Molecular phylogeny of Moenkhausia (Characidae) inferred from mitochondrial and nuclear DNA evidence

Moenkhausia is one of the most speciose genera in Characidae, currently composed of 75 nominal species of small fishes distributed across South American hydrographic basins, primarily the Amazon and Guyanas. Despite the large number of described species, studies involving a substantial number of its species designed to better understand their relationships and putative monophyly are still lacking. In this study, we analysed a large number of species of Moenkhausia to test the monophyly of the genus based on the phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes. The in-group included 29 species of Moenkhausia, and the out-group was composed of representatives of Characidae and other members of Characiformes. All species of Moenkhausia belong to the same clade (Clade C); however, they appear distributed in five monophyletic groups along with other different genera, which means that Moenkhausia is polyphyletic and indicates the necessity of an extensive revision of the group. © 2013 Blackwell Verlag GmbH.

Análise filogenética das espécies de Hemigrammus Gill, 1858 (Characiformes, Characidae)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Gorgocephalus yaaji n. sp (Digenea : Gorgocephalidae) from the brassy chub Kyphosus vaigiensis (Perciformes : Kyphosidae) off Lizard Island, northern Great Barrier Reef and further records of G-kyphosi

A new species Gorgocephalus yaaji is described in the intestine of Kyphosus vaigiensis from the waters off Lizard Island, Queensland, Australia. It differs from Gorgocephalus kyphosi by its broader body shape, the extension of the vitellarium into the forebody, a relatively longer forebody, cirrus-sac and post-caecal region, and a shorter distance between the ventral sucker and the ovary. It differs from Gorgocephalus manteri in its size, its tandem testes, and the ratios of width, ventral sucker to ovary distance and ovary to testes distance to body-length. Gorgocephalus kyphosi is reported in the pyloric caeca of K. vaigiensis from waters off Moorea, French Polynesia, and Lizard Island, Queensland, Australia. Measurements and an illustration are given of the latter species.

A Novel Isoform of the Hepatic Antimicrobial Peptide, Hepcidin (Hepc-CB1), from a Deep-Sea Fish, the Spinyjaw Greeneye Chlorophthalmus bicornis (Norman, 1939): Molecular Characterisation and Phylogeny

Hepcidin is cysteine-rich short peptide of innate immune system of fishes, equipped to perform prevention and proliferation of invading pathogens like bacteria and viruses by limiting iron availability and activating intracellular cascades. Hepcidins are diverse in teleost fishes, due to the varied aquatic environments including exposure to pathogens, oxygenation and iron concentration. In the present study, we report a 87-amino acid (aa) preprohepcidin (Hepc-CB1) with a signal peptide of 24 aa, a prodomain of 39 aa and a bioactive mature peptide of 24 aa from the gill mRNA transcripts of the deep-sea fish spinyjaw greeneye, Chlorophthalmus bicornis. Molecular characterisation and phylogenetic analysis categorised the peptide to HAMP2-like group with a mature peptide of 2.53 kDa; a net positive charge (?3) and capacity to form b-hairpin-like structure configured by 8 conserved cysteines. The present work provides new insight into the mass gene duplication events and adaptive evolution of hepcidin isoforms with respect to environmental influences and positive Darwinian selection. This work reports a novel hepcidin isoform under the group HAMP2 from a nonacanthopterygian deep-sea fish, C. bicornis

Endoparasite communities of five fish species (Labridae : Cheilininae) from Lizard Island: how important is the ecology and phylogeny of the hosts?

The parasite community of animals is generally influenced by host physiology, ecology, and phylogeny. Therefore, sympatric and phylogenetically related hosts with similar ecologies should have similar parasite communities. To test this hypothesis we surveyed the endoparasites of 5 closely related cheilinine fishes (Labridae) from the Great Barrier Reef. They were Cheilinus chlorounts, C. trilobatus, C. fasciatils, Epibulus insidiator and OxYcheilinus diagrainnia. VVe examined the relationship between parasitological variables (richness, abundance and diversity) and host characteristics (bodv weight, diet and phuylogeny). The 5 fishes had 31 parasite species with 9-18 parasite species per fish species. Cestode larvae (mostly Tetraphyllidea) were the most abundant and prevalent parasites followed by nematodes and digeneans. Parasites, body size and diet of hosts differed between fish species. In general, body weight, diet and host phylogeny each explained some of the variation in richness and composition of parasites among the fishes. The 2 most closely related species, Cheilinus chlorourus and C. trilobatus, had broadly similar parasites but the Other fish species differed significantly in all variables. However, there was no all -encompassing pattern. This may, be because different lineages of parasites may react differently to ecological variables. We also argue that adult parasites may respond principally to host diet. In contrast, larval parasite composition may respond both to host diet and predator-prey interactions because this is the path by which many, parasites complete their life-cycles. Finally, variation in parasite phylogeny and parasite life-cycles among hosts likely increase the complexity of the system making it difficult to find all-encompassing patterns between host characteristics and parasites, particularly when all the species in rich parasite communities are considered.

Molecular phylogeny of Sinocyclocheilus (Cypriniformes : Cyprinidae) inferred from mitochondrial DNA sequences

More than 10 species within the freshwater fish genus Sinoncyclocbeilus adapt to caves and show different degrees of degeneration of eyes and pigmentation. Therefore, this genus can be useful for studying evolutionary developmental mechanisms, role of natural selection and adaptation in cave animals. To better understand these processes, it is indispensable to have background knowledge about phylogenetic relationships of surface and cave species within this genus. To investigate phylogenetic relationships among species within this genus, we determined nucleotide sequences of complete mitochondrial cytochrome b gene (1140 bp) and partial ND4 gene (1032 bp) of 31 recognized ingroup species and one outgroup species Barbodes laticeps. Phylogenetic trees were reconstructed using maximum parsimony. Bayesian, and maximum likelihood analyses. Our phylogenetic results showed that all species except for two surface species S. jii and S. macrolepis clustered as five major monophyletic clades (I, II, III, IV, and V) with strong supports. S. jii was the most basal species in all analyses, but the position of S. macrolepis was not resolved. The cave species were polyphyletic and occurred in these five major clades. Our results indicate that adaptation to cave environments has occurred multiple times during the evolutionary history of Sinocyclocheilus. The branching orders among the clades I, II, III, and IV were not resolved, and this might be due to early rapid radiation in Sinocyclocheilus. All species distributed in Yunnan except for S. rhinocerous and S. hyalinus formed a strongly supported monophyletic group (clade V), probably reflecting their common origins. This result suggested that the diversification of Sinocyclocheilus in Yunnan may correlate with the uplifting of Yunnan Plateau. © 2005 Published by Elsevier Inc.

Morphological and molecular phylogenetic analysis of two Saprolegnia sp (Oomycetes) isolated from silver crucian carp and zebra fish

Two Saprolegnia isolates, JY isolated from silver crucian carp (Carassius auratus gibelio Bloch) and BMY isolated from zebra fish (Brachydanio rerio Hamilton) came from infections occurring concurrently in different locations in China. To confirm whether the two isolates were from the same Saprolegnia clone, comparative studies have been carried out based on their morphological, physiological and molecular characteristics. Observations showed that morphologically (both asexual and sexual organs) the two isolates were broadly similar and both isolates under-went repeated zoospore emergence. Comparing 704 base pairs of internal transcribed spacer (ITS) region and the 5.8S rDNA, we found isolates JY and BMY shared an identical ITS sequence with a minor variation (99.6 % similarity). Forty available sequences for representatives Saprolegnia spp. belonged to four phylogenetically separate clades. The two studied isolates fell within clade I that comprised a group of isolates which showed almost an identical ITS sequence but had been identified as a number of different morphological species. our findings suggest that isolates JY and BMY appear to belong to the S. ferax clade and this clade (1) contains a number of closely related phylogenetic species. This is distinct from the more common fish pathogenic isolates, which belong to the S. parasitica clade (III) and are characterized by having cysts decorated by bundles of long hooked hairs and two further clades (II and IV) containing largely saprotrophic or soil born species. (C) 2009 Published by Elsevier Ltd on behalf of The British Mycological Society.

Phylogeny and speciation of the eastern Asian cyprinid genus Sarcocheilichthys

The genus Sarcocheilichthys is a group of small cyprinid fishes comprising 10 species/sub-species widely distributed in East Asia, which represents a valuable model for understanding the speciation of freshwater fishes in East Asia. In the present study, the molecular phylogenetic relationship of the genus Sarcocheilichthys was investigated using a 1140 bp section of the mitochondrial cytochrome b gene. Two different tree-building methods, maximum parsimony (MP) and Bayesian methods, yielded trees with almost the same topology, yielding high bootstrap values or posterior probabilities. The results showed that the genus Sarcocheilichthys consists of two large clades, clades I and II. Clade I contains Sarcocheilichthys lacustris, Sarcocheilichthys sinensis and Sarcocheilichthys parvus, with S. parvus at a basal position. In clade II, Sarcocheilichthys variegatus microoculus is at a basal position; samples of the widespread species, Sarcocheilichthys nigripinnis, form a large subclade containing another valid species Sarcocheilichthys czerskii. Sarcocheilichthys kiangsiensis is retained at an intermediate position. Since S. czerskii is a valid species in the S. nigripinnis clade, remaining samples of S. nigripinnis form a paraphyly. This speciation process is attributed to geographical isolation and special environmental conditions experienced by S. czerskii and stable environments experienced by the other S. nigripinnis populations. This type of speciation process was suggested to be very common. Samples of Sarcocheilichthys sinensis sinensis and Sarcocheilichthys sinensis fukiensis that did not form their own monophyletic groups suggest an early stage of speciation and support their sub-species status. Molecular clock analysis indicates that the two major lineages of the genus Sarcocheilichthys, clades I and II diverged c. 8.89 million years ago (mya). Sarcocheilichthys v. microoculus from Japan probably diverged 4.78 mya from the Chinese group. The northern-southern clades of S. nigripinnis began to diverge c. 2.12 mya, while one lineage of S. nigripinnis evolved into a new species, S. czerski, c. 0.34 mya. (C) 2008 The Authors Journal compilation (C) 2008 The Fisheries Society of the British Isles.

The c-myc coding DNA sequences of cyprinids (Teleostei : Cypriniformes): Implications for phylogeny

The family Cyprinidae is one of the largest fish families in the world, which is widely distributed in East Asian, with obvious difference in characteristic size among species. The phylogenetic analysis of cyprinid taxa based on the functionally important genes can help to understand the speciation and functional divergench of the Cyprinidae. The c-myc gene is an important gene regulating individual growth. In the present study, the sequence variations of the cyprinid c-myc gene and their phylogenetic significance were analyzed. The 41 complete sequences of the c-myc gene were obtained from cyprinids and outgroups through PCR amplification and clone. The coding DNA sequences of the c-myc gene were used to infer molecular phylogenetic relationships within the Cyprinidae. Myxocyprinus asiaticus (Catostomidae), Misgurnus anguillicaudatus (Cobitidae) and Hemimyzon sinensis (Homalopteridae) were assigned to the outgroup taxa. Phylogenetic analyses using maximum parsimony (MP), maximum likelihood (ML), and Bayesian retrieved similar topology. Within the Cyprinidae, Leuciscini and Barbini formed the monophyletic lineage respectively with high nodal supports. Leuciscini comprises Xeno-cyprinae, Cultrinae, East Asian species of Leuciscinae and Danioninae, Gobioninae and Acheilognathinae, and Barbini contains Schizothoracinae, Barbinae, Cyprininae and Labeoninae. Danio rerio, D. myersi and Rasbora trilineata were supposed to separate from Leuciscinae and Barbini and to form another lineage, The positions of some Danioninae species were still unresolved. Analyses of both amino acid variation with parsimony information and two high variation regions indicated that there is no correlation between variations of single amino acid or high variation regions and characteristic size of cyprinids. In,addition, the species with smaller size were usually found to be basal within clades in the tree, which might be the results of the adaptation to the primitive ecology and survival pressure.

Non-monophyly of fish in the Sinipercidae (Perciformes) as inferred from cytochrome b gene

The sinipercids represent a group of 12 species of freshwater percoid fish, including nine in Siniperca and three species in Coreoperca. Despite several classification attempts and a preliminary molecular phylogeny, the phylogenetic relationships and systematic position of sinipercids remained still unsolved. The complete cytochrome b gene sequences from nine sinipercid species four non-sinipercid fish species were cloned, and a total of 12 cyt b sequences from 10 species of sinipercids and 11 cyt b sequences from 10 species of non-sinipercid fish also in Perciformes were included in the phylogenetic analysis. As expected, the two genera Siniperca and Coreoperca within sinipercids are recovered as monophyletic. However, nine species representing Moronidae, Serranidae, Centropomidae, Acropomatidae, Emmelichtyidae, Siganidae and Centrarchidae included in the present study are all nested between Coreoperca and Siniperca, which provides marked evidence for a non-monophyly of sinipercid fishes. Coreoperca appears to be closest to Centrachus representing the family Centrarchidae. Coreoperca whiteheadi and C. herzi are sibling species, which together are closely related to C. kawamebari. In the Siniperca, the node between S. roulei and the remaining species is the most ancestral, followed by that of S. fortis. S. chuatsi and S. kneri are sibling species, sister to S. obscura. However, the sinipercids do not seem to have a very clear phylogenetic history, for different methods of phylogenetic reconstruction result in different tree topologies, and the only conclusive result in favor of a paraphyletic origin of the two sinipercid genera is the parametric bootstrap test. The paraphyly of Sinipercidae may suggest that the "synapomorphs" such as cycloid scales, upon which this family is based, were independently derived at least twice within sinipercid fishes, and further study should be carried out to include the other two Siniperca species and to incorporate other genes.

Phylogeny of the East Asian cyprinids inferred from sequences of the mitochondrial DNA control region

With 210 genera and 2010 species, Cyprinidae is the largest freshwater fish family in the world. Several papers, based on morphological and molecular data, have been published and have led to some solid conclusions, such as the close relationships between North American phoxinins and European leuciscins. However, the relationships among major subgroups of this family are still not well resolved, especially for those East Asian groups. In the present paper, the mitochondrial DNA (mtDNA) control region, 896-956 base pairs, of 17 representative species of East Asian cyprinids was sequenced and compared with those of 21 other cyprinids to study their phylogenetic relationships. After alignment, there were 1051 sites. The comparison between pairwise substitutions and HKY distances showed that the mtDNA control region was suitable for phylogenetic study. Phylogenetic analysis indicated that there are two principal lineages in Cyprinidae: Cyprinine and Leuciscine. In Cyprinine, the relationships could be a basal Labeoinae, an intermediate Cyprininae, and a diversified Barbinae (including Schizothroaxinae). In Leuciscine, Rasborinae is at the basal position; Gobioninae and Leuciscinae are sister groups; the East Asian cultrin-xenocyprinin taxa form a large monophyletic group with some small affiliated groups; and the positions of Acheilognathinae and Tincinae are still uncertain.

Mitochondrial DNA phylogeny of two morphologically enigmatic fishes in the subfamily Schizothoracinae (Teleostei : Cyprinidae) in the Qinghai-Tibetan Plateau

The complete mitochondrial DNA (mtDNA) cytochrome b gene (1140 bp) was sequenced in Herzenstein macrocephalus and Gymnocypris namensis and in 13 other species and sub-species (n = 22), representing four closely related genera in the subfamily Schizothoracinae. Conflicting taxonomies of H. macrocephalus and G. namensis have been proposed because of the character instability among individuals. Parsimony, maximum likelihood and Bayesian methods produced phylogenetic trees with the same topology and resolved several distinctive clades. Previous taxonomic treatments, which variously placed these two species of separate genera or as sub-species, are inconsistent with the mtDNA phylogeny. Both H. macrocephalus and G. namensis appear in a well-supported clade, which also includes nine species of Schizopygopsis, and hence should be transferred to the genus Schizopygopsis. Morphological changes are further illustrated, and their adaptive evolution in response to the local habitat shifts during the speciation process appears to be responsible for conflicting views on the systematics of these two species and hence the contrasting taxonomic treatments. These species are endemic to the Qinghai-Tibetan Plateau, a region with a history of geological activity and a rich diversity of habitats that may have result in the parallel and reversal evolution of some morphological characters used in their taxonomies. Our results further suggest that speciation and morphological evolution of fishes in this region may be more complex than those previously expected. (c) 2007 The Authors Journal compilation (c) 2007 The Fisheries Society of the British Isles.

Geographic and host factors shape the evolution of a newly recognized subgroup within the U genogroup of the fish rhabdovirus IHNV

Thesis (Master's)--University of Washington, 2015

A study on the phylogeny and the ecology of ammonia-oxidizing bacteria using a new molecular marker based on the gene amoB

L'agricultura i la industrialització han causat un augment significatiu del nombre d'ambients rics en amoni. La presència de compostos nitrogenats redueix la qualitat de l'aigua, causant problemes de toxicitat, deteriorant el medi ambient i fins i tot afectant la salut humana. En conseqüència, la nitrificació s'ha convertit en un procés global que afecta al cicle del nitrogen a la biosfera. Els bacteris oxidadors d'amoni (AOB) són els responsables de l'oxidació de l'amoni a nitrit, i juguen un paper essencial en el cicle del nitrogen. Els primers oxidadors d'amoni foren aïllats a finals del segle XIX, però la lentitud del seu creixement i les dificultats per cultivar-los feren que fins als anys 80, amb els primers estudis emprant el gen 16SrDNA, no s'assolís un coneixement complert d'aquest grup bacterià. Actualment les bases de dades contenen multitud d'entrades amb seqüències corresponents a AOB. L'objectiu d'aquest treball era trobar, desenvolupar i avaluar eines útils i fiables per a l'estudi dels AOB en mostres ambientals. En aquest treball primer descrivim la utilització de la hibridació in situ amb fluorescència (FISH), mitjançant l'aplicació de sondes amb diana en el 16SrRNA dels AOB. La FISH ens va permetre detectar i recomptar aquest grup bacterià; no obstant, aquest mètode no permetia la detecció de noves seqüències, pel que es necessitava una nova eina. Amb aquesta intenció vam aplicar la seqüència de la sonda Nso1225 en una PCR. El fet d'amplificar específicament un fragment del 16SrDNA dels AOB va suposar el desenvolupament d'una nova eina molecular que permetia detectar la presència i diversitat d'aquests bacteris en ambients naturals. Malgrat tot, algunes seqüències pertanyents a bacteris no oxidadors d'amoni del subgrup β dels proteobacteris, eren també obtingudes amb aquesta tècnica. Així mateix, un dels inconvenients de l'ús del 16SrDNA com a marcador és la impossibilitat de detectar simultàniament els AOB que pertanyen als subgrups β i γ dels proteobacteris. El gen amoA, que codifica per la subunitat A de l'enzim amoni monooxigenasa (AMO), era aleshores àmpliament utilitzat com a marcador per a la detecció dels AOB. En aquest treball també descrivim la utilització d'aquest marcador en mostres procedents d'un reactor SBR. Aquest marcador ens va permetre identificar seqüències de AOB en la mostra, però la necessitat de detectar amoA mitjançant clonatge fa que l'ús d'aquest marcador requereixi massa temps per a la seva utilització com a eina en estudis d'ecologia microbiana amb moltes mostres. Per altra banda, alguns autors han assenyalat l'obtenció de seqüències de no AOB en utilitzar amoA en un protocol de PCR-DGGE. Amb la finalitat d'obtenir una eina ràpida i rigorosa per detectar i identificar els AOB, vam desenvolupar un joc nou d'oligonucleòtids amb diana en el gen amoB, que codifica per a la subunitat transmembrana de l'enzim AMO. Aquest gen ha demostrat ser un bon marcador molecular pels AOB, oferint, sense tenir en compte afiliacions filogenètiques, una elevada especificitat, sensibilitat i fiabilitat. En aquest treball també presentem una anàlisi de RT-PCR basada en la detecció del gen amoB per a la quantificació del gènere Nitrosococcus. El nou joc d'oligonucleòtids dissenyat permet una enumeració altament específica i sensible de tots els γ-Nitrosococcus coneguts. Finalment, vam realitzar un estudi poligènic, comparant i avaluant els marcadors amoA, amoB i 16SrDNA, i vàrem construir un arbre filogenètic combinat. Com a resultat concloem que amoB és un marcador adequat per a la detecció i identificació dels AOB en mostres ambientals, proporcionant alhora agrupacions consistents en fer inferències filogenètiques. Per altra banda, la seqüència sencera del gen 16S rDNA és indicada com a marcador en estudis amb finalitats taxonòmiques i filogenètiques en treballar amb cultius purs de AOB.

Ecological interactions between an invasive fish (Gambusia holbrooki) and native cyprinodonts: the role of salinity

Actualment una de les principals amenaces a la biodiversitat és la introducció d'espècies. Revisant 26 variables de les 69 espècies de peixos continental de la Península Ibèrica concloem que la filogènia, variabilitat i els usos de l'home són necessaris per entendre millor les diferències entres les espècies natives i invasores. Entre les especies més afectades per la introducció de peixos es troben els ciprinodontiformes endèmics del Mediterrani. Aportem les primers dades sobre l'ús d'hàbitats ocasionalment inundats i la selecció de preses del fartet (Aphanius iberus), observant un canvi ontogenètic, clarament relacionat amb el microhàbitat. També demostrem que la salinitat influeix en l'èxit invasor de la gamúsia, afectant la seva densitat i biologia reproductiva. Per altra banda, demostrem experimentalment que amb l'increment de salinitat la gambúsia disminueix la seva agressivitat i captura menys preses, reduint la seva eficàcia competitiva respecte dels ciprinodonts natius.