1,720,961 research outputs found
Biogeography of the old world native Xanthium strumarium
No full textThis dataset is composed of supplementary files regarding the related publication. We publish here: - XML files of the Beast2 dating and phylogenetic analyses; - BioGeoBEARS trees resulting from all models analysed - Biogeobears distance's matrix
Species delimitation in Xanthium sect. Acanthoxanthium
No full textThis dataset is composed of supplementary files regarding the related publication.
We publish here:
- XML files of the SPEEDEMON (Beast2) analysis;
- Clustering results from the ClusterTreeSetAnalyser of the SPEEDEMON analyses;
- Alignment of Chloroplast sequences;
- Alignment of concatenated Nuclear sequences of 391 loci from HybPhyloMaker;
- R script of the Geometric Morphometric analysis;
- Quartet Sampling tree
Recent Long‐Distance‐Dispersal Explains the Range Disjunction of the Old‐Word Cockleburs ( Xanthium strumarium )
No full textABSTRACT Aim In the present study, we focused in addressing questions concerning the biogeographic history of Xanthium strumarium , an Old World native species whose close relatives are generally all native to the American continent. Location The species distribution covers the Eurasian continent and some African regions and close islands. Methods We employed herbarium material and target enrichment (herbariomics) sequence data of over 700 single copy loci to estimate the divergence times of the species. Ancestral range reconstruction was employed to test different hypotheses on the events that determined the arrival, differentiation and dispersal of the ancestor of X. strumarium in the Old World. Results The crown age of X. strumarium was estimated to be ~156.58 ka. In the phylogenomic analysis, the individuals from the different geographic areas grouped mostly congruently based on their collection origin, the earliest diverging clade comprising samples from India, and then progressively clades including samples from Asia, Europe and Africa. The same pattern was observed in the biogeographic analysis, with a movement of the ancestral ranges going from east to west. The ancestral range of the species was inferred to be the Indian subcontinent. Main Conclusions Both the use of herbarium specimens as old as 240 years and the use of modern sequencing techniques clarified the phylogenetic relationships, divergence time and biogeography of Xanthium strumarium . Most probably, the ancestor of the species reached the Old World by way of a trans‐Pacific long‐distance dispersal from the Americas to Southeastern Asia, followed by westward colonisation of the Old World.Deutsche Forschungsgemeinschaft https://doi.org/10.13039/50110000165
The first complete chloroplast genome for the species-rich genus Anthemis (Asteraceae)
No full textOpen-Access-Publikationsfonds 202
Comparative plastome assembly of the yellow ironweed (Verbesina alternifolia) using Nanopore and Illumina reads
Full text linkChloroplast genomes (plastomes) represent a very important source of valuable information for phylogenetic and biogeographic reconstructions. The use of short reads (as those produced from Illumina sequencing), along with de novo read assembly, has been considered the “gold standard” for plastome reconstruction. However, short reads often cannot reconstruct long repetitive regions in chloroplast genomes. Long Nanopore (ONT) reads can help bridging long repetitive regions but are by far more error-prone than those produced by Illumina sequencing. Verbesina is the largest genus of tribe Heliantheae (Asteraceae) and includes species of economic importance as ornamental or as invasive weeds. However, no complete chloroplast genomes have been published yet for the genus. We utilized Illumina and Nanopore sequencing data and different assembly strategies to reconstruct the plastome of Verbesina alternifolia and evaluated the usefulness of the Nanopore assemblies. The two plastome sequence assemblages, one obtained with the Nanopore sequencing and the other inferred with Illumina reads, were identical, except for missing bases in homonucleotide regions. The best-assembled plastome of V. alternifolia was 152,050 bp in length and contained 80, 29, and four unique protein-coding genes, tRNAs, and rRNAs, respectively. When used as reference for mapping Illumina reads, all plastomes performed similarly. In a phylogenetic analysis including 28 other plastomes from closely related taxa (from the Heliantheae alliance ), the two Verbesina chloroplast genomes grouped together and were nested among the other members of the tribe Heliantheae s.str. Our study highlights the usefulness of the Nanopore technology for assembling rapidly and cost-effectively chloroplast genomes, especially in taxonomic groups with paucity of publicly available plastomes.Open-Access-Publikationsfonds 202
Interspecific competition with the American Xanthium orientale L. as a possible cause of the decline of the Old-World X. strumarium L.
No full textAbstract Xanthium is represented in Europe by three species complexes: X. strumarium L., X. orientale L., and X. spinosum L. The former two complexes are similar, in both morphology and ecological requirements. Xanthium strumarium is native to the Old World, whereas X. orientale originates from America and was accidentally introduced into Europe about two centuries ago. Since then, it has colonized the whole continent, while the native congener has become increasingly rare. Over two years, we conducted competition experiments to assess the impact of the introduced X. orientale on the fitness of the native X. strumarium. Germination time, dry biomass, number of burs (pistillate flower heads) and bur biomass were measured as proxies of fitness. Xanthium strumarium was grown alone (control), together with conspecifics (intraspecific competition) or with X. orientale plants (interspecific competition). We also evaluated the allelopathic effect of X. orientale over X. strumarium, by watering Xanthium seedlings with exudate of X. orientale dry leaves. Growth and reproductive traits of X. strumarium were significantly lower in individuals growing in proximity of X. orientale compared to the control, whereas intraspecific competition has a lower but still significant effect. Xanthium orientale, although, germinates and grows faster than the Old-World congener, and under interspecific competition regime, X. strumarium produces significantly lower biomass, number of burs and bur biomass. Watering with exudates negatively influences the germination and the growth of the two species. We therefore believe that interspecific competition of the introduced congener may be one of the causes explaining the drastic decline of X. strumarium populations in Europe in the past century
Species delimitation in Xanthium sect. Acanthoxanthium (Heliantheae, Asteraceae) and the neglected species Xanthium argenteum
No full textAbstract Xanthium is a genus of annual herbaceous plants that stands out within Asteraceae for being wind‐pollinated, diclinous monoecious, and bearing solitary pistillate flowers in peculiar spiny structures (burs). Xanthium sect. Acanthoxanthium is native to South America and characterized by the presence of trifurcate spines at the base of the leaves. Past taxonomic treatments of the section have been contradictory, some recognising up to six species, others reducing all to a single polymorphic species. Altogether, 42 samples of X. sect. Acanthoxanthium were analysed, the vast majority taken from herbarium specimens between 20 and 160 years old. We sampled multiple specimens of X. spinosum from throughout its broad range as well as those taxa with narrower distributions, covering the whole range of morphological variation in the section. When possible, we included types and original material. We used Hyb‐Seq techniques to obtain information from about 1000 single‐copy nuclear genes and complete plastomes. Phylogenomic data were submitted to coalescent‐based species delimitation approaches (SPEEDEMON). Additionally, we performed geometric morphometric analysis of leaf outlines. The results strongly support the identification of four lineages in the section favouring the acceptance of four of the hitherto described species, i.e., X. ambrosioides , X. argenteum , X. catharticum , and X. spinosum . These results were to some extent corroborated by morphometric analyses. While X. ambrosioides was well distinct from X. spinosum based on leaf morphology, such difference was not observed between X. spinosum and X. catharticum . However, X. catharticum differs from X. spinosum in its ecological requirements, being a species rather adapted to high‐mountain environments of the Neotropics. Intriguingly, X. argenteum – a taxon described from a single herbarium collection – was also inferred as a species
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
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