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47 results for “metabarcoding analysis”
Data from: DNA metabarcoding diet analysis for species with parapatric versus sympatric distribution: a case study on subterranean rodents
Closely related sympatric species commonly develop different ecological strategies to avoid competition. Ctenomys minutus and C. flamarioni are subterranean rodents parapatrically distributed in the southern Brazilian coastal plain, showing a narrow sympatric zone. To gain understanding on food preferences and possible competition for food resources, we evaluated their diet composition performing DNA metabarcoding analyzes of 67 C. minutus and 100 C. flamarioni scat samples, collected along the species geographical ranges. Thirteen plant families, mainly represented by Poaceae, Araliaceae, Asteraceae and Fabaceae, were identified in the diet of C. minutus. For C. flamarioni, 10 families were recovered, with a predominance of Poaceae, Araliaceae and Asteraceae. A significant correlation between diet composition and geographical distance was detected in C. minutus, whereas the diet of C. flamarioni was quite homogeneous throughout its geographical distribution. No significant differences were observed between males and females of each species. However, differences in diet composition between species were evident according to multivariate analysis. Our results suggest some level of diet partitioning between C. flamarioni and C. minutus in the sympatric region. While the first species is more specialized on few plant items, the second showed a more varied and heterogeneous diet pattern among individuals. These differences might have been developed to avoid competition in the region of co-occurrence. Resource availability in the environment also seems to influence food choices. Our data indicate that C. minutus and C. flamarioni are generalist species, but that some preference for Poaceae, Asteraceae and Araliaceae families can be suggested for both rodents.
Data from: A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal
Metabarcoding allows the genetic analysis of pooled samples of various sources. It is becoming popular in the study of animal diet, especially because it allows the analysis of the composition of feces without the need of handling animals. In this work, we studied the diet of the Pyrenean desman (Galemys pyrenaicus), a small semi-aquatic mammal endemic to the Iberian Peninsula and the Pyrenees, by sequencing COI minibarcodes from feces using next-generation sequencing techniques. For the identification of assembled sequences, we employed a tree-based identification method that used a reference tree of sequences of freshwater organisms. The comparison of freshly collected fecal samples and older samples showed that fresh samples produced significantly more sequencing reads. They also rendered more operational taxonomical units (OTUs), but not significantly. Our analyses of 41 samples identified 224 OTUs corresponding to species of the reference tree. Ephemeroptera, Diptera excl. Chironomidae, and Chironomidae were the most highly represented groups in terms of reads as well as samples. Other groups of freshwater organisms detected were Plecoptera, Trichoptera, Neuropteroida, Coleoptera, Crustacea, and Annelida. Our results are largely in line with previous morphological and genetic studies on the diet of the Pyrenean desman, but allowed the identification of a higher diversity of OTUs in each sample. Additionally, the bioinformatic pipeline we developed for deep sequencing of fecal samples will enable the quantitative analysis of the diet of this and other species, which can be highly useful to determine their ecological requirements.
Data from: 18S rRNA metabarcoding diet analysis of the predatory fish community across seasonal changes in prey availability
Predator-prey relationships are important ecological interactions, affecting biotic community composition and energy flow through a system, and are of interest to ecologists and managers. Morphological diet analysis has been the primary method used to quantify the diets of predators, but emerging molecular techniques using genetic data can provide more accurate estimates of relative diet composition. This study used sequences from the 18S V9 rRNA barcoding region to identify prey items in the gastrointestinal (GI) tracts of predatory fishes. Predator GI samples were taken from the Black River, Cheboygan Co., MI, USA (n=367 samples, 12 predator species) during periods of high prey availability, including the larval stage of regionally threatened lake sturgeon (Acipenser fulvescens Rafinesque 1817) in late May/early June of 2015 and of relatively lower prey availability in early July of 2015. DNA was extracted and sequenced from 355 samples (96.7%), and prey DNA was identified in 286 of the 355 samples (80.6%). Prey were grouped into 33 ecologically significant taxonomic groups based on the lowest taxonomic level sequences that could be identified using sequences available on GenBank. Changes in the makeup of diet composition, dietary overlap, and predator preference were analyzed comparing the periods of high and low prey abundance. Some predator species exhibited compositional changes in diet. Dietary overlap was slightly but significantly higher during the period of high prey abundance. There was little evidence for large changes in predator preference between the two periods. This study demonstrates the utility of molecular diet analysis in understanding predator-prey interactions in complex freshwater communities.
Metadata of sampling strategy during metabarcoding analysis (Journal publication supplement)
<p>The table presents supplementary materials and contains metadata of sampling strategy during metabarcoding analysis of four types of substrates in two ombrotrophic bog habitats, with other experimental and environmental parameters included in analyses. </p>
Supplementary material 1 from: Graupner N, Boenigk J, Bock C, Jensen M, Marks S, Rahmann S, Beisser D (2017) Functional and phylogenetic analysis of the core transcriptome of Ochromonadales. Metabarcoding and Metagenomics 1: e19862. https://doi.org/10.3897/mbmg.1.19862
KEGG orthologous genes of the core trancriptome of the herein investigated Ochromonadales (Poteriospumella lacustris strains JBC07, JBM10, JBNZ41; Poterioochromonas malhamensis DS; Spumella vulgaris 199hm; Pedospumella encystans JBMS11) used for phylogenetic analyses.
Data from: Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet
Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators' diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach highlights a highly complex interaction web and demonstrates that levels of trophic partitioning among coral reef fishes have likely been underestimated. Therefore, we strongly encourage further empirical approaches to dietary studies prior to making assumptions of trophic equivalency in food web reconstruction.
Data from: 18S rRNA metabarcoding diet analysis of the predatory fish community across seasonal changes in prey availability
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Data from: Advancing the integration of multi-marker metabarcoding data in dietary analysis of trophic generalists
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Data from: A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal
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Data from: DNA metabarcoding diet analysis for species with parapatric versus sympatric distribution: a case study on subterranean rodents
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Data from: A critical evaluation of how ancient DNA bulk bone metabarcoding complements traditional morphological analysis of fossil assemblages
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Data from: Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis
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ASV output data for all in the details: A first assessment for the viability of metabarcoding in diet composition analysis of African wild dogs (Lycaon pictus)
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Data from: DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea)
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Data from: Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet
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Ecological specialization and niche overlap of subterranean rodents inferred from DNA metabarcoding diet analysis
<p>Knowledge of how animal species use food resources available in the environment increases our understanding of ecological processes. However, obtaining this information using traditional methods is a hard task for species feeding on a large variety of food items in highly diverse environments. We amplified the DNA of plants for 306 scat and 40 soil samples, and applied an eDNA metabarcoding approach to investigate food preferences, degree of diet specialization and diet overlap of seven herbivore rodent species of the <i>Ctenomys</i> genus distributed in southern and midwestern Brazil.<b> </b>The metabarcoding approach revealed that species consume more than 60% of the plant families recovered in soil samples, indicating generalist feeding habits of ctenomyids. The Poaceae family was the most common food resource retrieved in scats of all species as well in soil samples. Niche overlap analysis indicated high overlap in the plant families and Molecular Operational Taxonomic Units consumed, mainly among the southern species.<b> </b>Interspecific difference in diet composition was influenced, among other factors, by the availability of resources in the environment. In addition, our results provide support for the hypothesis that the allopatric distributions of ctenomyids allow them to exploit the same range of resources when available, possibly because of the absence of interspecific competition.</p>
Data from: Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus)
Fecal samples are of great value as a non-invasive means to gather information on the genetics, distribution, demography, diet, and parasite infestation of endangered species. Direct shotgun sequencing of fecal DNA could give information on these simultaneously, but this approach is largely untested. Here we use two fecal samples to characterize the diet of two Red-Shanked Doucs Langurs (Pygathrix nemaeus) that were fed a known combination of foliage, fruits, vegetables and cereals. Illumina HiSeq sequencing produced ~70 million paired reads per sample, of which ~10000 (0.014%) and ~44000 (0.066%) respectively corresponded to chloroplast genomes. Sequences were matched against a database of available chloroplast 'barcodes' for angiosperms. The results were compared with 'metabarcoding' using PCR amplification of the P6 loop of trnL. Shotgun sequencing identified 7 and 9 of the likely 16 diet plants, against 6 and 5 plant species identified by metabarcoding. Metabarcoding produced thousands of reads that were consistent with the known diet, but the barcodes were too short to identify several diet plants to genus. Metagenomics could utilize multiple, longer barcodes that combined had greater power of identification, but rare diet items were not recovered. Read numbers for diet species in metagenomic and metabarcoding data were correlated, indicating that both approaches are useful for determining relative sequence abundance. Metagenomic reads were uniformly distributed across the chloroplast genomes; thus if chloroplast genomes were to be used as reference, the precision of identifications and species recovery would improve further. Metagenomics also recovered the host mitochondrial genome and numerous intestinal parasite sequences in addition to generating data useful for characterizing the microbiome.
Supplemental R code and csv files for statistical analysis on Doi et al. "Effects of species traits and ecosystem characteristics on species detection by eDNA metabarcoding in lake fish communities"
<p>Supplemental R code and csv files for statistical analysis on Doi et al. "Effects of species traits and ecosystem characteristics on species detection by eDNA metabarcoding in lake fish communities"</p>
Figure 3 from: Anslan S, Nilsson RH, Wurzbacher C, Baldrian P, Tedersoo L, Bahram M (2018) Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding. MycoKeys 39: 29-40. https://doi.org/10.3897/mycokeys.39.28109
Figure 3 - Number of OTUs per sample for Illumina data recorded from a) pipeline-generated OTU tables (median differences = 38 OTUs) and from b) filtered OTU tables (median differences = 12 OTUs). The Galaxy workflow was excluded here.
Figure 2 from: Anslan S, Nilsson RH, Wurzbacher C, Baldrian P, Tedersoo L, Bahram M (2018) Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding. MycoKeys 39: 29-40. https://doi.org/10.3897/mycokeys.39.28109
Figure 2 - OTU accumulation curves of the evaluated pipelines for a) PacBio and b) Illumina datasets.
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