Data sets

ML versus Bayes: 100 data sets of 1 single artificial locus each. 4 population exchange migrants round robin from 1 to 4 to 3 to 2 to 1. In each population a sample of 20 individuals with 10000 bp each was taken. The data sets are in MIGRATE format. (data here)(paper here)

[It would be very interesting for me and practical researchers, if these data set would be run with programs that compete with migrate: please let me know about such trials.]

Homburg Dataset from my master thesis discussing the strange occurrence of a species (Rana ridibunda) of waterfrogs in a parent-hybrid system (Rana lessonae and R. esculenta). The data set is a mixture of categorical and quantitative data.

Legend:

Variable                   States                                       Comments

Species                    ESC, LES, RID                           ESC=Rana esculenta (the hybrid),

                                                                              LES=Rana lessonae (the present parental species,

                                                                              RID=Rana ridibunda (parental species not present in the region)

Sex                          F, M, J                                      F=female, M=male, J=juvenile

location                   Aeuli, Homburg                        Aeuli=well-connected gravel pit near Buerglen (Thurgau,     

                                                                              Switzerland), Homburg=isolated gravel pit near Homburg (Thurgau)

Length                     [mm]\                                      Body length measured over the back in mm

Tibia                        [mm]                                       Length of Tibia [mm]

Cil                           [mm]                                       Length of the largest tubercle on the first toe in mm

Cia                          [mm]                                       Height of largest tubercle on first toe in mm

Dp                          [mm]                                       Length of first toe in mm

Weight                   [g]                                            Bodyweight in grams (unadjusted, "fresh" weight of live frogs)

Bcarea                    [sq micron?]                              Average area of red blood cells (to define ploidy, all are most

                                                                              likely diploid)

Bcstd                      [sq micron?]                              Standard deviation of Bcarea

Bcn                        number                                     Number of measured blood cells

agerings                  number                                     Number of arrest rings in finger bone (second)

Gpi                        S, F                                            Each individual is diploid: SS or SF or FF (S=slow, F=fast) [dimer]

LDH                      Rs, Rf, Lf, Li                                Rs and Rf are RID defining alleles, Li, Lf are LES defining

                                                                              alleles [tetramer]

Anatolia (Data set of 5 populations of water frogs): Allozyme data of 31 loci (data here), this data set contains comments (version of migrate 2.1.8 or newer can read this with problems, for older versions or other converters you need to excise all lines that start with #.

Programs

MIGTREE and MIGDATA (Peter Beerli) a commandline tool to simulate genealogies with and without migration events, and the generate data (DNA sequence data, microsatellite data, allozyme data).

Diverge (Peter Beerli) a simple tool for estimating divergence time of two individuals from different species, integrating over a wide range of possible ancestral population sizes. distributed in source and command line binaries for MacOSX. This program is "user-nasty" and not for the faint of heart.

Diverge3D (Peter Beerli) a simple tool for estimating divergence time of two individuals from different species]. It produces the likelihood surface for two parameters: ancestral population size and divergence time. Distributed in source only. This program is "user-nasty".