Thursday, May 12, 2016

How to identify a plant

When you encounter a plant that you do not know, it is natural to want to know previous post, I described some ecological disasters that resulted from scientists misidentifying plants used in experimental studies or in habitat restoration.  I also provided a reference where numerous incidences of accidental poisoning have occurred through consumption of misidentified food or medicinal plants.

Can you tell the difference between the two specimens below? Two people in Italy were recently hospitalized for confusing them.  The one on the left is fennel, the one on the right is poisonous Hemlock, two species out of hundreds in the carrot family, Apiaceae. Though there are clear differences, including flower color and leaf shape, you would have to know them from experience or have them identified by an expert before using them.
Photo by Alvesgaspar - Own work, CC
BY-SA 3.0, httpscommons.wikimedia.
Photo in public domain,
its name.  In some cases, it may be critical to ID it correctly: if you're using a plant in a scientific study, if it's something you may eat or take as a medicine, if your child has eaten something that might be poisonous, or if you're selling plants of some supposed horticultural or medicinal value.  The list goes on and on.  In my

So what do you do?  If it's important, you at some point will have to consult an expert.  You can use available tools to identify it yourself, or at least narrow down the possible identities.  If you have a deep interest in plants, learning identification skills can be time well spent.  It will sharpen your eye for detail and deepen your understanding of plant diversity and adaptation.  If, however, you are a mother in a panic about what your child just put into his mouth, skip this step!

In either case, you need to gather as much baseline information as possible:

1. Is it wild plant, or a cultivated one?  There are different tools for these fundamental categories.

        If it is a wild plant, and you know where it came from, you've already
greatly limited the number of possible plants. There are typically field guides, keys, pictorial guides, and specimen depositories (herbaria) for specific regions of the world, that you can avail yourselves of.

        If it is a cultivated plant, where it was growing is also important.  Plants cultivated in south Florida are quite different from what can be grown in Maine, and there are often regional guides for cultivated plants.

2. What plant parts do you have to work with? Though a good forensic botanist may be able to ID seeds, pollen grains, or wood fragments, generally a good sample of the foliage as well as the flowers and/or fruit is necessary for identification.  Photographs are helpful, but the actual physical material is important for examining small details.

If the above information and materials are fairly complete, you are in a good position to seek out an appropriate expert, or plunge on yourself.

The primary job of plant taxonomists is to inventory the plant
life of the Earth.  Here, taxonomists Heinar Streimann
and Peter Stevens work with local villagers to pack up
plant materials that will be dried and deposited in
 around the world as reference specimens.  Photo taken on an
expedition to Aseki, Papua New Guinea in 1972. When not
in the field, taxonomists continue their research in plant
diversity, teach students, and identify specimens sent in by
A.  Finding an expert.  Plant identification experts are called taxonomists or systematists, and they reside primarily at herbaria and botanical gardens. If there is such a facility locally, that will be your first contact. In most states, there is at least one major herbarium, usually at the primary state university or at your state's designated agricultural college.  In big states, like California, Florida, Texas, and New York, there are several major herbaria.  A local county agricultural extension agent may know many of the plants cultivated locally, and can also direct you to the nearest herbarium.  Outside of the US, each country has a similar network of regional and national herbaria.

Once you locate a herbarium and confirm that they are willing to look at your material you can take your specimens to them, or send them by mail if it's too far to drive there.  Once your materials are in the hand of a professional plant taxonomist, you are connected to the network.  If your local taxonomist can't fully ID your plant, he or she can at least narrow it down to a plant family, genus or other grouping and send it off to a specialist.  Some places will charge a fee, particularly for commercial purposes, others will do it for free.  If it's a common local plant, they may be able to give you the ID instantly.

But experts frequently turn to other experts for critical identification of uncommon plant materials.  Each typically has his or her own particular genus or family that they have spent years studying, which often have specialized terminology or details that require years of training and practice to recognize.  In the grass family, for example, we have to distinguish between paleas, lemmas, glumes, and awns, and in mosses we have calyptras, peristomes, opercula, etc. In the genus Sphagnum, the distinguishing characters not only have funny names, but can only be seen in special preparations under the light microscope.

Now, if you're that panicked mother, you've already wasted valuable time reading the above paragraphs.  You should already be at the hospital!  The baseline information, and a sample of the plant material will still be very important in identifying the poison and administering the appropriate antidote.  The information here will, however, help prepare you for future incidences and to avoid poisonous materials in the future.

B. Plunging on yourself.  How do you start?

You don't have to have a PhD in plant taxonomy to begin the identification process, narrow the plant ID to a handful of possibilities, or possibly even come up with the correct scientific name for the plant. It's a challenge, but can be a very rewarding learning process.  The tools available run the gamut from pictorial guides that anyone can use, to more technical keys that require some learning and practice.  There are books and a growing list of useful websites to help with identifying plant materials of a particular type or geographic origin.

Pictorial wildflower guides, like this one for
South Africa,can be very useful, but you must
pay close attention to detail - there are many
look-alikes due to similar adaptations for
You can begin with non-technical field guides that contain descriptions and color photographs, usually arranged by flower color, or sometimes by habitat.  These are available for many states, national parks, or other specific regions.  These are not usually comprehensive, but contain the most common species. If you come up with a possible match, you can do a web search for images to confirm.  But beware - you can get many erroneous hits, typically of other plants that might be on the same web page as the plant you're looking for.

You can move from that beginning to more formal floras or handbooks, which contain all known species for a specific area with technical descriptions and identification keys.   An identification key takes you through a series of either-or questions that progressively narrow the field of possibilities.  A key might begin
More advanced references,
like Wunderlin and Hansen's
Guide to the plants of Florida,
require the use of technical
keys and specialized
with "flowers red" vs "flowers yellow."  Depending on your choice, you're directed to a later subsection of the key that deals only with plants with red flowers or the one that deals only with yellow flowers.  So, if you were faced with a possible 1000 plants at the beginning of the exercise, after the first step, you could potentially be down to 500 possibilities (more or less, depending on how many red and yellow flowered plants are actually in the area).  You could get really lucky and find that there is only one red-flowered species in the area, and you have it.  Simple, right?

Well, not always.  Keys in general are notoriously difficult, even sometimes for trained taxonomists.  First, you have to learn a lot of specialized terminology. You have to know the names of all the parts of a flower, and the parts of each flower part, and there are typically special names for unique forms of flower or fruit parts found in particular families or genera.  

Professional taxonomists typically reduce the time they spend with keys with various shortcuts.  The most important of these is to learn to recognize the various plant families.   Keys to the families are particularly difficult as the technical characteristics that distinguish modern plant families tend to be rather obscure.

Someday, we might be able to just "google" a plant by entering in an image for "facial recognition."   An experienced taxonomist can often recognize instantly plants that he has seen before, sometimes even just by the hue and pattern of colors in a field.  I's the sames as when you see someone you know.  You don't have to measure the length of your spouse's earlobes or the precise color of their eyes to identify them.  A taxonomist likewise, doesn't have to laboriously count ovary locules or measure the length of anthers in order to identify a plant he or she has seen before.  So a similar sort of facial recognition of plants may be possible with computers in the future.  Another tool that may eventually allow for instant identification would be some kind of DNA scanner, a Star-Trekish tricorder, if you like.

For now we still need professional taxonomists, and in fact a large number of them will be needed to program the above technology!)  This is all the more reason that it should be alarming that taxonomists are dwindling in numbers, as I pointed out in my previous post, and as eloquently pleaded by the famous Indian taxonomist R. R. Rao.

Wednesday, April 20, 2016

Mosses of Central Florida 15. Physcomitrium collenchymum

Physcomitrium collenchymum forms extensive colonies, and an abundance
of spore capsules, in the wet soil along receding ponds. (Essig 20160328-1)

[For other mosses in this series, see the Table of Contents]

Physcomitrium collenchymum (Funariaceae) occurs along the receding edges of ponds during the dry season, and in other disturbed wet sites.  It evidently completes its life cycle rapidly, producing an abundance of spore-bearing capsules in the interval before the rains fill up the ponds again.
After losing their lids (calyptras) the capsules resemble
 wide-mouthed wine glasses and lack teeth around the margins.  

This species occurs in Florida and in other southeastern states, with outlying records in Kansas and Nova Scotia.  It is distinguished from the related species, P. pyriforme, by its globose, rather than inverted pear-shaped, capsules.  The capsules lack any teeth around the opening, which distinguishes them from many common mosses, such as Isopterygium.

The leaves have a strong midrib and clear, rectangular to angular cells with walls irregularly thickened.  The thickened appearance appears to be due to chloroplasts adhering to the walls.  Leaf cells are smooth, lacking any papillae (hard, pimple-like bumps).  This distinguishes this species from similar-looking members of the Pottiaceae.
The leaves of Physcomitrium have a strong midrib, and large rectangular
Note: photographs, geographic distributions and information about the naming history and synonyms of this and other mosses are currently being incorporated into the Atlas of Florida Plants.

Adhering chloroplasts give the cell walls a rough, thickened

Monday, March 21, 2016

The case for plant systematics in universities

The diverse creatures of planet Earth are being destroyed faster than taxonomists
can document them or have any chance to save them. Logging, agriculture,
mining, urban expansion, pollution, and other factors related to human population
growth are the causes of biodiversity loss. 
Every university biology department should hire a plant systematist.  Here are the reasons why.

1. We are in the midst of a "biodiversity crisis"  a massive extinction of species comparable to the one that saw the extinction of the dinosaurs.  This one could be even worse, however, because it is human-caused, and if we can't bring our wasteful practices, demand for natural resources, and unchecked population growth under control, the losses will be catastrophic.

Why is biodiversity so important?  The billions of species of life on this planet are not isolated, like zoo animals in their contained display areas.  Each species lives in the context of many other species with which it interacts in complex, unpredictable, and often unknown ways.  For simplicity, we can call this a food web.  The removal of a single species affects all the others, maybe in a minor way, but maybe in a catastrophic way.  The removal of wolves from an area, for example, usually results in  the overpopulation of deer and other grazers, and that in turn leads to decimation of herbaceous vegetation.  The removal of many species, or an entire biotic community at one time may lead to disruption of the water cycle, soil erosion, climate change, the cycling of  carbon dioxide and oxygen, or other serious ecosystem imbalances.

Plant taxonomists gather plant materials from the wild, store them as dried
specimens in herbaria, then  analyze, describe, name and classify them.
Herbaria thus represent depositories of a vast amount of information about
the kinds of plants that exist, their distributions, habitat preferences,
ecological interactions, and indigenous uses.
A particularly aggravating dimension of the crisis is that many of the species going extinct have never been named, described, or even been seen by scientists.  The traditional practice of taxonomy focuses on the collection of specimens, their preservation and storage in museums or herbaria, naming and describing those species, and developing classifications, practical identification keys, catalogues, and field guides to the species.

The discovery and documentation of the kinds of organisms on this planet, despite nearly three centuries of effort by dedicated taxonomists, is by the most generous of estimates, only half done.  A general consensus suggests however that we have documented only about 15% of the species that probably exist on Earth (Wilson 2004).  Whatever unique ecological, genetic, or biochemical properties might be possessed by the remaining 85% of the world's biodiversity could be lost forever before they are even known.  This is surely one of the most pressing issues facing humanity, considered by some to be even a greater challenge than mitigating the effects of climate change (Science Daily, January 2012). Wilson (2004) suggests, however, that completing the inventory of Earth's creatures could be completed within one generation, if the number of taxonomists working worldwide (estimated at 6000 in 2004) were doubled.  Modern techniques, including use of high-resolution imaging, genomic mapping, and communication of taxonomic information over the internet, will aid this process, but only in the hands of trained taxonomists.

2. One very real and concrete way in which plant systematics, specifically plant identification skills, is vital, is in both theoretical and applied ecological studies.  Alejandro Bortolus (2008) documented the many kinds of disastrous cascades of errors that can occur when ecologists fail to verify the identity of plant species cited or manipulated in their studies.  One example particularly stands out:

"During the late 1970s, a team of geneticists, managers, architects, politicians, biologists, and landscapers got involved in the transplant of propagules of the cordgrass Spartina foliosa from Humboldt Bay to Creekside Park in San Francisco, California, as part of a restoration project involving the only Spartina species native to the West Coast. Using an esthetic criterion, they selected gray clumped mats of S. densiflora, believing they were a good-looking growth form of the native S. foliosa, and they did not question the species identification (after all, it was the only Spartina species described for the region by then). In fact, biologists had mentioned that the plants on Humboldt Bay looked different from the San Francisco native, but no significant attempt was made to further identify it (which would have amended the error) until after it had been introduced into Creekside Park (30). It was not before a number of phenological and ecological differences became highly evident between the transplants and local specimens that botanists realized they were probably working with a different species than presently thought. About 30 years later, the transplanted specimens were correctly recognized as S. densiflora (31). By then, the repeated transplant of this species seamed to have triggered a latent invasive ability in S. densiflora, which after decades of apparent inactivity expanded its original distributional range, massively displacing native organisms and changing the entire physiognomy of regional landscapes along the West Coast" (Bortolus 2008).

One can imagine similar disasters in pharmacological studies of plant derived compounds, though I have not yet seen any compilations of errors in that field.  There are, however, many instances of poisoning or other harm caused by misidentification of herbs by commercial interests and amateurs (Lewis and Lewis, 2003, Chapter 3).  In a related field, one that could serve as a basis for pharmacological investigation, Luczai (2010) found a significant percentage of errors in Polish ethnobotanical papers, even when voucher specimens were deposited.  Failing to correctly identify plant materials in any kind of study most importantly disconnects the study from the body of literature associated with that species, and connects it with the wrong body of literature.

By misidentifying plant species in scientific studies, researchers risk more than disasters like that mentioned above.  One of the essential features  of a modern scientific paper is the "Materials and Methods" section, which if properly done, provides information necessary for the experiment in question to be verified by replication or other independent means.  If researchers do not explicitly state how and by whom their plant materials were identified, and/or did not file voucher specimens of each species, their results are non-replicable, unreliable, and potentially misleading.  This is bad science!

  Further quoting from Bortolus (2008): "62.5% of these modern [ecological] studies are devoid of any supporting information justifying or guaranteeing the correct identification of the organisms studied or manipulated.  Only 2.5% of the analyzed papers reported that specimen vouchers were deposited in a scientific institution.  Medicine, biochemistry, paleontology, and geomorphology are some of the disciplines in which misidentifications could generate great loss of time, knowledge, money, and even human lives."   These conclusions were  verified and amplified by Vink et al. (2012). So biologists of all stripes need taxonomists as partners, not only to prevent disastrous errors, but also to improve the design of their research so as to target the most relevant plant materials, and to enhance replicability and credibility of their research.   For that reason biology departments should be including plant taxonomists on their faculty.

The need for taxonomists, or systematists, to document the diversity of life has never been greater.   Yet ironically, the number of taxonomists being trained and employed, has declined drastically over the past few decades.   Why?

The National Science Foundation had a program from the mid 1990's to 2010 for training scientists in taxonomy, called PEET (Partnerships for Enhancing Expertise in Taxonomy)  mid-90's to about 2010.  It was successful in turning out a number of young taxonomists, but the problem was that they had a difficult time finding work as practicing taxonomists afterwards.  "But as many PEET alumni (peetsters) are experiencing, taxonomic expertise is rarely required, or even relevant, when it comes to securing a job, especially in academia." (Agnarsson and Kuntner 2007). So the prejudice against taxonomists was already entrenched at that time.  What about that prejudice?

In all fairness, Biology has been changing rapidly for several decades.  Academic departments have been scrambling to keep up with the newest expertise in genetics, theoretical ecology, and cell biology, typically with colleges relatively stingy about providing new faculty lines.  So older areas of expertise were sacrificed for the newer ones.  Except in institutions with well-established and productive botany programs, low enrollment botany departments, curricula, and degrees were often scrapped altogether.  Plant-based ecologists, geneticists, and cell biologists were often integrated into the new programs, but classical plant morphologists, anatomists, physiologists and taxonomists disappeared. Many herbaria were bundled up and shipped off to more stable botanical institutions.

However, there is a persistent perception by many biologists that taxonomy is old-fashioned, not engaged with cutting-edge practical or theoretical developments, or unimportant to those advanced fields.  For those that do recognize the value of taxonomy and perhaps utilize taxonomic information in their research, there is the belief that others can do it; that they can consult with taxonomists at other institutions if need be.  The fallacy is that such an attitude only strengthens the decline in the number of practicing taxonomists, making such collaboration even more difficult.

According to Wilson's estimate in 2004, we need 6000 more taxonomists globally to complete the biodiversity inventory of the Earth.  It's probably more than that now, since the last generation of taxonomists to find widespread employment, in the 1960's and 70's, has been retiring in droves during the last decade or two.  A large percentage of these will be plant taxonomists. Universities with varied biology programs can help reach that goal, and include:

      a. universities with unstaffed or understaffed herbaria, some of which have been essentially mothballed;
      b. universities with otherwise strong biology programs, particularly in ecology and evolution, where a major herbarium is nearby.  That would be the case, for example, in New York City, Washington, DC, Boston, St. Louis, MO, Claremont, CA, or Berkeley, CA;
      c. the existing major herbaria themselves, whether privately or governmentally funded, which should be encouraged to hire  additional taxonomists, including some who could teach part-time at local universities.

3.  Plant systematics is bigger than taxonomy.  Departments who feel that they cannot support a conventional plant taxonomist can benefit greatly from  a more broadly defined plant systematist, who could work with ecologists and geneticists on biodiversity issues.  Plant systematists include scientists who are taxonomically knowledgeable, but working on a broader array of related issues.  They ask questions like: what is the geographical and ecological range of each species? How does each survive and interact with other species?  How did these species evolve?  Why are some species endangered while others run amok when transported outside of their natural range? What properties of each species, particularly medicinal, nutritional, or structural, are directly useful to us as we face questions of survival and quality of life in the coming centuries?  (See Michener et al. 1970, for a more extensive discussion of systematics from the time of its emergence.).

Employing a plant systematist, who may not need regular or frequent use of a herbarium, opens up new opportunities for universities to get more involved in current issues associated with the biodiversity crisis. This crisis is gaining more and more attention in the media, by the public, and eventually (we hope) by politicians.  That means funding is and will be available for biodiversity research. Such funding opportunities require the participation of systematists.   Though the PEET program and the Systematic Biology and Biodiversity programs have been discontinued, funding from NSF is a moving target, and similar programs may rise from the dead.  Currently, NSF is offering an interesting program called  “Dimensions of Biodiversity,” which targets the interaction of phylogenetic, genetic, and functional aspects of biodiversity – a perfect opportunity for collaboration between plant systematists, ecologists and geneticists.  Grants for research related to biodiversity can also be obtained from the USDA, the Florida Fish and Wildlife Service, and the Natural Resources and Conservation Service. There are also many private organizations such as the Florida Native Plant Society, JRS Biodiversity Foundation, and the Rainforest Biodiversity Coalition, that fund research in biodiversity.

4. A final reason why university biology departments, particularly smaller ones, should hire plant systematists is this:  If you're going to hire just one "token" botanist to provide balance in your program, you would best be served to hire a plant systematist.  Plant systematists by nature have a broad knowledge of plants and their diverse adaptations.  They can undertake modest, inexpensive field projects with which to engage undergraduate students  They are also likely to be knowledgeable of plants useful in medicine, nutrition and technology. They have a lot of stories to tell, neat ways to engage students, recruiting some for further study, enlightening the rest against plant blindness.   In addition, the kind of information and expertise that a plant systematist can provide is vital to many other disciplines, including  environmental science, anthropology, historical geology, horticulture, pharmacology, medicine, forensics, organic chemistry, history, the fine arts, and material science.  A plant systematist would be a valuable resource to an entire university community.

Literature cited:

Agnarsson, Ingi and Matjaž Kuntner. 2007. Systematic Biology Volume 56, Issue 3Pp. 531-539.

Bortolus, Alejandro.  2008. Error Cascades in the Biological Sciences: The Unwanted Consequences of Using Bad Taxonomy in Ecology, Ambio Vol. 37, No. 2, March 2008, pp 114-118.

Lewis, W. H. and M. P. F. Elvin-Lewis. 2003. Medical Botany, ed. 2. John Wiley & Sons, Hoboken, NJ.

Łuczaj, Łukasz J.  2010. Plant identification credibility in ethnobotany: a closer look at Polish ethnographic studies. Journal of Ethnobiology and Ethnomedicine. 2010; 6: 36.

Michener, Charles D., John O. Corliss, Richard S. Cowan, Peter H. Raven, Curtis W. Sabrosky, Donald S. Squires, and G. W. Wharton. 1970. Systematics In Support of Biological Research. Division of Biology and Agriculture, National Research Council. Washington, D.C. 25 pp.

Vink, Cor J., Pierre Paquin and Robert H. Cruickshank. 2012.  Taxonomy and Irreproducible Biological Science. BioScience Volume 62, Issue 5Pp. 451-452.

Wilson, E. O. 2004. Taxonomy as a fundamental discipline. Phil. Trans. R. Soc. Lond. B. Volume: 359:739.

Thursday, November 19, 2015

Everything you wanted to know about plant cells, but were afraid to ask

 Plant cells, like animals and other eukaryotes, have nuclei, mitochondria and cell membranes, along with a fundamentally similar living cytoplasm, but they have some unique features that adapt them to function quite differently:

1. A cell wall.  This is not the same thing as a cell membrane, but laid down outside of it by secretions of cellulose and other materials from the cytoplasm.  A cell wall is more-or-less rigid, yet generally porous.  Its primary function is to prevent the cell from bursting as water flows in through osmosis.  Animal cells don't have a wall, and if placed in distilled water will expand until they burst.  As I explained in a recent post, plants utilize that intrinsic turgor pressure for a variety purposes, such as expansion of tissues during growth, transport of food and other materials around the plant, holding soft foliage upright, and movements like the closing of venus fly traps.  

2. A large central vacuole.  This is essentially a big bag of water in the center of each cell, surrounded by its own membrane.  This is key to the phenomenal growth rates of young plant parts.  The living cytoplasm occupies a relatively thin zone around the periphery of the cell. Water absorbed by the cell can be stored in the vacuole without diluting the cytoplasm, allowing cells to expand many fold.  The central vacuole also serves as a depository for waste materials and defensive chemical substances.

3. Plastids.  The most recognizable plastid is the chloroplast, which gives the plant its signature property of photosynthesis.  Other forms of plastids are modified to store various materials, such as starch, oils, or pigments.

Parenchyma cells are complete living cells with thin  walls and
active cytoplasm.  This image is from a video posted on 
Youtube, in which you can see the chloroplasts moving 
around the cell.
There are many specialized cell types in plants, but we can begin with the generic living plant cell, such as might be depicted in an introductory biology text.  It is a living cell, capable of many metabolic functions, including photosynthesis, energy metabolism, food storage, and synthesis of structural molecules and secondary plant compounds.  It has functional mitochondria, active plastids, and a functioning nucleus. It has a relatively thin cell wall, and can even divide under certain circumstances, or be changed into another kind of cell.  This is called a parenchyma cell.

The parenchyma cells in a potato tuber are filled with
starch-storing leucoplasts (purple-stained bodies). 
Parenchyma cells fill the interior of all plant organs, filling in around the vascular tissues.  In the leaves and young stems, plastids in the parenchyma cells develop as chloroplasts, in the roots they develop primarily as starch-storing leucoplasts.  In flower petals, they become pigment-storing chromoplasts.

A tissue is a distinctive grouping of cells in a particular region and with a particular function.  Parenchyma tissue is a mass of parenchyma cells, which may seem obvious, but as you'll see later, some tissues are a mixture of different kinds of cells.  Parenchyma cells may also be embedded within the vascular tissues.

A mass of parenchyma tissue on land would flop on the ground and quickly dry out.  It would be okay underwater, and in fact most algae consist of nothing but parenchyma.  So land plants need specialized tissues for internal structural support (sclerenchyma and collenchyma), an external waterproofing layer (epidermis or cork), and internal water and food conducting tissues (vascular tissues: xylem and phloem).

In comparison with parenchyma, specialized cell types are characterized by something being missing, something being exaggerated, or both.  In other words, they are structurally modified for specialized functions.  In sclerenchyma tissues and the water-conducting xylem, cell walls are quite thick and very rigid, while the cytoplasm is essentially non-functional or completely. Once mature, these cells function only as empty cell walls.

Fibers, as in this palm fruit, are most often bundled into thick
These thickened walls, called secondary cell walls, consist of multiple layers of cellulose that are laid down before the cytoplasm dies.  They and may also be impregnated with a hard, resin-like substance called lignin, which gives them additional strength and durability.  Fibers are long slender sclerenchyma cells, usually bundled together to make rope- or cable-like strands of support.  They are mostly found around vascular bundles, but may form separate strands as well.

Fibers are particularly well-developed in monocots, which lack wood.  The trunk of a palm tree is made up of thousands of fibrous bundles running through a parenchyma matrix. Palm leaves are likewise reinforced with fibrous bundles that act as support cables.  The softer leaves of banana plants are also supported by bundles of fibers, and one species (Musa textilis) is the source of the commercial Manila hemp fiber.  Softer fibers in the flax plant (Linum usitatissimum), a eudicot, are used to make the fine fabric known as linen.

The epidermal cells of the developing bean have been
modified into closely packed elongate sclereids.  
The term sclereid is used for a great variety of thick-walled cells that are not long and narrow. They may be shaped like grains of sand, clubs, pillars, spikey stars, and other odd shapes. They are usually in patches or layers that create a barrier against herbivorous intruders. The seed coat that surrounds mature seeds is often made up of elongate, pillar-like sclereids.

The shell of a walnut is mostly sclereids, densely packed and glued together like bricks to create a protective wall that can be breached only by animals with special tools, such as rodents with their chisel-like teeth.  The gritty patches of sclerieds just below the surface of a pear protect it from insects when it is small, but spread apart as it matures, making it palatable to the larger animals that disperse its seeds.  The outer husk of a coconut is made of fibers intermixed with light, airy tissues that allow the whole fruit to float on water.
The long "strings" that line the angles of a celery stalk are
made of collenchyma cells.  The thickened primary walls run
together to form a light colored matrix around the darker
Like the walnut shell. the heavy-duty inner shell of a coconut consists primarily of sclereids.   In nature, this shell can only be broken by a specialized crab (Birgus latro) that has enormous, powerful pincers.  Such crabs, the largest land-dwelling arthropods, live on islands in the Indian and Pacific Oceans, where it is believed that the coconut evolved.

Collenchyma is a specialized soft supportive tissue, where the rigidity comes from thick, water-filled cell walls. These are primary cell walls, consisting of a loose matrix of cellulose, unlike the dense secondary walls of sclerenchyma.  Collenchyma is rapidly produced and common in young, growing herbaceous stems and leaves.

In this succulent stem of Hoya, sclereids (S) form a continuous "brick wall" that protects the inner tissues.  Bundles
of fibers (F) serve as reinforcing cables inside the sclereid wall, and parenchyma (P) tissues fill the interior spaces.
The epidermis to the right has a thin, orange-stained cuticle. Vascular bundles are out of view to the left. 

A xylem vessel consists of a stack of thickened, cylindrical cell
walls (vessel elements) abandoned by the protoplasts that formed
 them.  Tracheids are single cells. 
Modified from
The tracheids and vessels that conduct water through the plant  also have thickened walls, but much larger hollow centers in their mature, functional state.  Fibers may be evolutionarily related to these conducting cells, and in wood (secondary xylem) they intergrade with one another.  Xylem tissue is a mix of tracheids, vessels, fibers, and parenchyma.

In this cross-section of wood from Celtis occidentalis (hackberry), wide vessels (V) are surrounded by narrow fibers (F). Rays of parenchyma (P) run through the wood at right angles to the vessels and fibers. Vessels are narrower and fibers have thicker walls in the late Summer and Fall (lower part of the picture), helping to mark the annual growth ring.  Wood is laid down by the cylindrical layer of dividing cells known as the vascular cambium, which slows down its activity during the late summer.

The cells that make up a sieve tube (sieve tube members) 
are partially broken down.  The nucleus, central vacuole, 
and mitochondria are gone, and the modified cytoplasm
serves as the medium for carrying dissolved sugar through
the tube. The end walls are also called sieve plates, for 
they contain large pores to accomodate the flowing
fluid. The companion cells are fully functioning 
parenchyma cells. Modified from

Phloem tissue consists of the food-conducting sieve tubes, companion cells, parenchyma and fibers.  The sieve tubes consist of a series of cells that contain a cytoplasm-like fluid, but lack nuclei and other organelles. Sugar and other organic substances are loaded into the fluid and flow from one part of the plant under the force of turgor pressure.  Large pores at the ends of the sieve tube elements allow the fluids to pass through freely.  Companion cells are specialized, metabolically active parenchyma cells that run parallel to the sieve tubes and perform some metabolic functions for them. They also help load the sugar into the phloem.

A vascular bundle, as seen here in a Ranunculus stem, is a
complex assemblage of xylem, phloem, narrow
parenchyma cells, and fibers, embedded in the mass
of larger parenchyma cells.
In this succulent stem, the epidermis is reinforced by a layer of sclereids,
 and covered by a thick cuticle. No stomata are visible in this picture. 
Stiff bristles emerge from the epidermal cells of maize leaves.
The outgrowths of epidermal cells are generally known as

Epidermal cells are living cells on the surface of plant organs and so are modifed for protection against water loss and invading organisms.  They don't usually contain chloroplasts, but are active in other ways, and under some circumstances can divide.  The epidermis usually contains specialized cells, including embedded sclereids, glandular cells and the important guard cells that open and close pores (stomata) in the epidermis, allowing for gas exchange.  Epidermal cells also secrete on their outer surface a cuticle, made of a hard polymer called cutin.  The cuticle prevents water loss from the plant, except through the stomata.  Some plants even secrete a layer of was over the cuticle for additional waterproofing.  The thick layer of wax on the leaves of the Carnauba wax palm (Copernicia prunifera) is used commercially to make fine, hard car waxes.  Epidermal cells may also sport a wide variety of hairs, bristles and scales, collectively known as trichomes.

Cork tissue may be laid down on older stems and roots through cell divisions in the epidermis, the parenchyma below the epidermis, or from older phloem tissues.  It consists of empty, thin-walled, waterproof cells.

Stomata are important elements of the epidermis.  They consist
of a pore flanked by a pair of guard cells that can change shape
to open or close the pore. This allows for gas exchange needed
for photosynthesis, or to seal the plant against water loss during
dry or inactive periods.  From micro-scopic.tumbler

The trichomes produced by the epidermal cells of a carnivorous sundew (Drosera)
contain glands that exude a sticky, digestive juice.

Within these basic cell types there is amazing variation in shape and distribution. Families, genera, and even species in some cases, can be recognized by the pattern of their internal tissues. The study of this variation is plant anatomy, which in turn is one of the most important tools in forensics, as well as in archeology and paleobotany.  In coming posts, I will explore some of this variation.

Friday, October 23, 2015

What is an adaptation?

What do we mean by adaptation?  We can use that word  both as a process and as the observable result of that process.   Adaptation is the process of evolutionary change under the guidance of natural selection.  It is the process in which populations become genetically modified to function more efficiently in their specific environment, to respond to changes in the environment, or to move into new environments.  The result of that process is new or altered characteristics that we refer to as adaptations.

An important working assumption, or hypothesis, in biology is that every observable characteristic or trait of an organism has some adaptive significance, or at least had adaptive significance sometime during the ancestry of the organism.  A related assumption is that the total set of adaptations (and hence the total set of observable characteristics) is unique for each species, and defines a unique ecological niche.  That in turn means that each species "fits" into the biosphere in a different way from every other species. Discovering the adaptive meaning of everything from leaf shape to flower color is to me the most exciting part of botany, or biology in general.

Let's just take one example: the shape of cactus stems.  First, of course, cactus stems are succulent, i.e. filled with water-storage tissue.  They gather water during the brief and infrequent rain storms, store it, and utilize it sparingly during the long dry spells.  It allows cacti to continue to function, even to bloom at predictable times, rather than become dormant during those dry periods. That is the signature adaptation made by early members of the cactus family.

Cactus stems are also, in the absence of leaves, photosynthetic.  The two major functions of cactus stems requires some interesting compromises. They need to gather light, but exposure to the intense sunlight and heat of the desert environment can potentially result in overheating and tissue damage.   Imagine leaving a plastic jug of water out in the full sun, with surrounding air temperatures over 100 degrees F.

The approximately 1500 species of the cactus family have evolved a variety of mechanisms to cope with this heating problem.  The evolution of many species from a single common ancestor is called adaptive radiation.

Many cacti are round but narrow,optimizing water storage while reducing
exposure along the sides at mid-day sun and optimizing exposure 
the early morning or late afternoon, Photo by RC Designer t-w-m-c
Most cacti have adaptations that minimize exposure during the hottest hours of the mid-day.  One strategy is to take on an erect and narrow shape.  This allows full exposure to early morning and late afternoon sun, when temperatures are somewhat cooler.  In the middle of the day, however, only the small tip of the stem faces directly into the sun, and the sides receive light obliquely.

Beavertail cacti (genus Opuntia) take that strategy a step further. Their stems develop as flattened segments, which expose even less surface to the noon-time sun, and even more direct exposure  early and late in the day.

The flattened segments of a beavertail cactus (Opuntia) gather
light optimally when the sun is low in the sky, and provide
minimal exposure in mid-day.  Photo by Stan Sherm, Wikipedia.
A spherical or barrel-shaped stem would seem to be all wrong - exposed maximally at high noon.   It is however the most efficient way to store water.  The round shape provides the minimum ratio of evaporative surface area to water storage volume, but it does potentially provide the greatest proportion of its surface facing directly to the noonday sun.  To compensate, barrel cacti often have large curved spines, or numerous long hair-like spines that provide protection from the intense sun.
Cactus spines, which are modified leaves, are particularly well-developed in
broadly rounded cacti, and serve both for protection against herbivores and for
shading from mid-day sun.  Photo by t-w-m-c

Most barrel cacti are ribbed, allowing expansion of the water-storage tissues, and
 also decreasing exposure of the surface tissues to direct sunlight.
Photo by F. B. Essig
Barrel cacti are often fluted, or corrugated, as well - their surfaces consist of accordion-like ridges and valleys.  This further reduces the amount of surface exposed to intense sunlight.   This fluting has a second function as well, allowing the stems to shrink or expand neatly as their internal water stores fluctuate.  The vascular tissues in these stems are concentrated into a series of parallel ribs, so as to allow the expansion of tissues between them.

Another aspect of adaptation is how they are chained together over time, one leading to another to arrive at the characteristic features of a current organism.  We can say that adaptive change is canalized, (see G. L.Stebbins and the process of adaptive modification) and develops momentum in a particular direction.  Certain kinds of change come naturally based on what has come before; others are extremely unlikely.  I have referred to this as "adaptive parsimony" in some of my other essays (see Were the first monocots syncarpous?A flying elephant is unlikely, but the evolution of flight is quite possible in lightweight animals that already leap around in trees (e.g. the ancestors of bats and flying squirrels). 

Another thing lightweight arboreal mammals can become is human.  When I taught introductory biology, I had the students do a thought experiment dealing with human evolution: could humans (or equally sentient beings) have evolved from some other starting point than primates adapted to life in the trees?  Could they have evolved from grazing ungulates or dog-like carnivores?  Could they have evolved from octopi or cuttlefish? Or from insects? The evolution of stereoscopic color vision, grasping hands with opposable thumbs, and rotatable arms in arboreal primates pre-adapted some of their descendants to walk upright and use their hands to craft and utilize tools and weapons - an essential ability for developing technology.  What other path to humanity could have occurred?  We also applied this logic to fictional aliens: how might Wookies or Huts have evolved (especially the huts!)?  Well, that's another story altogether.

Returning to plants, a number of my previous postings (including the ones mentioned above) have centered around logical chains of adaptations.  In the case of cacti, the original adaptations for storing water within the stems led to modifications of the stem to avoid overheating.  In other succulent plants, leaves were modified for water storage instead of the stems (aloes, sedums, etc.).  An aloe is not likely to abandon its water-filled leaves and transfer that function to its stem, just as a cactus is highly unlikely to sprout leaves and transfer water storage to them.  The modification of stems or leaves for water storage is an either/or situation, constrained by their separate canalized adaptive trends.

Stem segments of some epiphytic cacti, such as this Schlumbergera, have
become thin and leaf-like. Photo by Peter Coxhead, Wikipedia.
When some species of cactus adapted to life as epiphytes in tropical rain forests, overheating was not as big a problem, but they needed to absorb more of the light that came to them, They did not sprout leaves again, but instead developed flattened, leaf-like stem segments.  It was a simpler adaptive path.  They also ditched the stem fluting and heavy spines so as to expose more of their light-gathering surface.

Focusing on adaptation can be a highly useful way to teach botany.  It allows one to tell engaging stories that combine systematics (the differences among plants), ecology, anatomy, and physiology.

Friday, September 25, 2015

Dick Brummitt - champion of the paraphyletic

Botanist Dick Brummitt passed away on September 18, 2013.  I missed the opportunity to post a tribute to him at the time, and September of last year also flew by, so in the waning days of September 2015, I will at least mark the second anniversary of his passing.  He is someone we should remember.

Who was Dick Brummitt?  He had a long productive career as a plant taxonomist, primarily at the Royal Botanic Gardens at Kew.  He did what taxonomists do.  He went into the field collecting specimens, did generic revisions and worked on floras.  He did a lot of important work in Africa.  He is more widely known, however,  for his passionate and dogged defense of the peculiar beasts referred to as "paraphyletic taxa."   In a decades-long battle, he pitted himself against the advocates of the new phylogenetic taxonomy, who insisted that only monophyletic groups of organisms could be recognized as formal taxa.  I dedicated two earlier posts to this subject "the great botanical butter battle" and  "making the ancestor problem go away," so I will just briefly summarize it here.

A monophyletic taxon, you may recall, consists of a complete branch, or clade, of a phylogenetic tree: a common ancestor and all of its descendants.  In one of his most memorable essays, Brummitt declared himself to be a "bony fish."  This remark stemmed from the new phylogenetic taxonomy of vertebrates, in which amphibians were a subclade of the bony fish, reptiles (amniotes, if you prefer) a subclade of amphibians, and mammals and birds both subclades of reptiles.  "Mammals" and "bony fishes" are no longer equivalent classes as they were in previous classifications.  The new classification reflects better the evolutionary history of organisms, but raises some difficult practical questions.

What really irked Brummitt was the difficulty of naming ancestral groups.    If we wish to refer to just the bony fishes that did not become amphibians, reptiles, etc., what name can we give them? We cannot put them into a formal category, such as a class, phylum, or family  because they are a paraphyletic taxon.  Such a taxon contains a common ancestor (the first bony fish) and some of its descendants (bony fishes that remained bony fishes), but not all of its descendants (amphibians, etc.), so it is not a complete clade.  If we decide that the bony fish clade is a formal "class" then what are the mammals or birds - sub-sub-sub classes?

Brummitt argued that, taken to its logical conclusion, this situation would lead to a collapse of the taxonomic system, because, after all, bony fishes were just a subclade of an earlier group of vertebrates, the early vertebrates were a subclade of a still earlier group, and so on back to the first organisms.  Recognition of the branching clade structure of life is extremely valuable, but it has made the application of formal ranks difficult, inconsistent, and increasingly less useful.  Brummitt was right on that, and most taxonomists now avoid higher level taxa such as phyla, classes etc., referring instead to stem groups, clades, grades, and other references to portions of the phylogenetic tree.  Supporters of the "phylocode," advocate a system for naming clades without trying to stuff them into formal ranks.  This was a de facto recognition of one of the problems of phylogenetic classification perceived by Brummitt and other like-minded taxonomists.
The groups that we recognize as genera have arisen
sequentially from earlier genera.

With respect to lower level taxa, such as genera and species, we're kind of stuck, however.  We need to give organisms (including fossils) names, and there seems to be no good way to do that other than the traditional binomial: the genus plus the specific epithet.  So we need genera, and we need to be able to group organisms into genera even if they were ancestral to other genera.

For example, the very first species of our own genus, Homo, most certainly evolved from members of an earlier genus traditionally known as Australopithecus, making the latter genus paraphyletic. The same is true for every known genus and the genus that preceded it,  A genus that is monophyletic today might in several million years become paraphyletic by giving birth to new genera. Paraphyletic genera are therefore unavoidable.

Phylogenetic taxonomists have tried to avoid recognizing such genera - sometimes lumping paraphyletic genera with the nearest monophyletic genus, sometimes splitting paraphyletic genera into smaller monophyletic units, or by recognizing unavoidable groups of ancestral species (a"stem group" ) as some kind of special category.  All of these diminish the meaning of genera as comprehensible units of biodiversity.

Brummitt and others (see Hörandl  & Stuessy 2010) argued that paraphyletic genera (and other ranked taxa) should be simply recognized and named in our taxonomic system because they are unavoidable, natural units of evolutionary history.  

Literature cited:

Hörandl  & Stuessy. 2010. Paraphyletic groups as natural units of biological classification. Taxon 59 (6): 1641-1653.

Wednesday, August 26, 2015

The evolutionary perspective in teaching botany

[This essay is modified from one that I recently posted at the Oxford University Press blog site]
Many of us involved in teaching botany feel a sense of urgency in our profession.  Botany departments, botany majors, and botany curricula have gradually shrunk or disappeared from most colleges and universities in the US, and I suspect in many other parts of the world as well.  Too many students are graduating with little or no understanding of the unique ways in which plants meet the challenges of survival and reproduction in the Earth’s diverse ecosystems.  Biology faculty who don’t have training or experience with plants are often ill-prepared to relate to or take advantage of the unique contributions plants might make to their own teaching and research.

So if we have only a semester, or worse only a week or two, to teach the fundamentals of plant life, and to pass on the exhilaration we feel in the face of their diverse adaptations, how do we do it?  If our non-botanical colleagues or teaching assistants have been assigned to teach a beginning level segment on plants, how do we help them understand the basics and develop some enthusiasm for the subject matter? 

Some teachers prefer an ecological approach, emphasizing the pivotal and diverse roles of plants in the ecosystem.  Others prefer an approach emphasizing applications to human technology, agriculture, nutrition or medicine.   All of these approaches are useful in developing interest, but may end up being too superficial with respect to fundamental structure and function.  Traditional botany texts tend to be dry and encyclopedic.   Non-majors texts may be more appropriate for most of today’s audience, but they still tend to avoid a side of biology that I call the “why” questions. 

One must have the “what” before the “why,” but it is the latter that gives some context or meaning to the former.   The “what” is the factual material one finds in a textbook.  The “why” is the explanation of the “what.” For example, textbooks typically contain a little section on the differences between monocots and dicots (or now monocots and eudicots, awkwardly ignoring magnolids, waterlilies and other basal angiosperms).  We are told that dicots typically have net-veined leaves, vascular bundles arranged in a ring in the stem, and secondary (woody) growth, while monocots typically have parallel-veined leaves, vascular bundles scattered within the stem, and no secondary growth.  That is the “what,” at least in a simplistic sense, but there is typically no “why” to follow it.
The sword-shaped leaves of cat tails, have parallel
veins because new tissues are added at their bases,
 pushing them upward from their underground stem
systems, This lengthens each vein as the leaf lengthens.
The corresponding suppression of woody tissues in
the underground stems occurred as the stems adapted
 for clonal spreading rather than vertical growth. 

  Monocots are the newer invention in plant architecture, having developed their unique structures and way of growth as they split from ancient dicots.  Why do their leaves have parallel veins?  Why do they not have secondary growth?  How do they interact differently with the world than dicots, and how did their innovative structures come about? (Hint: it has to do with ancestral monocots going “underground.” ) See the caption to the right, and for a more extended exploration of these questions see my blog post: How the grass leaf got its stripes.

“Why,” in scientific terms, has to do with the process of adaptation. It’s the story of origins, of plants facing environmental challenges and evolving innovative ways to cope.  This is what makes botany interesting.  It is also a way to make sense of the fundamental features of plants, some of which may be dismissed as obscure and unimportant, but which are loaded with both meaning and utility. 

For another example, let’s take everyone’s favorite: life cycles.   Students already sophisticated enough to know that sperm and egg in animals are produced through the special kind of nuclear division called meiosis are truly puzzled by why that does not happen in plants.  Others are surprised that plants produce sperm and egg at all. Meiosis mixes chromosomes and reduces a double set (diploid) into a single one (haploid) in each of the resulting cells.  In animals the haploid cells combine into a diploid zygote, which develops into a new diploid individual  In algae and plants, however, it's more complicated. Bear with me, even the short version is convoluted!

In the evolutionary story of sexual reproduction in plants, we find that the algae similar to those that gave rise to land plants, and simpler land plants themselves, are haploid and do produce sperm and egg directly.  In both cases, however, the joining of sperm and egg does not result in a new plant, but rather in a short-lived diploid zygote that produces spores through meiosis. Spores are adapted for long-distance dispersal, and germinate to form new haploid plants that will eventually produce gametes.  So spores, not gametes, are produced through meiosis in plants.

A moss colony, such as this Isopterygium, is
both photosynthetic and gamete-producing (the
gametophyte generation).  It holds water within 
its spongy matrix, which sustains the  life of the
vegetative tissues and also provides a watery
pathway for sperm cells in search of eggs.
Because of this mode of reproduction, mosses
must remain small and close to the ground.  The
sporangium and its elongate stalk constitute the
sporophyte generation, a separate individual
resulting from the fertilization of the egg.
Spores will germinate to establish new 
genetically mixed moss colonies.  
The production of spores in green algae mostly occurs within individual cells, but in land plants, a small, diploid, multicellular body, technically a separate plant called a sporophyte, develops for that purpose.  The fact that plants alternate between haploid gamete-producing plants and diploid spore-producing plants is the “what” of plant reproduction.  Students might memorize dozens of life cycle diagrams, but won’t know “why” such things exist, or why they have to bother with such tedia, until the adaptive story is told.     

That story has primarily to do with the fact that plants cannot move around to find mates, and that if they simply released sperm cells to go off and find an egg on their own, it would lead at best to severe inbreeding.  Such a strategy works well enough in some marine invertebrates, like sea stars, where currents can help disperse the sperm cells, but on land, these tiny, fragile cells just don’t get very far.  Spores do the traveling for  plants, taking the place of mate selection in mobile animals.  Genetic diversity in plants depends on spores from different genetic backgrounds landing close to one another, so that when they develop into gamete-producing plants, suitable mates will be next to one another. 

In the early vascular plants, the diploid sporophyte
generation became the dominant part of the life cycle,
lifting spore-producing structures high into the air. 
Some of their descendants, including the ancestors 
of these giant douglas firs, evolved seeds and pollen 
grains - the more complex spore-derived vehicles that 
bear tiny egg- and sperm-producing individuals. 
Spores are launched best from an elevated vantage point, and so sporophytes tend to be stretch upward as much as possible.  In mosses, this can be only a few centimeters (see "Why are there no moss trees?") but this suffices to get spores above the low-growing moss foliage. In the land plants we call vascular plants, however, sporophytes became larger and larger, and in fact the trees, herbs, and grasses we see today are actually the sporophyte generation of the plant life cycle.  The egg- and sperm-producing “plants” (gametophytes) - the equivalent of the algal or moss colonies, are hidden within the embryonic seeds and pollen grains of these more advanced plants.

Yes, it’s complicated, but if the story unfolds from the perspective of how and why it evolved, it does make sense. And it is an important story.  Understanding how plants and algae reproduce impacts both agriculture and ecology.  

Plant Life – A Brief History,” provides the adaptive perspective of plant features for students, instructors, and others interested in the biology of plants.