Roslin, Tomas
- Institutionen för ekologi, Sveriges lantbruksuniversitet
- Helsingin yliopisto
Sammanfattning
The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent-coverage threshold to filter out false positives, (b) an internal-standard DNA spike-in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R-2 = .93, mitogenomes R-2 = .95) and a high repeatability across environmental-sample replicates (barcodes R-2 = .94, mitogenomes R-2 = .93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species-specific abundances, and phenology. SPIKEPIPE provides cost-efficient and reliable quantification of eukaryotic communities.
Nyckelord
Araneae; Arthropoda; biomonitoring; COI internal standard; community composition; DNA barcoding; insecta; metagenomics; mitogenomes; mitogenomics
Publicerad i
Molecular Ecology Resources
2020, volym: 20, nummer: 1, sidor: 256-267
Utgivare: WILEY
SLU författare
Globala målen (SDG)
SDG15 Ekosystem och biologisk mångfald
UKÄ forskningsämne
Ekologi
Molekylärbiologi
Biokemi
Publikationens identifierare
- DOI: https://doi.org/10.1111/1755-0998.13057
Permanent länk till denna sida (URI)
https://res.slu.se/id/publ/101387