## 8.4 R Exercise Week 5

**Task:** Assess fine-scale spatial genetic structure in *Pulsatilla vulgaris* within a single patch, A25: Test for IBD with Mantel rank correlation, and use a Mantel correlogram to assess the range of spatial autocorrelation.

**Hints:**

**Load packages**: You may want to load the packages`dplyr`

,`EcoGenetics`

and`adegenet`

. Alternatively, you can use`::`

to call functions from packages.**Import data, extract adults from A25**.- Use the code below to import the data into gstudio.
- Inspect a few rows of the data.
- Filter the dataset to retain adults (OffID == 0) from site A25 (Population == “A25”).

```
Pulsatilla.gstudio <- gstudio::read_population(path=system.file("extdata",
"pulsatilla_genotypes.csv",
package = "LandGenCourse"),
type="column", locus.columns=c(6:19),
phased=FALSE, sep=",", header=TRUE)
```

**Plot locations of individuals**: use`plot`

with the argument`asp = 1`

to plot the locations of the sampled individuals from site A25 to scale.**Convert to ecogen and genind**: use`EcoGenetics::gstudio2ecogen`

to convert to an`ecogen`

object. From there, use`EcoGenetics::ecogen2genind`

to convert to a`genind`

object.**Calculate genetic and Euclidean distance**:- Use
`adegenet::propShared`

to calculate the proportion of shared alleles at the individual level. (Do not convert to genpop). - Convert to a distance measure by calculating
`1 - propShared`

. - Check object class. If it is not
`dist`

, use`as.dist`

to convert to a`dist`

object. - Use
`dist`

to calculate Euclidean distance between individuals.

- Use
**Mantel test**:- Adapt code from section 4.a to plot pairwise genetic distance against Euclidean distance.
- Do you notice something unusial in the plot? Why are there so few different values of genetic distance?
- Do you think there is spatial autocorrelation? If so, up to what distance?
- Adapt code from section 4.b to test for IBD with a Mantel test, using Spearman rank correlation.

**Mantel correlogram**: adapt code from section 5.a to create and plot a Mantel correlogram. Interpret the results.

**Questions:** What is the range of spatial autocorrelation in *P. vulgaris* in site A25?

- Based on a plot of genetic distance against Euclidean distance?
- Based on where the Mantel correlogram reaches 0?
- Based on statistical significance tests for the Mantel correlogram (with default settings: one-sided alternative “less”, Holm’s adjustment)?