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2008
Havill, N. P., Campbell C. S., Vining T. F., & LePage B. (2008).  Phylogeny and Biogeography of Tsuga (Pinaceae) Inferred from Nuclear Ribosomal Its and Chloroplast DNA Sequence Data. (BayerR J., DonoghueM J., Ed.).Systematic Botany. 33,
2003
Bella, C. D., & Donoghue M. J. (2003).  Phylogeny and biogeography of Morinaceae (Dipsacales) based on nuclear and chloroplast DNA sequences. Organisms Diversity and Evolution. 3,
2002
Li, J. H., P D T., Yang S. X., & Donoghue M. J. (2002).  Phylogenetic relationships and biogeography of Stewartia (Camellioideae, Theaceae) inferred from nuclear ribosomal DNA ITS sequences. Rhodora. 104,
1998
Eriksson, T., Donoghue M. J., & Hibbs M. S. (1998).  Phylogenetic analysis of Potentilla using DNA sequences of nuclear ribosomal internal transcribed spacers (ITS), and implications for the classification of Rosoideae (Rosaceae). Plant Systematics and Evolution. 211,
1997
Sang, T., Donoghue M. J., & Zhang D. (1997).  Evolution of alcohol dehydrogenase genes in peonies (Paeonia): phylogenetic relationships of putative nonhybrid species. Molecular Biology and Evolution. 14,
Eriksson, T., & Donoghue M. J. (1997).  Phylogenetic Relationships of Sambucus and Adoxa (Adoxoideae, Adoxaceae) Based on Nuclear Ribosomal ITS Sequences and Preliminary Morphological Data. Systematic Botany. 22,