A new genus for Diplectanum setosum Nagibina, 1976 (Monogenea: Dipletanidae), a parasite of Psammoperca waigiensis (Cuvier) (Perciformes: Latidae) from Okinawa-jima Island,Japan

Systematic Parasitology - The diplectanid monogenean Diplectanum setosum Nagibina, 1976 is redescribed based on newly collected specimens from Psammoperca waigiensis (Cuvier) (Perciformes: Latidae)...     

Historical biogeography of amphibian parasites, genus Polystoma (Monogenea: Polystomatidae)

Aim  The present-day geographical distribution of parasites with a direct biological life cycle is guided mostly by the past dispersal and vicariance events that have affected their hosts. The Amphibia– Polystoma association (which satisfies these criteria) also exhibits original traits, such as host specificity and world-wide distribution. This biological model was thus chosen to investigate the common historical biogeography of its widespread representatives.
Location  North and South America, Eurasia and Africa.
Methods  We investigated the phylogeny of 12 species of neobatrachian parasites sampled from North and South America, Eurasia and Africa. Hosts belonged mostly to hyloids and ranoids of families Bufonidae, Hylidae, Leptodactylidae, Ranidae and Hyperoliidae. Phylogenetic reconstructions were inferred from maximum likelihood and maximum parsimony analyses from complete ITS1 sequences.
Results  The group of American species appeared paraphyletic with one species at the base of a Eurafrican clade, within which two lineages were seen: one composed of only Eurasian species, and the other of European and African species, with the two European species basal to an African clade.
Main conclusions  The route of Polystoma evolution is deduced from the phylogenetic tree and discussed in the light of host evolution. We conclude that Polystoma originated in South America on hyloids, after the separation of South America from Africa. The genus must have colonized North America in Palaeocene times and Eurasia by the mid-Cainozoic, taking advantage of the dispersal of either ancestral bufonids or hylids. Africa, however, appears to have been colonized more recently, during the Messinian period.     

Diplectanum yamagutii sp.n.(Monogenea, Monopisthocotylea, Diplectanidae), Parasite de Kyphosus cinerascens (Forsskål) à Hawaii

Diplectanum yamagutii sp.n., a gill parasite of Kyphosus cinerascens (Forsskål, 1775) off Hawaii is described from amongst the type-material deposited by Professor S. Yamaguti in the National Parasite Collection of the United States National Museum of Natural History at Beltsville (Maryland, USA). Diplectanum yamagutii sp.n., D. diplobulbus Yamaguti, 1968, D. nenue Yamaguti, 1968, D. spiculare Yamaguti, 1968 and D. kyphosi (Yamaguti, 1968) comb.n. are sympatric parasites of Kyphosus cinerascens off Hawaii. These five species are distinguished by the shape and size of the armature of both the cirrus and the haptoral sclerotised pieces.     

Diplectanidae (Monogenea) parasites of fish of the Kerkennah Islands (Tunisia)

Eleven Diplectanidae (Monogenea) gill parasites from various Sparidae and Serranidae of the Kerkennah Islands are noted. Three new species: Lamellodiscus hilii, L. bidens, L. impervius, parasites of Puntazzo puntazzo (Sparidae) are described.     

A phylogenetic analysis and revised classification of the Monocotylidae Taschenberg, 1879 (Monogenea)

The Monocotylidae Taschenberg, 1879 is revised based on a cladistic analysis of relationships between the constituent species and genera. The monophyly of the family is supported by three apomorphic character states: division of the haptor into one central and eight peripheral loculi; the ovary looping the right intestinal caecum; and tetrahedral eggs. The family is divided into six subfamilies: Calicotylinae Monticelli, 1903 (comprising Calicotyle Diesing, 1850, Dictyocotyle Nybelin, 1941); Dasybatotreminae Bychowsky, 1957 (comprising Anoplocotyloides Young, 1967, Dasybatotrema Price, 1938, Timofeevia n. g., Troglocephalus Young, 1967); Decacotylinae n. subfam. (comprising Decacotyle Young, 1967, Papillicotyle Young, 1967); Heterocotylinae n. subfam. (comprising Heterocotyle Scott, 1904, Neoheterocotyle Hargis, 1955, Nonacotyle Ogawa, 1991, Potamotrygonocotyle Mayes, Brooks & Thorson, 1981, Spinuris Doran, 1953); Merizocotylinae Johnston & Tiegs, 1922 (comprising Cathariotrema Johnston & Tiegs, 1922, Empruthotrema Johnston & Tiegs, 1922, Merizocotyle Cerfontaine, 1894, Squalotrema Kearn & Green, 1983, Triloculotrema Kearn, 1993); and Monocotylinae Taschenberg, 1879 (comprising Clemacotyle Young, 1967, Dendromonocotyle Hargis, 1955, Monocotyle Taschenberg, 1878). The Dendromonocotylinae Hargis, 1955 is removed from subfamilial status and the two genera previously assigned to the subfamily are reassigned to the Monocotylinae. Timofeevia is proposed for Timofeevia rajae (Timofeeva, 1983) n. comb. (formerly Dasybatotrema rajae). Mycteronastes Kearn & Beverley-Burton, 1990 and Thaumatocotyle Scott, 1904 are synonymised with Merizocotyle. Gymnocalicotyle Nybelin, 1941 is not considered a distinct taxon. Revised diagnoses and keys for subfamilies and genera of the Monocotylidae are provided.     

Diplectanum squamatum n.sp. (Monogenea:Diplectanidae) fro the gills of Cynoscion guatucupa (Sciecidae) in southwest Atlantic waters

Diplectanum squamatum n. sp. is described from the gills of the sciaenid Cynoscion guatucupa collected off Mar del Plata, Argentina. The new species is distinguished from other species of the genus by the morphology of the hamuli and the male copulatory organ, and presence of scales on the haptor and body. This is the first species of Diplectanum to be reported from southwest Atlantic waters and, with the possible exception of D. cayennense Euzet & Durette-Desset, 1974, the only species from the Atlantic coast of South America.     

Using uncorrelated discriminant analysis for tissue classification with gene expression data

The classification of tissue samples based on gene expression data is an important problem in medical diagnosis of diseases such as cancer. In gene expression data, the number of genes is usually very high (in the thousands) compared to the number of data samples (in the tens or low hundreds); that is, the data dimension is large compared to the number of data points (such data is said to be undersampled). To cope with performance and accuracy problems associated with high dimensionality, it is commonplace to apply a preprocessing step that transforms the data to a space of significantly lower dimension with limited loss of the information present in the original data. Linear discriminant analysis (LDA) is a well-known technique for dimension reduction and feature extraction, but it is not applicable for undersampled data due to singularity problems associated with the matrices in the underlying representation. This paper presents a dimension reduction and feature extraction scheme, called uncorrelated linear discriminant analysis (ULDA), for undersampled problems and illustrates its utility on gene expression data. ULDA employs the generalized singular value decomposition method to handle undersampled data and the features that it produces in the transformed space are uncorrelated, which makes it attractive for gene expression data. The properties of ULDA are established rigorously and extensive experimental results on gene expression data are presented to illustrate its effectiveness in classifying tissue samples. These results provide a comparative study of various state-of-the-art classification methods on well-known gene expression data sets     

Helminth parasites of the western painted turtle, Chrysemys picta belli (Gray), including Neopolystoma elizabethae n. sp. (Monogenea: Polystomatidae), a parasite of the conjunctival sac

Neopolystoma elizabethae n. sp. is described from the conjunctival sac of the western painted turtle Chrysemys picta belli (Gray), from the Upper Peninsula of Michigan. This is the first species found in this location from chelonians in North America. The new species differs from all other species of Neopolystoma in possessing a circle of 8 genital spines that are recurved and possess a crescent-shaped base. Eight additional species of helminths were found in the 5 turtles examined in this study. All are common parasites of North American freshwater turtles. An additional species of Monogenea (Polystomoidespauli) was found in the oral cavity. Four species of Digenea (Eustomos chelydrae, Allassostomoides chelydrae, Spirorchis kirki, and Spirorchis parvus) and 3 species of Nematoda (Spiroxys contorta, Serpinema trispinosus, and Amphibiocapillaria serpentina) were also found. The following are reported from Michigan for the first time: P. pauli, S. kirki, and A. serpentina.     

Morphometric stepwise discriminant analysis of the five genetically determined European taxa of the genus Mus

Univariate and multivariate analyses have been performed on skull and mandible measurements for the five biochemically defined groups of the genus Mus in Europe. Four of these taxa occur in Bulgaria; other samples came from France and Israel. This extensive biometrical analysis has allowed us to establish diagnostic keys for these taxa.     

Morphometric stepwise discriminant analysis of three genetically identified species within Pseudoterranova decipiens (Krabbe, 1878) (Nematoda: Ascaridida)

Univariate and multivariate statistical analyses have been performed on 19 morphometric variables of adult male specimens belonging to three genetically identified species within Pseudoterranova decipiens (Nematoda: Ascaridida) parasitic in the digestive tract of seals. Two morphometric keys are proposed for the identification of the three species. One key, which uses two variables, determines a frequency of error of 3.8% (3/79). The second key, which uses two canonical discriminant functions based on seven variables previously selected with a stepwise procedure, gives 100% (76/76) accurate classification.     

Monitoring plant community change: an application of quadrat classification + discriminant analysis

A procedure for monitoring plant community change was described using data from 189 quadrats (each 0.09 m² in area) from or near 11 Carex exserta meadow sites in the high Sierra Nevada, California, USA. Initially the quadrats were agglomerated into five clusters by the flexible clustering strategy (beta=–0.25) with the standard absolute distance resemblance function. Data for each quadrat were cover percentages for C. exserta, other plants, litter, soil, gravel, and rock. The five clusters appeared to define a cover gradient, from quadrats with mostly gravel and rock to those with mostly C. exserta, and were accordingly designated pioneer, low seral, mid-seral, high seral, and climax.Classification functions (from discriminant analysis) are used with values of the variables to classify individual quadrats on sites used to monitor change. A site is characterized at repeated observations by the proportions of quadrats in each class. Within-class (low seral vs. low seral) rather than between-class (pioneer vs. low seral) tests are made for presence of change. Confidence intervals for differences in proportions of quadrats or individual quadrat probabilities of class membership are computed. If the confidence intervals do not cover zero, values for time one versus time two differ significantly.     

Rhabdosargus haffara (Forsskål, 1775) and Sphyraena flavicauda Rüppell, 1833—new Red Sea immigrants in the Mediterranean

Two Red Sea species, the sparid Rhabdosargus haffara and the sphyraenid Sphyraena flavicauda , previously unrecorded in the Mediterranean, have been recently found in the vicinity of Tel-Aviv, coast of Israel.     

A view of early vertebrate evolution inferred from the phylogeny of polystome parasites (Monogenea: Polystomatidae)

The Polystomatidae is the only family within the Monogenea to parasitize sarcopterygians such as the Australian lungfish Neoceratodus poisteri and freshwater tetrapods (lissamphibians and chelonians). We present a phylogeny based on partial 18S rDNA sequences of 26 species of Polystomatidae and three taxon from the infrasubclass Oligonchoinea (= Polyopisthocotylea) obtained from the gills of teleost fishes. The basal position of the polystome from lungfish within the Polystomatidae suggests that the family arose during the evolutionary transition between actinopterygians and sarcopterygians, ca. 425 million years (Myr) ago. The monophyly of the polystomatid lineages from chelonian and lissamphibian hosts, in addition to estimates of the divergence times, indicate that polystomatids from turtles radiated ca. 191 Myr ago, following a switch from an aquatic amniote presumed to be extinct to turtles, which diversified in the Upper Triassic. Within polystomatids from lissamphibians, we observe a polytomy of four lineages, namely caudatan, neobatrachian, pelobatid and pipid polystomatid lineages, which occurred ca. 246 Myr ago according to molecular divergence-time estimates. This suggests that the first polystomatids of amphibians originated during the evolution and diversification of lissamphibian orders and suborders ca. 250 Myr ago. Finally, we report a vicariance event between two major groups of neobatrachian polystomes, which is probably linked to the separation of South America from Africa ca. 100 Myr ago.     

Graph constrained discriminant analysis: a new method for the integration of a graph into a classification process

Integrating gene regulatory networks (GRNs) into the classification process of DNA microarrays is an important issue in bioinformatics, both because this information has a true biological interest and because it helps in the interpretation of the final classifier. We present a method called graph-constrained discriminant analysis (gCDA), which aims to integrate the information contained in one or several GRNs into a classification procedure. We show that when the integrated graph includes erroneous information, gCDA's performance is only slightly worse, thus showing robustness to misspecifications in the given GRNs. The gCDA framework also allows the classification process to take into account as many a priori graphs as there are classes in the dataset. The gCDA procedure was applied to simulated data and to three publicly available microarray datasets. gCDA shows very interesting performance when compared to state-of-the-art classification methods. The software package gcda, along with the real datasets that were used in this study, are available online: http://biodev.cea.fr/gcda/.     

Morphometric and molecular analysis of the Encarsia inaron species-group (Hymenoptera: Aphelinidae), parasitoids of whiteflies (Hemiptera: Aleyrodidae)

Several series of host-reared specimens of an Encarsia species, initially thought to be the cosmopolitan Encarsia inaron (Walker), were collected in the Azores Islands (Portugal). Subsequent morphometric analysis supported the presence of two species: E. inaron and a new species, described herein as Encarsia estrellae Manzari & Polaszek sp. n. Encarsia estrellae was reared from Aleyrodes singularis Danzig, A. ?singularis, and Bemisia sp. afer-group on several host plants. In addition, the D2 region of the 28S rDNA gene was sequenced in eight individuals belonging to these species, as well as single representatives of two closely related and one distantly related species. Phylogenetic analysis of these DNA sequences, together with 23 additional Encarsia sequences retrieved from the European Molecular Biology Laboratory (EMBL) and GenBank databases, further supported the specific status of E. estrellae, and the placement of E. dichroa (Mercet) in the E. inaron species-group. Additionally, E. inaron is redescribed and some taxonomic problems in the E. inaron species-group are discussed.     

Morphometric analysis of four species of Eubothrium (Cestoda: Pseudophyllidea) parasites of salmonid fish: an interspecific and intraspecific comparison

Four species of the genus Eubothrium (E. crassum, E. fragile, E. rugosum and E. salvelini) were subjected to morphometric comparison. Discriminant analysis was conducted utilising 17 characters measured on the scolex and strobila of 101 specimens. Univariate statistics were first used to detect features that were useful for separating individual Eubothrium species and two different host populations of E. salvelini. Subsequent multivariate discriminant analysis, combining all the measured variables, made it possible to separate all four species. A comparison of the four taxa revealed that (1) E. fragile is the most distinct species, possessing a much smaller scolex than the other congeners, and its similarity with the other marine species E. crassum is not proven; (2) the two freshwater taxa, E. rugosum and E. salvelini are the most similar; (3) the characters most suitable for species differentiation are the length of the scolex, the width of the apical disc, the width of the neck and its area, the width of eggs and the number of testes; (4) the width of the apical disc was confirmed to be the most stable character at the intraspecific level (within E. salvelini host populations) and is therefore considered to be a trait of the highest discriminative power in the subset of four Eubothrium species.     

Comparison of discriminant function and classification tree analyses for age classification of marmots

We evaluated the predictive power of two classification techniques, one parametric – discriminant function analysis (DFA) and the other non-parametric – classification and regression tree analysis (CART), in order to provide a non-subjective quantitative method of determining age class in Vancouver Island marmots ( Marmota vancouverensis ) and hoary marmots ( Marmota caligata ). For both techniques we used morphological measurements of known-age male and female marmots from two independent population studies to build and test predictive models of age class. Both techniques had high predictive power (69–86%) for both sexes and both species. Overall, the two methods performed identically with 81% correct classification. DFA was marginally better at discriminating among older more challenging age classes compared to CART. However, in our test samples, cases with missing values in any of the discriminant variables were deleted and hence unclassified by DFA, whereas CART used values from closely correlated variables to substitute for the missing values. Therefore, overall, CART performed better (CART 81% vs DFA 76%) because of its ability to classify incomplete cases. Correct classification rates were approximately 10% higher for hoary marmots than for Vancouver Island marmots, a result that could be attributed to different sets of morphological measurements. Zygomatic arch breadth measured in hoary marmots was the most important predictor of age class in both sexes using both classification techniques. We recommend that CART analysis be performed on data-sets with incomplete records and used as a variable screening tool prior to DFA on more complete data-sets.