scholarly journals Harnessing the power of metabarcoding in the ecological interpretation of plant-pollinator DNA data: strategies and consequences of reads filtering

2021 ◽  
Author(s):  
Nicola Tommasi ◽  
Andrea Ferrari ◽  
Andrea Galimberti ◽  
Paolo Biella
Keyword(s):  
Species Interactions ◽  
High Throughput Sequencing ◽  
Point Of View ◽  
Biological Information ◽  
Fixed Amount ◽  
Dna Metabarcoding ◽  
Different Types ◽  
First Time ◽  
Plant Pollinator ◽  
Do So

DNA metabarcoding approaches to analyse complex mixtures of pollen has become the standard in pollination biology, especially in the light of recent threats affecting pollination. In spite of the increasing adoption of High Throughput Sequencing (HTS) approaches, these studies generate huge numbers of raw reads, some of which might be associated to false positives or infrequently recorded species with potentially little biological information. If these reads are not discarded (i.e. pruned), they can lead to changes in the ecological findings and lead to biased conclusions. In this study we reviewed 42 papers in the recent pollen DNA metabarcoding literature and focused on the type of pruning applied. We also tested whether the different types of those cut off threshold may leave a mark on the DNA metabarcoding data. To do so, we compared for the first time community composition, species richness and networks of species interactions (i.e. Connectace, Modularity, Connectivity and Shannon entropy) associated with the most relevant ways of treating HTS outputs: no cut (no reads filtering), or cutting levels obtained as proportional 1% of sample total reads, or as fixed amount of 100 reads, or from ROC (Receiver operator characteristic). Results clearly indicated that pruning type shapes species composition and that to apply or not a threshold dramatically impacts ecological indices, potentially increasing the risk of misinterpreting DNA metabarcoding data under an ecological point of view. Given the high methodological heterogeneity from the revised literature, we discuss in what conditions filtering types may be more appropriate, and also recommend to biologically justify the pruning threshold when analysing DNA metabarcoding raw reads, and to develop shared approaches to make future studies more comparable.

scholarly journals Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant—Pollinator DNA Data: Strategies and Consequences of Filtering Approaches

Diversity ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 437
Author(s):  
Nicola Tommasi ◽  
Andrea Ferrari ◽  
Massimo Labra ◽  
Andrea Galimberti ◽  
Paolo Biella
Keyword(s):  
Species Richness ◽  
High Sensitivity ◽  
Conservative Approach ◽  
Pollen Assemblage ◽  
Future Studies ◽  
Molecular Features ◽  
Dna Metabarcoding ◽  
Plant Pollinator ◽  
Very High ◽  
Do So

Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or maintaining false positives, contaminants, and rare taxa or molecular features could lead to different ecological results. Here, we reviewed how this choice has been addressed in 43 studies featuring pollen DNA metabarcoding, which highlighted a very high heterogeneity of filtering methods. We assessed how these strategies shaped pollen assemblage composition, species richness, and interaction networks. To do so, we compared four processing methods: unfiltering, filtering with a proportional 1% of sample reads, a fixed threshold of 100 reads, and the ROC approach (Receiver Operator Characteristic). The results indicated that filtering impacted species composition and reduced species richness, with ROC emerging as a conservative approach. Moreover, in contrast to unfiltered networks, filtering decreased network Connectance and Entropy, and it increased Modularity and Connectivity, indicating that using cut-off thresholds better describes interactions. Overall, unfiltering might compromise reliable ecological interpretations, unless a study targets rare species. We discuss the suitability of each filtering type,plead for justifying filtering strategies on biological or methodological bases and for developing shared approaches to make future studies more comparable.

scholarly journals Construction, validation and application of nocturnal pollen transport networks in an agro-ecosystem: a comparison using microscopy and DNA metabarcoding

2018 ◽  
Author(s):  
Callum J. Macgregor ◽  
James J.N. Kitson ◽  
Richard Fox ◽  
Christoph Hahn ◽  
David H. Lunt ◽  
...  
Keyword(s):  
Light Microscopy ◽  
Species Interactions ◽  
Interaction Networks ◽  
List Type ◽  
Transport Networks ◽  
Pollen Transport ◽  
Pollen Types ◽  
Dna Metabarcoding ◽  
Multiple Pollen ◽  
Plant Pollinator

AbstractMoths are globally relevant as pollinators but nocturnal pollination remains poorly understood. Plant-pollinator interaction networks are traditionally constructed using either flower-visitor observations or pollen-transport detection using microscopy. Recent studies have shown the potential of DNA metabarcoding for detecting and identifying pollen-transport interactions. However, no study has directly compared the realised observations of pollen-transport networks between DNA metabarcoding and conventional light microscopy.Using matched samples of nocturnal moths, we construct pollen-transport networks using two methods: light microscopy and DNA metabarcoding. Focussing on the feeding mouthparts of moths, we develop and provide reproducible methods for merging DNA metabarcoding and ecological network analysis to better understand species-interactions.DNA metabarcoding detected pollen on more individual moths, and detected multiple pollen types on more individuals than microscopy, but the average number of pollen types per individual was unchanged. However, after aggregating individuals of each species, metabarcoding detected more interactions per moth species. Pollen-transport network metrics differed between methods, because of variation in the ability of each to detect multiple pollen types per moth and to separate morphologically-similar or related pollen. We detected unexpected but plausible moth-plant interactions with metabarcoding, revealing new detail about nocturnal pollination systems.The nocturnal pollination networks observed using metabarcoding and microscopy were similar, yet distinct, with implications for network ecologists. Comparisons between networks constructed using metabarcoding and traditional methods should therefore be treated with caution. Nevertheless, the potential applications of metabarcoding for studying plant-pollinator interaction networks are encouraging, especially when investigating understudied pollinators such as moths.

scholarly journals On Statistical Analysis of Brain Variability

2020 ◽  
Author(s):  
Oliver Y. Chén ◽  
Huy Phan ◽  
Guy Nagels ◽  
Maarten de Vos
Keyword(s):  
Regression Models ◽  
Data Science ◽  
Law Of Large Numbers ◽  
Decomposition Methods ◽  
Large Numbers ◽  
Biological Studies ◽  
Different Types ◽  
First Time ◽  
Do So ◽  
Extract Information

A century ago, Sir R.A. Fisher introduced for the first time the concept of variance in biological studies. In this paper, we present a few new, modified, or integrated perspectives of variance that we feel would contribute to future thinking and practice of data science. We do so by focusing on brain and behavioral data, through which we hope one could extrapolate the discussions to other fields and data. Specifically: (1) We define different types of variation. (2) We demonstrate that both classic regression models and advanced statistical methods can be viewed as variance-decomposition methods. (3) We make a distinction between innate and acquired variability, linked through Bayesian updating. (4) We review and illustrate how to extract information from high-dimensional data and how to visualize them. Additionally, we introduce the Neural Law of Large Numbers. (5) We discuss the statistical basis for association, explanation, prediction, and causation, and recommend a strategy that may be useful to check if association-based findings can be raised to causal discoveries. Taken together, to understand the variation of data, one needs creative statistical thinking. Meanwhile, by incorporating insights learned from data, one can begin to design better statistical apparatuses.

My questions about emotionally focused couple therapy (EFT) and a few answers

2020 ◽  
Vol 14 (1) ◽  
pp. 23-41
Author(s):  
Anne Power
Keyword(s):  
Object Relations ◽  
Couple Therapy ◽  
Point Of View ◽  
Same Sex ◽  
Heterosexual Couple ◽  
Emotionally Focused Couple Therapy ◽  
Emotionally Focused ◽  
Do So

This article provides a brief overview of emotionally focused couple therapy (EFT) along with some reservations about the method. The article considers questions and critiques which are often raised about the model and does so from the point of view of a practitioner new to the method, who has become convinced of the value of the approach whilst not wanting to jettison an object relations understanding. The segregation between different groups of attachment researchers and practitioners is noted. To provide variation I occasionally use the term "marital" but I do so loosely, referring to a couple bond rather than to a wedded pair. The systemic pattern between a pursuer and a withdrawer which is discussed here could refer to a same-sex or a heterosexual couple, despite the different gender alignments which operate in each case.

Thanato-Laboratorien. Theorien von Tod und Sterben und Elias Canettis Buch gegen den Tod

2020 ◽  
Vol 4 (1) ◽  
pp. 67-86
Author(s):  
Elisabeth Heyne
Keyword(s):  
Human Life ◽  
Death And Dying ◽  
Point Of View ◽  
Visual Images ◽  
Elias Canetti ◽  
History Of ◽  
Series Of Experiments ◽  
First Time ◽  
Textual Form ◽  
Or History

AbstractAlthough visual culture of the 21th century increasingly focuses on representation of death and dying, contemporary discourses still lack a language of death adequate to the event shown by pictures and visual images from an outside point of view. Following this observation, this article suggests a re-reading of 20th century author Elias Canetti. His lifelong notes have been edited and published posthumously for the first time in 2014. Thanks to this edition Canetti's short texts and aphorisms can be focused as a textual laboratory in which he tries to model a language of death on experimental practices of natural sciences. The miniature series of experiments address the problem of death, not representable in discourses of cultural studies, system theory or history of knowledge, and in doing so, Canetti creates liminal texts at the margins of western concepts of (human) life, science and established textual form.

A Nabatean port on the Red Sea: note on the pottery finds from al-Qusayr (al-Wajh, Saudi Arabia)

2020 ◽  
Author(s):  
Caroline Durand
Keyword(s):  
Saudi Arabia ◽  
19Th Century ◽  
Red Sea ◽  
Point Of View ◽  
The Other ◽  
Trade Routes ◽  
Other Hand ◽  
Roman Egypt ◽  
Pottery Sherds ◽  
First Time

Al-Qusayr is located 40 km south of modern al-Wajh, roughly 7 km from the eastern Red Sea shore. This site is known since the mid-19th century, when the explorer R. Burton described it for the first time, in particular the remains of a monumental building so-called al-Qasr. In March 2016, a new survey of the site was undertaken by the al-‘Ula–al-Wajh Survey Project. This survey focused not only on al-Qasr but also on the surrounding site corresponding to the ancient settlement. A surface collection of pottery sherds revealed a striking combination of Mediterranean and Egyptian imports on one hand, and of Nabataean productions on the other hand. This material is particularly homogeneous on the chronological point of view, suggesting a rather limited occupation period for the site. Attesting contacts between Mediterranean merchants, Roman Egypt and the Nabataean kingdom, these new data allow a complete reassessment of the importance of this locality in the Red Sea trade routes during antiquity.

Decorative motifs on oil lamps from Grimm's 1973 excavations in Alexandria

2019 ◽  
Author(s):  
Heba Abdel Wahed Sayed
Keyword(s):  
Point Of View ◽  
Symbolic Meaning ◽  
Ancient History ◽  
Different Types ◽  
Decorative Motifs ◽  
Egyptian Culture ◽  
Late Roman

A collection of 30 clay oil lamps from Gunther Grimm's excavations in 1973 in the Western necropolis of Alexandria has been classified by Safaa Samir Abu Al Yazid from Tanta University and found to represent 12 different types ranging in time from the Hellenistic to the late Roman periods in Egypt's ancient history. The present paper looks at this collection from the point of view of the symbolic significance of the decorative motifs used in their decoration. These motifs— figural, floral and geometric—had obvious symbolic meaning to their users and signified more than a simple belief in certain deities. They also reflected Roman Egyptian culture.

Probabilistic Assessment of Reliability and Risk Values by Certification Results

2020 ◽  
pp. 52-67
Author(s):  
Vladimir A. Lapin ◽  
Erken S. Aldakhov ◽  
S. D. Aldakhov ◽  
A. B. Ali
Keyword(s):  
Seismic Risk ◽  
Housing Stock ◽  
Seismic Resistance ◽  
Probabilistic Assessment ◽  
Quantitative Estimates ◽  
Different Types ◽  
Reduce Risk ◽  
First Time ◽  
Structural Solutions ◽  
Practical Recommendations

For the first time in Almaty full passport of apartment stock of multiapartment building was carried out. The structure of the housing stock was revealed with the allocation of groups of buildings according to structural solutions and assessment of their seismic resistance. Based on the results of certification, quantitative estimates of failure probability values for different types of buildings were obtained. Formulas for estimation of quantitative value of seismic risk are obtained. The number of deaths in the estimated zem-shakes was estimated. The results of the assessments will be used for practical recommendations to reduce risk and expected losses in possible earthquakes.

Ground state molecular parameters of phosphine, PH3, from the simultaneous analysis of the high-resolution infrared, microwave and submillimeterwave spectra

1985 ◽  
Vol 50 (11) ◽  
pp. 2480-2492 ◽  
Author(s):  
Soňa Přádná ◽  
Dušan Papoušek ◽  
Jyrki Kauppinen ◽  
Sergei P. Belov ◽  
Andrei F. Krupnov ◽  
...  
Keyword(s):  
Fourier Transform ◽  
High Resolution ◽  
Ground State ◽  
Unitary Transformation ◽  
Point Of View ◽  
Acoustic Detection ◽  
Molecular Parameters ◽  
Microwave Spectrometer ◽  
Fourier Transform Spectra ◽  
First Time

Fourier transform spectra of the ν2 band of PH3 have been remeasured with 0.0045 cm-1 resolution. Ground state combination differences from these data have been fitted simultaneously with the microwave and submillimeterwave data to determine the ground state spectroscopical parameters of PH3 including the parameters of the Δk = ± 3n interactions. The correlation between the latter parameters has been discussed from the point of view of the existence of two equivalent effective rotational operators which are related by a unitary transformation. The ΔJ = 0, +1, ΔK = 0 (A1 ↔ A2, E ↔ E) rotational transitions in the ν2 and ν4 states have been measured for the first time by using a microwave spectrometer and a radiofrequency spectrometer with acoustic detection.

In the Labyrinth

2017 ◽  
Author(s):  
Andrew McNeillie
Keyword(s):  
The Right ◽  
First Time ◽  
Do So

It is now widely acknowledged, and far beyond Ireland, that Tim Robinson’s two volumes jointly known as Stones of Aran (‘Pilgrimage’ and ‘Labyrinth’) are modern classics, exemplary in every way of how to write about place and to do so with a formal, literary accomplishment that more than earns the right to nod at Ruskin’s own classic. In 2012, Robinson went back to Árainn, the largest of the three islands, for the first time in nearly ten years. He did so at the urging of Andrew McNeillie, with whom he spent two and a half days revisiting old haunts. This chapter makes account of the occasion and uses, in the process, a unique document provided by Robinson as an experiment in annotating his work. This prompts McNeillie to investigate some of his own annotations and footnotes to Aran.

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