Global genetic diversity and geographical and host-species distribution of beak and feather disease virus isolates

Psittacine beak and feather disease (PBFD) has a broad host range and is widespread in wild and captive psittacine populations in Asia, Africa, the Americas, Europe and Australasia. Beak and feather disease circovirus (BFDV) is the causative agent. BFDV has an ~2 kb single stranded circular DNA genome encoding just two proteins (Rep and CP). In this study we provide support for demarcation of BFDV strains by phylogenetic analysis of 65 complete genomes from databases and 22 new BFDV sequences isolated from infected psittacines in South Africa. We propose 94% genome-wide sequence identity as a strain demarcation threshold, with isolates sharing > 94% identity belonging to the same strain, and strain subtypes sharing> 98% identity. Currently, BFDV diversity falls within 14 strains, with five highly divergent isolates from budgerigars probably representing a new species of circovirus with three strains (budgerigar circovirus; BCV-A, -B and -C). The geographical distribution of BFDV and BCV strains is strongly linked to the international trade in exotic birds; strains with more than one host are generally located in the same geographical area. Lastly, we examined BFDV and BCV sequences for evidence of recombination, and determined that recombination had occurred in most BFDV and BCV strains. We established that there were two globally significant recombination hotspots in the viral genome: the first is along the entire intergenic region and the second is in the C-terminal portion of the CP ORF. The implications of our results for the taxonomy and classification of circoviruses are discussed. © 2011 SGM.

Personalized recommender systems integrating tags and item taxonomy

The social tags in Web 2.0 are becoming another important information source to profile users' interests and preferences to make personalized recommendations. To solve the problem of low information sharing caused by the free-style vocabulary of tags and the long tails of the distribution of tags and items, this paper proposes an approach to integrate the social tags given by users and the item taxonomy with standard vocabulary and hierarchical structure provided by experts to make personalized recommendations. The experimental results show that the proposed approach can effectively improve the information sharing and recommendation accuracy.

Taxonomy and redescription of the Yellow-footed Antechinus, Antechinus flavipes (Waterhouse) (Marsupialia: Dasyuridae)

We provide a taxonomic redescription of the ubiquitous and variable dasyurid marsupial Yellow-footed Antechinus, Antechinus flavipes (Waterhouse), which comprises three currently recognized subspecies whose combined geographic distribution spans almost the length and breadth of Australia. A. flavipes leucogaster Gray is confined to south-west Western Australia; A. flavipes flavipes is distributed in south-eastern Australia across four states—South Australia, Victoria, New South Wales and Queensland; A. flavipes rubeculus Van Dyck is confined to the wet tropics of Queensland. A. flavipes is readily distinguished from all extant congeners based on external morphology by the following combination of features: a grey head; orange-yellow toned flanks/rump, feet and tail base; pale eye-rings and a darkened tail tip. A. flavipes skulls are stout, being broad at the level of the rear upper molars, have small palatal vacuities and small entoconid cusps on the lower molars. However, notable differences among subspecies of A. flavipesprevent any obvious collection of skull characters being diagnostic for species-level discrimination among congeners. A. flavipes rubeculus is the largest of the three subspecies of Yellow-footed Antechinus and most similar in skull morphology to A. leo, A. bellus and A. godmani—all four species are geographically limited to tropical Australia. A. f. rubeculus is notably larger in many characters than its conspecifics: A. f. flavipes, the next largest, and A. f. leucogaster, the smallest of the group. A. f. flavipes and A. f. leucogaster diverge significantly at only a few skull characters, and both subspecies have cranial morphological affinities with the recently discovered A. mysticus, most notably A. f. leucogaster. Phylogenies generated from mt- and nDNA data strongly support Antechinus flavipes as monophyletic with respect to other members of the genus; within A. flavipes, each of the three recognized subspecies form distinctive monophyletic clades.

Taxonomy and redescription of the Atherton Antechinus, Antechinus godmani (Thomas) (Marsupialia: Dasyuridae)

We provide a taxonomic redescription of the dasyurid marsupial Atherton Antechinus, Antechinus godmani (Thomas). A. godmani is only rarely encountered and limited to wet tropical rainforests of north-east Queensland, Australia, between the towns of Cardwell and Cairns (a distribution spanning 135 kilometres from north to south). The distinctive species occurs at altitudes of over 600 meters asl, in all major rainforest types, and can be found with both the northern subspecies of the Yellow-footed Antechinus, A. flavipes rubeculus Van Dyck and the Rusty Antechinus, A. adustus (Thomas). A. god-mani is clearly separated from all congeners on the basis of both morphometrics and genetics. A. godmani can be distin-guished from all extant congeners based on external morphology by a combination of large size, naked-looking tail and reddish fur on the face and head. A. godmani skulls are characteristically large, with a suite of long features: basicranium, palate, upper premolar tooth row, inter-palatal vacuity distance and dentary. Phylogenies generated from mt- and nDNA data position Antechinus godmani as monophyletic with respect to other members of the genus; A. godmani is strongly supported as the sister-group to a clade containing all other antechinus, but excluding the south-east Australian Dusky An-techinus, A. swainsonii (Waterhouse) and Swamp Antechinus, A. minimus (Geoffroy). Antechinus godmani are genetically very divergent compared to all congeners (mtDNA: range 12.9–16.3%).

Seasonal occurrence and distribution of Bryde's whales in the Hauraki Gulf, New Zealand

The Hauraki Gulf is a large, shallow embayment located north of Auckland City (36°51′S, 174°46′E), New Zealand. Bryde's whales (Balaenoptera edeni) are the most frequently observed balaenopterid in these waters. To assess the use of the Hauraki Gulf for this species, we examined the occurrence and distribution in relation to environmental parameters. Data were collected from a platform of opportunity during 674 daily surveys between March 2003 and February 2006. A total of 760 observations of Bryde's whales were recorded throughout the study period during 371 surveys. The number of Bryde's whales sighted/day was highest in winter, coinciding with the coolest median sea-surface temperature (14.6°C). Bryde's whales were recorded throughout the Hauraki Gulf in water depths ranging from 12.1–59.8 m (mean = 42.3, SD = 5.1). Cow–calf pairs were most frequently observed during the austral autumn in water depths of 29.9–53.9 m (mean = 40.8, SD = 5.2). Data from this study suggest Bryde's whales in the Hauraki Gulf exhibit a mix of both “inshore” and “offshore” characteristics from the Bryde's whales examined off the coast of South Africa. Based on complete mitochondrial DNA sequences, Sasaki et al. (2006) recognized two sister species of Bryde's whales: Balaenoptera brydei and B. edeni, with the latter including small-type, more coastal Bryde's whales from Japan, Hong Kong, and Australia. Their samples and samples in previous analyses of small-type whales, all originated from eastern and southeastern Asia. These authors did not include the forms of Bryde's whales that occur in other regions, e.g., in the Pacific off Peru (Valdivia et al. 1981), in the Atlantic off Brazil (Best 1977) and in the western Indian Ocean off South Africa (Best 1977). Recent genetic analysis using mtDNA from the “inshore” and “offshore” forms from South Africa confirms the offshore form is B. brydei, and establishes that the inshore form is more closely related to B. brydei than to B. edeni (Penry 2010). These different forms do vary considerably in their habitat use and ecology (refer to Table 1 for a detailed comparison between the South African inshore and offshore forms, as described by Best (1967, 1977) and the Bryde's whales from New Zealand (Wiseman 2008). Recent genetic analysis on the Bryde's whales in the Hauraki Gulf suggests they are B. brydei (Wiseman 2008). However, pending resolution of the uncertainty within and between species of this genus, we follow the Society of Marine Mammal's committee on taxonomy, who state that B. edeni applies to all Bryde's whales.

Beyond Moa's Ark and Wallace's Line: extralimital distribution of new species of Austronothrus (Acari, Oribatida, Crotoniidae) and the endemicity of the New Zealand oribatid mite fauna

The genus Austronothrus was previously known from three species recorded only from New Zealand. Austronothrus kinabalu sp. nov. is described from Sabah, Borneo and A. rostralis sp. nov. from Norfolk Island, south-west Pacific. A key to Austronothrus is included. These new species extend the distribution of Austronothrus beyond New Zealand and confirms that the subfamily Crotoniinae is not confined to former Gondwanan landmasses. The distribution pattern of Austronothrus spp., combining Oriental and Gondwanan localities, is indicative of a curved, linear track; consistent with the accretion of island arcs and volcanic terranes around the plate margins of the Pacific Ocean, with older taxa persisting on younger island though localised dispersal within island arc metapopulations. Phylogenetic analysis and an area cladogram are consistent with a broad ancestral distribution of Austronothrus in the Oriental region and on Gondwanan terranes, with subsequent divergence and distribution southward from the Sunda region to New Zealand. This pattern is more complex than might be expected if the New Zealand oribatid fauna was derived from dispersal following re-emergence of land after inundation during the Oligocene (25 mya), as well as if the fauna emanated from endemic, relictual taxa following separation of New Zealand from Gondwana during the Cretaceous (80 mya).

Quality-aware review selection based on product feature taxonomy

As of today, user-generated information such as online reviews has become increasingly significant for customers in decision making process. Meanwhile, as the volume of online reviews proliferates, there is an insistent demand to help the users tackle the information overload problem. In order to extract useful information from overwhelming reviews, considerable work has been proposed such as review summarization and review selection. Particularly, to avoid the redundant information, researchers attempt to select a small set of reviews to represent the entire review corpus by preserving its statistical properties (e.g., opinion distribution). However, one significant drawback of the existing works is that they only measure the utility of the extracted reviews as a whole without considering the quality of each individual review. As a result, the set of chosen reviews may consist of low-quality ones even its statistical property is close to that of the original review corpus, which is not preferred by the users. In this paper, we proposed a review selection method which takes review quality into consideration during the selection process. Specifically, we examine the relationships between product features based upon a domain ontology to capture the review characteristics based on which to select reviews that have good quality and preserve the opinion distribution as well. Our experimental results based on real world review datasets demonstrate that our proposed approach is feasible and able to improve the performance of the review selection effectively.

Rotifera recorded from China, 1893-1997, with remarks on their composition and distribution

A search of the literature on rotifers recorded from China, includes today 477 valid species names and 42 subspecies or infrasubspecific variants in 84 genera and 28 families recorded since 1893. Chinese rotifera research is reviewed, and all recorded species are listed with current taxonomic status and their first localities in China. Most of the named taxa are widely distributed or cosmopolitan, with only a small number (about 3%) possibly restricted to China. This fauna exhibits 15 endemic taxa. The composition and distribution of Chinese Rotifera are briefly analyzed. It is likely that considerably more rotifers remain to be described from China as further study to be carried on and taxonomic resolution improves.

New wild Brassica oleracea L. germplasm at its western distribution limit in the Iberian Peninsula

An exploration and collection mission for wild Brassica oleracea populations was carried out in spring and summer of 2013. The aim of this collection was to expand the number of accessions of wild Brassica oleracea available for basic and applied research in plant breeding. In this paper we report a new accession of wild Brassica oleracea in an unexplored coastal area of Galicia, NW Iberian Peninsula. Details of population ecology and vegetation, soil, climate and geographic data were recorded for this population. The “Endangered” threat category for the region is proposed, and actions for in situ and ex situ conservation are proposed. Seeds will be added to the germplasm collections of University of Santiago de Compostela and Misión Biológica de Galicia (CSIC) for further research on diverse aspects of the dynamics and ecophysiology of the population along with characterization and evaluation of useful traits.

The deep-sea chiton Nierstraszella (Mollusca: Polyplacophora: Lepidopleurida) in the Indo-West Pacific: taxonomy, morphology and a bizarre ectosymbiont

This study investigated the taxonomy and distribution of the deep-sea polyplacophoran mollusc Nierstraszella Sirenko, 1992 in the Indo-West Pacific, based on a collection of 516 specimens collected in the Philippines and Solomon Islands. Although seven species names have historically been proposed in this group of chitons, all have been considered as synonyms of the monotypic N. lineata (Nierstrasz, 1905). Morphological examination of this new material reveals the presence of two species. N. lineata is distinct from N. andamanica (Smith, 1906), based on morphological characters given in the original species description and very distinctly different morphology of aesthete pores in the shell surface. Furthermore, populations of N. andamanica in the Philippines and Solomon Islands are locally colonized with the epibiotic (ectoparasitic) bryozoan Pseudobathyalozoon profundum d'Hondt, 2006. These bryozoans attach ventrally to the girdle of the host chiton and the erect zooids feed within the pallial cavity, among the chiton's gills.

INDIAN AND ANTARCTIC BRYOZOANS - TAXONOMY AND OBSERVATIONS ON TOXICOLOGY

This thesis embodies findings on a taxonomical investigation of a group of lower marine invertebrates belonging to the category coelomata. Bryozoans are well known both in fossil and recent taxonomical history. They comprise of about 5,000 living and 16000 fossil species. Bryozoans are well known for their taxonomic abundance and structural diversity,representing the various ecological niches ranging from the intertidal to the abyssal benthic. At a time when global marine biological diversity has become a concern of not only to the scientists but also to the policy makers,an understanding of species diversity and abundance are cardinal aspects of biological studies. Geological time scales which is known that by Pre-Cambrian, marine invertebrate diversity reach the maximum and this diversity has become more comprehensive as time advanced. Taxonomists a vanishing species of scientists have become more concerned in discerning patterns of species diversity. The basic tool for this is identification fo animals. with this idea in mind a detailed study of taxonomy of bryozoan was undertaken . The major part of this thesis is devoted to describe various species of bryozoans with detailed description and ecotypical variations.The pattern of distribution and abundance which are important aspects of animal groups have also been documented. Possible effects of heavy metal contamination on the tolerance and growth of bryozoans, a few species of which have been eliminated from the chronically polluted areas of Cochin backwaters have also been documented.

Studies on taxonomy and ecology of Mysidacea from the EEZ of India

Members of the order Mysidacea are important component in marine and estuarine plankton inhabiting all regions of the oceans. There are many brackish water species and few species occur in fresh water, some have become adapted to the specialized environments of caves and wells. They are omnivores, responsible for remineralisation of a substantial portion of the detritus in the water column. They form an important link in the food chain (between microbial producers and secondary consumers) and therefore play a major role in the cycling of energy within the aquatic ecosystem. In tropical and subtropical waters, swarms of mysids are exploited commercially and marketed as preserved cooked food. Mysids have been used in fish farming as live feed resource. They are also excellent experimental organism, extremely useful in the studies of potential impact of various pollutants in the aquatic environment. Mysids are also used in wood pulp effluent plants.Considering the significant role of mysids in the productivity of tropical and coastal ecosystems,the present study has been undertaken to extend our knowledge on the systematics, species composition, distribution,abundance and ecology of mysid fauna of the Indian EEZ and adjoining areas. The present study therefore will undoubtedly fumish valuable information on Mysidacea of the Indian waters.

Parasite distribution and histopathological studies on certain commercially important fishes of cochin area

In order to check the damage caused by the parasites, even though it is difficult in open waters, a proper understanding of the seasonal variation in the distribution of the parasite and other factors like age of the host, sex of the host, which affect distribution of parasite is a must. Although several workers have carried out investigations on the taxonomy of metazoan parasites of marine and brackish water Fishes of India, very little attempt is made to correlate such investigations with the host and the environment. In this thesis such an attempt is made by the researcher. In chapter one the literature related to the prevalence, mean intensity of infection, and histopathological changes caused by the metazoan parasites, in particular by helminths, copepods and isopods, was reviewed. Chapter two contains observations on the distribution pattern of parasites in relation to the season, sex, and size of the host. It was found that the prevalence rate of radiorynchus_indicus infecting the alimentary canal of Tachysurugs mgacuglatus, Ergasilus sp. infecting the gills of T maculatus, and Lernaeeniicus ramosus found on the body surface of Qeimgipteirfugs jagonicus was higher during monsoon season. But agarna malayi found in the opercular chamber and Ehilometra cephalus infecting the gonads of valamugil speiglari showed a higher prevalence rate during the postmonsoon season. This was discussed on the basis of the hydrographical characteristics prevailing in the study area during the three different seasons. It was also observed that the sex of the host did not influence significantly the distribution pattern of the parasites. The reasons for this were also discussed. Invariably, the size of the host was found to influence the parasite distribution pattern. It was observed that the prevalence rate showed an increase with increase in size of the fish. This was discussed on the basis of food habits of the host, along with other aspects An attempt was made in chapter three to study the histopathological effects of‘ the various parasites on their respective sites of attachments on host Fishes. It was found that except Rhadinorhyhchugs indicus, all other parasites produced damages of varying intensity, in the form of hypertrophy, rhyperplasia, haemorrhage, tissue disruption and ulcers. Interestingly, E. indicus, an acantho— cephalid with a powerful proboscis for attachment was found not to cause any serious damage to the intestine of the host Fish. All these aspects are included in the third and final chapter of the thesis.

The Systematics, Distribution and Bionomics of Deep sea fishes beyond depth 200m along the South west coast of India

Reducing fishing pressure in coastal waters is the need of the day in the Indian marine fisheries sector of the country which is fast changing from a mere vocational activity to a capital intensive industry. It requires continuous monitoring of the resource exploitation through a scientifically acceptable methodology, data on production of each species stock, the number and characteristics of the fishing gears of the fleet, various biological characteristics of each stock, the impact of fishing on the environment and the role of fishery—independent on availability and abundance. Besides this, there are issues relating to capabilities in stock assessment, taxonomy research, biodiversity, conservation and fisheries management. Generation of reliable data base over a fixed time frame, their analysis and interpretation are necessary before drawing conclusions on the stock size, maximum sustainable yield, maximum economic yield and to further implement various fishing regulatory measures. India being a signatory to several treaties and conventions, is obliged to carry out assessments of the exploited stocks and manage them at sustainable levels. Besides, the nation is bound by its obligation of protein food security to people and livelihood security to those engaged in marine fishing related activities. Also, there are regional variabilities in fishing technology and fishery resources. All these make it mandatory for India to continue and strengthen its marine capture fisheries research in general and deep sea fisheries in particular. Against this background, an attempt is made to strengthen the deep sea fish biodiversity and also to generate data on the distribution, abundance, catch per unit effort of fishery resources available beyond 200 m in the EEZ of southwest coast ofIndia and also unravel some of the aspects of life history traits of potentially important non conventional fish species inhabiting in the depth beyond 200 m. This study was carried out as part of the Project on Stock Assessment and Biology of Deep Sea Fishes of Indian EEZ (MoES, Govt. of India).