Fig 1.
Dot symbols indicate sampling sites along the Amazon River and its tributaries. From west to east: Mamirauá Sustainable Development Reserve, Tefé, Manaus, and Belém.
Fig 2.
Laboratory work flowchart showing detail between the main steps. Quantification determined how much DNA to add during PCR preparation or library construction.
Fig 3.
Manatee eDNA results from Tefé/Mamirauá Reserve.
Positive and negative manatee DNA results from sites within the Mamirauá Sustainable Development Reserve and Tefé. A yellow star indicates that one or both duplicates returned positive. Mamirauá Reserve is located between the Japurá River to the north and the Amazon River to the south. Tefé is the town south of the Amazon River seated on the Tefé River. Each symbol represents duplicate samples, one at the water surface and another one-meter sub-surface.
Fig 4.
Manatee eDNA results from Manaus.
Positive and negative manatee DNA results from sites near Manaus. Each symbol represents duplicate samples, one at the water surface and another one-meter sub-surface. A yellow star indicates that one or both duplicates returned positive. The Rio Negro runs along the city of Manaus before converging with the Amazon River in the east.
Fig 5.
Manatee eDNA results from Belém.
Positive and negative manatee DNA results from sites near Belém. Each symbol represents duplicate samples, one at the water surface and another one-meter sub-surface. A yellow star indicates that one or both duplicates returned positive. The city of Belém is bordered by Baía do Guajará to the west and Guamá River to the east. The Acará River runs southeast to northwest.
Fig 6.
Frequency of manatee eDNA detection.
Histogram comparing the frequencies of positive and negative Amazonian manatee DNA detections in the three study regions.
Fig 7.
Anthropological influence on manatee eDNA detection.
Manatee DNA detections in the three regions based on distance from anthropological influence. Twenty-one samples were detected in rural or protected areas and eight were detected in urban areas. Rural and urban categories were determined by overall amounts of boat traffic, settlements, and pollution in each sample area.
Fig 8.
Collection depth influence on manatee eDNA detection.
Manatee DNA detections based on collection depth. Fifteen positive samples were obtained at the surface, and fourteen detections were obtained at 60 cm sub-surface. There was not a statistically significant effect of water depth on manatee DNA detection.
Fig 9.
Water volume influence on manatee eDNA detection.
Volume of water in milliliters (mL) filtered during collection of each sample. Positive sample volumes spanned 350 mL to 900 mL; negative samples spanned 225 mL to 2000 mL. Volumes of samples 9 and 10 were not recorded.
Fig 10.
Storage temperature influence on manatee eDNA detection.
Histogram comparing the frequencies of positive and negative results for Amazonian manatee DNA detection between samples stored at 4°C and 28°C. The two left bars indicate positive and negative samples stored at 4°C, and the bars on the right indicate positive and negative samples stored at room temperature. There was not a statistically significant effect of temperature on detection frequencies.