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opencc-zeroDec 2022View details →

Trait-based sensitivity of large mammals to a catastrophic tropical cyclone: DNA metabarcoding data

Extreme weather events perturb ecosystems and increasingly threaten biodiversity1. Ecologists emphasize the need to forecast and mitigate the impacts of these incidents, which requires knowledge of how risk is distributed among species and environments, but the scale and unpredictability of extreme events complicates assessment1–4. These challenges are compounded for large animals ('megafauna'), which play crucial ecological roles but are hard to study5. Traits such as body size, dispersal ability, and habitat affiliation are among the hypothesized determinants of animals' vulnerability to natural hazards1,6,7. However, it has rarely been possible to test these propositions or, more generally, to link short- and longer-term effects of weather-related disturbance8,9. Here, we show how large herbivores and carnivores in Mozambique responded to Intense Tropical Cyclone Idai, the deadliest storm on record in Africa, across scales ranging from individual decisions in the hours after landfall to community-level responses nearly 20 months later. Animals occupying low-elevation habitats exhibited strong spatial responses to rising floodwaters. Body size predicted species' subsequent numerical responses: small-bodied species exhibited the greatest population declines. We trace this sensitivity to limited mobility, which increased likelihood of death during the flood and constrained animals' capacity to withstand food shortages afterward. Our results identify potentially general trait-based mechanisms underlying animal responses to severe weather and may help to inform strategies for wildlife conservation in a volatile climate. <ol> <li>Climate Change 2022: Impacts, Adaptation and Vulnerability. Contribution of Working Group II to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change [H.-O. Pörtner, D.C. Roberts, M. Tignor, E.S. Poloczanska, K. Mintenbeck, A. Alegría, M. Craig, S. Langsdorf, S. Löschke, V. Möller, A. Okem, B. Rama (eds.)]. Cambridge University Press. Cambridge University Press, Cambridge, UK and New York, NY, USA, (2022).</li> <li>Smith, M. An ecological perspective on extreme climatic events: A synthetic definition and framework to guide future research. J. Ecol. 99, 656-663 (2011).</li> <li>Ummenhofer, C. C., & Meehl, G. A. Extreme weather and climate events with ecological relevance: a review, Phil. Trans. R. Soc. B. 372, 20160135 (2017).</li> <li>Jentsch, A., Kreyling, J., & Beierkuhnlein, C. A new generation of climate-change experiments: events, not trends. Front. Ecol. Environ. 5, 365-374 (2007).</li> <li>Pringle, R. M., et. al. Impacts of large herbivores on terrestrial ecosystems. Current Biology 33, R584-R610 (2023).</li> <li>Spiller, D. A., Losos, J. B., & Schoener, T. W. Impact of a catastrophic hurricane on island populations. Science 281, 695-697 (1998). </li> <li>Schoener, T. W., & Spiller, D. A. Nonsynchronous recovery of community characteristics in island spiders after a catastrophic hurricane. PNAS 103, 2220-2225 (2006).</li> <li>Pruitt, N., Little, A. G., Majumdar, S. J., Schoener, T. W., & Fisher, D. N. Call-to-Action: A global consortium for tropical cyclone ecology. TREE 34, 588-590 (2019).</li> <li>Lin, T. C., Hogan, J. A., & Chang, C. T. Tropical cyclone ecology: a scale-link perspective. TREE 35, 594-604 (2020).</li> </ol>

opencc-zeroJan 2024View details →

COI metabarcoding data from arthropod pollinator communities in burned and unburned sites of California

Novel wildfire regimes are rapidly changing global ecosystems and pose significant challenges for biodiversity conservation and ecosystem management. In this study, we used DNA metabarcoding to assess the response of arthropod pollinator communities to large-scale wildfires across diverse habitat types in California. We sampled six reserves within the University of California Natural Reserve System (UCNRS), each of which was partially burned in the 2020 Lightning Complex wildfires in California. Using yellow pan traps to target pollinators, we collected arthropods from burned and unburned sites across multiple habitat types including oak woodland, redwood, scrub, chamise, grassland, forest, and serpentine habitats. We found no significant difference in alpha diversity values between burned and unburned sites; instead, seasonal variations played a significant role in arthropod community dynamics, with the emergence of plant species in Spring promoting increased pollinator richness at all sites. When comparing all sites, we found that burn status was not a significant grouping factor. Instead, compositional differences were largely explained by geographic differences, with distinct communities within each reserve. Within a geographic area, the response of arthropods to fire was dependent on habitat type. While communities in grasslands and oak woodlands exhibited recovery following burn, scrublands experienced substantial changes in community composition. Our study highlights the importance of examining community responses to wildfires across broad spatial scales and diverse habitat types. By understanding the nuanced dynamics of arthropod communities in response to fire disturbances, we can develop effective conservation strategies that promote resilience and maintain biodiversity in the face of increasing wildfire frequency and severity driven by climate change.

opencc-zeroJan 2024View details →

Bloodmeal metabarcoding of the argasid tick (Ornithodoros turicata Dugès) reveals extensive vector-host associations

Molecular methods to understand host feeding patterns of arthropod vectors are critical to assess exposure risk to vector-borne disease and unveil complex ecological interactions. We build on our prior work discovering the utility of PCR-Sanger sequencing bloodmeal analysis that work well for soft ticks (Acari: Argasidae), unlike for hard ticks (Acari: Ixodidae), thanks to their unique physiology that retains prior bloodmeals for years. Here, we apply bloodmeal metabarcoding using amplicon deep sequencing to identify multiple host species in individual Ornithodoros turicata soft ticks collected from two natural areas in Texas, United States. Of 788 collected O. turicata, 394 were evaluated for bloodmeal source via metabarcoding, revealing 27 different vertebrate hosts (17 mammals, 5 birds, 1 reptile, and 4 amphibians) fed upon by 274 soft ticks. Information on multiple hosts was derived from 167 individual O. turicata (61%). Metabarcoding revealed mixed vertebrate bloodmeals in O. turicata while same specimens yielded only one vertebrate species using Sanger sequencing. These data reveal wide host range of O. turicata and demonstrate the value of bloodmeal metabarcoding for understanding the ecology for known and potential tick-borne pathogens circulating among humans, domestic animals and wildlife such as relapsing fever caused by Borrelia turicatae. Our results also document evidence of prior feeding on wild pig from an off-host soft tick for the first time in North America; a critical observation in the context of enzootic transmission of African swine fever virus if it were introduced to the US. This research enhances our understanding of vector-host associations and offers a promising perspective for biodiversity monitoring and disease control strategies.

opencc-zeroMar 2024View details →

Environmental DNA metabarcoding differentiates between micro-habitats within the rocky intertidal

While the utility of environmental DNA (eDNA) metabarcoding surveys for biodiversity monitoring continues to be demonstrated, the spatial and temporal variability of eDNA, and thus the limits of the differentiability of an eDNA signal, remains under-characterized. In this study, we collected eDNA samples from distinct micro-habitats (~40 m apart) in a rocky intertidal ecosystem over their exposure period in a tidal cycle. During this period, the micro-habitats transitioned from being interconnected, to physically isolated, to interconnected again. Using a well-established eukaryotic (cytochrome oxidase subunit I) metabarcoding assay, we detected 415 species across 28 phyla. Across a variety of univariate and multivariate analyses, using exclusively taxonomically assigned data as well as all detected amplicon sequence variants (ASVs), we identified unique eDNA signals from the different micro-habitats sampled. This difference paralleled expected ecological gradients and increased as the sites became more physically disconnected. Our results demonstrate that eDNA biomonitoring can differentiate micro-habitats in the rocky intertidal only 40 m apart, that these differences reflect known ecology in the area, and that physical connectivity informs the degree of differentiation possible. These findings showcase the potential power of eDNA biomonitoring to increase the spatial and temporal resolution of marine biodiversity data, aiding research, conservation, and management efforts.

opencc-by-4.0Mar 2024View details →

Data from: European green crab predation in a Washington State estuary revealed with DNA metabarcoding

Fisher, MC, Grason, EW, Stote, A, Kelly, RP, Litle, K, & PS McDonald. (in review). Invasive European green crab (Carcinus maenas) predation in a Washington State estuary revealed with DNA metabarcoding.  Sequencing data files produced for Fisher et al. (in review) on an Illumina MiSeq (2x300bp) targeting a 418bp DNA sequence in the mitochondrial cytochrome C oxidase subunit I gene (cox1 or COI) Folmer region. Data are demultiplexed but otherwise un-processed. Sample data sheets used to load each sequencing run are included as excel spreadsheets in the appropriate zipped folder. The metadata file contains sample (green crab stomach / mock community) metadata and corresponding MiSeq run number(s).  Associated lab protocols are available on Github (<a href="https://github.com/mfisher5/Green-crab-dDNA/tree/main/doc" target="_blank" rel="noopener">Green-Crab-dDNA</a>) --- Abstract: Predation by invasive species can threaten local ecosystems and economies. The European green crab (Carcinus maenas), one of the most widespread marine invasive species, is an effective predator associated with clam and crab population declines outside of its native range. In the U.S. Pacific Northwest, green crab has recently increased in abundance and expanded its distribution, generating concern for estuarine ecosystems and associated aquaculture production. However, regionally-specific information on the trophic impacts of invasive green crab is very limited. We compared the stomach contents of green crabs collected on shellfish aquaculture beds versus natural intertidal sloughs in Willapa Bay, Washington, to provide the first in-depth description of European green crab diet at a particularly crucial time for regional management. We first identified putative prey items using DNA metabarcoding of stomach content samples. We compared diet composition across sites using prey presence/absence and an index of species-specific relative abundance. For eight prey species, we also calibrated metabarcoding data to quantitatively compare DNA abundance between prey items, and to describe an ‘average’ green crab diet at an intertidal slough and an actively cultivated Manila clam bed. From the stomach contents of 61 green crabs, we identified 54 unique taxa belonging to nine phyla. The stomach contents of crabs collected from cultivated Manila clam beds were significantly different from the stomach contents of crabs collected at natural intertidal sloughs. Across all sites, arthropods were the most frequently detected prey, with the native hairy shore crab (Hemigrapsus oregonensis) the single most common prey item. Of the eight species included in the quantitative model, two ecologically-important native species – the sand shrimp (Crangon franciscorum) and the Pacific staghorn sculpin (Leptocottus armatus) – were the most abundant in crab stomach contents, when present. In addition to providing timely information on green crab diet, our research demonstrates the novel application of a recently developed model for more quantitative DNA metabarcoding. This represents another step in the ongoing evolution of DNA-based diet analysis towards producing the quantitative data necessary for modeling invasive species impacts.

opencc-zeroMar 2024View details →

Data from: Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard

Species of the family Felidae (a group represented by cats) are thought to be obligate carnivores, specialized for hunting and consuming other animals. However, the detection of plants in the feces of felids raises questions about the role of plants in their diet. This is particularly true for the snow leopard (Panthera uncia), a big cat native to central and South Asia's high mountains. Our study aimed to comprehensively identify the prey and plants consumed by snow leopards as well as six other sympatric mammals. We applied DNA metabarcoding methods on 126 fecal samples collected from the Sarychat-Ertash Nature Reserve in Kyrgyzstan. We found that among the three most common plant families in snow leopard feces, Tamaricaceae (genus Myricaraia) was consumed often by snow leopards. The genus Myricaria frequently appeared in samples lacking any animal prey DNA, indicating that snow leopards might have consumed this plant especially when their digestive tracts were empty. We also observed a significant difference in plant composition between male and female snow leopards, and potentially between sampling seasons. We provide a comprehensive overview of the prey and plants detected in the feces of snow leopards and sympatric mammals. We believe our findings will help in formulating hypotheses and guiding future research to understand the adaptive significance of plant-eating behavior in felids and animal-plant relationships in the ecosystem.

F I G U R E 3 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches

F I G U R E 3 Comparison of trait-based metrics expressed in relative number of individuals computed from eDNA () and traditional electro-fishing (TEF;) samples in the five river stretches (RS), A, B, C, D and E. Trait categories: BEN, benthic; EUR, eurytopic; INS, insectivorous; OMN, omnivorous; PHY, phytophilic; POT, potamodromous; RHE, rheophilic; TOL, tolerant; PEL pelagic. Significance of the differences between eDNA and TEF metrics are shown: ns, not significant (P> 0.05)

F I G U R E 4 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches

F I G U R E 4 Boxplots (, median value;, interquartile range;, full range;, outliers) showing the variability in the eDNAadapted fish index (six metrics) computed at three sites (Brangues, Rhins and Usses) where 10 eDNA water samples were collected once. At each site, the eDNA-based six-metric fish index was computed for each of the 45 possible pairs of samples

F I G U R E 2 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches

F I G U R E 2 Comparison of trait-based metrics expressed in number of species computed from eDNA () and traditional electrofishing (TEF;) samples in the five river stretches (RS), A, B, C, D and E. Trait categories: BEN, benthic; EUR, eurytopic; INS, insectivorous; OMN, omnivorous; PHY, phytophilic; POT, potamodromous; RHE, rheophilic; TOL, tolerant; PEL pelagic. Significance of the differences between eDNA and TEF metrics are shown: P <0.05; P <0.01; ns, not significant (P> 0.05)

F I G U R E 1 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches

F I G U R E 1 Sampling locations along river stretches (RS) A to E () of the main channel of the Rhône River, France, using both traditional electro-fishing (TEF) and eDNA., Sites sampled every 2 months (September 2015– August 2016);, sites where ten eDNA water samples (filtration capsules) were collected once;, sites located on the tributaries or the Rhône River itself sampled once for eDNA. The 10 metric fish index and the adapted six-metric fish index were computed at all sites with a black filled symbol within natural water bodies

opencc-by-4.0Apr 2024View details →

Github Repository for: European green crab predation in a Washington State estuary revealed with DNA metabarcoding

Fisher, MC, Grason, EW, Stote, A, Kelly, RP, Litle, K, & PS McDonald. (2024). Invasive European green crab (Carcinus maenas) predation in a Washington State estuary revealed with DNA metabarcoding. DOI:10.1371/journal.pone.0302518 Github release v1.1 of the repository for Fisher et al. 2024, "European green crab predation in a Washington State estuary revealed with DNA metabarcoding." For the most updated repository, see: <a href="https://github.com/mfisher5/Green-crab-dDNA/tree/main/doc">github.com/mfisher5/Green-crab-dDNA</a> Contains the code and minimum dataset necessary to replicate study findings.   --- Abstract: Predation by invasive species can threaten local ecosystems and economies. The European green crab (Carcinus maenas), one of the most widespread marine invasive species, is an effective predator associated with clam and crab population declines outside of its native range. In the U.S. Pacific Northwest, green crab has recently increased in abundance and expanded its distribution, generating concern for estuarine ecosystems and associated aquaculture production. However, regionally-specific information on the trophic impacts of invasive green crab is very limited. We compared the stomach contents of green crabs collected on shellfish aquaculture beds versus natural intertidal sloughs in Willapa Bay, Washington, to provide the first in-depth description of European green crab diet at a particularly crucial time for regional management. We first identified putative prey items using DNA metabarcoding of stomach content samples. We compared diet composition across sites using prey presence/absence and an index of species-specific relative abundance. For eight prey species, we also calibrated metabarcoding data to quantitatively compare DNA abundance between prey items, and to describe an ‘average’ green crab diet at an intertidal slough and an actively cultivated Manila clam bed. From the stomach contents of 61 green crabs, we identified 54 unique taxa belonging to nine phyla. The stomach contents of crabs collected from cultivated Manila clam beds were significantly different from the stomach contents of crabs collected at natural intertidal sloughs. Across all sites, arthropods were the most frequently detected prey, with the native hairy shore crab (Hemigrapsus oregonensis) the single most common prey item. Of the eight species included in the quantitative model, two ecologically-important native species – the sand shrimp (Crangon franciscorum) and the Pacific staghorn sculpin (Leptocottus armatus) – were the most abundant in crab stomach contents, when present. In addition to providing timely information on green crab diet, our research demonstrates the novel application of a recently developed model for more quantitative DNA metabarcoding. This represents another step in the ongoing evolution of DNA-based diet analysis towards producing the quantitative data necessary for modeling invasive species impacts.

opencc-zeroJan 2022View details →

Semi‐quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island

Spatial variation in climatic conditions along elevation gradients provides an important backdrop by which communities assemble and diversify. Lowland habitats tend to be connected through time, whereas highlands can be continuously or periodically isolated, conditions that have been hypothesized to promote high levels of species endemism. This tendency is expected to be accentuated among taxa that show niche conservatism within a given climatic envelope. While species distribution modeling approaches have allowed extensive exploration of niche conservatism among target taxa, a broad understanding of the phenomenon requires sampling of entire communities. Species-rich groups such as arthropods are ideal case studies for understanding ecological and biodiversity dynamics along elevational gradients given their important functional role in many ecosystems, but community-level studies have been limited due to their tremendous diversity. Here, we develop a novel semi-quantitative metabarcoding approach that combines specimen counts and size-sorting to characterize arthropod community-level diversity patterns along two elevational gradients across two volcanoes on the island of Hawai`i. We find that arthropod communities between the two transects become increasingly distinct compositionally at higher elevations. Resistance surface approaches suggest that climatic differences between sampling localities are an important driver in shaping beta-diversity patterns, though the relative importance of climate varies across taxonomic groups. Nevertheless, the climatic niche position of OTUs between transects was highly correlated, suggesting that climatic filters shape the colonization between adjacent volcanoes. Taken together, our results highlight climatic niche conservatism as an important factor shaping ecological assembly along elevational gradients and suggest topographic complexity as an important driver of diversification.

opencc-by-4.0Feb 2022View details →

ITS1 metabarcoding revealing Phytophthora diversity in anthropized and natural ecosystems in Sicily, Italy

This dataset on Zenodo contains the raw sequencing data for: <a href="https://doi.org/10.3390/jof8040330">La Spada et al. (2022) DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems</a>. This a subset of 192 demultiplexed Illumina MiSeq raw sequencing samples run at the James Hutton Institute in January 2020, consisting of two 96-well plates labelled with the Illumina A and D multiplexing kits. There are 61 pairs of raw gzipped compressed FASTQ files (122 files), provided as a 930MB gzipped compressed tar-ball. From the D multiplexing kit, there are 27 Nature Reserve (NR) samples, 16 Botanical Garden (BG) samples, and 6 managed Citrus Orchard (CO) samples containing Phytophthora targeted ITS1 marker sequences, and 6 synthetic controls (prefix GL1D) which should have contained only four known synthetic sequences. Additionally included are the 6 synthetic controls (prefix GL1A) from the A multiplexing kit, which were clean. The filenames start with the sample name, followed by something like DH03_S183_L001_R1_001.fastq.gz where DH03 indicates well H03 on the 96-well plate labelled with the D multiplexing set, S183 is the MiSeq sample number (from 1 to 192), and R1 (or R2) indicate the Illumina forward (or reverse) paired read files.

opencc-zeroFeb 2022View details →

Data from: Metabarcoding of soil environmental DNA replicates plant community variation but not specificity

<blockquote> While metabarcoding of plant DNA from their environment is an exciting method that can supplement inventorying of live plant species, the accuracy and specificity has yet to be fully assessed over complex continuous landscapes. In this work, we evaluate plant community profiles produced via metabarcoding of soil by comparing them to a morphological survey. We assessed plant communities by metabarcoding of soil DNA in 130 sites along ecological gradients (nutrients, succession, moisture) in Denmark using chloroplast trnL region (10-143 bp) primer set and compared the resulting communities to communities produced with a longer nuclear ITS2 region (~216 bp) and a morphological survey. We found that the community variation observed within the morphological survey was well represented by molecular surveys, with significant correlation with both community composition and richness using both primer sets. While the majority of the ITS2 sequences could be assigned to species (over 80%), we had less success with the trnL sequences (70%), which was only possible after restricting the reference database to local species. We conclude that the community profiles produced by metabarcoding can be highly effective in performing large-scale macroecological studies. However, the discovery rates and taxonomic assignments produced via metabarcoding remained inferior to morphological surveys, but manual curation of databases improves the specificity of assignments made by the trnL primers, and improves the accuracy of the assignments made with the ITS2 primers. Finally, we suggest that a greater percentage of named diversity would be recovered by increasing soil sampling with the use of additional universal primer sets. </blockquote>

opencc-zeroMay 2022View details →

Data from: eDNA metabarcoding of log hollow sediments and soils highlights the importance of substrate type, frequency of sampling and animal size, for vertebrate species detection

Fauna monitoring often relies on visual monitoring techniques such as camera trappings, which have biases leading to underestimates of vertebrate species diversity. Environmental DNA (eDNA) has emerged as a new source of biodiversity data that may improve biomonitoring; however, eDNA based assessments of species richness remain relatively untested in terrestrial environments. We investigated the suitability of fallen log hollow sediment as a source of vertebrate eDNA, across two sites in south-western Australia - one with a Mediterranean climate and the other semi-arid. We compared two different approaches (camera trapping and eDNA metabarcoding) for monitoring of vertebrate species, and investigated the effect of other factors (frequency of species, timing of visits, frequency of sampling, body size) on vertebrate species detectability. Metabarcoding of hollow sediments resulted in the detection of higher species richness in comparison Hollow sediment detected higher species richness (29 taxa: six birds, three reptiles and 20 mammals) to metabarcoding of soil at the entrance of the hollow (13 taxa: three birds, two reptiles and eight mammals). We detected 31 taxa in total with eDNA metabarcoding and 47 with camera traps, with 14 taxa detected by both (12 mammals and two birds). By comparing camera trap data with eDNA read abundance, we were able to detect vertebrates through eDNA metabarcoding that had visited the area up to two months prior to sample collection. Larger animals were more likely to be detected, and so were vertebrates that were identified multiple times in the camera traps. These findings demonstrate the importance of substrate selection, frequency of sampling, and animal size, on eDNA based monitoring. Future eDNA experimental design should consider all these factors as they affect detection of target taxa.

opencc-zeroJun 2022View details →

Interspecific coprophagia by wild red foxes: DNA metabarcoding reveals a potentially widespread form of commensalism among animals

Vertebrate animals are known to consume other species' faeces, yet the role of such coprophagy in species dynamics remains unknown, not least due to the methodological challenges of documenting it. In a large-scale metabarcoding study of red fox and pine marten scats, we document a high occurrence of domestic dog DNA in red fox scats and investigate if it can be attributed to interspecific coprophagia. We tested whether experimental artifacts or other sources of DNA could account for dog DNA, regressed dog occurrence in the diet of fox against that of the fox' main prey, short-tailed field voles, and consider whether predation or scavenging could explain the presence of dog DNA. Additionally, we determined the calorific value of dog faeces through calorimetric explosion. The high occurrence of dog DNA in the diet of fox, the timing of its increase, and the negative relationship between dog and the fox's main prey, point to dog faeces as the source of DNA in fox scats. Dog faeces being highly calorific, we found that foxes, but not pine martens, regularly exploit them, seemingly as an alternative resource to fluctuating prey. Scattered accounts from the literature may suggest that interspecific coprophagia is a potentially frequent and widespread form of interaction among vertebrates. However, further work should address its prevalence in other systems as well as the implications for ecological communities. Tools such as metabarcoding offer a way forward.

opencc-zeroJun 2022View details →

Dietary metabarcoding datasets for the southern meadow jumping mouse (Zapus luteus luteus)

The southern meadow jumping mouse (Zapus luteus luteus) is Endangered in the US due to loss of riparian habitat and knowledge of diet can focus conservation efforts. Context and life stages of diet have been documented for other species of Zapus (seeds, insect larvae, and hypogeous fungi), possibly shifting toward greater diversity in seed predations prior to hibernation. Yet, challenges in field observation, thorough digestion, and lack of scalability have hindered a thorough survey of dietary taxonomies. We collected the feces of 165 Z. l. luteus from across the geographic range. Emphasizing granivorous diet, we used DNA metabarcoding to resolve its dietary taxonomies. With negligible impact of field contamination, we found a varied diet most frequently of graminoids, forbs, and lepidoptera. Detecting up to nine dietary taxa in individuals, Z. l. luteus consumed more and different combinations of plant taxa as they approached the known hibernation window. Our work emphasizes the importance of forbs and graminoids as the foundation of the diet, providing primary sustenance and habitat for insect prey. The breadth of different diet items they consume suggests plasticity in resource use, potentially accommodating diverse patterns of seed production throughout their active period. We also hypothesize that a peak in seed availability in the late season could play a role in their accumulation of pre-hibernation fat stores.

opencc-zeroJul 2022View details →

Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy: Data and Analyses

Marine communities undergo rapid changes because of human-induced ecosystem pressures. The Baltic Sea pelagic food web has experienced several regime shifts during the past century, resulting in a system where competition between planktivorous mesopredators is assumed to be high. While the two clupeids sprat and herring reveal signs of competition, the stickleback population has increased drastically during the past decades. Here, we investigate diet overlap between the three dominating planktivorous fish in the Baltic Sea, utilizing DNA metabarcoding on the 18S rRNA gene and the COI gene, targeted qPCR, and microscopy. Our results show niche differentiation between clupeids and stickleback and that rotifers play an important function in niche partitioning of stickleback, as a resource that is not being used, neither by the clupeids nor by other zooplankton. We further show that all the diet assessment methods used in this study are consistent but DNA metabarcoding describes the plankton-fish link at the highest taxonomic resolution. This study suggests that rotifers and other understudied soft-bodied prey may have an important function in the pelagic food web and that the growing population of pelagic stickleback is supported by the unutilized feeding niche offered by the rotifers.

opencc-by-4.0Nov 2021View details →

BeeDNA: microfluidic environmental DNA metabarcoding as a tool for connecting plant and pollinator communities

Data repository accompanying the paper 'BeeDNA: microfluidic environmental DNA metabarcoding as a tool for connecting plant and pollinator communities' by Harper et al. (2021). 1_Raw_Data.zip This zipped folder contains the raw sequence data (sorted by primer set and demultiplexed) for both sequencing runs (2019-10-24 and 2019-11-11). To decompress each file, run:  <pre><code>tar -xvf filename.bz2</code></pre> This will create a folder for each primer set containing the raw reads for each sample/control. 2_Anacapa_Bioinformatic_Processing.zip This zipped folder contains all files needed to perform bioinformatic processing with Anacapa. Please process sequence data belonging to each primer set individually (i.e. do not process sequence data belonging to different primer sets together). 3_metaBEAT_Bioinformatic_Processing.zip  This zipped folder contains the scripts and files needed to perform bioinformatic processing with metaBEAT. Before running the scripts, move the raw reads for each sample belonging to each primer set into the dedicated folder within metaBEAT_Bioinformatic_Processing, e.g. all .fastq files in Raw_Data > BF1_BR1 should be moved to metaBEAT_Bioinformatic_Processing > BF1-BR1 > raw_reads. To run metaBEAT, you will have to install Docker on your computer. Docker is compatible with all major operating systems, but see the Docker documentation for details. On Ubuntu, installing Docker should be as easy as: <pre><code>sudo apt-get install docker.io</code></pre> Once Docker is installed, you can enter the environment by typing: <pre><code>sudo docker run -i -t --net=host --name metaBEAT -v $(pwd):/home/working chrishah/metabeat /bin/bash</code></pre> This will download the metaBEAT image (if not yet present on your computer) and enter the 'container', i.e. the self contained environment (NB: sudo may be necessary in some cases). With the above command, the container's directory /home/working will be mounted to your current working directory (as instructed by $(pwd)). In other words, anything you do in the container's /home/working directory will be synced with your current working directory on your local machine. Please process sequence data belonging to each primer set individually (i.e. do not process sequence data belonging to different primer sets together). An example of expected outputs can be seen in the Jupyter Notebook for the BF1/BR1 primer set from the 2019-11-11 sequencing run. 4_Illinois_Invert_Reference_Database.zip This zipped folder contains all files that were used to generate the custom COI and 16S reference databases for invertebrates that occur in Illinois, U.S. You will need to have metaBEAT installed (see above) before you try to run any Jupyter Notebooks (.ipynb files). 5_ecoPCR.zip This zipped folder contains all files used to perform ecoPCR for each primer set evaluated for microfluidic eDNA metabarcoding. You will need to <a href="https://git.metabarcoding.org/obitools/ecopcr/wikis/home">install ecoPCR</a> before running any shell scripts. 6_Tidied_Data.zip This zipped folder contains the taxonomically assigned data for both sequencing runs produced by metaBEAT and Anacapa. These were copied over from the folders 2_Anacapa_Bioinformatic_Processing and 3_metaBEAT_Bioinformatic_Processing and rearranged into a more logical order. These files are used as the input for data analysis using R. 7_Data_Analysis.zip This zipped folder contains all scripts and metadata required to summarise and statistically analyse data in R.   Please contact Dr Lynsey Harper (lynsey.harper2@gmail.com) or Dr Mark Davis (davis63@illinois.edu) if you encounter any issues!