Oleksandr Holovachov

A phylogenetic tree of nematodes based on about 1200 full-length small subunit ribosomal DNA sequences

As a result of the scarcity of informative morphological and anatomical characters, nematode systematics have always been volatile. Differences in the appreciation of these characters have resulted in numerous classifications and this greatly confuses scientific communication. An advantage of the use of molecular data is that it allows for an enormous expansion of the number of characters. Here we present a phylogenetic tree based on 1215 small subunit ribosomal DNA sequences ( ca 1700 bp each) covering a wide range of nematode taxa. Of the 19 nematode orders mentioned by De Ley et al. (2006) 15 are represented here. Compared with Holterman et al. (2006) the number of taxa analysed has been tripled. This did not result in major changes in the clade subdivision of the phylum, although a decrease in the number of well supported nodes was observed. Especially at the family level and below we observed a considerable congruence between morphology and ribosomal DNA-based nematode systematics and, in case of discrepancies, morphological or anatomical support could be found for the alternative grouping in most instances. The extensiveness of convergent evolution is one of the most striking phenomena observed in the phylogenetic tree presented here – it is hard to find a morphological, ecological or biological characteristic that has not arisen at least twice during nematode evolution. Convergent evolution appears to be an important additional explanation for the seemingly persistent volatility of nematode systematics.

Linking DNA sequences to morphology: cryptic diversity and population genetic structure in the marine nematode Thoracostoma trachygaster (Nematoda, Leptosomatidae)

Derycke, S., De Ley, P., De Ley, I.T., Holovachov, O., Rigaux, A. & Moens, T. (2010). Linking DNA sequences to morphology: cryptic diversity and population genetic structure in the marine nematode Thoracostoma trachygaster (Nematoda, Leptosomatidae).—Zoologica Scripta, 39, 276–289.

The role of habitat heterogeneity in structuring the community of intertidal free-living marine nematodes

The role of habitat complexity has been widely neglected in the study of meiofaunal community patterns. We studied the intertidal nematode community of a structurally complex macrotidal beach exhibiting contrasting microhabitats (sandbars and runnels) to understand the influence of environmental gradients and habitat heterogeneity in the community structure. We tested whether topographical complexity affected (1) the zonation pattern in terms of abundance and diversity, and (2) local diversity by promoting compartmentalization into distinct faunal groups. Our analyses revealed three major faunal assemblages along the exposure gradient associated to differences in mean grain size and chlorophyll a. Diversity patterns involved a mid-intertidal peak, consistent with the intermediate disturbance hypothesis, and another peak at the limit with the subtidal region, consistent with the transition zone. These results highlight the predominance of environmental gradients in establishing intertidal zonation. However, microhabitats differed in environmental conditions and possessed significantly distinct nematofaunal communities. Runnels featured higher levels of taxonomic and functional diversity, many unique genera, and the community differed from the assemblage at the limit to the subtidal, stressing their role as distinct microhabitats. The nematofauna of the structurally complex beach was more diverse than the one from a homogeneous beach nearby, supporting the hypothesis that structural heterogeneity promotes diversity by compartmentalization and highlighting the importance of microhabitats in the assessment of biodiversity. Contrary to previous predictions, our results indicate potentially high regional marine nematode diversity in the Upper Gulf of California.

Small subunit ribosomal DNA-based phylogeny of basal Chromadoria (Nematoda) suggests that transitions from marine to terrestrial habitats (and vice versa) require relatively simple adaptations.

The phylum Nematoda is positioned the base of the superphylum Ecdysozoa and in terms of species number and abundance can be characterized as a highly successful group. Because of their relatively conserved morphology and many poor morphological descriptions, nematode taxonomy has been unstable for decades. However, the small and large subunit (SSU and LSU) ribosomal DNA (rDNA) sequences are remarkably powerful in resolving the internal relationships within this phylum. Studies on the basis of SSU rDNA sequences suggested a subdivision of the Nematoda into several numbered clades (Blaxter et al., 1998; Holterman et al., 2006). Over the last five years there has been a steep increase in the number of available sequences, and most recently Meldal et al. (2007) presented 46 new SSU rDNA sequences from marine taxa, a so far underrepresented group. For decades the hypothesis of Filipjev (1929) about the marine ancestry of nematodes has been widely accepted. Molecular analysis of Ecdysozoa on the basis of both small and large subunit ribosomal DNA sequence information seems to support Filipjev’s hypothesis (Mallatt and Giribet, 2006). Nematodes can be found in virtually all terrestrial, freshwater and marine habitats, and it is interesting to investigate on the basis of neutral molecular data where and how frequent fundamental habitat transitions occurred. We hypothesize that the taxonomic levels at which the transitions take place (class, order, family or genus level) are indicative for the number of physiological and/or morphological changes needed to

Description of Scottnema lindsayae Timm, 1971 (Rhabditida: Cephalobidae) from Taylor Valley, Antarctica and its phylogenetic relationship

The endemic Antarctic nematode Scottnema lindsayae is described from specimens collected in Taylor Valley, McMurdo Dry Valleys, Victoria Land. The recently collected material is compared with the original description and other subsequent descriptions of the species. A more complete scanning electron microscopy (SEM) study of the species is presented. The phylogenetic position of S. lindsayae is inferred using a secondary structure-based alignment of a partial sequence of nuclear Large Subunit (LSU) ribosomal DNA. Phylogenetic trees were inferred using base-paired substitution models implemented in PHASE 2 software and Bayesian inference, and show S. lindsayae as the sister group to Stegelletina taxa.

Description of Phasmarhabditis californica n. sp. and first report of P. papillosa (Nematoda: Rhabditidae) from invasive slugs in the USA

A new species of Phasmarhabditis and the known species P. papillosa were isolated from cadavers of invasive slugs in California. Phasmarhabditis papillosa is the type of the genus and has not previously been reported from the Americas. Both species are characterised based on morphology, morphometrics and molecular data. Molecular phylogenies were inferred from concatenated DNA sequence alignments of nearly complete SSU and the D2-D3 domains of the LSU rDNA. Phasmarhabditis californica n. sp. is characterised by a robust body, mature egg-laying specimens almost spindle-shaped when relaxed, 1.5 (1.3-1.8) mm long, tapering to a bluntly rounded anterior end with stoma about as long as lip region diam., six inner labial papillae and four outer cephalic papillae, pharynx with rounded to pyriform basal bulb, vulva located halfway along the body, hermaphroditic, didelphic, amphidelphic, and short, conoid tail constricted at one-third its length with prominent phasmids. Not a single male was found among five strains. Phasmarhabditis papillosa is gonochoristic and has a longer isthmus, pyriform basal bulb and longer, dome-shaped spicate female tail constricted halfway along its length. Sequence analysis revealed unambiguous autapomorphies for P. papillosa and P. californica n. sp. Phylogenetic analyses placed these two species in a monophyletic clade comprising Phasmarhabditis species and other gastropod-parasitic taxa. Morphology, genetic distance, reproductive strategy and nucleotide autapomorphies support the new taxon.

Nematodes from terrestrial and freshwater habitats in the Arctic.

Abstract We present an updated list of terrestrial and freshwater nematodes from all regions of the Arctic, for which records of properly identified nematode species are available: Svalbard, Jan Mayen, Iceland, Greenland, Nunavut, Northwest territories, Alaska, Lena River estuary, Taymyr and Severnaya Zemlya and Novaya Zemlya. The list includes 391 species belonging to 146 genera, 54 families and 10 orders of the phylum Nematoda.

Morphology, molecular characterisation and systematic position of the genus Cynura Cobb, 1920 (Nematoda: Plectida)

Descriptions of three known species of Cynura, i.e., C. cerambus, C. klunderi and C. papillata, are given, including SEM micrographs of C. cerambus and a tabular compendium for all species of the genus. The phylogenetic relationships of C. klunderi are inferred from molecular data. Bayesian analyses of small subunit (SSU) of rRNA sequences support a position nested among the Plectidae suggesting the secondary simplification in the morphology of pharyngeal valvular apparatus in Cynura and the ‘return’ from a terrestrial to a marine environment in this genus.

Redescription of Placodira lobata Thorne, 1937 (Rhabditida: Cephalobidae) with a discussion of the systematic position of the genus

A population of Placodira lobata from the USA is described using both light and scanning electron microscopy and compared with the descriptions of the type specimens of the same species. The phylogenetic relationships of the species are inferred from molecular data and places P. lobata in a clade that unites genera with mostly simple morphology of the labial region, like Cephalobus , Acrobeloides , Heterocephalobellus and Metacrobeles , but also includes species of Zeldia and Chiloplacus .

Nematodes from the Gulf of California. Part 1. The genera Ceramonema Cobb, 1920, Pselionema Cobb in Cobb, 1933 and Pterygonema Gerlach, 1954 (Nematoda: Ceramonematidae)

The morphology and morphometry of nematodes of six species of the family Ceramonematidae is described using light and scanning electron microscopy. In this paper, we describe two new species and redescribe two known species of Ceramonema and one new species each of Pselionema and Pterygonema. Ceramonema altogolfi sp. n. is characterised by the 0.8-1.3 mm long body, 187-247 body annules, weakly developed zygapophyses, presence of intracuticular vacuoles, sexual dimorphism in amphid shape, presence of vaginal sclerotisation, complex gubernaculum and relatively uniform anal and cloacal annules, whilst C. inguinispina sp. n. has a 0.8-1.1 mm long body, 135-191 body annules, weakly developed zygapophyses, presence of intracuticular vacuoles, sexual dimorphism in amphid shape, absence of vaginal sclerotisation, thorn-shaped precloacal projection, plate-like gubernaculum and double cloacal annule. Pselionema psednum sp. n. is distinguished by 1.4-1.7 mm long body, 251-292 body annules, weakly developed zygapophyses, absence of intracuticular vacuoles, sexual dimorphism in amphid shape and Pterygonema mexicanum sp. n. is characterised by having amphids lacking a central thorn-like projection and pharynx with a distinct posterior glandular bulb. Populations of Ceramonema rectum and Ceramonema cf. yunfengi are also described. The male cloacal region of the species examined appears to be a rich potential source of taxonomic characters that have as yet received insufficient attention for this family.