1. Phylogeny and Systematics
Chapter 25
Phylogeny and Systematics

2. Overview: Investigating the Tree of Life
Phylogeny is the evolutionary history of a species or group of related species
Biologists draw on the fossil record, which provides information about ancient organisms

4. Systematics is an analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct
Systematists use morphological, biochemical, and molecular comparisons to infer evolutionary relationships

6. Concept 25.1: Phylogenies are based on common ancestries inferred from fossil, morphological, and molecular evidence
To infer phylogenies, systematists gather information about morphologies, development, and biochemistry of living organisms
They also examine fossils to help establish relationships between living organisms

7. The Fossil Record Sedimentary rocks are the richest source of fossils
Sedimentary rocks are deposited into layers called strata
Video: Grand Canyon

8. LE 25-3
Rivers carry sediment to the ocean. Sedimentary rock layers containing fossils form on the ocean floor.
Over time, new strata are deposited, containing fossils from each time period.
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

9. 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

10. Animation: The Geologic Record
Though sedimentary fossils are the most common, paleontologists study a wide variety of fossils
Animation: The Geologic Record

11. LE 25-4 Leaf fossil, about 40 million years ago
Petrified trees in Arizona, about 190
million years old
Insects preserved whole in amber
Dinosaur bones being
excavated from sandstone
Casts of ammonites, about
375 million years old
Boy standing in a 150-million-year-old
dinosaur track in Colorado
Tusks of a 23,000-year-old mammoth, frozen whole
in Siberian ice

12. Morphological and Molecular Homologies
In addition to fossils, phylogenetic history can be inferred from morphological and molecular similarities in living organisms
Organisms with very similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences

13. Sorting Homology from Analogy
In constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy
Homology is similarity due to shared ancestry
Analogy is similarity due to convergent evolution

14. Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages

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

17. Evaluating Molecular Homologies
Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms

18. LE 25-6 1 2
Deletion 1 2
Insertion 1 2 1 2

20. Concept 25.2: Phylogenetic systematics connects classification with evolutionary history
Taxonomy is the ordered division of organisms into categories based on characteristics used to assess similarities and differences
In 1748, 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

21. Binomial Nomenclature
The two-part scientific name of a species is called a binomial
The first part of the name is the genus
The second part, called the specific epithet, is unique for each species within the genus
The first letter of the genus is capitalized, and the entire species name is latinized
Both parts together name the species (not the specific epithet alone)

22. Hierarchical Classification
Linnaeus introduced a system for grouping species in increasingly broad categories
Animation: Classification Schemes

23. LE 25-8 Panthera pardus Species Panthera Genus Felidae Family
Carnivora
Order
Mammalia
Class
Chordata
Phylum
Animalia
Kingdom
Eukarya
Domain

24. Linking Classification and Phylogeny
Systematists depict evolutionary relationships in branching phylogenetic trees

25. LE 25-9 Panthera pardus (leopard) Mephitis mephitis (striped skunk)
Lutra lutra
(European
otter)
Canis
familiaris
(domestic dog)
Canis
lupus
(wolf)
Species
Genus
Panthera
Mephitis
Lutra
Canis
Family
Felidae
Mustelidae
Canidae
Order
Carnivora

26. Each branch point represents the divergence of two species

27. LE 25-UN497 Leopard Domestic cat Common ancestor Wolf Leopard

28. “Deeper” branch points represent progressively greater amounts of divergence

29. A cladogram depicts patterns of shared characteristics among taxa
Concept 25.3: Phylogenetic systematics informs the construction of phylogenetic trees based on shared characteristics
A cladogram depicts patterns of shared characteristics among taxa
A clade is a group of species that includes an ancestral species and all its descendants
Cladistics studies resemblances among clades

30. Cladistics
Clades can be nested in larger clades, but not all groupings or organisms qualify as clades

31. A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants

32. LE 25-10a
Grouping 1
Monophyletic

33. A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants

34. LE 25-10b
Grouping 2
Paraphyletic

35. A polyphyletic grouping consists of various species that lack a common ancestor

36. LE 25-10c
Grouping 3
Polyphyletic

37. Shared Primitive and Shared Derived Characteristics
In cladistic analysis, clades are defined by their evolutionary novelties

38. A shared primitive character is a character that is shared beyond the taxon we are trying to define
A shared derived character is an evolutionary novelty unique to a particular clade

39. Outgroups
An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied
Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared primitive characteristics

40. Outgroup comparison assumes that homologies shared by the outgroup and ingroup must be primitive characters that predate the divergence of both groups from a common ancestor
It enables us to focus on characters derived at various branch points in the evolution of a clade

41. LE 25-11 TAXA (outgroup) Salamander Lancelet Lamprey Leopard Turtle
Tuna
Turtle
Hair
Amniotic (shelled) egg
CHARACTERS
Four walking legs
Hinged jaws
Vertebral column
(backbone)
Character table
Leopard
Turtle
Hair
Salamander
Amniotic egg
Tuna
Four walking legs
Lamprey
Hinged jaws
Lancelet (outgroup)
Vertebral column
Cladogram

42. Phylogenetic Trees and Timing
Any chronology represented by the branching of a phylogenetic tree is relative rather than absolute in representing timing of divergences

43. 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

44. LE 25-12
Drosophila
Fish
Lancelet
Amphibian
Bird
Rat
Human
Mouse

45. Ultrametric Trees
Branching in an ultrametric tree is the same as in a phylogram, but all branches traceable from the common ancestor to the present are equal length

46. LE 25-13 Drosophila Lancelet Fish Bird Human Rat Mouse Amphibian
Cenozoic
65.5
Mesozoic
251
Paleozoic
542
Neoproterozoic
Millions of
years ago

47. Maximum Parsimony and Maximum Likelihood
Systematists can never be sure of finding the best tree in a large data set
They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood

48. The most parsimonious tree requires the fewest evolutionary events to have occurred in the form of shared derived characters
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

49. LE 25-14 Human Mushroom Tulip Human 30% 40% Mushroom 40% Tulip
30%
40%
Mushroom
40%
Tulip
Percentage differences between sequences
25%
15%
15%
20%
15%
10% 5% 5%
Tree 1: More likely
Tree 2: Less likely
Comparison of possible trees

50. In considering possible phylogenies for a group of species, systematists compare molecular data for the species.
The most efficient way to study hypotheses is to consider the most parsimonious hypothesis, the one requiring the fewest evolutionary events (molecular changes)

51. Sites in DNA sequence 1 2 3 4 5 6 7 I II III IV I II III IV
LE 25-15ab
Sites in DNA sequence 1 2 3 4 5 6 7 I II
Species
III IV I II
III IV
Bases at
site 1 for
each species
Base-change
event

52. Phylogenetic Trees as Hypotheses
The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil
Sometimes the best hypothesis is not the most parsimonious

53. LE 25-16 Lizard Bird Mammal Four-chambered heart Mammal-bird clade
Lizard-bird clade

54. 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

55. Gene Duplications and Gene Families
Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes

56. Orthologous genes are genes found in a single copy in the genome
They can diverge only after speciation occurs

57. Ancestral gene Speciation Orthologous genes
LE 25-17a
Ancestral gene
Speciation
Orthologous genes

58. Paralogous genes result from gene duplication, so are found in more than one copy in the genome
They can diverge within the clade that carries them, often adding new functions

59. Ancestral gene Gene duplication Paralogous genes
LE 25-17b
Ancestral gene
Gene duplication
Paralogous genes

60. Genome Evolution
Orthologous genes are widespread and extend across many widely varied species
The widespread consistency in total gene number in organisms indicates genes in complex organisms are very versatile and that each gene can perform many functions

61. Concept 25.5: 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

62. Molecular Clocks
The molecular clock is a yardstick for measuring absolute time of evolutionary change based on the observation that some genes and other regions of genomes seem to evolve at constant rates

63. 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
It states that the rate of molecular change in these genes and proteins should be regular like a clock

64. Difficulties with Molecular Clocks
The molecular clock does not run as smoothly as neutral theory predicts
Irregularities result from natural selection in which some DNA changes are favored over others
Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty

65. Applying a Molecular Clock: The Origin of HIV
Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates
Comparison of HIV samples throughout the epidemic shows that the virus evolved in a very clocklike way

66. 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