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

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

6. 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

7. 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

8. 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

9. 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

10. Convergent evolution occurs when similar environmental pressures and natural selection
Produce similar (analogous) adaptations in organisms from different evolutionary lineages
Figure 25.5

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

12. 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

13. 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

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

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

16. 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

17. 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

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

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

20. A clade within a cladogram
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

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

22. 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

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

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

25. 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

26. 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

27. 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

28. 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

29. 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)

30. 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

31. 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

32. The End