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The genome of the tardigrade Hypsibius dujardini - Popgroup 49 Talk, Edinburgh Dec 18, 2015
No full textPresentation on <b>The genome of the tardigrade </b><b>Hypsibius dujardini </b>by Mark Blaxter, at the 49th Popgroup meeting held in Edinburgh, Dec 18, 2015
Fig. 2 Cae o in Caenorhabditis monodelphis sp. n.: defining CrossMark the stem morphology and genomics of the genus Caenorhabditis
No full textFig. 2 Cae o abolts mo ode ph s sp. n., matu e spe matozoa fema e post- ıte e sac, TEM A ovvs=spe m ce sPublished as part of Dieter Slos, Walter Sudhaus, Lewis Stevens, Wim Bert & Mark Blaxter, 2017, Caenorhabditis monodelphis sp. n.: defining CrossMark the stem morphology and genomics of the genus Caenorhabditis, pp. 1-15 in BMC Zoology 2 (4) on page 5, DOI: 10.1186/S40850-017-0013-2, http://zenodo.org/record/32231
Caenorhabditis monodelphis Dieter Slos & Walter Sudhaus & Lewis Stevens & Wim Bert & Mark Blaxter 2017
No full text<p> <i>Caenorhabditis monodelphis</i> 1 sp. n. Slos & Sudhaus</p> = <i>Caenorhabditis</i> sp. SB341 [7] <p>= <i>Caenorhabditis</i> sp. SB341 and <i>Caenorhabditis</i> sp. n.</p> <p>SB341 [36]</p> <p>= <i>Caenorhabditis</i> sp. n. 1 (SB341) and (lapse)</p> <p> <i>Caenorhabditis</i> sp. n. 4 (SB341) [10]</p> <p>= <i>Caenorhabditis</i> sp. 1 SB3 41 [6, 8, 37]</p> <p>= <i>Caenorhabditis</i> sp. 4 SB3 41 [38]</p> (Figs. 1, 2, 3 and 4; Table 1) Adult <p>Small species (female 0.7 2 - 1.0 4 mm, male 0.6 5 <i>–</i> 0.7 7 mm); cuticle thin, ca. 1 μm wide and finely annulated, 0.8 μm wide at midbody. Lateral field inconspicuous, about 9% of body width, consisting one ridge that can be traced anteriorly to the level of the median bulb and posteriorly at level of rectum in females and about 1½ spicules length anterior of the cloacal aperture in males. Six lips slightly protruding, each with one apical papilliform labial sensillum and a second circle of four sublateral cephalic sensilla in both sexes; amphids opening on the lateral lips, hardly discernible. Buccal tube long and slender, more than twice the width in lip region, pharyngeal sleeve envelopes nearly half of the stoma, the anterior as well as the posterior end of the tube appear slightly thickened, cheilostom inconspicuous, arcade cells forming the gymnostom sometimes visible; glottoid apparatus completely absent. Pharynx with a prominent median bulb, diameter more than 90% of diameter of terminal bulb; terminal bulb pyriform, with double chambered haustrulum, the anterior chamber smallish; cardia conspicuous, opens funnel-like in intestine. Nerve ring encircles isthmus in its anterior part in living specimens, more to the middle of the isthmus in heat relaxed or preserved specimens; deirids usually conspicuous in the lateral field at level of beginning of terminal bulb, sometimes not visible in heat relaxed animals; pore of excretory-secretory system hard to discern posterior of deirid level. Two gland cells ventral and slightly posterior of terminal bulb conspicuous in live specimens. Lateral canals visible in live specimens extending anteriorly to two stoma length from the anterior end and ending at rectum level in the female. Postdeirids usually very conspicuous dorsally of the lateral field at about 7 5% of body length in both sexes and about half the length between vulva and beginning of rectum (or at level of posterior end of uterus remnant) in females, sometimes not visible in heat relaxed specimens.</p> Female <p>Maximum body diameter clearly anterior of the vulva, vulva position 65% body length, a transverse slit, bordered in both ends by cuticular longitudinal flaps, vulva lips moderately protruding, four diagonal vulval muscles conspicuous; one pseudocoelomocyte exists anterior of gonad flexure ventrally. Genital tracts asymmetrical; posterior branch rudimentary, sac like, on the left hand side of intestine, without flexure, almost as long as body diameter at the level of the vulva, containing spermatozoa (Fig. 2); anterior branch right of intestine, reflexed dorsally close to the pharynx, flexure more than half the length of the gonad (measured from vulva to flexure); at the flexure oocytes in several rows, downstream in one row, oocytes predominantly growing in the last position, where granules are stored inside; sphincter between oviduct and uterus, only a few sperm cells in oviduct, most of them in uterus and blind sac; oviparous, one egg at a time in uterus (rarely two), segmentation starts in the uterus. Rectum a little S-shaped, rectal gland cells very small, posterior anal lip slightly protuberant. Tail short, panagrolaimid, dorsally convex, with offset tip tapering, smooth to somewhat telescope-like by cuticle forming a sleeve-like structure; tail tip with tiny hooks, mostly one dorsal, but also subventral (compare with <i>Poikilolaimus</i>); opening of phasmids located at 60 <i>–</i> 65% of tail length, shortly anterior of tip, phasmid glands not reaching anus level.</p> Male <p>Testis right of intestine, ventrally reflexed in a certain distance posterior of pharynx; flexure relatively short. One pseudocoelomocyte between pharynx and flexure ventrally. Bursa well developed, peloderan, anteriorly open, with smooth margin and sometimes terminally indented, posterior part of velum transversely striated.</p> <p>Nine pairs of genital papillae (GP) present, two of them anterior of the cloaca, genital papilla 1 (GP1) and GP2 spaced, GP3 to GP6 and GP7 to GP9 clustered, GP5 and GP7 point to the dorsal side of the velum, GP6 slightly bottle shaped, GP8 and GP9 fused at base, GP2 and GP8 not reaching the margin of velum. Phasmids forming small tubercles to the ventral side posterior of the last GP; formula of GPs: v1,v2/(v3,v4,ad,v5) (pd,v6,v7)ph. Precloacal sensillum small, precloacal lip simple (according to type A of W Sudhaus and K Kiontke [39]), postcloacal sensilla long filamentous. Spicules short and stout, tawny, separate, slightly curved, with prominent head; shaft with a transverse seam, with a prominent longitudinal ridge, a dorsal lamella, and an oval <i>“</i> window <i>”</i>, the tip notched. Gubernaculum dorsally projecting, flexible, in the distal part following the contour of the spicules, spoon shaped in ventral view.</p> Dauer larva <p>Unsheathed, mouth closed; stoma long, slender. Pharyngeal sleeve covering about half of the stoma; pharynx with welldeveloped median and terminal bulbs; corpus length ca. 52% of pharynx length. Nerve ring somewhat in the middle between the middle and terminal bulb. Genital primordium at about 60% of body length, elongated oval in shape. Tail conical. Amphids, lateral lines, position excretory pore, deirids and phasmids not observed.</p> <i>Aberration</i> <p>In one female a second set of <i>“</i> sensilla <i>”</i> were observed a short distance posterior to postdeirids, possibly a duplication of the postdeirids.</p> <i>Type carrier and locality</i> <p>Holotype and paratypes of <i>Caenorhabditis monodelphis</i> sp. n. were isolated from the tunnels of <i>Cis castaneus</i> (Herbst, 1793) (Ciidae, Coleoptera) in the bracket fungus <i>Ganoderma applanatum</i> (Polyporales) on a stump of the common beech (<i>Fagus sylvatica</i>) a few centimetres above the ground in Berlin-Grunewald in April 2 0 0 1. The same sample included individuals of <i>Diploscapter</i> sp., <i>Plectus</i> sp., <i>Oscheius dolichura</i> and one individual dorylaimid and mononchid.</p> <i>Type material</i> <p>Holotype male (collection number WT 3684) and five female and four male paratypes (WT 3685, WT 3686) are deposited in the National Plant Protection Organization Wageningen, The Netherlands. In addition, four female and four male paratypes, are deposited in the collection of Museum Voor Dierkunde at Ghent University, Ghent, Belgium, five female and three male paratypes in Museum für Naturkunde an der Humboldt-Universität zu Berlin, Berlin, Germany. Additional paratypes are available in the UGent Nematode Collection (slides UGnem158, 159 & 160) of the Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium.</p> <i>Diagnosis and relationship</i> <p> <i>Caenorhabditis monodelphis</i> sp. n. can be recognised as a <i>Caenorhabditis</i> based on the thickened GP6 and the clearly visible postdeirids. <i>Caenorhabditis monodelphis</i> sp. n. is distinguished from all other described <i>Caenorhabditis</i> species by the presence of a monodelphic genital tract in the female with a blind sac posterior the vulva, a panagrolaimid female tail shape, adults with only one ridge on the lateral field, a very long and slender stoma without visible glottoid apparatus and male with short, stout spicule with bifurcate tip.</p> <i>Ecology and biology</i> <p> <i>Caenorhabditis monodelphis</i> sp. n. is a gonochoristic species with both males and females. Females are oviparous and carry only one egg (rarely two eggs). Development from egg to adult took about 5 <i>–</i> 6 days in juice prepared from brown algae at room temperature. Development from dauer larva to adults was completed in less than 3 days at 20 ̊C on NA seeded with OP50. The lifespan of adults is at minimum 1 4 days for males and 1 7 days for females. One pair of adults produced 1 6 7 offspring in 8 days and the daily production of fertile eggs was 6 <i>–</i> 3 1 (mean 1 8; <i>n</i> = 1 4). After the reproductive phase, females lived 9 <i>–</i> 1 4 days (<i>n</i> = 3) with males present.</p> <p> <i>Caenorhabditis monodelphis</i> sp. n. has until now only been found in <i>Ganoderma</i> and <i>Fomes</i> in Germany and Belgium in relation with the ciid beetle <i>Cis castaneus</i>. The <i>Ganoderma</i> carrying <i>C. monodelphis</i> sp. n. from Oslo was not investigated for the presence of <i>C. castaneus</i>. In fungal fruiting bodies lacking the beetle <i>C. monodelphis</i> sp. n. was not found. Dauers of <i>C. monodelphis</i> sp. n. were found under the elytra of the beetle, but were not found internally when the beetle was further dissected. These findings indicate a phoretic association with the beetle. As only dauer larvae were isolated from beetles, while adults and larvae were present in the fruiting bodies, we infer that <i>C. monodelphis</i> sp. n. exit from dauer within the mushroom, develop to adulthood and start to reproduce. The food source of the species in natural conditions is not known, but they survive and reproduce easily on <i>E. coli</i> OP50 in culture.</p> <p> <i>Genome sequence of an inbred strain of Caenorhabditis</i> <i>monodelphis sp. n.</i></p> <p>We sequenced the genome of an inbred strain (JU1677) of <i>C. monodelphis</i> sp. n. using Illumina sequencing technology to ~110x coverage. The genome was assembled into 6,864 scaffolds, spanning 115.1 Mb with a scaffold N50 of 49.4 kb (Table 2). CEGMA (Core Eukaryotic Gene Mapping Approach) [40] scores suggested the assembly is of high completeness. We predicted 17,180 protein coding gene models using RNA-Seq evidence. These statistics, and the overall gene content and structure of the assembly were largely in keeping with those determined for other <i>Caenorhabditis</i> species. The genome was larger than that of <i>C. elegans</i> and <i>C. briggsae</i>, which are hermaphroditic species, but smaller than that of <i>C. remanei</i>, a gonochoristic species.</p> <p>We carried out preliminary comparisons of the structure and content of the <i>C. monodelphis</i> sp. n. genome with those of other sequenced <i>Caenorhabditis</i> species. The number of genes identified was lower than estimates for most other <i>Caenorhabditis</i> species. To compare the gene structures of <i>C. monodelphis</i> sp. n. to that of <i>C. elegans</i>, we identified 6,174 orthologous gene pairs and calculated gene structure statistics (Table 3, Fig. 5.). To minimize bias from erroneous gene predictions (such as merged or split genes), orthologous gene pairs which differed in CDS length by 20% were considered outliers. <i>C. monodelphis</i> sp. n. genes were typically longer than their orthologues in <i>C. elegans.</i> We also found a clear trend toward more coding exons per gene in <i>C. monodelphis</i> sp. n. than in <i>C. elegans</i> (Fig. 5a). A few examples of <i>C. monodelphis</i> sp. n. gene models compared to those of orthologues in <i>C. elegans</i> are shown (Fig. 5b). Although introns are, on average, shorter in <i>C. monodelphis</i> sp. n. than in <i>C. elegans,</i> <i>C. monodelphis</i> genes typically have a longer total span of introns than <i>C. elegans</i> transcripts (Table 3, Fig. 5.).</p> <p>a from anus to flexure in the female; from cloaca to flexure in the male b <i>n</i> = 7</p> <p>a Scaffolds shorter than 500 bp were not considered</p> <p> <i>C. monodelphis sp. n. is sister to other known</i> <i>Caenorhabditis</i></p> <p>We clustered a total of 634,56 4 protein sequences from <i>C. monodelphis</i> sp. n., twenty-two other <i>Caenorhabditis</i> species, and two rhabditomorph outgroup species (<i>Oscheius tipulae</i>; data courtesy of M. A. Félix, and <i>Heterorhabditis bacteriophora</i>) to define putative orthologues. We identified 34,425 putatively orthologous groups containing at least two members, 303 of which were either single copy or absent across all 25 species. These single copy orthologues were aligned, and the alignments concatenated and used to perform maximum-likelihood and Bayesian inference analysis using RAxML and PhyloBayes, respectively. Both analysis methods resulted in an identical topology, with the placement of <i>C. monodelphis</i> sp. n. arising basally to all other <i>Caenorhabditis</i> species (Fig. 6). All branches had maximal support except for three nodes within the <i>Elegans</i> super-group. Our analysis included data from several new and currently undescribed putative species of <i>Caenorhabditis</i>, including <i>C.</i> sp. 21 which is the sister taxon to the <i>Drosophilae</i> plus <i>Elegans</i> super-groups and <i>C.</i> sp. 31 which forms the first branch in the <i>Elegans</i> super-group. <i>C.</i> sp. 38 is placed within the <i>Drosophilae</i> super-group, while <i>C.</i> sp.</p> <p>26, <i>C.</i> sp. 32 (sister to <i>C. afra</i>) and <i>C.</i> sp. 40 (sister to <i>C. sinica</i>) are all members of the <i>Elegans</i> super-group. From these analyses we conclude that <i>C. monodelphis</i> sp. n. is sister to all other known <i>Caenorhabditis</i>.</p> <i>Stemspecies pattern reconstruction</i> <p>Our phylogenetic analyses were based on species with whole genome data available, and thus did not include the full known diversity of the genus. The stemspecies pattern was reconstructed based on ingroup and outgroup comparison. Previous molecular phylogenetic analyses of <i>Caenorhabditis</i> species using a small number of marker genes [1 0] placed <i>C. monodelphis</i> sp. n. and <i>C. sonorae</i> [4 1] as sister species, again arising at the base of the genus.</p> <p>The following morphological synapomorphies can be hypothesised to support a <i>C. monodelphis</i> sp. n. <i>– C. sonorae</i> clade: mouth opening triangular (Fig. 4b), spicule having a complicated tip (notched or dentated) and a longish thin walled <i>“</i> window <i>”</i> in the blade (Figs. 1i, 4l), postcloacal sensilla being filiform (Fig. 4k), and the female tail shortened to less than three times anal body width. Other similarities between both these species are plesiomorphic.</p> <p> <i>Caenorhabditis</i> and its sister group constitute the monophylum Anarhabditis within the Rhabditina. For convenience, we will call the sister clade of <i>Caenorhabditis</i> Protoscapter (Fig. 7): it comprises <i>“ Protorhabditis ”</i>, <i>Prodontorhabditis</i>, <i>Diploscapter</i> and <i>Sclerorhabditis</i> [4 2]. To reconstruct the characters of the stemspecies of <i>Caenorhabditis</i> it is necessary to consider the morphologies of all these taxa, and not only the taxa for which we have molecular data. <i>“ Protorhabditis ”</i> is paraphyletic. The <i>Oxyuroides</i> group is sister taxon of <i>Prodontorhabditis</i> [4 3, 4 4], and the <i>Xylocola</i> group may be sister taxon of <i>Diploscapter</i> / <i>Sclerorhabditis</i>. However, the two species <i>Protorhabditis elaphri</i> (Hirschmann in Osche, 1952) and <i>P. tristis</i> [4 5] appear to represent basal branches in Protoscapter (compare [43]). These last two species, despite the paucity of information available for them, are crucial for comparisons that will illuminate the stemspecies patterns of Anarhabditis, Protoscapter and <i>Caenorhabditis</i>.</p> <i>C. monodelphis</i> sp. n. C. elegans <p>All values are medians</p> <p>a orthologous gene pairs which differed in CDS length by 20% were not included</p> <p>By ingroup comparison we reconstruct the following characters of the stemspecies of Anarhabditis without differentiating them into apo- or plesiomorphies (on apomorphies see the legend of Fig. 7):</p> <p> <i>–</i> adults of small size (less than 1 mm); − lips not offset from anterior end; − four cephalic sensilla present in male and female; − stoma with pharyngeal sleeve (stegostom length nearly that of gymnostom); − median bulb of pharynx strongly developed, corpus intima with transverse ridging, terminal bulb with double haustrulum; − gonochoristic; − female tail elongate conoid; − gonads amphidelphic, the anterior branch right and the posterior left of intestine; − vulva at midbody, a transverse slit; − oviparous, usually only one egg at a time in the uteri; − male gonad on the right side, reflexed to the ventral; − bursa peloderan and anteriorly open, oval-shaped in ventral view, with smooth margin, terminally not notched; − 9 pairs of even genital papillae, two precloacal largely spaced, GP3 <i>–</i> 6 evenly spaced, the last three GPs forming a tight cluster; GP1, GP5 and GP7 terminate on the dorsal surface of the bursa velum; − phasmids open behind GP9, inconspicuous; − bursa formula thus v1,v2/v3,v4,ad,v5 (pd,v6,v7)ph; − male tail tip present; − 1 + 2 circumcloacal sensilla inconspicuous, precloacal lip simple; − spicules separate, stout, head not rounded, behind the shaft a slight ventral projection, dorsal part of blade weakly cuticularised (velum), its tip possibly not even (argued below); − gubernaculum simple spatulate; − dauerlarvae with double cuticle (ensheathed), not waving.</p>Published as part of <i>Dieter Slos, Walter Sudhaus, Lewis Stevens, Wim Bert & Mark Blaxter, 2017, Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis, pp. 1-15 in BMC Zoology 2 (4)</i> on pages 3-10, DOI: 10.1186/s40850-017-0013-2, <a href="http://zenodo.org/record/1156816">http://zenodo.org/record/1156816</a>
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
Szitenberg_et_al_15-ReproPhylo
No full text<p>The analysis from the manuscript "ReproPhylo: a python package for reproducible phylogenomics" with Max John, Mark Blaxter and David Lunt</p
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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