Assessing intraspecific genetic diversity from community DNA metabarcoding data
- Published
- Accepted
- Subject Areas
- Biogeography, Bioinformatics, Molecular Biology, Freshwater Biology
- Keywords
- high-throughput sequencing, metabarcoding, ecosystem assessment, haplotyping, population genetics
- Copyright
- © 2017 Elbrecht et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. Assessing intraspecific genetic diversity from community DNA metabarcoding data. PeerJ Preprints 5:e3269v1 https://doi.org/10.7287/peerj.preprints.3269v1
Abstract
DNA metabarcoding provides species composition data for entire communities, yet information on intraspecific diversity is usually lost during data analysis. The capacity to infer intraspecific genetic diversity within whole communities would, however, represent a leap forward for ecological monitoring and conservation. We developed an amplicon-based sequence denoising approach that allows the identification of haplotypes from metabarcoding data sets and demonstrate its power with two freshwater macroinvertebrate data sets.
Author Comment
Initial version of the manuscript, soon to be submitted to nature ecology & evolution. We would love to get some feedback/criticism from you before submitting it!
Supplemental Information
Figure S1: Schematic overview of errors affecting metabarcoding data and clustering / denoising strategies to reduce them
Figure S2: Effect of different quality filtering (may ee) on reads of the singe species mock sample
Figure S3: Effect of different alpha values in read denoising of the singe species mock sample
Figure S4: Detailed plots of four example taxa from the denoised monitoring samples, showing haplotype maps & networks, similarity between replicates and sequence alignment for all BF/BR primer sets
Figure S5: Overview of the haplotyping strategy used here and their implementation in the JAMP R package
Table S1: Finland haplotype table (for all 4 different primer combinations)
Scripts S1: Metabarcoding and denoising pipeline, and additional scripts used to produce the figures
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