A number of factors help biologists decide whether an organism belongs to a new species. In the case of Homo floresiensis, the new hominid presented a unique combination of primitive and more recently evolved (derived) features not found in any other taxon. Some of the important characteristics used to differentiate among hominids are: brain size (earlier hominids had brains with volumes around 400-450 cm3, while modern humans have brains averaging 1,300 cm3); jaw shape (during human evolution, jaws have become less elongated, with the development of more pronounced chins); and bipedal posture (whether or not they walked on two legs). Homo floresiensis presents a small brain volume, but has facial and dental features more similar to Homo erectus, the closest known relative to modern humans. In addition, Homo floresiensis appears to have walked on two legs.

The Family Hominidae contains humans, great apes and their extinct relatives (http://tolweb.org/tree?group=Hominidae). Members of this family also are referred to as "hominids." The Tribe Hominini consists of several, related genera (Homo, Ardipithecus Australopithecus and Paranthropus) with bipedal posture, among other shared, derived characteristics. Members of this tribe are called "hominins." Current evidence now points toward three species of the genus Homo: Homo sapiens (modern humans), Homo erectus and Homo floresiensis.

To understand how and why organisms function the way they do, and how they interact with one another, we must observe patterns in development and evolution. Think about the scope of the Life Science Content Standards: understanding the cell; molecular basis of heredity; biological evolution; interdependence of organisms, matter, and energy; organization in living systems; and behavior of organisms. Classification is a scientific approach to grouping organisms based on current knowledge gathered from all of these fields.

It is more important to understand how and why classification systems are organized than to memorize each individual level. Classification systems encompass a wide, dynamic body of knowledge that is being modified continually.

Classification systems attempt to solve the problem of providing meaningful groupings of organisms.  The Swedish scientist, Carolus von Linnaeus, is credited with introducing binomial nomenclature and hierarchical classification as an organized way of naming and describing organisms and their relationships to one another.  Binomial nomenclature refers to the use of a two-part name for each species (one name designating genus and one designating species).

Linnaeus described a hierarchical classification system using seven taxonomic categories, or taxa (Kingdom, Phylum, Class, Order, Family, Genus, Species).  Beginning with species, each category becomes progressively more comprehensive.  For example, while the leopard, tiger and domestic cat all belong to different genera, they are grouped together in the same family.

Taxonomy is the science of classification.  When taxonomic systems include hypothesized evolutionary relationships among groups, the field generally is referred to as Phylogenetics.  Systematics is a larger field involving classifying organisms based on their phylogenetic relationships.  Systematics can be thought of as the study of biological diversity and how that diversity evolved.  In a sense, Charles Darwin introduced systematics in his revolutionary work, The Origin of Species.  He wrote, "The natural system is founded on descent with modification; that the characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, and, in so far, all true classification is genealogical" (Darwin, 1859).

Early naturalists identified plants and animals by observable structural similarities and referred to organisms using long complicated phrases.  This was known as the "polynomial system."  In this system, a plant might be described by phrases of 12 or more words.  It is not surprising that polynomial names could become very complex and were often misinterpreted when translated from one language to another.

In the 1700s, Carolus von Linnaeus, sometimes referred to as the Father of Classification, described a binomial system, which was published in his early work, System Naturae (1735).  Although he created the two-word system as a short-cut for users of this work, the system was rapidly adopted as a manageable way of naming species.  
 
In the binomial nomenclature system, genus and species-just two names-replace the long string of words used in the polynomial system.  The meaning of words can differ from language to language and from country to country.  For example, in Great Britain, the word "buzzard" refers to an organism Americans call a hawk.  For this reason, scientific names are written in Latin to maintain a uniform system of naming across all languages.

In the binomial system, genus is always a noun, underlined (or italicized), and capitalized; species is a descriptive term, underlined (or italicized), and not capitalized.  Some examples of binomial names include: Quercus rubra (red oak), Panthera pardus (leopard), or Homo sapiens (human).

Carolus von Linnaeus created a hierarchical classification system using seven taxonomic categories, or taxa (Kingdom, Phylum, Class, Order, Family, Genus, Species).  These categories are based on shared physical characteristics, or phenotypes, within each group.  Beginning with kingdom, each successive level of classification becomes more and more specific.  Organisms within the same order have more in common with one another than organisms within the same class. For example, all species of bears are mammals, but not all mammals are bears.  A useful pneumonic tool to help students remember the hierarchical classification system is: "King Phillip Came Over For Green Soup," with the first letter of each word representing each category, beginning with kingdom and ending with species.

In the 18th Century, organisms were considered to belong to one of two kingdoms, Animalia or Plantae. As biologists gathered more information about the diverse forms of life on Earth, it became evident that the two-kingdom system did not accurately reflect relationships among different groups of organisms, and the number of kingdoms increased. In 1969, Robert Whittaker proposed a five-kingdom system consisting of monerans, protists, fungi, plants and animals. In the last few years, comparative studies of nucleotide sequences of genes coding for ribosomal RNA and other proteins have allowed biologists to recognize important distinctions between bacteria and archaebacteria. The graphic on this slide illustrates the phylogenetic relationships drawn from this information using a three-domain and a six-kingdom arrangement, compared to the traditional five kingdom system.

Evolutionary classification, or phylogenetics, creates classification that represents hypothesized relationships among groups of organisms.  Systematists use a combination of fossil records, comparative anatomy, cladistical analyses and molecular data to understand the patterns of relationships among organisms. 

The fossil record is an accumulation of all fossils found within layers of sedimentary rock and helps to reconstruct a geological time scale.  Fossils are the remnants or impressions of organisms that lived in the past.
 
Homologies are similarities among species attributed to the inheritance of a feature from a common ancestor.  Important information about common ancestry can be discovered by comparing different organisms' anatomical, embryological and molecular homologies.  A classic example of homologous structures is the comparison of the basic groups of bones in the forelimbs of different groups of vertebrates (whale, alligator, penguin and human).  Although each forelimb is adapted for a different use, the bones are formed in the same way during embryological development, suggesting descent from a common ancestor.
 
Cladistics is based on the idea that members of a group share a common evolutionary history and are more closely related to members within their group than to other organisms.  These groups are recognized as sharing unique, derived features not present in distant ancestors.  A cladogram is a branching diagram that illustrates hypothesized relationships based on shared, derived characteristics.

Comparative sequencing: Scientists also can compare DNA and RNA sequences among different organisms to unravel evolutionary relationships and common ancestry.  These sequences can be used in comparison studies to determine phylogenetic relationships that can not be compared between morphological or fossil data.  Ribosomal RNA, chloroplast DNA, and mitochondrial DNA have proven particularly useful in these kinds of studies.

Molecular clock studies compare sequences of macromolecules (proteins and nucleic acids) among species, assuming that these macromolecules evolve at constant rates throughout time, and for different lineages.  Changes in sequences (nucleotide or amino acid substitutions, or mutations) are used to develop ideas about the evolutionary divergence of species.  The molecular clock hypothesis has been a powerful technique for determining evolutionary events of the remote past for which the fossil record and other evidence is lacking or insufficient.  The reliability of this hypothesis is currently under debate in the scientific community.

Sometimes, biologists group organisms into categories that represent common ancestries, not just physical similarities.  Early naturalists used physical characteristics and later, fossil data, attempting to represent evolutionary relationships among organisms.  Today, modern classification systems use fossil data, physical characteristics and DNA/RNA information to draw increasingly more accurate branching diagrams.

Phylogenetic trees, or phylogenies, represent hypothesized evolutionary relationships among organisms and may include extinct as well as modern species. Cladograms are based only on characteristics observable in existing species. The branching patterns in a cladogram are defined by the presence of unique, evolving innovations (derived characteristics) shared by all members of the group.

Identification is the process of finding the named group to which an organism belongs.  Dichotomous keys are useful tools to help identify different organisms and usually are found in field guides.  Identification in the field is based on features that are observable to the eye; therefore, it is important to remember that a key is an identification tool and is not synonymous with phylogenetic diagrams, which communicate hypothesized evolutionary history.
Dichotomous keys are constructed of contrasting pairs of statements.  To use a dichotomous key, begin with the first pair of statements and follow the directions at the end of each statement until you reach the name of the organism you are trying to identify.  With each new organism, always start at the beginning of the key (1a and 1b).  The ability to use dichotomous keys is an important skill and should be incorporated into instruction throughout the year.
It is important to note that when constructing a dichotomous key, each pair of contrasting descriptions must deal with the same characteristic.  For example the margin of the leaf might be used for the first pair of descriptors, and the shape of the leaf might be used for another pair. An incorrect pair of statements might be: 
1a)  Is the leaf heart shaped?
1b)  Are the edges lobed

Viruses are extremely diverse. The International Committee on Taxonomy of Viruses (ICTV) has organized them into over 70 different families. Criteria used in classifying viruses include the type of nucleic acid that serves as the genetic material, the shape of the capsid, and whether or not the virus has a membranous envelope. 

The genetic material of viruses can be made up of either DNA or RNA. Almost all DNA viruses contain double-stranded DNA as their genome. The DNA can be arranged as linear or circular molecules. Most RNA viruses have single-stranded genomes, which can be found on one or more segments, depending on the virus. When the single RNA strand contains information that is immediately translatable (analogous to mRNA), the virus is categorized as a positive (+) strand RNA virus. RNA viruses that contain the complement of a (+) strand are referred to as negative (-) strand RNA viruses.

Capsids are made up of many copies of protein subunits, often consisting of only a single type of protein. The arrangements of subunits determines the symmetry and shape of the capsid. There are three main types of capsid structure: helical, polyhedral, and complex. For helical viruses, the subunits are assembled in a helix, and the viruses are rod-shaped. The subunits of polyhedral viruses are arranged into an icosahedron (a structure with 20 equilateral triangular faces). These viruses generally have a spherical structure. Complex viruses have capsid structures that do not fit into either of the other categories and are not well understood. Bacteriophages are an example of such a virus.

Some viruses contain an envelope consisting of a lipid bilayer that surrounds the capsid. Viruses acquire an envelope when they bud out through the membrane of a host cell. Virus proteins become inserted into the lipid bilayer and play an important role when viruses infect another host cell. Viruses that lack an envelope are known as naked viruses.