F-Statistics

Nora Mitchell January 31, 2017

Goals for Today’s Lab

I

Install R packages hierfstat and adegenet

I

Work through tutorial

I

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

I

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.

I

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 ...

#### Recommend Documents

here - GitHub
Sep 14, 2015 - Highlights. 1 optimizationBenchmarking tool for evaluating and comparing ...... in artificial intelligence, logic, theoretical computer science, and various application ...... can automatically be compiled to PDF [86],ifaLATEX compiler

1 - GitHub
Mar 4, 2002 - is now an integral part of computer science curricula. ...... students have one major department in which they are working OIl their degree.

J - GitHub
DNS. - n~OTHOCTb aamiCI1 Ha IAJI i. FILE - CllHCOK HOUepOB OCipaCiaTbiBaeu~ tlJai'i~OB i. RCBD - KO~HqecTBO OCipaCiaTbiB86Y~ ~E3;. PRT.

Geomega - GitHub
2: Number of these atoms in the material (integer). Old style ..... A directional 3D strip detector, where some information of the electron direction is retained (*).

33932 - GitHub
for automotive electronic throttle control, but are applicable to any low voltage DC servo ... degree of heatsinking provided to the device package. Internal peak-.

here - GitHub
Feb 16, 2016 - 6. 2 Low Level System Information. 7. 2.1 Machine Interface . .... devspecs/abi386-4.pdf, which describes the Linux IA-32 ABI for proces- ...... rameters described for the usual personality routine below, plus an additional.

Syllabus - GitHub
others is an act of plagiarism, which is a serious offense and all involved parties will be penalized according ... Academic Honesty Policy Summary: Introduction.

here - GitHub
can start it for free, but at some point you need to pay to advance through (not sure of the ... R for Everyone, Jared Lander, http://www.amazon.com/Everyone-Advanced-Analytics-Graphics-Addison-Wesley/ ... ISLR%20First%20Printing.pdf.