Learning Unit 1: Phylogeny and Systematics
Textbook pages: 519 – 538
PHYLOGENY : THE EVOLUTIONARY HISTORY OF A SPECIES OR GROUP OF SPECIES
SYSTEMATICS: A DISCIPLINE FOCUSED ON CLASSIFYING ORGANISMS AND DETERMINING THEIR
EVOLUTIONARY RELATIONSHIPS .
TAXONOMY: THE SCIENTIFIC DISCIPLINE OF HOW ORGANISMS ARE NAMED AND CLASSIFIED.
HOMOLOGIES: PHENOTYPIC AND GENETIC SIMILARITIES DUE TO SHARED ANCESTRY .
ANALOGY: THE SIMILARITY FUNCTION AND SUPERFICIAL RESEMBLANCE OF STRUCTURES THAT HAVE DIFFERENT ORIGINS. SIMILAR
STRUCTURES IN COMPLETELY UNRELATED SPECIES DEVELOPED INDEPENDENTLY AS ADAPTATIONS TO A COMMON FUNCTION DUE
TO SIMILAR ENVIRONMENTAL PRESSURES AND NATURAL SELECTION .
CLADISTICS: AN APPROACH TO SYSTEMATICS IN WHICH COMMON ANCESTRY IS THE PRIMARY CRITERION USED TO CLASSIFY
ORGANISMS.
MONOPHYLETIC : A GROUP OF ORGANISMS CONSISTING OF A COMMON ANCESTRAL SPECIES AND ALL OF ITS DESCENDANTS .
PARAPHYLETIC : A GROUP OF ORGANISMS CONSISTING OF A COMMON ANCESTRAL SPECIES AND SOME , BUT NOT ALL , OF ITS
DESCENDANTS .
POLYPHYLETIC : A GROUP OF ORGANISMS CONSISTING OF DISTANTLY RELATED SPECIES BUT DOES NOT INCLUDE THEIR MOST
RECENT COMMON ANCESTOR.
ORTHOLOGOUS GENES: HOMOLOGOUS GENES FOUND IN DIFFERENT GENE POOLS AFTER A SPECIATION EVENT.
PARALOGOUS GENES: RESULT FROM GENE DUPLICATION AND ARE FOUND IN MORE THAN ONE COPY IN THE SAME GENOME.
THESE GENES DIVERGE (MUTATE) FROM ONE ANOTHER WITHIN A SPECIES . THIS GIVES RISE TO A NEW GENE THAT HOLDS A NEW
FUNCTION, ALTHOUGH THIS FUNCTION MAY BE RELATED TO THAT OF THE ANCESTRAL GENE .
A KEY STEP TO RECONSTRUCTING PHYLOGENIES IS TO DISTINGUISH HOMOLOGOUS FEATURES FROM
ANALOGOUS ONES
Describe the binomial nomenclature system.
Binomial nomenclature is the nomenclature (terminology) that biologists use when naming and referring to
organisms, to avoid ambiguity. The organism’s Latin scientific name is used and consists of two parts (a binomial).
The first part is the name of the genus (plural – genera) to which the organism belongs and is always capitalized. The
second part of the name is the specific epithet, which is unique for each species within the genus, and is not
capitalized. The entire binomial is written in italics. Example – Homo sapiens
Explain the hierarchical system of classification.
Hierarchical classification is the grouping of species into a hierarchy of increasingly inclusive categories. Species that
appear to be closely related are grouped into the same genus. Related genera are grouped into the same family.
Families are grouped into orders, orders into classes, classes into phyla (singular – phylum), phyla into kingdoms and
kingdoms into domains.
A taxon (plural – taxa) is the named taxonomic unit at any level of the hierarchy. Example – Homo is the taxon at the
genus level in the case of humans.
1
, Taxa broader than the genus are not italicized, only capitalized
List the different hierarchical classification groupings.
Listed from broadest to narrowest:
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Discuss cladistic analysis on which systematics is based.
The basis of cladistic analysis is data on traits of the organisms that we are interested in. A clade is a group of species
that includes an ancestral species and all its descendants. Each clade can be nested within larger clades. A valid clade
is monophyletic.
A shared ancestral (primitive) character is found in both the clade being analysed, as well as older (ancestral) clades.
A shared derived character is unique to a clade and is useful in establishing a phylogeny.
Outgroup comparison is used to differentiate shared ancestral characters from shared derived characters by. An
outgroup is a species or group of species that is closely related to the species that we are studying but known to be
less closely related than any members of the study group are to one another.
A cladogram presents the chronological sequence of branching during the evolutionary history of a set of organisms.
NOTE: A cladogram is NOT a phylogenetic tree but may merely act as the base for one.
2
,In a phylogram, the length of a branch reflects the number of genetic changes that have taken place in a particular
DNA or RNA sequence in a lineage.
Discuss the principle of parsimony and maximum likelihood.
Principle of Parsimony: First investigate the simplest explanation that is consistent with the facts.
Maximum Likelihood: Identifies the tree most likely to have produced a given set of DNA data, based on certain
probability rules about how DNA sequences change over time.
Phylogenetic trees are simply hypotheses and the principle of parsimony just helps us create the simplest hypothesis.
The Tree of Life
The Tree of Life consists of three great domains – Bacteria, Archaea and Eukarya
3
, Learning Unit 2: Prokaryotes and the Origins of Metabolic Diversity
Textbook pages: 625 – 644
PHOTOTROPHS : ORGANISMS THAT OBTAIN ENERGY FROM LIGHT .
CHEMOTROPHS: ORGANISMS THAT OBTAIN ENERGY FROM CHEMICALS.
AUTOTROPHS: O RGANISMS THAT NEED ONLY CO2 OR RELATED COMPOUNDS AS A CARBON SOURCE .
HETEROTROPHS: O RGANISMS THAT REQUIRE AT LEAST ONE ORGANIC NUTRIENT TO MAKE OTHER ORGANIC COMPOUNDS.
Name the two main branches of prokaryotic evolution.
Bacteria and Archaea are the two main branches of prokaryotic evolution.
The fact that prokaryotes can survive extreme conditions, which most eukaryotes cannot, accounts for the fact that
they are far more abundant on Earth. Although they are extremely small (0.5 – 5 micrometres in diameter) when
compared to eukaryotes (10 – 100 micrometres in diameter), prokaryotes are well organized and achieve all of an
organism’s life functions within a single cell.
Describe the structure, function and reproduction of bacteria.
The cell wall maintains cell shape, protects the cell and prevents it from bursting in hypotonic environments.
Most bacterial cell walls contain peptidoglycan. There are 2 types of cell walls – gram-positive and gram-negative.
Gram-positive: simple, thick cell walls. Gram-negative: thin, more complex cell walls – peptidoglycan layer
surrounded by plasma membrane and outer membrane – are more resistant antibiotics and host’s immune defence.
In a hypertonic environment, prokaryotes plasmolyze (lose water and
shrink away from cell wall). This inhibits reproduction. That’s why salt
can be used to preserve food – it prevents food-spoiling prokaryotes
from rapidly multiplying.
4
Textbook pages: 519 – 538
PHYLOGENY : THE EVOLUTIONARY HISTORY OF A SPECIES OR GROUP OF SPECIES
SYSTEMATICS: A DISCIPLINE FOCUSED ON CLASSIFYING ORGANISMS AND DETERMINING THEIR
EVOLUTIONARY RELATIONSHIPS .
TAXONOMY: THE SCIENTIFIC DISCIPLINE OF HOW ORGANISMS ARE NAMED AND CLASSIFIED.
HOMOLOGIES: PHENOTYPIC AND GENETIC SIMILARITIES DUE TO SHARED ANCESTRY .
ANALOGY: THE SIMILARITY FUNCTION AND SUPERFICIAL RESEMBLANCE OF STRUCTURES THAT HAVE DIFFERENT ORIGINS. SIMILAR
STRUCTURES IN COMPLETELY UNRELATED SPECIES DEVELOPED INDEPENDENTLY AS ADAPTATIONS TO A COMMON FUNCTION DUE
TO SIMILAR ENVIRONMENTAL PRESSURES AND NATURAL SELECTION .
CLADISTICS: AN APPROACH TO SYSTEMATICS IN WHICH COMMON ANCESTRY IS THE PRIMARY CRITERION USED TO CLASSIFY
ORGANISMS.
MONOPHYLETIC : A GROUP OF ORGANISMS CONSISTING OF A COMMON ANCESTRAL SPECIES AND ALL OF ITS DESCENDANTS .
PARAPHYLETIC : A GROUP OF ORGANISMS CONSISTING OF A COMMON ANCESTRAL SPECIES AND SOME , BUT NOT ALL , OF ITS
DESCENDANTS .
POLYPHYLETIC : A GROUP OF ORGANISMS CONSISTING OF DISTANTLY RELATED SPECIES BUT DOES NOT INCLUDE THEIR MOST
RECENT COMMON ANCESTOR.
ORTHOLOGOUS GENES: HOMOLOGOUS GENES FOUND IN DIFFERENT GENE POOLS AFTER A SPECIATION EVENT.
PARALOGOUS GENES: RESULT FROM GENE DUPLICATION AND ARE FOUND IN MORE THAN ONE COPY IN THE SAME GENOME.
THESE GENES DIVERGE (MUTATE) FROM ONE ANOTHER WITHIN A SPECIES . THIS GIVES RISE TO A NEW GENE THAT HOLDS A NEW
FUNCTION, ALTHOUGH THIS FUNCTION MAY BE RELATED TO THAT OF THE ANCESTRAL GENE .
A KEY STEP TO RECONSTRUCTING PHYLOGENIES IS TO DISTINGUISH HOMOLOGOUS FEATURES FROM
ANALOGOUS ONES
Describe the binomial nomenclature system.
Binomial nomenclature is the nomenclature (terminology) that biologists use when naming and referring to
organisms, to avoid ambiguity. The organism’s Latin scientific name is used and consists of two parts (a binomial).
The first part is the name of the genus (plural – genera) to which the organism belongs and is always capitalized. The
second part of the name is the specific epithet, which is unique for each species within the genus, and is not
capitalized. The entire binomial is written in italics. Example – Homo sapiens
Explain the hierarchical system of classification.
Hierarchical classification is the grouping of species into a hierarchy of increasingly inclusive categories. Species that
appear to be closely related are grouped into the same genus. Related genera are grouped into the same family.
Families are grouped into orders, orders into classes, classes into phyla (singular – phylum), phyla into kingdoms and
kingdoms into domains.
A taxon (plural – taxa) is the named taxonomic unit at any level of the hierarchy. Example – Homo is the taxon at the
genus level in the case of humans.
1
, Taxa broader than the genus are not italicized, only capitalized
List the different hierarchical classification groupings.
Listed from broadest to narrowest:
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Discuss cladistic analysis on which systematics is based.
The basis of cladistic analysis is data on traits of the organisms that we are interested in. A clade is a group of species
that includes an ancestral species and all its descendants. Each clade can be nested within larger clades. A valid clade
is monophyletic.
A shared ancestral (primitive) character is found in both the clade being analysed, as well as older (ancestral) clades.
A shared derived character is unique to a clade and is useful in establishing a phylogeny.
Outgroup comparison is used to differentiate shared ancestral characters from shared derived characters by. An
outgroup is a species or group of species that is closely related to the species that we are studying but known to be
less closely related than any members of the study group are to one another.
A cladogram presents the chronological sequence of branching during the evolutionary history of a set of organisms.
NOTE: A cladogram is NOT a phylogenetic tree but may merely act as the base for one.
2
,In a phylogram, the length of a branch reflects the number of genetic changes that have taken place in a particular
DNA or RNA sequence in a lineage.
Discuss the principle of parsimony and maximum likelihood.
Principle of Parsimony: First investigate the simplest explanation that is consistent with the facts.
Maximum Likelihood: Identifies the tree most likely to have produced a given set of DNA data, based on certain
probability rules about how DNA sequences change over time.
Phylogenetic trees are simply hypotheses and the principle of parsimony just helps us create the simplest hypothesis.
The Tree of Life
The Tree of Life consists of three great domains – Bacteria, Archaea and Eukarya
3
, Learning Unit 2: Prokaryotes and the Origins of Metabolic Diversity
Textbook pages: 625 – 644
PHOTOTROPHS : ORGANISMS THAT OBTAIN ENERGY FROM LIGHT .
CHEMOTROPHS: ORGANISMS THAT OBTAIN ENERGY FROM CHEMICALS.
AUTOTROPHS: O RGANISMS THAT NEED ONLY CO2 OR RELATED COMPOUNDS AS A CARBON SOURCE .
HETEROTROPHS: O RGANISMS THAT REQUIRE AT LEAST ONE ORGANIC NUTRIENT TO MAKE OTHER ORGANIC COMPOUNDS.
Name the two main branches of prokaryotic evolution.
Bacteria and Archaea are the two main branches of prokaryotic evolution.
The fact that prokaryotes can survive extreme conditions, which most eukaryotes cannot, accounts for the fact that
they are far more abundant on Earth. Although they are extremely small (0.5 – 5 micrometres in diameter) when
compared to eukaryotes (10 – 100 micrometres in diameter), prokaryotes are well organized and achieve all of an
organism’s life functions within a single cell.
Describe the structure, function and reproduction of bacteria.
The cell wall maintains cell shape, protects the cell and prevents it from bursting in hypotonic environments.
Most bacterial cell walls contain peptidoglycan. There are 2 types of cell walls – gram-positive and gram-negative.
Gram-positive: simple, thick cell walls. Gram-negative: thin, more complex cell walls – peptidoglycan layer
surrounded by plasma membrane and outer membrane – are more resistant antibiotics and host’s immune defence.
In a hypertonic environment, prokaryotes plasmolyze (lose water and
shrink away from cell wall). This inhibits reproduction. That’s why salt
can be used to preserve food – it prevents food-spoiling prokaryotes
from rapidly multiplying.
4
