No, it uses the chip's SPI ports for programming. Take a look at, for example, the data sheet on the ATmega64 that supports both JTAG and SPI programming.
Having a few JTAG dongles sitting around here (TI MSP430, Cypress something (clear blue plastic box), a Xilinx Parallel 3, and an Altera ByteBlasterMV clone (dang, these things do accumulate)) does anyone know if the Atmel JTAG software can be fooled into using one of the others?