Illumina_Read_Files

Illumina_Read_File

Genetic Distances

Intraspecific and interspecific genetic distances within Hawaiian Tetragnatha species for 4 mitochondrial and 3 nuclear loc

Sequence files for nine loci for all seperate arthropod specimens

Sequence files for nine loci for all seperate arthropod specimen

Mitochondrial genomes used for primer design

Mitochondrial genomes used for primer desig

Sequence files for specimen pools for all loci

Sequences for all loci, which were amplified for the arthropod specimen pool

Illumina read files for DNA degradation experiment

The dataset contains read files of microbial 16S and arthropod COI amplicons. The sample name comprises 1. the amplified locus, 2. the DNA integrity (H/L) and 3. the temperature treatment (RT/FT

OTU_tables

OTU tables used for the analyses

Illumina read files for PCR condition experiment

Samples are named with a unique identifier followed by the used primer (ARF1/mICOIintF), followed by the according PCR conditions. a & b represent exact replicates, 51C an increase of annealing temperature by 5 °C and 22X a reduction of PCR cycle number by 1

Simpson indices and their associations for the DNA degradation experiment.

<p><b>A-D)</b> Association of Shannon indexes between high and low molecular weight DNA fraction for exact replicates of the same sample for <b>A)</b> samples stored in the freezer (red squares) or stored at room temperature (black circles) and amplified for COI <b>B)</b> Samples from actual Malaise traps amplified for COI. <b>C)</b> samples stored in the freezer (red squares) or stored at room temperature (black circles) and amplified for bacterial 16SrDNA. <b>D)</b> Samples from actual Malaise traps amplified for microbial 16SrDNA. The X-axis represents the high molecular weight and the Y-axis the low molecular weight fraction. Dashed lines represent linear regression lines.</p

The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota

<div><p>PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias could thus be a significant issue, skewing diversity estimates. Here, we estimate the effect of differential DNA degradation on the recovery of community diversity of Hawaiian arthropods and their associated microbiota. We use a simple DNA size selection protocol to test for degradation bias in mock communities, as well as passively collected samples from actual Malaise traps. We compare the effect of DNA degradation to that of varying PCR conditions, including primer choice, annealing temperature and cycle number. Our results show that DNA degradation does indeed bias community analyses. However, the effect of this bias is of minor importance compared to that induced by changes in PCR conditions. Analyses of the macro and microbiome from passively collected arthropod samples are thus well worth pursuing.</p></div