If you look at the PIO section of the datasheet page 654, you will see that a PIO line can be pulled_up by:
PIOx->PIO_PUER |= PIO_PUER_Py; // Where x is A,B,C or D and 0<= y <=31
alternately a pull_up can be disabled by:
PIOx->PIO_PUDR |= PIO_PUDR_Py;
I guess that during UART initialization, PA8 and PA9 are both pulled_up.