Systematics and genetic variation in commercial shape Kappaphycus and shape Eucheuma (Solieriaceae, Rhodophyta)

The systematics and taxonomy of Kappaphycus and Eucheuma (Solieriaceae) is confused and difficult due to morphological plasticity, lack of adequate characters to identify species and commercial names of convenience. These taxa are geographically widely dispersed through cultivation. Commercial, wild and herbarium sources were analysed; molecular markers provided insights into taxonomy and genetic variation, and where sources of genetic variation may be located. The mitochondrial cox2-3 and plastidal RuBisCo spacers were sequenced. There is a clear genetic distinction between K. alvarezii (“cottonii”) and K. striatum (“sacol”) samples. Kappaphycus alvarezii from Hawaii and some samples from Africa are also genetically distinct. Our data also show that all currently cultivated K. alvarezii from all over the world have a similar mitochondrial haplotype. Within Eucheuma denticulatum (“spinosum”) most African samples are again genetically distinct. Our data also suggest that currently cultivated E. denticulatum may have been “domesticated” several times, whereas this is not evident for the cultivated K. alvarezii. The present markers used do not distinguish all the morpho-types known in cultivation (e.g. var. tambalang, “giant” type) but do suggest that these markers may be useful to assess introductions and species identification in samples.     

Origins, taxa, names and meanings

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DNA barcodes as a tool in biodiversity research: testing pre-existing taxonomic hypotheses in Delphic Apollo butterflies (Lepidoptera,Papilionidae)

Numerous studies have demonstrated that DNA barcoding is an effective tool for detecting DNA clusters, which can be viewed as operational taxonomic units (OTUs), useful for biodiversity research. Frequently, the OTUs in these studies remained unnamed, not connected with pre-existing taxonomic hypotheses, and thus did not really contribute to feasible estimation of species number and adjustment of species boundaries. For the majority of organisms, taxonomy is very complicated with numerous, often contradictory interpretations of the same characters, which may result in several competing checklists using different specific and subspecific names to describe the same sets of populations. The highly species-rich genus Parnassius (Lepidoptera: Papilionidae) is but one example, such as several mutually exclusive taxonomic systems have been suggested to describe the phenotypic diversity found among its populations. Here we provide an explicit flow chart describing how the DNA barcodes can be combined with the existing knowledge of morphology-based taxonomy and geography (sympatry versus allopatry) of the studied populations in order to support, reject or modify the pre-existing taxonomic hypotheses. We then apply this flow chart to reorganize the taxa within the Parnassius delphius species group, solving long-standing taxonomic problems.     

Trioxys similis n. sp. (Hym. Braconidae,Aphidiinae), eine neue Blattlaus-Schlupfwespe aus Frankreich

Summary In the present paper the author describes the new speciesTrioxys (Trioxys) similis n. sp. (Hymenoptera: Braconidae, Aphidiinae), which has been reared in France from the peach aphid, presumablyMyzus persicae (Sulzer 1776). Considering the fact that this aphid is a world wide distributed pest causing heavy damages by transmission of numerous plant viruses, attention is drawn to use this braconid parasite as a limiting factor in biological control.Trioxys similis n. sp. belongs to the group of species “Trioxys angelicae (Hal. 1833) s. l.”, the biology and taxonomy of which is briefly discussed. The existence of various strains of one parasite species, differing only in their host range or host preference is a major problem both of applied entomology and of insect taxonomy. It is suggested to name these morphologically indistinguishable forms according to terms used in microbiological nomenclature. Finally, the following names have been changed as being homonyms, and new names are proposed instead of them:Aphidius constrictus Benoit 1955=Aphidius benoiti n. n., †Trioxys obscuriformis Quilis 1940=†Trioxys fossilis n. n.

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Beitrag zur Kenntnis der palaearktischenAphidiinae.     

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.     

Automated group assignment in large phylogenetic trees using GRUNT: GRouping,Ungrouping, Naming Tool

Background  

Accurate taxonomy is best maintained if species are arranged as hierarchical groups in phylogenetic trees. This is especially important as trees grow larger as a consequence of a rapidly expanding sequence database. Hierarchical group names are typically manually assigned in trees, an approach that becomes unfeasible for very large topologies.     

Selected subspecies names from Richter,Plantae Europeae,Vol. 1, 1890

The bookK. Richter, Plantae europeae, Vol. 1, 1890, is analyzed from the viewpoint of nomenclature of subspecies names. 264 subspecies names interesting from the standpoint of contemporary taxonomy and nomenclature are selected from the total number of 840 subspecies names for a commented list. Seventeen important cases are dealt with separately in greater detail. Eleven new nomenclatural combinations (two for species, nine for subspecies) are proposed in the Appendix. Types for two generic names (Acorellus Palla andJuncellus C. B. Clarke) are proposed. A new term “parabasionym” is applied for names establishing the priority of infraspecific epithets in the rank in question. The need to respect the newly accepted principle of priority of autonymic subspecies names at proposing new nomenclatural combinations is stressed. Examples ofRichter’s subspecies names having priority, subspecies names with necessary changes in their authorship and names having a possible importance as parabasionyms are enumerated in separate lists.     

Proposed validation of the specific namescrenatus Bruguière, 1789, andrenggeri Oppel, 1863 (Class Cephalopoda,Order Ammonoidea) from the Oxfordian stage of the upper jurassic

Ammonites crenata Bruguière (1789) is one of the oldest species names used in modern ammonite taxonomy. This is a nomen dubium that is probably a synonym of what modern authors callCreniceras renggeri (Oppel 1863), a common species of the early Oxfordian.Ammonites crenatus Bruguière in Oppel (1863) is a stratigraphically junior taxon of the middle Oxfordian. Nevertheless, there is a possibility, however improbable it may be, thatAmmonites crenata Bruguière andAmmonites crenatus Oppel are synonyms. Therefore it is proposed here to retain the current usage of the namescrenatus Bruguière emend. d’Orbigny (1847) andrenggeri Oppel.     

Recent Taxonomic Developments with <Emphasis Type="Italic">Candida</Emphasis> and Other Opportunistic Yeasts

Increases in susceptible patient populations and advances in identification methods have resulted in the continued recognition of novel yeasts as agents of human infection. Most of these agents are members of the well-recognized genera Candida, Cryptococcus, Trichosporon, and Rhodotorula. Some of these agents are “cryptic species,” members of species complexes, and may not be detectable using classical carbohydrate assimilation-based methods of yeast identification. Such species require DNA- or MALDI-based methods for correct identification, although sporadic isolates may not routinely require delineation to the individual species level. The coming end of the fungal taxonomy rules requiring separate names for sexual and asexual forms of the same fungus will hopefully allow greater clarity, as names for medically important yeast can now be based on the needs of the medical mycology community and the common goal of better communication between laboratory and clinician.     

Current advances in Phellinus sensu lato: medicinal species, functions, metabolites and mechanisms

Twenty-six species of Phellinus sensu lato, reported as medicinal mushrooms, are enumerated in this review. The species’ names were checked and revised according to contemporary taxonomy and the latest version of the International Code of Botanical Nomenclature (Vienna Code); two misapplied names of Phellinus baumii Pilát and Phellinus himalayensis Y.C. Dai in previous reports are also discussed. Of the 20 types of medicinal functions, the most shared functions are antitumor and improving immunity, both of which may be viewed as the basal functions of Phellinus s. l. In addition, alleviating septic shock, anti-inflammatory, and antioxidation are also a routine functions mentioned often. The main medicinal metabolites, including several kinds of polysaccharides and polyphenols, are introduced. Different methods and conditions could purify various polysaccharides with difference in activity level even from the same species, while all polyphenols are hispidin and its derivatives in general. Three aspects of mechanism contribute to antitumor activities of polysaccharides: (1) promoting an immune response, (2) inducing cell apoptosis, and (3) inhibiting metastasis. Other general mechanisms of the metabolites in antioxidant activity, and in treating diabetes, as well as complications are summarized. We also elaborate on potential scientific strategies for obtaining the medicinal metabolites from Phellinus s. l., such as artificial cultivation, the discoveries of more species with medicinal functions, the utilization of species growing quickly, and the optimization of culture conditions and media supplements in fermentation.     

Panbiogeography and the amateur naturalist with reference to conservation implications

Abstract

The minimal-spanning-tree as a method of plotting dispersal in panbiogeographic methodology is a useful tool for the general naturalist or recreational biologist, as it enables observations of plant or animal distributions to be associated with the geological processes of an area in a disciplined but convenient way. This is achieved by plotting the known distribution of the taxa, using the current taxonomy, on a map and connecting these points by the shortest-distance tree. Interpretations arrived at by this methodology not only provide a framework for understanding of evolutionary processes but they stress the dynamics of the geological and biological systems. Panbiogeography emphasises the importance of biological communities and the significance of these areas at a regional or national level. This type of area recognition aids conservation advocates, as it helps to set priorities of areas identified as needing protection. Inland saline areas of Central Otagoare discussed by way of an example. This approach produces novel predictions about these areas that aid the interpretation of their conservation status. Panbiogeography highlights the need to advocate conservation of restricted species not only in strategic areas but throughout their natural range. Panbiogeography, by stressing the importance of the actual distribution of taxa is therefore useful in the Protected Natural Areas Programme as it enables the significance of the ecological district to be effectively assessed. Transfers of birds, reptiles, and insects are discussed in the context of panbiogeography and some of the dangers are pointed out of placing species on island refuges where they may never have been.     

Isoenzyme and Total Protein Analysis by Agarose Isoelectric Focusing, and Taxonomy of the Genus Acanthamoeba

Thirty axenically grown reference strains belonging to 15 different Acanthamoeba spp. were investigated for isoenzyme patterns by agarose isoelectric focusing in the pH range 3–10. Zymograms of acid phosphatase, leucine amino peptidase, malate dehydrogenase, propionyl esterase, glucose phosphate isomerase, phosphoglucomutase, and alcohol dehydrogenase were compared. The same strains were also analyzed for protein patterns separated by agarose isoelectric focusing in a pH gradient of 5–8. The results suggested changes in taxonomy within morphology group II of Pussard & Pons. Acanthamoeba paradivionensis becomes a synonym of A. divionensis. Although this species seems to be related to A. rhysodes, it could not be concluded that the species names are synonyms since the type strain of A. rhysodes was not available for comparison. In the subgroup A. polyphaga–A. quina–A. lugdunensis, A. lugdunensis becomes the species name for pathogenic strains of this subroup, A. quina for the nonpathogenic strains, while A. polyphaga is the species name for an atypical strain. Two strains of A. castellanii showed different zymograms from strain Neff of this species, but related protein patterns. In group III, A. pustulosa is found to be a synonym of A. palestinensis, while one strain of A. lenticulata is also found to belong to the A. palestinensis species. All other species names in both morphology groups could be retained as valuable, on the basis of the techniques used. Group I was not investigated, as axenic cultures could not be obtained.     

A revision of the desert shrub Fagonia (Zygophyllaceae)

The taxonomy of the desert shrub genus Fagonia is revised in detail. In total 167 names are accounted for, lectotypes are selected for 33 names, and two names are neotypified. A key to the 34 species is presented, as well as distribution maps for each species. Three new species are described and illustrated, F. densispina and F. latistipulata from Somalia, and F. hadramautica from Yemen. Of the accepted species, 24 are restricted to the Old World and eight to the New World. Most of the Old World species are confined to the Saharo‐Sindian region, with two extending to parts of Macaronesia. Eight species are endemic to the Somali‐Masai region, and two are restricted to southern Africa. In the New World four species are endemic to Baja California, two to northern Baja California and adjacent parts of southwestern USA, one to the province of Coahuila in northeastern Mexico, and one to Chile and Peru. The names of all four species of Fagonia currently on the IUCN Red List of Threatened Plants are put into synonymy.