Polystomatidae (Monogenea) of African Anura: Polystoma dawiekoki n. sp. parasitic in Ptychadena anchietae (Bocage)

Polystoma dawiekoki n. sp. is described as a new species of the Polystomatidae parasitic in the urinary bladder of the plain grass frog Ptychadena anchietae. This parasite was collected at Mkuze town and Mkuze Game Reserve in northern Kwazulu-Natal Province, in the Kruger National Park in Mpumalanga Province, South Africa, and at Bulwa in Tanga Province, East Usambara Mountains, Tanzania. It is distinguished from other African Polystoma species by a combination of characters, including the body size, size and shape of marginal hooklets and the haptor length to body length ratio. The presence of adult, as well as subadult, parasites in the same individuals, as is known for Eupolystoma, represents a significant evolutionary departure from the pattern of transmission typical of Polystoma in most of the other anuran hosts.     

Comparing the efficacy of morphologic and DNA-based taxonomy in the freshwater gastropod genus Radix (Basommatophora, Pulmonata)

Background  

Reliable taxonomic identification at the species level is the basis for many biological disciplines. In order to distinguish species, it is necessary that taxonomic characters allow for the separation of individuals into recognisable, homogeneous groups that differ from other such groups in a consistent way. We compared here the suitability and efficacy of traditionally used shell morphology and DNA-based methods to distinguish among species of the freshwater snail genus Radix (Basommatophora, Pulmonata).     

Revision of the systematics of the genus Calliptamus Serville 1831, (Orthoptera: Acrididae: Calliptaminae) in Algeria using morphological,chemical, and genetic data

Summary. The genus Calliptamus contains swarming orthopterans that cause serious damage in Algerian agricultural systems. However, it remains difficult to identify species within this genus; a thorough understanding of the group’s systematics and the utilization of novel taxonomic criteria are needed. We used morphological analysis along with two other methods of species identification – chemotaxonomy with cuticular compounds and DNA barcoding involving the COI gene – to classify 81 individual grasshoppers collected at two different sites in the Sétif region (northeastern Algeria). The chemotaxonomic analyses yielded ambiguous results, but DNA barcoding allowed us to differentiate two Calliptamus species found in Algeria: Calliptamus barbarus (Costa 1836), and Calliptamus wattenwylianus (Pantel 1896). Several morphological criteria used in identification keys appear to reflect differences among morphotypes rather than differences between species, and their taxonomic specificity is not supported by the barcoding data. The number of spines on the hind tibia is the only morphological criterion that reflected genetic differences between species; it is thus considered to be a taxonomically useful feature for identifying species in this genus.     

Genomic taxonomy of vibrios

Background  

Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i. e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios.     

A new species of the mazocraeid genus Cribromazocraes Mamaev, 1981, from the freshwater clupeid Hilsa ilisha (Ham.) from the Kanpur District,India

Cribromazocraes llewellyni n. sp. is described from a freshwater clupeid Hilsa ilisha (Ham.) from the Kanpur District, India. It is characterised by the presence of unbranched intestinal caeca, the number and arrangement of the genital spines, the shape of the clamp sclerites and the presence of marginal hooklets. This is the first record of the genus Cribromazocraes Mamaev, 1981 from India.     

Integrated method for single-cell DNA extraction, PCR amplification, and sequencing of ribosomal DNA from harmful dinoflagellates Cochlodinium polykrikoides and Alexandrium catenella

A simplified technique was developed for DNA sequence-based diagnosis of harmful dinoflagellate species. This protocol integrates procedures for DNA extraction and polymerase chain reaction (PCR) amplification into a single tube. DNA sequencing reactions were performed directly, using unpurified PCR products as the DNA template for subsequent sequencing reactions. PCR reactions using DNA extracted from single cells of Cocodinium polykrikoides and Alexandrium catenella successfully amplified the target ribosomal DNA regions. DNA sequencing of the unpurified PCR products showed that DNA sequences corresponded to the expected locus of ribosomal DNA regions of both A. catenella and C. polykrikoides (each zero genetic distance and 100% sequence similarity). Using the protocol described in this article, there was little DNA loss during the purification step, and the technique was found to be rapid and inexpensive. This protocol clearly resolves the taxonomic ambiguities of closely related algal species (such as Alexandrium and Cochlodinium), and it constitutes a significant breakthrough for the molecular analysis of nonculturable dinoflagellate species.     

Morphology and molecular characterization of Polystoma goeldii n. sp. (Monogenea,Polystomatidae) parasite from the urinary bladder of Physalaemus ephippifer (Steindachner) (Anura,Leptodactylidae)

Polystomatid flatworms of amphibians are represented in the Neotropical realm by species of Mesopolystoma, Nanopolystoma, Parapseudopolystoma, Polystoma, Riojatrema and Wetapolystoma but only species of Polystoma are known from Brazil, namely Polystoma cuvieri, P. knoffi, P. lopezromani and P. travassosi. During a survey of monogeneans infecting amphibians in the north-eastern region of Pará State, the Cayenne Caecilian Typhlonectes compressicauda was found to be infected with Nanopolystoma tinsleyi and the Veined Tree Frog Trachycephalus typhonius was found to harbor Polystoma lopezromani. A yet unknown species of Polystoma was also encountered in the urinary bladder of the Steindachner's Dwarf Frog, Physalaemus ephippifer. This new species, which is the second species reported from Physalaemus spp., is described herein as Polystoma goeldii n. sp. and its life cycle is also illustrated. The new species can be distinguished from Polystoma spp. from other neotropical realm by a combination of characteristics, including hamuli morphology, outer/inner hamuli length ratio, haptor/total body length ratio, genital bulb/total body length ratio, genital spine number and COI molecular characters.     

Identification of phlebotomine sand flies (Diptera: Psychodidae) from leishmaniasis endemic areas in southeastern Mexico using DNA barcoding

Leishmaniasis, a vector‐borne disease transmitted to humans through the bite of phlebotomine sand flies, is of public health significance in southeastern Mexico. Active and continuous monitoring of vectors is an important aspect of disease control for the prediction of potential outbreaks. Thus, the correct identification of vectors is paramount in this regard. In this study, we employed DNA barcoding as a tool for identifying phlebotomine sand flies collected in localized cutaneous leishmaniasis endemic areas of Quintana Roo, Mexico. Specimens were collected using CDC light and Shannon traps as part of the Mexican Ministry of Health surveillance program. DNA extraction was carried out using a nondestructive protocol, and morphological identification based on taxonomic keys was conducted on slide‐mounted specimens. Molecular taxonomic resolution using the 658‐bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene was 100% congruent with the morphological identification. Seven species were identified: Lutzomyia cruciata (Coquillett 1907), Lutzomyia longipalpis (Lutz & Neiva 1912), Psathyromyia shannoni (Dyar 1929), Dampfomyia deleoni (Fairchild & Hertig 1947), Dampfomyia beltrani/steatopyga (Vargas & Díaz‐Nájera 1951), Bichromomyia olmeca olmeca (Vargas & Díaz‐Nájera, 1959), and Brumptomyia mesai (Sherlock 1962). Mean intraspecific divergence ranged from 0.12% to 1.22%, while interspecific distances ranged from 11.59% to 19.29%. Neighbor‐joining (NJ) analysis using the Kimura 2‐parameter model also showed specimens of the same species to be clustered together. The study provides the first cox1 sequences for three species of sand flies and indicates the utility of DNA barcoding for phlebotomine sand flies species identification in southeastern Mexico.     

AN OVERVIEW OF LARDIZABALACEAE

This overview provides a taxonomic revision of the family Lardizabalaceae. Seven genera are accepted here (Akebia, Boquila, Decaisnea, Lardizabala, Sargentodoxa, Sinofranchetia and Stauntonia); as a result of molecular and morphological data Archakebia is included in Akebia and Holboellia and Parvatia are united with Stauntonia. The number of species in the family is increased to 40, resulting from elevation of some varietal and subspecific names to species level, although it should be noted that the differences between species of Stauntonia are often minute, both morphologically and genetically, and may not warrant recognition. To facilitate identification, keys to the genera and species are provided and taxonomic discussions are given. Horticultural information and illustrations are provided for every genus.     

Polystomatidae (Monogenea) of Anura in southern Africa: Polystoma testimagna n. sp. parasitic in Strongylopus f. fasciatus (Smith, 1849)

Polystoma testimagna n. sp. is described as a new species of the Polystomatidae, parasitic in the urinary bladder of the striped stream frog Strongylopus f. fasciatus collected in the Vernon Crookes Nature Reserve, Natal, South Africa. Parasite prevalence was found to be 50.0% and 27.7% in two successive years, and the mean intensity was 1.5 and 1.6, respectively. The species occurs together with another Polystoma species in the same water body and within one kilometre from a third species. Aspects of host specificity are discussed and data on the ecology and distribution of the host presented.     

Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi

Background  

During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public databases such as GenBank increases exponentially, only a minuscule fraction of all organisms have been sequenced, leaving taxon sampling a momentous problem for sequence-based taxonomic identification. When querying GenBank with a set of unidentified sequences, a considerable proportion typically lack fully identified matches, forming an ever-mounting pile of sequences that the researcher will have to monitor manually in the hope that new, clarifying sequences have been submitted by other researchers. To alleviate these concerns, a project to automatically monitor select unidentified sequences in GenBank for taxonomic progress through repeated local BLAST searches was initiated. Mycorrhizal fungi – a field where species identification often is prohibitively complex – and the much usedITSlocus were chosen as test bed.     

Bushmeat genetics: setting up a reference framework for the DNA typing of African forest bushmeat

The bushmeat trade in tropical Africa represents illegal, unsustainable off‐takes of millions of tons of wild game – mostly mammals – per year. We sequenced four mitochondrial gene fragments (cyt b, COI, 12S, 16S) in >300 bushmeat items representing nine mammalian orders and 59 morphological species from five western and central African countries (Guinea, Ghana, Nigeria, Cameroon and Equatorial Guinea). Our objectives were to assess the efficiency of cross‐species PCR amplification and to evaluate the usefulness of our multilocus approach for reliable bushmeat species identification. We provide a straightforward amplification protocol using a single ‘universal’ primer pair per gene that generally yielded >90% PCR success rates across orders and was robust to different types of meat preprocessing and DNA extraction protocols. For taxonomic identification, we set up a decision pipeline combining similarity‐ and tree‐based approaches with an assessment of taxonomic expertise and coverage of the GENBANK database. Our multilocus approach permitted us to: (i) adjust for existing taxonomic gaps in GENBANK databases, (ii) assign to the species level 67% of the morphological species hypotheses and (iii) successfully identify samples with uncertain taxonomic attribution (preprocessed carcasses and cryptic lineages). High levels of genetic polymorphism across genes and taxa, together with the excellent resolution observed among species‐level clusters (neighbour‐joining trees and Klee diagrams) advocate the usefulness of our markers for bushmeat DNA typing. We formalize our DNA typing decision pipeline through an expert‐curated query database – DNAbushmeat – that shall permit the automated identification of African forest bushmeat items.     

中国吴茱萸属(广义)叶结构特征及其分类学意义北大核心CSCD

该研究以中国产芸香科广义吴茱萸属18种3变种为材料,于体视显微镜下观察叶结构特征。结果发现:(1)吴茱萸属叶脉为羽状脉。(2)二级脉有花环状弓形脉和简单弓形脉两种类型,极少数存在内二级脉,间二级脉存在或缺失。(3)三级脉不规则网状或极少数弱贯穿,边缘三级脉环状。(4)四级脉不规则网状或自由分支。(5)五级脉不规则网状或自由分支,脉间区发育差或中等,游离端小脉末端简单或管状异形,边缘末级脉大多数不完整,极少数环状。(6)基于重要的外部形态学特征和叶结构特征观察结果,编制了广义吴茱萸属植物的分组检索表。研究表明,吴茱萸属这些类群的二级脉与更高级脉序形成的结构极为稳定,同时又存在种间差异,故广义吴茱萸属植物叶结构特征可以为更准确地鉴定一些疑难种和混淆种提供佐证,具有重要的系统分类学价值。     

Molecular characterisation and development of rapid molecular methods to identify species of Gracilariaceae from the Atlantic coast of Morocco

In Gracilariaceae, species identification is traditionally based on gross morphology; therefore the taxonomic status of terete individuals remains frequently problematic due to the lack of diagnostic characters to identify specimens. Different morphospecies have been recorded along the Atlantic coast of Morocco; however, no clear diagnostic characters were available to discriminate between terete species. Rapid molecular techniques have been developed recently to resolve many taxonomic problems and to re-assess the global diversity and biogeography in algae. In this study, molecular markers were used as DNA barcoding to characterise species. The sequence of the Rubisco spacer allowed identification of six species of Gracilariaceae: Gracilaria gracilis, Gracilaria dura, Gracilaria conferta, Gracilaria vermiculophylla, Gracilaria multipartita and Gracilariopsis longissima. In order to identify species with certainty, two simple and rapid methods based on the amplification of rDNA ITS and PCR-RFLP of the large subunit of the Rubisco were developed.     

Citizen monitoring of invasive species: wing morphometry as a tool for detection of alien Tetropium species

The increasing threat of alien wood‐boring insect has resulted in the initiation of large‐scale monitoring programmes. These programmes are most often based on pheromone‐bailed traps, which allow the early detection and monitoring of invasive species. This approach is expensive because it entails the processing and accurate identification of large numbers of specimens. One of the most often suggested solutions to this problem is citizen participation in the monitoring of invasive species. Such an approach has the potential for reducing costs as well as providing data from a larger number of sites. However, citizens vary in taxonomic expertise and experience which can result in identification errors. This may be particularly important in the case of wood borers which include many morphologically similar species. In this study, we develop and discuss a semi‐automated method of identifying four morphologically similar and invasive Tetropium spp. wood borers as a potential tool for citizen‐based monitoring programmes. Identification is based on wing measurements and requires neither specialist knowledge nor expensive equipment. The method correctly identified the species of Tetropium with an error ranging from 1.3% for T. fuscum to 7.5% for T. cinnamopterum. We found that experience level of the individual user was not essential for correct identification; on average, inexperienced volunteers correctly identified the Tetropium species in 93% of cases. Further development of this method may be a significant step to overcoming the taxonomical impediment to citizen monitoring of taxonomically challenging groups of insects.     

Evaluation of the taxonomic diversity of prosthecate bacteria belonging to the genera <Emphasis Type="Italic">Brevundimonas</Emphasis> and <Emphasis Type="Italic">Caulobacter</Emphasis> isolated from various eurasian ecosystems by analysis of the 16S rRNA genes

A taxonomic study of 35 cultures of prosthecate bacteria of the genera Brevundimonas and Caulobacter isolated from various soil and aquatic ecosystems of Eurasia was performed by amplified ribosomal DNA restriction analysis (ARDRA) and 16S rRNA gene sequencing. The most widespread groups of prosthecate bacteria belonging to these genera were revealed; at least two new species belonging to the genus Brevundimonas were found. The genus Brevundimonas includes both prosthecate and non-prosthecate species; however, it is quite possible that some Brevundimonas species may exhibit heterogeneity in such an important taxonomic characteristics as the ability to form prosthecae.     

DNA barcoding as a tool for coral reef conservation

DNA Barcoding (DBC) is a method for taxonomic identification of animals that is based entirely on the 5′ portion of the mitochondrial gene, cytochrome oxidase subunit I (COI-5). It can be especially useful for identification of larval forms or incomplete specimens lacking diagnostic morphological characters. DBC can also facilitate the discovery of species and in defining “molecular taxonomic units” in problematic groups. However, DBC is not a panacea for coral reef taxonomy. In two of the most ecologically important groups on coral reefs, the Anthozoa and Porifera, COI-5 sequences have diverged too little to be diagnostic for all species. Other problems for DBC include paraphyly in mitochondrial gene trees and lack of differentiation between hybrids and their maternal ancestors. DBC also depends on the availability of databases of COI-5 sequences, which are still in early stages of development. A global effort to barcode all fish species has demonstrated the importance of large-scale coordination and is yielding promising results. Whether or not COI-5 by itself is sufficient for species assignments has become a contentious question; it is generally advantageous to use sequences from multiple loci.     

Molecular diversity and distribution of eastern Atlantic and Mediterranean dogfishes Squalus highlight taxonomic issues in the genus

The alpha taxonomy of the globally distributed shark genus Squalus has been under intense investigation recently, and many new species have been described over the last decade. However, taxonomic uncertainty remains about several taxa. Without consistent nomenclature and the ability to reliably distinguish between the different Squalus species, basic data collection, downstream conservation and management efforts are seriously compromised. To aid in clarifying the taxonomic status of Squalus species in the eastern Atlantic and Mediterranean, we assessed species diversity at the molecular level and evaluated the consistency in species identification in the region. Samples from all nominal Squalus species recognized in the above regions were collected in an international effort and sequenced for regions of the mitochondrial COI and ND2 genes. These data were further analysed alongside publicly available sequences, including 19 of the 26 Squalus species globally recognized, to compare the regional genus‐level diversity with that found elsewhere. Our results confirm inconsistent species identification in the eastern Atlantic and Mediterranean Squalus, particularly concerning S. blainville and S. megalops, and reinforce the need to revise the status of S. megalops and S. mitsukurii as they may include several distinct species distributed around the world. The status of S. blainville is also discussed in the light of the current findings and its problematic taxonomic history.