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Scarlett became notable for his excavations over many decades on several paleontological deposits on New Zealand like Te Aute, Lake Poukawa, or the Pyramid Valley swamp where he unearthed and described the fossil remains of a Late Quaternary avifauna including bones of the Eyles' Harrier (Circus eylesi), the New Zealand Owlet-nightjar, the Scarlett's Duck (which was named by Storrs L. Olson), and the Hodgens' Waterhen.