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.     

Revision of Comesomatidae (Nematoda)

The gross and fine morphology of the family Comesomatidae is reviewed and the systematic position of its members revised. Significant differentiating characters of the Comesomatidae within the Chromadorida are: a copulatory apparatus provided with apophyses, a female reproductive system with outstretched ovaries, the presence of marginal tubes within the oesophagus, and a non-sclerotized and enlarged tail tip. For classification within the family the following three main characters are used: the structure of the buccal cavity, the structure of the copulatory apparatus, and the arrangement of the cephalic sense organs. Structure of the Sabatieria type is considered basic. The genera are rearranged in three subfamilies as follows: Sabatieriinae ( Cervonema, Laimelia, Pierrickia, Sabatieria (syn. Actarjania), Scholpaniella ), Dorylaimopsinae (Dorylaimopsis (syn. Mesonchium), Hopperia, Metasabatieria, Paramesonchium, Vasostoma ), Comesomatinae ( Comesoma, Metacomesoma, Paracomesoma. ) Six species of Comesomatidae are described from the øresund, Denmark: Cervonema macramphis sp.n.; Laimelia filipjevi nom. nov. (syn. Sabatieria longicaudata Filipjev, 1922); Sabatieria hilarula De Man, 1922; S. ornata (Ditlevsen, 1918); S. punctata (Kreis, 1924); Dorylaimopsis punctata Ditlevsen, 1918. Representatives of these species constitute more than 40% of the total number of nematodes in the region.     

Fine Structure of the Head and Cervical Region of Ceramonema carinatum (Chromadorida: Ceramonematidae)

Structure of the head and cervical region of Ceramonema carinatum (Chromadorida: Ceramonematidae) was described from transmission electron microscopy of serial transverse and longitudinal sections of two females. An unbroken massive cortical layer encompasses the head, except where three thin liplets surround the mouth. A large flask-shaped buccal cavity, with simpler less dense cuticle identical with that of the pharynx, abuts the body cuticle just within the mouth. Myoepithelial ceils constituting the buccal and pharyngeal regions were described. Sixteen head sensilla, the amphids, and dorsal and ventral internal sensilla were identified and described, each with associated sheath and socket cells. Ultrasturcture of the head was compared with that of other nematodes. Arrangement of sensilla resembled that of Monhysterida and Rhabditida with some significant variations, such as prominent longitudinally arranged intracellular organelles containing many microtubules associated with the amphids. The buccal cavity was almost entirely pharyngeal in character. A well-developed system of structural fibrils and abundant hemidesmosomes were notable features.     

近岸海洋线虫与细菌、古菌的共现性及其对碳、氮循环的影响

【目的】初步探究海洋线虫与微生物的相互作用对碳、氮循环的影响。【方法】利用16S r RNA和18S r RNA基因高通量测序方法,对33个近岸沉积物样品中细菌、古菌和真核生物的多样性进行调查;对海洋线虫与细菌、海洋线虫与古菌的共现性进行网络分析,并采用Spearman统计学方法,识别出与海洋线虫共现性呈显著相关性的微生物种类。【结果】在夏季,红树林和潮间带泥滩样品中线虫OTU平均相对丰度基本呈随深度增加而递减趋势;冬季的红树林样品中发现相类似变化规律,只有在冬季潮间带泥滩样品中线虫OTU平均相对丰度在深层较高于表层。相对丰度最高的海洋线虫隶属于单宫目(47%)、色矛目(19%)、刺嘴目(16%)和垫刃目(9%),它们与热源体古菌、深古菌、γ-和δ-变形菌等微生物有显著正/负相关关系。【结论】在香港米埔湿地沉积物中,与相对丰度最高的5种线虫显著相关的几大类微生物均在碳、氮、硫等元素循环方面起十分重要的作用,暗示海洋线虫与微生物潜在的相互作用对元素地球化学循环具有重要影响。研究结果有助于深入了解线虫在生态系统中未被揭示的生态功能,有助于更清晰地认识海洋线虫在底栖生态系统中所扮演的角色。     

NEWLY RECORDED SPECIES OF FREE-LIVING NEMATODES FROM CHINA (CHROMADORIDA,ENOPLIDA ARAEOLAIMIDA)

The present paper embodies 11 species belonging to Chromadorida, Enoplida and Araeolaimida. All of these species are recorded from China for the first time. The genera Achromadora, Ironus, Triplina, Cylindrolaimus and Paraplectonema are are also first reported in the country.       

Chromadorida (Nematoda) from Guadeloupe and Polynesia with evidence of intersexuality

Spirobolbolaimus boucherorum sp.n. (Microlaimidac) and Sabatieria maboyae sp.n. (Comesomatidae) arc described, and Dorylaimopsis pellucidum (Cobb, 1920) is discussed. Intersex specimens have been found in all three species. Spirobolbolaimus boucherorum sp.n. is characterized by its multispiral amphidcal fovea, number and localization of the cervical setae arranged in six rows posterior to the amphids, and large banana-shaped sperm. Sabatieria maboyae sp.n., a member of the S. pulchra group, possesses long posteriorly located cervical setae and long spicules.     

Nicascolaimus punctatus gen. et sp. n. (Nematoda, Axonolaimoidea), with notes on sperm dimorphism in free-living marine nematodes

Nicascolaimus punctatus gen. et sp.n. (Axonolaimidae) from an Australian beach links the families Axonolaimidae and Comesomatidae, mainly by the combination of a long conical stoma, loop-shaped amphids and a punctate cuticle with ring pores. The anterior and posterior testes and the respective spermatozoa are very different in structure. The occurrence of sperm dimorphism in aquatic nematodes is reviewed, and new observations on Axonolaimus helgolandicus Lorenzen, 1972 and Microlaimus aff. paraborealis Allgén, 1940 are communicated. Particular reference is made to the peculiar spermatogenesis in Rhabdodemania species (Enoplida), resulting in three different structural types filling the vesicula seminalis.     

Structure of the Cuticle of Metadasynemoides cristatus (Chromadorida: Ceramonematidae)

Structure of the cuticle of Metadasynemoides cristatus (Chromadorida: Ceramonematidae) is examined by light, scanning, and transmission electron microscopy. The nematode has more than 600 annuli, and each annulus has eight cuticular plates. Eight longitudinal ridges, beginning on the cephalic capsule, extend the whole length of the body. Where a ridge traverses an annulus, it forms a complicated articulating structure of overlapping vanes. Within the electron-dense cortical layer, from which the cuticular plates are formed, there are spaces crossed by fine fibrillae, forming what have been termed "vacuoles" by light microscopists. There is an epicuticle and a continuous lucent basal layer. There appears to be no median layer. The cuticle lining of the esophagus and that forming the circum-oral ridge is of much simpler construction.     

The nematode fauna in the sulphide–rich brine seep and adjacent bottoms of the East Flower Garden, NW Gulf of Mexico. II. Monhysterida

Eight nematode species of the order Monhysterida are described from the East Flower Garden at 72 m depth in the north–western Gulf of Mexico. The material is from sandy and rocky bottom samples influenced or beyond the influence o f a sulphide–rich brine seep. Seven species are new to science: Monhystera anoxybiotica sp.n., Gonionchus intermedius sp.n., Theristus (Theristus) coplatus sp.n., Theristus (Theristus) rezaki sp.n., Xyala oxybiotica spa., Desmolaimoides thiobioticus gen. et sp.n. and Linhomoeus gittingsi sp.n. Specimens of a Linhomoeus species are also described. The species is probably new to science, but the available material only includes females and juveniles.     

Freshwater nematodes of the Galápagos

Freshwater nematodes of the Galápagos archipelago were studied from four samples collected in 1988. Eighteen species, two of which are new to science, belonging to five orders, Enoplida, Dorylaimida, Mononchida, Monhysterida and Chromadorida, are described. Alaimus wittmeri n.sp. is characterised by having a smooth cuticle, a more posteriorly enlarged pharynx, a posteriorly situated amphidial fusus, obscure but anteriorly situated excretory pore, a mono-opisthodelphic ovary, and by the absence of sexual dimorphism in the lip region, the absence of pre-vulval uterine sac, the presence of males that have few (4–7) and weak ventromedian supplements and absence of mucro on tail tip. Monhystera floreanae n. sp. is distinguished by its females having a small body (L = 492–634 µm) with a narrow lip region, narrow posteriorly located amphidial openings, a small value for the c'-ratio (c' = 6.0–7.5), weak vaginal sphincter, by the absence of post-vaginal gland cells, absence of males and absence of crystalloid bodies. The difficulty in the use of crystalloid bodies as diagnostic character in the genus Monhystera is discussed. Two forms, a big form and a small form, which are similar except in measurements are reported for Achromadora micoletzkyi. SEM photos of ruptured cuticle of A. micoletzkyi and A. semiarmata show unique intra-cuticular structures. Comparison of these structures in the two species is made. Papilliform instead of setiform outer labial sensilla are also observed in A. micoletzkyi. The presence of the male and fine crystalloid bodies in Achromadora semiarmata, dorsal body pore in Prismatolaimus dolichurus and Prismatolaimus kenyensis, forty longitudinal cuticular ridges around the mid-body of Stomachoglossa pachyderma, crystalloid bodies in Ironus dentifurcatus are reported here for the first time. SEM photos of twelve species: Monhystera floreanae n. sp., Monhystera somereni, Alaimus wittmeri n. sp., Monhystrella hastata, Paramphidelus dolichurus, Eutobrilus annetteae, Ironus dentifurcatus, Chronogaster cameroonensis, Rhabdolaimus terrestris, Stomachoglossa pachyderma, Achromadora micoletzkyi and Achromadora semiarmata, are also presented.The richest nematode fauna was found in El Junco (San Cristobal), the only permanent freshwater lake on the archipelago. The nine species recorded from the lake are probably only a fraction of the total nematode fauna. The very recent man made reservoir La Toma has a relatively high diversity, due to its vicinity to El Junco. It is argued that the freshwater nematodes from San Cristobal probably arrived there through passive transport by birds.The freshwater bodies encountered on Floreana are very different from those on San Cristobal and so is their nematode fauna. Part of the species found on these islands may have been transported by land birds, others may have invaded the freshwater from terrestrial habitats.Apart from the two new species, the other ones have a wide to very wide distribution (cosmopolitan, southern hemisphere, ...), so that endemism of freshwater nematodes is very low, if it exists at all. This is due to easy dispersal capacities of nematodes on the one hand and the recent colonization (not more than 10 000, max. 40 000 years) on the other hand.     

The Nematode Fauna in the Sulphide-Rich Brine Seep and Adjacent Bottoms of the East Flower Garden, NW Gulf of Mexico. I Chromadorida

Sixteen nematode species of the order Chromadorida are described from the East Flower Garden at 72 m depth in the north-western Gulf of Mexico. The material is from sandy bottom samples influenced or beyond the influence of a sulphide-rich brine seep. Fifteen species are new to science: Acantholaimus quadridentatus sp.n., Prochromadorella papillata sp.n., Austranema mexicanum sp.n., Rhips anoxybiotica sp.n., Filitonchoides thiobioticus gen. et sp.n., Paracyatholaimus spinulaosus sp.n., Marylynnia punctata sp.n., Marylynnia johanseni sp.n., Acanthopharyngoides bidentatus sp.n., Desmodora (Croconema)punctata sp.n., Desmodora (Desmodora) curvispiculum sp.n., Desmodora (Pseudochromadora) bulbosa sp.n., Chromaspirinia longisetosa sp.n., Prochaetosoma brighti sp.n. and Ixonema powelli sp.n. A specimen of Bathyepsilonema is also described and is probably new to science, but the available material only includes a female.     

The influence of ionic composition on the distribution of nematode species in springs of the province of Granada (Spain)

The ionic composition of 38 mineral springs in the province of Granada (Spain), and the distribution of 45 species of nematodes belonging to orders Monhysterida, Araeolaimida, Chromadorida and Enoplida were examined. Water chemistry is used to make two diagrams representing anionic and cationic composition. Diagrams for anionic composition (given the greater variance seen in the springs considered) are used to illustrate the distribution of individual species. The results obtained from species distribution and the correlation between species made it possible to group species which could be associated with springs where each of the anions considered predominated. A greater number of species groups was found to inhabit springs in which chloride concentrations was less than 50% of the total concentration of anions.     

Structure of the Cuticle of Ceramonema carinatum (Chromadorida: Ceramonenatidae)

The cuticle of Ceramonema carinatum (Chromadorida: Ceramonematidae) is described and illustrated from scanning and transmission electron microscopy. Each of ca. 200 annules is composed of a single ring with eight external flat faces (plates), which are divided by longitudinal ridges formed by pairs of parallel upstanding vanes. Vanes and plates overlap those of the adjacent annules. Longitudinal ridges extend from the cephalic capsule to the tail spike. On the cephalic capsule a simple ridge extends each of the eight ridges to a position just anterior to the amphid. Cuticular plates are formed from the electron-dense cortical layer and contain lacunae filled with fine fibrils. The vanes are denser, with laminations on a central core. In the annular grooves between the plates there is an electron-lucent layer, which it is suggested, by comparison with other nematodes, is the basal layer. An epicuticle overlies the cortical plates, the vanes, and the interannular lucent layer. Cuficular structure is compared with that of other Ceramonematidae and related nematodes.     

Relative position of the cheirogaleidae in strepsirhine phylogeny: A comparison of morphological and molecular methods and results

An examination of previous morphological and molecular studies of strepsirhine systematics suggests a conflict between the two types of data. Cladistic analyses of morphological data have indicated that the Malagasy primate family Cheirogaleidae is the sister taxon of the Afro-Asian lorisiforms and that together, cheirogaleids and lorisiforms comprise a monophyletic clade that excludes the Malagasy lemuriforms. Molecular studies, on the other hand, have consistently found that cheirogaleids and lemuriforms together are monophyletic to the exclusion of lorisiforms. Both types of studies, however, have suffered from methodological weaknesses: the morphological studies looked at too few characters and the molecular studies looked at too few taxa. This study examines a large and diverse morphological data set as well as molecular data from a comprehensive sample of strepsirhine taxa. The data sets are considered independently and jointly. When they are analyzed independently, the morphological data give weak support, and the molecular data strong support, to the hypothesis of Malagasy primate monophyly. When the two data sets are combined in a single analysis, the results are decisive. The “total evidence” approach yields compelling support to the hypothesis that cheirogaleids and remaining Malagasy lemuriforms comprise a monophyletic assemblage that excludes lorisiforms. © 1994 Wiley-Liss, Inc.     

Integration of morphological data sets for phylogenetic analysis of Amniota: the importance of integumentary characters and increased taxonomic sampling

Several mutually exclusive hypotheses have been advanced to explain the phylogenetic position of turtles among amniotes. Traditional morphology-based analyses place turtles among extinct anapsids (reptiles with a solid skull roof), whereas more recent studies of both morphological and molecular data support an origin of turtles from within Diapsida (reptiles with a doubly fenestrated skull roof). Evaluation of these conflicting hypotheses has been hampered by nonoverlapping taxonomic samples and the exclusion of significant taxa from published analyses. Furthermore, although data from soft tissues and anatomical systems such as the integument may be particularly relevant to this problem, they are often excluded from large-scale analyses of morphological systematics. Here, conflicting hypotheses of turtle relationships are tested by (1) combining published data into a supermatrix of morphological characters to address issues of character conflict and missing data; (2) increasing taxonomic sampling by more than doubling the number of operational taxonomic units to test internal relationships within suprageneric ingroup taxa; and (3) increasing character sampling by approximately 25% by adding new data on the osteology and histology of the integument, an anatomical system that has been historically underrepresented in morphological systematics. The morphological data set assembled here represents the largest yet compiled for Amniota. Reevaluation of character data from prior studies of amniote phylogeny favors the hypothesis that turtles indeed have diapsid affinities. Addition of new ingroup taxa alone leads to a decrease in overall phylogenetic resolution, indicating that existing characters used for amniote phylogeny are insufficient to explain the evolution of more highly nested taxa. Incorporation of new data from the soft and osseous components of the integument, however, helps resolve relationships among both basal and highly nested amniote taxa. Analysis of a data set compiled from published sources and data original to this study supports monophyly of Amniota, Synapsida, Reptilia, Parareptilia, Eureptilia, Eosuchia, Diapsida, Neodiapsida, Sauria, Lepidosauria, and Archosauriformes, as well as several more highly nested divisions within the latter two clades. Turtles are here resolved as the sister taxon to a monophyletic Lepidosauria (squamates + Sphenodon), a novel phylogenetic position that nevertheless is consistent with recent molecular and morphological studies that have hypothesized diapsid affinities for this clade.     

ARTHROPOD PHYLOGENY: A COMBINED APPROACH

Abstract— Ribosomal and ubiquitin protein coding sequence data are generated from 20 arthropods and five close relatives. These molecular data are combined with morphological characters derived from the literature to approach arthropod phylogenetics from the perspective of total evidence. Trilobita were included in the analysis through morphological comparison alone. The overall data strongly support arthropod monophyly. Recent molecular analyses which have yield different results are shown to have been based on few characters, few taxa or both. The most parsimonious explanation of the data is (Annelida + (Onychophora + (Trilobita + Chelicerata) + (Crustacea + (Myriapoda + Hexapoda))))). The data are largely concordant both internally among data sets and externally with previous cladistic anatomical analyses.     

Morphological heterogeneity of Bordetella pertussis populations and clones (based on electron microscopy data)

Populations belonging to different serovars of B. pertussis museum strains and antibiotic-resistant clones obtained from them have been studied by electron microscopy. As a result, morphological heterogeneity and differences in the ultrastructure of the cells with respect to the cell-wall structure, the character of the cytoplasm, the size of the cells, cytoplasmic inclusions and intracellular links have been demonstrated and, proceeding from these data, two main morphological variants of the cells have been defined. The cells of the morphological variant characterized by the pliciform surface of the outer membrane and the pronounced periplasmic space prevail among the populations of the museum strains. The possibility of the isolation of antibiotic-resistant clones, differing in their morphological structure and functional properties from the initial population, has been shown. The morphological diversity of B. pertussis population is the necessary condition for the existence and development of microbial populations.     

Nematodes from the Strait of Magellan and the Beagle Channel (Chile): Description of four new species of the Comesomatidae

Four nematode species of the Comesomatidae from the Strait of Magellan and the Beagle Channel, Chile, are described as new to science. Comesoma hermani n. sp. can be separated from similar species, Comesoma bermudense Jensen & Gerlach, 1977, Comesoma minimum Chitwood, 1937 and Comesoma chilense Jensen & Gerlach, 1977 by the difference of body length, cephalic setae length, the ratio of the subcephalic setae to cephalic setae length and the ratio of spicule to anal body diameter. Dorylaimopsis magellanense n. sp. is identified by the lateral differentiation of 3–4 longitudinal rows of enlarged dots, the curved spicules are prominently jointed and with a ventral protrusion. Hopperia beaglense n. sp. could be easily recognised by both the rounded tail tip and anterior head end which differs from all the species of this genus except H. dorylaimopsoides (Allgén, 1959), which has, however, a smaller de Man ratio 'a' and reflexed ovaries. Hopperia arntzi n. sp. has a shorter body length which differs from the closest species, Hopperia americana Ward, 1984 and Hopperia muscatensis Warwick, 1973. Furthermore, the de Man ratio 'a' is different between our specimens and the other two species. An identification key to all known species of the genus Hopperia is provided.