Molecular dietary analyses of western capercaillies (Tetrao urogallus) reveal a diverse diet

ABSTRACTConservation strategies centred around species habitat protection rely on species’ dietary information. One species at the focal point of conservation efforts is the herbivorous grouse, the western capercaillie (Tetrao urogallus). Traditional microhistological analysis of crop contents or faeces and/or direct observations are time-consuming and at low taxonomic resolution. Thus, limited knowledge on diet is hampering conservation efforts. Here we use non-invasive environmental DNA (eDNA) metabarcoding on DNA extracted from faeces to present the first large-scale molecular dietary analysis of capercaillies. Faecal samples were collected from seven populations located in Norway (Finnmark, Troms, Trøndelag, Innlandet) and France (Vosges, Jura, Pyrenees) (n=172). We detected 122 plant taxa belonging to 46 plant families of which 37.7% of the detected taxa could be identified at species level. The average dietary richness of each sample was 7 ± 5 SD taxa. The most frequently occurring plant groups with the highest relative read abundance (RRA) were trees and dwarf shrubs, in particular, Pinus and Vaccinium myrtillus, respectively. There was a difference in dietary composition (RRA) between samples collected from the different locations (adonis F5,86= 11.01, p <0.05) and seasons (adonis F2,03= 0.64, p <0.05). Dietary composition also differed between sexes at each location (adonis F1,47 = 2.77, p <0.05), although not significant for all data combined. In total, 35 taxa (36.84% of taxa recorded) were new capercaillie food items compared to existing knowledge. The non-invasive molecular dietary analysis applied in this study provides new ecological understanding of capercaillies’ diet which can have real conservation implications. The broad variety of diet items indicates that vegetation does not limit food intake. This plasticity in diet suggests that other factors including disturbed mating grounds and not diet could be the main threat to their survival.

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Dietary analysis of an uncharacteristic population of the Mountain Pygmy-possum(Burramys parvus)in the Kosciuszko National Park, New South Wales, Australia

PeerJ ◽

10.7717/peerj.6307 ◽

2019 ◽

Vol 7 ◽

pp. e6307 ◽

Cited By ~ 1

Author(s):

Tahneal Hawke ◽

Hayley Bates ◽

Suzanne Hand ◽

Michael Archer ◽

Linda Broome

Keyword(s):

Seasonal Variation ◽

National Park ◽

Climatic Variability ◽

Critically Endangered ◽

Conservation Strategies ◽

Dietary Composition ◽

Southern Population ◽

Northern Population ◽

Dietary Analysis ◽

Critically Endangered Species

BackgroundThe Mountain Pygmy-possum (Burramys parvus) is a critically endangered marsupial, endemic to alpine regions of southern Australia. We investigated the diet of a recently discovered population of the possum in northern Kosciuszko National Park, NSW, Australia. This new population occurs at elevations well below the once-presumed lower elevation limit of 1,600 m.Goals and MethodsFaecal material was analysed to determine if dietary composition differed between individuals in the newly discovered northern population and those in the higher elevation southern population, and to examine how diet was influenced by rainfall in the southern population and seasonal changes in resource availability in the northern population.Results and DiscussionThe diet ofB. parvusin the northern population comprised of arthropods, fruits and seeds. Results indicate the diet of both populations shares most of the same invertebrate orders and plant species. However, in the absence of preferred food types available to the southern population, individuals of the northern population opportunistically consumed different species that were similar to those preferred by individuals in higher altitude populations. Differing rainfall amounts had a significant effect on diet, with years of below average rainfall having a greater percentage composition and diversity of invertebrates. Seasonal variation was also recorded, with the northern population increasing the diversity of invertebrates in their diet during the Autumn months when Bogong Moths (Agrotis infusa) were absent from those sites, raising questions about the possum’s dependence on the speciesConclusionsMeasurable effects of rainfall amount and seasonal variation on the dietary composition suggest that predicted climatic variability will have a significant impact on its diet, potentially impacting its future survival. Findings suggest that it is likely thatB. parvusis not restricted by dietary requirements to its current pattern of distribution. This new understanding needs to be considered when formulating future conservation strategies for this critically endangered species.

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Improving herpetological surveys in eastern North America using the environmental DNA method

Genome ◽

10.1139/gen-2015-0218 ◽

2016 ◽

Vol 59 (11) ◽

pp. 991-1007 ◽

Cited By ~ 35

Author(s):

Anaïs Lacoursière-Roussel ◽

Yohann Dubois ◽

Eric Normandeau ◽

Louis Bernatchez

Keyword(s):

Large Scale ◽

Habitat Type ◽

Environmental Dna ◽

Conservation Strategies ◽

Natural Environments ◽

Detection Rates ◽

Survey Tool ◽

Declining Species ◽

Species Specific ◽

Wood Turtle

Among vertebrates, herpetofauna has the highest proportion of declining species. Detection of environmental DNA (eDNA) is a promising method towards significantly increasing large-scale herpetological conservation efforts. However, the integration of eDNA results within a management framework requires an evaluation of the efficiency of the method in large natural environments and the calibration of eDNA surveys with the quantitative monitoring tools currently used by conservation biologists. Towards this end, we first developed species-specific primers to detect the wood turtle (Glyptemys insculpta) a species at risk in Canada, by quantitative PCR (qPCR). The rate of eDNA detection obtained by qPCR was also compared to the relative abundance of this species in nine rivers obtained by standardized visual surveys in the Province of Québec (Canada). Second, we developed multi-species primers to detect North American amphibian and reptile species using eDNA metabarcoding analysis. An occurrence index based on the distribution range and habitat type was compared with the eDNA metabarcoding dataset from samples collected in seven lakes and five rivers. Our results empirically support the effectiveness of eDNA metabarcoding to characterize herpetological species distributions. Moreover, detection rates provided similar results to standardized visual surveys currently used to develop conservation strategies for the wood turtle. We conclude that eDNA detection rates may provide an effective semiquantitative survey tool, provided that assay calibration and standardization is performed.

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Metabarcoding for parallel identification of species, sex and diet: an application to the conservation of globally-threatened Gyps vultures

10.1101/756247 ◽

2019 ◽

Author(s):

Mousumi Ghosh-Harihar ◽

Nehal Gurung ◽

Harsh Shukla ◽

Ishani Sinha ◽

Awadhesh Pandit ◽

...

Keyword(s):

National Parks ◽

Large Scale ◽

Sequence Data ◽

Indian Subcontinent ◽

Spatial Association ◽

Taxonomic Resolution ◽

Conservation Strategies ◽

Species Identity ◽

Factors Affecting ◽

Identification Of Species

AbstractAn understanding of the factors affecting the diet composition of critically endangered Gyps vultures in the Indian subcontinent has important applications to the design of effective conservation strategies. After suffering a massive decline (~99%) in numbers caused by veterinary use of the nephrotoxic drug diclofenac, vultures now persist in very low numbers, mostly concentrated within or near National Parks. This spatial association might be attributed to the availability of wild ungulate carcasses free from toxic veterinary drugs. Hence, quantification of vulture diets and the factors affecting them is critical to test this hypothesis. Here, we describe and validate a robust “field-to-benchtop-to-desktop” metabarcoding workflow for assessing the species- and sex-specific diet of these obligate scavengers from non-invasively collected faecal samples. Seven metabarcodes targeting mitochondrial and nuclear genes were used to simultaneously determine the vulture species identity, sex and species consumed. The amplicons were sequenced using an Illumina Miseq platform. We included controls and three replicates per sample to establish a series of non-arbitrary thresholds to filter the sequence data and eliminate cross-contamination, PCR/sequencing errors and false positives. Using this strategy enabled identification of species and sex for all samples. Diet species-specific sequences could be identified with high taxonomic resolution for 93% of samples. Out of the seven metabarcodes, just four were sufficient to meet the objectives. From this preliminary analysis, domestic livestock seem to be the most frequently consumed diet item across samples from inside and outside protected habitats. Our method provides a rapid and reliable tool for describing large-scale variation in consumption of domestic versus wild species in the diet of these species, paving the way for a better understanding of the role protected areas play in persistence and recovery of the remaining Gyps vulture populations in the wild.

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eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants

Scientific Reports ◽

10.1038/s41598-021-85488-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Louise Nørgaard ◽

Carsten Riis Olesen ◽

Kristian Trøjelsgaard ◽

Cino Pertoldi ◽

Jeppe Lund Nielsen ◽

...

Keyword(s):

Negative Impact ◽

Environmental Dna ◽

Diet Analysis ◽

Taxonomic Resolution ◽

Generalist Predators ◽

Field Observations ◽

Natural Ecosystems ◽

Survey Techniques ◽

Non Invasive ◽

Identification Techniques

AbstractWith an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently been described as “biodiversity capsules” and suggested as a complementary tool for improving current biodiversity assessments. In this study, using faecal samples from two generalist omnivore species, the Eurasian badger and the red fox, we evaluated the applicability of eDNA metabarcoding in determining dietary composition, compared to macroscopic diet identification techniques. Subsequently, we used the dietary information obtained to assess its contribution to biodiversity assessments. Compared to classic macroscopic techniques, we found that eDNA metabarcoding detected more taxa, at higher taxonomic resolution, and proved to be an important technique to verify the species identification of the predator from field collected faeces. Furthermore, we showed how dietary analyses complemented field observations in describing biodiversity by identifying consumed flora and fauna that went unnoticed during field observations. While diet analysis approaches could not substitute field observations entirely, we suggest that their integration with other methods might overcome intrinsic limitations of single techniques in future biodiversity surveys.

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Multi-marker DNA metabarcoding reflects tardigrade diversity in different habitats

Genome ◽

10.1139/gen-2019-0218 ◽

2020 ◽

Author(s):

Lasse Topstad ◽

Roberto Guidetti ◽

Markus Majaneva ◽

Torbjørn EKREM

Keyword(s):

Large Scale ◽

Environmental Dna ◽

Distribution Patterns ◽

Taxonomic Resolution ◽

Dna Metabarcoding ◽

The World ◽

Microhabitat Distribution ◽

Environmental Surveys ◽

Reference Sequences ◽

Alpine Environments

Like meiofauna in general, tardigrades are often neglected in ecological and environmental surveys. Tardigrades occur in all parts of the world, from deep marine sediments to alpine environments, and are present in most ecosystems. They are therefore potentially good candidates for biomonitoring programs. However, sampling of these minute animals is both tedious and time-consuming, impeding their inclusion in large-scale ecological surveys. In this study we argue that using a multi-marker metabarcoding approach on environmental DNA partly can overcome this barrier. Samples of moss, lichens and leaf litter were investigated both by morphology-based methods and DNA metabarcoding, and the results were compared in terms of tardigrade diversity and community composition of the sampled microhabitats. DNA metabarcoding using three markers detected more species of tardigrades than identification by morphology in most samples. Also, metabarcoding detected the same community differences and microhabitat distribution patterns as morphology-based methods. In general, metabarcoding of litter samples was unreliable, with only one out of three markers consistently amplifying and detecting tardigrades. The low availability of tardigrade reference sequences in public databases restricts the taxonomic resolution in eDNA surveys, but this impediment is partly circumvented by utilizing multiple markers

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Meta-Governance

10.1093/oso/9780198825074.003.0008 ◽

2018 ◽

Author(s):

Morten Egeberg ◽

Jarle Trondal

Keyword(s):

Large Scale ◽

Central Government ◽

Focal Point ◽

Reform Process ◽

Government Agencies ◽

Reform Processes ◽

The Government ◽

Central Government Agencies ◽

Instrumental Control

Chapter 8 draws attention to meta-governance and how the governing of reforms is affected by how reform processes are organized. The chapter asks how reformers can ensure support for large-scale reforms that are likely to attract profound resistance. The focal point of the chapter is a study of geographical decentralization of central government agencies. The chapter argues that successful meta-governance can be provided for by careful organization of the reform process. The empirical case studied is a large-scale relocation of government agencies in Norway during the early 2000s. In carrying out this reform, the government succeeded against the odds. Most importantly, research has revealed huge constraints on the instrumental control of large-scale reforms in general and of geographical relocation of organizations in particular. Yet, this chapter shows that large-scale reforms can be successfully achieved through careful crafting of the reform organization.

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GIANA allows computationally-efficient TCR clustering and multi-disease repertoire classification by isometric transformation

Nature Communications ◽

10.1038/s41467-021-25006-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Hongyi Zhang ◽

Xiaowei Zhan ◽

Bo Li

Keyword(s):

T Cell ◽

T Cell Receptor ◽

Large Scale ◽

Cell Receptor ◽

Alignment Algorithm ◽

Computationally Efficient ◽

Antigen Specificity ◽

Non Invasive ◽

Isometric Transformation ◽

Specific Receptors

AbstractSimilarity in T-cell receptor (TCR) sequences implies shared antigen specificity between receptors, and could be used to discover novel therapeutic targets. However, existing methods that cluster T-cell receptor sequences by similarity are computationally inefficient, making them impractical to use on the ever-expanding datasets of the immune repertoire. Here, we developed GIANA (Geometric Isometry-based TCR AligNment Algorithm) a computationally efficient tool for this task that provides the same level of clustering specificity as TCRdist at 600 times its speed, and without sacrificing accuracy. GIANA also allows the rapid query of large reference cohorts within minutes. Using GIANA to cluster large-scale TCR datasets provides candidate disease-specific receptors, and provides a new solution to repertoire classification. Querying unseen TCR-seq samples against an existing reference differentiates samples from patients across various cohorts associated with cancer, infectious and autoimmune disease. Our results demonstrate how GIANA could be used as the basis for a TCR-based non-invasive multi-disease diagnostic platform.

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Large-scale visualization of dispersion of liquid-exfoliated two-dimensional nanosheets

Chemical Communications ◽

10.1039/d1cc01101d ◽

2021 ◽

Author(s):

Xingyu Cui ◽

Wen ying Shi ◽

Chao Lu

Keyword(s):

Aqueous Solution ◽

Large Scale ◽

Fluorescence Microscope ◽

Visualization Method ◽

Two Dimensional ◽

Non Invasive

An ultrafast, non-invasive and large-scale visualization method has been developed to evaluate the dispersion of two-dimensional nanosheets in aqueous solution with fluorescence microscope by formation of excimers from improvement of...

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Dynamic relationships between spontaneous and evoked electrophysiological activity

Communications Biology ◽

10.1038/s42003-021-02240-9 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Soren Wainio-Theberge ◽

Annemarie Wolff ◽

Georg Northoff

Keyword(s):

Neural Activity ◽

Large Scale ◽

Behavioral Outcomes ◽

Low Frequencies ◽

Scale Free ◽

Non Invasive ◽

Spontaneous Neural Activity ◽

Electrophysiological Signals ◽

Evoked Activity ◽

Dynamic Relationships

AbstractSpontaneous neural activity fluctuations have been shown to influence trial-by-trial variation in perceptual, cognitive, and behavioral outcomes. However, the complex electrophysiological mechanisms by which these fluctuations shape stimulus-evoked neural activity remain largely to be explored. Employing a large-scale magnetoencephalographic dataset and an electroencephalographic replication dataset, we investigate the relationship between spontaneous and evoked neural activity across a range of electrophysiological variables. We observe that for high-frequency activity, high pre-stimulus amplitudes lead to greater evoked desynchronization, while for low frequencies, high pre-stimulus amplitudes induce larger degrees of event-related synchronization. We further decompose electrophysiological power into oscillatory and scale-free components, demonstrating different patterns of spontaneous-evoked correlation for each component. Finally, we find correlations between spontaneous and evoked time-domain electrophysiological signals. Overall, we demonstrate that the dynamics of multiple electrophysiological variables exhibit distinct relationships between their spontaneous and evoked activity, a result which carries implications for experimental design and analysis in non-invasive electrophysiology.

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Beyond Newgrange: Brú na Bóinne in the later Neolithic

Proceedings of the Prehistoric Society ◽

10.1017/ppr.2021.6 ◽

2021 ◽

pp. 1-30

Author(s):

Stephen Davis ◽

Knut Rassmann

Keyword(s):

Large Scale ◽

Morphological Characteristics ◽

World Heritage ◽

Geophysical Survey ◽

World Heritage Site ◽

Late Neolithic ◽

Non Invasive ◽

Heritage Site ◽

New Evidence

The Brú na Bóinne World Heritage Site, Ireland is best known for its megalithic monuments, in particular the great developed passage tombs of Knowth, Dowth, and Newgrange, and its abundance of megalithic art. However, our understanding of the wider Brú na Bóinne landscape has changed beyond all recognition in the last decade owing to the application of modern, non-invasive survey technologies – in particular LiDAR and large-scale geophysical survey – and most recently as a result of the hot, dry summer of 2018 which revealed a series of remarkable cropmarks between Newgrange and the River Boyne. Despite a lack of excavation it can be argued, based on their morphological characteristics, that many of the structures revealed belong within the corpus of late Neolithic ritual/ceremonial structures, including earthen henges, square-in-circle monuments, palisaded enclosures, and pit/post-alignments. These display both extraordinary diversity, yet also commonality of design and architecture, both as a group and with the passage tombs that preceded them. This paper provides an up-to-date survey of the late Neolithic and presumed late Neolithic landscape of Brú na Bóinne. It provides new evidence and new insights from ongoing survey campaigns, suggesting parallels within the British Neolithic but also insular development within some monument classes.

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