Lab 5. Herbals; An Introduction to Taxonomy Biology 1B Saddleback College

Dr. Jane Horlings

IntroductionTo identify specimens in a logical and efficient manner, specimens may be grouped according to morphological characteristics. If we were to organize a tool box, we might group fasteners in one compartment, pliers in another, screwdrivers in another, and so on. Within the fastener compartment, we might divide up the screws from the nails, the nuts from the bolts. In a similar fashion, we may "compartmentalize" biological specimens. We can easily see the division between salmon and blue birds, between chimpanzees and flamingos. Indeed, many of our zoos are organized like this; the primate house houses the primates, the antelope corral houses the various antelope species.

These divisions are clearly based on morphological similarities as well as differences. It is because of a shared evolutionary history that all birds look alike, or that all primates appear to have similar characteristics. Based on our knowledge of the evolutionary history of organisms inferred from the fossil record, we can classify organisms. The study of this classification system is known as taxonomy (naming and grouping) or systematics (relating the classification to phylogeny= evolutionary relationships).

The Greeks and Romans were the first to develop a system of naming plants and animals. Books about animals were called Beastiaries; books on plants were called Herbals. The modern system of naming (nomenclature) was developed in the 1700s by Carollus Linnaeus (1707-1778), a Swedish biologist.

Read about Linnaeus at http://www.ucmp.berkeley.edu/history/linnaeus.html and http://www.systbot.uu.se./dept/history/linneaus.html

• Describe a bit of his life:

Linnaeus saw the taxonomic groupings as an expression of God's mind. Although creationism was later replaced by the evolutionary theory, his classification system stood. Linnaeus' Species Plantarum (plants), published in 1753, and Systema Naturae (animals), published in 1758 marked the official beginning of the organized and scientific naming of species and higher categories. Linnaeus organized all things into the plant, animal and mineral kingdoms

Linnaeus believed that species were created once and were fixed over time. He classified organisms based on arbitrarily weighted characteristics. After the

publication of Origin of Species in 1859 by Charles Darwin, the study of taxonomy began to consider evolutionary relationships as well.

• Describe the current taxonomic system of classification. Refer to: Classification of Living Things. An introduction to the principles of taxonomy with a focus on human classification categories. http://anthro.palomar.edu/animal/default.htm

Describe:

The Scientific NomenclatureLinnaeus' system is now known as binomial nomenclature; a "two name" system which uniquely identifies all living things. The two names are the genus and species name. To date, there are approximately 1.5 million species of animals named and described. The naming of organisms follows very rigid rules. The scientific name of an organism consists of two parts; first the name of the genus, which is always capitalized and underlined; followed by the name of the species, which is not capitalized, but is underlined.

The species name is considered the basic unit of classification. For example, the cultivated pansy plant is Viola tricolor. This name is unique to that particular species. A related species, the long-spurred violet, shares the same genus, but has its own unique species name; Viola rostrata. This system of scientific names is important in international biology, as this system crosses language barriers. The fruit of the orange tree may be known as "orange" in English, and "naranja" in Spanish, but scientists may converse about Citrus sinensis and understand each other, as all taxonomic terms are now standardized into the International Code of Botanical Nomenclature.

One cannot list just the species name without the genus name, as both must be mentioned, although you may shorten the scientific name to just the initial of the genus name with the species name, such as V. tricolor.

More information on taxonomic nomenclature can be found at this site: Glossary. Definitions of terms related to taxonomy. http://www.sel.barc.usda.gov/scalenet/glossary.htm

List 5 words that you have lookedup at this site and define:1.

2.3.4.5.

The KingdomBefore we delve into the classification under the umbrella of Botany, I would like to mention the overall classification of living things. Many biologists follow the Five Kingdom scheme, proposed by R. Whittaker in 1969. This groups all living things into the following kingdoms: Kingdom Monera (prokaryotic organisms; bacteria); Kingdom Protista (eukaryotic unicells or colonies; photosynthetic or heterotrophic); Kingdom Fungi (typically multicellular, non-photosynthetic organisms with cell walls); Kingdom Plantae (typically multicellular, photosynthetic organisms with cell walls); and Kingdom Animalia (typically multicellular non-photosynthetic organisms without cell walls). More recent work has pointed out that the Monerans should be split into two kingdoms; Eubacteria and Archaebacteria. This would result in a 6 kingdom scheme.

Several groups of living things are considered by various biologists to be members of different groups. For example, in some of the following labs, we will examine single-celled plant-like organisms that I would classify as algae, but others may consider to be plants.

Botanical TaxonomyThe Plant and Fungal Kingdoms may be further subdivided into divisions, classes, orders, families, genera and species. Animals are subdivided into phyla, rather than divisions, but the other groupings are the same. For example, study the following schematic:

Corn The Edible MushroomKingdom/Phylum Plantae Fungi

Division Anthophyta BasidiomycotaClass Monocotyledones HymenomycetesOrder Commeninales AgaricalesFamily Poaceae AgaricaceaeGenus Zea Agaricus

Species mays bisporus

Note that family names (of most plants, at least) end in -aceae. Names of plant orders end in -ales. Some groups of plants have been classified into intermediate levels, designated by prefixes of sub- and super-. Other groupings include confusing levels such as Tribes, Series, and Infraclasses. We won't delve that deeply!

However, it is useful to know that below the species level, there may be subspecies, varieties and races. These organisms are capable of interbreeding and usually can produce fertile offspring, but are often geographically isolated from one another. These distinctions may be important when defining an endangered species. For example, if the southern subspecies of a particular plant is

endangered, but the northern subspecies is not endangered, can or should you classify the southern subspecies as endangered? This may have important legal implications in the future.

• Study the specimens set out at the various stations around the lab. Make notes on the various divisions and what characteristics distinguish them. In the protist, fungal and plant kingdoms, 25 divisions are presently recognized.

This is the classification scheme that we will follow this semester. This differs in some ways from the scheme presented by other texts. Note that the term Division is now commonly replaced by the term Phylum (also applicable to animals as well).

Taxonomic Name Common Name ProkaryotesKingdom Eubacteria EubacteriaKingdom Archaebacteria Archaebacteria

EukaryotesKingdom Protista *Heterotrophic protists

Division Oomycota Water moldsDivision Chytridomycota ChytridsDivision Acrasiomycota Cellular slime moldsDivision Myxomycota Plasmodial slime molds

*Photosynthetic protists (“algae”)Division Chrysophyta Diatoms and chrysophytesDivision Pyrrophyta DinoflagellatesDivision Euglenophyta EuglenoidsDivision Rhodophyta Red algaeDivision Phaeophyta Brown algaeDivision Chlorophyta Green algae

Kingdom FungiDivision Zygomycota ZygomycetesDivision Ascomycota AscomycetesDivision Basidiomycota Basidiomycetes

Kingdom Plantae *Bryophytes

Division Hepaticophyta LiverwortsDivision Anthocerotophyta HornwortsDivision Bryophyta Mosses

*Seedless vascular plantsDivision Psilotophyta Whisk fernsDivision Lycophyta LycophytesDivision Sphenophyta HorsetailsDivision Pterophyta Ferns

*Vascular plants with seeds

Division Cycadophyta CycadsDivision Ginkgophyta GinkgoDivision Coniferophyta ConifersDivision Gnetophyta GnetophytesDivision Anthophyta/Magnoliophyta Angiosperms

* Groupings that are not of a true taxonomic status

• Referring to your textbook, web pages and the specimens at various stations around the room, and answer the following questions and complete necessary sketches.

I. ProkaryotesA. Kingdom Eubacteria• These are the true bacteria; exhibiting various modes of metabolism. List and describe the major categories of bacterial metabolism (refer to text):1.2.3.4.

Refer to: Diversity of Life: Kingdom Monera. Lots of links to more information.http://www.geocities.com/RainForest/6243/diversity2.html - BacteriaList five characteristics of the true bacteria (new name Kingdom Eubacteria, older name Kingdom Monera)1.2.3.4.5. B. Kingdom Archaebacteria• This group of unusual bacteria are often found in very inhospitable habitats. List and describe the three major groups of Archaebacteria. Refer to:Archaebacteria: Life on Mars? Information on thermophiles, including cyanobacterial species, as well as halophiles.http://waynesword.palomar.edu/ploct97.htm

orArchaea. Many links to pages with more information on the genomes of these bacteria.http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?name=Archaea

or

Archaebacteria. Information on the three groups of archaea.http://fox.rollins.edu/~egregory/Archaebacteria.html

Describe what makes the archaebacteria different from the typical bacteria:

II. EukaryotesA. Kingdom Protista Heterotrophic Protists

1. Division Oomycota, the water molds• What historical event was initiated by a growth of a terrestrial mildew? See: The Irish Potato Famine Fungus, Phytophthora infestans.http://www.siu.edu/~ebl/leaflets/blight.htm

• How might a water mold affect a fish in an aquarium?

2. Division Chytridomycota, the Chytrids• What characterizes organisms in this obscure group?

3. Division Acrasiomycota, the Cellular slime molds• Mycologists classically study the slime molds, even though we do not current classify them as true molds. What do mycologists typically study? See: MykoWeb. Information on mycology; links, and even recipes. http://www.mykoweb.com/index.html

• How are the cellular slime molds different from the plasmodial slime molds?Refer to: Introduction to the Slime Molds. Information and many links.http://www.ucmp.berkeley.edu/protista/slimemolds.html

4. Division Myxomycota, the Plasmodial slime molds• What does the term coenocytic mean? • What is the plasmodium stage?

Photosynthetic Protists (“algae”)• How are algae different from protozoans?

5. Division Chrysophyta, the Diatoms and Chrysophytes

For information, refer to:Eureka: Diatoms Biology. A very well done site on diatoms. Any question you have will probably be covered here. http://hjs.geol.uib.no/diatoms/biology/index.html-ssi

• What type of photosynthetic pigments dominate in this group?

• What do phycologists study?

• What is an unusual feature of the diatoms?

6. Division Pyrrophyta, the Dinoflagellates

Refer to: Dinoflagellates. Much information and links on dinoflagellates.http://www.geo.ucalgary.ca/~macrae/palynology/dinoflagellates/dinoflagellates.html

• Sketch Ceratium:

• What are two ecologically important roles that dinoflagellates play? Refer to: "Red Tides" and Harmful Algal Blooms. This site is supported by the NSF, Woods Hole Oceanographic Institution and NOAA, and definitely is the place to start to learn more about harmful algal blooms. http://habserv1.whoi.edu/hab/

andPfiesteria. Go right to the source for information on Pfiesteria piscicida at this site from North Carolina State University’s Aquatic Botany page. NCSU was the first laboratory to identify this microorganism. http://www.pfiesteria.org/

7. Division Euglenophyta, the Euglenoids• How are euglenoids different from green algae?

• Some euglenoids are heterotrophic. Define heterotrophic:

7. Division Rhodophyta, the Red algae

Red Algae: Rhodophyta. Clickable genus names show a photograph and information of many genera. http://www.sonoma.edu/biology/algae/Red.html

• Where do most red algae live?

• Brown algae dominate in cold waters. Where do red algae dominate?

8. Division Phaeophyta, the Brown algae

Life History and Ecology of the Phaeophyta. From the U.C. Berkeley Museum.http://www.ucmp.berkeley.edu/chromista/browns/phaeolh.html

andKelp Forests. Nice pictures and much information about kelp forest communities.http://life.bio.sunysb.edu/marinebio/kelpforest.html

• What are kelps?

10. Division Chlorophyta, the Green algae

Introduction to the Green Algae. From the Berkeley Museum, and a link to a page on red algae.http://www.ucmp.berkeley.edu/greenalgae/greenalgae.html

andGreen Algae: Chlorophyta. Clickable genus names show a photograph and information of many genera. http://www.sonoma.edu/biology/algae/Green.html

• What is the evolutionary significance of this group? • The term seaweed refers to large, marine members of this group and what two other groups?

B. Kingdom Fungi1. Division Zygomycota, the Zygomycetes

Zygomycota. A description, and a diagram of the life cycle of this bread mold.http://www.uwinnipeg.ca/~simmons/lb2pg05.htm

• What are mycorrhizae?

• Where might you find a zygomycete growing in your kitchen?

2. Division Ascomycota, the Ascomycetes

Ascomycota. A good description and diagrams of the sac fungi.http://www.uwinnipeg.ca/~simmons/lb2pg06.htm

andSac Fungi. Photographs and text from the Natural Perspective.http://www.perspective.com/nature/fungi/ascomycota.html

• What ascomycetes might you eat?

3. Division Basidiomycota, the Basidiomycetes

Basidiomycota. A very informative site on the basidiomycetes, with diagrams of life cycles, and links to photos.http://www.uwinnipeg.ca/~simmons/lb2pg07.htm

andArizona’s Tree of Life page on Basidiomycota. Much information on life cycles, references, and pictures.http://phylogeny.arizona.edu/tree/eukaryotes/fungi/basidiomycota/basidiomycota.html andThe Club Fungi. Links to photographs and information on the basidiomycetes.http://web1.manhattan.edu/fcardill/plants/fungi/basidio.html

• What basiomycetes might you eat?

• What basidiomycetes cause plant diseases?

C. Kingdom Plantae Bryophytes

The Bryology Home Page, from the Missouri Botanical Garden is a good starting place with lots of links.http://www.mobot.org/MOBOT/tropicos/most/

• Characterize this group:

1. Division Hepaticophyta, the Liverworts• How did the liverworts get their name?See: Hepatophyta. Many good images for familiarization with this group, and review.http://www.science.siu.edu/landplants/Hepatophyta/hepatophyta.html

2. Division Anthocerotophyta, the Hornworts• How do the hornworts differ from liverworts? Compare: Introduction to the Anthocerotophyta. From the U.C. Berkeley Museum of Paleontology.http://www.ucmp.berkeley.edu/plants/anthocerotophyta.html

toMosses. Information and photographs.http://www.bio.umass.edu/biology/conn.river/liverwts.html

3. Division Bryophyta, the Mosses

View photographs of mosses at: Bryophyta. Description and diagrams of mosses. Includes interactive quiz questions. Go to the next page to learn about reproduction in mosses.http://www.uwinnipeg.ca/~simmons/lb3pg4.htm

• Define: rhizoids:hint: glossary at: http://www.gardenweb.com/glossary/

Seedless vascular plantsDefine: vascular tissue:http://www.botany.hawaii.edu/faculty/webb/BOT410/Phloem/Phloem-1.htm

4. Division Psilotophyta, the whisk ferns• Sketch a whisk fern:

5. Division Lycophyta, the Lycophytes• What are common names for lycophytes?

• Describe members of this group. Resources:Division Lycophyta. Information on the various orders within this division (phylum).http://web1.manhattan.edu/fcardill/plants/vascular/lycophy.html

andLycophyta. Many images of representative species.http://www.science.siu.edu/landplants/Lycophyta/lycophyta.html

andIntroduction to the Lycophyta. From the UCMP.http://www.ucmp.berkeley.edu/plants/lycophyta/lycophyta.html

andLycophyta. More information and images.http://www.wisc.edu/botit/Botany_130/Div/Phyla/Lycophyta/Lycophyta.html

6. Division Sphenophyta, the Horsetails• Describe the horsetails of the Cambrian Period.

• Describe the botanical diversity during this period. Refer to:Links to Other Sites Related to Plant Evolution. Just like the title says!http://www.science.siu.edu/landplants/otherSites.html

• Describe the wide variety of extant horsetails. Refer to: Sphenophyta. Great images. Lots of them!http://www.science.siu.edu/landplants/Sphenophyta/sphenophyta.html

7. Division Pterophyta, the Ferns

Describe the diverse morphology of the ferns. Refer to:Morphological and Anatomical Diversity in the Ferns. Go to the next page for information on fern reproduction.http://www.uwinnipeg.ca/~simmons/lb3pg7.htm

• What is a fiddlehead? You should find this at: Ferns. Good description and graphic of fern life cycles.http://www.edc.com/~jkimball/BiologyPages/F/Ferns.html

orhttp://web1.manhattan.edu/fcardill/plants/vascular/ferns.html

• What plants contributed to the coal forests of the Carboniferous?

Vascular plants with seeds• What is the importance of seeds?

8. Division Cycadophyta, the Cycads

Cycads. Information and absolutely beautiful photographs.http://www.nd.edu/~fboze/cycads.htm

• What is another name for a cycad?

9. Division Ginkgophyta, the Ginkgo

Ginkgophyta. Links to images.http://www.wisc.edu/botit/Botany_130/Div/Phyla/Ginkgophyta/Ginkgophyta.html

• Why is the ginkgo often planted in cities?

9. Division Coniferophyta, the Conifers

Refer to: Coniferophyta. Information, many useful links.http://www.wisc.edu/botit/Botany_130/Div/Phyla/Coniferophyta/Coniferophyta.html

The Conifers. Photographs of various genera.http://online.anu.edu.au/Forestry/teaching/t6/bd.html

Coniferophyta. Photographs of various genera. Good link to life cycle of conifers.

http://www.science.siu.edu/landplants/Coniferophyta/coniferophyta.html

• What is the reproductive structure of a conifer?

• What are the leaves of conifers?

• Approximately how many species of conifers have been identified?

10. Division Gnetophyta, the Gnetophytes

Refer to:Subdivision Gneticae. Photographs of gnetophytes.http://web1.manhattan.edu/fcardill/plants/gymno/gnetes.html

andGnetophyta. Links to images.http://www.wisc.edu/botit/Botany_130/Div/Phyla/Gnetophyta/Gnetophyta.html

• What is unusual about this taxonomic group?

11. Division Anthophyta, the Angiosperms- often also referred to more recently in texts as Phylum Magnoliophyta.

Anthophyta. A great place to start. Links to information on everything from pistils to leaf types. A great link to information on families. A wealth of information, though a few links don’t exist (yet).http://www.nsci.plu.edu/~jmain/b340web/pages/anthophy.htm

andFlowering Plants. Information, photographs and links about the diversity of angiosperms.http://waynesword.palomar.edu/trmar98.htm

andAnthophyta. Many links to information on angiosperms.http://www.science.siu.edu/landplants/Anthophyta/anthophyta

• Approximately how many species of Angiosperms have been identified?

• Questions to answer:1. If there were no human beings to classify them, would there be genera, families, orders, etc? Why ? (hint: key word starts with an “E”)

2. What should be done if it is discovered that a species has been named more than once?

3. Why is Linnaeus's system referred to as binomial nomenclature?

4. How would you abbreviate Stenocereus thurberi?

5. In what kingdom did Linnaeus classify fungi?

6. Why did Linnaeus not classify bacteria?

Notes on lab 5:

Web Sites for Lab 5.

Classification of Living Things. An introduction to the principles of taxonomy with a focus on human classification categories.http://daphne.palomar.edu/animal/default.htm

Plant Nomenclature. Information on naming and taxonomy of plants. Look at the information on "nyms."http://130.17.2.215/boty3700/nomenclature.htm

Carol Linnaeus. Information on the life of this famous early taxonomist.http://www.ucmp.berkeley.edu/history/linnaeus.html

Carl von Linne. More biographical information.http://www.systbot.uu.se./dept/history/linneaus.html

Taxonomic Resources and Expertise Directory (TRED). Find a new species in your back yard? This is the place to find information regarding how to classify it.http://www.nbii.gov/datainfo/syscollect/tred/

Species 2000. To goal of this organization is to provide a uniform and validated index of names of all known species of organisms.http://www.sp2000.org/

Integrated Taxonomic Information System (ITIS). More information, supported by the USGS and other cooperating agencies, focusing on the biota of North America. ITIS is part of Species 2000, an international project to classify and list all of the world’s known species.http://www.itis.usda.gov/plantproj/itis/index.html

Glossary. Definitions of terms related to taxonomy.http://www.sel.barc.usda.gov/scalenet/glossary.htm

Biology 120 Phylogeny Exercise. Extensive information on taxonomy and phylogeny.http://www.utm.edu/~rirwin/b120lab.htm

Introduction to Phylogeny. This site is great! It is part of a virtual museum from the University of California, Berkley. It is a bit confusing to navigate at first, but nevertheless provides much information and some nice images. Within most taxa, you can click to learn more about a group's fossil record, life history and ecology, systematics, or morphology. Includes just about all organisms. Help files, glossary, and a navigating tool called Web Lift are available. http://www.ucmp.berkeley.edu/exhibit/phylogeny.html

Methods of Classification

Journey into the World of Cladistics. This site includes an introduction, a discussion of methodology, implication, and the need for cladistics.http://www.ucmp.berkeley.edu/clad/clad4.html

What is Cladistics? A short but informative introduction to cladistics.http://fossilnews.com/1996/cladistics.html

References About Phylogenetic Biology. A very long list of references (not links) on phylogenetic biology.http://phylogeny.arizona.edu/tree/home.pages/references.html

Glossary of Phylogenetic Systematics. An extensive glossary of the terminology necessary to understand systematics.http://members.tripod.de/GBechly/glossary.htm

Cladistics. A glossary.http://www.dorak.free-online.co.uk/clade.html

General Botanical References

Botanical Society of America. Information on the American Journal of Botany and many web links.http://www.botany.org/

Careers in Botany. This is from the Botanical Society of America. Many associated links.http://www.botany.org/bsa/careers/

Internet Directory for Botany. An enormous amount of resources (over 3,700 botany-related links).http://www.helsinki.fi/kmus/botmenu.html

Phylum Directory. A great site that links you to pages with photographs, photomicrographs, and information on vascular plants. From the University of Wisconsin at Madison.http://www.wisc.edu/botit/Botany_130/Div/Phyla/Phylum_directory.html

General Botany. This consists of over 2,000 pictures organized within the context of an introductory botany course from the University of Wisconsin at Madison.http://www.wisc.edu/botit/img/bot/130/

Names of Wildflowers. A description of how common names are often misnomers; others are very descriptive.http://daphne.palomar.edu/wayne/pljuly98.htm

Embryophytes. Arizona’s Tree of Life Page. A description of the taxonomy of this group with links to some groups.http://phylogeny.arizona.edu/tree/eukaryotes/green_plants/embryophytes/embryophytes.html

Why Study Plants? See why botany is a very important field of study.http://koning.ecsu.ctstateu.edu/plant_physiology/WhyPlants.html

Botanical Record-Breakers. Including the world's fastest reproducing plants, the world's fastest growing plants, and the most painful botanical encounters.http://daphne.palomar.edu/wayne/ww0601.htm

Index. An index to more information from a botany class.http://www.nsci.plu.edu/~jmain/b359web/pages/359index.htm

Botany Society of America Image Collection. Over 800 images are available for instructional use.http://images.botany.org/

Internet Directory for Botany. An extremely large searchable index.http://www.botany.net/IDB/

GardenWeb Glossary of Botanical Terms. A very user-friendly dictionary of botanical terms with definitions.http://www.gardenweb.com/glossary/

California State University Bio. Web. A comprehensive list of searchable sites of interest to botanists.http://arnica.csustan.edu/site.asp

CalPhotos: Plants. Over 20,000 photos of plants. A comprehensive database on the flora of California. Produced by the U. California Berkeley Digital Library Project. Very well done!http://elib.cs.berkeley.edu/photos/flora/

Missouri Botanical Garden Site’s Other Sources of Information. An extensive list of other sites.http://www.mobot.org/MOBOT/otherwww.html

Botany Online: The History of a Science.http://ostracon.biologie.uni-kl.de/b_online/e01/01.htm

Flowering Plants, Image Gallery. Bookmark this site: it links to pages on everything from floral structure to thorns. Great photographs. Based on the flora of Texas.http://www.csdl.tamu.edu/FLORA/tfp/tfphome1.html