It’s very important to understand the Native VLAN and VLAN 1 concept and what impact for Layer 2 protocol communication.
Cisco switch uses some of Layer 2 protocols like CDP/VTP/DTP/PAgP/UDLD/BPDU are using by default VLAN 1 to communicates with the other switches. Switch sends it to reserverd 01:00:0C:CC:CC:CC MAC address it’s a kind of Layer 2 multicast group so all Cisco switches are looking for these frames. What is a connection with VLAN 1 and native VLAN. By default VLAN 1 is Native VLAN what is means is that is not taged at all. I’ve done a small test to figure it out VLAN 1, Native VLAN and protocols relationship. I have connected the PC with Wireshark directly to the Cisco 3550 switch and configure interface fa0/24 as below:
interface FastEthernet0/24
switchport trunk encapsulation dot1q
switchport mode trunk
channel-group 1 mode desirable 1

What I get on Wireshark is STP, CDP, DTP and PAgP protocols, so all is working fine. Let’s add the switchport trunk allowed vlan 10 command and see the capture:
interface FastEthernet0/24
switchport trunk encapsulation dot1q
switchport trunk allowed vlan 10
switchport mode trunk
channel-group 1 mode desirable 1

As we see nothing has changed. All layer protocols are transmited. It’s important to understand here what switchport trunk allowed vlan command exactly do. Command Reference says that it „sets the list of allowed VLANs that transmit traffic from this interface in tagged format when in trunking mode”. OK so what about vlan 1? Is it allowed or not. As VLAN 1 by default is not tagged so it will not be filtered out what capture has confirmed. Let’s make last test and change the native vlan to different on, for example VLAN 10:
interface FastEthernet0/24
switchport trunk encapsulation dot1q
swtchport trunk native vlan 10
switchport trunk allowed vlan 10
switchport mode trunk
channel-group 1 mode desirable 1
Thanks to this we have changed the Native VLAN from 1 to VLAN 10 so now VLAN 1 is tagged but due to command switchport trunk allowed vlan 10 is filtered out. So let’s see what we have in capture now.

We have got just STP and DTP.

Conclusion:
STP and DTP frames have no relation to VLAN, so are always transmited over Native VLAN.
CDP/VTP/PAgP/UDLD are always transmited over VLAN 1, if Native VLAN is 1 then will be transmited in untagged form, if VLAN 1 is tagged (Native VLAN is other VLAN then 1), protocols will be tagged with 1.

I hope this has clarified the concept.