@article{fdi:010085702,
  title = {{E}valuating bioinformatics pipelines for population-level inference using environmental {DNA}},
  author = {{M}ac{\'e}, {B}. and {H}ocd{\'e}, {R}{\'e}gis and {M}arques, {V}. and {G}uerin, {P}.{E}. and {V}alentini, {A}. and {A}rnal, {V}. and {P}ellissier, {L}. and {M}anel, {S}.},
  editor = {},
  language = {{ENG}},
  abstract = {{E}nvironmental {DNA} is mainly not only used at the interspecific level, to quantify spe-cies diversity in ecosystems, but can also be used to quantify intraspecific genetic variability, thus avoiding the need to sample individual tissue. {H}owever, errors in the amplification and sequencing of e{DNA} samples can blur this intraspecific signal and strongly over- estimate genetic diversity. {E}xisting bioinformatics pipelines therefore need to be tested to evaluate whether reliable levels of intraspecific genetic variability can be derived from e{DNA} samples. {H}ere, we compare the ability of twelve metabar-coding pipelines to detect intraspecific genetic variability combining five programs. {A}ll pipelines have common pre- processing steps, a processing data step using pro-grams among obiclean; {DADA}2; {SWARM}; and {LULU}. {A}n additional chimera removal step is also investigated based on two programs ({VSEARCH} or {DADA}2). {T}he case study was the natural intraspecific variation within {M}ullus surmuletus in experimental settings. {W}e developed specific primers for this species, located on the mitochondrial {D}-  loop fragment (barcode {MS}-{DL}06). {T}hirty- nine individuals were collected from the {M}editerranean {S}ea, placed into four aquariums, and their {DNA} was sequenced on this marker to build an intraspecific reference database. {A}fter filtering the aquarium water, {DNA} was extracted, amplified, and sequenced using the primer pair developed. {W}e then quantified the number of true haplotypes returned by each pipeline and its capacity to eliminate most of the erroneous sequences. {W}e show that the program {DADA}2 with a two- parent chimeric sequence removal step is the best tool to estimate intraspecific diversity from e{DNA}. {F}urthermore, our approach was also able to detect true {M}. surmuletus haplotypes in two e{DNA} samples collected in the {M}editerranean {S}ea. {W}e conclude that the combination of an appropriate intrapopulation barcode and a denoising pipeline like {DADA}2 with a chimeric sequence removal step is promising to make population- level inference using environmental {DNA} possible.},
  keywords = {{MEDITERRANEE} ; {FRANCE} ; {VILLEFRANCE} {SUR} {MER} {BAIE}},
  booktitle = {},
  journal = {{E}nvironmental {DNA}},
  volume = {4},
  numero = {3},
  pages = {674--686},
  ISSN = {2637-4943},
  year = {2022},
  DOI = {10.1002/edn3.269},
  URL = {https://www.documentation.ird.fr/hor/fdi:010085702},
}