Aug 31 Required Readings

C.W. Cunningham and T. Collins, 1998 Beyond area relationships: Extinction and recolonization in marine molecular biogeography. pp. 297-322 in Molecular Approaches to Ecology and Evolution (R. DeSalle, Schierwater, B., eds.). Birkhauser Verlag, Basel, Switzerland.

Aug 31 Additional Readings Mentioned in Class

Brooks, D. R. 1985. Historical ecology: a new approach to studying the evolution of ecological associations. Annals of the Missouri Botanical Garden 72:660-680.

Sept 7 Required Readings

p. 61-72 IN
Grosberg, R. K. and C. W. Cunningham 2001 Genetic structure in the sea: from populations to communities.  Pages 61-84 in Marine Community Ecology (M. D. Bertness, S. Gaines, and M. E. Hay, eds.), Sinauer Associates, Sunderland, MA.

Slatkin, M. 1993. Isolation by distance in equilibrium and nonequilibrium populations. Evolution 47:264-279.

Crisp, M. D., and L. G. Cook. 2005. Do early branching lineages signify ancestral traits? Trends in Ecology & Evolution 20:122-128.

Sept 14 Required Readings

Edwards, S. V., and P. Beerli. 2000. Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54:1839-1854.

Sept 21 Required Reading
Marko 2004
Petit et al 2002
Wares 2005 is the paper that discusses isolation by distance with the dataset discussed on Sept. 14 and given below
Wares.2005

(these files should all work for Windows or Mac versions of Arlequin 2.0)
ArlequinDatasetNexusFormat
ArlequinDatasetConvertingtoArlequinFormatStep1
ArlequinDatasetConvertingtoArlequinFormatStep2
ScreenShots of Arlequin Run
Assignment: follow these steps with a new file (but delete the Mantel section for simplicity as in the following file
ArlequinDatasetConvertingtoArlequinFormatStep3

Here is a file with an "AMOVA section added
ArlequinDatasetConvertingtoArlequinFormatStep4

Sample Distance File

Mytilus edulis Arlequin File

Alternate Depiction of Haplotypes in Arlequin File: 1

Alternate Depiction of Haplotypes in Arlequin File: 2

Sept 28 Required Readings

Gene Genealogies, Variation and Evolution CH1
J.Hein, M. Schierup, C.Wiuf, 2006

Oct 5 Required Readings

Nielsen, R., and J. Wakeley. 2001. Distinguishing migration from isolation: a Markov Chain Monte Carlo approach. Genetics 158:885-896.

Gene Genealogies, Variation and Evolution CH4
J.Hein, M. Schierup, C.Wiuf, 2006

S2.txt

AMIC.txt

ICEUR.txt

New Improved Worksheet for MDIV.xls
This includes already-made and labelled graphs,but you need to save as a whole new file for each outfile.txt you paste in (copying a worksheet and pasting doesn't work)

Step By Step for Running and MDIV program on Soma

Readings for October 12

Alexandrino 2002

Knowles and Maddison 2002

Knowles 2004

Templeton 2004

Readings for October 19

Rogers and Harpending 1992

Saillard et al 2000

XA.SAILLARD WORKSHEET

XA.SAILLARD DATASET (Nexus)

XA.SAILLARD DATASET (PHYLIP)

XA.PHYLOGRAM