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Sources of Data for Botanical Classification and Identification


"Molecular biology, with its associated trinity of DNA, RNA, and proteins, has diverted a number of systematists from measuring petal lengths along the primrose path to phylogeny to a course supposedly more closely aligned with the inheritance of the individual taxon."  —Raymond Petersen, PhD

To a non-scientist, the world of plant taxonomy may seem to have been in a state of turmoil for the past few decades as some scientific names have experienced radical alterations. Not only have specific epithets and genera changed, but many plant families have changed as well. Certainly, a number of changes revealed by DNA analyses have been surprising to even the hardened plant taxonomist.

Systematists often quote botanical tomes from the 18th century; so, without a doubt, research on plant DNA has re-invigorated this somewhat staid science. Who in centuries past could have envisioned that the mare’s tail (Hippuridaceae), many of the figworts (Scrophulariaceae), and the water starwort families (Callitrichaceae) are actually plantains (Plantaginaceae)?1 Who could have predicted that many verbenas (Verbenaceae) — such as beautyberry (Callicarpa), glorybower (Clerodendrum), and chaste tree (Vitex) — are mints (Lamiaceae), and that maples (Acer) are soapberries (Sapindaceae)?1,2

In recent years, plant DNA studies have helped clarify many taxonomical hypotheses. Paleobotanists have known for decades that the lycopods (lycophytes) are not really “fern allies,” and that they have had a separate evolutionary path from the rest of plants since the zosterophylls (Zosterophyllophyta) appeared in the Silurian Period approximately 430 million years ago. A DNA study from 2011 confirmed these propositions.3 In 1971, David Bierhorst4 caused an uproar by classifying the whiskferns (Psilotum and Tmesipteris) as leafless ferns — not extremely primitive plants related to the first land plants (Rhyniophyta), as was believed at the time — and DNA analyses have confirmed this as well.3 However, I still have trouble recognizing horsetails (Equisetum) as highly modified ferns as DNA studies have indicated.3

Genetic research also has split plant taxa. The former genus Lycopodium, for example, now is recognized as comprising several genera, the most prominent of which is Huperzia (now probably best put in its own family, Huperziaceae, separate from the Lycopodiaceae).5,6

Perhaps the most radical change that DNA has revealed has been in the phylogeny of flowering plants. We no longer classify plants as monocotyledons or dicotyledons; it’s just not that simple. Today, scientists also recognize basal angiosperms, monocots, and eudicots (which can be further divided into basal eudicots, rosids, minor core eudicots, and asterids). Among living taxa, Amborella trichopoda (Amborellaceae) from New Caledonia is recognized as the most basal angiosperm, and the genus Acorus (Acoraceae) — or sweetflag of North America and Eurasia — is recognized as the most basal monocot. Without a doubt, DNA analyses have supplied the crucial evidence that allowed this mystery to be unraveled.

When DNA was first applied to plant classification, it was viewed as the field’s salvation and ultimate source of data. Using morphological or other characteristics was considered second-rate.However, we now know that there are caveats to DNA studies. As a result, many plant taxonomists have adopted a multidisciplinary approach to classification, which includes the use of genetic information. However, scientists differ on the amount of weight that should be applied to each factor in statistical or cladistic interpretations (i.e., methods of hypothesizing relationships among organisms), but DNA evidence often is very highly rated.

For example, two major botanical forensics books by Coyle7 and Hall and Byrd8 suggest using not only genetic data, but also algology (the study of algae), plant identification, plant anatomy and morphology, and palynology (the study of pollens and spores) to solve crimes and serve as evidence in court cases. Restated, each source of data has its use depending upon the available evidence, and each can contribute significantly. Likewise, in botanical classification and identification, data from these areas — in addition to others such as karyology (chromosome numbers, ploidy, etc.), secondary metabolites (alkaloids, essential oils, flavonoids, etc.), ecology, and genetics (crossability, sterility of hybrids, etc.) — all can provide useful information.

We now know the actual expression of nuclear DNA is modified by small messenger RNA chains (i.e., epigenetic changes), so the genotype reflected in the coding regions of nuclear DNA may not actually determine the phenotype, or expression, of the genes. In addition to epigenetics, two major discoveries in recent years have caused us to be careful when interpreting DNA data: (1) horizontal or lateral gene transfer and (2) non-maternal inheritance of organelles.

Normally, organisms acquire their genes through vertical transfer; that is, from parent to offspring. However, in horizontal or lateral gene transfer, genes are transferred via viruses, bacteria, fungi, or parasites.9,10 Researchers have demonstrated a large number of horizontal or lateral gene transfers, which is not an anomaly. The process is most prominent among bacteria, which calls into question phylogenies that assume only vertical gene transfer.11 Researchers have reported animal-to-animal and plant-to-plant gene transfers, but natural animal-to-plant and plant-to-animal gene transfers have not yet been discovered. Knowledge that horizontal or lateral gene transfer is normal suggests that GMOs (genetically modified organisms) are not something totally new and manmade. The crown gall bacterium (Agrobacterium tumefaciens, Rhizobiaceae) — routinely used by botanists to insert genes into other organisms — has been performing this task since it first evolved. What is different today is the speed and direction of certain gene transfers.

Most general biology textbooks state that organelles such as chloroplasts and mitochondria (both of which carry their own DNA) are transmitted only maternally, not paternally. Previously, scientists viewed the egg as a sac of cytoplasm with a nucleus and organelles, while the sperm was considered merely stripped down nuclear DNA. We now know that it is not that simple. Chloroplast and mitochondrial genomes can be inherited maternally, paternally, or even biparentally, not only in plants, but also in some animals.12,13 In many cases, we can group the method of inheritance by plant family, but many exceptions exist. For example, in the passionflowers (Passiflora spp., Passifloraceae), chloroplasts may be inherited maternally, paternally, or biparentally depending upon the species.14 Obviously, previous studies that assumed only maternal inheritance of chloroplast DNA and mitochondrial DNA will have to be re-examined.

What’s a novice to do to keep pace with all of these changes in plant classification? A good introduction is the book that I previously reviewed in HerbalGram, Botany in a Day, 6th ed., by Thomas J. Elpel.15,16 This book just touches the surface of the controversies surrounding plant taxonomy today as analytical methods continue to evolve and new information becomes available. Still, for a novice trying to find the most commonly accepted name (a term many taxonomists prefer over “correct” name, which invokes religion and politics), there are several websites that I routinely use and recommend:

  • GRIN, the Germplasm Resources Information Network (, funded by the United States Department of Agriculture, is where I go first for questions about a species’ most commonly accepted name. It also provides background literature and links to other pertinent sites. The only limitation to this database is that it focuses on higher plants of economic importance, not all plants.
  • The Plant List ( attempts to provide the accepted Latin name for all species of vascular plants (flowering plants, conifers, ferns, and their allies) and bryophytes (mosses and liverworts). The Plant List is a joint effort of the Royal Botanic Gardens at Kew and the Missouri Botanical Garden.
  • ITIS, the Integrated Taxonomic System (, provides taxonomic information on plants, animals, fungi, and microbes found around the world. ITIS was created by a partnership of US, Canadian, and Mexican agencies (ITIS-North America), as well as other organizations.
  • IPNI, the International Plant Names Index (, is a database of the names and associated basic bibliographical details of seed plants, ferns, and lycophytes. The Index is the product of a collaboration among the Royal Botanic Gardens at Kew, Harvard University’s Herbaria, and the Australian National Herbarium. IPNI provides the history of a plant name; it is not formulated to make judgments pertaining to the most commonly accepted name.
  • Tropicos® ( contains nomenclatural, bibliographic, and specimen data on tropical plant species in the Missouri Botanic Garden’s electronic databases collected over the past 25 years.

What’s next on the horizon? Scientists are still questioning if Linnaean nomenclature best reflects taxonomic relationships, but since commerce and other facets of our existence are closely tied to existing binomials, the chances are good that this system will remain. In the area of DNA research, previous studies have focused on chloroplast and mitochondrial DNA, which are comparatively short chains, or nuclear markers, that do not comprise the entire genome. With the cost of whole genome analysis decreasing, we now see papers like the one published in the December 12, 2014, issue of Science,17 which revealed new classifications of birds based on such analyses. The surprising result of these whole genome analyses is that the non-coding regions of nuclear DNA (which regulate gene expression and were once mistakenly called “junk DNA”) are often more diagnostic than coding regions (those genes that code for specific proteins).

Without a doubt, botanical names will continue to change. Science, even systematic science, is not absolute truth; it continues to evolve as knowledge increases. Yet, while DNA studies have revealed insights and changes in the systematics and phylogeny of various taxa, the majority of plant taxa based on traditional methods (including comparative morphology) has remained unaltered. Sundews (Drosera) are still in the sundew family (Droseraceae), and peppermint (Mentha x piperita) is still in the mint family (Lamiaceae).

Arthur O. Tucker, PhD, is emeritus professor and co-director of the Claude E. Phillips Herbarium at Delaware State University in Dover. He has published widely on the systematics and chemistry of herbs in both scientific and popular journals and is the co-author of The Encyclopedia of Herbs (Timber Press, 2009), which attempts to summarize the latest scientific information on herbs of flavor and fragrance for the average reader.

Acknowledgements. The author wishes to thank Raymond Petersen, PhD, Susan Yost, PhD, and Thomas Zanoni, PhD, for proofreading.


  1. Olmstead R. Whatever happened to the Scrophulariaceae? Fremontia. 2002;30(2):13-22.
  2. Harrington MG, Edwards KJ, Johnson SA, Chase MW, Gadek PA. Phylogenetic inference in Sapindaceae sensu lato using plastid matK and rbcL DNA sequences. Syst Bot. 2005;30:366-382.
  3. Lehtonen S. Towards resolving the complete fern tree of life. PLoS ONE. 2011;6(10):e24851. Available at: Accessed December 21, 2014.
  4. Bierhorst D. Morphology of Vascular Plants. New York, NY: Macmillan; 1971.
  5. Yatsentyuk SP, Vallejo-Roman KM, Samigullin TH, Wilkstrom N; Troitsky AV. Evolution of Lycopodiaceae inferred from spacer sequencing of chloroplast rRHA genes. Russ J Genet. 2001;37:1068-1073.
  6. Ji Sheng-Guo, Huo Ke-Ke, Wang Jun, Pan Sheng-Li. A molecular phylogenetic study of Huperziaceae based on chloroplast rbcL and psbA-trnH sequences. J Syst Evol. 2008;46:213-219.
  7. Coyle HM. Forensic Botany: Principles and Applications to Criminal Casework. Boca Raton, FL: CRC Press; 2005.
  8. Hall DW, Boyd JH. Forensic Botany, A Practical Guide. Chichester, England: Wiley-Blackwell; 2012.
  9. Bushman F. Lateral DNA Transfer: Mechanisms and Consequences. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 2001.
  10. Syvanen M, Kadi C, eds. Horizontal Gene Transfer, 2nd ed. New York: Chapman & Hall; 2002.
  11. Badger JH, Eisen JA, Ward NL. Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders ‘Rhodobacterales’ and Caulobacterales. Intern J Syst Evol Microbiol. 2005;55:1021-1026.
  12. Greiner S, Sobanski J, Bock R. Why are most organelle genomes transmitted maternally? Bioessays. 2014;36:1-15.
  13. Wolfe AD, Randle CP. Recombination, heteroplasmy, haplotype polymorphism, and paralogy in plastid genes: Implications for plant molecular systematics. Syst Bot. 2004;29:1011-1020.
  14. Hansen AK, Escobar LK, Gilbert LE, Jansen RK. Paternal, maternal, and biparental inheritance of the chloroplast genome in Passiflora (Passifloraceae): Implications for phylogenetic studies. Amer J Bot. 2007;94:42-46.
  15. Elpel TJ. Botany in a Day: The Patterns Method of Plant Identification, 6th ed. Pony, MT; HOPS Press: 2013.
  16. Tucker AO. Botany in a Day: The Patterns Method of Plant Identification. 6th ed. [review] HerbalGram. 2014;103:69. Available at: Accessed December 21, 2014.
  17. Pennisi E. Bird genomes give new perches to old friends. Science. 2014;346:1275-1276.