FN Archimer Export Format
PT J
TI Evaluating bioinformatics pipelines for population‐level inference using environmental DNA
BT 
AF Mace, Bastien
   Hocdé, Régis
   Marques, Virginie
   Guerin, Pierre‐Edouard
   Valentini, Alice
   Arnal, Véronique
   Pellissier, Loïc
   Manel, Stéphanie
AS 1:1;2:2;3:1,2;4:1;5:3;6:1;7:4,5;8:1;
FF 1:;2:;3:;4:;5:;6:;7:;8:;
C1 CEFE, Univ. Montpellier, CNRS EPHE‐PSL University, IRD Montpellier, France
   MARBEC, Univ. MontpellierCNRSIfremerIRD Montpellie, France
   SPYGEN, Le Bourget ‐du‐Lac, France
   Landscape Ecology Department of Environmental Systems Science Institute of Terrestrial Ecosystems ETH Zürich Zürich, Switzerland
   Unit of Land Change Science, Swiss Federal Research Institute WSL Birmensdorf, Switzerland
C2 UNIV MONTPELLIER, FRANCE
   UNIV MONTPELLIER, FRANCE
   SPYGEN, FRANCE
   ETH ZURICH, SWITZERLAND
   WSL, SWITZERLAND
UM MARBEC
TC 0
UR https://archimer.ifremer.fr/doc/00751/86255/91558.pdf
   https://archimer.ifremer.fr/doc/00751/86255/91559.docx
LA English
DT Article
DE ;bioinformatics;environmental DNA;fish;genetic diversity;marine ecology
AB Environmental DNA is mainly not only used at the interspecific level, to quantify species diversity in ecosystems, but can also be used to quantify intraspecific genetic variability, thus avoiding the need to sample individual tissue. However, errors in the amplification and sequencing of eDNA samples can blur this intraspecific signal and strongly over-estimate genetic diversity. Existing bioinformatics pipelines therefore need to be tested to evaluate whether reliable levels of intraspecific genetic variability can be derived from eDNA samples. Here, we compare the ability of twelve metabarcoding pipelines to detect intraspecific genetic variability combining five programs. All pipelines have common pre-processing steps, a processing data step using programs among obiclean; DADA2; SWARM; and LULU. An additional chimera removal step is also investigated based on two programs (VSEARCH or DADA2). The case study was the natural intraspecific variation within Mullus surmuletus in experimental settings. We developed specific primers for this species, located on the mitochondrial D-loop fragment (barcode MS-DL06). Thirty-nine individuals were collected from the Mediterranean Sea, placed into four aquariums, and their DNA was sequenced on this marker to build an intraspecific reference database. After filtering the aquarium water, DNA was extracted, amplified, and sequenced using the primer pair developed. We then quantified the number of true haplotypes returned by each pipeline and its capacity to eliminate most of the erroneous sequences. We show that the program DADA2 with a two-parent chimeric sequence removal step is the best tool to estimate intraspecific diversity from eDNA. Furthermore, our approach was also able to detect true M. surmuletus haplotypes in two eDNA samples collected in the Mediterranean Sea. We conclude that the combination of an appropriate intrapopulation barcode and a denoising pipeline like DADA2 with a chimeric sequence removal step is promising to make population-level inference using environmental DNA possible. 
PY 2022
PD MAY
SO Environmental DNA
SN 2637-4943
PU Wiley
VL 4
IS 3
BP 674
EP 686
DI 10.1002/edn3.269
ID 86255
ER

EF