This page contains details of generally applicable techniques for analysing genetic data from hybridising populations, appropriate for when hybridisation is rare, plus information on more general population genetic analyses. The hybridisation methodologies were developed for the analysis of a hybrid zone between native Scottish red deer and introduced Asian sika deer (genus Cervus) in Argyll, Scotland. Full details of this study can be found in the paper:

Goodman, S. J., N. H. Barton, G. Swanson, K. Abernethy and J. M. Pemberton (1999) Introgression through rare hybridisation: a genetic study of a hybrid zone between red and sika deer (genus Cervus) in Argyll, Scotland. Genetics (in press).

This paper will appear in the May 1999 edition of the Journal GENETICS.

The information is contained in Mathematica 3.0 notebooks. If you do not have a copy of Mathematica you can get a free copy of a 'Mathreader', which will let you view the notebooks but not run the analyses, from Wolfram Research. At present the files are archived as Macintosh "Stuffit" files, we hope to make PC ZIP files available shortly. The Stuffit compression/decompression software is available from Aladdin Systems.

There are two sets of notebooks. The first describes a specific example of our analysis approach applied to rare hybridisation between red and sika deer in Argyll Scotland. It contains full details of the analyses described in the above paper. This includes an appendix to the paper which describes our maximum likelihood method for calculating null allele frequencies.

The general population genetic analyses are in the Application library. This is a collection of varied routines, listed below. You need to down load both to run the deer analysis. After decompressing the deer note book you need to place the file "MS.nb" in the Mathematica style sheets folder. To install the Applications folder replace the empty "Applications" folder that comes with Mathematica 3.0 with the new one, and "Rebuild Help Index...". The documentation then appears in the Help browser.

	Download Analysis of red and sika deer hybridisation note book	Down load the applications library (3.5Mb).

APPLICATIONS LIBRARY

This set of Mathematica 3.0 packages contain a variety of routines which are useful for population genetics - especially, for problems involving multiple genes. They are divided (somewhat arbitrarily) into three sections:

Genealogies:
- describing genealogies
- inferring genealogies from infinite-sites data
- implementing the Griffiths-Tavare likelihood methods

Multilocus:
- multilocus selection and recombination (see Barton & Turelli, Genetics, 1991)
- exact model of selection on a set of unlinked genes
- exact recursions for genotype frequencies at up to ~5 loci
- models of habitat preference (in progress...)
- manipulating multilocus data
- estimating multilocus linkage disequilibria

Utilities:
- automatic numbering of equation, figures and tables in manuscripts
- a few methods for tridiagonal matrices
- a few routines for multinomial sampling and such


Many of the packages are under construction, or are the basis of manuscripts in preparation. Please send queries/comments to Nick Barton.

Please watch this space for further information.

DISCLAIMER
These files on this page are available without charge. In downloading the files the user accepts the following conditions of use:

• The author reserves the right to make changes without notifing users.

• Users accept that neither the author, nor any institution with which he has been associated, accepts responsibility for the accuracy of the results generated by the packages or conclusions based on the results of the programs nor for the use to which they are put. ie. THIS SOFTWARE IS PROVIDED ``AS IS'' WITH NO EXPRESS OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.

• No charge is made to other parties for services reliant on the packages without express permission from the author.

• The use of any material from this site is specifically acknowledged in any publications incorporating results produced by the packages, citing the paper listed above or other citation discussed with the author

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