To cite the adephylo package:

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

A BibTeX entry for LaTeX users is

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