Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures

Background In order to understand the role of herbivores in trophic webs, it is essential to know what they feed on. Diet analysis is, however, a challenge in many small herbivores with a secretive life style. In this paper, we compare novel (high-throughput pyrosequencing) DNA barcoding technology for plant mixture with traditional microhistological method. We analysed stomach contents of two ecologically important subarctic vole species, Microtus oeconomus and Myodes rufocanus, with the two methods. DNA barcoding was conducted using the P6-loop of the chloroplast trnL (UAA) intron. Results Although the identified plant taxa in the diets matched relatively well between the two methods, DNA barcoding gave by far taxonomically more detailed results. Quantitative comparison of results was difficult, mainly due to low taxonomic resolution of the microhistological method, which also in part explained discrepancies between the methods. Other discrepancies were likely due to biases mostly in the microhistological analysis. Conclusion We conclude that DNA barcoding opens up for new possibilities in the study of plant-herbivore interactions, giving a detailed and relatively unbiased picture of food utilization of herbivores

Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures

Abstract Background In order to understand the role of herbivores in trophic webs, it is essential to know what they feed on. Diet analysis is, however, a challenge in many small herbivores with a secretive life style. In this paper, we compare novel (high-throughput pyrosequencing) DNA barcoding technology for plant mixture with traditional microhistological method. We analysed stomach contents of two ecologically important subarctic vole species, Microtus oeconomus and Myodes rufocanus, with the two methods. DNA barcoding was conducted using the P6-loop of the chloroplast trnL (UAA) intron. Results Although the identified plant taxa in the diets matched relatively well between the two methods, DNA barcoding gave by far taxonomically more detailed results. Quantitative comparison of results was difficult, mainly due to low taxonomic resolution of the microhistological method, which also in part explained discrepancies between the methods. Other discrepancies were likely due to biases mostly in the microhistological analysis. Conclusion We conclude that DNA barcoding opens up for new possibilities in the study of plant-herbivore interactions, giving a detailed and relatively unbiased picture of food utilization of herbivores.</p

Megafauna diet data

Fasta file containing sequence data

Data from: Fifty thousand years of arctic vegetation and megafaunal diet

Although it is generally agreed that the arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we additionally explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr BP (before present). For much of the period investigated, arctic vegetation consisted of dry steppe tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25–15 kyr BP), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr BP, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such our findings question the predominance of a late Quaternary graminoid-dominated arctic “mammoth steppe”

Reference database Boreal (gh)

Fasta file of the Boreal reference database (P6 loop of the trnL

Reference database Arctic (ITSAst)

Fasta file of the Arctic reference database (ITSAst

Data from: Fifty thousand years of arctic vegetation and megafaunal diet

Although it is generally agreed that the arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we additionally explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr BP (before present). For much of the period investigated, arctic vegetation consisted of dry steppe tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25&ndash;15 kyr BP), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr BP, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such our findings question the predominance of a late Quaternary graminoid-dominated arctic &ldquo;mammoth steppe&rdquo;.,Sheep diet dataFasta file containing the sequence dataovis_sequence_data.fastaMegafauna diet dataFasta file containing sequence data.megafauna_diet_sequence_data.fastaNematoda sequence dataFasta file containing the raw sequence data.nematoda_sequence_data.fastaNematoda filtered sequence dataFasta file containing the filtered sequence data.nematoda_filtered_sequence_data.fastaMegafauna sequence dataFasta file containing the sequence data.megafauna_sequence_data.fastaMegafauna filtered dataTabulated file containing the filtered data.megafauna_filtered_data.txtSheep diet filtered dataTabulated file containing filtered data of sheep diet.ovis_filtered_data.txtFull permafrost datasetcsv file containing the full permafrost dataset.permafrost.fulldata.csvReference database Arctic (gh)Fasta file of the Arctic reference database (P6 loop of the trnL)references.arctic-gh.fastaReference database Arctic (ITSAst)Fasta file of the Arctic reference database (ITSAst)references.arctic-ITSAst.fastaReference database Arctic (ITSCyp)Fasta file of the Arctic reference database (ITSCyp)references.arctic-ITSCyp.fastaReference database Arctic (ITSPoa)Fasta file of the Arctic reference database (ITSPoa)references.arctic-ITSPoa.fastaReference database Boreal (gh)Fasta file of the Boreal reference database (P6 loop of the trnL)references.boreal-gh.fastaReference database EMBL (gh)Fasta file of the EMBL reference database (P6 loop of the trnL)references.embl-gh.fastaReference database EMBL (ITSAst)Fasta file of the EMBL reference database (ITSAst)references.embl-ITSAst.fastaReference database EMBL (ITSCyp)Fasta file of the EMBL reference database (ITSCyp)references.embl-ITSCyp.fastaReference database EMBL (ITSPoa)Fasta file of the EMBL reference database (ITSPoa)references.embl-ITSPoa.fasta,</span

Sheep diet data

Fasta file containing the sequence dat

Megafauna filtered data

Tabulated file containing the filtered data

Reference database Arctic (ITSCyp)

Fasta file of the Arctic reference database (ITSCyp