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81.
Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes 总被引:1,自引:0,他引:1
Hendrik Giebner Kathrin Langen Sarah J. Bourlat Sandra Kukowka Christoph Mayer Jonas J. Astrin Bernhard Misof Vera G. Fonseca 《Molecular ecology resources》2020,20(5):1333-1345
Environmental DNA studies targeting multiple taxa using metabarcoding provide remarkable insights into levels of species diversity in any habitat. The main drawbacks are the presence of primer bias and difficulty in identifying rare species. We tested a DNA sequence‐capture method in parallel with the metabarcoding approach to reveal possible advantages of one method over the other. Both approaches were performed using the same eDNA samples and the same 18S and COI regions, followed by high throughput sequencing. Metabarcoded eDNA libraries were PCR amplified with one primer pair from 18S and COI genes. DNA sequence‐capture libraries were enriched with 3,639 baits targeting the same gene regions. We tested amplicon sequence variants (ASVs) and operational taxonomic units (OTUs) in silico approaches for both markers and methods, using for this purpose the metabarcoding data set. ASVs methods uncovered more species for the COI gene, whereas the opposite occurred for the 18S gene, suggesting that clustering reads into OTUs could bias diversity richness especially using 18S with relaxed thresholds. Additionally, metabarcoding and DNA sequence‐capture recovered 80%–90% of the control sample species. DNA sequence‐capture was 8x more expensive, nonetheless it identified 1.5x more species for COI and 13x more genera for 18S than metabarcoding. Both approaches offer reliable results, sharing ca. 40% species and 72% families and retrieve more taxa when nuclear and mitochondrial markers are combined. eDNA metabarcoding is quite well established and low‐cost, whereas DNA‐sequence capture for biodiversity assessment is still in its infancy, is more time‐consuming but provides more taxonomic assignments. 相似文献
82.
Sour rot is a disease complex that causes serious damage in viticulture. The common vinegar fly Drosophila melanogaster (Diptera: Drosophilidae) is associated with sour rot in overripe or otherwise damaged grapes. Drosophila suzukii (Diptera: Drosophilidae) is an invasive species, which is suspected to induce sour rot in previously undamaged grapes due to the flies' ability to infest healthy, undamaged soft fruits with its serrated ovipositor. As a consequence, infection of healthy grapes by D. suzukii may facilitate the colonization by D. melanogaster. We investigated the single and combined effects of D. suzukii and D. melanogaster on sour rot development by measuring volatile acidity under near-natural conditions in the vineyard, along with laboratory experiments under controlled climate. In 2017, the combined field and laboratory experiments suggested that the presence of D. suzukii and D. melanogaster increased the volatile acidity levels at a similar rate. In 2018, the field experiments showed an only marginal increase in sour rot development in treatments with both Drosophila species. Under more favourable laboratory conditions, the presence of D. suzukii, but not D. melanogaster triggered sour rot emergence. A facilitating effect of D. suzukii infestation for D. melanogaster was not detectable. These findings suggest that D. suzukii does in fact have the potential to trigger sour rot, but will probably rarely do so under field conditions in the vineyard, at least in the studied region. Instead, our study showed that D. melanogaster can have a similar impact on sour rot development as D. suzukii, emphasizing the need of comparative studies. 相似文献
83.
Koffler Christoph Amor Ben Carbajales-Dale Michael Cascio Joseph Conroy Alison Fava James A. Gaudreault Caroline Gloria Thomas Hensler Connie Horvath Arpad Humbert Sebastien Manzardo Alessandro Margni Manuele Osset Philippe Sinistore Julie Vigon Bruce Wallace Michele L Wang Michael Prox Martina 《The International Journal of Life Cycle Assessment》2020,25(3):478-482
The International Journal of Life Cycle Assessment - 相似文献
84.
Sophia E. Kimmig Joscha Beninde Miriam Brandt Anna Schleimer Stephanie Kramer‐Schadt Heribert Hofer Konstantin Brner Christoph Schulze Ulrich Wittstatt Mike Heddergott Tanja Halczok Christoph Staubach Alain C. Frantz 《Molecular ecology》2020,29(3):466-484
Urbanization affects key aspects of wildlife ecology. Dispersal in urban wildlife species may be impacted by geographical barriers but also by a species’ inherent behavioural variability. There are no functional connectivity analyses using continuous individual‐based sampling across an urban‐rural continuum that would allow a thorough assessment of the relative importance of physical and behavioural dispersal barriers. We used 16 microsatellite loci to genotype 374 red foxes (Vulpes vulpes) from the city of Berlin and surrounding rural regions in Brandenburg in order to study genetic structure and dispersal behaviour of a mobile carnivore across the urban‐rural landscape. We assessed functional connectivity by applying an individual‐based landscape genetic optimization procedure. Three commonly used genetic distance measures yielded different model selection results, with only the results of an eigenvector‐based multivariate analysis reasonably explaining genetic differentiation patterns. Genetic clustering methods and landscape resistance modelling supported the presence of an urban population with reduced dispersal across the city border. Artificial structures (railways, motorways) served as main dispersal corridors within the cityscape, yet urban foxes avoided densely built‐up areas. We show that despite their ubiquitous presence in urban areas, their mobility and behavioural plasticity, foxes were affected in their dispersal by anthropogenic presence. Distinguishing between man‐made structures and sites of human activity, rather than between natural and artificial structures, is thus essential for better understanding urban fox dispersal. This differentiation may also help to understand dispersal of other urban wildlife and to predict how behaviour can shape population genetic structure beyond physical barriers. 相似文献
85.
Plant species differ in their ecological amplitude, with some species occurring in very different habitats under strongly differentiated environmental conditions. We were interested in to what extent the occurrence of Linum catharticum in dry calcareous grasslands (Bromion) and wet litter meadows (Molinion), two habitats on opposing ends concerning, for example, moisture level, is reflected on the genetic and epigenetic level. Using AFLP (amplified fragment length polymorphisms) and MSAP (methylation sensitive amplification polymorphisms) analyses, we studied the genetic and epigenetic variation of L. catharticum from calcareous grasslands and litter meadows. From each habitat, we included five study sites with 16 individuals per sampling location. We observed lower genetic than epigenetic diversity, but considerable differentiation among habitats, which was stronger on the genetic than the epigenetic level. Additionally, we observed a strong correlation of genetic and epigenetic distance, irrespective of geographic distance. The dataset included a large portion of fragments exclusively found in individuals from one or the other habitat. Some epigenetic fragments even occurred in different methylation states depending on the habitat. We conclude that environmental effects act on both the genetic and epigenetic level, producing the clear differentiation among plant individuals from calcareous grasslands and litter meadows. These results may also point into the direction of ecotype formation in this species. 相似文献
86.
Beheshti Hossein Strotbek Christoph Arif M. Asif Klingl Andreas Top Oguz Frank Wolfgang 《Plant molecular biology》2021,107(4-5):293-305
Plant Molecular Biology - This study focused on the key regulatory function of Physcomitrium patens GRAS12 gene underlying an increasing plant complexity, an important step in plant... 相似文献
87.
Pedrotta Tiziana Gobet Erika Schwörer Christoph Beffa Giorgia Butz Christoph Henne Paul D. Morales-Molino César Pasta Salvatore van Leeuwen Jacqueline F. N. Vogel Hendrik Zwimpfer Elias Anselmetti Flavio S. Grosjean Martin Tinner Willy 《Vegetation History and Archaeobotany》2021,30(6):789-813
Vegetation History and Archaeobotany - Knowledge about the vegetation history of Sardinia, the second largest island of the Mediterranean, is scanty. Here, we present a new sedimentary record... 相似文献
88.
89.
Manfred Schartl Susanne Kneitz Jenny Ormanns Cornelia Schmidt Jennifer L. Anderson Angel Amores Julian Catchen Catherine Wilson Dietmar Geiger Kang Du Mateo Garcia-Olazábal Sudha Sudaram Christoph Winkler Rainer Hedrich Wesley C. Warren Ronald Walter Axel Meyer John H. Postlethwait 《Current biology : CB》2021,31(5):911-922.e4
90.