Chapter Outline

1. Systematic Biology
1. Systematic biology (systematics) is the study of understanding the evolutionary history of life on Earth.
2. Systematic biology uses traits to infer the evolutionary relationships among organisms.

A.    The Field of Taxonomy

1. Taxonomy is the branch of biology concerned with identifying, naming, and classifying organisms.
2. A taxon is a group containing an organism or group of organisms that exhibit a set of shared traits.
3. Classification is the process of naming and assigning organisms or groups of organisms to a taxon.
4. The aim of taxonomists is to classify all living things on earth.
5. Early taxonomists relied on physical characteristics to classify organisms.
6. Today taxonomists classify organisms into natural groups based on their evolutionary history by constructing a phylogeny.

B.     Linnean Taxonomy
1.     Carolus Linnaeus (1707–1778) developed binomial system to name species.
2.     Binomial nomenclature names organisms using a two-part Latin name.
a.     The first part is the genus; closely related species are assigned to the same genus.
b.     The second part is the specific epithet, which refers to one species within that genus.
i.      It usually provides something descriptive about an organism.
c.     A scientific name consists of both genus (capitalized) and specific epithet (lower-case; e.g., Lilium buibiferum and Lilium canadense).
d.     Both names are italicized (when typed) or underlined (when written by hand).
e.     The genus can be abbreviated when used with a specific epithet if the full name was previously given.
3.     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.
C.     Linnaean Classification Hierarchy
1.     Aristotle classified life into 14 groups (e.g., mammals, birds, etc.), and subdivided them by size.
2.     Ray grouped animals and plants according to how he thought they were related.
3.     Linnaeus grouped plants by flower parts; his categories were published in Systema Naturae in 1735
4.     Today, taxonomists use seven categories of classification: species, genus, family, order, class, phylum, and kingdom.
a.     A higher category, the domain, has recently been added to these seven categories.
b.     The higher the category, the more inclusive it is.
c.     Members of a domain share general characters; members of a species share quite specific characters.
d.     The classification hierarchy is useful because it organizes the diversity of life.
e.     As new information is discovered, the classification hierarchy may change.
5.     Although Linnaeus set the standard for classification in a hierarchical system, there were no set rules for classifying organisms.
a.     The International Code of Zoological Nomenclature (ICZN) was accepted in 1961 as the universal guide for naming taxonomic groups.

1. The Three-Domain System
1. A five-kingdom system was established in 1969 by R. H. Whittaker and consisted of the kingdoms: Monera, Protista, Fungi, Plantae, and Animalia.
2. Organisms were classified according to:

i.      Type of cell (prokaryotic or eukaryotic)
ii.     Complexity (unicellular or Multicellular)
iii.    Type of nutrition

1. Defining the Domains
2. In the 1970s Carl Woese and colleagues discovered that there were two groups of prokaryotic organisms and their rRNA sequence was so different from each other that these prokaryotic organisms should be classified in separate domains.
1. Prokaryotic organisms are placed in the domain Bacteria and domain Archaea.
2. Eukaryotic organisms are placed in the domain Eukarya
3. Domain Bacteria
4.   The bacteria are prokaryotic unicellular organisms that reproduce asexually.
5. Cyanobacteria are large photosynthetic prokaryotes.
6. Most bacteria are heterotrophic.
7. Bacteria are important in ecosystems because they break down organic remains, thereby keeping chemical cycling going.
8. Some bacteria are parasitic and cause disease.
9. Domain Archaea
10. Like bacteria, archaea are prokaryotic unicellular organisms that reproduce asexually.
11. The archaea live in extreme environments: methanogens in anaerobic swamps, halophiles in salt lakes, and thermoacidophiles in hot acidic environments.
12. The archaea cell wall is diverse but not the same as the bacterial cell wall.
13. Domain Eukarya
14. Eukaryotes are unicellular or multicellular organisms, always with a membrane-bound nucleus.
15. Sexual reproduction is common; various types of life cycles are seen.
16. Protists and fungi are eukaryotes, as are plants and animals (these kingdoms will be studied in detail in later chapters in the text and in this instructor’s manual).

E.     DNA Bar Coding of Life (Nature of Science reading)
1.     The Consortium for the Barcode of Life (CBOL) believes that any scientist will be able to identify a species using a handheld scanner.
2.     According to this Consortium, there will be a database of DNA sequences, and this scanner would tap into the database and identify an organism.
3.     DNA barcoding could catalog biodiversity, identify crop pests, identify antivenom for snakebite victims, and identify illegal trade of endangered animals.
4.     In 2008, two seniors from a New York City high school did a project on the identification of fish sold in markets and sushi restaurants in Manhattan.
a.     Sixty fish samples were collected from four restaurants and 10 grocery stores.
b.     Two of the four restaurants, and six of the 10 grocery stores sold fish that were mislabeled.
c.     Most of the mislabeled fish were being sold as more expensive species.
19.3  Phylogeny
1.     Classification reflects phylogeny; one goal of systematics is to create phylogenetic trees.
2.     Phylogeny is the evolutionary history of a group of organisms.
A.    Interpreting a Phylogeny
1.     A phylogenetic tree indicates common ancestors and lines of descent or lineages.
2.     When a new character evolves, a new evolutionary path diverges from the old, and a new lineage is formed.
3.     Different lineages diverging from a common ancestor have ancestral traits—characteristics shared by the ancestor and the species in its lines of descent.
4.     A derived trait is present only in a specific line of descent.
a.     They define closer and closer evolutionary characteristics, and therefore provide a more detailed phylogeny.
5.     Determining whether a trait is a derived characteristic or an ancestral characteristic is relative to its location within a phylogeny.
6.     Because classification is hierarchical, it is possible to use classification categories to construct a phylogenetic tree.
B.     Cladistics
1.     Cladistics analyzes primitive and derived traits and constructs cladograms on the basis of shared derived traits.
2.     A cladogram is a diagram showing relationships among species based on shared, derived traits; a cladogram thus traces the evolutionary history of the group being studied.
a.     A clade is an evolutionary branch that includes a common ancestor and all its descendent species.
3.     Constructing a Cladogram
a.     First step: construct a table of derived traits of the taxa being compared.
b.     Any trait found in the outgroup as well as the ingroup is a shared ancestral trait.
c.     The ingroup exhibits the derived trait for which the evolutionary relationship is being determined.
5.     How to Judge a Cladogram

1. Cladists are guided by the principle of parsimony—the minimum number of assumptions is most logical.
2. The best cladogram is one in which the fewest number of shared derived traits are left unexplained or that minimizes the number of assumed evolutionary changes.
3. This approach is vulnerable if convergent evolution produces what appears to be common ancestry.

C.     Tracing Phylogeny

1. Traditionally, systematic biologists relied on morphological data to study evolutionary relationships, which can be misleading.
2. Fossil Traits
3. Because fossils can be dated, fossils can establish the age of a species.
4. It can be difficult to associate fossils with currently living groups; e.g., a new view of turtle fossils could place them closer to crocodiles.
5. The fossil record is often incomplete because soft-bodied organisms do not fossilize well.
6. Most organisms decay and the chances of becoming a fossil are low.
7. Morphological Traits
8. Homology is structural similarity that stems from having a common ancestor; homology helps indicate when species belong to a related group.
9. Homologous structures are related to each other through common descent but may differ in function (e.g., the forelimbs of a horse and the wings of a bat).
10. Convergent evolution is acquisition of similar traits in distantly related lines of descent as a result of adaptation to similar environmental conditions; convergentevolution may make it difficult to distinguish homologous from analogous structures.
11. Analogous structures have the same function but do not have a common ancestry (e.g., the wings of an insect and the wings of a bat).

        4.     Behavioral Traits 
a.     Since many different species may display some common behaviors, this may substantiate the morphological data that some species are related through evolution.
5.     Molecular Traits
a.     Speciation occurs when mutations bring about changes in base pair sequences of DNA.
b.     Each distinct lineage accumulates changes in DNA base pair sequences and amino acid sequences in proteins over time.
c.     Advances in analyzing nucleotide and amino acid sequences make abundant data available to researchers.
d.     Protein Comparisons
i.      Earlier studies used immunological reactions to antibodies, made by injecting a rabbit with cells of one species, to determine the relatedness of two species.
ii.     Amino acid sequences are now used to determine the differences in proteins between two species.

1. Cytochrome c is a protein found in all aerobic organisms; the amino acid differences in cytochrome c between chickens and humans is 13 but between chickens and ducks is only 3.

iii.    Since the number of universal proteins is limited, most new studies use RNA and DNA.
e.     Molecular Clocks
i.      Nucleic acid changes are not tied to adaptation; the fairly constant changes provide a molecular clock to construct a timeline of evolutionary history.
ii.     Comparison of mtDNA sequences equated a 5.1% nucleic acid difference among songbird species to 2.5 million years.
iii.    The fossil record can then be used to calibrate the clock and confirm the hypothesis drawn from molecular data.