Mood palpably altered with two rooks in tree (8,6)
I believe the answer is:
lombardy poplar
'tree' is the definition.
(Lombardy poplar is an example)
'mood palpably altered with two rooks' is the wordplay.
'two rooks' means two substitutions for 'rook'.
'altered with' is an anagram indicator.
'rook' becomes 'r' (abbreviation in chess).
'rook' becomes 'r' (abbreviation in chess).
'mood'+'palpably'='moodpalpably'
'moodpalpably' anagrammed with 'r' makes 'lombardypopla'.
'lombardypopla'+'r'='LOMBARDY POPLAR'
'in' is the link.
(Another definition for lombardy poplar that I've seen is " tree".)