18. CLASSIFICATION: Taxonomy


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Students, you are required to read the textbook for the instructor to be able to teach the concepts the course encompasses. (From FOUNDATION SKILLS in the Biology Department Master Syllabus.) Do not just read these notes, to succeed in this class -- at least if you wish to have a high grade, you MUST use your textbook as a LEARNING TOOL! The textbook -- especially the figures, will help clarify things you did not understand in class or from reading the lecture notes.
MAIN TOPICS OUTLINE

18.1 GROUNDS FOR CLASSIFICATION
18.11 Cell types
18.12 All organisms are related
18.13 Reasons for classification

18.2 KINGDOMS AND DOMAINS

18.3 TAXONOMY

18.31 Binomial system of nomenclature

18.31.1 International Rules
18.31.2 Two names

18.32 Logical taxonomic groups

18.32.1 Viruses
18.32.2 Taxonomic groups & Taxonomic hierarchy
18.32.3 Dichotomous keys



LECTURE OBJECTIVES
1. Discuss grounds for classification.
2. Discuss reasons that biologists disagree about how many kingdoms of organisms exist.
3. Know and characterize (list several characteristics for) the five / six kingdoms
4. Explain Carl von Linné's contribution to the field of taxonomy.
5. List, in order, the categories (taxa) used in today's hierarchy of classification, and classify selected organisms -- including humans, using the system.
6. Recognize what constitutes a scientific species name
7. Explain the use of a dichotomous key.
8. Distinguish between classification, taxonomy, and phylogeny.
9. Define selected key terms


Key Terms:
def. Animalia: Taxonomic group including animals.
def. Archaea: One of the prokaryotic domains, in the domain classification system.
def. Binomial System: Assignment of two names to each organism, the first of which designates the genus and second of which is the specific epithet.
def. Class: A group of organisms of closely related orders.

def. Classification: Grouping and naming of objects into logical categories owing to their joint possession of attributes.
def. Dichotomous Key: Taxonomic tool used to help identify organisms.
def. Domain: The largest grouping (taxa) used in the 3 group classification of organisms, the three domains are Eubacteria (or just Bacteria), Archaea, and Eukarya.

def. Eukaryotic cell: A cell that possesses a nucleus and other organelles.
def. Endosymbiosis: A mutually beneficial interdependence between two species, one of
which resides permanently inside the other's body. [Compare with "symbiosis".]
def. Endosymbiotic Theory: A theory about the origin of the eukaryotic cell suggesting that
some organelles found in eukaryotic cells may have originated as free-living prokaryotes.
def. Bacteria: One of the prokaryotic domains, in the domain classification system.
def. Eukarya: The eukaryotic domain, in the domain classification system.
def. Evolution: Progressive change due to genetic adaptation of a population to its environment.
def. Family: A group of organisms of closely related genera.
def. Fungi: Taxonomic group including mushrooms and allies.
def. Genus name: In the binomial system of nomenclature, the first name in Latin -- always capitalized, given to a group of closely related species.
def. Genus: A group of organisms of closely related species.
def. Hierarchy: an arrangement in which larger groups include smaller groups, which include still smaller groups.
def. Kingdom: The largest grouping (taxa) used in the 5 or 6 group classification of organisms.
def. Monera: Taxonomic group including bacteria. Another classification system includes the Archaea and the Bacteria as domains for prokaryotic organisms. (See Domain below.)
def. Nomenclature: Language of biological classification (the language used in the science of taxonomy).
def. Order: A group of organisms of closely related families.
def. Phylogeny: Evolutionary history of a group of organisms.
def. Phylum: A group of organisms of closely related classes (pl. phyla).
def. Plantae: Taxonomic group including plants.
def. Prokaryotic cell: Cell lacking the organelles found in eukaryotic cells.
def. Protista: Taxonomic group including organisms that cannot be placed in any other kingdom.
def. Scientific species name: the unique two names given to a scientifically described organism, given to a group of organisms considered to be of the the same species -- the name being a binomial consisting of the genus name and the specific epithet.
def. Species: A group of organisms (population) that can interbreed under natural conditions to produce fertile offspring that are reproductively isolated from other organisms (valid for sexually reproducing organisms only).
def. Specific epithet: In the binomial system of nomenclature, the second name in Latin -- not capitalized, given to a group of organisms that are of the same species. (Some use "species" instead of "specific epithet".)
def. Systematics: Science that studies the diversity of life, encompasses taxonomy and phylogeny.
def. Taxa: The logical categories used in naming and classifying organisms in the classification hierarchy (sing. Taxon)
def. Taxonomist: A biologist that identifies and classifies organisms.
def. Taxonomy: Science that identifies and classifies (naming and grouping) organisms into logical categories.
def. Virus: A noncellular infectious agent, consisting of DNA or RNA coated with protein, which functions as an obligate intracellular parasite.






18.11


18.1 Grounds for Classification

def. Evolution: Progressive change due to genetic adaptation of a population to its environment.
def. Classification: Grouping and naming of objects into logical categories owing to their joint possession of attributes.
def. Taxa: The logical categories used in naming and classifying organisms in the classification hierarchy (sing. Taxon)
def. Taxonomy: Science that identifies and classifies (naming and grouping) organisms into logical categories.
def. Phylogeny: Evolutionary history of a group of organisms.
def. Systematics: Science that studies the diversity of life, encompasses taxonomy and phylogeny.
def. Taxonomist: A biologist that identifies and classifies organisms.


Classification is the grouping and naming of organisms (after the evolutionary relationships)

18.12


18.11 Cell types

def. Prokaryotic cell: Cell lacking the organelles found in eukaryotic cells.
def. Eukaryotic cell: A cell that possesses a nucleus and other organelles.
def. Endosymbiosis: A mutually beneficial interdependence between two species, one of
which resides permanently inside the other's body. [Compare with "symbiosis".]
def. Endosymbiotic Theory: A theory about the origin of the eukaryotic cell suggesting that
some organelles found in eukaryotic cells may have originated as free-living prokaryotes.

Bacteria (=Prokaryotic cell type) and Humans (=Eukaryotic cell type). Because bacteria are different from us, we can use antibiotics against many diseases caused by these organisms, without hurting our own body.

Streptomycin – combines with prokaryotic ribosomes and prevent them from
producing proteins. Does not hurt eukaryotic (our) ribosomes.
Penicillin – cell wall in eukaryotic cells: cellulose
cell wall in prokaryotic cells: not cellulose

18.13


18.12 All organisms are related

All present-day organisms evolved from “protocells” (see below), and are considered related (this is called “common descent”).

1. Molecules in the early atmosphere and early oceans formed prebionts
2. Prebionts are forerunners of protocells.
3. Protocells evolved into prokaryotes (Monera).
4. Some prokaryotic cells gave rise to eukaryotes (Protista).
5. Members of the Protista evolved into the other Kingdoms (Fungi, Plantae, and Animalia)


Similarities considered evidence of common descent:

1. DNA is the universal genetic material (different combinations – but same chemicals).
2. Protein is the structural chemical and the chemical of enzymes.
3. ATP is the source of energy.
4. Cells are the units of life.

18.2


18.13 Reasons for classification

-- to communicate information (language) -- NOMENCLATURE
-- to make order of all organisms on Earth (classify) -- TAXONOMY

def. Taxonomy: Science that identifies and classifies (naming and grouping) organisms into logical categories.
def. Nomenclature: Language of biological classification (the language used in the science of taxonomy).

Animation: Primate Phylogeny





18.3


18.2 Kingdoms and Domains

Biologists today debate whether living organisms on Earth should be classified into 5 or 6 major groups called Kingdoms, or into 3 major groups called Domains (which in turn is divided into kingdoms).

def. Kingdom: The largest grouping (taxa) used in the 5 or 6 group classification of organisms.
def. Taxa: The logical categories used in naming and classifying organisms (sing. Taxon)
def. Monera: Taxonomic group including bacteria. Another classification system includes the Archaea and the Bacteria as domains for prokaryotic organisms. (See Domain below.)
def. Protista: Taxonomic group including organisms that cannot be placed in any other kingdom.
def. Fungi: Taxonomic group including mushrooms and allies.
def. Plantae: Taxonomic group including plants.
def. Animalia: Taxonomic group including animals.
---
def. Domain: The largest grouping (taxa) used in the 3 group classification of organisms, the three domains are Eubacteria (or just Bacteria), Archaea, and Eukarya.
def. Bacteria: One of the prokaryotic domains, in the domain classification system.
def. Archaea: One of the prokaryotic domains, in the domain classification system.
def. Eukarya: The eukaryotic domain, in the domain classification system.

Here is a compromise of these two ideas used, classifying all living organisms into 6 kingdoms -- but not using domain. (Two kingdoms are prokaryotic -- Euacteria & Archaebacteria. Four kingdoms are eukaryotic, and would be in the Domain Eukarya -- Protista, Fungi, Plantae, & Animalia. The “Eukarya” is not a true taxon, but can be used as a convenient name to group the four eukaryotic kingdoms together.)


KINGDOM EUBACTERIA (-- former kingdom Monera)
KINGDOM ARCHAEBACTERIA (-- former kingdom Monera)
KINGDOM PROTISTA
KINGDOM FUNGI
KINGDOM PLANTAE
KINGDOM ANIMALIA





18.31


18.3 Taxonomy

def. Taxonomy: Science that identifies and classifies (naming and grouping) organisms into logical categories.
def. Taxa: The logical categories used in naming and classifying organisms in the classification hierarchy (sing. Taxon)


Aristotle: Greek philosopher, mid 300th B.C.,
the first person to attempt a logical classification system.
– divided plants into:
• trees
• shrubs
• herbs

Linné (Linnaeus): Swedish medical doctor and botanist
mid 1700’s.
1758 Systema Naturae (father of modern taxonomy)
(Carl von Linné vs. Carolus Linnaeus)

Linné came up with a classification system based on:

i. Binomial system of nomenclature (see 18.31.1) -- all organisms have two names in Latin
ii. Logical taxonomic groups (taxa) (see 18.31.2) -- all organisms placed into logical groups called taxa


18.31.1


18.31 Binomial system of nomenclature

18.31.2


18.31.1 International Rules

• Naming of organisms follows certain international rules.

For animals: International Code of Zoological Nomenclature.


1. Each described organism has a scientific name:

--two names in Latin (which are always in italics or underlined)
i. genus name (always capitalized)
ii. specific epithet (always written in lowercase)


2. Only one species can have a certain scientific name.


3. Names cannot be changed (unless there is compelling evidence to justify doing so).


18.32


18.31.2 Two names

def. Genus name: In the binomial system of nomenclature, the first name in Latin -- always capitalized, given to a group of closely related species.
def. Genus: A group of organisms of closely related species.
def. Specific epithet: In the binomial system of nomenclature, the second name in Latin -- not capitalized, given to a group of organisms that are of the same species. (Some use "species" instead of "specific epithet".)
def. Species: A group of organisms (population) that can interbreed under natural conditions to produce fertile offspring that are reproductively isolated from other organisms (valid for sexually reproducing organisms only).
def. Binomial System: Assignment of two names to each organism, the first of which designates the genus and second of which is the specific epithet.
def. Scientific species name: the unique two names given to a scientifically described organism, given to a group of organisms considered to be of the the same species -- the name being a binomial consisting of the genus name and the specific epithet.

A species name: ‹ a binomial (having two names: a genus name + a specific epithet)

1. Scientific species name for humans: Homo sapiens

2. Scientific species names for dogs, wolfs, and coyotes:


Canis familiaris Domestic dog
Canis lupus Wolf
Canis latrans Coyote


All three are in the genus "group" called Canis.
Canis -- genus name
familiaris -- specific epithet
Canis familiaris -- scientific species name

Animation: Primate Phylogeny

18.32.1


18.32 Logical taxonomic groups (taxa)

-- Organisms placed in logical groups.

def. Taxa: The logical categories used in naming and classifying organisms in the classification hierarchy (sing. Taxon)
def. Kingdom: The largest grouping (taxa) used in the 5 or 6 group classification of organisms.


18.32.2


18.32.1 Viruses

def. Virus: A noncellular infectious agent, consisting of DNA or RNA coated with protein, which functions as an obligate intracellular parasite.

• Where does viruses fit into the classification system? (Which kingdom?)

Monera, Protista, Fungi, Plantae, Animalia

Eubacteria, Archaebacteria
, Protista, Fungi, Plantae, Animalia


• A virus is a nucleic acid particle coated with protein.

-- Not capable of living by themselves (must be inside cells)
-- Most biologists consider them non-living
-- They are some of the smallest things known (usually need a electron microscope to see them)
-- Often host-specific: can only infect certain organisms, and only certain cells in the host
-- antibiotics do not work on viruses!!!

• Examples:
Herpes
Rabies
Common cold
Influenza ("flu")
Measles
Hepatitis
Mumps
HIV (AIDS)
West Nile
SARS
Bird flu

Animation: Primate Phylogeny

18.32.3


18.32.2 Taxonomic groups & Taxonomic hierarchy


Kingdoms are further subdivided into smaller units (taxa with a reduced number of species).

The smallest unit (= species) only contains ONE type of organism (1 species).

This arrangement is called a HIERARCHY -- an arrangement in which larger groups include smaller groups, which include still smaller groups.

def. Kingdom: Largest grouping used in the classification of organisms (a group of organisms of closely related phyla).
def. Phylum: A group of organisms of closely related classes (pl. phyla).
def. Class: A group of organisms of closely related orders.
def. Order: A group of organisms of closely related families.
def. Family: A group of organisms of closely related genera.
def. Genus (taxa): A group of organisms of closely related species.
def. Genus (name): In the binomial system of nomenclature, the first name in Latin -- always capitalized, given to a group of closely related species.
def. Species (taxa): A group of organisms that can interbreed under natural conditions to produce fertile offspring that are reproductively isolated from other organisms (valid for sexually reproducing organisms only).
def. Specific epithet: In the binomial system of nomenclature, the second name in Latin -- not capitalized, given to a group of organisms that are of the same species. (Some use "species" instead of "specific epithet".)
def. Scientific species (name): Unique name given to a scientifically described group of organisms considered to be of the the same species -- the name being a binomial consisting of the genus name and the specific epithet.
- - -
def. Hierarchy: an arrangement in which larger groups include smaller groups, which include still smaller groups.

Classification hierarchy below the Kingdom. Each kingdom encompasses these groups (taxa).

Kingdom
Phylum
Class
Order
Family
Genus
Species


“Kings Play Chess On Fine Grain Sand”

Example (portion of the Animal kingdom):

Animalia
Chordata
Mammalia
(Mammals)
Carnivora (Meat eaters)

Felidae
Felis
familiaris Domesticated cat (also Felis domesticus & Felis catus)
Panthera
tigris
leo

Canidae
Canis
familiaris Domesticated dog
lupus Wolf
Vulpes
vulpes Red fox

Rodentia (Rodents)

Muridae
Rattus
rattus Black rat
norvegicus Brown rat

Primates (Primates)
Hominidae
Homo
sapiens Human



e.g.: a brown rat is included in the genus Rattus, which is included in the family Muridae, which is included in the order Rodentia, which is included in the class Mammalia, which is included in the phylum Chordata, which is included in the kingdom Animalia.

or similar: Rio Grande City is included in Starr County, which is included in Texas, which is included in the United States, which is included in North America, which is included on planet Earth.



18.32.3 Dichotomous key

def. Dichotomous Key: Taxonomic tool used to help identify organisms.

• Taxonomic tool used to help identify organisms.
• To identify an organism the reader is given usually two choices (di choto), and after each choice a number or a name is given. (One follows the key until a name is reached.)


EXAMPLE OF A VERY SIMPLE DICHOTOMOUS KEY FOR ANIMALS


1a. Animal with wings ......................................................................................................................................... 2
1b. Animal without wings ................................................................... 4


2a. Wings covered with hair or feathers .......................................................................................................... 3
2 b. Wings covered with minute scales or not covered ......................................................................... Insect


3a. Wings covered with hair ........................................................................................................................... Bat
3 b. Wings covered with feathers ................................................................................................................... Bird

4a. Animal with .... ......................................................................................................................................... 5
4b. Animal with .... ......................................................................................................................................... 6

Cont...............



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