Naming and Classifying Organisms
A. Taxonomy
1. Taxonomy is the branch of biology concerned with identifying and naming organisms.
a. Naming and identifying organisms began with the Greeks and Romans.
b. Much later, John Ray, a British naturalist, argued that each organism should have a set name.
B. Assigning a Two-Part Name
1. The number of known organisms expanded greatly in the mid-eighteenth century due to European travel.
2. Swedish naturalist Carolus Linnaeus (1701-1778) developed binomial system to name species.
3. A binomial system of nomenclature names organisms using a two-part Latin name.
a. The first part is the genus; many species can be assigned to the same genus if closely related.
b. The second part is the specific epithet and usually provides something descriptive about the organism.
c. A scientific name consists of both genus and specific epithet (e.g., Lilium/buibiferum and Lilium canadense).
d. Both names must be italicized or underlined, and the first letter of only the genus name is capitalized.
4. Common names vary with different languages, lump many species under one name or have various names for the same species, and the same name may refer to different organisms in different regions.
5. The job of naming is unfinished.
a. There are estimated to be between 3 and 20 million species living on earth.
b. We have currently named one million species of animals and a half million plant species.
c. Some groups, such as birds, are nearly all known; some insect groups are mostly unknown.
C. What Is a Species?
1. Linnaeus considered each species to have a unique structure that made it distinct.
a. Distinguishing species on structure can be a problem because variations occur among members.
b. In addition, males and females may have different form, as well as juveniles and adults.
(Fig. 28.3)
2. The biological definition of a species states a species can interbreed and share the same gene pool.
a. Distinguishing species on the basis of reproductive isolation can also be a problem.
b. Some species do not reproduce sexually.
c. Some species hybridize.
d. Reproductive isolation can be difficult to observe.
3. When a species has a wide geographic range, variant types may tend to interbreed where they overlap; these populations may be named as subspecies.
a. The rat snakes Elaphe obsoleta obsoleta and Elaphe obsoleta bairdi are subspecies of Elaphe obsoleta.
b. Including the subspecies makes this a trinomial, or three-part, name.
4. In this chapter, a classification approach is taken to the definition of species.
a. Classification establishes categories to assign species on the basis of their relationship to other species.
b. Species is a taxonomic category below the rank of genus.
c. Species share a more recent common ancestor with species in same genus than with those in other taxa.
d. Taxa are groups of organisms in a classification category; Rosa or Felis are taxa in the category genus.
e. A common ancestor is an ancestor held in common by at least two lines of descent.
D. Now Let's Classify
1. Aristotle classified life into 14 groups (e.g., mammals, birds, etc.), and subdivided them by size.
2. Ray groups animals and plants according to how he thought they were related.
3. Linnaeus grouped plants simply by their flower parts; his categories were published in Systema Naturae.
4. Classification of an organism begins when it is named; then a species is assigned to a particular genus.
5. Today, we use a minimum of seven categories of classification: species, genus, family, order, class, phylum or division (plants), and kingdom.
a. The higher the category, the more inclusive it is.
b. Members of a kingdom share general characters; members of a species share quite specific characters.
c. Characters are any structural, chromosomal, or molecular feature that distinguishes groups.
d. Additional levels of classification can be added by adding super-, sub-, or infra- (e.g., suborder).
28.2. Constructing Phylogenetic Trees
A. Systematics is the study of the diversity of organisms using information from all levels of organization, from the cellular to the population level.
1. It includes the fields of taxonomy and classification.
2. Classification should reflect phylogeny, and one goal of systematics is to create phylogenetic trees.
a. Phylogeny is the evolutionary history of a group of organisms.
b. A phylogenetic tree is a branching diagram that indicates common ancestors and lines of descent.
c. A primitive character is a trait that is present in a common ancestor and all members of a group.
d. A derived character is present only in a specific lineage and is not present in the common ancestor.
e. Different lineages diverging from a common ancestor may have different derived characters.
3. All species placed in a group should have common ancestry; they should form a monophyletic group.
B. When Parts Are Similar
1. Homology is similarity in a structure due to having a common ancestry.
2. Homologous structures in different organisms are related to each other through common descent, but they may differ in their structure and function (e.g., the forelimbs of a horse and the wings of a bat).
3. Analogous structures have the same function but are not derived from the same organ in a common ancestor (e.g., the wings of an insect and the wings of a bat).
4. Homology helps indicate when species belong to a related group; however, convergent evolution and parallel evolution sometimes make it difficult to distinguish homologous from analogous structures.
5. Convergent evolution is acquisition of the same or similar traits in distantly related lines of descent, as a result of adaptation to similar environmental conditions.
a. Both euphorbia and cacti are adapted to a hot, dry environment and are both similar.
b. Details of flower structure indicate these two groups are not closely related.
6. Parallel evolution is acquisition of similar characters in related lineages without being present in a common ancestor.
C. When Genes Are Similar
1. When two lineages first diverge from a common ancestor, the genes and proteins are nearly identical.
2. Each lineage accumulates changes over time.
3. Many changes are neutral and accumulate at a fairly constant rate; such changes can be used as a kind of molecular clock to indicate evolutionary time.
4. Immunological techniques can roughly judge the similarity of two species; the strength of the antibody reaction reveals the relatedness of the species.
5. DNA hybridization separates the DNA strands of two species and combines the strands; the more closely related the two species, the more the DNA strands stick together.
6. Panda evolution
a. Chinese giant panda resembled a bear, has a false thumb, but its bones and teeth resembled a raccoon.
b. The red panda has similar features but lacks the false thumb.
c. Results of DNA hybridization suggest the giant panda diverged from the bear lineage and the red panda diverged from the raccoon lineage
7. Chimpanzees and humans
a. DNA hybridization shows chimpanzees closer to humans than to other apes.
b. Yet humans are kept in a separate family and chimpanzees are with the ape family.
c. However, DNA differences do not reflect adaptational differences that are real and important.
8. DNA studies are of limited usefulness if DNA differences are not relative to important characters.
D. When Fossils Are Available
1. The fossil record is often incomplete because soft-bodied organisms do not fossilize well, most organisms decay and the chances of becoming a fossil are low, fossils must survive powerful geological forces and be exposed where someone will find them.
2. Because fossils can be dated, available fossils can establish the age of a species.
3. If the fossil record is complete enough, a lineage can sometimes be traced through time.
4. However, fossils cannot determine if a feature is primitive or derived.
E. Who Constructs Phylogenetic Trees
1. The traditional school stresses common ancestry and the degree of structural difference among divergent groups in order to construct phylogenetic trees.
a. The traditional school athe tenet that mammals and birds evolved from reptilian ancestors, even though the reptile group is monophyletic---it does not include all groups from all ancestors.
b. But the reptile group is no longer monophyletic---it does not include all groups from all ancestors.
2. The cladistic school analyzes primitive and derived characters and constructs cladograms on the basis of shared derived characters.
a. A cladogram is a diagram showing relationships among species based on shared, derived characters.
b. To cladists, the traditional method of determining phylogeny is arbitrary.
c. In the bird example, birds are more closely related to dinosaurs and crocodiles than they are different.
d. Cladists would not use "reptiles" because it does not include all organisms derived from reptiles.
e. A cladogram is built based on shared characteristics; but they must use judgment gathering this data.
f. A cladogram is not a phylogenetic tree.
g. Cladists are guided by principle of parsimony---the minimum number of assumptions is most logical.
h. This approach is vulnerable if convergent evolution produces what appears to be common ancestry.
i. Reliability of cladograms is dependent on knowledge and skill of particular investigator gathering data.
3. The numerical phenetic school clusters species on the basis of the number of shared similarities, regardless of whether they might be convergent, parallel, or depend on one another.
a. Systematists of this school do not believe that a classification that actually reflects phylogeny can be constructed; it is better to rely strictly on a method that does away with personal prejudices.
b. Results of their analysis are depicted in a phenogram.
c. Phenograms vary for same group of organisms, depending on how the data are collected and handled.
28.3. Deciding the Number of Kingdom
A. Naming the Kingdoms
1. Early biologists recognized two kingdoms: animals (kingdom Animalia) and plants (kingdom Plantae).
2. After the microscope revealed many unicellular animals that were not plantlike or animal-like, Ernst Haeckel proposed the kingdom Protista.
3. Haeckel originally placed bacteria and cyanobacteria in Monera since they lacked a nucleus.
4. R. H. Whittaker suggested a five kingdom system that is based on cell type, reproduction, and motility:
a. Members of Monera lack a true nucleus, are unicellular, obtain organic molecules by absorption or photosynthesis, and reproduce asexually; includes bacteria and cyanobacteria.
b. Members of Protista are eukaryotic, unicellular, or multicellular, organisms that obtain organic molecules by absorption, ingestion, or photosynthesis; includes algae, protozoa, water and slime molds.
c. The Plantae are eukaryotic, multicellular organisms obtaining organic molecules by photosynthesis, are nonmotile, and reproduce asexually (i.e., vegetative reproduction) or sexually; it includes plants.
d. Members of the kingdom Animalia are eukaryotic, multicellular organisms that obtain their organic molecules by ingestion, are generally motile, and reproduce asexually and sexually; includes animals.
e. Members of the Fungi are eukaryotic, predominantly multicellular organisms that obtain their organic molecules by secreting digestive enzymes into their environment and absorbing organic nutrients, are nonmotile, and reproduce both asexually (i.e., budding) and sexually; mushrooms and molds.
5. Three domains have been suggested
a. DNA and ribosomal RNA sequencing suggests that the Archaea (formerly called archaebacteria) should not be considered bacteria.
b. Three domains are now recognized. They are Bacteria, Archaea, and Eukarya.