Mac Pro early2008 El Cap. LOGIC BOARD compatibility w/ later models
No. The machines are totally different as soon as you take the side off, visually &amp; electronically.

The top ⅓ is visually similar, though the 08 uses PATA connections in the optical bay, the 09 has SATAII.

As for the rest, these are just the visible highlights...

The 08 mounts the CPUs directly to the motherboard, 'sideways' like a standard PC, with separate removable RAM daughterboards onto which individual sticks are installed.
At the front is a large dual fan assembly.

  

08 pics EveryMac &amp; OWC

The 2009 has an entirely different structure - both the CPUs &amp; RAM are on a removable daughterboard, the huge front fan assembly has been replaced by a single fan &amp; a nice PCI card release, far improved over the 08's 'fiddle around underneath like a PC' structure.



09 pic OWC

OWC's picture also hints at (well, advertises;-) one more thing about the 09.
It can reasonably simply be upgraded to 2012 5,1 firmware &amp; will take dual 6-core Westmere's rather than the original Nehalems.
It can also be updated to Sierra 10.12 once the firmware has been upgraded.

I forgot to mention that the memory isn't compatible either.
The 08 takes DDR2 [expensive these days]
The 08 takes DDR3 [much cheaper]

Also, &amp; you really can't tell without sitting two side by side, the drive sleds are different sizes. To move a drive from an 08 to an 09 you must use the correct sled or the pins don't match up to the motherboard when you slide them in.

The 08's still a good machine for its age, but the 09 upgraded to [actually higher than originally purchasable] 2012 spec is still quite the beast.

I have one of each, 08 &amp; upgraded 09. Both going strong.

Purely my own opinion, but I'd be tempted to trade up the 08 to an 09 - you can get them very easily on eBay etc, fully upgraded &amp; ready to go. [Mine is a dual 6-core 3.46GHz, 64GB RAM, cost £1600, UKP. I added a decent graphics card &amp; still had change from 2 grand.]