This page contains links to software, papers, notes, data sets, and other materials used in a graduate seminar in statistical phylogeography at the University of Connecticut held during Spring Semester 2011.

Contents 1 Schedule 2 Software 2.1 For allelic data (microsatellites, SNPs, AFLPs) 2.2 For haplotype (i.e., sequence) data 2.3 For both types of data 2.4 Getting your data into the computer 3 Bibliography

Schedule

Meetings Tuesday at 4:00pm (except where noted below in magenta type) in the Bamford Room, TLS 171B

You'll find the papers referred to in the Mendeley bibliography

Date	Topic	Lead
Jan 18	Snow day
Jan 25	Overview; Introduction to Structure & Structurama Papers to read: Pritchard et al. (2000), Evanno et al. (2005), Hulsenbeck & Andolfatto (2007) You may also want to take a look at my notes on Structure from PopGen HTML PDF A few notes on Structure PDF	Holsinger
Feb 1	Snow day
Feb 8	Structure, Structurama, Clumpp, & distruct Papers to read: Jakobsson & Rosenberg (2007) You may also want to look at Santafé et al.(2008). It's heavy going, and I haven't had a chance to study it closely yet, but the approach seems promising. If you want to read something in addition to Jakobsson & Rosenberg, Kalinowski (2010) is a lot easier, and more likely to be relevant than Santafé et al. (Thanks to Elizabeth for reminding me about it.) A few notes on label switching PDF	Theiss
Feb 15 (2:30pm)	BayesAss+ Paper to read: Wilson & Rannala (2003), Faubet et al. (2007) A few notes on BayesAss+ PDF	Golden
Feb 22	Geneland Papers to read: Guillot et al. (2005) and Guillot et al. (2008) You might also want to take a look at Chen et al. (2007) and François & Durand (2010) A few notes on Geneland PDF	Lewis
Mar 1	BIMr Paper to read: Faubet & Gaggiotti (2008) A few notes on BIMr PDF	Holsinger
March 8	Spring break
March 15 (2:30pm)	Migrate-N (and LAMARC) Papers to read: Beerli & Felsenstein (2000), Beerli (2004) A few notes on Migrate PDF	Holsinger
March 22	IMa2 Papers to read: Nielsen & Wakeley (2001), and Hey & Nielsen (2004) And a technical paper that may interest a few of you Hey & Nielsen (2007) A few notes on IMa PDF	Wade
March 29	∂a∂i -- diffusion approximation for demographic inference Papers to read: Ellison et al. (2011), Gutenkunst et al. (2009) A few notes on ∂a∂i PDF	Holsinger
April 5	Approximate Bayesian Computation: DIYABC, PopABC Papers to read: Ascunce et al. (2011), Cornuet et al. (2008), Lopes et al. (2009) A few notes on ABC PDF	Chen
April 12	ABC -- the debate Papers to read (listed in the order of appearance): Nielsen & Beaumont (2009), Templeton (2010a), Beaumont et al. (2010) For the debate in the specific context of human phylogeography, you may also want to read: Fagundes et al. (2007), Templeton (2010b), Berger et al. (2010), Templeton (2010c)	Holsinger
April 19 (2:30pm)	BEAST -- Bayesian skyline plots Papers to read: Drummond & Rambaut (2007), Kuhner (2009), Ho & Shapiro (2011) A few notes on Skyline plots PDF	Batta Lona
April 26	PhyloMapper Paper to read: Lemmon & Lemmon (2008)	Lemmon
May 3	Estimating species trees from gene trees: STEM, SpedeSTEM, BEST, and StarBEAST Papers to read: Kubatko et al. (2009), Carstens & Dewey (2010), Edwards et al. (2007), Liu (2008), Heled & Drummond (2010) You might also want to take a look at Liu & Yu (2011), which is scheduled to appear in May	Holsinger

Software

For allelic data (microsatellites, SNPs, AFLPs)

• Structure
  • CLUMPP
  • distruct
  • Structure Harvester -- automatically produce plots of ln P(X|K) and the Evanno et al. (2005) criterion
  • CorrSieve -- calculates Evanno et al. (2005) and other statistics to choose K (available through CRAN for R)
• Structurama
• BayesAss+
  Scroll down the page to find it.
• BIMr
  Scroll down the page to find it.
• Geneland
  Geneland is a package for R.
• TESS
• Genetics Landscapes GIS Toolbox
  For use within ArcGIS.
• ∂a∂i -- diffusion approximation for demographic inference

For haplotype (i.e., sequence) data

• GeoDis
• BEAST
• BEST
• STEM
• PhyloMapper

For both types of data

• Migrate-N
  • LAMARC
• IMa2
• DIYABC
• POPABC

Getting your data into the computer

These programs are for allelic data, e.g., microsatellites or AFLPs.

• PGDSpider
• Formatomatic
• CREATE

Bibliography

Bibliography on Mendeley.

Note: The bibliography is publicly accessible, but only those whom I invite will be able to add to it. Click the "Ask to join group" button if you're interested.

Free desktop (Windoze, Mac OS X, and Linux) and iPad clients for Mendeley are available. They sync with bibliographies on the web. You may find it useful to get one of these clients, since the web bibliography doesn't sort references by author (or at least I haven't figured out how to get it to sort them by author yet).