28.0 Introduction

1. Biological World Is Very Diverse
1. Differences Separate the Various Groups of Organisms fig 28.1
2. Life on Earth Varies from Bacteria to Whales to Trees

28.1 Biologists name organisms in a systematic way

1. The Classification of Organisms
1. Early Naming of Organisms
1. Necessary as a point of reference for scientific discussions
2. Genus (genera, pl.): Basic unit of grouping
3. Names written in, or given Latin form
4. Classification specialists called systematists (systematics) or taxonomists (taxonomy)

2. The Polynomial System
1. Additional descriptive terms added to genus names to designate a species
2. Polynomial name: String of Latin words and phrases
1. Extremely long and cumbersome
2. Lack of uniformity caused confusion

3. The Binomial System
1. Developed by Carl Linnaeus
2. Derived two-part naming system from polynomials
3. Two-part name called a binomial

4. A Closer Look at Linnaeus
1. Example comparing two oaks from North America fig 28.2
1. Quercus phellos described the thin-leaved, tooth-less willow oak
2. Quercus rubra named the leaf of the bristly, deeply lobed red oak

2. Considered polynomial the organism's true name

2. Species Names
1. Format of Naming
1. Species epithet is second part of binomial name
2. Is meaningless if used alone
3. Genus can be abbreviated: G. species

2. International Associations of Taxonomists Oversee Naming
1. Names established by rigid set of rules
1. Provide uniform means of communication
2. Reduce confusion as local names may describe different organisms fig 28.3

2. Provide constant point of reference throughout scientific world

3. The Taxonomic Hierarchy
1. Genera Grouped into Larger Classifications
1. A single family includes many related genera
1. Family Fagaceae: Oaks, beeches, chestnuts and others
2. Family Sciuridae: Tree squirrels, marmots and others fig 28.4

2. Certain features can be surmised from unit associations

2. Taxonomic System
1. Family, order, class, phylum, kingdom, domain fig 28.5
2. In plants, fungi and algae phylum also called division
3. Comparative hierarchal descriptions of various organisms tbl 28.1
1. Categories may include several or only one taxon
2. Taxon implies set of characteristics and group of organisms

4. Printing conventions
1. Genus capitalized, species not capitalized
2. Both genus and species italicized or underlined
3. All other taxonomic unit names capitalized, but no distinctive print style

4. What Is a Species?
1. Criteria Not Absolute
1. Individuals of one species may appear quite dissimilar
2. Capable of hybridizing with one another
3. Offspring may appear different from one another
4. Individuals from different species do not generally hybridize
5. Criteria apply for organisms that regularly outcross
6. Different characterizations for asexually reproducing organisms

2. Defining Species
1. Compare morphological features and ecology
2. Remain constant, do not normally interbreed

3. How Many Species Are There?
1. 1.4 million species currently named and described
1. Some groups well known: Flowering plants, vertebrate animals, butterflies
2. More than 90% of species in these groups already named

2. Other groups less well known only 5% of nematode, fungi, mite species recognized
3. Actual number of species estimated at 10 million

4. Most Species Live in the Tropics
1. 6 to 7 million in tropics alone
2. Only 400,000 tropical species now described
3. Estimates apply for eukaryotes only
4. Functionally impossible to estimate number of prokaryote species

28.2 Taxonomy is the science of classifying organisms

1. Evolutionary Taxonomy
1. Defining Taxonomy's Role in Biology
1. Linnaean approach of classifying and naming
2. Darwinian approach of tracing evolutionary history

2. Classifying by Morphological Similarity
1. Observations of characteristics to distinguish and name new species
2. Must make subjective judgement on which characteristics are more important
3. Numerical taxonomy (phenetics) applies numbers to evaluation of characteristics
1. Use as many characteristics as possible
2. No additional emphasis initially prescribed to any one character
3. Avoids confusion associated with parallel evolution
1. Analogous characteristics are similar characteristics of unrelated organisms
2. Homologous characteristics associated with common evolutionary descent

4. Subsequent applications assign weight (emphasis) to certain characteristics

3. Classifying by Evolutionary Relationships
1. Cladistic school of taxonomy at opposite end of spectrum from phenetic school
2. Consider only evolutionary relatedness, not morphological comparisons
3. Classifies organisms by historical order in which evolutionary branches arise
4. Use biochemical characteristics, DNA sequence divergence, along with morphology
5. Basic object of cladistics
1. Ascertain characteristics that indicate common ancestry
2. Construct hypotheses about group's ancestral condition and derived characters
3. Derived characters shared by all members of branch, but not existent before branch
4. Example: Vascular plant cladogram (evolutionary tree) fig 28.6

6. Construction of accurate cladograms requires correct interpretation of features
1. Cladistic approach seems most appropriate to analyze evolutionary history
2. Cladistics shows order of descent, not extent of divergence

4. Taxonomy Today
1. Utilizes information from phenetics and cladistics
2. Accounts for degree of differences and evolutionary history
3. Example of conflicts
1. Birds in own class, crocodiles grouped with reptiles
2. Crocodiles more closely related to birds, share derived features fig 28.7
3. Birds retain own class due to degree of divergence from common ancestor with crocodiles

28.3 All living organisms are grouped into one of a few major categories

1. The Kingdoms of Life
1. The Six Kingdoms of Life
1. Originally only two kingdoms: Animals and plants fig 28.8a
2. Kingdoms added through scientific discovery fig 28.8b
3. Most biologists now identify six kingdoms fig 28.8c
4. Four kingdoms are eukaryotic
1. Animalia and Plantae are mostly multicellular
2. Fungi contain multicellular forms and single-celled yeasts
3. Fundamental differences among multicellular kingdoms
1. Different morphology, motility and nutrition
2. Each kingdom evolved from different single-celled ancestor

5. Protists are unicellular
1. Arbitrary grouping
2. Include algae

6. Archaebacteria and Eubacteria contain prokaryotic organisms

2. Domains
1. Archaebacteria are very different from other organisms
2. Caused adoption of taxonomic level higher than kingdom fig 28.8d
1. Archaebacteria in one domain
2. Eubacteria is another domain
3. Eukaryotes in a third domain

2. Domain Archaea (Archaebacteria)
1. Ancient Group of Organisms
1. Early divergence from Eubacteria fig 28.9
2. Inhabit extreme habitats
3. Share key characteristics tbl 28.2
1. Cell walls lack peptidoglycans present in other bacteria
2. Possess unusual lipids, characteristic ribosomal RNA sequences
3. Some genes possess introns like eukaryotes

4. Divided into three groups

2. Methanogens
1. Obtain energy by using hydrogen gas to reduce carbon dioxide to methane gas
2. Evolved early in history of earth, pre-photosynthesis
3. Are strict anaerobes, readily poisoned by oxygen in air
4. Ten closely-related species
1. Live in swamps, marshes, animal intestines
2. Release 2 billion tons of methane per year

3. Extreme Thermophiles
1. Live in very hot places, temperatures from 60º to 80º C
2. Usually have metabolic systems based on sulfur
3. Examples
1. Sulfolobus of Yellowstone oxidize elemental sulfur to sulfuric acid
2. Inhabit 105º C water of deep-sea hydrothermal vents

4. Extreme Halophiles
1. Live in very salty places, salinity between 15 to 20%
2. Use red pigment bacteriorhodopsin in photosynthesis

3. Domain Bacteria (Eubacteria)
1. Are Most Abundant Organisms
1. More bacteria in one mouth than mammals living on earth
2. Tiny, unable to see with unaided eye
3. Play critical role in earth's ecology
1. Extract nitrogen from air for all organisms
2. Key involvement in cycling of carbon and sulfur
3. Do most of world's photosynthesis

2. Many Different Kinds of Bacteria
1. Evolutionary relationships not well understood
2. Comprise 12 to 15 major groups
3. Comparing rRNA sequences to reveal relationships

3. One "Tree Of Life" Presentation fig 28.10
1. Eubacteria at "root" of tree
2. Archaebacteria, eukaryotes more closely related to each other than to eubacteria
3. Archaebacteria and eubacteria are prokaryotes

4. Domain Eukarya (Eukaryotes)
1. Evolution of Eukaryotes
1. Only bacteria existed on earth for 2 billion years
2. First appeared 1.5 billion years ago

2. Three Largely Multicellular Kingdoms
1. Fungi, plants and animals are well-defined evolutionary groups
1. Each stems from different single-celled ancestor
2. Largely multicellular

2. Derived from ancestor classified as Protista

3. A Fourth Very Diverse Kingdom
1. Unicellular eukaryotes lumped together in Protista
1. Lacking rationale to put them with fungi, plants or animals
2. Have great biological significance

2. Characteristics of the six kingdoms tbl 28.3

4. Symbiosis and the Origins of Eukaryotes
1. All eukaryotes possess complex cellular organization
1. Extensive endomembrane system, divides cell into compartments
2. Some cellular components not derived from endomembrane system

2. Example: Energy-producing mitochondria
1. Approximate size of bacteria, contain DNA
2. DNA similar to DNA of purple sulfur bacteria
3. Are descendants of purple sulfur bacteria, incorporated in early eukaryotic history

3. Some protists acquired chloroplasts and are photosynthetic
1. Chloroplasts derived from symbiotic cyanobacteria
2. Defining characteristic of groups that possess them

4. Mitochondria and chloroplasts developed via endosymbiosis
1. Both contain own ribosomes, more similar to bacterial ribosomes
2. Manufacture own membranes
3. Divide independently of cell
4. Contain chromosomes similar to those found in bacteria

5. Other symbionts: Basal bodies, centrioles, flagella, cilia

5. Key Characteristics of Eukaryotes
1. Multicellularity
1. Unicellular body plan is very successful
1. Bacteria occur in nearly every habitat
2. Protists diverse in form and biochemistry

2. Multicellularity allows novel adaptations to environment
1. Distinct cell differentiation possible
2. Greater complexity of activities
3. Has arisen independently many times

3. True multicellularity
1. Occurs only in eukaryotes
2. Coordinates activities of individual cells
3. Bacteria and some protists may form colonial aggregates fig 28.11

4. Some protists exhibit simple multicellularity fig 28.12
1. Green algal protists were ancestors of plants
2. Fungi and animals arose from unicellular ancestors

5. Groups giving rise to these kingdoms still exist

2. Sexuality
1. Major characteristic of eukaryotes
2. Process is regular, results are predictable
3. Alternation between syngamy and meiosis
1. Syngamy: Produces cell with two sets of chromosomes
2. Meiosis: Produces cells with one set of chromosomes

4. Differs greatly from genetic exchange in bacteria
5. Cells of animals and plants are diploid during some part of life cycle
6. Few eukaryotes complete life cycle in haploid condition
7. Offspring of sexual eukaryotic organisms vary widely
1. Due to segregation during meiosis
2. Resulting from crossing over in meiosis
3. Provides raw material for evolution

8. Sexual organisms evolve rapidly in relation to demands of environment
9. Protist sexual reproduction
1. May only occur in times of stress
2. Many are haploid throughout entire life, an ancestral condition

3. Life Cycles fig 28.13
1. Zygotic meiosis
1. Zygote is the only diploid cell
2. Zygote immediately undergoes meiosis

2. Gametic meiosis
1. Gametes are only haploid cells
2. Exemplified by animals
3. Gametes fuse giving rise to a zygote

3. Sporic meiosis: Alternation of generation
1. Exhibited by plants
2. Alternates between multicellular haploid phase and multicellular diploid phase
3. Diploid form undergoes meiosis to produce haploid spores
4. Haploid spores give rise to haploid phase
5. Haploid form produces haploid gametes
6. Gametes fuse to produce diploid zygote

6. Viruses: A Special Case
1. Viruses Not Classified as Living Organisms
1. Do not satisfy basic criteria of life
2. Are acellular, not composed of cells
3. Do not carry out metabolism, photosynthesis, cellular respiration, fermentation

2. Present Special Classification Problem
1. Viruses not included in any kingdom
2. Simple construction: Bits of nucleic acid surrounded by protein coat
1. Capable of replication within a cell
2. Machinery of host cells directed to manufacture viral material fig 28.14

3. Are solely nucleic acid fragments derived from prokaryotes or eukaryotes
4. Infect organisms from all taxonomic groups fig 28.15