Boatmen initially shoot two under Darwin’s ship (6)
I believe the answer is:
beagle
'darwin's ship' is the definition.
(Charles Darwin voyaged on the Beagle)
'boatmen initially shoot two under' is the wordplay.
'initially' indicates taking the first letters.
'shoot two under' becomes 'eagle' (I've seen this in another clue).
The initial letter of 'boatmen' is 'b'.
'b'+'eagle'='BEAGLE'
(Other definitions for beagle that I've seen before include "Short-haired dog" , "Type of hound" , "hunting animal with smooth coat" , "Small hunting dog" , "Darwin voyaged in this ship" .)