Download Unit 11: Classification (And REALLY quick survey of kingdoms

Taxonomy
Unit 11: Classification
(And REALLY quick survey of
kingdoms)
Honors Biology
• Branch of biology concerned with
identifying and naming organisms.
• Naming and identifying organisms began
with the Greeks and Romans.
• Middle ages, organisms were described
using long Latin descriptions.
• Much later, John Ray, a British naturalist
argued that each organism should have a
set name.
The Dichotomous Key:
•device for identifying an unknown
organism, set up as a sequence of
choices between two (sometimes more)
statements
– Couplets, which are based on
characteristics of the organism.
•By making the correct choice, the
name of the organism will be revealed.
A sample dichotomous key:
•couplets together
1a. Flower open with distinct petals .................................go to 2
1b. Flower neither open nor has distinct petals ......... Aquilegia
2a. Petals usually striped to tip; multiple filaments
project just outside of center ….....................................Clematis
2b. Petals faint or no striping; no filaments outside of
center………………………………....................................... go to 3
3a. Pollen held close to center.................................... Ranuculus
3b. Pollen on stamens away from center .....................Anemone
Constructing Keys
• Use constant characteristics
• Use measurements
• Make the choice a positive one - something
"is" instead of "is not".
• If possible, start the couplet with the same
word.
• If possible, start different couplets with
different words.
Using a Key
The Binomial System
• Always read both choices, even if the first
seems to be the logical one at first.
• Be sure you understand the meaning of
the terms involved. When measurements
are given, measure
• If the choice is not clear, for whatever
reason, try both divisions. If you end up
with two possible answers, read
descriptions of the two choices to help
you decide.
Linnaeus’s System of Classification
• Carolus Linnaeus (1701-1778) developed a binomial
system to name species.
• A binomial system of nomenclature names
organisms using a two-part Latin name.
– First part is the genus; closely related species are assigned
to the same genus.
– Second part is the specific epithet; it usually provides
something descriptive about an organism, its discoverer, or
where it was discovered (this part is also called the species
part of the name)
– A scientific name consists of both genus and specific
epithet (e.g., Lilium buibiferum and Lilium canadense).
– Both names are italicized if in print or underlined if
handwritten; the first letter of only the genus is capitalized.
– The genus can be abbreviated when used with a specific
epithet if the full name was given before.
Classification of Ursus arctos
Grizzly bear
Modern
biologists have
added Domain
above the level
of Kingdom
Kingdom
Phylum
Class
Order
Family
Genus
Species
•
•
•
•
•
•
•
King
Phillip
Came
Over
From
Germany
Singing
Black bear Giant
panda
Red fox Albert
squirrel
Coral
snake
Sea star
KINGDOM Animalia
PHYLUM Chordata
CLASS Mammalia
ORDER Carnivora
FAMILY Ursidae
GENUS Ursus
SPECIES Ursus arctos
Common names
•
•
•
•
vary with different languages
lump many species under one name
have various names for the same species
same name may refer to different
organisms in different regions.
What is a FROGMOUTH?
What is an elk?
•elk, name applied to several large members of the
deer family. It most properly designates the largest
member of the family, Alces alces, found in the
northern regions of Eurasia and North America. In
North America this animal is called moose. The
name elk is used in North America to designate a
different animal, the wapiti, closely related to the
red deer of Europe. The prehistoric Irish elk,
Megaceros giganteus, is still another species,
related to the fallow deer. It was found in Europe
and W Asia in Pleistocene times and had an 11-ft
(3.3-m) antler span, the largest of any deer.
Naming
• The job of naming is unfinished.
– 3 - 20 million species live on Earth.
– one million species of animals and a half
million plant species are named
– Some groups, such as birds, are nearly all
known; some insect groups, bacteria, and
protists are mostly unknown.
– As more molecular evidence is gathered,
entire phylogenetic tree branches must be
moved to reflect new information
What is a Fish?
• Starfish?
• Jellyfish?
• Crayfish?
What Is a Species?
• Linnaeus considered each species to have a unique
structure that made it distinct.
– Distinguishing species on structure can be a problem
because variations occur among members.
– Males and females may have different forms, as well
as juveniles and adults.
• The biological definition of a species states a species
can interbreed and share the same gene pool.
• Distinguishing species on the basis of reproductive
isolation can also be a problem
– Some species do not reproduce sexually.
– Some species hybridize.
– Reproductive isolation can be difficult to observe.
• When a species has a wide geographic
range, variant types may tend to
interbreed where they overlap; these
populations may be named as subspecies.
– The rat snakes Elaphe obsoleta obsoleta and
Elaphe obsoleta bairdi are subspecies of
Elaphe obsoleta.
– Including the subspecies makes this a
trinomial, or three-part, name.
From the standpoint of classification:
– categories are established to assign species on
the basis of their relationship to other species.
• Species is a taxonomic category below the
rank of genus.
– Species share a more recent common ancestor
with species in same genus than with those in
other taxa.
– A taxon is a group of organisms in a classification
category; Rosa or Felis are taxa at the genus
level.
– A common ancestor is valid if there are at least
two lines of common descent
Homology
• Homology is a character similarity due to
having a common ancestry.
• Homologous structures are related to each
other through common descent but may
differ in structure and function (e.g., the
forelimbs of a horse and the wings of a bat)
– 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).
– Homology helps indicate when species belong to
a related group.
Example
• Panda evolution
– Chinese giant panda resembles a bear, has
a false thumb, but bones and teeth
resembled a raccoon
– The red panda has similar features but
lacks the false thumb
– Results of DNA hybridization suggest the
giant panda diverged from the bear lineage
and the red panda diverged from the
raccoon lineage.
Classification Categories
• We use eight categories (taxons) for
classification: species, genus, family, order,
class, phylum (or division for plants),
kingdom, and domain
– The higher the category, the more inclusive it is.
– Members of a domain share general characters;
members of a species share specific characters.
• Characters are any structural, chromosomal, or
molecular feature that distinguishes groups.
– Additional levels of classification can be added by
adding super-, sub-, or infra- (e.g., suborder).
Molecular Data
• Speciation occurs when mutations bring about
changes in base pair sequences of DNA
• Each distinct lineage accumulates changes in
DNA base pair sequences and amino acid
sequences in proteins over time.
• Molecular changes are numerical and can
sometimes sort out relationships obscured by
convergence.
• Advances in analyzing nucleotide and amino
acid sequences make abundant data available
to researchers.
Cladistic Systematics
• Cladistics analyzes primitive and derived characters
and constructs cladograms on the basis of shared
derived characters
• Cladogram is a diagram showing relationships among
species based on shared, derived characters.
• Constructing a Cladogram
– First step is to construct a table of characters of
the taxa being compared.
– Homologies shared by certain lineages are shared
derived characters.
– A clade is an evolutionary branch that includes a
common ancestor and all its descendent species.
Some Definitions
• Classification reflects phylogeny; one goal of
systematics is to create phylogenetic trees.
– Systematics is the study of the diversity of organisms
using information from cellular to population levels
– Phylogeny is the evolutionary history of a group of
organisms.
– A phylogenetic tree indicates common ancestors and
lines of descent.
• A primitive character is a trait that is present in a
common ancestor and all members of a group
• An outgroup is a taxon that is outside the
group of interest; it is included for
comparison
• A derived character is present only in a
specific line of descent.
– Different lineages diverging from a common
ancestor may have different derived
characters
This simple cladogram shows
primitive / derived characters
• Each larger
circle
represents
a group of
primitive
characters;
the smaller
circle are
groups that
share a set
of derived
characters
Cladogram of Six
Kingdoms and Three
Domains
DOMAIN
ARCHAEA
DOMAIN
EUKARYA
Kingdoms
DOMAIN
BACTERIA
Eubacteria
Archaebacteria
Protista
Plantae
Fungi
Animalia
• Traditional
Classification is
based on structural
similarities, without
an attempt to find
genetic or
evolutionary
relationships.
Three-Domain System
• Cladistics, or
evolutionary
classification, bases
classification on derived
characters, such as the
molted skeleton and
segmentation found in
all crustaceans.
Cladistics attempts to
classify based on
evolutionary history.
The diagram produced
is a cladogram.
Domain Bacteria; Kingdom
Eubacteria
•
Unicellular, prokaryotic
• Cell walls
– Thick, rigid, contain peptidoglycan
• Autotrophic by photosythesis, or Heterotrophic
• Some require oxygen (aerobic); others are
killed by oxygen (anaerobic)
• Examples : Escherichia coli, Mycobacterium
•
tuberculosis, Salmonella enteridis
Domain Archaea : Kingdom
Archaebacteria
• Unicellular and prokaryotic
•
•
•
•
Cell walls without peptidoglycan
Autotroph or Heterotroph
Aerobic and anaerobic forms
Habitats
– live in extreme environments
– Arctic Ice, geysers, hot springs, brine (like
the Great Salt Lake), deep ocean volcanic
vents
• Sequencing of rRNA suggests all organisms
evolved along three distinct lineages: domains
Bacteria, Archaea, and Eukarya.
• Bacteria diverged first; Archaea and Eukarya are
more closely related than either is to bacteria.
• The archaea live in extreme environments:
– methanogens in anaerobic swamps
– halophiles in salt lakes
– thermoacidophiles in hot acidic environments
Domain Eukarya : Kingdom Protista
•
•
•
•
•
Eukaryotic organisms not classified as
plants, animals, or fungi
Most unicellular, some multicellular
Cell wall with cellulose
Autotrophic by photosynthesis, or
Heterotrophic
A miscellaneous category to put organisms
that do not fit elsewhere; most likely to be
revised in near future
Domain Eukarya : Kingdom Fungi
• Multicellular and Unicellular
• Cell walls of chitin
• Heterotrophic by absorption; secrete digestive
enzymes into food, then absorb usable
molecules
• Examples : Yeast, Molds, Mushrooms
Domain Eukarya : Kingdom Plantae
•
•
•
•
•
Domain Eukarya : Kingdom Animalia
•
•
•
•
Multicellular; mostly motile
No cell walls
Heterotrophic by ingestion
Examples: sponges, jellyfish, flatworms,
earthworms, mollusks, arthropods, starfish,
frogs
Multicellular and nonmotile
Cell walls made of cellulose
Photosynthetic autotrophs
Food stored as starch
Examples: mosses, ferns, conifers, flowering
plants
• STOP 2011
Domain Bacteria
In Depth
Bacteria and Viruses
• Bacteria occur in many shapes and sizes.
Most bacteria have one of three basic
shapes: rod-shaped, sphere-shaped, or
spiral-shaped.
• Rod-shaped bacteria are called bacilli
(singular, bacillus). An example of bacilli is
Escherichia coli.
• Sphere-shaped bacteria are called cocci
(singular, coccus). An example of cocci is
Micrococcus luteus.
Domain Bacteria, continued
Three Bacterial Cell Shapes
• Spiral shaped bacteria are called spirilla
(singular, spirillum). An example of spirilla
bacteria includes Spirillum volutans.
• Cocci that form chains similar to a string of
beads are called streptococci.
• Cocci that form clusters similar to a bunch
of grapes are called staphylococci.
Domain Bacteria, continued
Gram Staining
• Gram Stain
– Most species of bacteria are classified into two
categories based on the structure of their cell walls
as determined by a technique called the Gram
stain.
– Gram-positive bacteria have a thick layer of
peptidoglycan in their cell wall, and they appear
purple under a microscope after the Gram-staining
procedure.
– Gram-negative bacteria have a thin layer of
peptidoglycan in their cell wall, and they appear
reddish-pink under a microscope after the Gramstaining procedure.
Gram Stain
Click below to watch the Visual Concept.
Important Bacterial Groups
• Bacteria are also classified by their biochemical
properties and evolutionary relationships.
• Proteobacteria
Visual Concept
– Proteobacteria are one of the largest and most
diverse groups of bacteria, and contain several
subgroups that are extremely diverse.
– Members of this group include bacteria of the genus
Rhizobium, the genus Agrobacterium, and the
bacterium Escherichia coli.
Important Bacterial Groups,
continued
• Gram-Positive Bacteria
– Not all of the bacteria in this group are Gram-positive.
Biologists place a few species of Gram-negative
bacteria in this group because these species are
genetically similar to Gram-positive bacteria.
– Members of this group include the streptococcal
species, Clostridium botulinum, Bacillus anthracis,
and members of the genus Mycobacteria.
Important Bacterial Groups,
continued
Important Bacterial Groups,
continued
• Gram-Positive Bacteria, continued
– Actinomycetes are Gram-positive bacteria,
some species of which produce antibiotics.
• Antibiotics are chemicals that inhibit the
growth of or kill other bacteria.
Streptomycin and tetracycline are
examples of antibiotics that are used
medicinally.
Important Bacterial Groups,
continued
• Spirochetes
• Cyanobacteria
– Cyanobacteria use photosynthesis to get energy
from sunlight, and make carbohydrates from water
and carbon dioxide. During this process, they create
oxygen as a waste product.
– Once called blue-green algae, cyanobacteria are
now known to be bacteria because they lack a
membrane-bound nucleus and chloroplasts.
Important Bacterial Groups,
continued
• Chlamydia
– Gram-negative coccoid pathogens of the
group Chlamydia live only inside animal cells.
The cell walls of chlamydia do not have
peptidoglycan. Chlamydia trachomatis causes
the sexually transmitted infection called
chlamydia.
– Spirochetes are Gram-negative, spiral-shaped
bacteria that move by means of a corkscrew-like
rotation. Some are aerobic.
– Spirochetes can live freely or as pathogens.
Pathogenic spirochetes include Treponema pallidum,
the causative agent of syphilis, and Borrelia
burgdorferi, which causes Lyme
disease.
Structure and Function
• The major structures of a prokaryotic cell
include a cell wall, a cell membrane, cytoplasm,
ribosomes, and sometimes a capsule, pili,
endospores, and flagella.
• Cell Wall
– Most prokaryotes have a cell wall. Bacterial cell
walls contain peptidoglycan. Archaeal cell walls do
not have peptidoglycan; instead, some contain
pseudomurein, a compound made of unusual
lipids and amino acids.
Structure and Function,
continued
•
Structure and Function,
continued
DNA
• Cell Membrane and Cytoplasm
– Bacterial and archaeal cell membranes are
lipid bilayers that have proteins. However, the
lipids and proteins of archaeal cell walls differ
from those of bacterial cell walls.
– The cytoplasm is a semifluid solution that
contains ribosomes, DNA, small organic and
inorganic molecules, and ions.
Structure and Function,
continued
• Capsules and Pili
– Many bacteria have an outer covering of
polysaccharides called a capsule that
protects the cell against drying, pathogens, or
harsh chemicals.
– Pili are short, hairlike protein structures on
the surface of some bacteria that help
bacteria connect to each other and to
surfaces, such as those of a host cell.
•
Structure and Function,
Endospores continued
– Prokaryotic DNA is a single closed loop of
double-stranded DNA attached at one point to
the cell membrane.
– Along with a single main chromosome, some
prokaryotes have plasmids, which are small,
circular, self-replicating loops of doublestranded DNA.
Bacterial Capsule
Click below to watch the Visual Concept.
Visual Concept
Structure and Function,
continued
• Prokaryotic Movement
– Some Gram-positive bacteria can form a
thick-coated, resistant structure called an
endospore when environmental conditions
become harsh.
– Many prokaryotes have long flagella that
allow the prokaryotes to move toward food
sources or away from danger.
Structural Characteristics of a
Bacterial Cell
Parts of a Prokaryotic Cell
Click below to watch the Visual Concept.
Visual Concept
Nutrition and Metabolism
• Prokaryotes obtain nutrients either from
the nonliving environment or by utilizing
the products or bodies of living organisms.
– Heterotrophs obtain carbon from other
organisms.
– Autotrophs obtain their carbon from CO2.
– Chemotrophs get energy from chemicals in
the environment.
Bacteria and Health
• Antibiotics and Antibiotic Resistance
– A mutation in the DNA of a single bacterium
can confer resistance to an antibiotic.
– Cells with the mutant gene have a selective
advantage when the antibiotic is present.
– Mutant cells take over the population when
the normal cells die.
– This is a common example of evolution that
is easily observed within a human lifetime
Reproduction and
Recombination
• Genetic recombination in bacteria can
occur by the following three ways:
– transformation (taking in DNA from the
outside environment)
– conjugation (exchanging DNA with other
bacteria via pili)
– transduction (transmission of bacterial DNA
via viruses).
Bacteria and Health,
• Emerging Infectious Diseases Caused
by Bacteria
– The number of certain bacterial diseases has
increased because of the increase in the
number of antibiotic resistant bacteria, the
movement of people into previously
untouched areas, and global travel.
Bacteria in Industry
• Many species of bacteria are used to
produce and process different foods, to
produce industrial chemicals, to mine for
minerals, to produce insecticides, and to
clean up chemical and oil spills.
• Biologists have learned to harness
bacteria to recycle compounds in a
process called bioremediation, which
uses bacteria to break down pollutants.
Characteristics of Viruses
• Viral Size and Structure
– Viruses are nonliving particles containing
DNA or RNA and are surrounded by a protein
coat called a capsid.
– Some viruses also have an envelope that is
derived from a host cell’s nuclear membrane
or cell membrane.
Vectors of Viral Diseases
• Vectors, or hosts, of viral diseases include
humans, animals, and insects.
Discovery of Viruses
• Researchers in the late 1800s discovered
that something smaller than bacteria could
cause disease.
• In 1935, Wendell Stanley demonstrated
that viruses were not cells when he
crystallized TMV, the virus that causes
tobacco mosaic disease in tobacco and
tomato plants.
Characteristics of Viruses
• Classification of Viruses
– Viruses can be classified based on whether
they have RNA or DNA, whether the RNA or
DNA is single or double stranded and circular
or linear, by capsid shape, and whether or not
they have an envelope.
Human Viral Diseases
• Viruses cause many human diseases,
including the common cold, flu, hepatitis,
rabies, chickenpox, certain types of
cancer, and AIDS.
• Chickenpox and Shingles
– Chickenpox and shingles are caused by the
same varicella-zoster herpesvirus.
Human Viral Diseases
• Viral Hepatitis
– Hepatitis, or inflammation of the liver, can be
caused by at least five viruses.
– Hepatitis A and hepatitis E can be spread by
fecally contaminated food and water.
– Hepatitis B, C, and D are spread by sexual
contact, by contact with infected blood and
serum, and by the use of contaminated
needles.
Human Viral Diseases
• Acquired Immune Deficiency
Syndrome (AIDS)
– The human immunodeficiency virus (HIV) is
an RNA virus spread by sexual contact, by
contact with infected body fluids, and from
mother to fetus.
– HIV targets macrophages and thus damages
the body’s immune system. The disease
called acquired immune deficiency syndrome
(AIDS) results.
Human Viral Diseases
• Viruses and Cancer
– Some viruses contain oncogenes that can
cause cancer, while other viruses convert
proto-oncogenes, which usually control cell
growth, to oncogenes.
– The human papillomavirus (HPV) causes
genital warts and 93% of all cervical cancers
Emerging Viral Diseases
• Emerging viruses usually infect animals
isolated in nature but can jump to humans
when contact occurs in the environment.
– “Jump” means that the virus has mutated so
that it can infect a human
• The mutation usually occurs at least
decades before the virus has an opportunity
to infect humans
• The mutation rate has been very important
in the evolutionary history of viruses
DONE !