1. Reconstructing Evolutionary Trees
Chapter 14

2. Phylogeny
A phylogenetic tree is an illustrated summary of the history of a group of organisms.
It describes the pattern and timing of speciation events.
It describes the relationship of different taxa to one another.

3. The Logic of Phylogeny Inference
14.1

4. Challenges to Creating Phylogenic Trees
Characters used in a phylogenitic analysis have to be independent of one another.
Characters used in phylogeny inference have to be homologous.
Traits that are shared among species because they are homologous and that are similar because they were modified in a common ancestor are called synapomorpies.

5. Evolutionary relationships can be inferred by analyzing synapomorphies

6. Synapomorphies identify evolutionary branch points
Genetic separation causes homologous traits to change independently.
These changed traits are synapomorphies that identify populations belonging to different descending lineages.

7. Synapomorphies are Nested
As you move through time and trace a tree from its bottom to its top, each branching event adds one or more shared, derived traits.
Cladistic method

8. Establishing the direction of Change

9. Feathers are a a Hallmark of birds
Based on their structure, the feathers of modern and fossil birds are clearly homologous, and synaptomorphic.
Employing outgroup analysis one can tell the direction and polarity of change through time.

10. Outgroup Analysis
The character (feathers) in the ingroup is compared to that trait in a close relative (the outgroup) that clearly branched off earlier.
Skeletal structures show that theropod dinosaurs are birds closest realtives.

12. Several dromaeosaur species have simple featherlike structures projecting from their skin
The presence of feather in nonflying dinosaurs also confirmed that the evolution of feathers predated the evolution of flight in birds.

13. The problem of Homoplasy
Reversals remove similarity that is caused by descent from a common ancestor

14. Phylogenetic hypotheses for whales