1. Phylogeny and Systematics
Chapter 25
Phylogeny and Systematics

2. History of Life (See Table 26.1) 4500 Eras
Boundaries between units in the Geologic Time Scale are marked by dramatic biotic change
A figure from Ch. 26…
4500
Origin of Earth

3. 5 Kingdom classification system in use through the late 1900s

4. 5 Kingdom classification system in use through the late 1900s gave way to Woese’s 3 Domains

5. 5 Kingdom classification system in use through the late 1900s gave way to Woese’s 3 Domains and multiple Kingdoms

6. “Did King Philip Come Over For Gumbo Sunday?”
Fig. 25.8
“Did King Philip Come Over For Gumbo Sunday?”
Taxon (taxa) = the named taxonomic unit(s) at any level in this taxonomic hierarchy
Each taxonomic level is more inclusive or comprehensive than the previous one (moving from species toward domains).
Panthera = genus
pardus = specific epithet that refers to one species in the genus Panthera

7. Linnaeus convinced us to use a hierarchical classification system
Darwin provided us with the mechanism by which evolution results in descent with modification
Taxonomy – naming & classifying organisms
Systematics – naming & classifying organisms according to their evolutionary relationships
These two contributions (from Linnaeus and Darwin) combine in the modern branches of biology known as taxonomy, systematics, phylogenetics, and systematic phylogenetics.
Systematic Phylogenetics
Phylogenetics – reconstructing the evolutionary relationships among organisms

8. Macroevolution & Phylogeny
Phylogenetic tree
– hypothesized genealogy traced back to the last common ancestor (i.e., the most recent) through hierarchical, dichotomous branching
Note that this is a highly pruned tree!
Cladistics – the principles that guide the production of phylogenetic trees, a.k.a., cladograms

9. Macroevolution & Phylogeny
Phylogenetic tree, phylogeny, or cladogram
Node – branch point, speciation event
Note that this is a highly pruned tree!

10. Macroevolution & Phylogeny
Phylogenetic tree, phylogeny, or cladogram
Note that this is a highly pruned tree!
Lineage or clade – an entire branch

11. Macroevolution & Phylogeny
Phylogenetic tree, phylogeny, or cladogram
Note that this is a highly pruned tree!
Lineage or clade – an entire branch

12. Macroevolution & Phylogeny
Phylogenetic tree, phylogeny, or cladogram
Note that this is a highly pruned tree!
Lineage or clade – an entire branch

13. Macroevolution & Phylogeny
Phylogenetic tree, phylogeny, or cladogram
Note that this is a highly pruned tree!
A clade is a monophyletic group, i.e., an ancestral species and all of its descendents

14. Macroevolution & Phylogeny
Phylogenetic tree, phylogeny, or cladogram
Note that this is a highly pruned tree!
A clade is a monophyletic group, i.e., an ancestral species and all of its descendents

15. Macroevolution & Phylogeny
Phylogenetic tree, phylogeny, or cladogram
Note that this is a highly pruned tree!
A clade is a monophyletic group, i.e., an ancestral species and all of its descendents

16. Macroevolution & Phylogeny
Phylogenetic tree, phylogeny, or cladogram
Note that this is a highly pruned tree!
A paraphyletic group consists of an ancestor and some of its descendents

17. Macroevolution & Phylogeny
Phylogenetic tree, phylogeny, or cladogram
Note that this is a highly pruned tree!
A polyphyletic group lacks the common ancestor of species in the group

18. Macroevolution & Phylogeny
Note that this is a highly pruned tree!
Fig. 25.9
Taxonomic groups often reflect true clades…

19. Macroevolution & Phylogeny
However, tension sometimes exists between taxonomic tradition and cladistic hypotheses…
Note that phylogenetic trees can be oriented any which way.

20. Macroevolution & Phylogeny
E.g., If the Class Reptilia is to be monophyletic, birds must be included!

21. Macroevolution & Phylogeny
How are phylogenetic trees constructed?

22. Macroevolution & Phylogeny
The fossil record is especially valuable, and the only option for many extinct taxa

23. Macroevolution & Phylogeny
However, we almost never have a continuous record from one species to the next

24. Macroevolution & Phylogeny
Cladistic principles allow us to construct hypothesized phylogenetic trees

25. Cladistic Analysis
Fossils provide morphological data for extinct species, whereas comparisons of multiple types of traits – including molecular – do so for extant species

26. Cladistic Analysis
Similar characters (e.g., morphological, behavioral, molecular, etc. traits or features) suggest relatedness…
Wasps [Hymenoptera]

27. Cladistic Analysis
But, not all similarity derives from common ancestry!
Mantisfly [Neuroptera]
Convergent evolution can produce superficially similar traits that lack homology with one another

28. Cladistic Analysis Homologous characters share common ancestry
Lack of similarity among taxa results from divergence

29. Cladistic Analysis Analogous characters do not share common ancestry
Similarity among taxa results from convergence

30. Cladistic Analysis
As a general rule, the more homologous characters shared by two species, the more closely they are related
Sequences of DNA & RNA (nucleotides) and proteins (amino acids) are used as characters; as a general rule, the more recently two species shared a common ancestor, the more similar their sequences

31. Each nucleotide can be treated as a character
Cladistic Analysis
Each nucleotide can be treated as a character
Character changes (mutations) from the ancestral to the derived state include:
Substitutions
…AGCTCTAGG…
…AGCTATAGG…
Insertions
A = adenine; C = cytosine; G = guanine; T = thymine
…AGCTCTAGG…
Mutations
…AGCTGATCTAGG…
Deletions
…AGCTCTAGG…
…AGCTCTAGG…

32. All similar characters
Cladistic Analysis
Shared Primitive Characters (ancestral)
Analogies
All similar characters
Homologies
Shared Derived Characters(unique to a clade)
This flowchart summarizes types of similarities among species…
The sequence of branching in a cladogram then represents the sequence in which evolutionary novelties (shared derived characters) evolved

33. Ingroup = the group whose relationships we are trying to resolve
Cladistic Analysis
Ingroup vs. Outgroup
Ingroup = the group whose relationships we are trying to resolve
Fig

34. Cladistic Analysis Ingroup vs. Outgroup
Outgroup = a species (or group) known to have an older most recent common ancestor with the ingroup than the ingroup’s most recent common ancestor
Fig

35. Cladistic Analysis Ingroup vs. Outgroup
An outgroup helps identify shared ancestral and shared derived characters (unique to a clade)
Fig

36. Parsimony & Occam’s Razor
Cladistic Analysis
Parsimony & Occam’s Razor
The most parsimonious tree is the one that requires the fewest evolutionary events (appearance of shared derived characters)
Fig

37. Parsimony & Occam’s Razor
Cladistic Analysis
Parsimony & Occam’s Razor
On this most parsimonious cladogram, each key character originated (evolved) once
Fig

38. Cladistic Analysis An example… See Fig. 25.15 for another example
Outgroup
Ingroup
See Fig for another example

39. Cladistic Analysis An example… See Fig. 25.15 for another example
Outgroup
Ingroup
Create potential topologies for the tree
See Fig for another example

40. Cladistic Analysis An example… See Fig. 25.15 for another example
Outgroup
Ingroup
Create potential topologies for the tree
The first topology requires 7 changes, the second 9, and the third 8.
Map the characters onto the trees
Choose the most parsimonious tree
See Fig for another example

41. Macroevolution & Phylogeny
Sometimes the most parsimonious arrangement for one character is not the most accurate overall…
Bird-mammal clade
Lizard-bird clade
Fig

42. Macroevolution & Phylogeny
Don’t confuse the age of a clade with the age of its component species
African Rift Lake Cichlid
Alligator Snapping Turtle
~ 200,000 yr
~ 20,000,000 yr
Based on the cladogram, which species is likely to be older?
Once a clade arises, speciation events can continue to occur within it.

43. Macroevolution & Phylogeny
The overall trend is increasing diversity, with periodic episodes of extinction
Fig. 26.8

44. Macroevolution & Phylogeny
Cretaceous mass extinction
Asteroid impacts may have caused mass extinction events
Cretaceous mass extinction marks boundary between Cretaceous and Tertiary Periods.
Permian mass extinction
Extinction of >90% of species

45. Macroevolution & Phylogeny
K-T impact event

46. Macroevolution & Phylogeny
Continental drift is responsible for many cladogenic events & biogeograhic distribution patterns
E.g., Proteaceae – a plant family that originated in Gondwana

47. Continental drift results from plate tectonics
Fig

48. Macroevolution & Phylogeny
Some biogeographic similarities result from common ancestry (common descent)
E.g., all bromeliads are found in the New World Tropics & Sub-Tropics

49. Macroevolution & Phylogeny
Some biogeographic similarities result from convergent evolution (convergent adaptive modification)
E.g., cactus of Americas compared to euphorbs of Africa
Cactus
Euphorb