F-Statistics

Nora Mitchell January 31, 2017

Goals for Today’s Lab

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Install R packages hierfstat and adegenet

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Work through tutorial

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Work through example

Variance Components In R, the packages adegenet and hierfstat can be used to compute FIS , FST , and FIT using variance components. (1 − FIS )(1 − FST ) = 1 − FIT

Hierarchical F-Stat

Install the R packages adegenet and hierfstat!

Tutorial

Work through the Jombart (2015) tutorial parts 1, 2.1, 3, 4.1, 4.2, and 5 on your own / with partner

Practice problem This dataset takes 7 microsatellite loci from 16 North American populations (516 individuals) of the invasive plant Polygonum cespitosum found in two different habitats from Matesanz et al. (2014)

Practice problem

To do: 1. Download “polygonum.stru”’ 2. Test for HWE 3. Compute hierarchical f-stats 4. Add level for habitat and compute f-stats again

Next Week

Individual Assignment in Structure! Project # 2!

Works Cited

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Matesanz, S., K. E. Theiss, K. E. Holsinger, and S. E. Sultan. 2014. Genetic Diversity and Population Structure in Polygonum cespitosum: Insights to an Ongoing Plant Invasion. PLoS One 9:e93217.

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Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.

F-Statistics - GitHub

Page 1. F-Statistics. Nora Mitchell. January 31, 2017. Page 2 ... Work through the Jombart (2015) tutorial parts 1, 2.1, 3, 4.1, 4.2, and 5 on your own / with partner ...

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