In the earliest studies of biodiversity

• classifications were based on subjective logic

• system was to order "like" organisms which reflected a "natural order" (kosmos)

• scientific names were long, cumbersome sentences that described the organism.

1735 - Swedish botanist Carl Linne (a.k.a. Linnaeus) published Systema naturae,outlining a new system of binomial nomenclature. It's still in use today.

In the Linnaean system, every scientific name consists of an organism's Genus and species, the names of which are always GREEK, LATIN or LATINIZED versions of other languages or terms.

Example: Oryctolagus cuniculus

Each species is nested in every taxonomic level above genus in ever more INCLUSIVE groups:

DOMAIN - Kingdom - Phylum - Class - Order - Family - Genus (plural = genera) - species
(Insert clever mnemonic device here)

In general, scientific names have a specific meaning, usually describing the species. For example, Eleutherodactylus planirostris, the Greenhouse Frog:

• eleutheros is Greek for...

• dactyl is Greek for...

• plani is Greek for...

• rostris is Greek for...

Many species are at least partially named after people, but these proper names, too, must be Latinized:

Example: Chilomeniscus savagei
• chilo is Greek for...

• meniscus is Greek for...

• And "savagei" is the Latinization of the last name of Dr. Jay Savage, eminent herpetologist (and professor emeritus at the University of Miami).

What is a Taxon?

For example, the name of the taxon containing all domestic dogs is Canis familiaris. The order to which all dogs belong (along with a host of other flesh-eating mammals with specialized cutting teeth called carnassials) is Carnivora.

2. The taxon's rank

For example, the taxon Mammalia is assigned the taxonomic rank of Class. The taxon's rank has no true biological significance. It serves only to help the biologist locate the taxon within the hierarchy.

The relative rank of a given organism within its larger and smaller groupings is more relevant than the rank itself, which is subject to change.

For example, it's important to know that all members of Felis are classified within the larger taxon "Carnivora," and that all carnivores are classified within the still larger taxon "Mammalia." It's less important to struggle to recall that "Carnivora" is an order and "Mammalia," is a class (especially since those ranks can change with new data).

Many institutions now use rankless system in publication, in which taxa are described only by their name, with rank being tacitly understood. An author using this system will write "Mammalia" rather than "Class Mammalia" to avoid confusion as the ranks shift and change along with new information.

3. The taxon's content

All the students in this class are members of the genus Homo and the species Homo sapiens. This is the biologically relevant aspect of the taxon. By grouping specific individuals within a single species, related species within a single genus, related genera within a single family and so on, the systematist tells us which organisms are believed to be most closely related to one another, in terms of common evolutionary ancestry.

The Levels of Taxonomy

• classification: the ordering of organisms into groups based on their relationships

• alpha taxonomy - the describing and naming of species
• beta taxonomy - arranging species into a system of higher classification (genus through Kingdom and Domain)
• gamma taxonomy - study of the biological aspects of species, such as intraspecific variation and the actual mechanisms of speciation.

Who Keeps Track of All This?

1930 - ICBN (...Botanical...) formed

1947 - ICBacterial Nomenclature formed

In any one system, no two species can have the same scientific name. However, sometimes there is overlap between systems, with animal and plant sharing the same genus name:

e.g. : Heliconius is a butterfly (note that genus name is masculine)

Heliconia is a plant (note that genus name is feminine)

• Masculine ending: -us
  
• Feminine ending: -a
  
• ...and there are many endings which are neither masculine nor feminine.

A Few Rules of Nomenclature

1. the three codes are independent of one another.
2. a taxon bears only one correct name
3. no two species or genera (within one code) may have the same name
4. name must be latin or latinized
5. correct name is based upon publication priority (whoever described something first gets to give it the name, and if two species are discovered to have the same name, the first one gets to keep it, and the later one has to be changed.)
6. For plant families and animal superfamilies, the name of the family or superfamily must be based on that of a type genus, the first genus ever described in a given family (plants) or superfamily (animals)

Examples:
The Pea Family is named Fabaceae because the very first genus of leguminous plants ever described was given the name Faba, by Linnaeus.)

The Daisy Family is named Asteraceae because the first genus described was Aster

The Practical Application of Taxonomy

Knowledge of classification at the alpha, beta and gamma levels can save you and the ecosystems around you.

A Parasite's Tale

Early 1900's - sporadic, localized outbreaks of malaria (caused by
• Plasmodium, a protozoan blood parasite, and transmitted by a vector species, female mosquitoes of the genus Anopheles) were believed to be caused by Anopheles maculipennis. Puzzling: This was a widespread species. Why were outbreaks so localized?

• Work by two systematists (Hackett in 1937 and Bates in 1940) revealed that "A. maculipennis" was actually several *sibling* species, each of which had a distinct ecology, diurnal periodicity and habitat.

• Knowing this, those in charge of eradication efforts were able to specifically target the responsible species and wipe out the problem.

Evil Fern Weevil

• 1920's - Hawaiian forest preserves' fern populations were severely threatened by the invasion of an exotic fern weevil (Syagrius fulvitarsis). No one knew where it was native, and it was highly reproductive and difficult to control.

• 1921 - systematist Pemberton identified a single museum specimen, labeled with locality, as Australian.

• The beetle's natural predators from Australia could then be determined and (after careful study) used as biological control.

Ecological Side Note...

Florida examples:
• Cajeput (Paperbark) tree (Melaleuca quinquenervia)
• Australian pine (Casuarina equisetifolia)
• Brazilian pepper(Schinus terebinthifolius)
  --all very invasive, pernicious "weed" species that out-compete native species and can eventually lead to native species extinction.

  They are also allelopathic--producing toxic compounds that are meant to deter growth of other competing plants nearby.
  (As we already know, this can be valuable to humans seeking bioactive compounds--but don't assume that a product labeled "natural" is safe. Those plants mean business.)

For more information on Exotic Infasive Plant Species in southern Florida, visit:

A taxon has dimensions in space (geographical range) and time (its evolutionary history).

Let's have a look at evolutionary relationships of apes.

• Gibbons (Hylobates spp.)
• Orangutans (Pongo pygmaeus)
• Gorillas (Gorilla gorilla)
• Chimpanzees (Pan troglodytes)
• Bonobos (Pan paniscus)
• Humans (Homo sapiens)

This phylogenetic tree (from Human Molecular Genetics - Evans, 2004) is based upon amino acid sequences in a protein known as ASPM, which is believed by some to be involved in the formation of the central nervous system (brain and spinal cord) in vertebrates.

• K_s = frequency of synonymous changes in the gene (mutations that don't change the amino acid sequence of the protein)
• K_a = frequency of nonsynonymous substitutions in the gene (mutations that do cause a change the amino acid sequence of the protein)

A high K_a/K_s ratio means that the number of amino acid changes in that lineage is greater than would be predicted by random chance. This suggests that the protein sequence has been under selective pressure, though no one knows for certain (yet) what ASPM does.

The more symplesiomorphies a taxon within your study group shares with the outgroup, the more likely it is that it has a recency of common descent with that outgroup, and may be more primitive with respect to the other members of the assemblage.

The more synapomorphies two groups exhibit, the more recent their common ancestor. For example, if the phylogenetic tree of the Great Apes above is correct, you can surmise that humans and chimpanzees exhibit more synapomorphies (shared, derived characters) than do humans and gorillas. Similarly, Gorillas, chimpanzees, and humans exhibit more synapomorphies (as a group) than do Gibbons and humans.

Any taxon's evolutionary history and phylogenetic relationships can be diagrammed with a phylogenetic tree such as this one showing the relationships among the Animalia.

You will construct phylogenetic trees in your Systematics Lab. Be sure to read and try it out before the lab.

Constructing Phylogenies That Reflect Common Ancestry

• Monophyletic taxon: includes only those taxa derived from a single common ancestor.

• Polyphyletic taxon: includes taxa derived from more than one common ancestor.
  

• Paraphyletic taxon: includes only some of the descendants of a common ancestor, but not all of them.

In some cases, true evolutionary relationships cannot be determined with the data available, or a group may be in the process of being classified. In this case, members of a group may be placed (hopefully temporarily!) into a FORM TAXON.

Form taxon: a taxon whose members are included in the group more on the basis of shared, known similarities in morphology, physiology, etc. than on known evolutionary relationships. (e.g., "Kingdom" Protista, "Kingdom" Monera, "Phylum" Deuteromycota)

THREE SCHOOLS OF THOUGHT IN EVOLUTIONARY BIOLOGY

Classical Evolutionary System

The Phenetic System

• a system of convenience, somewhat akin to the library's Dewey Decimal System.

• based on measurable, morphological characters, not evolutionary relationships

• all morphological features are considered equally important in this system (no characters are "weighted" with more significance)

• characters are chosen at random, to eliminate bias.

• classifications made on the basis of overall % of shared similarity.

• Problem: any rank higher than species is often polyphyletic, due to CONVERGENCE of morphological characters.

The Cladistic System

• devised by German biologist Willi Hennig and published in 1950.

  Four Tenets of Cladism:

  1. cladogenesis (speciation) is the only quantifiable feature of evolution.

  2. all taxa must be monophyletic

  3. all evolutionary relationships must be measured in terms of recency of common descent.

  4. the rank of a taxon is automatically determined by the age of the common ancestor.

  Phyla had all branched off by the pre-Cambrian

  Classes, by the Cambrian and Devonian

  Orders by the Carboniferous and Permian

  Families by the Triassic & Early Cretaceous

  Tribes by the Late Cretaceous and Oligocene

  Genera by the Miocene

  All cladogenesis now taking place is at the species level.
  (Let's think about this for a moment...)

In the Cladistic System:

• only derived characters are informative in determining evolutionary relationships.
  
• The more shared, derived characters two taxa exhibit, the more recent their common ancestry.
  
• degree of specialization after a branch point gives no further useful information about evolutionary relationships (or classification)

• Over time, an ancestral stem taxon gives rise to daughter (= sibling) taxa.
• The branching of a single, ancestral taxon into two new taxa is known as cladogenesis. (Look up the meaning of "cladogenesis" in your Word Root Dictionary.)
  
• Fossils are treated the same as extant taxa: a fossil organism can not be said to be ancestral to an extant taxon. It can be said ONLY that a particular fossil taxon shares a common ancestor with a particular extant taxon.

• The Cladist uses shared, derived characters to devise a phylogenetic tree that is (hoped to be) based on recency of descent from a common ancestor.
• Such a phylogenetic tree is called a CLADOGRAM.

• More than one cladogram may be consistent with the data. In this case the systematist chooses the most parsimonious (i.e., the simplest; the tree with the fewest steps, which is thus the simplest explanation of the relationships) to be the "working hypothesis."
• This doesn't mean that the cladist believes that evolution is always parsimonious. But until more data become available, the simplest explanation is the model of choice.

• organisms are ranked and classified SOLELY on the basis of recency of common ancestry.
  
• The time dimension of the phylogenetic tree is the most important; physical differentiation after cladogenesis is relatively unimportant.

Where Classical Evolutionary Taxonomy and Cladistics Part Ways...

In the Classical system, birds are accorded separate Class status, even though they share a most recent common ancestor with crocodilians and dinosaurs. The Classical Evolutionary Taxonomist would say that characters such as feathers (modified scales), homeothermy(the ability to maintain constant body temperature metabolically) and endothermy(the ability to produce body heat metabolically) make birds sufficiently different from other reptiles that they should be placed in their own class.

In the Cladistic system, birds are considered part of Reptilia because of their common ancestry with other reptiles. To give them separate status simply because of their specializations obfuscates true evolutionary relationships. To the Cladist:

• feathers are a synapomorphy that link all birds together, with respect to all other vertebrates (none of which have scales modified to form feathers).
• If one considers only birds, however, feathers become a symplesiomorphy shared by all birds. Their presence offers no further useful information in separating birds into smaller, less inclusive taxa.

A recent cladogram of terrestrial vertebrate relationships can be seen here, at the Tree of Life. And of special interest are the relationships between the vertebrates known as Amniota. (hey look! there's us!)

Be sure to read "Concept 25.4" in your text: Genes, Genomes and Genome evolution AND "Concept 25.5": Molecular Clock.