Wednesday,
Jan. 22
|
Introduction to instructors - contemporary issues in
phylogenetic systematics - what is at stake? (BDM) |
Tree Thinking: Chap. 1 |
LAB 01: Discussion: student interests; get acquainted
roundtable; tour of systematics collections, labs, and
resources in VLSB |
Friday,
Jan. 24
|
Introduction - history & philosophy of phylogenetics
(BDM)
Lecture notes
|
Tree Thinking: Chaps. 1 & 2
Supplemental:
Mishler. 2009.
Three centuries of paradigm changes in biological
classification: is the end in sight? Taxon 58:61-67. B.D.
Mishler. 2014.
History and theory in the development of phylogenetics in
botany. In A. Hamilton (ed.), The Evolution of
Phylogenetic Systematics, pp. 189-210. UC Press.
|
|
Monday,
Jan. 27 |
Introduction - the Hennig Principle: homology;
synapomorphy; rooting; integrating fossils (BDM)
Lecture notes |
Required Reading: Tree Thinking: Chap. 4, pages
90-93
|
|
Wednesday,
Jan. 29 |
Morphological data I: ontogeny & structure of plants
vs. animals; character analysis; what is a data matrix?
(BDM)
Lecture notes |
B.D. Mishler. 2005.
The logic of the data matrix in phylogenetic analysis. In
V.A. Albert (ed.) Parsimony, Phylogeny, and Genomics, pp.
57-70. Oxford University Press.
|
LAB 02: Hypotheses of
homology; How to handle phylogenetic data and trees;
Introduction to Nexus and Newick files; Morphological data
matrix. Introduction to FigTree and Mesquite.
|
Friday,
Jan. 31
|
Morphological data II: Character coding [primary homology,
polarity, additivity, etc.] (guest lecture: Kip Will)
Lecture notes
|
Tree Thinking: pp 77-95, 399-403
Rieppel, O. (2015). Homology: A Philosophical and
Biological Perspective. Handbook of Paleoanthropology,
295-315.
|
|
Monday,
Feb. 3
|
Molecular data I: General introduction; types of molecular
data (DNA hybridization; allozymes; restriction sites, DNA
sequences, ESTs; comparative genomics) (BDM)
Lecture notes
|
Maddison, W. P. and D.R. Maddison. 2011. Mesquite: a
modular system for evolutionary analysis. Version 3.61
Chapter on Analyzing Molecular Data |
|
Wednesday,
Feb. 5
|
Molecular data II: Sequence alignment (BDM)
Lecture notes
|
Tree Thinking: pp 86-89, 195-200 |
LAB 03: introduction to
GENBANK and FASTA files; BLAST; sequence analysis and
alignment (Clustal, Muscle, AliView)
PROJECT TOPIC DUE -- turn in 1 paragraph
description and discuss in class
|
Friday,
Feb. 7
|
Phylogenetic trees I: reconstruction; models, algorithms
& assumptions (BDM)
Lecture notes
|
Tree Thinking: pp 35-53. |
|
Monday,
Feb. 10
|
Phylogenetic trees II: Phenetics; distance-based
algorithms (BDM)
Lecture notes
|
Tree Thinking: pp 231-238. |
|
Wednesday,
Feb. 12
|
Phylogenetic trees III: Parsimony; Measures of support and
robustness (BDM)
Lecture notes
|
Tree Thinking: pp 95-106, 173-215, 271-284
|
LAB 04 : Distance and
parsimony inference using PAUP; UPGMA, neighbor-joining,
bootstrap, jackknife, and Bremer support |
Friday,
Feb. 14
|
Phylogenetic trees IV: Maximum likelihood; molecular
evolution and phylogenetics (Guest lecture: Carrie Tribble)
Lecture slides
|
Required: Tree Thinking: pp 217
- 231, 238 - 247
Recommended:
Felsenstein, Joseph. "Evolutionary trees from DNA
sequences: a maximum likelihood approach." Journal of
molecular evolution 17.6 (1981): 368-376.
|
|
Monday,
Feb. 17
|
holiday
|
Wednesday,
Feb. 19 |
Phylogenetic trees V: Bayesian methods and Markov Chain
Monte Carlo (Guest lecture: Carrie Tribble)
Lecture slides
|
Required: Tree Thinking: pp 247
- 258
Recommended: Lecture Notes
from 2016
Holder,
Mark, and Paul O. Lewis. "Phylogeny estimation:
traditional and Bayesian approaches." Nature reviews
genetics 4.4 (2003): 275. |
LAB 05: Maximum likelihood
and CIPRES supercomputer web interface |
Friday,
Feb. 21 |
Phylogenetic trees VI: Dating in the 21st century: clocks,
& calibrations; proper use of fossils
(Guest lecture: Carrie Tribble)
Lecture slides
|
Tree Thinking: pp 53-58
Chen, Ming-Hui, Lynn Kuo, and Paul O. Lewis. "Bayesian
inference of species divergence times." Bayesian
Phylogenetics. Chapman and Hall/CRC, 2014. 307-348.
|
|
Monday,
Feb. 24 |
Phylogenetic trees VII: Tree-to-tree comparisons;
consensus methods; supertrees (guest lecture: Kip Will)
Lecture notes
|
|
|
Wednesday,
Feb. 26 |
Classification I -- introduction to
phylogenetic classifications; monophyly, information content
(BDM)
Lecture notes
|
Tree Thinking: pp 107-131 |
LAB 06: Bayesian
Phylogenetics,MCMC Convergence Diagnostics,and Divergence
Time Estimation
|
Friday,
Feb. 28 |
Classification II -- phylogenetic taxonomy
including incorporation of fossils; Phylocode (BDM)
Lecture notes
|
Preface
to the Phylocode
Tree thinking: pp 131-133.
|
|
Monday,
Mar. 2
|
Introduction to statistical thinking in phylogenetics
(Guest lecture: David Ackerly)
Lecture notes
|
Tree Thinking: Beginning of Chapter 10 pp. 305 -
312 |
|
Wednesday,
Mar. 4 |
Classification III -- species concepts;
speciation (BDM)
Lecture notes
|
B.D.
Mishler and J.S. Wilkins. 2018. The hunting of the SNaRC:
a snarky solution to the species problem. Philosophy,
Theory, and Practice in Biology. 10: 1-18.
|
LAB 07:
Intro to R;
Basic Phylogenetic Functions in
R
|
Friday,
Mar. 6
|
Classification IV -- DNA barcoding and DNA
taxonomy (BDM)
Lecture notes
|
K.W.
Will, B.D. Mishler, and Q.D. Wheeler. 2005. The perils of
DNA barcoding and the need for integrative taxonomy.
Systematic Biology 54: 844-851. |
|
Monday,
Mar. 9
|
Qualitative character evolution within a cladogram I:
discrete states; ancestral state reconstructions (Guest
lecture: David Ackerly)
Lecture notes
|
Required:
Tree Thinking: pp. 77-99, 312-322
Maddison WP,
Maddison DR (2000) MacClade 4 (pdf manual), Sunderland MA:
Sinauer, chapters 3, 4, and 22.
Recommended:
Maddison
WP, Slatkin M (1991) Null models for the number of
evolutionary steps in a character on a phylogenetic tree.
Evolution 45: 1184-1197.
|
|
Wednesday,
Mar. 11
|
Qualitative character evolution within a cladogram II:
comparing two or more characters (Guest lecture: David
Ackerly)
Lecture notes
Lecture slides
|
Required:
Pagel
M. (1994) Detecting correlated evolution on phylogenies: a
general method for the comparative analysis of discrete
characters. Proc. R. Soc. Lond. B, 255, 37-45
Schluter
D., Price T., Mooers A. & Ludwig D. (1997) Likelihood
of ancestor states in adaptive radiation. Evolution, 51,
1699-1711
Recommended:
Pagel
M. (1999) The maximum likelihood approach to
reconstructing ancestral character states of discrete
characters on phylogenies. Syst. Biol., 48, 612-622
|
LAB 08: Phylogenetics in R:
Trait Evolution in a phylogenetic context
|
Friday,
Mar. 13
|
Quantitative character evolution within a cladogram I:
intro; ancestral trait reconstruction; phylogenetic
conservatism (Guest lecture: David Ackerly)
Lecture notes
Lecture slides
|
Felsenstein
J. 1985. Phylogenies and the comparative method. Amer.
Nat. 125:1-15
Oakley
TH, Cunningham CW. 2000. Independent contrasts succeed
where ancestral reconstruction fails in a known
bacteriophage phylogeny. Evolution 54:397-405
|
|
Monday,
Mar. 16
|
Classification V -- nomenclature; Zoological
& Botanical Codes; practical systematics, monography
(Guest lecture: Kip Will)
Lecture notes
|
TBD
|
|
Wednesday,
Mar. 18
|
Quantitative character evolution within a cladogram II:
independent contrasts and trait correlations (Guest lecture:
David Ackerly)
Lecture notes
Lecture slides
|
Required:
Hansen,
T. 1997. Stabilizing selection and the comparative
analysis of adaptation. Evolution 51:1341- 1351.
Ackerly,
D. D. 2009. Conservatism and diversification of plant
functional traits: Evolutionary rates versus phylogenetic
signal. Proceedings of the National Academy of Sciences
USA 106:19699-19706.
Blomberg,
S. P., and T. Garland, Jr. 2002. Tempo and mode in
evolution: phylogenetic inertia, adaptation and
comparative methods. J. Evol. Biol. 15:899-910.
Strongly Recommended:
Blomberg,
S. P., T. Garland, and A. R. Ives. 2003. Testing for
phylogenetic signal in comparative data: Behavioral traits
are more labile. Evolution 57:717-745. (Focus on pp.
719-723 on methods for measuring phylogenetic signal.)
Harmon,
L. J., J. B. Losos, T. J. Davies, et al.. 2010. EARLY
BURSTS OF BODY SIZE AND SHAPE EVOLUTION ARE RARE IN
COMPARATIVE DATA Evolution 64:2385-2396.
|
PHYLOGENY FOR YOUR PROJECT DUE in writing + discuss
progress on comparative analyses
LAB 09: Introduction to
RevBayes
|
Friday,
Mar. 20
|
Phylogenies and Community Ecology (Guest
lecture: David Ackerly)
Lecture notes
Lecture slides
QUIZ 1 handed out
|
Required:
Cavender-Bares,
J., D. D. Ackerly, D. Baum, and F. A. Bazzaz. 2004.
Phylogenetic overdispersion in Floridian oak communities.
Amer. Nat. 163:823-843.
Cavender-Bares,
J., K. H. Kozak, P. V. A. Fine, and S. W. Kembel. 2009.
The merging of community ecology and phylogenetic biology.
Ecology letters 12:693-715.
Recommended:
Webb,
C. O., et al.. 2002. Phylogenies and community ecology.
Annu. Rev. Ecol. Syst. 33:475-505. |
|
Mar. 23 - 27
|
SPRING
BREAK
|
Monday,
Mar. 30
|
Phylogenetics and adaptation (BDM)
Lecture notes
|
Coddington, Jonathan A. "The roles of homology and
convergence in studies of adaptation." (1994). |
|
Wednesday
Apr. 1
|
Evolution and development - heterochrony (BDM)
Lecture notes
|
Fink,
W.L. 1982. The Conceptual Relationship Between Ontogeny
and Phylogeny. Paleobiology 8: 254-264. |
LAB 10: Systematic databases
and community phylogenetics
Rmd file
|
Friday,
Apr. 3
|
Biogeography I: finding and cleaning spatial data; niche
modeling; niche evolution; climate change (IGR)
Lecture slides
|
TBD
|
|
Monday,
Apr. 6
|
Comparing sister clades within a cladogram: the shape of
evolution (Guest lecture: David Ackerly)
Lecture notes
Lecture slides
|
Required:
Morlon,
H. (2014). Phylogenetic approaches for studying
diversification. Ecology Letters, 17(4), 508-525.
Recommended:
Rabosky,
D. L., & Glor, R. E. (2010). Equilibrium speciation
dynamics in a model adaptive radiation of island lizards.
Proceedings of the National Academy of Sciences, 107(51),
22178-22183.
Jetz,
W., Thomas, G. H., Joy, J. B., Hartmann, K., & Mooers,
A. O. (2012). The global diversity of birds in space and
time. Nature, 491(7424), 444-448.
|
|
Wednesday,
Apr. 8
|
Tempo and mode in macroevolution; patterns of
diversification and extinction (Guest lecture: David
Ackerly)
Lecture notes
|
Goldberg,
Emma E., et al. "Species selection maintains
self-incompatibility." Science 330.6003 (2010): 493-495.
Lagomarsino,
Laura P., et al. "The abiotic and biotic drivers of rapid
diversification in Andean bellflowers (Campanulaceae)."
New Phytologist 210.4 (2016): 1430-1442.
|
LAB 11: Diversification models:
Pure-Birth and Birth-Death Process; Joint character
evolution and diversification analyses using BiSSE
Lab files
|
Friday,
Apr. 10
|
Adaptive radiations (BDM)
Lecture
|
Rosemary
G. Gillespie, 2013. Adaptive radiation: convergence and
non-equilibrium. Current Biology 23: R71R74
|
|
Monday,
Apr. 13
|
Phylogenetic trees VIII: Below the "species level;"
phylogeography; dealing with reticulation (Guest lecture:
Chris Martin)
Lecture slides
|
Tree Thinking: Chapt 6
Section 6.3 in Coop, G. 2020. Population and
quantitative genetics.
|
|
Wednesday,
Apr. 15 |
Coalescence theory and connections to population genetics
(Guest lecture: Chris Martin)
Lecture slides
|
Hahn
and Nakhleh (2015) Irrational exuberance for resolved
species trees, International Journal of Organic Evolution,
70-1:7-17.
|
Discuss progress on projects in class
LAB 12: Coalescence theory: gene
tree-species tree reconstruction using
RevBayes and the multispecies coalescent
lab files
|
Friday,
Apr. 17 |
Molecular Evolution (BDM)
Lecture notes
|
Wolfe KH,
Li W (2003) Molecular evolution meets the genomics
revolution. Nature Genetics 33(3s), 355-365 |
|
Monday,
Apr. 20
|
Gene family evolution; phylogenomics; evo-devo (BDM)
Lecture notes
|
Boussau B, Daubin V (2010) Genomes as documents of
evolutionary history. Trends in Ecology & Evolution
25(4), 224-232.
|
|
Wednesday,
Apr. 22
|
Biogeography II: basic principles; ecological vs.
historical approaches; vicariance vs. dispersal (BDM)
Lecture notes
|
Tree Thinking: pp 349-355 |
LAB 13: Probabilistic
biogeographic models using BioGeoBEARS
|
Friday,
Apr. 24 |
Biogeography III: spatial phylogenetics;
phylobetadiversity & biome recognition, and other
spatial issues (BDM)
Lecture notes
Lecture slides
|
A.H.
Thornhill, B.D. Mishler, N. Knerr, C.E. Gonzalez-Orozco,
C.M. Costion, D.M. Crayn, S.W. Laffan, and J.T. Miller.
2016. Continental-scale spatial phylogenetics of
Australian angiosperms provides insights into ecology,
evolution and conservation. Journal of Biogeography. 43:
2085–2098. |
|
Monday,
Apr. 27 |
Phylogenetics and conservation biology (BDM)
Lecture notes
Lecture slides
|
M.M.
Kling, B.D. Mishler, A.H. Thornhill, B.G. Baldwin, and
D.D. Ackerly. 2018. Facets of phylodiversity: evolutionary
diversification, divergence, and survival as conservation
targets. Philosophical Transactions Royal Society
B. 374: 20170397.
Pollock, L.J., Thuiller, W. and Jetz, W., 2017. Large
conservation gains possible for global biodiversity
facets. Nature, 546(7656), p.141.
|
|
Wednesday,
Apr. 29 |
Comparing cladograms; cospeciation methods (BDM)
Lecture notes
Lecture slides
|
Percy,
Diana M., Roderic DM Page, and Quentin CB Cronk.
"Plant–insect interactions: double-dating associated
insect and plant lineages reveals asynchronous
radiations." Systematic Biology 53.1 (2004): 120-127.
Vienne,
DM de, et al. "Cospeciation vs host‐shift speciation:
methods for testing, evidence from natural associations
and relation to coevolution." New Phytologist 198.2
(2013): 347-385.
|
INITIAL COMPARATIVE ANALYSES DUE in writing +
discuss progress on projects in class
LAB 14: Introduction to
BIODIVERSE
Lab files
|
Friday,
May 1
|
Coevolution; symbiosis (BDM)
|
TBD
|
QUIZ 2 handed out (due that evening)
|
May 4 - 8
|
READING &
FINALS WEEKS |
TBD
|
Student
minisymposium |
| TBD |
Final
projects due by midnight |