PHYOGENY & THE TREE OF LIFE
Campbell and Reece, Chapter 26
definitions
Phylogeny

evolutionary
history of a
species or group of
species
Systematics

discipline focused
on classifying
organisms &
determining their
evolutionary
relationships
Taxonomy
how
organisms are
classified and
named
 each step
called a taxon

(plural: taxa)
BINOMIAL NOMENCLATURE
Man’s
Genus
species:
Homo
sapiens
used to avoid ambiguity
 the Latin scientific name
for each individual
species
 is the Genus species
portion of taxonomy

3 DOMAINS

DOMAIN ARCHAEA
 Prokaryotes
 many
live in Earth’s extreme
environments
 as molecularly close to eukaryotes
as Domain Bacteria
 includes multiple kingdoms
(notice position of domain Archaea)
Domain Archaea
methanogen
thermophile
Domain Bacteria
Prokaryotic
 very diverse group
 use every major mode of nutrition &
metabolism
 beneficial: photoautotrophs, alcoholic
fermentation, Vit K production
 pathologic: strep throat, flesh-eating
disease, ulcers, Rheumatic fever

Domain Bacteria
Gram Positive Bacteria
Streptococcus
(cocci)
Gram Negative Bacteria
Legionella pneumophilia
(rods)
Domain Bacteria
Spirochetes
(spirillia)
Domain Eukarya

Eukaryotic cells
 more
complex, become specialized
 able to form multicellular organisms
 greatest diversity
Domain Eukarya
Plants
Fungi
Domain Eukarya
Animal
Protozoa
Domain Eukarya
Algae Cells
Algal “bloom”
Linnean Classification
PHYLOGENETIC TREES
show the evolutionary history of a
group of organisms
 represented by a branching diagram
 each branch point represents the
divergence of 2 evolutionary lineages
from a common ancestor

Phylogenetic Trees

Branch Point
 sister
 basal
taxa
taxa
Phylogenetic Trees
What you can learn


patterns of descent
common ancestors
What you cannot learn



does not show
phenotypic similarity
cannot tell ages of
species based on where
branches are in the
“tree”
sister taxa did not evolve
from each other; they
have a common ancestor
(that could be extinct)
Uses of Phylogenetic Tree
1.
If “close” relatives
found they could
be source of
beneficial alleles
that could be
transferred to
hardier taxa via
genetic
engineering
2. Using DNA samples
are now able to
differentiate legal
species from illegal
species of whale,
tuna
Phylogenies are inferred from
morphological & molecular data

Homology: similarity in characteristics
resulting from a shared ancestry
Homologous Chromosomes in
same species

When
chromosomes
duplicate in S
Phase of Cell
Cycle see genes
in same loci of
each sister
chromatid
Homologous Chromosomes
across Species with Common
Ancestor

Genes or certain
DNA sequences
also homologous
if they descended
from sequences
carried by a
common ancestor

Organisms that
share very
similar
morphologies or
DNA sequences
are likely to be
more closely
related than
organisms with
vastly different
structures

There are
examples of
organisms that
look very
different but
have very similar
DNA sequences
because species
underwent
adaptive
radiation.
Homology vs. Analogy

Analogy is similarity due to convergent
evolution: occurs when similar
environmental pressures & natural
selection produce similar (analogous)
adaptations even though organisms have
different ancestors.

homoplasies: analogous structures that
arose independently (Greek: to mold in
same way)
 Examples:
 bird
& bat wing: their common ancestor
did not fly
The more complex the structure
found in 2 species the more
likely it is that they have a
shared ancestor
Molecular Evidence
of Evolutionary Relationships


DNA sequence similarities have been
documented among prokaryotes &
eukaryotes: (comparative genomics)
High degree of sequence similarity noted in
some eukaryotic nuclear genes to Archaea
& mitochondrial genes are similar to
Bacteria
Using DNA to map an
organism’s evolutionary history


The more recently 2 species have branched
from a common ancestor, the more similar
their DNA sequences should be
The longer ago 2 species have been on
separate evolutionary paths, the more their
DNA should have diverged
Different genes evolve
at different rates
Nuclear DNA


changes slowly
useful for
investigating
relationships
between taxa that
diverged hundreds
of millions of yrs
ago
Mitochondrial DNA


evolves rapidly
useful to
investigate more
recent
evolutionary
events


Eukaryotic genes consist of numerous
coding regions (exons) that are separated
by noncoding regions (introns)
both transcribed into pre-mRNA and then
intron sequences are removed

in humans 90% of
the exons are
homologous to
exons found in
Drosophila &
Caenorhabditis
(nematode worms

Puffer Fish is
vertebrate with
smallest known
genome (1/7th
human genome) &
yet has all exons
present in humans

in chromosomes:
“homologous”
means sequences
are so similar that
they are not likely
due to chance so
are considered the
result of common
ancestry
Duplication in human genome

both of genes &
chromosome
segments

1.
2.
Based on these duplications & new
combinations of exons it seems that
the vertebrate evolution has required very
few new proteins
evolutionary change involves making new
genes by rearranging functional domains
into novel combinations (called “exon
shuffling”)
Exon Shuffling


Important source of genetic variation (in
addition to mutations & crossing over)
still investigating mechanism
Homologous Genes


60% of human genes that encode proteins
are homologous to genes from other
organisms
high degree of conservation of both genes
& exons among widely diverse organisms
from all 3 Domains is strong evidence for
their common ancestry
Nonfunctional Sequences


another bit of strong evidence for
relatedness among diverse organisms is the
similarity in DNA sequences that have no
apparent function.
one category of these are pseudogenes
Pseudogenes 2 kinds:

1. arises from DNA
replication 
mutations  STOP
codons in one of
duplicates; other
no mutation

2. Processed
Pseudogenes:
arise during
transcription or
translation: lack a
promoter sequence
so cannot be
transcribed

To date, 2909
pseudogenes in
human genome
Other functionless DNA
LINEs



Long Interspersed
Nucleotide
Element
Families: 1,2,3
Are
retrotransposons
SINEs



Short Interspersed
Nucleotide
Element
Also 3 families in
humans
Specific LINEs &
SINEs found only
in cloven-hooved
mammals & whales
Retroviruses


RNA virus
Infects cell and turns its single strand 
double strand which inserts into host
genome
RetrovirusRetrotransposon


Retrovirus inserts self into host genome but
somewhere along the way genes for
capsids lost
If LINEs in different species are
homologous it is considered to be strong
evidence that these 2 species share a
common ancestor where that particular
LINE first became established
Review:




Phylogeny can be inferred from
–the fossil record,
–morphological homologies
–molecular homologies


Phylogenetic trees are used to depict
hypotheses about the evolutionary history
of a species
Shared characters are used to construct
phylogenetic trees
 Shared
ancestral characters group organisms
into clades
 Shared derived characters distinguish clades
& form branching points in the tree of life
Shared Characteristics are used
to Construct Phylogenetic Trees


Cladistics: an approach to systematics in
which organisms are placed into groups
based primarily on common descent
Clades:groups organisms are placed in:
1
clade will include ancestor & all its
descendants
 3 types:
1. Monophyletic Group


equivalent to a
clade
ancestral species
& all its
descendants
2. Paraphyletic Group

consists of an
ancestral species
& some of its
descendants
3. Polyphyletic Group

Some members of
this group will
have different
ancestors
Name That Group:
Shared Derived
Character
Shared Ancestral
Character

character that
originated in an
ancestor of the
taxon

an evolutionary
novelty unique to a
clade.
Shared Ancestral
Character
Shared Derived
Character
How to Build a Cladogram

http://ccl.northwestern.edu/simevolution/obonu/cla
dograms/Open-This-File.swf
Making a Phylogenetic Tree


SHOULD BE POSSIBLE TO DETERMINE
THE CLADE ANY SHARED DERIVED
CHARACTER 1ST APPEARED
Construct a CHARACTER TABLE:
1
axis has list of organisms, 1 has characters
CHARACTER TABLE
FROG
AMNION
HAIR,
MAMMARY
GLANDS
GESTATION
LONG
GESTATION
IGUANA
DUCK-BILLED
PLATYPUS
KANGAROO
BEAVER

Important step in cladistics is the
comparison of the
 Ingroup:
the taxa whose phylogeny is being
investigated
 Outgroup: the taxon that diverged before the
lineage leading to the members of the ingroup
 Use
to identify the derived characters that
define the branch points in the phylogeny of
the ingroup
PHYLOGENETIC TREES

WHEN CONSTRUCTING A
PHYLOGENETIC TREE, SCIENTISTS USE
PARSIMONY, LOOKING FOR THE
SIMPLEST EXPLANATION FOR
OBSERVED PHENOMENA

SYSTEMATISTS USE MANY KINDS OF
EVIDENCE, BUT EVEN THE BEST TREE
REPRESENTS ONLY THE MOST LIKELY
HYPOTHESIS
Shared characters are used to
construct phylogenetic trees

The phylogenetic tree of reptiles shows
that crocodiians are the closest living
relatives of birds

Crocodiles & Birds share:
 4-chambered
heart
 “singing” to defend territories
 parental care of eggs within nests
Phylogenetic Trees with
Proportional Branch Lengths


branch lengths are
proportional to the
amount of genetic
change in each
lineage
So the longer the
line the more
genetic changes
have occurred
Principle of Maximum Parsimony



1st investigate the
simplest explanation
that is consistent
with the facts
aka “Occum’s
Razor”
for phylogenies
based on DNA: the
most parsimonious
tree requires the
fewest base changes
Principle of Maximum Likelihood

given certain
probability rules
about how DNA
sequences change
over time, a tree
can be made that
reflects the most
likely sequence of
evolutionary
events

currently using computer programs to
search for trees that are parsimonious &
have a high probability
Phylogenetic Trees
as Hypotheses


Scientists can make & test predictions
based on the assumption that a phylogeny
(the hypothesis) can be supported or not.
Prediction: features shared by 2 groups of
closely related organisms are also present
in their common ancestor & all of its
descendants
An organism’s evolutionary
history is documented in its
genome: 2 Types of
Homologous Genes
Orthologous Genes


Exact copies found
in different species
Origin: common
ancestor
Paralogous Genes

Homology result of
gene duplication:
multiple copies of
a gene in same
species all came
from same gene
Genome Evolution

1.
2.
By investigating entire genomes of
different species see 2 patterns:
Lineages that diverged long ago can share
orthologous genes
# of genes a given species has does not
seem to increase thru duplication at same
rate as increase in phenotype changes
Molecular Clocks


is a yardstick for measuring the absolute time
of evolutionary change based on the
observation that some genes & other regions
of genomes appear to evolve at constant rates.
is based on assumption that the # of nucleotide
substitutions in orthologous genes is
proportional to the time that has elapsed since
the species branched from their common
ancestor (known as divergence time)
Molecular Clocks

calibration of a molecular clock is done by
graphing the # of genetic differences
against the dates of evolutionary branch
points that are known from fossil record

finding the average rates of genetic change
from such graphs can be used to estimate
dates of events that cannot be discerned
from fossil record




genes that appear to follow molecular clock
are really only acting in statistically
average rate of change
of course parts of the genome appear to
have evolved in irregular bursts
some genes seem to have different rates of
change in different organisms
some genes evolve a million times faster
than others
Neutral Theory



states much of the evolutionary change in
genes & proteins has no effect on fitness &
therefore is not influenced by natural
selection
many new genes are harmful so are quickly
removed
differences in the clock rate for different
genes are a function of how important a
gene is
Problems with Molecular Clocks


1.
2.
Natural selection favors some DNA
changes
Many scientists remain skeptical about:
the “Neutral Theory”,
about using the molecular clock beyond
time span documented by fossil record
(about 550 million years)
Dating the Origin of HIV with a
Molecular Clock


HIV is
descended from
viruses that
infected chimps
& other
primates but did
not cause same
AIDS-like
illness
When did this
happen?
HIV Strains



multiple strains
have infected
humans
multiple strains
implies multiple
origins
most widespread
strain in HIV-M

using molecular
clock best guess is
HIV-M strain 1st
spread to humans
in the 1930’s
Is the tree of Life Really a
Ring of Life?


there has been
substantial
movements of genes
between organisms
in the 3 domains
mechanism:
horizontal gene
transfer: plasmids,
viral infection,
maybe even fusion
of organisms
Ring of Life

some scientists
think horizontal
gene transfer so
common that early
history of life
should be
represented as a
ring with 3
domains emerging
from the ring