Laboratory Studies of Organisms

Classification and phylogeny linking different organisms,

a survey of key characters illustrating their diversity.
 Sections 1(microbes) & 2 (animals): Laboratory work

• Reports to be finished in class: up to 3 marks each for each report 27 ttl

• Final practical exam 10 microbe, 10 animal 20 ttl

• Tutorial and Theory

• Quizzes up to 1 each, 9 quizzes, drop the lowest 8 ttl

• Final, multiple choice theory exam (~60 questions) 12 ttl

Total 67

• Section 3 (plants): Lab work

• Quizzes 5

• Final practical exam 13

• Theory

• Final Theory exam 15

• Total 33
 • Texts

• Required Campbell, N. A. et al. 2008. Biology 8th Edition. Benjamin

Cummings, New York.
Laboratory Manual

Lab coat

• Suggested Van De Graaff, K. M. and J. L. Crawley, 1996. A photographic

atlas for the biology laboratory. Morton, Englewood, Colorado.
• Instructors:
• Parts 1&2 (Microbes&Animals) Dr. Gray Stirling
• SP375.25; Tel: 848 2424 Loc. 3343;
• e-mail:dstirlin@alcor.concordia.ca
• Part 3 (Plants) Dr. B. Mangat:-
• SP401-7; Tel 848 2424 Loc. 3406;
• e-mail: mangatbs@alcor.concordia.ca
• Technician: Sue Parisella:-
• SP 375-33; Tel: 848 2424 Loc. 3371;
• e-mail: sparis@vax2.concordia.ca
The joy of naming and the
currency of classification

The unit of Linnaean classification is the

species- a group of individuals sharing
unique characters. The binomial (Latin)
species name includes (1) Genus and (2)
species name.

Species are combined into increasingly

more inclusive groups (Genus, Family,
Order etc.) based on character similarity
judgments. Generally this is a hierarchical
organization of taxonomic information,
wherein species are grouped into more
inclusive taxa
 • Classifying life
Species Genus Family Order Class Phylum Kingdom Domain
Ursus
ameri-
canus
(American
black bear)

Ursus

Species are combined into a

hierarchy of increasingly moreUrsidae
inclusive groups (Genus, Family,
Order etc.) based on character Carnivora

similarity judgments, in particular

shared, key character states ( that Mammalia

flag membership in one or another

taxa.
Chordata

Linnean classification began as,

and still is an information system. Animalia

A natural classification system

Eukarya
would take ancestor- descendent
relations into account.
• Classification groups species by similar key character combinations, into a
taxonomic hierarchy. Phylogenies hypothesize the nature of ancestral
relationships and diversification, and then test those hypotheses using:
(1) the number of shared characters (2) morphological and genetic character
homologies - similarity by descent with modification.

Taxonomy
Phylogeny
Current biology texts divide organisms into 3 most inclusive taxa

Bacteria are the most diverse 4 µm
and widespread prokaryotes
and are now divided among multiple
kingdoms. Each of the rod-shaped
structures in this photo is a bacterial cell.
DOMAIN ARCHAEA
Protists (multiple kingdoms) Kingdom Plantae consists of
100 µm
are unicellular eukaryotes and multicellula eukaryotes that carry
their relatively simple multicellular out photosynthesis, the conversion
relatives.Pictured here is an assortment of of light energy to food.
protists inhabiting pond water. Scientists are
currently debating how to split the protists
into several kingdoms that better represent
evolution and diversity.

Many of the prokaryotes known
0.5 µm
as archaea live in Earth‘s
extreme environments, such as salty lakes
and boiling hot springs. Domain Archaea
includes multiple kingdoms. The photo
shows a colony composed of many cells.
Kindom Fungi is defined in part by the
nutritional mode of its members, such
as this mushroom, which absorb
nutrientsafter decomposing organic
material.
Kindom Animalia consists of
multicellular eukaryotes that
ingest other organisms.
 The 3 domains and their
major lineages are
organized into a natural
classification system based
on inheritance and
The Biol 227 Project…
diversification.
 Tutorial 1:

Topics:
Classification and Phylogeny
Eons and Evolution- geological time and biological change
Viruses- a short introduction to living cells that are not
organisms.
Begin with species: a biologically unique group,
a class of individuals sharing one or more
unique characters and a biological unit in
classification and phylogeny.
The only group that (may) has an empirical meaning is the species, which were
(1) originally largely defined morphologically by reference to a type and an authority,
Currently,
(2) Isolation species concept *(Biological species concept on pp 488) : mechanisms causing
reproductive isolation is the dominant definition in the ecological literature, but it depends
on the result and not the process of speciation and it is difficult to apply to asexual species.
(3) Phylogenetic species concept:* a group of organisms with a unique genetic history or the
smallest monophyletic group on a phylogenetic tree.
(4) Bar Code a portion of the cytochrome c, DNA sequence (in animals) is scanned and the
level of sequence variation is used to determine whether a group sharing this level of variation
is different enough to be a separate species.
Palentological species concept: morphologically distinct species known only from the fossil
record.
Evolutionary species concept: an evolutionarily independent group
Recognition species concept: individuals who recognize each other for mating and other
interactions.
Ecological species concept*: occupying a distinct niche.
Phylogeny of
Bacteria, Archaea Ancestry and Evolution
and Eukarya. Bacteria

Two taxonomic
Kingdoms
(Plantae,
Animalia), then 5,
now 3 Domains, Eukarya
Origin
with ‘prokaryote’ or
‘microbe’ having a
classification but
not a cladistic-
phylogenetic
meaning. (see ch Archaea
Sequence Change
26.6)
Re-drawn from:- Pace, N. R.
2006. Time for a change. Comparisons of ribosomal RNA sequences reveal a
Nature 441: 289 three domains tree of life, rendering the term
“prokaryote” obsolete
•The most modern genetic evidence repeatedly supports Darwin 1959
conjecture, all living organisms appear to have a common origin or life on
earth is monophyletic (an ancestor and all its descendents).

tip
branch
node
root

•plants, animals, fungi, protists and prokaryotes share a common ancestor .

The key to phylogenetic relationships is not the name, but an
understanding of ‘homology’,the definition involving similarity,
ancestry and evolution (modification with descent from an ancestor).
*Campbell ‘homology’- characters whose similarity is due to (most recent) common
ancestry, even though their functions may vary.
R. Owen (1848). The same organ in different animals under every variety of form and function.
Mindell and Meyer 2001. ‘The criteria for defining homology are similarity between
morphological or physiological characters and inheritance of similar characters from a recent
common ancestor.’
But note, the problem between genetic and morphological similarity..
E. Abouheif 1997. ‘Among (many) concepts of homology, the historical (emphasis on phylogeny)
and biological (emphasis on shared developmental patterns), homology can exist independently
at different levels of integration (gene, embryonic origins, morphological structures, behaviour
etc.).’
Galis, F. 1996 ‘is it unreasonable to infer the homologies of structures from genetic data without
considering the developmental pathways ? Is genetic similarity, just as morphological similarity,
insufficient to demonstrate homology conclusively ?’
From: N. Shubin, C. Tabin and S. Carroll 2009. Nature 457

Structural similarity appears due to

parallel evolution, but genetic
similarity appears homologous.
Evidence for evolution:
(1) Observation of evolution, e.g. Galapagos finches, Trinidad
guppies, pesticide and antibiotic resistance etc.
(2) Homology (a) Similarity between the morphology of
various living and/or extinct organisms.
(b) Similarity in development among diverse
organisms (evo-devo)
(c) Genes shared among diverse living
organisms.
Evidence for evolution:
Homology among similar genes shared among diverse living
organisms. A phylogenetic tree is a graphical representation of
(hypothetical) ancestral relationships between organisms-or
molecules.
Homologous genes may be:
orthologs- have a common function
paralogs - duplication and drift in function
xenologs- horizontal transfer, independent of 1 organism
Thus, (1) a gene tree is not necessarily the same as an organism tree,
(because of xenologs) or, and
(2) molecular sequences may transcend species longevity (dinosaurs
are extinct, but many dinosaur molecules are expressed in modern birds).
Time Frame, Organismsand Environment
associated with Evolution of Major Taxa

Geological methods using observed average rates of

sedimentation, continental uplift and drift to estimate a
fossils age, checked by
Radioactive dating methods and more recently
Molecular clocks (ch 26.5) provide methods of dating the
origins of earth, its oceans and changes in the pattern of life.
First, notice the earth is older than its oceans, life formed in
its oceans, prokaryotic cells proceeded more complicated
eukaryotes, O2 requiring single celled eukaryotes appear
before multicellular.
From 3.8 to 2 billion years ago, the only organisms were prokaryotes,
eukaryotes and multicellular organisms evolved after the shift to a higher
oxygen environment .

eons eons
Carroll (2001) argues the low concentration of atmospheric oxygen
constrained prokaryote size, precluded the formation of supporting
skeletons and limited their structural complexity.
 The Time of Eukaryote Origin(s)
Eons

The Precambrian super Eon includes the formation of

the earth, unicellular life, evolution of atmospheric
oxygen and multicellular origins.
Carroll (2001) ‘The most significant
evolutionary events to occur in the mid Proterozoic
(approximately 1.5 billion years ago) were the
endosymbiosis between species of the Archaea and
Eubacteria, which led to the origin of the
mitochondria and the chloroplasts of eukaryotes’.
What ‘living’ cells are not classified as organisms ?
Viruses
Viruses are not organisms
DNA
 Viruses cannot self-
replicate, they use host
replication and
metabolism systems to
make more viruses..

 Viruses consist of:

(1) RNA or DNA
(2) A protein capsid and
possibly an envelope
derived from the host’s
plasma or nuclear T-even
membrane bacteriophage
Virus classification:
DNA may be (a) single stranded
or (b) double stranded

RNA may be (a) single stranded

or (b) double stranded
•Virus genetic material is either: (1) or (2) enveloped virus enclosed
nonenveloped capsid enclosed, or by both a capsid and a
surrounded by just a shell of protein membrane-like envelope.
called a capsid. A T4 virus is
HIV is an enveloped virus.
nonenveloped.
•(1) A lytic
replication cycle,
in which viral
particles are made
and released from
the cell, usually
resulting in the
death of the host.
(2) A lysogenic growth cycle, in which viral genes are
incorporated into the host's chromosome and are transmitted to the
host's daughter cells. Subsequently they may become lytic
although the environmental cues or thresholds are not well
understood. HIV and other viruses are capable of lysogeny

(3) A temperate phage has both lytic and lysogenic phases

in its life cycle
+ 9ml physiological buffer only
T streaking to get bacterial colonies Viral plaques
Background Reading:
Ch 24 Read about species concepts (pp 488, 492).
Ch 25 The history of life on earth, know the Eons in the
pre-Cambrian Eras (table 25.1)
Chapter 26. Read phylogeny and the tree of life to get a
start on cladistics, reading phylogenetic trees etc.
If you are unfamiliar with these topics, I suggest you read
these 3 chapters superficially now, become familiar with
them. We will return to them throughout the course.
Quiz: multiple choice questions:

Define homology: classification and phylogeny.

Evidence for evolution

Species definitions (phylogenetic, biological, barcode)

Geological time: eons and beginning of eukaryote

evolution.

Virus classification (naked, etc. single, double stranded,

lytic, lysogenic.)