2. 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.

3. “Paleontological chart” from Edward Hitchcock’s Elementary Geology, first published in 1840.

7. Reading a Phylogenetic Tree
Outgroup
Node
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

8. Understanding a phylogeny is a lot like reading a family tree
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.
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.
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.

9. Similarly, each lineage has ancestors that are unique to that lineage and ancestors that are shared with other lineages — common ancestors.

10. 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.

11. 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.

12. 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:

13. Phylogenetic thinking – birds are dinosaurs.
Birds evolved from dinosaurs.
Cannot clip a branch that includes
a) dinosaurs and b) more dinosaurs without including c) birds.
Q: Using tree thinking, are all reptiles cold-blooded? Is this a good definition of reptiles?
Evo. Edu. Outreach (2009) 2:

14. 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:

15. 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.

16. 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 (

17. So when reading a phylogeny, it is important to keep three things in mind:
1. Evolution produces a pattern of relationships A B C D among lineages that is tree-like, not ladder-like.
2. Just because we tend to read phylogenies from left to right, there is no correlation with level of "advancement."
3. 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 phylogenies at left are equivalent
University of California Museum of Paleontology's Understanding Evolution (

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

20. 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.

21. Synapomorphies are integral to studying phylogenetic trees because:
a) they identify evolutionary branch points
b) they are nested. As you proceed from the base of the tree to the tips, each branching event adds one or more shared, derived traits.

23. A shared derived character is one that two lineages have in common, and a derived character is one that evolved in the lineage leading up to a clade and that sets members of that clade apart from other individuals.
Four limbs is a shared derived character inherited from a common ancestor that helps set apart this particular clade of vertebrates.
However, the presence of four limbs is not useful for determining relationships within the clade in green above, since all lineages in the clade have that character.

24. Homologous characters — characters in different organisms that are similar because they were inherited from a common ancestor that also had that character.
An example of homologous characters is the four limbs of tetrapods. Birds, bats, mice, and crocodiles all have four limbs . Sharks and bony fish do not. The ancestor of tetrapods evolved four limbs, and its descendents have inherited that feature — so the presence of four limbs is a homology.

25. Analogies are the result of convergent evolution.
The structural dissimilarities between a bird wing and bat wing suggests that they were not inherited from a common ancestor with wings.
Independent evolution of a character – the wing.
Bird and bat wings are analogous — that is, they have separate evolutionary origins, but are superficially similar because they have both experienced natural selection that shaped them to play a key role in flight.
Analogies are the result of convergent evolution.
In what way are bird and bat wings homologous?

27. A reversal – When a derived trait can revert to an ancestral trait either through a mutation, or selection.

28. 3 Assumptions to Cladistics
1. Change in characteristics occurs in lineages over time.
2. Any group of organisms is related by descent from a common ancestor.
3. There is a bifurcating, or branching, pattern of lineage-splitting.

29. What about primitive and derived characters?
The use of the term “primitive” have inaccurate connotations.
Often the original (or plesiomorphic) character state 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."

30. Reconstructing trees: A step by step method
Choose the taxa whose evolutionary relationships interest you.
Determine the characters and examine each taxon to determine the character states. Use homologies, not analogies.
Determine the polarity of characters — in other words, figure out the order of evolution for each character.
For example, did the beetle species under consideration all evolve from an ancestor with five antennal segments — and only later did six evolve, or was it the other way around?
4. Group taxa by synapomorphies, not by symplesiomorphies.
Synapomorphies are derived or "changed" character states shared by two taxa.
Symplesiomorphies An ancestral character state (i.e., a plesiomorphy) shared by two or more lineages in a particular clade.

31. Synapomorphy versus symplesiomorphy

32. Reconstructing trees: A step by step method
1. All taxa go on the endpoints of the tree, never at nodes.
2. All nodes must have a list of synapomorphies, which are common to all taxa above the node (unless the character is later modified).
3. All synapomorphies appear on the tree only once unless the character state was derived separately by evolutionary parallelism.

33. Using Parsimony to Recreate Phylogenetic Trees
Parsimony - choose the simplest scientific explanation that fits the evidence.
Hypothesis 1 requires six evolutionary changes.
Hypothesis 2 requires seven evolutionary changes, with a bony skeleton evolving independently, twice.