1. Phylogeny and the Tree of Life
Chapter 26
Phylogeny and the Tree of Life

2. Phylogeny and Systematics
Phylogeny: the evolutionary history of a species – based on common ancestries inferred from:
Fossil records
Morphological & biochemical resemblances
Molecular evidence
Systematics: a discipline that focuses on classifying organisms and their evolutionary relationships.

3. The Fossil Record Sedimentary rock are the richest source of fossils.
The fossil record is a substantial, but incomplete, chronicle of evolutionary history.
The history of life on Earth is punctuated by mass extinctions
Biologists draw on the fossil record
Which provides information about ancient organisms

4. 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 22.3

5. The Fossil Record The fossil record Fossils reveal
Is based on the sequence in which fossils have accumulated in such strata
Fossils reveal
Ancestral characteristics that may have been lost over time

6. Biologists also use systematics
As an analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct
Currently, systematists use
Morphological, biochemical, and molecular comparisons to infer evolutionary relationships

7. 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
NOTE: DNA sequence comparisons are the BEST evidence of close relation.

8. Sorting Homology from Analogy
A potential misconception in constructing a phylogeny
Is similarity due to convergent evolution, called analogy, rather than shared ancestry
It is important in phylogeny to sort HOMOLOGY from ANALOGY.
Homologous structures – common ancestry
Analogous structures – convergent evolution by similar environmental pressures

9. Convergent Evolution and Analogous Structures
Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages
Figure 25.10

10. Homoplasies
Analogous structures or molecular sequences that evolved independently are also called homoplasies

11. Taxonomy
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

12. Binomial Nomenclature
Is the two-part format of the scientific name of an organism
Was developed by Carolus Linnaeus
The binomial name of an organism or scientific epithet
Is latinized
Is the genus and species

13. Hierarchical Classification
Linnaeus also introduced a system for grouping species in increasingly broad categories
If organisms A, B, and C belong to the same order but to different families and if organisms D, E, and F belong to the same family but to different genera, which pair of organisms would show the greatest degree of structural homology?
Panthera
pardus
Felidae
Carnivora
Mammalia
Chordata
Animalia
Eukarya
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
A and B?
A and C?
B and D
C and F
E and F
Figure 25.7

14. Linking Classification and Phylogeny
Systematists depict evolutionary relationships in branching phylogenetic trees
Panthera pardus (leopard)
Mephitis mephitis (striped skunk)
Lutra lutra (European otter)
Canis familiaris (domestic dog)
Canis lupus (wolf)
Panthera
Mephitis
Lutra
Canis
Felidae
Mustelidae
Canidae
Carnivora
Order
Family
Genus
Species
Figure 25.8

15. Linking Classification and Phylogeny
Each branch point
Represents the divergence of two species
Leopard
Domestic cat
Common ancestor

16. Linking Classification and Phylogeny
“Deeper” branch points
Represent progressively greater amounts of divergence
Leopard
Domestic cat
Common ancestor
Wolf

17. Cladistics
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

18. Cladistics
Clades
Can be nested within larger clades, but not all groupings or organisms qualify as clades

19. A valid clade is monophyletic
Monophyletic Clades
A valid clade is monophyletic
Signifying that it consists of the ancestor species and all its descendants
(a) Monophyletic. In this tree, grouping 1, consisting of the seven species B–H, is a monophyletic group, or clade. A mono- phyletic 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.
Grouping 1 D C E G F B A J I K H
Figure 25.9a

20. Paraphyletic Clades A paraphyletic clade
Is a grouping that consists of an ancestral species and some, but not all, of the descendants
(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.) D C E B G H F J I K A
Grouping 2
Figure 25.9b

21. A polyphyletic grouping
Polyphyletic Clades
A polyphyletic grouping
Includes numerous types of organisms that lack a common ancestor
Grouping 3
(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. Further- more, 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. D C B E G F H A J I K
Figure 25.9c

22. Cladograms
Phylogenetic trees are constructed to reflect the hierarchial classification of taxonomic groups nested within more inclusive groups.
Today, most systematists practice cladistics.
A phylogenetic diagram based on cladistics is called a cladogram – and a valid cladogram is monophyletic. 22

23. Anatomy of the Cladogram

24. Characters and Cladograms
The term “character” is referring to any feature that a particular taxon possesses.
2 Types:
Shared Primitive Characters: a homology common to a taxon more inclusive than the one being defined.
Shared Derived Characters: an evolutionary novelty unique to a particular clade (also called synapomorphies).
The sequence of branching in a cladogram represents the sequence in which SHARED DERIVED CHARACTERS evolved. 24

25. Shared Primitive and Shared Derived Characteristics
In cladistic analysis
Clades are defined by their evolutionary novelties
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
A shared derived character
Is an evolutionary novelty unique to a particular clade
also called synapomorphies

26. Classification Using Cladograms
To refine evolutionary classification, biologists now prefer a method called cladistics
Cladistics considers only those characteristics that are new characteristics that arise as lineages evolve over time
Characteristics that appear in recent parts of a lineage but not in its older members are called derived characters (synapomorphies). 26

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

28. The outgroup comparison
Outgroup Comparisons
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
TAXA
Turtle
Leopard
Tuna
Lamprey
Lancelet (outgroup) 1
Hair
Amniotic (shelled) egg
Four walking legs
Hinged jaws
Vertebral column (backbone)
Amniotic egg
Vertebral column
(a) Character table. A 0 indicates that a character is absent; a 1 indicates that a character is present.
(b) Cladogram. Analyzing the distribution of these derived characters can provide insight into vertebrate phylogeny.
CHARACTERS
Figure 25.11a, b

29. Performing Outgroup Comparison
See text page 543
See figure 26.11
Understand outgroup v/s ingroup and how both are used to build cladograms. 29

30. 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

31. 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
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

32. Parsimony
Create “tree” that explains data envoking the fewest number of evolutionary events.

33. Principle of Maximum Likelihood
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 Follow the numbered steps as we apply the principle of parsimony to a hypothetical phylogenetic problem involving four closely related bird species.
Species I
Species II
Species III
Species IV I II
III IV
Sites in DNA sequence
Three possible phylogenetic hypothese 1 2 3 4 5 6 7 A G T
Bases at site 1 for each species
Base-change event
1 First, draw the possible phylogenies for the species (only 3 of the 15 possible trees relating these four species are shown here).
2 Tabulate the molecular data for the species (in this simplified example, the data represent a DNA sequence consisting of just seven nucleotide bases).
3 Now focus on site 1 in the DNA sequence. A single base- change event, marked by the crossbar in the branch leading to species I, is sufficient to account for the site 1 data.
Species
Figure 25.15a

34. Principle of Maximum Likelihood
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 GG AA T G
10 events
9 events
8 events
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).
Two base
changes
6 At site 7, the three trees also differ in the number of evolutionary events required to explain the DNA data.
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.)
Figure 25.15b

35. Phylogenetic Trees as Hypotheses
The best hypotheses for phylogenetic trees
Are those that fit the most data: morphological, molecular, and fossil
Sometimes there is compelling evidence that the best hypothesis is not the most parsimonious
See figure 25.16

36. Tools for Tracing Evolutionary History
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

37. Molecular Clocks Molecular clocks help track evolutionary time
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
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
Does not run as smoothly as neutral theory predicts

38. 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

39. 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
Eukarya
Archaea
4 Symbiosis of chloroplast ancestor with ancestor of green plants 1
3 Symbiosis of mitochondrial ancestor with ancestor of eukaryotes 4
Billion years ago 3 2
2 Possible fusion of bacterium and archaean, yielding ancestor of eukaryotic cells 2 3
1 Last common ancestor of all living things 1
Origin of life 4

40. Timeline of Classification
– 322 B.C. Aristotle
2 Kingdom Broad Classification – Plants or Animals
Carl Linnaeus
2 Kingdom Multi-Divisional Classification
(Kingdom, Phylum, Class, Order, Family Genus, Species)
3. Evolutionary Classification – (After Darwin)
Group By lines of Evolutionary Descent
4. Five Kingdom System – 1950s
(Whittaker) – 1950s – Plantae, Fungi, Animalia, Protista, Monera
6. Three Domain System – late 1990s
late 1990s – Bacteria, Archaea, Eukarya 40

41. Linnaeus System Evolves from TWO Kingdoms to FIVE
As we learned more about different kinds of life, there needed to be more Kingdoms
1800’s – Added Kingdom Protista
Amoeba, Slime Molds
1950’s – Added Fungi and Monera
Fungi distinguished from Plants
Prokaryotes (no nucleus) bacteria given category
1970’s – Split Kingdom Monera into 2 separate Kingdoms
Eubacteria – bacteria with peptidoglycan
Archaebacteria – bacteria without peptidoglycan 41

42. The Five-Kingdom System
Reflected increased knowledge of life’s diversity
Kingdom is highest – most inclusive taxonomic category
Five Kingdoms include:
Monera
Protista
Plantae
Fungi
Animalia
Recognized 2 types of cells: prokaryotes & eukaryotes 42

43. The Five-Kingdom System
Described classification as:
Plantae, Fungi, Animalia, Protista, Monera
recognizes only 2 types of cells: prokaryotic and eukaryotic
sets all prokaryotes apart from eukaryotes
prokaryotes are in their own kingdom (Monera)
distinguished 3 kingdoms of eukaryotes based on mode of nutrition
protista were all eukaryotes that did not fit the definition of plants, fungi, or animals

44. Whittaker’s five-kingdom system

45. Figure 26.16 Our changing view of biological diversity

46. The Three-Domain System
Molecular analyses have given rise to the most current classification system – the Three Domain System
Domain is larger than kingdom (superkingdoms)
The 3 Domain System is the most recent classification system and includes:
Bacteria
Archaea
Eukarya 46

47. The Three Domain System
Describes classification as:
Not all prokaryotes are closely related (not monophyletic)
Prokaryotes split early in the history of living things (not all in one lineage)
Archaea are more closely related to Eukarya than to Bacteria
Eukarya are not directly related to Eubacteria
There was a common ancestor for all extant organisms (monophyletic)
Eukaryotes are more closely related to each other (than prokaryotes are to each other)

48. Classification of Living Things
Section 18-3
Classification of Living Things
Go to Section: 48