1,721,066 research outputs found
The Anadara trapezia transcriptome : a resource for molluscan physiological genomics
No full textIn this study we undertook deep sequencing of the blood cockle, Anadara trapezia, transcriptome to generate genomic\ud
resources for future functional genomics analyses. Over 27 million high quality paired end reads were assembled\ud
into 75 024 contigs. Of these contigs, 29 013 (38.7%) received significant BLASTx hits and gene ontology\ud
(GO) terms were assigned to 13 718 of these sequences. This resourcewill facilitate physiological genomic studies\ud
to test the gene expression response of A. trapezia to various environmental stresses
Seed dispersal, germination and fine-scale genetic structure in the stream lily, Helmholtzia glaberrima (philydraceae)
No full textSeed dispersal in aquatic habitats is often considered to be a complex multistage process, where initial seed shadows are redistributed by water (hydrochory). The roles of hydrochory in seed dispersal and influencing population genetic structure were examined in Helmholtzia glaberrima using both ecological and genetic techniques. Ecological experiments showed that water can redistribute seeds and seedlings over local scales and that hydrochory can provide the potential for very long distance seed and seedling dispersal. Patterns of seedling genetic structure were affected by micro-drainages that direct water flow within populations and influence water-borne seed dispersal on a local scale. Strong non-equilibrium dynamics and persistent founder effects were responsible for the patterns of genetic structure observed among established populations of H. glaberrima. Classical metapopulation models best described dispersal patterns, while water-borne seed dispersal could potentially explain patterns of genetic differentiation within a stream system, it could not explain the distribution of genetic variation among stream systems. The current study found that although hydrochory influenced seed dispersal and seedling genetic structure within a population, it had little effect on the spatial pattern of genetic variation among established populations of H. glaberrima. Moreover, even though prolonged buoyancy and viability in water provide the potential for long-distance hydrochory, results presented here do not support the hypothesis that flowing water is an effective long distance seed dispersal vector for H. glaberrima. Taken together, these results suggest that the relative importance of gene flow via water-born seed dispersal in H. glaberrima may be low compared with that of some other riparian species
Understanding the genetic basis of invasiveness
No full textInvasive species provide excellent study systems to evaluate the ecological and evolutionary processes that contribute to the colonization of novel environments. While the ecological processes that contribute to the successful establishment of invasive plants have been studied in detail, investigation of the evolutionary processes involved in successful invasions has only recently received attention. In particular, studies investigating the genomic and gene expression differences between native and introduced populations of invasive species are just beginning and are required if we are to understand how plants become invasive. In the current issue of Molecular Ecology, Hodgins et al. () tackle this unresolved question, by examining gene expression differences between native and introduced populations of annual ragweed, Ambrosia artemisiifolia. The study identifies a number of potential candidate genes based on gene expression differences that may be responsible for the success of annual ragweed in its introduced range. Furthermore, genes involved in stress response are over-represented in the differentially expressed gene set. Future experiments could use functional studies to test whether changes in gene expression at these candidate genes do in fact underlie changes in growth characteristics and reproductive output observed in this and other invasive species
Micro-geographic landscape features demarcate seedling genetic structure in the stream lily, Helmholtzia glaberrima
No full textCopyright © 2007 Elsevier B.V. All rights reserved.Peter J. Prentis and Peter B. Matherhttp://www.elsevier.com/wps/find/journaldescription.cws_home/503303/description#descriptio
Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with Chlorella-Like Species (Chlorophyta).
Full text linkSeveral different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. Chlorella is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of Chlorella-like organisms is easily confused. Here we report a comprehensive barcoding analysis of Chlorella-like species from Chlorella, Chloroidium, Dictyosphaerium and Actinastrum based on rbcL, ITS, tufA and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of Chlorella-like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in C. sorokiniana, D. ehrenbergianum and C. Vulgaris. The tufA proved to be the most efficient barcoding locus, which thus could be as potential "specific barcode" for Chlorella-like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among rbcL, ITS and tufA genes. The best resolution for species differentiation appeared in tufA analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of rbcL, ITS and tufA sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Genetic structure of invasive weed Parthenium hysterophorus in Australia and Pakistan
No full textUnderstanding the patterns of genetic structure in the introduced range of invasive species can help elucidate invasion histories and levels of gene flow among populations. Parthenium weed (Parthenium hysterophorus L.; PW) is native to the Gulf of Mexico and central South America but has become globally invasive during the last three decades and little is known about the genetics of this species in its invasive range. The present study was conducted to determine the genetic structure of 95 individual samples from 11 populations (9 from Pakistan and 2 from Australia) of PW using ISSR fingerprinting. A total of 30 ISSR primers were screened; of which eight were selected due to their high polymorphism and reproducibility. In toto 147 bands were amplified, which ranged in size from 200-2000 bp; among which 97 were polymorphic. Genetic diversity within the populations both from Pakistan and Australia ranged between 0.193-0.278. Approximately 18% of genetic variation occurred among and 82% within populations. Principal Coordinate Analysis showed that within the 95 samples two groups were present: one contained samples collected mainly from Pakistan and the second group included the Australian samples along with two populations from Pakistan. Overall, there was limited gene flow among PW populations in Pakistan, although the genetic diversity within populations was high. The degree of genetic variation inferred from various population diversity measures can predict different events of founding populations, which have passed through complicated processes of invasion, experiencing genetic bottlenecks. Taken together, results showed that PW in Pakistan is genetically heterogeneous and may have been the result of multiple introductions
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