This PDF file includes:

• appendix S1. The Kerguelen Islands: Historical information on rabbit introduction.
  
• appendix S2. Supplementary results.
  
• appendix S3. Amplification of plant and mammal taxa using the P007 and g-h primers.
  
• table S1. Detection of NPPs in the analyzed sediment samples.
  
• table S2. Detection of sedDNA in the analyzed sediment samples.
  
• table S3. Estimation of breakpoints in the erosion rate performed using a dynamic programming algorithm (59).
  
• table S4. Average climatic variables during the period 1912–2013, calculated on the basis of the 2014 version of the University of Delaware time series of monthly global gridded high-resolution station data (60).
  
• table S5. Match between primers and sequences from plants and mammals living in Kerguelen.
  
• fig. S1. Data from core POU14P1 with photograph, grain size median, LOI550 (organic matter), and NCIR.
  
• fig. S2. Age-depth model for the upper 65 cm of the sediment core POU14P1 based on radiocarbon (blue) and short-lived radionuclides derived ages (green).
  
• fig. S3. Constrained RDA, showing the relationship between the proxies of rabbit abundance (sedDNA and Sporormiella) and the abundance of different plant taxa.
  
• fig. S4. Temporal variation of the accumulation rate of spores of coprophilous fungi (Sporormiella sp.), measured as concentration (spores/cm³).

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Other Supplementary Material for this manuscript includes the following:

• Data file (Microsoft Excel format).