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Assessing intraspecific genetic diversity from community DNA metabarcoding data

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RT @VascoElbrecht: Great talk by @JessicaHellmann on the importance of genetic diversity and migration corridors to counter species extinct…
Great talk by @JessicaHellmann on the importance of genetic diversity and migration corridors to counter species extinction due to climate change! I'm sure you will like or approach to extract genetic diversity of full ecosystems using #metabarcoding data https://t.co/uJb3Ra09Vr
Here is the #haplotypes per OTU plot for the Finland data: Bit noisier, as haplotypes in single locations, are kept. https://t.co/uJb3Ra09Vr https://t.co/dtUbdhtAiU
@alpineedna @francis_thomsen @SiCreerProf @hollybik population genetics with eDNA? Yes please! =) already works on a #metabarcoding scale, see https://t.co/uJb3RahKMZ great position!
New #JAMP version! Now includes all the final filtering steps for HTS #denoising used in our recent @PeerJPreprints: https://t.co/uJb3Ra09Vr https://t.co/M9XITVmmgY
RT @VascoElbrecht: New @PeerJPreprints: Denoising #metabarcoding data reveals intraspecific genetic diversity of macroinvertebrates! https:…
RT @VascoElbrecht: Ever wondered how haplotyping in our recent @PeerJPreprints (https://t.co/HcvWDxBwbg) is done? I'm currently writing a s…
76 days ago
RT @VascoElbrecht: Ever wondered how haplotyping in our recent @PeerJPreprints (https://t.co/HcvWDxBwbg) is done? I'm currently writing a s…
Ever wondered how haplotyping in our recent @PeerJPreprints (https://t.co/HcvWDxBwbg) is done? I'm currently writing a short tutorial = ) https://t.co/AXrib2nBCz
RT @Jorge_dona_: Assessing intraspecific genetic diversity from community DNA metabarcoding data https://t.co/i42AWSsLki via @PeerJPreprin…
77 days ago
RT @VascoElbrecht: Fingers crossed @leeselab @dirch3! If anyone would like to add some additional feedback, here is the @PeerJPreprints htt…
Fingers crossed @leeselab @dirch3! If anyone would like to add some additional feedback, here is the @PeerJPreprints https://t.co/HcvWDxBwbg https://t.co/BpxSSpL1dm
@naturhistoriska @metagusano @_SLU @Stockholm_Uni @2017Kaw100 @didrikbiolog @deepsthlmuni @PPennington_Lab @AycoTack @KTHinfo awesome, looking forward to see the large scale #metabarcoding data. You could use haplotyping​ for phylogeography https://t.co/HcvWDxBwbg
Assessing intraspecific genetic diversity from community DNA metabarcoding data https://t.co/i42AWSsLki via @PeerJPreprints
Metabarcoding based haplotyping #PrePrint (https://t.co/HcvWDxBwbg) submitted to @NatureEcoEvo. Very nice & convenient submission process!
86 days ago
RT @VascoElbrecht: New @PeerJPreprints: Denoising #metabarcoding data reveals intraspecific genetic diversity of macroinvertebrates! https:…
87 days ago
RT @VascoElbrecht: New @PeerJPreprints: Denoising #metabarcoding data reveals intraspecific genetic diversity of macroinvertebrates! https:…
88 days ago
RT @metabar_papers: Assessing intraspecific genetic diversity from community DNA metabarcoding data https://t.co/MO0kB7fVSA
RT @metabar_papers: Assessing intraspecific genetic diversity from community DNA metabarcoding data https://t.co/MO0kB7fVSA
RT @metabar_papers: Assessing intraspecific genetic diversity from community DNA metabarcoding data https://t.co/MO0kB7fVSA
RT @VascoElbrecht: New @PeerJPreprints: Denoising #metabarcoding data reveals intraspecific genetic diversity of macroinvertebrates! https:…
RT @VascoElbrecht: New @PeerJPreprints: Denoising #metabarcoding data reveals intraspecific genetic diversity of macroinvertebrates! https:…
RT @VascoElbrecht: New @PeerJPreprints: Denoising #metabarcoding data reveals intraspecific genetic diversity of macroinvertebrates! https:…
89 days ago
RT @dirch3: First joined one with @VascoElbrecht @PeerJPreprints https://t.co/P1nbQ6lOSo many to follow
RT @metabar_papers: Assessing intraspecific genetic diversity from community DNA metabarcoding data https://t.co/MO0kB7fVSA
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Supplemental Information

Figure S1: Schematic overview of errors affecting metabarcoding data and clustering / denoising strategies to reduce them

DOI: 10.7287/peerj.preprints.3269v1/supp-1

Figure S2: Effect of different quality filtering (may ee) on reads of the singe species mock sample

DOI: 10.7287/peerj.preprints.3269v1/supp-2

Figure S3: Effect of different alpha values in read denoising of the singe species mock sample

DOI: 10.7287/peerj.preprints.3269v1/supp-3

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

DOI: 10.7287/peerj.preprints.3269v1/supp-4

Figure S5: Overview of the haplotyping strategy used here and their implementation in the JAMP R package

DOI: 10.7287/peerj.preprints.3269v1/supp-5

Table S1: Finland haplotype table (for all 4 different primer combinations)

DOI: 10.7287/peerj.preprints.3269v1/supp-6

Scripts S1: Metabarcoding and denoising pipeline, and additional scripts used to produce the figures

DOI: 10.7287/peerj.preprints.3269v1/supp-7

Manuscript work file for providing feedback

Please use track changes / comment functions. Thank you for your feedback.

DOI: 10.7287/peerj.preprints.3269v1/supp-8

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Vasco Elbrecht conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Ecaterina Edith Vamos conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Dirk Steinke wrote the paper, reviewed drafts of the paper.

Florian Leese conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Haplotype sequences are available in supporting Table S1

Data Deposition

The following information was supplied regarding data availability:

Raw data is already available in SRA (NCBI), see SRR5295658, SRR5295659, SRR4112287

Bioinformatic package is available on GitHub:

github.com/VascoElbrecht/JAMP

Funding

This study is part of the European Cooperation in Science and Technology (COST) Action DNAqua-Net (CA15219). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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