Chapter 25

Phylogeny and Systematics

PowerPoint Lectures for Biology, Seventh Edition
Neil Campbell and Jane Reece

Lectures by Chris Romero
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• Overview: Investigating the Tree of Life • This chapter describes how biologists trace phylogeny
– The evolutionary history of a species or group of related species

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• Biologists draw on the fossil record
– Which provides information about ancient organisms

Figure 25.1
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• Biologists also use systematics
– As an analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct

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• Currently, systematists use
– Morphological, biochemical, and molecular comparisons to infer evolutionary relationships

Figure 25.2
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• Concept 25.1: Phylogenies are based on common ancestries inferred from fossil, morphological, and molecular evidence

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The Fossil Record • Sedimentary rocks
– Are the richest source of fossils – Are deposited into layers called strata
1 Rivers carry sediment to the ocean. Sedimentary rock layers containing fossils form on the ocean floor. 2 Over time, new strata are deposited, containing fossils from each time period. 3 As sea levels change and the seafloor is pushed upward, sedimentary rocks are exposed. Erosion reveals strata and fossils.

Younger stratum with more recent fossils Older stratum with older fossils

Figure 25.3

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• The fossil record
– Is based on the sequence in which fossils have accumulated in such strata

• Fossils reveal
– Ancestral characteristics that may have been lost over time

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• Though sedimentary fossils are the most common
– Paleontologists study a wide variety of fossils

(c) Leaf fossil, about 40 million years old

(b) Petrified tree in Arizona, about 190 million years old (a) Dinosaur bones being excavated from sandstone

(d) Casts of ammonites, about 375 million years old (f) Insects preserved whole in amber

Figure 25.4a–g

(g) Tusks of a 23,000-year-old mammoth, frozen whole in Siberian ice

(e) Boy standing in a 150-million-year-old dinosaur track in Colorado

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Morphological and Molecular Homologies • In addition to fossil organisms
– Phylogenetic history can be inferred from certain morphological and molecular similarities among living organisms

• In general, organisms that share very similar morphologies or similar DNA sequences
– Are likely to be more closely related than organisms with vastly different structures or sequences

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Sorting Homology from Analogy • A potential misconception in constructing a phylogeny
– Is similarity due to convergent evolution, called analogy, rather than shared ancestry

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• Convergent evolution occurs when similar environmental pressures and natural selection
– Produce similar (analogous) adaptations in organisms from different evolutionary lineages

Figure 25.5
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• Analogous structures or molecular sequences that evolved independently
– Are also called homoplasies

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Evaluating Molecular Homologies
• Systematists use computer programs and mathematical tools – When analyzing comparable DNA segments from different organisms
1

Ancestral homologous DNA segments are identical as species 1 and species 2 begin to diverge from their common ancestor.

1 C C A T C A G A G T C C 2 C C A T C A G A G T C C

A C G G A T A G T C C A C T A G G C A C T A T C A C C G A C A G G T C T T T G A C T A G

Deletion
2

Deletion and insertion mutations shift what had been matching sequences in the two species.

1 2

C C A T C A G A G T C C C C A T C A G A G T C C

Figure 25.7

G T A Insertion

3

Homologous regions (yellow) do not all align because of these mutations.

1 2

C C A T C C A T

C A

A G T C C C A G A G T C C

G T A

4

Figure 25.6

Homologous regions realign after a computer program adds gaps in sequence 1.

1 2

C C A T C C A T G T A

C A C A G

A G T C C A G T C C

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• Concept 25.2: Phylogenetic systematics connects classification with evolutionary history • Taxonomy
– Is the ordered division of organisms into categories based on a set of characteristics used to assess similarities and differences

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Binomial Nomenclature • Binomial nomenclature
– Is the two-part format of the scientific name of an organism – Was developed by Carolus Linnaeus

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• The binomial name of an organism or scientific epithet
– Is latinized – Is the genus and species

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Hierarchical Classification • Linnaeus also introduced a system
– For grouping species in increasingly broad categories
Panthera Species pardus Genus Family Order Class Phylum Kingdom Panthera Felidae Carnivora Mammalia Chordata Animalia Eukarya

Figure 25.8

Domain

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Linking Classification and Phylogeny • Systematists depict evolutionary relationships
– In branching phylogenetic trees
Species Genus

Panthera Mephitis Canis Canis Lutra lutra pardus mephitis familiaris lupus (European (leopard) (striped skunk) otter) (domestic dog) (wolf)

Panthera

Mephitis

Lutra

Canis

Family

Felidae

Mustelidae

Canidae

Order

Carnivora

Figure 25.9
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• Each branch point
– Represents the divergence of two species

Leopard

Domestic cat

Common ancestor
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• “Deeper” branch points
– Represent progressively greater amounts of divergence

Wolf

Leopard

Domestic cat

Common ancestor
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• Concept 25.3: Phylogenetic systematics informs the construction of phylogenetic trees based on shared characteristics • A cladogram
– Is a depiction of patterns of shared characteristics among taxa

• A clade within a cladogram
– Is defined as a group of species that includes an ancestral species and all its descendants

• Cladistics
– Is the study of resemblances among clades
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Cladistics • Clades
– Can be nested within larger clades, but not all groupings or organisms qualify as clades

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• A valid clade is monophyletic
– Signifying that it consists of the ancestor species and all its descendants
Grouping 1 D C E G F H J I K

B A (a) Monophyletic. In this tree, grouping 1, consisting of the seven species B–H, is a monophyletic group, or clade. A monophyletic group is made up of an ancestral species (species B in this case) and all of its descendant species. Only monophyletic groups qualify as legitimate taxa derived from cladistics.

Figure 25.10a

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• A paraphyletic clade
– Is a grouping that consists of an ancestral species and some, but not all, of the descendants Grouping 2
D C E G F H J I K

B A (b) Paraphyletic. Grouping 2 does not meet the cladistic criterion: It is paraphyletic, which means that it consists of an ancestor (A in this case) and some, but not all, of that ancestor’s descendants. (Grouping 2 includes the descendants I, J, and K, but excludes B–H, which also descended from A.)

Figure 25.10b

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• A polyphyletic grouping
– Includes numerous types of organisms that lack a common ancestor
Grouping 3 D C E G F H J I K

B A (c) Polyphyletic. Grouping 3 also fails the cladistic test. It is polyphyletic, which means that it lacks the common ancestor of (A) the species in the group. Furthermore, a valid taxon that includes the extant species G, H, J, and K would necessarily also contain D and E, which are also descended from A.

Figure 25.10c

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Shared Primitive and Shared Derived Characteristics

• In cladistic analysis
– Clades are defined by their evolutionary novelties

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• A shared primitive character
– Is a homologous structure that predates the branching of a particular clade from other members of that clade – Is shared beyond the taxon we are trying to define

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• A shared derived character
– Is an evolutionary novelty unique to a particular clade

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Outgroups • Systematists use a method called outgroup comparison
– To differentiate between shared derived and shared primitive characteristics

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• As a basis of comparison we need to designate an outgroup
– which is a species or group of species that is closely related to the ingroup, the various species we are studying

• Outgroup comparison
– Is based on the assumption that homologies present in both the outgroup and ingroup must be primitive characters that predate the divergence of both groups from a common ancestor
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• The outgroup comparison
– Enables us to focus on just those characters that were derived at the various branch points in the evolution of a clade
Salamander Lancelet (outgroup) TAXA Tuna Lamprey CHARACTERS Hair Amniotic (shelled) egg Four walking legs Hinged jaws Vertebral column (backbone)

0 0 0 0 0

0 0 0 0 1

0 0 0 1 1

0 0 1 1 1

0 1 1 1 1

Leopard

Turtle

1 1 1 1 1
(a) Character table. A 0 indicates that a character is absent; a 1 indicates that a character is present.

Turtle Salamander Tuna Lamprey Lancelet (outgroup)

Leopard Hair

Amniotic egg Four walking legs Hinged jaws (b) Cladogram. Analyzing the distribution of these derived characters can provide insight into vertebrate phylogeny.

Figure 25.11a, b

Vertebral column

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Phylogenetic Trees and Timing • Any chronology represented by the branching pattern of a phylogenetic tree
– Is relative rather than absolute in terms of representing the timing of divergences

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Phylograms
• In a phylogram – The length of a branch in a cladogram reflects the number of genetic changes that have taken place in a particular DNA or RNA sequence in that lineage
os Dr hil op a

e nc La

Am

ph ib

Fi

let

sh

ia n

an

H um

Figure 25.12
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M ou

Bi

R

rd

at

se

Ultrametric Trees
• In an ultrametric tree – The branching pattern is the same as in a phylogram, but all the branches that can be traced from the common ancestor to the present are of equal length
ila

hib i Am p
sh Fi

an
rd Hu ma n R at M ou se el et Bi

D ro s

op h

Cenozoic

Mesozoic

Paleozoic

Proterozoic

Figure 25.13
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Millions of years ago

542

251

65.5

La nc

Maximum Parsimony and Maximum Likelihood • Systematists
– Can never be sure of finding the single best tree in a large data set – Narrow the possibilities by applying the principles of maximum parsimony and maximum likelihood

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• Among phylogenetic hypotheses
– The most parsimonious tree is the one that requires the fewest evolutionary events to have occurred in the form of shared derived characters

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• Applying parsimony to a problem in molecular systematics

Human Human Mushroom 0

Mushroom 30% 0

Tulip 40% 40% 0

Tulip

Figure 25.14

(a) Percentage differences between sequences

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• Applying parsimony to a problem in molecular systematics

25%

15%

15%

20%

15%

10% 5% 5%

Tree 1: More likely

Tree 2: Less likely

Figure 25.14

(b) Comparison of possible trees

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• The principle of maximum likelihood
– States that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events
APPLICATION In considering possible phylogenies for a group of species, systematists compare molecular data for the species. The most efficient way to study the various phylogenetic hypotheses is to begin by first considering the most parsimonious—that is, which hypothesis requires the fewest total evolutionary events (molecular changes) to have occurred. TECHNIQUE 1 Follow the numbered steps as we apply the principle of parsimony to a hypothetical phylogenetic problem involving four closely related bird species. First, draw the possible phylogenies for the species (only 3 of the 15 possible trees relating these four species are shown here).

Species I I II III IV

Species II

Species III

Species IV

I

III

II

IV

I

IV

II

III

Three possible phylogenetic hypothese 1 2 Tabulate the molecular data for the species (in this simplified example, the data represent a DNA sequence consisting of just seven nucleotide bases). Species I II III IV I A 3 Now focus on site 1 in the DNA sequence. A single basechange event, marked by the crossbar in the branch leading to species I, is sufficient to account for the site 1 data. G Base-change event G A G G G II G Sites in DNA sequence 2 5 6 3 4 7 G G A G III G G G G A G A G G IV G G G G A A G G A A T G T G

Bases at site 1 for each species

Figure 25.15a

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4 Continuing the comparison of bases at sites 2, 3, and 4 reveals that each of these possible trees requires a total of four base-change events (marked again by crossbars). Thus, the first four sites in this DNA sequence do not help us identify the most parsimonious tree.

I

II

III

IV

I

III

II

IV

I

IV

II

III

5 After analyzing sites 5 and 6, we find that the first tree requires fewer evolutionary events than the other two trees (two base changes versus four). Note that in these diagrams, we assume that the common ancestor had GG at sites 5 and 6. But even if we started with an AA ancestor, the first tree still would require only two changes, while four changes would be required to make the other hypotheses work. Keep in mind that parsimony only considers the total number of events, not the particular nature of the events (how likely the particular base changes are to occur).

I II GG GG GG

III AA

IV AA AA

I III GG AA GG

II GG

IV AA GG

I IV GG AA GG

II GG

III AA GG

GG I T T T II G III T

Two base changes

GG III T II G IV G G I T T IV G

GG II G III T T

6 At site 7, the three trees also differ in the number of evolutionary events required to explain the DNA data.

IV G T

I T T

T III IV I III II IV I IV

T II III

RESULTS To identify the most parsimonious tree, we total all the base-change events noted in steps 3–6 (don’t forget to include the changes for site 1, on the facing page). We conclude that the first tree is the most parsimonious of these three possible phylogenies. (But now we must complete our search by investigating the 12 other possible trees.)

I

II

Figure 25.15b
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8 events

9 events

10 events

Phylogenetic Trees as Hypotheses • The best hypotheses for phylogenetic trees
– Are those that fit the most data: morphological, molecular, and fossil

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• Sometimes there is compelling evidence
– That the best hypothesis is not the most parsimonious
Lizard Bird Mammal

Four-chambered heart

(a) Mammal-bird clade

Lizard

Bird

Mammal

Four-chambered heart Four-chambered heart

Figure 25.16a, b

(b) Lizard-bird clade

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• Concept 25.4: Much of an organism’s evolutionary history is documented in its genome • Comparing nucleic acids or other molecules to infer relatedness
– Is a valuable tool for tracing organisms’ evolutionary history

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Gene Duplications and Gene Families • Gene duplication
– Is one of the most important types of mutation in evolution because it increases the number of genes in the genome, providing further opportunities for evolutionary changes

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• Orthologous genes
– Are genes found in a single copy in the genome – Can diverge only once speciation has taken place
Ancestral gene

Speciation

(a)

Figure 25.17a

Orthologous genes

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• Paralogous genes
– Result from gene duplication, so they are found in more than one copy in the genome – Can diverge within the clade that carries them, often adding new functions
Ancestral gene

Gene duplication

Figure 25.17b

(b)

Paralogous genes

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Genome Evolution • Orthologous genes are widespread
– And extend across many widely varied species

• The widespread consistency in total gene number in organisms of varying complexity
– Indicates that genes in complex organisms are extremely versatile and that each gene can perform many functions

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• Concept 25.5: Molecular clocks help track evolutionary time

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Molecular Clocks • The molecular clock
– Is a yardstick 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

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Neutral Theory • Neutral theory states that
– Much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection – And that the rate of molecular change in these genes and proteins should be regular like a clock

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Difficulties with Molecular Clocks • The molecular clock
– Does not run as smoothly as neutral theory predicts

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Applying a Molecular Clock: The Origin of HIV • Phylogenetic analysis shows that HIV
– Is descended from viruses that infect chimpanzees and other primates

• A comparison of HIV samples from throughout the epidemic
– Has shown that the virus has evolved in a remarkably clocklike fashion

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The Universal Tree of Life
• The tree of life – • Is divided into three great clades called domains: Bacteria, Archaea, and Eukarya

The early history of these domains is not yet clear
Bacteria 0 Eukarya Archaea 4 Symbiosis of chloroplast ancestor with ancestor of green plants Symbiosis of mitochondrial ancestor with ancestor of eukaryotes Possible fusion of bacterium and archaean, yielding ancestor of eukaryotic cells Last common ancestor of all living things

1 Billion years ago 4 3

3

2

2 2

3 1 1 Origin of life

Figure 25.18

4

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