NOTES: Chapter 26 Phylogeny and the Tree of Life
NOTES: Chapter 26
Phylogeny and the Tree of Life
Phylogeny: the evolutionary history of a
species or group of species
● Systematics: discipline focused on classifying organisms and determining their evolutionary relationships
● The fossil record: the ordered array of fossils, within layers, or strata, of sedimentary rock
● Paleontologists: collect and interpret fossils
a “family tree”…
Linnaeus
convinced us to
use a hierarchical
classification
system
Darwin provided us
with the mechanism by
which evolution results
in descent with
modification
● Taxonomy – naming & classifying organisms
● Systematics – naming & classifying
organisms according to
their evolutionary relationships
● Phylogenetics – reconstructing the
evolutionary relationships
among organisms
Systematics
Phylogenetics
Binomial Nomenclature
● In the 18th century, Carolus Linnaeus published a
system of taxonomy based on resemblances
● Two key features of his system remain useful
today: two-part names for species and
hierarchical classification
Aptenodytes forsteri
● The two-part scientific name of a species is called a binomial
● The first part of the name is the genus
● The second part is unique for each species within the genus
● The first letter of the genus is capitalized, and the entire species name is
italicized
● Both parts together
name the species
Binomial Nomenclature
Chelonia mydas
Hierarchical Classification
● The taxonomic groups from
broad to narrow are domain,
kingdom, phylum, class, order,
family, genus, and species
● A taxonomic unit at any level of
hierarchy is called a taxon
Species:
Panthera pardus
Genus:
Panthera
Family:
Felidae
Order:
Carnivora
Class:
Mammalia
Phylum:
Chordata
Domain:
Bacteria
Kingdom:
Animalia Domain:
ArchaeaDomain:
Eukarya
5 Kingdom classification system in
use through the late 1900s
5 Kingdom classification system in
use through the late 1900s
gave way to Woese’s 3 Domains
5 Kingdom classification system in
use through the late 1900s
gave way to Woese’s 3 Domains
and multiple Kingdoms
“Did King Philip
Come Over From
Great Spain?”
The Major Lineages of Life: the 5 Kingdom System
Living organisms (now PLUS 3 domains!)
Prokaryotic Eukaryotic
Simple/unicells Multicellular
Autotrophic Heterotrophic
Absorptive Ingestive
nutrition nutrition
(Animalia)(Fungi)
(Plantae)
(Protista)
(Monera)
Linking Classification and
Phylogeny
● Systematists
depict evolutionary
relationships in
branching
phylogenetic
trees
Order Family
Pantherapardus(leopard)
Genus Species
Canislatrans(coyote)
Taxideataxus(Americanbadger)
Lutra lutra(Europeanotter)
Canislupus(gray wolf)
Felid
ae
Ca
rniv
ora
Pa
nth
eraT
ax
idea
Mu
stelida
e
Lu
tra
Ca
nid
ae
Can
is
Macroevolution & Phylogeny
–
hypothesized genealogy
traced back to the last
common ancestor (i.e., the
most recent) through
hierarchical, dichotomous
branching
● Phylogenetic tree -
● A phylogenetic tree represents a hypothesis about
evolutionary relationships
● Each branch point represents the divergence of
two species
● Sister taxa are groups that share an immediate
common ancestor
Phylogenetic Trees
● A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree
● A basal taxon diverges early in the history of a group and originates near the common ancestor of the group
● A polytomy is a branch from which more than two groups emerge
Phylogenetic Trees
Branch point:where lineages diverge
ANCESTRALLINEAGE
This branch pointrepresents thecommon ancestor oftaxa A–G.
This branch point forms apolytomy: an unresolvedpattern of divergence.
Sistertaxa
Basaltaxon
Taxon A
Taxon B
Taxon C
Taxon D
Taxon E
Taxon F
Taxon G
Macroevolution & Phylogeny
Phylogenetic tree, phylogeny, or cladogram
● Node – branch point,
speciation event
Constructing Phylogenetic
Trees● Sorting homology vs. analogy...
● Homology: likenesses attributed to common or shared ancestry
● Analogy: likenesses attributed to similar ecological roles and natural selection
● Convergent evolution: species from different evolutionary branches that resemble one another due to similar ecological roles
Phylogenies – HOMOLOGY
HOMOLOGIES: Similar characters (e.g.,
morphological, behavioral, molecular, etc. traits or
features) suggest relatedness…
Wasps
[Hymenoptera]
● Homologous characters share common ancestry
**Lack of similarity among taxa results from
DIVERGENCE
Phylogenies – HOMOLOGY
● As a general rule, the more homologous
characters shared by two species, the
more closely they are related
● Sequences of DNA & RNA (nucleotides) and
proteins (amino acids) are used as characters; as a
general rule, the more recently two species shared a
common ancestor, the more similar their sequences
Phylogenies – HOMOLOGY
Phylogenies - ANALOGY
But, not all similarity derives from common ancestry!
CONVERGENT EVOLUTION: can produce superficially
similar traits that lack homology with one another
● Analogous characters do not share common
ancestry
**Similarity among taxa results from CONVERGENCE
Phylogenies - ANALOGY
Evaluating Molecular
Homologies:
● Systematists use computer programs and
mathematical tools when analyzing comparable
DNA segments from different organisms
● Molecular systematics uses DNA and other
molecular data (i.e. amino acid sequences) to
determine evolutionary relationships
Deletion
Insertion
1
1
1
1
2
2
2
2
2
1
3
4
Cladistic Analysis
Each nucleotide can be treated as a character
Character changes (mutations) from the ancestral
to the derived state include:
Substitutions
Insertions
Deletions
…AGCTCTAGG…
…AGCTATAGG…
…AGCTCTAGG…
…AGCTGATCTAGG…
…AGCTCTAGG…
…AGCTCTAGG…
Mutations
Shared characters are used to
construct phylogenetic trees
● Once homologous characters have been
identified, they can be used to infer a phylogeny
CLADISTICS:
● Cladistics groups organisms by common
descent
● A clade is a group of species that includes
an ancestral species and all its descendants
● Clades can be nested in larger clades, but
not all groupings of organisms qualify as
clades
● A valid clade is monophyletic, signifying
that it consists of the ancestor species and
all its descendants
(a) Monophyletic group (clade)
Group
A
B
C
D
E
F
G
● A paraphyletic grouping consists of an ancestral
species and some, but not all, of the descendants
CLADISTICS:
(b) Paraphyletic group
Group
A
B
C
D
E
F
G
● A polyphyletic grouping consists of various
species with different ancestors
CLADISTICS:
(c) Polyphyletic group
Group
A
B
C
D
E
F
G
(a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group
Group
Group
Group
A
B
C
D
E
F
G
A
B
C
D
E
F
G
A
B
C
D
E
F
G
Macroevolution & Phylogeny
A clade is a monophyletic group, i.e., an
ancestral species and all of its descendents
Phylogenetic tree, phylogeny, or cladogram
Macroevolution & Phylogeny
Taxonomic groups often reflect true clades…
Shared Ancestral and Shared
Derived Characters
● In comparison with its ancestor, an organism has
both shared and different characteristics
● A shared ancestral character is a character that
originated in an ancestor of the taxon
● A shared derived character is an evolutionary
novelty unique (“new”) to a particular clade
● A character can be both ancestral and derived,
depending on the context
Ancestral vs. Derived Characters
Inferring Phylogenies Using
Derived Characters
● When inferring evolutionary relationships, it is
useful to know in which clade a shared derived
character first appeared
TAXA Lancelet
(outgroup)
Lamprey
Bass
Frog
Turtle
Leopard
Vertebral
column
(backbone)
Four walking
legs
Hinged jaws
Amnion
Hair
Vertebral
column
Hinged jaws
Four walking legs
Amnion
Hair
(a) Character table (b) Phylogenetic tree
CH
AR
AC
TE
RS
Lan
cele
t
(ou
tgro
up
)
Lam
pre
y
Bass
Fro
g
Tu
rtle
Leo
pard
0
0
0
0
0
1
0
0
0
0
1
1
0
0
0
1
1
1
0
0
1
1
1
1
0
1
1
1
1
1
TAXA
Vertebral
column
(backbone)
Four walking
legs
Hinged jaws
Amnion
Hair
(a) Character table
CH
AR
AC
TE
RS
Lan
cele
t
(ou
tgro
up
)
Lam
pre
y
Bass
Fro
g
Tu
rtle
Leo
pard
0
0
0
0
0
1
0
0
0
0
1
1
0
0
0
1
1
1
0
0
1
1
1
1
0
1
1
1
1
1
Lancelet
(outgroup)
Lamprey
Bass
Frog
Turtle
Leopard
Vertebral
column
Hinged jaws
Four walking legs
Amnion
Hair
(b) Phylogenetic tree
Cladistic Analysis
All
similar
characters
Analogies
Homologies
Shared
Primitive
Characters
(ancestral)
Shared
Derived
Characters
(unique to a clade)
**The sequence of branching in a cladogram then
represents the sequence in which evolutionary
novelties (shared derived characters) evolved
● An OUTGROUP is a species or group of species
that is closely related to the INGROUP, the
various species being studied
● The outgroup is a group that has diverged before
the ingroup
● Systematists compare each ingroup species with
the outgroup to differentiate between shared
derived and shared ancestral characteristics
Ingroup vs. Outgroup
● Characters shared by the outgroup and ingroup
are ancestral characters that predate the
divergence of both groups from a common
ancestor
Cladistic Analysis
Ingroup vs. Outgroup
An outgroup helps identify shared ancestral and
shared DERIVED CHARACTERS (unique to a
clade)
Phylogenetic Trees with
Proportional Branch Lengths
● In some trees, the length of
a branch can reflect the
number of genetic changes
that have taken place in a
particular DNA sequence in
that lineage
Lancelet
Drosophila
Zebrafish
Frog
Chicken
Human
Mouse
● In other trees, branch length can represent
chronological time, and branching points can be
determined from the fossil record
Mouse
Human
Chicken
Frog
Zebrafish
Lancelet
Drosophila
Present
CENOZOICMESOZOICPALEOZOIC
Millions of years ago
542 251 65.5
Phylogenetic Trees as Hypotheses
● The best hypotheses for phylogenetic trees fit the
most data: morphological, molecular, and fossil
● Phylogenetic bracketing allows us to predict
features of an ancestor from features of its
descendants
-For example, phylogenetic bracketing allows us to
infer characteristics of dinosaurs
Lizards
and snakes
Crocodilians
Ornithischian
dinosaurs
Saurischian
dinosaurs
Birds
Common
ancestor of
crocodilians,
dinosaurs,
and birds
● Birds and crocodiles share several features:
four-chambered hearts, song, nest building,
and brooding
● These characteristics likely evolved in a
common ancestor and were shared by all of its
descendants, including dinosaurs
● The fossil record supports nest building and
brooding in dinosaurs
Phylogenetic Trees as Hypotheses
Front limb
Hind limb
Eggs (a) Fossil remains of
Oviraptor and eggs(b) Artist’s reconstruction of the dinosaur’s
posture based on the fossil findings
An organism’s evolutionary history is
documented in its genome
● Comparing nucleic acids or other molecules to
infer relatedness is a valuable approach for tracing
organisms’ evolutionary history
● DNA that codes for rRNA changes relatively slowly
and is useful for investigating branching points
hundreds of millions of years ago
● mtDNA evolves rapidly and can be used to explore
recent evolutionary events (i.e. human ancestral
groups)
Molecular clocks help track
evolutionary time
● To extend molecular phylogenies beyond the fossil
record, we must make an assumption about how
change occurs over time
Molecular Clocks
Molecular Clocks
● A molecular clock uses constant rates of evolution
in some genes to estimate the absolute time of
evolutionary change
● In orthologous genes (genes found in different
species; e.g. cytochrome c for E.T.C.), nucleotide
substitutions are proportional to the time since they
last shared a common ancestor
● In paralogous genes (similar genes found within
one species; e.g. olfactory receptor genes in
humans), nucleotide substitutions are proportional
to the time since the genes became duplicated
● Molecular clocks are
calibrated against
branches whose dates
are known from the
fossil record
● Individual genes vary
in how clocklike they
are
Molecular Clocks
Divergence time (millions of years)
Nu
mb
er o
f m
uta
tio
ns
90
60
30
30 60 90 120
0