1. Phylogeny and Systematics
Chapter 25
Phylogeny and Systematics

2. Overview: Investigating the Tree of Life
This chapter describes how biologists trace phylogeny
The evolutionary history of a species or group of related species

3. Biologists draw on the fossil record
Which provides information about ancient organisms
Figure 25.1

4. Biologists also use systematics
As an analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct

5. Currently, systematists use
Morphological, biochemical, and molecular comparisons to infer evolutionary relationships
Figure 25.2

6. Concept 25.1: Phylogenies are based on common ancestries inferred from fossil, morphological, and molecular evidence

7. 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

8. 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

9. Though sedimentary fossils are the most common
Paleontologists study a wide variety of fossils
Figure 25.4a–g
(a) Dinosaur bones being excavated from sandstone
(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
(d) Casts of ammonites, about 375 million years old
(f) Insects preserved whole in amber
(b) Petrified tree in Arizona, about 190 million years old
(c) Leaf fossil, about 40 million years old

10. 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

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

12. occurs when similar environmental pressures and natural selection
Convergent evolution
occurs when similar environmental pressures and natural selection
Produce similar (analogous) adaptations in organisms from different evolutionary lineages
Figure 25.5
Marsupial Australian mole, and eutherian North American mole

13. Analogous structures or molecular sequences that evolved independently
Are also called homoplasies

14. Evaluating Molecular Homologies
Systematists use computer programs and mathematical tools
When analyzing comparable DNA segments from different organisms
Figure 25.6
C C A T C A G A G T C C
C C A T C A G A G T C C
C C A T C A G A G T C C
G T A
Deletion
Insertion
C C A T C A A G T C C
C C A T G T A C A G A G T C C
C C A T C A A G T C C
C C A T G T A C A G A G T C C
1 Ancestral homologous DNA segments are identical as species 1 and species 2 begin to diverge from their common ancestor.
2 Deletion and insertion mutations shift what had been matching sequences in the two species.
3 Homologous regions (yellow) do not all align because of these mutations.
4 Homologous regions realign after a computer program adds gaps in sequence 1. 1 2
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
Figure 25.7

15. 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

16. Binomial Nomenclature
Is the two-part format of the scientific name of an organism
Was developed by Carolus Linnaeus

17. The binomial name of an organism or scientific epithet
Is latinized
Is the genus and species

18. Hierarchical Classification
Linnaeus also introduced a system
For grouping species in increasingly broad categories
Panthera
pardus
Felidae
Carnivora
Mammalia
Chordata
Animalia
Eukarya
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Figure 25.8

19. 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 25.9

20. Each branch point Represents the divergence of two species Leopard
Domestic cat
Common ancestor

21. “Deeper” branch points
Represent progressively greater amounts of divergence
Leopard
Domestic cat
Common ancestor
Wolf

22. 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 (taxonomic units)
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

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

24. 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 25.10a

25. 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 25.10b

26. 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 25.10c

27. Shared Primitive and Shared Derived Characteristics
In cladistic analysis
Clades are defined by their evolutionary novelties

28. 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

29. A shared derived character
Is an evolutionary novelty unique to a particular clade

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

31. 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

32. 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

33. 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

34. 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
Drosophila
Lancelet
Amphibian
Fish
Bird
Human
Rat
Mouse
Figure 25.12

35. 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
Drosophila
Lancelet
Amphibian
Fish
Bird
Human
Rat
Mouse
Cenozoic
Mesozoic
Paleozoic
Proterozoic
542
251
65.5
Millions of
years ago
Figure 25.13

36. 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

37. 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

38. Applying parsimony to a problem in molecular systematics
Human
Mushroom
Tulip
40%
30%
(a) Percentage differences between sequences
Figure 25.14

39. Applying parsimony to a problem in molecular systematics
Tree 1: More likely
(b) Comparison of possible trees
Tree 2: Less likely
15% 5%
20%
10%
25%
Figure 25.14

40. Three possible phylogenetic hypothese
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

41. Figure 25.15b I II III IV GG AA T G 10 events 9 events 8 events
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

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

43. Sometimes there is compelling evidence
That the best hypothesis is not the most parsimonious
Lizard
Four-chambered heart
Bird
Mammal
(a) Mammal-bird clade
(b) Lizard-bird clade
Figure 25.16a, b

44. Comparing nucleic acids or other molecules to infer relatedness
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

45. Gene Duplications and Gene Families
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

46. Orthologous genes Are genes found in a single copy in the genome
Can diverge only once speciation has taken place
Ancestral gene
Speciation
Orthologous genes
(a)
Figure 25.17a

47. 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
Paralogous genes
Figure 25.17b
(b)

48. Orthologous genes are widespread
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

49. Concept 25.5: Molecular clocks help track evolutionary time

50. 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

51. 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

52. Difficulties with Molecular Clocks
The molecular clock
Does not run as smoothly as neutral theory predicts

53. 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

54. 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
Figure 25.18