of the species Diastolaimus grossus have been obtained from bark of trees in Bosnia and Herzegovina and the Czech Republic. The species is described and characterized in detail using morphological techniques (light and electron scanning microscopy) and morphometrical (Gower General Similarity coefficient of morphological characters) and molecular analyses, including phylogenetic analysis of all related and already sequenced species of the family Chambersiellidae. Morphological and molecular analyses, based on 18S and 28S ribosomal DNA sequences, show that the family Chambersiellidae is polyphyletic, being the subfamily Chambersiellinae related with Cephalobomorpha and Tylenchomorpha, and the subfamily Macrolaiminae is located into Panagrolaimomorpha. The genus Diastolaimus, previously belonging to Macrolaiminae, is transferred to Chambersiellinae. Diastolaimus mexicanus is proposed as a junior synonym of D. grossus.

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.  

Comparative study of four known species of the genus Acrobeles von Linstow, 1877 (Nematoda, Cephalobidae) with 'single' and 'double' cuticle from coastal dunes in Spain

The nematode genus Acrobeles is composed of two morphological groups distinguished by the presence ('double' cuticle) or absence ('single' cuticle) of the refringent inner layer of the cuticle. In the present study, four species of this genus, two with 'single' cuticle (Acrobeles ciliatus and Acrobeles cylindricus) and two with 'double' (Acrobeles aenigmaticus and Acrobeles complexus) are studied from coastal dunes in Spain. This study provides detailed morphological and morphometrical analyses for the four species, while molecular analysis, based on 18S and 28S ribosomal DNA, is provided for A. complexus. The four species are studied with scanning electron microscopy, which is obtained for the first time for A. cylindricus. These analyses revealed morphological and molecular differentiations between both groups, appearing as two related monophyletic entities. The subgenera Acrobeles and Seleborca, formerly considered as separate genera, are proposed to accommodate both groups.

Morphological and Molecular Data Reveal Two New Species of Viannaia (Nematoda: Viannaiidae), Parasitizing Opossums (Mammalia: Didelphidae) in Mexico

Two new species of Viannaia from the intestine of the North American opossums, Didelphis virginiana (Virginia opossum), and Philander opossum (gray four-eyed opossum), are described based on morphological and molecular data, through an integrative taxonomic approach. Maximum likelihood and Bayesian inference analyses for each dataset and the concatenated dataset were performed using a mitochondrial cytochrome c oxidase subunit 1 (COI) gene, and the nuclear ribosomal internal transcribed spacer region (ITS1-5.8S-ITS2). The phylogenetic analyses revealed 2 new species that occur in Mexico, one from the western state of Colima and another from the southern state of Chiapas. Our phylogenetic trees for both molecular markers and concatenated datasets yielded similar topologies with high bootstrap values and posterior probabilities. Viannaia is recovered as a monophyletic group, but the family Viannaiidae appears as non-monophyletic, due to the position of Travassostrongylus scheibelorum, similar to previous studies. Finally, the morphology of Viannaia and Hoineffia is discussed.

On the identity of Eucephalobus oxyuroides (de Man, 1876) Steiner, 1936 (Rhabditida, Cephalobidae), with an updated taxonomy of the genus and notes about its phylogeny

The identity of Eucephalobus oxyuroides is discussed after studying two Iberian populations that fit the original description of the species. A new characterization is consequently provided as follows: 0.49 to 0.70 mm long body, lip region continuous with the adjoining body and bearing short probolae prongs, neck 132 to 158 µm long, spermatheca 23 to 47 µm long or 1.0 to 1.8 times the corresponding body diameter, post-vulval uterine sac 40 to 54 µm long or 2.0 to 2.5 times as long as the body diameter, V  =  58 to 64, female tail conical elongate with very acute terminus (60-79 µm, c = 7.1-10.0, c′ = 4.9-5.8), male tail conical (36-49 µm, c =10.9-14.3, c′ = 2.4-3.4) with an elongate acute mucro, and spicules 21 to 22 µm long. Previous records of the species are revised. An emended diagnosis of the genus is proposed, and its taxonomy is updated with a list of species, key to their identification and illustrations. The evolutionary relationships of Eucephalobus, as derived from the analyses of 18S and 28S rDNA fragments, reveals that it occupies a basal position within the subfamily Cephalobidae.

The mitochondrial genome of Acrobeloides varius (Cephalobomorpha) confirms non-monophyly of Tylenchina (Nematoda)

The infraorder Cephalobomorpha is a diverse and ecologically important nematode group found in almost all terrestrial environments. In a recent nematode classification system based on SSU rDNA, Cephalobomorpha was classified within the suborder Tylenchina with Panagrolaimomorpha, Tylenchomorpha and Drilonematomorpha. However, phylogenetic relationships among species within Tylenchina are not always consistent, and the phylogenetic position of Cephalobomorpha is still uncertain. In this study, in order to examine phylogenetic relationships of Cephalobomorpha with other nematode groups, we determined the complete mitochondrial genome sequence of Acrobeloides varius, the first sequenced representative of Cephalobomorpha, and used this sequence for phylogenetic analyses along with 101 other nematode species. Phylogenetic analyses using amino acid and nucleotide sequence data of 12 protein-coding genes strongly support a sister relationship between the two cephalobomorpha species A. varius and Acrobeles complexus (represented by a partial mt genome sequence). In this mitochondrial genome phylogeny, Cephalobomorpha was sister to all chromadorean species (excluding Plectus acuminatus of Plectida) and separated from Panagrolaimomorpha and Tylenchomorpha, rendering Tylenchina non-monophyletic. Mitochondrial gene order among Tylenchina species is not conserved, and gene clusters shared between A. varius and A. complexus are very limited. Results from phylogenetic analysis and gene order comparison confirms Tylenchina is not monophyletic. To better understand phylogenetic relationships among Tylenchina members, additional mitochondrial genome information is needed from underrepresented taxa representing Panagrolaimomorpha and Cephalobomorpha.

Morphological and molecular characterization of Acrobeloides saeedi Siddiqi, De Ley and Khan, 1992 (Rhabditida, Cephalobidae) from India and comments on its status

Two cultured populations of Acrobeloides saeedi are described from India. Morphologically and morphometrically this material agrees with other species of the Maximus-group (A. bodenheimeri, A. longiuterus, and A. maximus), especially with A. longiuterus. However, molecular studies based on 18 S, 28 S and ITS rDNA confirmed the Indian material is well differentiated from all of these species. According to this, A. saeedi is considered a valid taxon distinguished mainly from A. bodenheimeri by having dextral female reproductive system (vs sinistral), from A. longiuterus by having larger females (1.03-1.57 vs 0.57-0.88 mm) and from A. maximus by having seta-like labial processes (vs absent) and males as frequent as females (vs males very infrequent). Molecular and phylogenetic studies revealed the present specimens to be conspecific to undescribed Acrobeloides sp. population from Iran, and hence, both regarded to be conspecific to each other. In addition, other similar species are revised: Acrobeloides ishraqi is considered new junior synonym of A. saeedi, Acrobeloides mushtaqi is considered new junior synonym of A. bodenheimeri, while Acrobeloides gossypia is also considered junior synonym of A. saeedi.

Description of Acrobeles aenigmaticus sp. n. (Rhabditida: Cephalobidae), an unusual species with a poorly developed vulva, from the Kalahari Desert (Ngamiland, Botswana)

Acrobeles aenigmaticus sp. n. is described from the North-West District (Ngamiland) of Botswana, which forms part of the Kalahari Desert. This new species is characterised by its body length, ‘double’ cuticle bearing numerous interannular punctations, lateral fields with two longitudinal incisures, lips triangular bearing triangular tines with variation in their morphology, labial probolae bifurcated with prongs bearing triangular tines, pharyngeal corpus 2.8-3.8 times the isthmus length, spermatheca 0.8-1.8 times the body diam., post-vulval sac 1.3-2.2 times the body diam., vagina bent to the left side, vulva located left subventral and very reduced, female tail conoid-elongate, male tail conoid, spicules 24-29 μm and gubernaculum 13-17 μm in length. Molecular characterisation of 18S and 28S rRNA shows the relationship of this species with other species of Acrobeles that also present a ‘double’ cuticle, as well as with other cephalobids (e.g., Cervidellus alutus) with the same characteristic in terms of its cuticle.

Description of Rotylenchus rhomboides n. sp. and a Belgian population of Rotylenchus buxophilus (Tylenchomorpha: Hoplolaimidae)

During a survey in the Botanical garden of Ghent University, a new species Rotylenchus rhomboides n. sp. and a population of Rotylenchus buxophilus were found. Rotylenchus rhomboides n. sp. is characterized by the presence of a rhomboid-like widening of the mid-ridge of lateral field at the level of vulva, a feature previously unknown within the genus. The population of the new species, composed only by females, has a rounded labial region with 4 to 5 annuli, robust stylet (31–37 μm long), short dorsal esophageal gland (9–19 μm) overlap of the intestine, vulva located slightly posterior to mid-body, and hemispherical or rounded tail shape with large phasmids located 3 to 5 annuli anterior to the level of anus. The hierarchical cluster analysis based on morphological features indicated that the new species closely resembles R. corsicus, R. gracilidens, and R. rugatocuticulatus. The DNA analyses of the D2-D3 of 28S rDNA, ITS rDNA, and COI mtDNA sequences of Rotylenchus rhomboides n. sp. show a close relationship with R. buxophilus, R. goodeyi, R. laurentinus, R. pumilus, and R. incultus, all of which can also be differentiated from the new species by morphological features. The combination of morphological, morphometric, and molecular characteristics confirmed the new species and the first report of R. buxophilus on yam (Dioscorea tokoro) in Belgium.

Antechiniella septentrionalis n. sp. (Spirurida: Acuariidae), a new intestinal nematode parasite of the tundra vole Microtus oeconomus (Pallas) (Rodentia: Muridae) in the north-east of Russia

Antechiniella septentrionalis n. sp. (Spirurida: Acuariidae) is described from the duodenum of a tundra vole, Microtus oeconomus (Pallas), collected in the Magadan region in the north-east part of Russia. It differs from A. suffodiax (Beveridge &amp; Barker, 1975) and A. sertatum Smales, 1991 mainly in having a larger number of postcloacal papillae (5–6 pairs vs 4 pairs), a differently shaped left spicule, the disposition of precloacal papillae in two rows vs one, and oblong vs oval eggs. Other differences include the different disposition of ovaries in A. septentrionalis n. sp and A. suffodiax and the different structure of deirids in A. septentrionalis n. sp. and A. sertatum. The new species was characterized molecularly (partial sequences for 18S rRNA, 28S rRNA and cox1 mtDNA). The phylogenetic analyses performed showed the affinity of the new species to the members of the Acuariidae and other spirurid nematodes.

Redescription of Macrolaimus canadensis Sanwal, 1960 and M. ruehmi Andrássy, 1966 (Nematoda, Rhabditida, Chambersiellidae), and new data on M. crucis Maupas, 1900

Three species belonging to the genus Macrolaimus, namely M. canadensis, M. crucis and M. ruehmi, have been obtained from areas of natural vegetation in Bosnia and Herzegovina, Corsica (France), the Czech Republic and Spain. These three species are characterized by the body length of males and females, stomatal proportion of the gymnostom and cheilostom, excretory pore position, postvulval uterine sac length, male and female tail length and morphology, and the length and morphology of the spicules and gubernacula. The occurrence of M. crucis in Spain has, as a result of this study, now also been expanded to a larger area of the southern Iberian Peninsula. Morphological and morphometrical analyses showed that M. canadensis and M. ruehmi are very similar, sharing apomorphic characters. In contrast, M. crucis has plesiomorphic characters. Description, measurements and illustrations are provided for these three species.

Description of Myolaimus mycophilus Slos & Bert sp. n. (Rhabditida: Myolaimidae)

Myolaimus mycophilus Slos & Bert sp. n. was isolated from mushrooms from different locations in Belgium and cultured on nutrient agar seeded with Escherichia coli OP50. Myolaimus mycophilus sp. n. is characterised by a unique combination of the following characters: adults with lateral fields not differentiated, buccal cavity triangular, cheilostom anisomorphic, female with a post-vulval uterine sac as long as the corresponding body diam., wrinkled eggshell, male with seven pairs of genital papillae, cloacal aperture covered by a trapezoidal cloacal flap and with a single ventral papilla at its base. The new species and M. goodeyorum Andrássy, 1984 were molecularly characterised by sequencing the 18S and D2-D3 28S expansion segments of rDNA. Phylogenetic relationships were reconstructed based on concatenated analyses and the phylogenetic placement of Myolaimus, an intriguing genus within the Rhabditida, is discussed.

Panagrellus levitatus sp. n. (Rhabditida: Panagrolaimidae), a nematode suppressing Drosophila melanogaster in laboratory cultures

A new nematode species recovered from the laboratory culture ofDrosophila melanogasteris described and illustrated. The mass reproduction ofPanagrellus levitatussp. n. in the fly culture occurred several times and resulted in a significant reduction of the fly population. Nematode outbreaks happened after the introduction ofD. melanogasterto the culture from natural sources. The new species is morphologically similar toP. ulmi. Partial LSU rDNA and SSU rDNA sequences were obtained and subjected to phylogenetic analysis that demonstrated the affinity of the new species withPanagrellussp. ‘MC2014’ from a red palm weevil. For the first time, the dauer juveniles ofPanagrelluswere described.

On the identity of Chiloplacus magnus Rashid & Heyns, 1990 and C. insularis Orselli & Vinciguerra, 2002 (Rhabditida: Cephalobidae), two confusable species

Two very similar species of the genus Chiloplacus, namely C. magnus and C. insularis, are re-described and compared based on type material as well as Iberian specimens. Relevant new information is obtained for their characterisation and for elucidating their identity with more accuracy. Special mention is deserved by the findings regarding: i) the morphology of the lateral field at vulval level; and ii) the location of the vulva, which is either midventral or subventral, two remarkable traits that were originally overlooked. Chiloplacus magnus is distinguished by having the left lateral field expanded at vulval level and the vulva displaced to a subventral position, whereas C. insularis displays the usual pattern of the genus. The evolutionary relationships of the Iberian C. magnus are explored by means of D2-D3 sequence analysis. Chiloplacus similis is regarded as identical to C. magnus and is proposed as a new junior synonym of the latter.

Acrobeloides varius sp. n. (Rhabditida: Cephalobidae) from South Korea

A new Acrobeloides is described and illustrated from samples collected in rice farmland in South Korea. Acrobeloides varius sp. n. exhibits morphological characters of other acrobeloids, including a corpus with elongate spindle-like swelling and lateral incisures that extend to the tail end region. However, this new species is distinguished from other acrobeloids by having lateral incisures that change in number from one to five, three low rounded labial probolae, and a conical pointed tail end with a small spike-shaped mucron. In this study, a detailed morphological comparison of Acrobeloides species is provided, along with new molecular sequence data from the D2-D3 regions of LSU, SSU and partial mtDNA cox1 region from the new species, which can be used as molecular barcode sequences.

The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle

The entomopathogenic nematode Steinernema carpocapsae has been widely used for the biological control of insect pests. It shares a symbiotic relationship with the bacterium Xenorhabdus nematophila, and is emerging as a genetic model to study symbiosis and pathogenesis. We obtained a high-quality draft of the nematode’s genome comprising 84,613,633 bp in 347 scaffolds, with an N50 of 1.24 Mb. To improve annotation, we sequenced both short and long RNA and conducted shotgun proteomic analyses. S. carpocapsae shares orthologous genes with other parasitic nematodes that are absent in the free-living nematode C. elegans, it has ncRNA families that are enriched in parasites, and expresses proteins putatively associated with parasitism and pathogenesis, suggesting an active role for the nematode during the pathogenic process. Host and parasites might engage in a co-evolutionary arms-race dynamic with genes participating in their interaction showing signatures of positive selection. Our analyses indicate that the consequence of this arms race is better characterized by positive selection altering specific functions instead of just increasing the number of positively selected genes, adding a new perspective to these co-evolutionary theories. We identified a protein, ATAD-3, that suggests a relevant role for mitochondrial function in the evolution and mechanisms of nematode parasitism.

Discovery of a free-living nematode phylogenetically related to vertebrate parasites of the genus Strongyloides (Nematoda : Strongyloidoidea): morphological, anatomical and molecular characterisation

Nematodes are important, largely because they frequently act as parasites and threaten the health of plants, animals and even humans. Here, we describe an interesting free-living nematode from land snails on Luofu Mountain, Guangdong, China. Alloionema luofuensis, sp. nov. is phylogenetically related to slug-parasite A. appendiculatum and the well-known vertebrate parasites Strongyloides spp. based on small subunit (SSU) and the D2-D3 domain of large subunit (LSU) rDNA sequences. The new species possesses an extremely transparent body and is easily maintained using C. elegans culture media, suggesting a possible application prospect of this free-living nematode as a comparative model system for its related parasites. Morphology and anatomy of the gonochoristic A. luofuensis, sp. nov. adult were described and illustrated. The species is characterised by a filiform tail bisexually, ‘rhabditiform’ oesophagus and ‘rhabditid-like’ female anatomy, but its male caudal region is completely different from that of typical rhabditid nematodes, being absent from an enveloping bursa. It is the first marker taxon characterised morphologically as well as molecularly from the family Alloionematidae, a group of nematodes with hyperdiverse molecular genetic variations underlying highly conserved anatomy. Further molecular and genetic studies on A. luofuensis, sp. nov. populations hold promise to provide insight into evolution of the clade consisting of vertebrate parasites of the heterogonic nematode genus Strongyloides. This is because of its unusual high levels of heterozygosity maintained by the conserved rRNA genes of partial SSU and the D2-D3 domain of LSU for the type isolate of this species.

Soil and litter nematode diversity of Mount Hamiguitan, the Philippines, with description of Bicirronema hamiguitanense n. sp. (Rhabditida: Bicirronematidae)

The nematode diversity in soil and litter was investigated on Mount Hamiguitan, the Philippines, along four eco-habitats from elevations of 75-1600 m a.s.l. A total of 155 and 467 nematodes were identified to 39 and 62 genera from litter and soil, respectively. The nematode assemblages and diversity did not show any relation to eco-habitat or elevation. Bacterivorous nematodes were the most common group (37.5%). Acrobeloides was most abundant from the soil and Aphelenchoides from the litter. Bicirronema hamiguitanense n. sp. is herein described based on morphology, morphometrics and molecular data. The new species has the following diagnostic features: a wide lateral field one-fifth of its body diam. with four incisures forming two ornamented ridges; gubernaculum with proximal thickening; spicules (35-38 μm) and gubernaculum (18-20 μm) longer than B. caledoniense; and with 37 molecular autapomorphies supporting its new species status. The phylogenetic position of the new species within Cephalobomorpha is discussed.

Phylogenetic analysis of entomoparasitic nematodes, potential control agents of flea populations in natural foci of plague

Entomoparasitic nematodes are natural control agents for many insect pests, including fleas that transmit Yersinia pestis, a causative agent of plague, in the natural foci of this extremely dangerous zoonosis. We examined the flea samples from the Volga-Ural natural focus of plague for their infestation with nematodes. Among the six flea species feeding on different rodent hosts (Citellus pygmaeus, Microtus socialis, and Allactaga major), the rate of infestation varied from 0 to 21%. The propagation rate of parasitic nematodes in the haemocoel of infected fleas was very high; in some cases, we observed up to 1,000 juveniles per flea specimen. Our study of morphology, life cycle, and rDNA sequences of these parasites revealed that they belong to three distinct species differing in the host specificity. On SSU and LSU rRNA phylogenies, these species representing three genera (Rubzovinema, Psyllotylenchus, and Spilotylenchus), constitute a monophyletic group close to Allantonema and Parasitylenchus, the type genera of the families Allantonematidae and Parasitylenchidae (Nematoda: Tylenchida). We discuss the SSU-ITS1-5.8S-LSU rDNA phylogeny of the Tylenchida with a special emphasis on the suborder Hexatylina.

Phylogenetic analysis of ruminant Theileria spp. from China based on 28S ribosomal RNA gene

Species identification using DNA sequences is the basis for DNA taxonomy. In this study, we sequenced the ribosomal large-subunit RNA gene sequences (3,037-3,061 bp) in length of 13 Chinese Theileria stocks that were infective to cattle and sheep. The complete 28S rRNA gene is relatively difficult to amplify and its conserved region is not important for phylogenetic study. Therefore, we selected the D2-D3 region from the complete 28S rRNA sequences for phylogenetic analysis. Our analyses of 28S rRNA gene sequences showed that the 28S rRNA was useful as a phylogenetic marker for analyzing the relationships among Theileria spp. in ruminants. In addition, the D2-D3 region was a short segment that could be used instead of the whole 28S rRNA sequence during the phylogenetic analysis of Theileria, and it may be an ideal DNA barcode.

Monophyly of clade III nematodes is not supported by phylogenetic analysis of complete mitochondrial genome sequences

Background

The orders Ascaridida, Oxyurida, and Spirurida represent major components of zooparasitic nematode diversity, including many species of veterinary and medical importance. Phylum-wide nematode phylogenetic hypotheses have mainly been based on nuclear rDNA sequences, but more recently complete mitochondrial (mtDNA) gene sequences have provided another source of molecular information to evaluate relationships. Although there is much agreement between nuclear rDNA and mtDNA phylogenies, relationships among certain major clades are different. In this study we report that mtDNA sequences do not support the monophyly of Ascaridida, Oxyurida and Spirurida (clade III) in contrast to results for nuclear rDNA. Results from mtDNA genomes show promise as an additional independently evolving genome for developing phylogenetic hypotheses for nematodes, although substantially increased taxon sampling is needed for enhanced comparative value with nuclear rDNA. Ultimately, topological incongruence (and congruence) between nuclear rDNA and mtDNA phylogenetic hypotheses will need to be tested relative to additional independent loci that provide appropriate levels of resolution.

Results

For this comparative phylogenetic study, we determined the complete mitochondrial genome sequences of three nematode species, Cucullanus robustus (13,972 bp) representing Ascaridida, Wellcomia siamensis (14,128 bp) representing Oxyurida, and Heliconema longissimum (13,610 bp) representing Spirurida. These new sequences were used along with 33 published nematode mitochondrial genomes to investigate phylogenetic relationships among chromadorean orders. Phylogenetic analyses of both nucleotide and amino acid sequence datasets support the hypothesis that Ascaridida is nested within Rhabditida. The position of Oxyurida within Chromadorea varies among analyses; in most analyses this order is sister to the Ascaridida plus Rhabditida clade, with representative Spirurida forming a distinct clade, however, in one case Oxyurida is sister to Spirurida. Ascaridida, Oxyurida, and Spirurida (the sampled clade III taxa) do not form a monophyletic group based on complete mitochondrial DNA sequences. Tree topology tests revealed that constraining clade III taxa to be monophyletic, given the mtDNA datasets analyzed, was a significantly worse result.

Conclusion

The phylogenetic hypotheses from comparative analysis of the complete mitochondrial genome data (analysis of nucleotide and amino acid datasets, and nucleotide data excluding 3^rd positions) indicates that nematodes representing Ascaridida, Oxyurida and Spirurida do not share an exclusive most recent common ancestor, in contrast to published results based on nuclear ribosomal DNA. Overall, mtDNA genome data provides reliable support for nematode relationships that often corroborates findings based on nuclear rDNA. It is anticipated that additional taxonomic sampling will provide a wealth of information on mitochondrial genome evolution and sequence data for developing phylogenetic hypotheses for the phylum Nematoda.

Integrating molecular and morphological approaches for characterizing parasite cryptic species: implications for parasitology

Herein we review theoretical and methodological considerations important for finding and delimiting cryptic species of parasites (species that are difficult to recognize using traditional systematic methods). Applications of molecular data in empirical investigations of cryptic species are discussed from an historical perspective, and we evaluate advantages and disadvantages of approaches that have been used to date. Developments concerning the theory and practice of species delimitation are emphasized because theory is critical to interpretation of data. The advantages and disadvantages of different molecular methodologies, including the number and kind of loci, are discussed relative to tree-based approaches for detecting and delimiting cryptic species. We conclude by discussing some implications that cryptic species have for research programmes in parasitology, emphasizing that careful attention to the theory and operational practices involved in finding, delimiting, and describing new species (including cryptic species) is essential, not only for fully characterizing parasite biodiversity and broader aspects of comparative biology such as systematics, evolution, ecology and biogeography, but to applied research efforts that strive to improve development and understanding of epidemiology, diagnostics, control and potential eradication of parasitic diseases.

Resolving phylogenetic incongruence to articulate homology and phenotypic evolution: a case study from Nematoda

Modern morphology-based systematics, including questions of incongruence with molecular data, emphasizes analysis over similarity criteria to assess homology. Yet detailed examination of a few key characters, using new tools and processes such as computerized, three-dimensional ultrastructural reconstruction of cell complexes, can resolve apparent incongruence by re-examining primary homologies. In nematodes of Tylenchomorpha, a parasitic feeding phenotype is thus reconciled with immediate free-living outgroups. Closer inspection of morphology reveals phenotypes congruent with molecular-based phylogeny and points to a new locus of homology in mouthparts. In nematode models, the study of individually homologous cells reveals a conserved modality of evolution among dissimilar feeding apparati adapted to divergent lifestyles. Conservatism of cellular components, consistent with that of other body systems, allows meaningful comparative morphology in difficult groups of microscopic organisms. The advent of phylogenomics is synergistic with morphology in systematics, providing an honest test of homology in the evolution of phenotype.

Diversity of free-living marine nematodes (Enoplida) from Baja California assessed by integrative taxonomy

We used morphological and molecular approaches to evaluate the diversity of free-living marine nematodes (order Enoplida) at four coastal sites in the Gulf of California and three on the Pacific coast of Baja California, Mexico. We identified 22 morphological species belonging to six families, of which Thoracostomopsidae and Oncholaimidae were the most diverse. The genus Mesacanthion (Thoracostomopsidae) was the most widespread and diverse. Five allopatric species, genetically and morphologically differentiated, were found in two localities in the Gulf of California (M. sp1 and M. sp2) and three in the Pacific coast (M. sp3, M. sp4 and M. sp5). Overall, we produced 19 and 20 sequences for the 18S and 28S genes, respectively. Neither gene displayed intraspecific polymorphisms, which allowed us to establish that some morphological variation was likely either ontogenetic or due to phenotypic plasticity. Although 18S and 28S phylogenies were topologically congruent (incongruence length difference test, P > 0.05), divergences between species were much higher in the 28S gene. Moreover, this gene possessed a stronger phylogenetic signal to resolve relationships involving Rhabdodemania and Bathylaimus. On the other hand, the close relationship of Pareurystomina (Enchilidiidae) with oncholaimids warrants further study. The 28S sequences (D2D3 domain) may be better suited for DNA barcoding of marine nematodes than those from the 18S rDNA, particularly for differentiating closely related or cryptic species. Finally, our results underline the relevance of adopting an integrative approach encompassing morphological and molecular analyses to improve the assessment of marine nematode diversity and advance their taxonomy.

Comparative, three-dimensional anterior sensory reconstruction of Aphelenchus avenae (nematoda: Tylenchomorpha)

The anterior sensory anatomy (not including amphids) of the nematode Aphelenchus avenae (Tylenchomorpha) has been three-dimensionally reconstructed from serial, transmission electron microscopy thin sections. Models, showing detailed morphology and spatial relationships of cuticular sensilla and internal sensory receptors, are the first computerized reconstruction of sensory structures of a Tylenchomorpha nematode. Results are analyzed with respect to similarly detailed reconstructions of Rhabditida outgroup nematodes, Acrobeles complexus (Cephalobomorpha) and Caenorhabditis elegans (Rhabditomorpha). Homologies identified in A. avenae demonstrate the general conservation of the anterior sensory system between freeliving nematodes and the largely plant parasitic Tylenchomorpha. A higher degree of similarity is shown between A. avenae and A. complexus, with common features including: the presence of a second, internal outer labial dendrite (OL1); a second cephalic dendrite in the female (CEP2/CEM); an accessory process loop of inner labial dendrite 1; and terminus morphology and epidermal associations of internal sensory receptors BAG and URX. Unique to A. avenae is a pair of peripheral, lateral neurons of unknown homology but with axial positions and intercellular relationships nearly identical to the "posterior branches" of URX in A. complexus. Knowledge of homologies and connectivity of anterior sensory structures provides a basis for expansion of the experimental behavioral model of C. elegans to the economically important nematodes of Tylenchomorpha.

Methylation of the sterol nucleus by STRM-1 regulates dauer larva formation in Caenorhabditis elegans

In response to pheromone(s), Caenorhabditis elegans interrupts its reproductive life cycle and enters diapause as a stress-resistant dauer larva. This decision is governed by a complex system of neuronal and hormonal regulation. All the signals converge onto the nuclear hormone receptor DAF-12. A sterol-derived hormone, dafachronic acid (DA), supports reproductive development by binding to DAF-12 and inhibiting its dauer-promoting activity. Here, we identify a methyltransferase, STRM-1, that modulates DA levels and thus dauer formation. By modifying the substrates that are used for the synthesis of DA, STRM-1 can reduce the amount of hormone produced. Loss of STRM-1 function leads to elevated levels of DA and inefficient dauer formation. Sterol methylation was not previously recognized as a mechanism for regulating hormone activity. Moreover, the C-4 sterol nucleus methylation catalyzed by STRM-1 is unique to nematodes and thus could be a target for therapeutic strategies against parasitic nematode infections.

Three-dimensional reconstruction of the stomatostylet and anterior epidermis in the nematode Aphelenchus avenae (Nematoda: Aphelenchidae) with implications for the evolution of plant parasitism

A three-dimensional model of the stomatostylet and associated structures has been reconstructed from serial thin sections of Aphelenchus avenae, a representative of Tylenchomorpha, a group including most plant parasitic nematodes. The reconstruction is compared with previous work on bacteriovorous cephalobids and rhabditids to better understand the evolution of the stylet and its associated cells. Two arcade syncytia ("guide ring") line the stylet shaft, supporting the hypothesis that the stylet shaft and cone (into which the shaft extends and which is not lined by syncytia) are homologous with the gymnostom of cephalobids, the sister taxon of tylenchids. Epidermal syncytia, HypA, HypB, HypC, and HypE, line the cephalic framework, vestibule, and vestibule extension, congruent with the hypothesis that these components are homologous with the cephalobid cheilostom. Relative to outgroups, HypC is expanded in A. avenae, enclosing sensilla that fill most of the cephalic framework. The homolog of syncytium HypD in the cephalobid Acrobeles complexus is not observed in A. avenae. Arcade syncytia are reduced compared with those of cephalobids. Stylet protractor muscles in A. avenae are homologous with the most anterior set of radial muscles of cephalobids. Observations to date test and verify our previous hypotheses of homology of the stomatostylet with respect to the stoma of bacteriovorous outgroups. Reconstruction of the stegostom and pharynx will provide further tests of homology and evolution of feeding structure adaptations for plant parasitism.

Molecular evolution in Panagrolaimus nematodes: origins of parthenogenesis, hermaphroditism and the Antarctic species P. davidi

BACKGROUND

As exemplified by the famously successful model organism Caenorhabditis elegans, nematodes offer outstanding animal systems for investigating diverse biological phenomena due to their small genome sizes, short generation times and ease of laboratory maintenance. Nematodes in the genus Panagrolaimus have served in comparative development and anhydrobiosis studies, and the Antarctic species P. davidi offers a powerful paradigm for understanding the biological mechanisms of extreme cold tolerance. Panagrolaimus nematodes are also unique in that examples of gonochoristic, hermaphroditic and parthenogenetic reproductive modes have been reported for members of this genus. The evolutionary origins of these varying reproductive modes and the Antarctic species P. davidi, however, remain enigmatic.

RESULTS

We collected nuclear ribosomal RNA gene and mitochondrial protein-coding gene sequences from diverse Panagrolaimus species and strains, including newly discovered isolates from Oregon, to investigate phylogenetic relationships in this nematode genus. Nuclear phylogenies showed that the species and strains historically identified as members of Panagrolaimus constitute a paraphyletic group, suggesting that taxonomic revision is required for Panagrolaimus and related nematode lineages. Strain-specific reproductive modes were mapped onto the molecular phylogeny to show a single origin of parthenogenesis from a presumably gonochoristic ancestor. The hermaphroditic strains were all placed outside a major monophyletic clade that contained the majority of other Panagrolaimus nematodes. Phylogenetic analyses of mitochondrial sequences showed that substantial molecular and geographic diversity exists within the clade of parthenogenetic strains. The Antarctic species P. davidi was found to be very closely related to two Panagrolaimus strains from southern California. Phylogenetic and molecular clock analyses suggested that P. davidi and the California strain PS1579 shared a common ancestor in the very recent evolutionary past.

CONCLUSION

Our study provides a phylogenetic framework for understanding the evolutionary origins and diversification patterns of varying reproductive modes within Panagrolaimus and important insights into the origin of the Antarctic species P. davidi. Panagrolaimus offers a powerful nematode model for understanding diverse evolutionary phenomena including the evolution of asexuality and the adaptive evolution of extreme cold tolerance.