Research ArticleECOLOGY

Environmental DNA illuminates the dark diversity of sharks

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Science Advances  02 May 2018:
Vol. 4, no. 5, eaap9661
DOI: 10.1126/sciadv.aap9661
  • Fig. 1 Sampling design and analyses of surveys across the New Caledonian archipelago, southwestern Pacific.

    (A) Sampling design in the New Caledonian archipelago (red stars, eDNA; blue pentagons, BRUVS; green dots, UVC). (B) Sample size (UVC, n = 2758; BRUVS, n = 385; eDNA, n = 22). (C) Cumulated number of shark species detected. (D) Frequency of samples with sharks detected. (E) Violin plot showing detected shark species richness, significantly different between techniques (P < 0.001, Kruskal-Wallis test), with eDNA detecting more shark species (2.5 ± 1.9) compared to BRUVS (0.8 ± 0.8) and UVC (0.2 ± 0.5) (P < 0.001, Dunn’s tests). White dots are mean values; thick black bars correspond to interquartile ranges; thin black lines are 95% confidence intervals.

  • Fig. 2 Detection of shark species with different sampling methods.

    Venn diagram showing the species detected by eDNA (n = 22 samples, S = 13 species), UVC (n = 2758 samples, S = 9 species), and BRUVS (n = 385 samples, S = 9 species). Scientific drawings courtesy of M. Dando.

  • Fig. 3 Number of shark species per sample in contrast to human impacts.

    Violin plot showing detected shark species richness by the different methods in (A) impacted areas (Nouméa, the capital city) and (B) wilderness areas (Chesterfield, D’Entrecasteaux, Great Northern Lagoon, Petri, and Astrolabe). White dots are mean values; thick black bars correspond to interquartile ranges; thin black lines are 95% confidence intervals. Differences between methods are highly significant for both types of areas (P < 0.001, Kruskal-Wallis tests), with eDNA detecting more species per sample than BRUVS and UVC (P < 0.001, Dunn’s tests).

  • Fig. 4 Sample-based rarefaction curves.

    (A) Theoretical illustration of dark diversity measured by traditional methods, simply unseen but illuminated by eDNA, revealing a lower amount of dark diversity (absent species). Rarefaction curves showing accumulated sampled shark diversity measured by the different techniques (green, UVC; blue, BRUVS; red, eDNA). (B) Based on all samples. (C) Zoomed in to 30 samples. Error bars indicate SD. (D) Estimated rarefaction curves for UVC, BRUVS, and eDNA when increasing sampling effort, based on the best common model (rational function).

  • Table 1 Models fitted for species rarefaction curves obtained from UVC, BRUVS, and eDNA using the nls function in the stats package and the AICc for small sample bias (package AICmodavg).

    The best-fitting model for each sampling technique is in bold, whereas the overall best-fitting model (all three techniques) is underlined.

    ModelFormulaAsymptoticNumber of parametersAICc
    UVCBRUVSeDNA
    PowerS = aXbNo2−434552814
    ExponentialS = a + b log(X)No219121023
    Negative exponentialS = a(1 − ebX)Yes2494028124
    Negative exponentialS = a + (ba)ecXYes3609−67519
    MonodS = a/(1 + bX− 1)Yes223211855
    Rational functionS = (a + bX)/(1 + cX)Yes32562421−49

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/4/5/eaap9661/DC1

    fig. S1. Number of shark species per sample in overlapping collection sites.

    table S1. Full sequences of the 24 tagged primer sets used.

    table S2. Metabarcoding pipeline for COI Elasmobranchii Fields et al. primers.

  • Supplementary Materials

    This PDF file includes:

    • fig. S1. Number of shark species per sample in overlapping collection sites.
    • table S1. Full sequences of the 24 tagged primer sets used.
    • table S2. Metabarcoding pipeline for COI Elasmobranchii Fields et al. primers.

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