Phylogenetic relationships of catostomid fishes (Actinopterygii: Cypriniformes) based on mitochondrial ND4/ND5 gene sequences

Family Catostomidae is a diverse group of benthic freshwater fishes that are distributed across North America and in parts of East Asia. In this study, the phylogenetic relationships of Catostomidae is examined using 3436 nucleotides of mitochondrial ND4 and ND5 protein coding genes and intervening tRNAs. All 13 genera and 60 species of catostomids were sampled to represent diversity of the family. Catostomidae and its four subfamilies were found to be monophyletic; however, relationships of the subfamilies are not strongly supported with bootstrapping. The analysis provides strong support for recognizing four tribes in subfamily Catostominae.     

Contribution to the taxonomy of the family Campulidae Odhner, 1926 (Digenea) by means of a morphometric multivariate analysis

Digeneans of the family Campulidae occur exclusively in marine mammals, particularly in cetaceans. Their taxonomy is confused, being based on adult morphology only. We used a multivariate discriminant analysis of morphometric data to provide new evidence on the taxonomy of the Campulidae. Measurements of 217 specimens from 21 species of all seven genera of the family were taken. The percentage of specimens correctly assigned into their own species was 96.3%. The first three discriminant functions accounted for most of the variation between the species, which were grouped together in suprageneric groups along the first and the second function. The ordination pattern observed conforms partly with the established taxonomy of the Campulidae. Variation along the first discriminant function can be interpreted as a gradient of the vitelline extension and the maximum width to length ratio. This function separates three groups of species, corresponding to the Hunterotrematinae, Orthosplanchninae and Campulinae-Lecithodesminae. The last two subfamilies are separated along the second axis, the Lecithodesminae having longer bodies and suckers than the Campulinae. This study also provides some evidence at the generic and specific level.     

Biometric variability of Hadwenius tursionis (Marchi, 1873) (Digenea,Campulidae) from the intestine of the bottlenose dolphin Tursiops truncatus (Montagu, 1821)

The species discrimination in the family Campulidae is largely based on morphometric characters (absolute measurements and ratios). To assess the variability of this characters we have studied the campulid species Hadwenius tursionis from four Mediterranean bottlenose dolphins Tursiops truncatus from the Western Mediterranean. In H. tursionis most absolute measurements differed significantly across the infrapopulations, showing high coefficients of variation. Only egg dimensions appeared to be fairly conservative. Body ratios were less variable than absolute measurements, but growth patterns did vary significantly between the infrapopulations studied. None of the ratios previously used in relation to other species of the family Campulidae indicated either isometric or allometric growth in this case. Only the ratios concerning the size of the gonads and the shape of the gonads and suckers showed isometry. It is concluded that absolute measurements and ratios should be used with caution in relation to the separation of species of the family Campulidae unless their intrinsic variability can be established beforehand.     

Mitochondrial gene order change in Schistosoma (Platyhelminthes: Digenea: Schistosomatidae)

In the flatworm genus Schistosoma, species of which include parasites of biomedical and veterinary importance, mitochondrial gene order is radically different in some species. A PCR-based survey of 19 schistosomatid spp. established which of 14 Schistosoma spp. have the ancestral (plesiomorphic) or derived gene order condition. A phylogeny for Schistosoma was estimated and used to infer the origin of the gene order change which is present in all members of a clade containing Schistosoma incognitum and members of the traditionally recognised Schistosoma indicum, Schistosoma mansoni and Schistosoma haematobium spp. groups. Schistosoma turkestanicum, with the plesiomorphic gene order state, is sister to this clade. Common interval analysis suggests change in gene order, from ancestral to derived, consisted of two sequential transposition events: (a) nad1_nad3 to nad3_nad1 and (b) [atp6,nad2]_[nad3,nad1,cox1,rrnL,rrnS,cox2,nad6] to [nad3,nad1,cox1,rrnL,rrnS,cox2,nad6]_[atp6,nad2], where gene order of fragments within square brackets remain unchanged. Gene order change is rare in parasitic flatworms and is a robust synapomorphy for schistosome spp. that exhibit it. The schistosomatid phylogeny casts some doubt on the origin of Schistosoma (Asian or African), highlights the propensity for species to host switch amongst mammalian (definitive) hosts, and indicates the likely importance of snail (intermediate) hosts in determining and defining patterns of schistosome radiation and continental invasion. Mitogenomic sampling of Schistosoma dattai and Schistosoma harinasutai to determine gene order, and within key species, especially S. turkestanicum and S. incognitum, to determine ancestral ranges, may help discover the geographic origins of gene order change in the genus. Samples of S. incognitum from India and Thailand suggest this taxon may include cryptic species.     

A complete species-level phylogeny of the Hylobatidae based on mitochondrial ND3-ND4 gene sequences

The Hylobatidae (gibbons) are among the most endangered primates and their evolutionary history and systematics remain largely unresolved. We have investigated the species-level phylogenetic relationships among hylobatids using 1257 bases representing all species and an expanded data set of up to 2243 bases for select species from the mitochondrial ND3-ND4 region. Sequences were obtained from 34 individuals originating from all 12 recognized extant gibbon species. These data strongly support each of the four previously recognized clades or genera of gibbons, Nomascus, Bunopithecus, Symphalangus, and Hylobates, as monophyletic groups. Among these clades, there is some support for either Bunopithecus or Nomascus as the most basal, while in all analyses Hylobates appears to be the most recently derived. Within Nomascus, Nomascus sp. cf. nasutus is the most basal, followed by N. concolor, and then a clade of N. leucogenys and N. gabriellae. Within Hylobates, H. pileatus is the most basal, while H. moloch and H. klossii clearly, and H. agilis and H. muelleri likely form two more derived monophyletic clades. The segregation of H. klossii from other Hylobates species is not supported by this study. The present data are (1) consistent with the division of Hylobatidae into four distinct clades, (2) provide the first genetic evidence for all the species relationships within Nomascus, and (3) call for a revision of the current relationships among the species within Hylobates. We propose a phylogenetic tree as a working hypothesis against which intergeneric and interspecific relationships can be tested with additional genetic, morphological, and behavioral data.     

Molecular differentiation and phylogeny of entomopathogenic nematodes (rhabditida: heterorhabditidae) based on ND4 gene sequences of Mitochondrial DNA.

We determined partial ND4 gene sequences of mitochondrial DNA from 15 heterorhabditid nematode isolates, representing 5 species collected from different regions of the world, by using polymerase chain reaction (PCR) and direct-sequencing of PCR products. Aligned nucleotide as well as amino acid sequences were used to differentiate nematode species by comparing sequence divergence and to infer phylogeny of the nematodes by using maximum parsimony and likelihood methods. Robustness of our phylogenetic trees was checked by bootstrap tests. The 15 nematode isolates can be divided into 7 haplotypes based on DNA sequences. On a larger scale, the sequence divergence revealed 4 distinct groups corresponding to 4 described species. No sequence divergence was detected from 5 isolates of Heterorhabditis bacteriophora or between Heterorhabditis marelatus to Heterorhabditis hepialius. Our sequence data yielded phylogenetic trees with identical topologies when different tree-building methods were used. Most relationships were also confirmed by using amino acid sequences in maximum parsimony analysis. Our molecular phylogeny of Heterorhabditis species support an existing taxonomy that is based largely on morphology and the sequence divergence of the ND4 gene permits species identification.     

Evolutionary relationships among the Schistosomatidae (Platyhelminthes:Digenea) and an Asian origin for Schistosoma

Schistosome blood flukes parasitize birds, mammals, and crocodilians and are responsible for causing one of the great neglected diseases of humanity, schistosomiasis. A phylogenetic study of 10 schistosome genera using approximately 1,100 bases of the large subunit of the nuclear ribosomal gene complex revealed 2 major clades. One clade is entirely mammalian and includes the genera Schistosoma and Orientobilharzia. A close examination of relationships in this group suggests that the medically important Schistosoma arose in Asia and not in Africa as generally presumed and is paraphyletic. The second clade is primarily avian, consisting of 6 genera of exclusively avian parasites and 2 genera of North American mammal flukes. These results indicate a secondary host capture of mammals on the North American continent. This study provides little evidence concerning the ancestral molluscan or vertebrate schistosome host but does demonstrate that host switching has been an important feature of schistosome evolution. Evidence also indicates that the reduced sexual dimorphism characteristic of some avian schistosomes is derived evolutionarily.     

A new species of Crepidostomum (Allocreadiidae: Digenea) from northeastern Finland,with comments on its possible origin

Crepidostomum wikgreni n. sp. is described from the gall-bladder and intestine of the whitefish Coregonus acronius in Lake Yli-Kitka in NE Finland. It is morphologically similar to Crepidostomum farionis, with which it occurs sympatrically and sometimes concurrently; but it differs in that the eggs are much larger, i.e. 96±6.5 m mean-length, as opposed to 71±4.7 m mean-length for C. farionis in the same host and locality.It is suggested that the new species has arisen from C. farionis after deglaciation and since c. 8,400 BP, at which time the waters of the Lake Kitka System were isolated from those in the rest of Finland and flowed eastwards into the White Sea Basin. The isolation of the White Sea Basin appears to have been maintained by watersheds running north-south close to the Fenno-Soviet border and east-west through central Karelia. It is further suggested that C. farionis currently occurring in Lake Yli-Kitka is a recent re-introduction brought about by the translocation of fish-stocks.     

Sphaeridiotrema globulus and Sphaeridiotrema pseudoglobulus (Digenea): species differentiation based on mtDNA (Barcode) and partial LSU-rDNA sequences

Flukes belonging to Sphaeridiotrema are important parasites of waterfowl, and 2 morphologically similar species Sphaeridiotrema globulus and Sphaeridiotrema pseudoglobulus, have been implicated in waterfowl mortality in North America. Cytochrome oxidase I (barcode region) and partial LSU-rDNA sequences from specimens of S. globulus and S. pseudoglobulus, obtained from naturally and experimentally infected hosts from New Jersey and Quebec, respectively, confirmed that these species were distinct. Barcode sequences of the 2 species differed at 92 of 590 nucleotide positions (15.6%) and the translated sequences differed by 13 amino acid residues. Partial LSU-rDNA sequences differed at 29 of 1,208 nucleotide positions (2.4%). Additional barcode sequences from specimens collected from waterfowl in Wisconsin and Minnesota and morphometric data obtained from specimens acquired along the north shore of Lake Superior revealed the presence of S. pseudoglobulus in these areas. Although morphometric data suggested the presence of S. globulus in the Lake Superior sample, it was not found among the specimens sequenced from Wisconsin or Minnesota.     

Phylogeny and evolution of the Drosophila nasuta subgroup based on mitochondrial ND4 and ND4L gene sequences

The sequences of the mitochondrial ND4 gene (1339 bp) and the ND4L gene (290 bp) were determined for all the 14 extant taxa of the Drosophila nasuta subgroup. The average A + T content of ND4 genes is 76.5% and that of ND4L genes is 83.5%. A total of 114 variable sites were scored. The ND4 gene sequence divergence ranged from 0 to 5.4% within the subgroup. The substitution rate of the ND4 gene is about 1.25% per million years. The base substitution of the genes is strongly transition biased. Neighbor-joining and parsimony were used to construct a phylogeny based on the resultant sequence data set. According to these trees, five distinct mtDNA clades can be identified. D. niveifrons represents the most diverged lineage. D. sulfurigaster bilimbata and D. kepulauana form two independent lineages. The other two clades are the kohkoa complex and the albomicans complex. The kohkoa complex consists of D. sulfurigaster sulfurigaster, D. pulaua, D. kohkoa, and Taxon-F. The albomicans complex can be divided into two groups: D. nasuta, D. sulfurigaster neonasuta, D. sulfurigaster albostrigata, and D. albomicans from Chiangmai form one group; and D. pallidifrons, Taxon-I, Taxon-J, and D. albomicans from China form the other group. High genetic differentiation was found among D. albomicans populations. Based on our phylogenetic results, we hypothesize that D. niveifrons diverged first from the D. nasuta subgroup in Papua New Guinea about 3.5 Mya. The ancestral population spread to the north and when it reached Borneo, it diversified sequentially into the kohkoa complex, D. s. bilimbata, and D. kepulauana. About 1 Mya, another radiation occurred when the ancestral populations reached the Indo-China Peninsula, forming the albomicans complex. Discrepancy between morphological groupings and phylogenetic results suggests that the male morphological traits may not be orthologous.     

GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions

Background  

The ever-expanding population of gene expression profiles (EPs) from specified cells and tissues under a variety of experimental conditions is an important but difficult resource for investigators to utilize effectively. Software tools have been recently developed to use the distribution of gene ontology (GO) terms associated with the genes in an EP to identify specific biological functions or processes that are over- or under-represented in that EP relative to other EPs. Additionally, it is possible to use the distribution of GO terms inherent to each EP to relate that EP as a whole to other EPs. Because GO term annotation is organized in a tree-like cascade of variable granularity, this approach allows the user to relate (e.g., by hierarchical clustering) EPs of varying length and from different platforms (e.g., GeneChip, SAGE, EST library).     

Effects of Plagiorchis elegans (Digenea: Plagiorchiidae) infection of Biomphalaria glabrata (Pulmonata: Planorbidae) on a challenge infection with Schistosoma mansoni (Digenea: Schistosomatidae)

Prior exposure of Biomphalaria glabrata to the eggs of an incompatible digenean, Plagiorchis elegans, rendered this snail host less suitable to a compatible species, Schistosoma mansoni. Although P. elegans failed to develop patent infections in B. glabrata, it reduced the production of S. mansoni cercariae by 88%. Concomitantly, host attributes such as reproduction, growth, and survival were compromised. The effect of P. elegans infection was most severe among snails that, in addition, had developed patent schistosome infections. Although few S. mansoni cercariae were produced, egg production by B. glabrata was only 4% of control values. Furthermore, no doubly infected snails survived for more than 3 wk after patency, whereas controls experienced no mortality during the same time period. The above effects were attributable to the establishment and persistence of P. elegans sporocysts in the tissues of the incompatible snail host. Their indirect antagonistic interaction with thelarval stages of S. mansoni may be mediated, in part, through their long-term stimulation of the host's internal defense mechanisms. These findings are discussed with a view to use P. elegans and other plagiorchiid digeneans as agents in the biological control of snails and snail-borne diseases.     

New primers for amplifying and sequencing the mitochondrial ND4/ND5 gene region of the Cypriniformes (Actinopterygii: Ostariophysi)

We provide 15 new primers for amplifying and sequencing the mitochondrial ND4/ND5 gene region of the Cypriniformes in an attempt to resolve relationships of this diverse group of freshwater fishes with extensive taxonomic sampling. Sequences from this region have the following desirable characteristics for phylogenetic analyses, some of which are lacking from the more commonly used cyt b and 12S/16S rRNA genes: they are (1) easy to align, (2) relatively long (ca. 3.4 kb), and (3) contain more phylogenetically informative variation at 1st and 2nd codon positions. Moreover, the ND4/ND5 gene region is easy to amplify and sequence when employing the protocol suggested herein.     

The Synthesium Brachycladiidae Odhner, 1905 (Digenea) association with hosts based on nuclear and mitochondrial genes

Synthesium pontoporiae, exclusive parasite of the endangered dolphin, Pontoporia blainvillei, is endemic and restricted to the South Atlantic and belongs to the Brachycladiidae family Odhner, 1905. The study of this family has been limited by the difficulty of accessing the parasites from their marine mammal hosts and as a consequence there is a paucity of genetic information available. Herein we present a genetic analysis using 18S rDNA sequences of S. pontoporiae and S. tursionis and the ND3 mtDNA sequence of S. pontoporiae. The genetic analysis of 18S rDNA sequences of brachycladiids and acanthocolpids determined two major clusters associated with their definitive hosts, marine mammals and fishes, respectively. Considering the tree topology of brachycladiids ND3 mtDNA gene, two clusters were defined, one with the Synthesium species. This work contributes with fundamental genetic information on S. pontoporiae, and suggests a Brachycladiidae genetic evolution related to their hosts.     

The origin of Dendrosenecio within the Senecioneae (Asteraceae) based on chloroplastDNA EVIDENCE

Chloroplast DNA restriction-site variation was surveyed using 15 enzymes for 37 accessions from the tribe Senecioneae (Asteraceae), plus two outgroup species, in order to determine the placement within the tribe of the giant senecios (Den-drosenecio). The survey revealed 176 phylogenetically informative mutations and 121 autapomorphic mutations. Dendro-senecio is diagnosed by a minimum of 15 mutations, which suggests that the giant senecios evolved from a relatively isolated lineage within the Senecioneae, and this conclusion is supported by earlier evidence from chromosome counts and phytochemistry. Among the taxa sampled, the closest relatives of Dendrosenecio are Cineraria deltoidea and two species of Euryops. Support was not found for suggestions in the literature that the closest relatives of Dendrosenecio are species in Solanecio or Senecio subgen. 'Crociseris.' The position of the Dendrosenecio/Cineraria/Euryops clade is weakly supported as basal to the majority of other senecionoid genera. The tussilaginoid genera sampled (Ligularia, Petasites, Roldana, and Tussilago) are monophyletic in our analysis, with the surprising inclusion of Pericallis hybrida as the sister-taxon to Roldana suffulta. The sister-group to the Dendrosenecio/Cineraria/Euryops clade includes all species of Delairea, Gynura, Kleinia, Packera, Senecio, and Solanecio sampled. Within Senecio, subgenera Senecio and ‘Crociseris’ form a monophyletic core, with subgenus ‘Kleinioidei’ being broadly paraphyletic or possibly polyphyletic.     

A new species of the genus Zalophotrema (Digenea: Campulidae), Zalophotrema atlanticum n. sp., from the liver of the striped dolphin Stenella coeruleoalba (Meyen, 1833) (Cetacea: Delphinidae) in Atlantic waters

Zalophotrema atlanticum n. sp. from the liver of a striped dolphin, Stenella coeruleoalba (Meyen, 1833), stranded in the Canary Islands is described. This new species differs from the other Zalophotrema species in body dimensions and relative size and position of the suckers and cirrus-sac. This is the first record of a species of the genus Zalophotrema in the striped dolphin, and the Atlantic Ocean constitutes a new locality record for this genus.