Notes
on the Web - Unit Two - Part 2
Diversity of Life,
Taxonomy, Classification, and Phylogeny
Bruce G. Stewart
General
Objectives and Study Guide
Your
objectives for these Notes on the Web and associated readings and exercises
are:
- To state the range
for number of species estimated to exist on Earth today and the approximate
number of extant (living) species named already in scientific literature;
- To name, describe,
characterize, and give examples of each of the five kingdoms of life;
- To define taxonomy and understand its importance
in the study of life;
- To list and define each major hierarchal category
in the modern Linnean system of classification of life;
- To describe the meaning and use of binomial
nomenclature and identify common sources of names;
- To write scientific names in proper style and
state the reason for that style;
- To define phylogeny and understand its purpose
in the study of life;
- To define cladistics and understand its function
in the study of life;
- To know common terms and facts that relate to
diversity, taxonomy, classification and phylogeny;
- To know specific terms important in cladistics
and describe their role in the construction of cladograms.
Related
Textbook Readings:
- For General Biology (BIO 1114) Class only– Johnson
and Losos (2008) Chapter 18
- For General Zoology (ZOO 1114) Class only –
Chapter 10 (Hickman, Roberts, Larson, and I'Anson 2004)
Diversity
of Life on Earth Today
Estimates for the number of species existing on Earth in present times range
from 5 million to 30 million! The fossil record shows clearly that this wonderful
diversity of life evolved over the eons and that extant species (those living
today) are descendants of a great historical pattern of evolution. All living
things share many characteristics, while distinctive differences also exist
among the various groups that are adapted to take advantages to different habitats
and resources. To make sense of the vast array of living forms, we must classify
them in categories that take into account the similarities and differences that
demonstrate their relationships to one another. Table 2.2-1 below summarizes
the broad kingdom categories of a common classification system used in biology.
Know the five kingdoms of life and their characteristics from this table.
| TABLE
2.2-1. Kingdoms of Life and Their General Characteristics |
| Kingdom |
Types
of Organisms |
Some
General Characteristics |
| Monera |
Bacteria
and Cyanobacteria (also known as blue-green algae) |
Single-celled
or colonial prokaryotes; some (cyanobacteria) can photosynthesize: others
absorb their nutrients |
| Protista |
Protozoans
such as amoebas, green algae, and other single-celled or colonial protozoans
and algae |
Single-celled
or colonial eukaryotes; some (those with chloroplasts) can photosynthesize;
others capture their food |
| Fungi |
Molds,
Mildews, and Mushrooms |
Multicellular
(often complex) eukaryotic organisms) that may appear plant-like but cannot
photosynthesize; they absorb their nutrients |
| Plantae |
Green
Plants |
Multicellular
(often complex) eukaryotic organisms that have chloroplasts and can photosynthesize |
| Animalia |
Animals |
Multicellular
(often complex) eukaryotic organisms that capture and ingest their food;
cannot photosynthesize; often very mobile creatures |
Taxonomy
|
Taxonomy. Study of the principles
of scientific classification; systematic ordering and naming of organisms.
(Hickman, et al. 2004) |
Who
can make sense of things with no name? Who can arrange millions of things
in some sensible fashion? Even if they have names, the task of making sense of
millions of things is almost overwhelming. Imagine going to an automotive parts
store to get a single part for your vehicle. Combined there are literally 10's
of thousands of models, years, makes, and other variations in manufacture of
automobiles. Then consider the number of unique parts for each vehicle type. The
key to a functional automotive parts business is knowing part names, knowing how
to classify them, and know how to organize them in a way that parts can be
inventoried and located for sale. Thus, I can go to the automotive parts store
and easily obtain a specific "fuel filter" for a "1991"
"Toyota" "four-wheel drive pickup" with a "22R
four-cylinder" " "fuel injection" engine!
The
world of biology is far more diverse and complex than our entire automotive
industry. There are a conservatively estimated 12.5 million species on Earth
today (Cox 1999)! How are we to make sense of this bewildering array of
diversity? How are we going to even name them? Well, the problem has been
tackled. Aristotle (384-322BC) tried and succeeded in making some sense of the
some 500 kinds of living things he knew. Others followed.
However, it wasn't until the 1700's that the naming and classification
system used in general outline today came into being. Carolus Linnaeus
(1707-1778), a Swedish botanist, published his classification system in 1758 in
a book titled Systema Naturae. Later in the 10th edition of
his famous work, Linnaeus refined a very special way of naming species. This
method is called binomial nomenclature, meaning a "two name"
"naming system." In
this system, for example, you belong to the species Homo sapiens. Let's
show the categories (called taxa) that modern taxonomists use to show the
position of the human species in the living world.
|
Kingdom |
Animalia |
| |
Phylum |
Chordata |
| |
Class
|
Mammalia |
| |
Order |
Primates |
| |
Family
|
Homidae |
| |
Genus
|
Homo |
| |
Species
|
Homo sapiens |
Knowing the characteristics of
each of these taxa (singular = taxon) we can easily understand our relationship
to other species. For example, we are living things in the Kingdom Animalia
and therefore are animals. Recall from earlier studies that our kingdom is one
of five kingdoms of life. We are in the Phylum Chordata and therefore have a
dorsal hollow nerve cord, notochord, pharyngeal slits or pouches, and a variety
of other features in common with such groups as reptiles, birds, fishes, mammals,
and amphibians. There are over 30 other animal phyla! We are in the Class Mammalia,
and therefore have hair, mammary glands, endothermy (generate our own body heat),
four-chambered heart, and other characteristics we share with all mammals. There
are 20 orders in the Class Mammalia, but we are in the Order Primates. The order
Primates composes a wonderful group of species who, amongst other things, share
the presence of nails, a clavicle, orbits encircled with bone, enlarged cerebrum,
opposable innermost digit of at least one pair of limbs, pendulous penis, testes
in scrotum, two pectoral mammary glands. If you would like to read more on the
Order Primates, try the following link:
When we get down to the Family Homidae, we are
dealing with a group of genera (plural for genus) that are very similar. For
example, hominids are bipedal (can walk erect on two feet) and they show
advanced ability for tool use. Genera
in the Family Homidae include Australopithecus, Ardipithicus, Paranthropus, and
Homo. We belong to the Genus Homo. Members of our own genus are
extremely similar indeed. So similar, in fact, that we would surely recognize
these species as being "human."
We belong to the species Homo sapiens, however, two other species
known from the fossil record include Homo habilis and Homo erectus.
One of the great tasks in biology is simply to
name and classify all organisms. Please realize that this is a never ending
project. Experts estimate that there may be as many as 5-30 million species on
Earth! Furthermore, as we learn more about the relationships of organisms
already known, our classification changes to reflect this new knowledge. Armed
with more knowledge, biologists have also constructed subdivisions of the basic
seven taxonomic categories to reflect our greater understanding. For example,
Phyla (plural for Phylum) are subdivided into Subphyla. Classes are subdivided
in to Subclasses, and so on. Now lets look at an interesting bit of information
about the meaning of species names.
Species names are binomial (two names) and should
never ever be written as a single word. The first part of the species
name is the genus and the second part is called the specific epithet. The words
are "Latinized" and are uniformly accepted around the world. That is
part of the genius in Linnaeus' system. That is, it is a system that can be used
by all so as to allow clear communication amongst biologists everywhere.
My father calls a Northern Cardinal a
"Redbird." I call it a Northern Cardinal. There is another
"Redbird" that lives in our area, the Summer Tanager. Which
"Redbird" are we talking about? For biologists, there is no doubt that
Cardinalis cardinalis is the Northern Cardinal and Piranga rubra
is the Summer Tanager. Biology must be precise so that no confusion or doubt
occurs just because we are not communicating clearly. Latinized standard
scientific names are absolutely necessary to accomplish this.
Beyond the purpose of having a unique binomial
name for each species, species names can have additional meanings. Here are a
few examples to illustrate.
| Species
|
Common Name |
Notes on Meaning |
|
Canis rufus |
Red
Wolf |
"rufus"
means reddish brown |
|
Lepus californicus |
Black-tailed
Jackrabbit |
"californicus"
refers to a geographic area where the species happens to be common
|
|
Strigiphilus garylarsoni
|
A species
of chewing louse that lives only on owls!
No common name. |
"garylarsoni"
stands for the great cartoonist, Gary Larson, whose syndicated comic
strip, The Far Side, often depicted intellectually stimulating animal
humor |
|
Coluber constrictor |
Racer
|
"constrictor"
refers to the prey killing behavior of this snake species |
| Brassierea
vivens |
None... it is one of thousands of species
of diatoms, a type of microscopic photosynthesizing single-celled protist. |
"Bassierea"
means "bra" and "vivens" means "living,"
thus the entire species name means literally "living bra!" See
the photographs below to see why! |
|
Clitoria mariana |
Butterfly
Pea (Click for image) |
"Clitoria"
means "clitoris," and was named by Carolus Linnaeus in 1753,
presumably after this human anatomical structure. The specific epithet
"mariana" is a bit of a mystery. Did Linnaeus name this small
blue lilac flower after an acquaintance? This was something reported
in botany class notes when I was in college in about 1973-4. However,
see my footnote for caution on this detail and a surprise reference
I found as I searched for the answer on the Internet! 1 |
 |
|
Electron
micrographs of Brassierea vivens. Left is external view of
"valve;" right is internal view of valve. Two valves compose
the "test" made of silica that encloses the actual living
cell which is not present in these specimens. Photographs above kindly
provided by Dr. Barbara M. Winsborough and are here used with her permission.
This species represented a new genus and species at the time of description!
(Hein and Winsborough 1999). |
Isaak (2006) has a very thorough and entertaining
site with volumes of examples of meanings and reasons for scientific names.
Please remember, however, that while there may be many meanings attached to
the naming of species, the most important single factor is that the combination
of genus and specific epithet must be unique. In zoology, the International
Commission for Zoological Nomenclature is the official body that helps maintain
consistency in naming animals. The International Commission for Botanical Nomenclature
does the same job for the plant kingdom.
Phylogeny
Taxonomic arrangements in biology ideally illustrate
the evolutionary relationships of living and fossil species. There are many
areas of evidence available to taxonomists to help them in there work. These
include morphology, physiology, behavior, molecular genetics, and many others.
Once the data have been gathered, mathematical techniques have become increasingly
important. One of the most important of these is cladistics. This technique
is discussed in your textbook and should be reviewed when you read your chapter
readings.
In a nutshell, cladistics is a method for REVEALING evolutionary
relationships. Since biological taxonomy seeks to reflect evolutionary relationships
(such as is described in your notes), cladistics aids in that effort. Fundamentally,
cladistics is a method that uses shared derived characters (called synapomorphies)
to unite taxa with common ancestry. For example, members of the Subphylum Vertebrate
(fishes, amphibians, reptiles, birds, mammals) all have a vertebral column.
They are placed in the same broad group (in this case a subphylum). Unique derived
characters called apomorphies then show groups on their own evolutionary branch.
For example, birds have epidermally-derived feathers that are not found in the
other vertebrates.
All of these things are relative. For example, WITHIN birds,
feathers represent a synapomorphy (shared derived character) that helps unite
all bird species. Other characters would be apomorphies that help distinguish
taxa with the bird class.
You should visit and study materials at two external links that
provide information on cladistics. The first gives a general overview of cladistics.
It is the American Museum of Natural History Cladistics Page found at the following
link:
The second site from the University of California Museum of
Paleontology has a more detailed description of cladistics, its methods and
terminology, and its implications. Here is the link:
The UCMP site has a glossary
that has all but one of the terms that I would like you to know (plus many more
you don't need to learn now). Here are the definition of the specific ones to
learn. These come from either the UCMP site, your textbook, or Mayden and Wiley
(1992)..
- Cladistics - a specific
method of determining ancestry, decendant taxa, and their phylogenetic relationships.
It seeks especially to determine the most likely evolutionary relationships.
- Cladogram - "Cladograms
are phylogentic trees with specific connotations of implied ancestry and with
a relative time axis. Thus, a cladogram is one kind of phylogenetic tree,
a common ancestry tree." "Some authors have preferred to distinguish
between a cladogram and a phylogenetic tree, while others do not..."
(Mayden and Wiley 1992)
- Apomorphy - a derived
character shared by an ancestral taxon and its decendants, but is not found
in other taxa. If two characters are considered "homologous" then
the apomophy is the one that has developed from the prior state.
- Synapomorphy - an apomorphy
share by more than one taxon, indicating a clade with monophyletic origins
- Pleisiomorphy - the "primitive"
condition of a character that later was modified (as an apomorphy) in a decendant.
- Character - "...
a feature of an organism that is heritable. By feature we mean any observable
part of, or attribute of, and organism." (Mayden and Wiley 1992)
- Derived Character - basically
the same as an apomorphy.
- Primitive Character -
basically the same as a pleisiomorphy
- Outgroup - "...
any group used in a cladistics analysis that is not included in the ingroup
under study." (Mayden and Wiley 1992)
- Ingroup - the group of
taxa under study to determine their evolutionary relationships following the
method of cladistics.
- Parsimony - choosing
the most probable path of evolution in an ingroup based on the fewest appearances
of new evolutionary novelties (apomophies) required.
- Phylogenetics - the study
of evolutionary relationships of species and other taxa, including construction
of relationships (cladograms), analysis of evolutionary transformations of
characters of organisms, and providing a basis for improved classification
systems.
- Monophyletic - is a group
that includes its most recent ancestor and all of its decendants. It is a
"natural taxon" that may be named according the the Rules of Nomenclature
(e.g. monitored by the International Commission on Zoological Nomenclature).
- Lineage - a series of
ancestral-decendant organisms
1.
Footnote on the origin and meaning of the specific epithet "mariana"
in the species name of the butterfly pea, Clitoria mariana.
Upon placing my class notes on the Internet in about 1998, I became increasingly
conscience of errors and accuracy in my class lecture materials. After all,
in live classes I could interject much more and offer direct verbal cautions,
clarifications, and corrections to my materials quite easily. However, converting
these notes to electronic media for the students on the web carried with it
a greater responsibility to confirm the detailed accuracy of the written content.
I am still working on this, and will likely be doing so until I retire. One
of the items that kept entering my mind was the origin of the species name,
Clitoria mariana. My college botany professor had given us one of those
taxonomic tidbits in lecture one day that I never forgot. "Clitoria"
meant "clitoris," and "mariana" was in reference to an "acquaintance"
of Carolus Linnaeus, the "Father of Taxonomy." So... when I began
organizing notes for my own teaching years later, I included this as an example
how species come to have their names. Then the doubt crept in. Was this REALLY
true? Was I perpetuating an error in fact? If so, it would not be the first
time I had discovered that some "common knowledge" turned out to be
without foundation. So I decided to search for some answers. Unfortunately (from
the library resource perspective only!), I am located in a very rural area and
teach at a small two-year where I do not have easy access to scientific database
services. So I began using Google and Google Scholar to search. I did find some
other sources that indicated either directly or implied that Linnaeus used the
genus "Clitoria" in reference to human anatomy (Isaak 2006,
Yanega 2007, Milius 2001, and Goldacre 2004). Isaak (2006) seemed to be the
the most thoroughly referenced site and Yanega (2007) seemed to be "scientific"
content, though I remain uncertain as to the degree of peer-review (if any)
either site may have received. Peer-review on the details of taxonomic meanings
mentioned in the others seemed rather unlikely. As for "mariana,"
there was mention of this being named after an acquaintance of Linnaeus in Goldacre
(2004) and Milius (2001). Thus, I need to bite the bullet and do a proper scientific
database search to find more answers. The search will have to continue.
Finally, here is a reason for great
caution in believing what you find on Internet. I found a blog (www.metafilter.com)
that had a thread dealing with how scientists can have a sense of humor. It
had mention of Clitoria mariana and its supposed meaning. It had a
link to a page that described this meaning and low and behold when I click on
it... it was my page! The blog writer wrote in reference to some other sites,
"If you are tempted to wonder what the Father of Taxonomy might have thought
of the irreverence of those last two collections, keep in mind that Linnaeus
himself named this plant "Clitoria Mariana" in honor of an 'acquaintance',
according to this page." (http://www.metafilter.com/33155/Are-you-an-Asinus-Petasatus-Then-youll-love-this)
"This page" was an earlier version of my very own Notes on the Web!
So in my own search for the confirmation of my answer to my taxonomic question,
I found at least one site with a reference to my own unconfirmed and questionable
answer! Later in this same blog, a poster noted that another page had "a
more prosaic explanation, that "the genus is thought to take its name from
kleio, to shut up, in reference to the habit these peas have of seeding long
before the flower drops off". But this was written in 1900, and may just
be a bit of Victorian prudery." Now, doesn't all of this make one want
to find the "true" meaning? Who was "Maryanne?" Or was "mariana"
even a reference to a person at all? And to add to the mystery, Isaak (2006)
listed "Murray Bruce" as the contributor on his information on "Clitoria."
I just hope this is not some strange reference to Bruce Stewart from
Murray State College!
Sources mentioned in footnotes::
Goldacre, Ben. 2004. Alternative medicine at NHS? IN Bad Science. http://www.badscience.net/2004/02/alternative-medicine-on-the-nhs
(accessed: 23 June 2008)
Isaak, Mark. 2006. Curiosities
of biological nomenclature. http://home.earthlink.net/~misaak/taxonomy.html#moreInfo
(accessed: 23 June 2008)
Milius, Susan. 2001. A fly
called Iyaiyai. IN Science News. http://findarticles.com/p/articles/mi_m1200/is_21_159/ai_75563131
May 26, 2001. (accessed: 23 June 2008)
Yanega, Doug. 2007. Doug's
Personal Page (with Curious Scientific Names). http://cache.ucr.edu/~heraty/yanega.html
(accessed: 23 June 2008)
Literature Cited
(In Progress)
Cox, George. 1996. Conservation Biology: Concepts and Applications, 2nd.
ed. McGraw-Hill Science/Engineering/Math. 384pp.
Hein, Michael K. and Barbara M. Winsborough. 1999. Brassierea
vivens Gen. ET SP. Nov., a new benthic marine diatom from the Bahamas.
Diatom Research 14(2): 273-283.
Isaak, Mark. 2006. Curiosities
of biological nomenclature. http://home.earthlink.net/~misaak/taxonomy.html#moreInfo
(accessed: 23 June 2008)
Mayden, Richard L. and E. O.
Wiley. 1992. The fundamentals of phylogenetic systematics, pp. 114-185 IN
Systematics, historical ecology, and North American freshwater fishes, Mayden,
R.C. Ed. Stanford University Press. Stanford, California.969pp.
Additional Resources
Definitions
of Apomorphy & Pleisiomorphy from the Peripitus Home Page
© 2007, 2008 Bruce
G. Stewart
