6,032 research outputs found
Desert‐like badlands and surrounding (semi‐)dry grasslands of Central Germany promote small‐scale phenotypic and genetic differentiation in Thymus praecox
No full text
Comparative plastome assembly of the yellow ironweed (Verbesina alternifolia) using Nanopore and Illumina reads
No full textChloroplast 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
Phylogenetic and taxonomic insights into Betula: low-coverage whole genome sequencing and plastome analysis with focus on the rare Ukrainian endemic species Betula klokovii Zaverucha
No full textBetula klokovii Zaverucha is a rare endemic species of Ukraine that is still not well taxonomically studied. In the current pilot study, we performed low-coverage whole genome sequencing for B. klokovii, related species (B. pendula Roth and B. pubescens Ehrh.) and the assumed hybrid B. klokovii × B. pendula, assessed the genomic structure of taxa with different mapping settings using UMAP non-linear dimension reduction algorithm, extracted and assembled whole plastomes.
Single Nucleotide Polymorphism (SNP) analysis based on low-coverage whole genome sequencing (LC-WGS) followed by UMAP visualization reveals the separation of B. klokovii from the other analysed taxa. The best taxonomic resolution was achieved with reads filtered for contamination. In contrast, the best result in obtaining complete plastome assemblies was achieved via NOVOPlasty pipeline and raw reads.
The size for the eight newly assembled plastid genomes ranges between 160,535 and 160,625bp, GC content is 36,1%. We annotated 130 genes (113 unique) for all eight assemblies. In addition, we investigated B. klokovii’s relationships with 20 other birch species and two intraspecific taxa by reconstructing plastome-based Bayesian inference and maximum likelihood phylogenies. Overall, plastome phylogeny provides a better resolution in comparison to phylogenies based on a few plastid or nuclear molecular markers. However, it could be affected by chloroplast capture, and some other factors like quality of sequencing and assembly, and is not suitable to detect hybrids when used alone.
In particular, we found that B. klokovii is likely a separate taxon that is closely related to B. pubescens but morphologically and genetically distinct. The study shows that genome-wide SNP data and plastome phylogenies have a certain potential for addressing issues with specific taxa within the genus Betula L. However, to fully leverage the potential of this approach, we suggest collecting a much larger number of birch plastome sequences to be sequenced and assembled. For a better understanding of birch phylogeny there is a need for reference-grade chromosome scale genome assemblies for polyploid species
Population size affected by environmental variability impacts genetics, traits, and plant performance in Trifolium montanum L.
No full textAbstract Population size, genetic diversity, and performance have fundamental importance for ecology, evolution, and nature conservation of plant species. Despite well‐studied relationships among environmental, genetic, and intraspecific trait variation (ITV), the influence of population size on these aspects is less understood. To assess the sources of population size variation, but also its impact on genetic, functional trait, and performance aspects, we conducted detailed population size estimations, assessed 23 abiotic and biotic environmental habitat factors, performed population genetic analyses using nine microsatellite markers, and recorded nine functional traits based on 260 Trifolium montanum individuals from 13 semi‐dry grassland locations of Central Europe. Modern statistical analyses based on a multivariate framework (path analysis) with preselected linear regression models revealed that the variation of abiotic factors (in contrast to factors per se) almost completely, significantly explained fluctuations in population size (R2 = .93). In general, abiotic habitat variation (heterogeneity) was not affected by habitat area. Population size significantly explained genetic diversity (NA: R2 = .42, Ho: R2 = .67, He: R2 = .43, and I: R2 = .59), inbreeding (FIS: R2 = .35), and differentiation (GST: R2 = .20). We also found that iFDCV (ITV) was significantly explained by abiotic habitat heterogeneity, and to a lesser extent by genetic diversity He (R2 = .81). Nevertheless, habitat heterogeneity did not statistically affect genetic diversity. This may be due to the use of selectively neutral microsatellite markers, and possibly by insufficient abiotic selective pressures on habitats examined. Small T. montanum populations in nonoptimal habitats were characterized by reduced genetic and functional trait diversity, and elevated genetic inbreeding and differentiation. This indicates reduced adaptability to current and future environmental changes. The long‐term survival of small populations with reduced genetic diversity and beginning inbreeding will be highly dependent on habitat protection and adequate land‐use actions
species complex
No full textAbstract The time frame and geographical patterns of diversification processes in European temperate‐montane herbs are still not well understood. We used the sexual species of the Ranunculus auricomus complex as a model system to understand how vicariance versus dispersal processes in the context of Pleistocene climatic fluctuations have triggered speciation in temperate‐montane plant species. We used target enrichment sequence data from about 600 nuclear genes and coalescent‐based species tree inference methods to resolve phylogenetic relationships among the sexual taxa of the complex. We estimated absolute divergence times and, using ancestral range reconstruction, we tested if speciation was enhanced by vicariance or by dispersal processes. Phylogenetic relationships among taxa were fully resolved with some incongruence in the position of the tetraploid R. marsicus. Speciation events took place in a very short time at the end of the Mid‐Pleistocene Transition (830–580 thousand years ago [ka]). A second wave of intraspecific geographical differentiation occurred at the end of the Riss glaciation or during the Eemian interglacial between 200 and 100 ka. Ancestral range reconstruction suggests a widespread European ancestor of the R. auricomus complex. Vicariance has triggered allopatric speciation in temperate‐montane plant species during the climatic deterioration that occurred during the last phase of the Mid‐Pleistocene Transition. Vegetation restructuring from forest into tundra could have confined these forest species into isolated glacial macro‐ and microrefugia. During subsequent warming periods, range expansions of these species could have been hampered by apomictic derivatives and by other congeneric competitors in the same habitat.German Research Foundation http://dx.doi.org/10.13039/50110000165
complex and its role in a geographical parthenogenesis scenario
No full textAbstract The larger distribution area of asexuals compared with their sexual relatives in geographical parthenogenesis (GP) scenarios has been widely attributed to the advantages of uniparental reproduction and polyploidy. However, potential disadvantages of sexuals due to their breeding system have received little attention so far. Here, we study the breeding system of five narrowly distributed sexual lineages of Ranunculus notabilis s.l. (R. auricomus complex) and its effects on outcrossing, inbreeding, female fitness, and heterozygosity. We performed selfing and intra‐ and interlineage crossings by bagging 481 flowers (59 garden individuals) followed by germination experiments. We compared seed set and germination rates, and related them to genetic distance and genome‐wide heterozygosity (thousands of RADseq loci). Selfings (2.5%) unveiled a significantly lower seed set compared with intra‐ (69.0%) and interlineage crossings (69.5%). Seed set of intra‐ (65%) compared to interpopulation crossings (78%) was significantly lower. In contrast, all treatments showed comparable germination rates (32%–43%). Generalized linear regressions between seed set and genetic distance revealed positive relationships in general and between lineages, and a negative one within lineages. Seed set was the main decisive factor for female fitness. Germination rates were not related to genetic distance at any level, but were positively associated with heterozygosity in interlineage crossings. Experiments confirmed full crossability and predominant outcrossing among sexual R. notabilis s.l. lineages. However, up to 5% (outliers 15%–31%) of seeds were formed by selfing, probably due to semi‐self‐compatibility in a multi‐locus gametophytic SI system. Less seed set in intrapopulation crossings, and higher seed set and germination rates from crossings of genetically more distant and heterozygous lineages (interlineage) indicate negative inbreeding and positive outbreeding effects. In GP scenarios, sexual species with small and/or isolated populations can suffer from decreased female fitness due to their breeding system. This factor, among others, probably limits range expansion of sexuals.Potential disadvantages of sexual plant species due to their breeding system have received little attention in geographical parthenogenesis (GP) scenarios so far. We compared seed set and germination rates of five sexual lineages of Ranunculus notabilis s.l (R. auricomus complex) and related them to genetic distance and genome‐wide heterozygosity. Results suggest that inbreeding depression particularly affects intrapopulation (intralineage) crossings, and that positive outbreeding effects particularly influence interlineage crossings. In GP scenarios, sexual species with small and/or isolated populations can suffer from decreased female fitness due to their breeding system. imageOpen-Access-Publikationsfonds 202
Kevin Brockmeier, Fiction Reading
No full textOctober 25, 2013, Ulrich Museum of Art, Wichita State UniversityAward winning author Kevin Brockmeier, reads from his work.University Libraries, Department of English, Department of Women's Studies, Watermark Books & Cafe, Ulrich Museum of Ar
Dr. Kevin Pelletier – Faculty Author Interview
No full textDr. Kevin Pelletier, Associate Professor of English, discusses his new book, Apocalyptic Sentimentalism: Love and Fear in US Antebellum Literature, published recently by the University of Georgia Press. The book provides powerful insights into the relationship between nineteenth-century sentimentality, religious discourse, and antislavery reform
- …
