To cite the adephylo package:

Jombart T., Dray S. (2008) adephylo: exploratory analyses for the phylogenetic comparative method.

Corresponding BibTeX entry:

  @Article{,
    title = {adephylo: exploratory analyses for the phylogenetic
      comparative method.},
    journal = {Bioinformatics},
    year = {2010},
    author = {T. Jombart and S. Dray},
    volume = {26},
    pages = {1907-1909},
    doi = {10.1093/bioinformatics/btq292},
  }