Phyloseminar- Fall 2015

Professor Brian O’Meara (bomeara@utk.edu)

TA. Rosana Zenil-Ferguson (roszenil@gmail.com)

Mondays 12:20 -1:10

Buehler Hall 476

Aug/24

Introduction to Birth and Death Models

Nee, Sean, et al. "Extinction rates can be estimated from molecular phylogenies." Philosophical Transactions of the Royal Society B: Biological Sciences 344.1307 (1994): 77-82.
http://rstb.royalsocietypublishing.org/content/royptb/344/1307/77.full.pdf

Aug/31

R tutorial. Simulating birth and death processes as diversification. Basic estimations of speciation and extinction

Introduction to lineage through time concept

Sept/7

Labor Day

Sept/14

Problems in the estimation of extinction rates

  1. Rabosky, Daniel L. "Extinction rates should not be estimated from molecular phylogenies." Evolution 64.6 (2010): 1816-1824.

http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2009.00926.x/epdf

2. Beaulieu, Jeremy M., and Brian C. O'Meara. "Extinction can be estimated from moderately sized molecular phylogenies." Evolution 69.4 (2015): 1036-1043.

http://onlinelibrary.wiley.com/doi/10.1111/evo.12614/epdf

Sept/21

Magallón, Susana, and Michael J. Sanderson. "Absolute diversification rates in angiosperm clades." Evolution 55.9 (2001): 1762-1780.

http://www.bioone.org/doi/abs/10.1554/0014-3820(2001)055%5B1762:ADRIAC%5D2.0.CO%3B2

Sept/28

BiSSE

Maddison, Wayne P., Peter E. Midford, and Sarah P. Otto. "Estimating a binary character's effect on speciation and extinction." Systematic Biology 56.5 (2007): 701-710.

http://sysbio.oxfordjournals.org/content/56/5/701.full.pdf+html

Oct/5

R tutorial. Using diversitree (BiSSE, MuSSE, QuaSSE)

http://www.zoology.ubc.ca/prog/diversitree/

Oct/12

Alternatives to BiSSE

Beaulieu, Jeremy M., and Brian C. O'Meara. "Detecting hidden diversification shifts in models of trait-dependent speciation and extinction." bioRxiv (2015): 016386.

http://www.biorxiv.org/content/biorxiv/early/2015/03/13/016386.full.pdf

Oct/19

BAMM

Rabosky, Daniel L. "Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees." PLoS One 9, no. 2 (2014): e89543.

http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0089543&representation=PDF

Oct/26

R tutorial. BAMM for the estimation of speciation and extinction linked to a phenotype.
http://bamm-project.org/

Nov/2

Diversification and fossil record

Etienne, Rampal S., et al. "Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record." Proceedings of the Royal Society of London B: Biological Sciences (2011): rspb20111439.

http://rspb.royalsocietypublishing.org/content/279/1732/1300

Nov/9

R tutorial. R package DDD. Estimation of diversity dependent speciation.

Nov/16

Time Dependent Diversification

*This article might change

May, Michael R., Sebastian Höhna, and Brian R. Moore. "A Bayesian Approach for Detecting Mass-Extinction Events When Rates of Lineage Diversification Vary." bioRxiv (2015): 020149.
http://biorxiv.org/content/biorxiv/early/2015/06/02/020149.full.pdf

Nov/23

Nov/30

R tutorial. R package TESS. Time heterogenous speciation and extinction.