Essential Question:

How do phylogenies
show evolutionary
relationships?
What is Phylogeny?

Figure 20.2 - What is

the evidence for the
phylogeny and how do
we know that a legless
body form evolved
independently from
legged ancestors? How
does natural selection
drive the evolution of a
snakelike body form?
Identify the three most
important facts about
binomial
nomenclature.

Three domains and the

classifications. Which
are the most specific
and the most general?
Figure 20.4
Classification and
Phylogeny

Phylogenetic trees do

Notes

Phylogeny is the evolutionary history of a species or group

of species. This information is used to make sense of
diversity.
Based on DNA sequence data, it reveals that the eastern
glass lizard and snakes evolved from lizards with legs, but
from different lineages of legged lizards. It seems like their
limbless body forms evolved independently.
Natural selection most likely drove these legless lizards to
evolve as certain environments such as grasslands
required burrowing in order to find shelter and protection
from predators. The legs of these organisms reduced in
size and even disappeared as the species adapted to their
environments.
The first part of a binomial is the genus to which the
species belong. The second part, called the specific
epithet, is unique for each species within the genus. The
first letter of the genus is capitalized and the entire name
is italicized. Scientific names are latinized and involve a
Latin root in its naming. For example, Homo sapiens which
is the scientific name for humans.
The three domains are Bacteria, Eukarya, and Archaea.
The classification order is from the most general Domain,
Kingdom, Phylum, Class, Order, Family, Genus, to Species.
Species is the most specific classification for an organism.
The taxon is the named taxonomic unit at any level of the
hierarchy. A Phylogenic Tree is the evolutionary history of
a group of organisms that is represented on a branching
diagram.

show phenotypic
similarity.

The sequence of
branching does not
show actual ages.

Is there an
evolutionary
relationship between
adjacent taxa on a
phylogenetic tree?
Explain.
What do researchers
use phylogenetic trees
for?

Morphological and
Molecular Homologies

Homologies vs
analogies including
convergent evolution

Phylogenetic trees show patterns of descent, not

phenotypic similarity. Although closely related organisms
often resemble each other from common ancestry, they
may not if their lineages evolved at different rates or faced
different environments.
The sequence of branching does not show actual ages
because diagrams are made from the patterns of descent.
For example, the tree in Figure 20.4 doesnt show that the
wolf evolved more recently than the otter. It only shows
the most recent common ancestor of the wolf and coyote.
You cannot assume that a taxon on a phylogenetic tree
evolved from the taxon next to it. Figure 20.4 does not
show that wolves evolved from coyotes. We only know that
wolves and coyotes came from a common ancestor.
Phylogeny trees on maize from DNA helped researchers
identify two species of wild grasses that may be maizes
closest living relatives. The relatives can be used as
reservoirs of beneficial alleles that can be transferred to
cultivated maize by genetic engineering. Phylogenetic
trees are also used to infer species identities by comparing
the relatedness of DNA from other organisms. Researchers
have used this to investigate whether whale meat was
illegally harvested from protected species or species that
can be harvested legally (Minke whales).
Homologies are phenotypic and genetic similarities due to
shared ancestry. For example, the similarity in the number
and arrangement of bones in the forelimbs of mammals is
due to their descent from a common ancestor. This is
known as a morphological homology. Some morphological
divergence between related species can be more
significant while having small genetic divergence. For
example, Hawaiian silversword plants are physically
diverse; some are tall trees while others are dense bushes
but are very genetically similar.
An analogy is s similarity due to a convergent evolution
rather than shared ancestry. For example, the marsupial
Australian mole and North American mole have very
similar burrowing characteristics such as an elongated
body and a pad of thickened skin that protects a tapered

nose. However their internal anatomy is very dissimilar,

their common ancestor lived 140 million years ago and
was not mole-like. Their analogous characteristics evolved
independently in these two lineages as they adapted to
similar environments (convergent evolution)
What are the
challenges for using
DNA sequences to
determine common
ancestry?

Cladistics and
classifying organisms

Compare and contrast

shared ancestral trait
and shared derived
trait. What is the role
of a derived trait in the
phylogenetic tree?
What is an outgroup
and why do we need
one?

What is the deal with

branch length on
phylogenetic trees?

The first step after sequencing molecules is to align

comparable sequences from the species being studied. If
they are very closely related, the sequences only differ at
a few sites. However if a base of the sequence is missing,
it moves back the pattern which can overlook a good
match. The molecular comparison between the Australian
mole and North American mole has shown that there are
many differences since their common ancestor and that
they are not closely related. In organisms that do not
appear to be closely related but have many accidental
base matches are called molecular homoplasies.
Cladistics uses common ancestry as the primary criterion
for classifying organisms which places species into groups
called clades. A monophyletic group consists of an
ancestral species and all of its descendants. A
paraphyletic group consists of an ancestral group and
some of its descendants. A polyphyletic group includes
taxa with different ancestors.
A shared ancestral character originated in an ancestor of
the taxon. For example, a backbone for mammals. A
shared derived character is an evolutionary novelty unique
to a clave such as hair to mammals, not all mammals have
hair but some claves do. A derived trait can differentiate
claves from a common ancestor
An outgroup is a species or group of species from an
evolutionary lineage that is known to have diverged before
the lineage. By comparing members between ingroups
and outgroups, we can determine which characters were
derived at branch points. For example, all of the
vertebrates in the ingroup have backbones which was
present in the ancestral vertebrate, but not in the
outgroup. While lampreys dont have a hinged jaw, other
members in the ingroup do, this helps identify an early
branch point in the vertebrate clade.
Some tree diagrams have proportional branch lengths to

Parsimony and
scientific research

What is a molecular
clock? How does it
measure absolute
time? Is it absolute?
Molecular clocks and
HIV-1M

Three domain system,

why is the five
kingdom theory
flawed?

Horizontal gene
transfer

amount of evolutionary change or to the time at which

particular events occurred. However even though the
branches of a phylogenetic tree may have different
lengths, all the different lineages that descend form a
common ancestry have survived for the same number of
years.
Maximum parsimony means firstly investigating the
simplest explanation that is consistent with facts.
Scientists have developed programs that are parsimonious
to find a phylogenetic tree that best describes
evolutionary history. They examine many possible trees
and select the tree that require the fewest evolutionary
changes.
A molecular clock is an approach for measuring the
absolute time of evolutionary change based on the
observation that some genes and other regions of
genomes appear to evolve at constant rates. This is not
absolute though, some genes evolve at a different rate
and the data is mostly an average rate of change.
Phylogenetic analysis showed that HIV, the virus that
causes AIDS descended from viruses that infect primates.
HIV-1 M is the most widespread strain in humans;
researchers compared the gene sequences which showed
that the virus evolved in a clocklike fashion. Going
backward in time using the molecular clock showed that
the strain first spread to humans during the 1930s.
The kingdom theory is flawed because some prokaryotes
differ as much from each other as they do with
eukaryotes. The three domains: Eukarya (true nuclei),
Archaea (prokaryotes in unusual environments, Bacteria
(prokaryotes) highlights that most of life has been about
single celled organisms.
Horizontal gene transfer is a when genes are transferred
from one genome to another through mechanisms like
exchange of transposable elements and plasmids, viral
infection, and fusions of organisms. This is so common
that it suggests the early history of life is a tangled
network of branches and that all of the domains are
connected in some manner.