Principal Investigator
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Project Title
| Migration rates between Rhynchosporium secalis populations |
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Brief Description for General Publications
The project will estimate migration rates between barley pathogen populations (Rhynchosporium secalis) around the world to determine effects of breech of quarantine and historical movement of barley seed. The outcome of this work will assist barley breeders and quarantine officers, as well as contribute to our basic understanding of fungal pathogen evolution and migration. This project aims to identify the migration patters of a fungal plant pathogen around the world using the program Migrate (Beerli, P. and J. Felsenstein (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. PNAS 98(8): 4563-4568.), available from the web. http://popgen.csit.fsu.edu/ Migrate estimates effective population sizes and past migration rates between n populations assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses maximum likelihood or Bayesian inference to jointly estimate all parameters. Estimates of all migration rates and all population sizes, assuming constant mutation rates among loci or a gamma distributed mutation rate among loci. Profile likelihood tables, Percentiles, Likelihood-ratio tests, and simple plots of the log-likelihood surfaces for all populations and all loci. The calculations are done per locus and is relatively quick (2 days) for 2 or 3 loci and only 2 or 3 populations. However, I have 14 loci, and 7 sets of data with 5-10 populations each. One run on my G5 computer with dual processor takes anything from 4-21 days. The analyses also need to be repeated twice to ensure repeatabilty of results. |