PBG270 Spring 2006: To tree or not to tree

PBG270 Spring 2006
To tree or not to tree: When to use phylogenetics and when to use population genetics to answer questions

Mondays at 12:10 in Storer 2342.
All email addresses, except where noted, are @ucdavis.edu

to connect to readings from off campus, or go to this page.

April 3: Intro meeting. Reading: Emerson, Paradis, and Thébaud, 2001 [PDF]. Revealing the demographic histories of species using DNA sequences. TREE 16(12) 707-716.
April 10: Phylogeography 1: Range expansion/refugia

Jason McLachlan, jsmclachlan
Reading: Carstens et al. 2004 "Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group" Systematic Biology 53(5): 781-792.
April 17: Phylogeography 2: Inferring population substructure

Maggie Sherriffs, msherriffs
Dean Leavitt, dhleavitt
Karen Mabry, kemabry
Reading: Double et al. 2005 "Dispersal, philopatry, and infidelity: dissecting local genetic structure in superb fairy wrens (Malurus cyaneus)" Evolution 59(3) 625-635.
April 24: Estimating gene flow 1

Lisa Reimer, ljreimer
Hillary Thomas, hqthomas
Tara Theimann, tcthiemann
Reading: Navia et al. 2005. "The invasive coconut mite Aceria guerreronis (Acara: Eriophyidae): origin and invasion sources inferred from mitochondrial (16S) and nuclear (ITS) sequences" Bulletin of Entomological Research 95: 505-516.
May 1: Estimating gene flow 2

Ian Wang, ijwang
Stephanie Porter, ssporter
Reading: Falush et al. 2003. "Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies" Genetics 164: 1567-1587.
Background: Pritchard et al. 2000. "Inference of population structure using multilocus genotype data" Genetics 155: 945-959.
Program: Structure is available here.
May 8: Phylogeography 3: Population size

Nate Hardy, nbhardy
Shannon Flynn, slf_210 AT yahoo.com
Readings (2):
Hey and Nielsen 2004. "Multilocus methods for estimating population sizes, migration rates, and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis." Genetics 167: 747-760.
Won and Hey 2004. "Divergence population genetics of chimpanzees" Molecular Biology and Evolution 22(2): 297-307.
May 15: Phylogeography 4

Andrea Lucky, alucky
Christopher Searcy, casearcy
Beverly Ajie, bcajie
Readings (2):
Irwin 2002. "Phylogeographic breaks without geographic barriers to gene flow" Evolution 56(12): 2383-2394.
Wakeley 2000. "The effects of subdivision on the genetic divergence of populations and species" 54(4): 1092-1101.
May 22: Inferring species boundaries 1

Bob Thomson, rcthomson
Renata Eberl, reberl
Reading: Wiens and Penkrot 2002. "Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus)" Systematic Biology 51(1): 69-91.
May 31 [Wednesday]: Inferring species boundaries 2

Michael Branstetter, mgbranstetter
Raquel Muniz-Salazar, rmunizsalazar
Shelah Morita, simorita
Readings (2):
Sites and Marshall 2004. "Operational criteria for delimiting species" Annual Review of Ecology, Evolution, and Systematics 35: 199-227.
Ross and Shoemaker 2005. "Species delimitation in native South American fire ants" Molecular Ecology 14:3419-3438.
June 5: Additional topics 1

Annie Sherwood and Jeff Firestone
Reading: Li et al. 2004. "Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia" Nature 430: 209-213.
June 12: Additional topics 2

Volunteer?

Some possible readings (feel free to suggest more):
Background

Emerson, Paradis, and Thébaud, 2001. Revealing the demographic histories of species using DNA sequences. TREE 16(12) 707-716. A classic overview paper. Includes list of software.
Rosenberg & Nordborg, 2002, Nature Reviews Genetics. Intro to coalescence, distinction between phylogenetic approaches and approaches that don't seek a tree
Wakeley, 200X Coalescent Theory: An Introduction (textbook excerpts). Has a good intro to some of the models, measures, and math involved with coalescence.
Charlesworth et al, 2003. The effects of genetic and geographic structure on neutral variation. An Rev Ecol Evo Syst 34: 99-125.

Inferring species boundaries

Estimating gene flow

Beerli and Felsenstein, 1998. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. PNAS 98 (8): 4563-4568. The math behind the program Migrate.
Beerli 2006. Comparison of Bayesian and maximum-likelihood inference of population genetic parameters. Bioinformatics 22(3): 341-345. A comparison of the efficacy of Bayesian and ML approaches.

Phylogeography-level questions

Arbogast et al, 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. An Rev Ecol Syst 33:707-740. The first half is about calibrating phylogenetic trees (so not relevant for this discussion); the second half deals with population processes (pop size, divergence between populations, etc).
Hey and Nielsen 2004. Multilocus methods for estimating population sizes, migration rates, and divergence time, with applications to divergence of Drosophila pseudoobscura and D. persimilis. Genetics 162(2): 747-760. Parameter-rich way of investigating the divergence of two species.
Hey 2005. On the Number of New World Founders: A Population Genetic Portrait of the Peopling of the Americas. PLOS Biology 3(6)e193.
Manel et al, 2003. Landscape genetics: combining landscape ecology and population genetics. TREE 18(4) 189-197.
Walker and Avise 1998. Principles of phylogeography as illustrated by freshwater and terrestrial turtles in the southeastern United States. An Rev Ecol Syst 29: 23-58.
Carstens et al, 2004. Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandyei species group. Syst Biol 53(5): 781-792. An empirical study that uses many approaches, from trees to coalescent models to nested clade analysis.

Assigning individuals to species

Matz and Nielsen, 2005. A likelihood ratio test for species membership based on DNA sequence data. Phil Trans Roy Soc B 360:1969-1974.