( ( Density differences ) ( ( ( were probably ) ( ( caused ( by ( ( the upwelling ) ( of ( deep ( copepod aggregations ) ) ) ) ) ) ( from ( Juan ( de ( Fuca Strait ) ) ) ) ) ) . ) )
(ROOT (S (NP (JJ Density) (NNS differences)) (VP (VBD were) (ADVP (RB probably)) (VP (VBN caused) (PP (IN by) (NP (NP (DT the) (NN upwelling)) (PP (IN of) (NP (JJ deep) (JJ copepod) (NNS aggregations))))) (PP (IN from) (NP (NNP Juan) (FW de) (NNP Fuca) (NNP Strait))))) (. .)))
Density differences were probably caused by the upwelling of deep copepod aggregations from Juan de Fuca Strait.
(ROOT (S (NP (JJ Deep) (NNS currents)) (VP (VBP are) (VP (VBN caused) (PP (IN by) (NP (NP (NNS differences)) (PP (IN in) (NP (NN density))))) (PP (IN at) (NP (NP (DT the) (NN top) (CC and) (NN bottom)) (PP (IN of) (NP (DT the) (NN ocean))))))) (. .)))