"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
By
Arthur O. Tucker, 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 (Clerodendron),
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 (www.ars-grin.gov/cgi-bin/npgs/html/taxgenform.pl/) 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.
- PLANTS
(www.theplantlist.org/)
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). PLANTS
is a joint effort of the Royal Botanic Gardens at Kew and the Missouri Botanical Garden.
- ITIS, the Integrated Taxonomic System (www.itis.gov/), 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 (www.ipni.org/ipni/plantnamesearchpage.do/), 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® (www.tropicos.org/) contains nomenclatural, bibliographic, and specimen data
on tropical plant species in the Missouri Botanic Gardens’ electronic databases
collected over the past 25 years.
What
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). |