Error in dis[sppInSample,sppInSample]:subscript out of bounds

Hello,
I am new to R and am encountering an error message that I cannot find a solution for.
I am attempting to calculate MPD (mean pairwise distance), without weighting for abundance, with a community species list and a phylogenetic tree in newick format with branch lengths.
I have read in both list and tree .txt files and calculated PD without any problem.
To calculate MPD I have entered:>MPD1=mpd(list,cophenetic(tree))
Error:Error in dis[sppInSample, sppInSample] : subscript out of bounds
Thank you for you helpCheersMarion.