Mitochondrial DNA data reveal cryptic species within Taenia krabbei

Cysticerci of Taenia sp. from two elks (Alces alces) in Finland were characterized using morphological criteria and sequences of two mitochondrial DNA regions. The host species, size, structure and location of the cysticerci indicated that they might belong to Taenia krabbei, a circumpolar species occurring in a sylvatic life cycle in wild canids and cervids. Based on the number, length and shape of the rostellar hooks, the specimens could not be unambiguously defined as belonging to T. krabbei, T. cervi, T. ovis or T. solium. In the phylogenetic analysis, based on mitochondrial nucleotide sequence data, Taenia sp. was placed as a sister species of T. solium, distant from T. krabbei isolates previously characterized from Svalbard. This indicates that the Finnish and the Svalbard isolates, resembling T. krabbei, cannot represent a single species. The results suggest that careful morphological and genetic analyses of further isolates from intermediate and definitive hosts are required to define the taxonomic status of these two cryptic species.     

Species identification in the genus Saprolegnia (Oomycetes): Defining DNA-based molecular operational taxonomic units

The lack of a robust taxonomy in the genus Saprolegnia is leading to the presence of incorrectly named isolates in culture collections and of an increasing number of misassigned sequences in DNA databases. Accurate species delimitation is critical for most biological disciplines. A recently proposed approach to solve species delimitation (taxonomic diagnosis system) of difficult organisms is the definition of molecular operational taxonomic units (MOTUs). We have used 961 sequences of nrDNA ITS from culture collections (461 sequences) and GenBank (500 sequences), to perform phylogenetic and clustering optimization analyses. As result, we have identified 29 DNA-based MOTUs in agreement with phylogenetic studies. The resulting molecular clusters support the validity of 18 species of Saprolegnia and identify 11 potential new ones. We have also listed a number of incorrectly named isolates in culture collections, misassigned species names to GenBank sequences, and reference sequences for the species. We conclude that GenBank represents the main source of errors for identifying Saprolegnia species since it possesses sequences with misassigned names and also sequencing errors. The presented taxonomic diagnosis system might help setting the basis for a suitable identification of species in this economically important genus.     

Genetic richness and diversity in Cryptosporidium hominis and C. parvum reveals major knowledge gaps and a need for the application of “next generation” technologies — Research review

Cryptosporidium species (apicomplexan protists) are a major cause of diarrhoeal disease (= cryptosporidiosis) in humans worldwide. The impact of cryptosporidiosis is also compounded by the spread of HIV/AIDS and a lack of cost-effective anti-cryptosporidial chemotherapeutics or vaccines. Mitigation of the impact of cryptosporidiosis in humans needs to focus on prevention and control strategies, built on a sound understanding of the epidemiology of Cryptosporidium species. Refined epidemiological studies rely on the use of molecular tools employing informative genetic markers. Currently, the 60-kDa glycoprotein gene (gp60) is the most suitable and widely used genetic marker for Cryptosporidium species infecting humans. Here, we undertake an analysis of all publicly-available gp60 sequence data and associated literature for C. hominis and C. parvum, and yield useful insights into the richness, diversity and distribution of genetic variants, and link these variants to human cryptosporidiosis. This global analysis reveals that, despite high genetic richness in Cryptosporidium isolates from humans, there is a surprisingly low diversity. It also highlights limited knowledge about the genetics of cryptosporidiosis in developing nations and in many animals that might act as infection sources. Clearly, there is a major need for more comprehensive studies of Cryptosporidium infecting humans and other animals in Africa and Asia. As molecular technologies improve and become affordable, future studies should utilize “next generation” sequencing and bioinformatic platforms to conduct comparative ‘genome sequence surveys’ to test the validity of current genetic classifications based on gp60 data. Complemented by in vitro and in vivo investigations, these biotechnological advances will also assist significantly in the search for new intervention strategies against human cryptosporidiosis.     

Cryptosporidium fayeri: Diversity within the GP60 locus of isolates from different marsupial hosts

The highly polymorphic 60 kDa glycoprotein (GP60) of Cryptosporidium is an important tool for investigating the epidemiology of this parasite. Characterization of the GP60 gene has only been performed for 3 of the 20 known Cryptosporidium species, and has already enabled sub-typing and source tracking of species with human significance. We have characterised a fourth species, Cryptosporidium fayeri, at the GP60 locus using isolates (n = 26) from different marsupial hosts to assess the diversity of GP60 within this species. The analysis demonstrated that C. fayeri isolates could be assigned to 6 subtypes which were associated with host species and locality. The intra-species diversity for the host-adapted C. fayeri was less than the diversity for human pathogenic species suggesting that the GP60 locus is under less selective pressure in these than host-adapted species.     

Biology of Cryptosporidium from marsupial hosts

The majority of biological data on Cryptosporidium has been collected from humans and domestic animal hosts which creates a bias in knowledge on the biodiversity and evolution of this parasite genus. Further to understanding Cryptosporidium biology are studies encompassing broad hosts that represent diverse taxa sampled across wide geographic ranges. Marsupials represent a group of wildlife hosts from which limited information on Cryptosporidium is available. As marsupial hosts are an ancient mammalian lineage they represent an important group for studying parasite evolution. This review summarises information of the biology, epidemiology and evolution of Cryptosporidium in marsupial hosts, and discusses the importance of further understanding interactions in this parasite-host system.     

The phylogenetic placement of hypocrealean insect pathogens in the genus Polycephalomyces: An application of One Fungus One Name

Understanding the systematics and evolution of clavicipitoid fungi has been greatly aided by the application of molecular phylogenetics. They are now classified in three families, largely driven by reevaluation of the morphologically and ecologically diverse genus Cordyceps. Although reevaluation of morphological features of both sexual and asexual states were often found to reflect the structure of phylogenies based on molecular data, many species remain of uncertain placement due to a lack of reliable data or conflicting morphological characters. A rigid, darkly pigmented stipe and the production of a Hirsutella-like anamorph in culture were taken as evidence for the transfer of the species Cordyceps cuboidea, Cordyceps prolifica, and Cordyceps ryogamiensis to the genus Ophiocordyceps. Data from ribosomal DNA supported these species as a single group, but were unable to infer deeper relationships in Hypocreales. Here, molecular data for ribosomal and protein coding DNA from specimens of Ophiocordyceps cuboidea, Ophiocordyceps ryogamiensis, Ophiocordyceps paracuboidea, Ophiocordyceps prolifica, Cordyceps ramosopulvinata, Cordyceps nipponica, and isolates of Polycephalomyces were combined with a broadly sampled dataset of Hypocreales. Phylogenetic analyses of these data revealed that these species represent a clade distinct from the other clavicipitoid genera. Applying the recently adopted single system of nomenclature, new taxonomic combinations are proposed for these species in the genus Polycephalomyces, which has been historically reserved for asexual or anamorphic taxa.     

种级异物同名处理及属名变动影响分析

讨论《国际动物命名法规》(简称《法规》)关于种级单元异物同名的处理及相关规定。以斧须隐翅虫亚科Oxyporinae的同名问题为例,笔者分析了属级单元名称变动对种级单元同名关系的影响。一些古老的属级单元有很长且比较复杂的分类历史,深入分析可将各类变化归纳为六类,其中三类与原同名有关,二类与后同名有关,余一类不再影响种级同名关系。文中讨论了第4版《法规》中与种级同名关系有关的若干重要变动,通过分析比较,说明《法规》的这类变动如何影响动物分类名称的稳定性与正确性。这些分析,可望有助于避免产生新的次同名,也有助于正确恰当地解决已有的同名问题。     

Constraints in naming parts of the Tree of Life

There are now overlapping codes of nomenclature that govern some of the same names of biological taxa. The International Code of Zoological Nomenclature (ICZN) uses the non-evolutionary concept of a "type species" to fix the names of animal taxa to particular ranks in the nomenclatural hierarchy. The PhyloCode, in contrast, uses phylogenetic definitions for supraspecific taxa at any hierarchical level within the Tree of Life (without associating the names to particular ranks), but does not deal with the names of species. Thus, biologists who develop classifications of animals need to use both systems of nomenclature, or else operate without formal rules for the names of some taxa (either species or many monophyletic groups). In addition, the ICZN does not permit the unique naming of many taxa that are considered to be between the ranks of genus and species. Hillis and Wilcox [Hillis, D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 34, 299-314] provided recommendations for the classification of New World true frogs that utilized the ICZN to provide names for species, and the PhyloCode to provide names for supraspecific taxa. Nonetheless, they created new taxon names that followed both sets of rules, to avoid conflicting classifications. They also recommended that established names for both species and clades be used whenever possible, to stabilize the names of both species and clades under either set of rules, and to avoid conflicting nomenclatures. Dubois [Dubois, A., 2006. Naming taxa from cladograms: a cautionary tale. Mol. Phylogenet. Evol., 42, 317-330] objected to these principles, and argued that the names provided by Hillis and Wilcox [Hillis, D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 34, 299-314] are unavailable under the ICZN, and that the two nomenclatural systems are incompatible. Here, I argue that he is incorrect in these assertions, and present arguments for retaining the established names of New World true frogs, which are largely compatible under both sets of nomenclatural rules.     

Burkholderia tuberum sp. nov. and Burkholderia phymatum sp. nov., nodulate the roots of tropical legumes

The taxonomic status of five root nodule isolates from tropical legumes was determined using a polyphasic taxonomic approach. Two isolates were identified as B. caribensis, an organism originally isolated from soil in Martinique (the French West Indies). One isolate was identified as Burkholderia cepacia genomovar VI, a B. cepacia complex genomovar thus far only isolated from sputum of cystic fibrosis patients. The remaining two isolates were identified as novel Burkholderia species for which we propose the names Burkholderia tuberum sp. nov. and Burkholderia phymatum sp. nov. The type strains are LMG 21444T and LMG 21445T, respectively.     

Paragonimus paishuihoensis Metacercariae in Freshwater Crabs,Potamon lipkei,in Vientiane Province,Lao PDR

Among Paragonimus species, P. paishuihoensis is one of the most mysterious and poorly understood species. Metacercariae are characterized by having a unique dendritically branched excretory bladder. However, the morphology of the adult worm remains unknown. To date, metacercariae of this species have been reported only in China and Thailand. In this study, we first found P. paishuihoensis metacercariae in freshwater crabs, Potamon lipkei, in Hinheub District, Vientiane, Lao PDR, with a prevalence of 77.7% and the average intensity of 10.3 (range 1-28) metacercariae per crab. The molecular data based on ITS2 and CO1 markers indicated that P. paishuihoensis from Laos and Thailand were almost completely identical and were close to members of the Paragonimus bangkokensis/Paragonimus harinasutai complex. Attempts to infect experimental animals (cats, dogs, and rats) with P. paishuihoensis were unsuccessful, suggesting that these animals might be unsuitable definitive hosts for the species. Further studies are necessary to elucidate the taxonomic status and life cycle of P. paishuihoensis.     

Integrative taxonomy and preliminary assessment of species limits in the Liolaemus walkeri complex (Squamata,Liolaemidae) with descriptions of?three?new species from Peru

Species delimitation studies based on integrative taxonomic approaches have received considerable attention in the last few years, and have provided the strongest hypotheses of species boundaries. We used three lines of evidence (molecular, morphological, and niche envelopes) to test for species boundaries in Peruvian populations of the Liolaemus walkeri complex. Our results show that different lines of evidence and analyses are congruent in different combinations, for unambiguous delimitation of three lineages that were “hidden” within known species, and now deserve species status. Our phylogenetic analysis shows that L. walkeri, L. tacnae and the three new species are strongly separated from other species assigned to the alticolor-bibronii group. Few conventional morphological characters distinguish the new species from closely related taxa and this highlights the need to integrate other sources of data to erect strong hypothesis of species limits. A taxonomic key for known Peruvian species of the subgenus Lioalemus is provided.     

Intra-specific variation of Kudoa spp. (Myxosporea: Multivalvulida) from apogonid fishes (Perciformes), including the description of two new species, K. cheilodipteri n. sp. and K. cookii n. sp., from Australian waters

Kudoa spp. from the musculature and intestinal mucosa of species of the teleost family Apogonidae were examined for their taxonomic identity. Two novel species are characterised: Kudoa cheilodipteri n. sp. from the musculature of Cheilodipterus quinquelineatus Cuvier, Ostorhinchus cyanosoma (Bleeker) and O. aureus (Lacépède); and Kudoa cookii n. sp. from the submucosa of the intestines of O. cookii (Macleay) only. Both species are characterised using morphology, small subunit ribosomal DNA (SSU rDNA), large subunit ribosomal DNA (LSU rDNA), and biological characters. Three new host records, O. cyanosoma, O. aureus and Apogon doederleini, and associated geographical, morphological and genetic data are also provided for Kudoa whippsi Burger & Adlard, 2010. Morphological and molecular intra-specific variation of all isolates assigned to K. whippsi is also examined. Phylogenetic analyses further support the idea that tissue tropism is a distinguishing character between morphologically similar species; species reported here display close relatedness to morphologically similar species infecting the same tissue within their hosts.     

The Praon dorsale–yomenae s.str. complex (Hymenoptera,Braconidae, Aphidiinae): Species discrimination using geometric morphometrics and molecular markers with description of a new species

In this paper we apply an integrative approach combining morphometric and molecular analyses to explore parasitoids of the Praon dorsale–yomenae s.str. complex. These parasitoids occur in natural and agricultural ecosystems throughout the Palaearctic and parasitize aphid hosts belonging to the tribe Macrosiphini. The P. dorsale–yomenae species complex represents a morphologically cryptic group, consisting of several hidden taxa with specific host adaptations and distributions. For the morphometric analyses we used a large dataset comprising 230 female specimens that emerged from 30 different species of aphid hosts throughout the Palaearctic. The molecular analysis included a reduced dataset of 44 specimens that emerged from 19 aphid hosts. The mitochondrial cytochrome oxidase subunit I (COI) and the nuclear second expansion segment of the 28S rRNA gene (28SD2) were used to estimate a genetic diversity within this complex. Although all Praon species clustered closely together in the 28SD2 tree, confirming their close relatedness, the molecular characterization based on COI identified five clearly separate taxa with sequence divergences in the range of 4.7–8.9%. These taxa also exhibited significant differences in forewing shape as revealed by geometric morphometric analyses. Classical morphometric analyses revealed the length of m-cu vein as a new taxonomic character, but suggested that one commonly used trait, the color pattern of the Rs + M and m-cu veins, cannot be used for species distinction as it was highly variable in one of the taxa. Based on the combined morphometric and genetic data, we confirm the species status of Praon dorsale, P. yomenae, P. longicorne and P. volucre, and describe and illustrate a new parasitoid species of the “dorsale–yomenae” group, i.e. Praon staticobii n.sp. associated with Staticobium limonii on Limonium angustifolium.     

Phylogenetic relationship of Phytophthora cryptogea Pethybr. & Laff and P. drechsleri Tucker

The phylogeny and taxonomy of Phytophthora cryptogea and Phytophthora drechsleri has long been a matter of controversy. To re-evaluate this, a worldwide collection of 117 isolates assigned to either P. cryptogea, P. drechsleri or their sister taxon, Phytophthora erythroseptica were assessed for morphological, physiological (pathological, cultural, temperature relations, mating) and molecular traits. Multiple gene phylogenetic analysis was performed on DNA sequences of nuclear (internal transcribed spacers (ITS), ß-tubulin, translation elongation factor 1α, elicitin) and mitochondrial (cytochrome c oxidase subunit I) genes. Congruence was observed between the different phylogenetic data sets and established that P. drechsleri and P. cryptogea are distinct species. Isolates of P. drechsleri form a monophyletic grouping with low levels of intraspecific diversity whereas P. cryptogea is more variable. Three distinct phylogenetic groups were noted within P. cryptogea with an intermediate group providing strong evidence for introgression of previously isolated lineages. This evidence suggests that P. cryptogea is an operational taxonomic unit and should remain a single species. Of all the morphological and physiological traits only growth rate at higher temperatures reliably discriminated isolates of P. drechsleri and P. cryptogea. As a homothallic taxon, P. erythroseptica, considered the cause of potato pink rot, is clearly different in mating behaviour from the other two species. Pathogenicity, however, was not a reliable characteristic as all isolates of the three species formed pink rot in potato tubers. The phylogenetic evidence suggests P. erythroseptica has evolved from P. cryptogea more recently than the split from the most recent common ancestor of all three species. However, more data and more isolates of authentic P. erythroseptica are needed to fully evaluate the taxonomic position of this species.     

Molecular phylogeny,taxonomy, and distribution of French Unio species (Bivalvia,Unionidae)

A plethora of unionid names was established in the nineteenth century by the “Nouvelle Ecole”. Although naiad morphological plasticity is well documented, the currently recognized fauna, with 17 species and subspecies included in the French checklist for the Unio genus, is still based upon morphological characters only. Insights have been provided from molecular data elsewhere in Europe and North Africa, but the French fauna remains unstudied. We present a molecular phylogeny of the Unio genus in France based on COI, 16S and 28S genes; taking up all available data in Europe plus 273 specimens collected in all main French drainages. The results show that there are either three valid species in France, with U. pictorum and U. mancus synonymized, or five, with the subspecies U. crassus courtillieri elevated to species level. Subspecies were generally not recovered, which questions the evolutionary units tacitly implied by subspecific names. Although sampling topotypes is the most reliable way to evaluate the status of a nominal subspecies, major human-induced changes in aquatic hydrosystems challenge the method. Nevertheless, operational taxonomy has to rely on ground-truthed data and we propose to reduce the actual number of valid taxa in France to the seven observed operational taxonomic units.     

Morphology and molecular taxonomy of Evlachovaea-like fungi,and the status of this unusual conidial genus

The entomopathogenic anamorphic genus Evlachovaea was described to differ from other fungi in forming its conidia obliquely to the axis of the conidiogenous cell and with successive conidia having alternate orientations with a zipper- or chevron-like arrangement resulting in flat, ribbon-like chains. Morphological and molecular studies of six Evlachovaea-like isolates baited from Central Brazilian soils using Triatoma infestans (a vector of Chagas disease) and of other entomopathogens with Evlachovaea-like conidiogenesis led to a re-evaluation of the status of this little known fungal genus. The Brazilian isolates formed two distinct groups based on gene sequences for both the internal transcribed spacer (ITS) and translation elongation factor (EF-1α) genes, morphology, and growth patterns; both groups also differed from the type species, Evlachovaea kintrischica. More detailed studies of these fungi indicated that the alternatingly oblique orientations of forming conidia are neither a stable nor invariant character (even on single phialides). Furthermore, the molecular cladistic analysis unambiguously placed the Evlachovaea isolates firmly within the genus Isaria (Hypocreales: Cordycipitaceae). The ITS sequences of E. kintrischica were very similar or even identical to those of Isaria amoenerosea and Isaria cateniobliqua, thereby suggesting that E. kintrischica is a synonym of one of these species, and that the genus Evlachovaea must be treated as a later synonym of Isaria, which must now be recognized to include several highly divergent modes of conidiogenesis. These taxonomic findings are discussed in the context of dramatic changes recently imposed on the nomenclatural standards used to determine the correct names of all pleomorphic fungi.