Fundamental frequency contour

[Constanza Ordoñez]

Hello, I'm trying to get the fundamental frequency contour of dolphin's whistles. My whistle of interest is between 3 and 6 kHz, I've some noise on the background and other signals in other frequency, so I filtered between 3 and 6kHz. The problem is that when I estimate the fundamental frequency (with fund() )  I get values under 3kHz and I don't get why is that possible. 

 

Can you help me or do you have another way of getting the fundamental freq. contour? 

Thank you very much.