2. Investigating the Evolutionary History of Life2

3. How are phylogenetic trees useful?
Assumptions
Mutations that are not expressed are maintained. They are neutral.
They should accumulate at a constant rate = the mutation rate.
This serves as a molecular clock.
Kittler et al. (2003,2004) compare genetic differences in lice between chimpanzees and humans.
Also considered fossil record.
Common ancestor of chimps and humans – 5.5. mya.
Able to determine # of base changes during that time between chimp lice and human lice
– the molecular clock.
Then applied that rate of change to the difference between human head lice (Pediculus humanus capitis) and body lice (Pediculus humanus corporis)
A. Head B. Body

4. How are phylogenetic trees useful?
Ethiopian lineage of head lice.
Assumptions
The rate of mutation accumulations between Chimp lice - Human lice =
Human head lice / Body lice.
Multiply the rate of change by the number of differences ~ 107, 000 years.
Origin of body lice was not more than 107,000 years ago.
Since Pediculus humanus corporis lives in clothing (though it feeds on the body), we can infer that humans began wearing clothing not more than 107,000 years ago.

5. Phylogenetic trees existed before OOS, but they were more like organizational charts.
Jean-Baptiste Lamarck sketchy diagram for animals in 1809.
Augustin Augier’s detailed tree of life for plants in 1801
in 1858, just a year before the Origin of Species, Heinrich Georg Bronn published a hypothetical phylogenetic tree labeled with letters.
Vestiges of the Natural History of Creation, anonymously published by Robert Chambers in 1844, had an even sketchier one, where fish, reptiles, and birds are represented by branches from a path leading to mammals.

6. Phylogenetic trees existed before OOS, or histories of life.
Indeed, once the tree of life image became associated with transmutations, Hitchcock dropped the image from later editions, since he strongly disagreed with the transmutation hypotheses of Lamarck, Haeckel, Darwin and others.
“Paleontological chart” from Edward Hitchcock’s Elementary Geology, first published in 1840.

7. The first phylogenetic tree

8. The first real phylogenetic tree.
The root of the tree – the common ancestor

9. The only figure in Darwin’s Origin of Species

10. Linking Classification and Phylogeny
Systematicists depict evolutionary relationships in branching phylogenetic trees
Much like a family tree
Sister
Cousin Vinny
Cousin Flossie
Time
Ancestors Me 10

11. Reading a Phylogenetic Tree
A phylogeny, or evolutionary tree, represents the evolutionary relationships among a set of organisms or groups of organisms, called taxa (singular: taxon).
Because no one was present to observe the splitting of taxa from a common ancestor, many evolutionary biologists consider a phylogenetic tree to be a hypothesis of those relationships

12. Reading a Phylogenetic Tree
Tips – descendent species
Node
Root
The root is the common ancestor of the species in the tree.
The tips represent the descendant taxa (often species)
The nodes represent the common ancestor of those descendants.

13. Reading a Phylogenetic Tree
Sister groups
Outgroup
Node
Two descendants that split from the same node are called sister groups.
The outgroup is a taxa that is outside the group of interest.
It stems from the base of the tree and provides perspective to the group of organisms being examined.

14. Character state – One of the variant conditions of a character (e. g
Character state – One of the variant conditions of a character (e.g. melanic or typical moth color. Or presence and absence of a trait. ).
Derived character state - same as apomorphy; a derived character / trait is inferred to be a modified version of a more primitive condition of that character and therefore inferred to have arisen later in the evolution of the clade.
Clade - a group of organisms that share a common ancestor; lineage; a monophyletic group.
Monophyletic group - terms applied to a group of organisms that includes an ancestral species and all of its descendants; e.g. Aves, Mammalia. This group is a complete branch of the tree of life, the phylogeny of life. Such a branch is called a clade.

15. Beak is the character, the state is its length.
Long
Character – beak length
Short

16. Apomorphy – a derived, or evolutionary novel character
Apomorphy – a derived, or evolutionary novel character. It is context specific.
When all four species are considered, the presence of the mask is considered novel relative to the presence of the ancestral form.

17. Plesiomorphy - An original character state for the taxa under consideration
When just the three species are considered, the presence of the mask is considered a pre-existing trait, or ancestral. This is called a plesiomorphy.

18. Apomorphy and plesiomorphy illustrated together
What about primitive and derived characters?You might hear people use the term "primitive" instead of plesiomorphic and "derived" instead of apomorphic. However, many biologists avoid using these words because they have inaccurate connotations. We often think of primitive things as being simpler and inferior — but in many cases the original (or plesiomorphic) state of a character is more complex than the changed (or apomorphic state). For example, as they have evolved, many animals have lost complex traits (like vision and limbs). In the case of snakes, the plesiomorphic characteristic is "has legs" and the apomorphic characteristic is "doesn't have legs."
Changed state
Original state

19. A synapomorphy  is a trait that is shared by two or more taxa and inferred to have been present in their most recent common ancestor, whose own ancestor in turn is inferred to not possess the trait.
The mask is a synapomorphy because it is shared by the most recent common ancestor.
But not this ancestor.

21. A clade is a grouping that includes a common ancestor and all the descendants (living and extinct) of that ancestor. Using a phylogeny, it is easy to tell if a group of lineages forms a clade. Imagine clipping a single branch off the phylogeny — all of the organisms on that pruned branch make up a clade.

22. Taxonomically, an organism accumulates all the names of all the clades to which it belongs.
A member of the most recent clade is also a member of all the ancestral (preceding clades).
Evo. Edu. Outreach (2009) 2:

23. Clade - a group of organisms that share a common ancestor; lineage; a monophyletic group.

24. Transition - a change in the character state along a branch.

25. Note that each one of these groups can be separated by “one snip”.
They are each a clade (monophyletic).

26. Practice to review – phylogenetic trees

27. Phylogenetically thinking – birds are dinosaurs.
Birds evolved from dinosaurs.
Cannot clip (make a clade) a branch that includes:
a) dinosaurs and b) more dinosaurs without including c) birds.
Q: Using tree thinking, are all reptiles cold-blooded? Can reptiles be defined as being cold-blooded?
Evo. Edu. Outreach (2009) 2:

28. Conclusion – Birds are descendants of dinosaurs.
Using tree thinking and the concept of clades, we can see that Ostriches belong to every clade preceding them (their ancestors).
Conclusion – Birds are descendants of dinosaurs.
Evo. Edu. Outreach (2009) 2:

29. These are all clades (monophyletic)
Depending on how many branches of the tree you are including however, the descendants at the tips might be different populations of a species, different species, or different clades, each composed of many species.

30. Note that two scissor snips rules out that this is a clade.
A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants.
Note that two scissor snips rules out that this is a clade. 30

31. Note that the taxa (tips) do not have the same common ancestor.
A polyphyletic grouping consists of various taxa with different ancestors.
Note that the taxa (tips) do not have the same common ancestor. 31

32. Paraphyletic group – a group that is monophyletic, except some descendant(s) have been removed.

34. Reading Phylogenetic Trees
Understanding a phylogeny is a lot like reading a family tree. The root of the tree represents the ancestral lineage, and the tips of the branches represent the descendants of that ancestor. As you move from the root to the tips, you are moving forward in time.
Evolution.berkeley.edu

35. Reading Phylogenetic Trees
When a lineage splits (speciation), it is represented as branching on a phylogeny. When a speciation event occurs, a single ancestral lineage gives rise to two or more daughter lineages.
Evolution.berkeley.edu

36. Reading Phylogenetic Trees
Phylogenies trace patterns of shared ancestry between lineages. Each lineage has a part of its history that is unique to it alone and parts that are shared with other lineages.
Evolution.berkeley.edu

37. Reading Phylogenetic Trees
Similarly, each lineage has ancestors that are unique to that lineage and ancestors that are shared with other lineages — common ancestors.
Evolution.berkeley.edu

38. Reading Phylogenetic Trees
Evolution produces a pattern of relationships among lineages that is tree-like, not ladder-like.
Evolution.berkeley.edu

39. Reading Phylogenetic Trees
Just because we tend to read phylogenies from left to right, there is no correlation with level of "advancement."
One form of a trait may be ancestral to another more derived form, but to say that one is primitive and the other advanced implies that evolution entails progress — which is not the case.
An organism's position on a phylogeny only indicates its relationship to other organisms, not how adaptive or specialized or extreme its traits are.
Evolution.berkeley.edu

40. Reading Phylogenetic Trees
Just because we tend to read phylogenies from left to right, there is no correlation with level of "advancement."
Evolution.berkeley.edu

41. Reading Phylogenetic Trees
Aristotle's vision of a Great Chain of Being, above. We now know that this idea is incorrect.
Reading Phylogenetic Trees
Although mosses branch off early on the tree of life and share many features with the ancestor of all land plants, living moss species are not ancestral to other land plants. Nor are they more primitive. Mosses are the cousins of other land plants.
University of California Museum of Paleontology's Understanding Evolution (

42. Reading Phylogenetic Trees
For any speciation event on a phylogeny, the choice of which lineage goes to the right and which goes to the left is arbitrary. The following phylogenies are equivalent:
Evolution.berkeley.edu

43. Synapomorphies – A derived character state that is shared by two or more taxa and is postulated to have evolved in (been modified by) their common ancestor.

44. Practice Reading Phylogenetic Trees