1. Overview: Investigating the Tree of Life
The discipline of systematics classifies organisms and determines their evolutionary relationships (phylogeny) and is the study of biodiversity
Systematists use fossil, molecular, and genetic data to infer evolutionary relationships
Phylogeny is the evolutionary history of a species or group of related species

2. Phylogenies are inferred from morphological and molecular data
To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms
Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences

3. Linking Classification and Phylogeny
Systematists use phylogenetic trees
These diagrams are genealogies of probable evolutionary groups based on relationships of taxonomic groups

4. A phylogenetic tree represents a hypothesis about evolutionary relationships
Each branch point represents the divergence of two species

5. What We Can and Cannot Learn from Phylogenetic Trees
Phylogenetic trees do show patterns of descent
Phylogenetic trees do not indicate when species evolved or how much genetic change occurred in a lineage
It shouldn’t be assumed that a taxon evolved from the taxon next to it

6. Concept : Phylogenies show evolutionary relationships
Taxonomy is the ordered division and naming of organisms

7. 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: binomial nomenclature: two-part names for species and descending categories -hierarchical classification, taxons

8. 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

9. Hierarchical Classification
Linnaeus introduced a system for grouping species in increasingly broad categories
The taxonomic groups in descending categories domain, kingdom, phylum, class, order, family, genus, and species
A taxonomic unit at any level of hierarchy is called a taxon

10. Figure 26.3 Hierarchical classification
Species:
Panthera
pardus
Genus: Panthera
Family: Felidae
Order: Carnivora
Class: Mammalia
Figure 26.3 Hierarchical classification
Phylum: Chordata
Kingdom: Animalia
Bacteria
Domain: Eukarya
Archaea

11. Linnaean classification and phylogeny can differ from each other
Systematists have proposed the PhyloCode, which recognizes only groups that include a common ancestor and all its descendents

12. Lizards and snakes Crocodilians Ornithischian dinosaurs Common
Fig
Lizards
and snakes
Crocodilians
Ornithischian
dinosaurs
Common
ancestor of
crocodilians,
dinosaurs,
and birds
Saurischian
dinosaurs
lFigure A phylogenetic tree of birds and their close relatives
Birds

13. Monophyletic – grouping consists of a single ancestor that gave rise gave rise to all descendents ( single tribe )
Ideal example for systematics

14. (a) Monophyletic group (clade)
Fig a A B
Group I C D E F
Figure 26.10a Monophyletic, paraphyletic, and polyphyletic groups G
(a) Monophyletic group (clade)

15. A polyphyletic grouping consists of various species that lack a common ancestor
Do not reflect evolutionary history

16. (b) Polyphyletic group
Fig c A B C D
Group II E F
Figure 26.10c Monophyletic, paraphyletic, and polyphyletic groups G
(b) Polyphyletic group

17. A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants
Do not reflect evolutionary history

18. (c) Paraphyletic group
Fig b A B C D
Group III E F
Figure 26.10b Monophyletic, paraphyletic, and polyphyletic groups G
(c) Paraphyletic group

19. Sorting Homology from Analogy
When constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy
Homology same structure different function, is similarity due to shared ancestry ex- bat skeleton to bird skeleton
Analogy structure from a different ancestor with similar function, is similarity due to convergent evolution ex bat wing analogous to bird wing

20. Fig. 26-7
Figure 26.7 Convergent evolution of analogous burrowing characteristics Australian mole, American mole have different internal anatomy, physiology, reproductive systems ex marsupial vs placental yes they have a common ancestor 140 million years ago but analogous characters developed in these lineages to adapt similar life styles

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

22. Shared characters are used to construct phylogenetic trees
Once homologous characters have been identified, they can be used to infer a phylogeny

23. Molecular Support 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
DNA that codes for rRNA changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago

24. Tools of the trade Nucleic Acids
DNA hybridization measures a closely related species by the tightness between DNA H bonds
Ex- found a giant panda is a bear
a raccoon is a lesser panda
Restriction maps are used to compare mitochondrial DNA because it mutates 10X faster than the genome
Ex – used to study Native American groups
DNA sequence of actual nucleotides analysis helps construct phylogenic trees

25. Proteins Compare amino acid sequences
Hemoglobin c and cytochrome c are ancient proteins in all aerobic species
Ex- humans compare to a chimp identical aa, dog differs by 13 aa
However only 2% of the genome codes for protein

26. Concept 26.5: 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

27. Molecular Clocks
A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change
Valid if mutation rates are constant

28. Molecular clocks are calibrated against branches whose dates are known from the fossil record

29. 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
Application of a molecular clock to one strain of HIV suggests that that strain spread to humans during the 1930s

30. Index of base changes between HIV sequences
Fig
0.20
0.15
Computer model
of HIV
Index of base changes between HIV sequences
0.10
Range
Figure Dating the origin of HIV-1 M with a molecular clock
0.05
1900
1920
1940
1960
1980
2000
Year

31. Difficulties with Molecular Clocks
The molecular clock does not run as smoothly as neutral theory predicts
Neutral evolution means that mutation rates are constant
Adaptation doesn’t fit into this idea
Irregularities result from natural selection in which some DNA changes are favored over others
Working with DNA has it problems (2 in notes)

32. Science of Systematics
Two new approaches Phenetics and Cladistics
Phenetics – bases taxonomy difference on measurable similarities and differences
Compares anatomical characteristics
Doesn’t sort out homology from analogy
Phenetics contends that if enough phenotypes are examined homology will prevail

33. Cladistics
Cladistics phylogenic systematics, groups organisms by common descent
A clade is a group of species that includes an ancestral species and all its descendants

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

35. 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 ancestral characteristics
Outgroup is clearly not related

36. Maximum parsimony assumes that the tree that requires the fewest evolutionary changes (appearances of shared derived characters) is the most likely
Synamorphies -appearances of shared derived characters

37. Shared Ancestral and Shared Derived Characters
In comparison with its ancestor, an organism has both shared and different characteristics

38. A shared ancestral character is a character that originated in an ancestor of the taxon
A shared derived character is an evolutionary novelty unique to a particular clade
A character can be both ancestral and derived, depending on the context

39. Inferring Phylogenies Using Derived Characters
When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared

40. Amniotic (shelled) egg 1 1
Fig a
TAXA
(outgroup)
Lancelet
Salamander
Lamprey
Leopard
Tuna
Turtle
Vertebral column
(backbone) 1 1 1 1 1
Hinged jaws 1 1 1 1
CHARACTERS
Four walking legs 1 1 1
Figure Constructing a phylogenetic tree
Amniotic (shelled) egg 1 1
Hair 1
(a) Character table

41. Vertebral column Hinged jaws Four walking legs Amniotic egg Lancelet
Fig b
Lancelet
(outgroup)
Lamprey
Tuna
Vertebral
column
Salamander
Hinged jaws
Figure Constructing a phylogenetic tree
Turtle
Four walking legs
Amniotic egg
Leopard
Hair
(b) Phylogenetic tree

42. Computer programs are used to search for trees that are parsimonious and likely

43. Three phylogenetic hypotheses: I I III
Fig
Species I
Species II
Species III
Three phylogenetic hypotheses:
Figure Applying parsimony to a problem in molecular systematics I I
III II
III II
III II I

44. Site 1 2 3 4 Species I C T A T I I III Species II C T T C II III II
Fig
Site 1 2 3 4
1/C
Species I C T A T I I
III
1/C
Species II C T T C II
III II
1/C
Species III A G A C
III II I
1/C
1/C
Ancestral
sequence A G T T
Figure Applying parsimony to a problem in molecular systematics

45. Site 1 2 3 4 Species I C T A T I I III Species II C T T C II III II
Fig
Site 1 2 3 4
1/C
Species I C T A T I I
III
1/C
Species II C T T C II
III II
1/C
Species III A G A C
III II I
1/C
1/C
Ancestral
sequence A G T T
3/A
2/T
3/A I I
III
2/T
3/A
4/C II
III II
4/C
4/C
2/T
III II I
3/A
4/C
2/T
4/C
2/T
3/A
Figure Applying parsimony to a problem in molecular systematics

46. Site 1 2 3 4 Species I C T A T I I III Species II C T T C II III II
Fig
Site 1 2 3 4
1/C
Species I C T A T I I
III
1/C
Species II C T T C II
III II
1/C
Species III A G A C
III II I
1/C
1/C
Ancestral
sequence A G T T
3/A
2/T
3/A I I
III
2/T
3/A
4/C II
III II
4/C
4/C
2/T
III II I
3/A
4/C
2/T
4/C
2/T
3/A
Figure Applying parsimony to a problem in molecular systematics I I
III II
III II
III II I
6 events
7 events
7 events

47. 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 descendents
Phylogeny gained strength with cladistics using morphology, biochemistry, paleontology and comparative biology.

48. Concept 26.6: New information continues to revise our understanding of the tree of life
Recently, we have gained insight into the very deepest branches of the tree of life through molecular systematics

49. From Two Kingdoms to Three Domains
Early taxonomists classified all species as either plants or animals
Later, five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia
More recently, the three-domain system has been adopted: Bacteria, Archaea, and Eukarya
The three-domain system is supported by data from many sequenced genomes
Animation: Classification Schemes

50. EUKARYA BACTERIA ARCHAEA Fig. 26-21 Land plants Dinoflagellates
Green algae
Forams
Ciliates
Diatoms
Red algae
Amoebas
Cellular slime molds
Euglena
Trypanosomes
Animals
Leishmania
Fungi
Sulfolobus
Green nonsulfur bacteria
Thermophiles
(Mitochondrion)
Figure The three domains of life
Spirochetes
Halophiles
Chlamydia
COMMON
ANCESTOR
OF ALL
LIFE
Green
sulfur bacteria
BACTERIA
Methanobacterium
Cyanobacteria
ARCHAEA
(Plastids, including
chloroplasts)

51. BACTERIA Green nonsulfur bacteria (Mitochondrion) Spirochetes
Fig a
Green nonsulfur bacteria
(Mitochondrion)
Spirochetes
Chlamydia
COMMON
ANCESTOR
OF ALL
LIFE
Green
sulfur bacteria
Figure The three domains of life
BACTERIA
Cyanobacteria
(Plastids, including
chloroplasts)

52. ARCHAEA Sulfolobus Thermophiles Halophiles Methanobacterium
Fig b
Sulfolobus
Thermophiles
Halophiles
Figure The three domains of life
Methanobacterium
ARCHAEA

53. EUKARYA Dinoflagellates Land plants Forams Ciliates Red algae Amoebas
Fig c
EUKARYA
Land plants
Dinoflagellates
Green algae
Forams
Ciliates
Diatoms
Red algae
Amoebas
Cellular slime molds
Euglena
Trypanosomes
Animals
Leishmania
Figure The three domains of life
Fungi

54. A Simple Tree of All Life
The tree of life suggests that eukaryotes and archaea are more closely related to each other than to bacteria
The tree of life is based largely on rRNA genes, as these have evolved slowly

55. There have been substantial interchanges of genes between organisms in different domains
Horizontal gene transfer is the movement of genes from one genome to another
Horizontal gene transfer complicates efforts to build a tree of life

56. Bacteria Eukarya Archaea 4 3 2 1 Billions of years ago Fig. 26-22
Figure The role of horizontal gene transfer in the history of life 4 3 2 1
Billions of years ago

57. Is the Tree of Life Really a Ring?
Some researchers suggest that eukaryotes arose as an endosymbiosis between a bacterium and archaean
If so, early evolutionary relationships might be better depicted by a ring of life instead of a tree of life

58. Fig
Eukarya
Bacteria
Archaea
Figure A ring of life

59. Monophyletic group A A A B B B C C C D D D E E E F F F G G G
Fig. 26-UN3
Monophyletic group A A A B B B C C C D D D E E E F F F G G G
Paraphyletic group
Polyphyletic group