Larval host records of butterflies in Japan

Using Japanese literature, we created a consolidated list of host records of butterflies in Japan. The list used the host records described in eight major illustrated reference books, two checklists, and 14 other pieces of literature. The presence of larvae on plants, the observation of larvae eating plants or insects in the field were considered as host records. We collected all species recorded in Japan. Scientific, family, and Japanese names of butterflies were consolidated using the BINRAN database (http://binran.lepimages.jp/). Scientific and Japanese names of host plants were based on the YList database (http://ylist.info/). If scientific names of host plants were not found in YList, we used scientific names based on The Plant List (http://www.theplantlist.org/). Family names of host plants were based on the Catalogue of Life database (http://www.catalogueoflife.org/). Scientific, family, and Japanese names of host insects were based on the MOKUROKU database (http://konchudb.agr.agr.kyushu-u.ac.jp/mokuroku/) for Hymenoptera and the catalogue of the Paraneoptera of Japan published by the Entomological Society of Japan for Hemiptera. We also provided the references of each host record and the original names described in the referred literature. Two datasets, HostDB and ReferenceDB, were created to include 3600 records of butterfly larval hosts in Japan, along with scientific and Japanese names of each species and a literature list. These datasets will be useful for basic and applied biological studies of butterflies. Data files are stored in the Ecological Research Data Archives (http://db.cger.nies.go.jp/JaLTER/ER_DataPapers/) and available from http://hostbj.lepumus.net/. These datasets are published under the Creative Commons License Attribution-ShareAlike 4.0 (CC BY-SA, https://creativecommons.org/licenses/by-sa/4.0/).     

Ergothioneine production with Aspergillus oryzae

To establish a reliable and practical ergothioneine (ERG) supply, we employed fermentative ERG production using Aspergillus oryzae, a fungus used for food production. We heterologously overexpressed the egt-1 and -2 genes of Neurospora crassa in A. oryzae and succeeded in producing ERG (231.0 mg/kg of media, which was 20 times higher than the wild type).

Abbreviations: ERG: ergothioneine; HER: hercynine; Cys-HER: hercynylcysteine-sulfoxide; SAM: S-adenosylmethionine; SAH: S-adenosylhomocysteine; l-His: l-histidine; l-Cys: l-cysteine; LC-ESI-MS: liquid chromatography-electrospray ionization-mass spectrometry     

Aquatic vascular plants in Japanese lakes

This data paper describes the native vascular aquatic plant floras of 268 Japanese lakes recorded from 1899–2011. The data were compiled from 201 literature sources, most of which were written in Japanese and published in local journals or individual reports rather than in major scientific journals. The literature was searched using web-based services (i.e., Google Scholar, http://scholar.google.com/; CiNii, http://ci.nii.ac.jp/en; JDreamII, http://pr.jst.go.jp/jdream2/; and ISI, http://apps.webofknowledge.com) and by private communication with experts or local governments. Scientific names were consolidated under currently-accepted nomenclature. Four datasets, FloraDB, LakeDB, SpeciesDB, and LiteratureDB, were created to include records of the flora of each lake in each year, the names and locations of the lakes, the scientific names and synonyms of the aquatic vascular plants, and a literature list, respectively. These data can be used to study long-term changes in the species composition and/or richness of aquatic plants in Japanese lakes.     

Book reviews

Patterns of thought in Africa and the West: Essays on magic, religion and science , by Robin Horton. Cambridge University Press, Cambridge, 1997. xi, 471pp., figures, notes, bibliography, index. ISBN 0–521–36926–6 (paperback).

Women's experiences with HIV/AIDS: An international perspective , edited by Lynellyn D. Long and E. Maxine Ankrah. Columbia University Press, New York, 1996. x, 426pp., tables, references, notes on contributors, index. ISBN 0–231–10605‐X (paperback).

A healing place: Indigenous visions for personal empowerment and community recovery , by Kayleen M. Hazelhurst. Central Queensland University Press, Rockhampton, 1996. xiii, 274pp., notes, illustrations, references. ISBN 0–908140–87–8 (paperback).

Reading the skin: Adornment, display and society among the Wahgi , by Michael O'Hanlon. Crawford House Press, Bathurst, 1989. 139pp., map, photographs, orthography and kinship terms, glossary, notes, bibliography, index. ISBN 1–86333–003–8 (hardback).

Paradise: Portraying the New Guinea Highlands , by Michael O'Hanlon. Crawford House Press, Bathurst, 1993. 99pp., maps, photographs, notes, bibliography, index. ISBN 1–86333–078‐X (paperback).

To sing with pigs is human: The concept of person in Papua New Guinea , by Jane C. Goodale. University of Washington Press, Seattle, 1995. xvi, 269pp., map, tables, figure, musical scores, photographs, bibliography, index. ISBN 0–295–94736–2 (paperback).

Resplendent sites, discordant voices: Sri Lankans and international tourism , by Malcolm Crick. Harwood Academic Publishers, Chur, 1994. x, 237pp., maps, tables, photographs, bibliography, index. ISBN 3–7186–5564–0 (hardback).

Impasse of the angels: Scenes from a Moroccan space of memory , by Stefania Pandolfo. University of Chicago Press, Chicago, 1997. xi, 389pp., photograph, notes, index. ISBN 0–226–64532–0 (paperback).

Mal'uocchiu: Ambiguity, evil eye, and the language of distress , by Sam Migliore. University of Toronto Press, Toronto, 1997. xiv, 159pp., tables, figures, glossary, notes, bibliography, index. ISBN 0–8020–7922–9 (paperback).

Satmar: Two generations of an urban island: The life, thought and culture of an Hasidic Jewish community in America , by Israel Rubin. Peter Lang, New York, 1997. xii, 341pp., tables, figures, notes, index. ISBN 0–8204–0759–3 (hardback).

UFO crash at Roswell: The genesis of a modern myth , by Benson Saler, Charles A. Ziegler and Charles B. Moore. Smithsonian Institution Press, Washington DC, 1997. xii, 198pp., maps, tables, figures, appendices, notes, bibliography, index. ISBN 1–56098–751–0 (hardback).     

Morphological and sexual traits in Atlas and Iberian Pied Flycatchers Ficedula hypoleuca speculigera and F. h. iberiae: a comparison

Capsule: There are significant biometric differences between Pied Flycatchers from Iberian and north African populations which are consistent with proposals to classify the two forms into separate species.

Aims: To determine the similarities and differences in the main biometrical and plumage sex traits between populations of the Iberian Pied Flycatcher Ficedula hypoleuca iberiae and the Atlas Flycatcher Ficedula hypoleuca speculigera.

Methods: Biometric and plumage traits of 193 breeding individuals of Iberian Pied Flycatchers and 43 Atlas Flycatchers were measured in 2014 with standardized protocols.

Results: Both sexes of Atlas Flycatchers were larger than Iberian Pied Flycatchers in skeletal (tarsus) and wing size and also differed in bill morphology, which was wider but shallower in speculigera than iberiae, with females (but not males) having shorter bills than iberiae females. Males differed in mantle colour and forehead patch size, with speculigera males being darker and displaying larger forehead patches than iberiae males. As in populations of iberiae, some speculigera females also expressed a white forehead patch.

Conclusion: We demonstrate significant phenotypic differences between Iberian Pied Flycatchers and Atlas Flycatchers with respect to size and traits of ecological and evolutionary relevance, supporting the recently proposed scenarios on their independent evolution.     

The long and the short of it: long-styled florets are associated with higher outcrossing rate in Senecio vulgaris and result from delayed self-pollen germination

Background: It has been reported that some plants of the self-compatible species Senecio vulgaris produce capitula containing long-styled florets which fail to set seed when left to self-pollinate, although readily set seed when self-pollinated by hand.

Aims: To determine if production of long-styled florets is associated with higher outcrossing rate in S. vulgaris, and whether long-styles occur in non-pollinated florets, whereas short-styles are present in self-pollinated florets.

Methods: The frequency of long-styled florets was compared in the radiate and non-radiate variants of S. vulgaris, known to exhibit higher and lower outcrossing rates, respectively. In addition, style length was compared in emasculated florets that were either self-pollinated or left non-pollinated.

Results: Long-styled florets were more frequent in the higher outcrossing radiate variant. Following emasculation, long styles occurred in non-pollinated florets, while short styles were present in self-pollinated florets. The two variants did not differ in style length within the non-pollinated or within the self-pollinated floret categories.

Conclusions: A high frequency of long-styled florets is associated with higher outcrossing rate in S. vulgaris and results from delayed self-pollination and pollen germination on stigmas.     

Morphological differentiation of Icelandic Redpolls,Acanthis flammea islandica

Capsule The analyses support the grouping of the three Acanthis species, although a large split is observed between the A. hornemanni subspecies.

Aims To investigate the morphological variation in A. f. islandica among different periods of the year and its morphological differentiation from the other subspecies A. f. flammea and A. f. rostrata, and also from the redpoll species, A. cabaret and the two subspecies of A. hornemanni, exilipes and hornemanni.

Methods The subspecies status of the Icelandic population was evaluated with Amadon's rule, by comparing its variation of traits to the distribution of the traits in different species/subspecies of the group.

Results A. f. islandica is characterized by intermediate wing, bill and tail lengths. Based on the 75% rule, wing length and bill depth can be used to discriminate A. f. islandica from both extreme morphs of redpolls (currently classified as different species); A. hornemanni and A. cabaret, and tail and wing length can distinguish A. f. islandica from its conspecifics A. f. flammea. The overall morphological divergence within the redpoll complex is not supported by association to the studied nuclear markers.

Conclusion The taxonomic status of the three redpoll species is supported by Amadon's rule, however the subspecies status of the Icelandic Redpoll remains unclear.     

Editorial Retraction

Upon a thorough investigation, it has been determined that the paper titled “Integrating Microbial Composting and Vermicomposting for Effective Utilization of By-Products of Sugar Cane-Processing Industries” by Shweta, Rahul Kumar, B.L. Singh, and Verma Deepshikha published in the Bioremediation Journal, 2010, Volume 14, pages 158–167, was simultaneously submitted and published in two journals. The same study with minor textual variations titled “Composting of sugar-cane waste by-products through treatment with microorganisms and subsequent vermicomposting” also written by Shweta, Rahul Kumar, B.L. Singh, and Verma Deepshikha published in the Elsevier publication, Bioresource Technology, 2010, 6707–6711, three months prior to publishing in Bioremedation Journal.

As a result the article published in Bioremediation Journal has been retracted and should not be cited in the electronic or print version of the journal.

Dr. Hanadi S. Rifai

Editor-in-Chief

Bioremediation Journal

Please click here to view the article to which this statement of retraction relates.     

Morphology,geographical variation and the subspecies of Marsh Tit Poecile palustris in Britain and central Europe

Capsule All British Marsh Tits belong to subspecies Poecile palustris dresseri, being smaller than nominate P. p. palustris of central Europe.

Aims Determining the subspecies of Marsh Tit in Britain to test whether ssp. P. p. palustris occurs in northern England and Scotland, by assessing regional variation in size compared with central European birds.

Methods 1147 wing length and 250 tail length measurements from 953 Marsh Tits were compared between eight British locations to test for regional variation. Biometrics were compared between birds from Britain and six locations within the continental European range of ssp. palustris.

Results There was no regional variation in wing or tail lengths among British Marsh Tits, indicating that all resident birds belong to ssp. dresseri. There was no evidence supporting the existence of ssp. palustris in northern England. British birds were significantly smaller than those from continental Europe, with proportionately shorter tails, consistent across all age and sex classes.

Conclusion All British Marsh Tits should be considered as ssp. dresseri, with ssp. palustris being limited to continental Europe. With no evidence of regional variation in size within Britain, reliable sexing methods based on biometrics could be applied in demographic studies throughout the country.     

The role of recruitment and dispersal limitation in tree community assembly in Amazonian forests

Background: Species composition of plant communities is shaped by the interplay between dispersal limitation, environmental filters and stochastic events.

Aims: The aim of this work was to investigate the effects of dispersal limitation and environmental filtering on tree recruitment. To accomplish this, we employed the unified neutral theory of biodiversity and biogeography to examine migration within the metacommunity, defined as a set of interacting local communities linked by the dispersal of multiple potentially interacting species.

Methods: We sampled 12,975 individuals with dbh ≥ 1 cm in 26 1-ha permanent plots, including habitats of terra firme, transitional forests, várzea and campinarana, on the upper Madeira River, Brazilian Amazon.

Results: Campinarana drew individuals from outside the metacommunity species pool at a mean probability of recruitment of 0.06, a much lower probability than terra firme (0.31), transitional (0.21) and várzea forests (0.22). Environmental variables, such as water table depth, soil texture and fertility, were related to differences in community assembly.

Conclusions: Species abundance distribution and diversity patterns of plant assemblages in a large river landscape in the Amazon highlight the importance of environmental heterogeneity that conditions beta-diversity. The high variation in recruitment probabilities from the metacommunity species pool to local communities suggests high habitat variability in the process of maintaining patterns of local diversity.     

Habitat use and tree selection of a declining Afro-Palaearctic migrant at sub-Saharan staging and wintering sites

Capsule: Wood Warblers Phylloscopus sibilatrix showed significant selection for tree species and woodland characteristics at staging and wintering sites in sub-Saharan Africa.

Aims: To investigate home range size, habitat and tree species selection of Wood Warblers at a staging site in Burkina Faso (Koubri) and a wintering site in Ghana (Pepease).

Methods: Comparing habitat recorded at locations of radio-tagged birds and at control points, we investigated whether there was habitat and tree species selection. We also compared home range size of individual birds between the two sites.

Results: Home range size did not differ between the two sites. There was significant selection for tree species at both Koubri and Pepease: Anogeissus leiocarpus and Albizia zygia, respectively. At Koubri, there was significant avoidance of the most common tree species (Azadirachta indica, Mangifera indica (both non-native), Vitellaria paradoxa and Acacia spp.). In addition, there was a preference for taller trees and greater tree density at both sites. However, the probability of a point being used declined with increasing number of taller (>14?m) trees.

Conclusion: Fine-scale selection of woodland habitats suggests that Wood Warblers are likely to suffer the consequences of ongoing land-use change in their West African wintering grounds.     

Similarities in mRNA expression of peripheral blood drug metabolizing enzymes and cancer marker genes with biopsy samples of head and neck cancer patients

Purpose: To develop peripheral blood mRNA expression profiles of drug metabolizing enzymes (DMEs) as a surrogate to monitor tobacco induced head and neck squamous cell carcinoma (HNSCC), attempts were made to investigate (i) similarities in alterations with the cancer marker genes in biopsy samples and (ii) if alterations similar to that seen in biopsy samples are reflected in peripheral blood.

Methods: Total RNA from eight soft gingival tissues and eight biopsy samples of HNSCC patients and total DNA and RNA from blood of healthy controls (n?=?150) and HNSCC patients (n?=?150) was processed for expression and genotyping studies. Blood from patients receiving chemo-radiotherapy was processed for follow-up study.

Results: qRT-PCR revealed significant increase in mRNA expression of DMEs in biopsy and blood samples of HNSCC patients when compared to controls. Similar alterations were observed in cancer marker genes in these samples. Patients with variant genotypes of DMEs showed greater magnitude of alterations in mRNA expression when compared to wild type controls. Responders of chemo-radiotherapy showed significant decline in induction of mRNA expression of DMEs and cancer marker genes

Conclusions: The data suggest that peripheral blood expression profiles could be used to monitor tobacco-induced HNSCC as well as the treatment response.     

Gene Ontology annotation of the rice blast fungus, <Emphasis Type="Italic">Magnaporthe oryzae</Emphasis>

Background

Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html. However, a comprehensive manual curation remains to be performed. Gene Ontology (GO) annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly.

Methods

A similarity-based (i.e., computational) GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked.

Results

In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO). In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57%) being annotated with 1,957 distinct and specific GO terms. Unannotated proteins were assigned to the 3 root terms. The Version 5 GO annotation is publically queryable via the GO site http://amigo.geneontology.org/cgi-bin/amigo/go.cgi. Additionally, the genome of M. oryzae is constantly being refined and updated as new information is incorporated. For the latest GO annotation of Version 6 genome, please visit our website http://scotland.fgl.ncsu.edu/smeng/GoAnnotationMagnaporthegrisea.html. The preliminary GO annotation of Version 6 genome is placed at a local MySql database that is publically queryable via a user-friendly interface Adhoc Query System.

Conclusion

Our analysis provides comprehensive and robust GO annotations of the M. oryzae genome assemblies that will be solid foundations for further functional interrogation of M. oryzae.

     

Plant sex and phenological stage affect interactions with rhizosphere nematode communities

Background: In dioecious plants, females and males associate differently with mycorrhizal fungi, but interactions with other rhizosphere organisms are less well studied.

Aims: We investigated the effect of plant sex on rhizosphere nematode communities associated with Corema album, a dioecious shrub occurring in coastal habitats.

Methods: Rhizosphere samples were collected from males and females in three populations (150 plants), during fruiting and flowering. Nematode communities were characterised and compared between plant sexes through statistical analyses of the abundance of trophic groups, plant parasitic nematode (PPN) genera and ecological indices.

Results: Free-living nematodes showed no statistically significant differences owing to plant sex. Conversely, PPN community composition was significantly different between plant sexes during fruiting but not flowering, suggesting that physiological requirements over the annual phenological cycle of the plant influence ecological interactions with the rhizosphere.

Of the 13 PPN genera identified, the ectoparasitic Criconema and Hemicriconemellawere more abundant in the rhizosphere of males during fruiting, whereas the endoparasitic Meloidogyne associated more frequently with females, suggesting that plant host suitability is related to PPN feeding strategy.

Conclusions: It appears that interactions of individuals of different sexes of C. album with the rhizosphere nematode community vary with phenological stage, especially for PPN.     

Genetic profiling of the critically endangered palm species Medemia argun using newly developed chloroplast DNA markers

Background: Medemia argun is a rare wild palm tree species. Its global existence is assumed to include the main population of about 1000 trees in the Nubian Desert of Sudan and some scattered individuals in southern Egypt. The species had previously been assumed to be extinct, but then reported to be extant about 20 years ago.

Aims: To assess genetic variation and explore population genetic structure of M. argun, through development and analysis of microsatellite markers.

Methods: The genome sequence mining approach was applied in order to identify microsatellites in the chloroplast genome of Bismarckia nobilis, a species closely related of M. argun. A set of 49 markers were designed, and their characteristics are now provided. Seven chloroplast DNA markers were developed for use in the genetic characterisation of this threatened species.

Results: Five markers were found polymorphic in M. argun, which enabled the assessment of the genetic diversity of the species. Significant genetic differentiation was observed among generations and collection sites, accompanied by low genetic variation. The seven markers developed were polymorphic among the wild relatives Hyphaene thebaica and Borassus aethiopum.

Conclusions: This is the first study to report molecular markers for M. argun. Our results suggest that the genetic consequences of population fragmentation in M. argun are beginning to be evident.     

The taxonomic status and range extension of Grimmia exquisita J.Muñoz (Grimmiaceae,Bryophyta)

Introduction. We found an unusual specimen collected in 1975 from Xinjiang Province, China which may represent Grimmia exquisita J.Muñoz. However, this species is known only from the type localities and its taxonomic status is still controversial.

Methods. A voucher of the Chinese specimen is deposited in IFP herbarium. This specimen was studied with the typical anatomical and morphological methods applied within Grimmia (Maier, 2010).

Key Results. The Chinese species represents G. exquisita. After examining the type specimens of G. exquisita, we confirmed that it should be recognised as a distinct species.

Conclusions. This study expands the distribution area of G. exquisita to East Asia. The Chinese specimen was discovered in a rather different habitat to its types and consequently, G. exquisita may be a more widely distributed species. Evaluation of the Grimmia specimens in many different herbaria is needed.     

Habitat associations of young Black Grouse Tetrao tetrix broods

Capsule: In the Scottish Highlands, Black Grouse Tetrao tetrix females with young broods selected areas rich in wet flushes, grasses and Sphagnum mosses.

Aims: To identify associations between young Black Grouse broods and habitat characteristics.

Methods: We located brood-rearing Black Grouse females in four areas of moorland-forest mosaic in the Scottish Highlands. Each brood was paired with a random reference location 100?m away. We recorded cover of different habitats and fine-scale vegetation and structure within squares of 1 and 0.25?ha, respectively. Associations between brood occurrence and habitat and vegetation variables were examined at the two scales.

Results: Black Grouse broods were positively associated with wet flushes (1?ha), and with Heather Calluna vulgaris, sedges Carex spp., grasses, Sphagnum mosses and taller vegetation with intermediate levels of height variability (0.25?ha).

Conclusions: This study highlights the importance of wet habitats for young Black Grouse chicks. In addition, relatively tall field-layer vegetation comprising Heather, sedges, grasses over a layer of Sphagnum mosses attracted brood-rearing Black Grouse females. Many management practices associated with peatland restoration, including drain-blocking, Sphagnum re-establishment and the avoidance of burning on deep peat soils, are therefore consistent with favourable habitat management for Black Grouse.