Mating
system, relatedness and genetic distance/diversity programs
updated
November 2009
Written by Kermit Ritland
University of British Columbia
MLTR for windows – Version 3.4 (November
2009). This program is described in Ritland (2002 Heredity). Windows version of
MLTR, maximum likelihood estimation of mating systems using genetic marker
data. Includes methods to characterize biparental inbreeding; allows arbitrary
numbers of groups, loci, alleles (described in Ritland 2002). Allows megagametophyte data, dominant
markers, genotyping errors, and individual-level estimates with method of
moment estimators (dominance not included in this case). Every year or two I have an improvement.
MLTET
- estimates multilocus t and F for autotetraploids. I am working on a version for correlated
matings. Contact Kermit for more complicated versions of this, which can
include apomixes and automixes. Tetraploids do strange things.
MLT
- DOS the original multilocus estimation program (for diploids). This is of historical interest.
Pairwise relatedness and
individual inbreeding, and quantitative traits
Mark (I
plan to expand this program shortly, and provide adequate documentation. Thanks
all for your comments. Due October 2009). This program implements various
analyses involving pairwise relatedness and individual inbreeding coefficients,
many described in Ritland (2000).
Also the current Animal model for association genetics will be
incorporated, albeit not a mixed model. The current program implements (1) the
procedure for estimating heritability using inferred relatedness, as described
in Ritland (1996), (2) isolation by distance analysis and the spatial variance
of gene identity (Ritland and Travis 2004), (3) individual inbreeding
coefficients and inbreeding genetic load (Ritland and Travis 2004), and just
pairwise relatedness. Four
alternative measures of relatedness can be used, and these can also be
evaluated for your specific data with a Monte Carlo simulation. In addition, a
measure of relatedness based upon D-square (mean squared difference of allele
size) can also be specified; this is appropriate longer-distance relatedness at
microsatellite loci.
Genetic distance and
diversity (co-dominant markers)
GDD
and GD - Programs for estimating genetic distance and diversity (GD does
standard errors of branch lengths). This is something I wrote a long time ago.
Again of historical interest. My two programs now are MLTR for Windows, and
Mark (also for Windows). Sorry Mac Guys, but I just program in Fortran.