Steps to reproduce:

1) Download attached project 'DrawMeshInstancedShadows.zip' and open in Unity
2) Open scene 'scene' and press Play
You will see that trees are not affected by Directional light

Expected result: Trees should be affected by Directional light (check attached image 'expected.png')
Actual result: Trees are not affected by Directional light (check attached image 'actual.png')

Reproduced with:
5.6.0a6, 5.6.1p4, 2017.1.0b9. 2017.2.0a3

Workaround:
Select gameObject 'Renderer' in the Hierarchy window and set DrawMode to 'Graphics Draw Instanced'

Note: I wasn't able to test with older than 5.6.0a6 release of Unity due to errors in the Console window