Preface to the study guide
1
“Reading guide Preface / Ch 1: Phylogenetic trees & their importance in modern biology”
Chapter commentary
1.1
Vocab summary
1.2
PREFACE (pages xv and xvi)
1.2.1
Course notes
1.3
CHAPTER 1: Phylogenetic trees & their importance in modern biology
1.3.1
Course notes
1.4
(Introduction)
1.5
“The importance of phylogenetic trees”
1.6
“From individuals to populations to species”
1.7
“Visualizing & modeling how traits evolve”
1.8
“Understanding what it means to be related”
1.9
“Organizing knowledge of biological diversity”
1.9.1
Related references
1.10
“Reconstructing history”
1.10.1
Related references
1.11
“Tree thinking and biological literacy”
2
“DRAFT - Reading guide Chapter 2: Tree thinking & its importance in the development of evolutionary thought”
Chapter commentary
2.1
Vocab summary
2.2
Notes
2.3
(Introduction)
2.4
“Before Charles Darwin” (OPTIONAL)
2.5
“Charles Darwin’s role in the development of tree thinking”
2.6
“Evidence for evolution and common ancestry”
2.7
“The emergence of phylogenetic systematics”
2.8
“Vestiges of ladder thinking in the popular understanding of evolution”
2.9
Chapter 2 Quiz
2.9.1
General biology questions:
2.9.2
Computational biology questions:
2.9.3
Interesting questions:
2.10
Further reading
3
“Reading guide Chapter 3: What a phylogenetic tree represents”
Chapter commentary
3.1
Notes
3.2
Objectives
3.3
(Introduction)
3.4
“Continuity of reproduction from the population to the tree of life”
3.5
“Asexual organisms”
3.6
“Tree terminology and conventions”
3.7
“Tree topology”
3.8
“Different tree styles”
3.9
“Merging and pruning” (SKIP)
3.10
“The time axis” (SKIP)
3.10.1
Related papers
3.11
“Branch lengths & evolutionary rate” (SKIP)
3.12
“Communicating phylogenetic uncertainty” (SKIP)
3.12.1
“Consensus trees” (SKIP)
3.12.2
Related papers
3.12.3
“Characterizing uncertainty” (SKIP)
3.13
“Unrooted trees”
3.14
Tree-to-tree distances
3.15
Chapter 3 Quiz
3.15.1
Intro bio
3.15.2
Computational biology
4
“DRAFT - Reading guide Chapter 4: Trait Evolution”
Chapter commentary
4.1
(Introduction)
4.2
Trait evolution in a single lineage
4.3
Trait evolution in a branching lineage
4.4
Ancestral & derived character states
4.5
The evolution of DNA sequences
4.6
An introduction to homology
4.6.1
Further reading
4.6.2
Further reading
4.7
Homplasy and consistency
4.8
Parsimony as a way to infer history of traits
4.8.1
Further reading
4.9
Chapter quiz
4.9.1
Intro bio
4.9.2
Computational biology
5
“Reading guide Chapter 6: Gene trees and species trees”
Chapter commentary
5.1
Gene duplication (pg 151)
5.2
Further reading
5.3
Chapter quiz
5.3.1
Intro bio
5.3.2
Computational biology
6
“Creating and rendering this book”
References
A Reading Guide to Tree Thinking: An Introduction to phylogenetic Biology
Chapter 6
“Creating and rendering this book”
bookdown
::
render_book
(
"index.Rmd"
,
"bookdown::gitbook"
)