Award details

Bayesian inference of the genealogy of a predominantly selfing population from multi locus genotype data

Reference	BBS/E/C/00004474
Principal Investigator / Supervisor	Professor Angela Karp
Co-Investigators / Co-Supervisors	Dr Kevin Dawson
Institution	Rothamsted Research
Department	Rothamsted Research Department
Funding type	Research
Value (£)	29,705
Status	Completed
Type	Institute Project
Start date	14/04/2003
End date	13/08/2006
Duration	40 months

Abstract

The aim of this project is to develop a Bayesian inference programme for making inferences about the genealogy of selfing lines and the outcrossing rate, from multi-locus genotypic data. The idea behead the Bayesian approach proposed here, is to focus attention on the recent genealogy of the sampled individuals. For every sample of genotypes, there will be many possible genealogies, - some more plausible than others. Multi-locus genotypic data will contain strong information about some aspects of this genealogy (such as the number of recent outcrossing events, and the number of distinct selfing lines), and less information about other aspects (such as the genealogical relationships between individuals belonging to the same selfing line). The basic approach will be to choose a prior distribution appropriate for the genealogy of a sample from a small predominantly selfing population (recently separated from a larger population), and then use an MCMC (Markov chain Monte Carlo) algorithm to sample the full posterior distribution of all the parameters (and hidden random variables) of the model. In this way, we will be able to compute the marginal posterior distribution of any parameter or hidden random variable of interest. Objectives: 1. Develop software for making Bayesian inferences about the genealogy of selfing lines and the outcrossing rate, from multi-locus genotypic data. 2. Test the performance of the Bayesian inference programme against simulated data sets. 3. Apply the Bayesian inference programme to real data (microsatellite data from the invasive herbaceous weed, Barren Brome Anisantha sterilis). 4. Evaluate alternative sampling strategies. In particular, compare the effect of genotyping more individuals, versus the effect of scoring more marker loci, on the reliability of the inferences about the outcrossing rate.

Summary

unavailable

Committee	Closed Committee - Agri-food (AF)
Research Topics	X – not assigned to a current Research Topic
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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