I was cracking some Pawnee pecans and noticed that this past summer's drought didn't effect nut fill as much as it created kernel color defects. In the photo at right the upper two kernel halves are plump and exhibit normal kernel color for Pawnee. The lower two kernel halves have dark blotches and prominent veins. Look carefully at the lower two kernels and you will see that they are also not as plump as the upper kernels. The area between the dorsal groves looks shrunken and the meats are not fully expanded all the way to the tip of the kernel.
You can find both types of kernels produced by the same tree. Without enough available water this past summer, the tree was unable to completely fill out the kernels of all nuts produced.
I've tasted both normal and darkened kernels and found little difference in flavor. However, the dark blotches can be a big "turn-off" to consumers. If Pawnee had just produced some kernels with less than perfect kernel fill and no color changes, no one would probably notice. Blotchy kernel darkening associated with incomplete nut fill seems to be unique to this year's Pawnee crop.