exercise.qmd

---
title: "Insula beetles exercise"
editor: visual
---

## *Insula* beetles excercise {#sec-exercise}

After you have finished the DAISIEprep and DAISIE practicals, you can begin applying these techniques to the *Insula* dataset.

## Questions to answer in your report {#sec-questions}

The aim is to be able to answer the following questions:

A.  How many times has *Insula* colonised the Caribbean islands?
B.  How many times has *Insula* colonised Jamaica?
C.  How many radiations have occurred on Jamaica?
D.  What are the rates of colonisation, speciation and extinction for *Insula* in Jamaica?
E.  Is there evidence for diversity-dependence in the *Insula* species of Jamaica?
F.  Is there evidence for equilibrium dynamics on the island of Jamaica?
G.  How has the diversity of *Insula* on Jamaica changed through time (according to DAISIE simulations)?

In sum, you need to load the phylogeny into R, use DAISIEprep to extract the DAISIE datalist. Then, fit DAISIE to that datalist to estimate parameters (extinction, colonisation, speciation, carrying capacity, and simulate islands), and to simulate islands. Make use of the DAISIEprep and DAISIE tutorials as well as the *Insula* tree, tables and figures provided. With these analyses you will be able to answer all the [questions](#sec-questions)

You can find all the relevant data here:

-   [Insula.tre](data/Insula.tre) the phylogenetic tree of *Insula* (to be loaded into R for analyses, but also visualized using Figtree): note that the species have numbers instead of latin names (Spec 1, Spec 2, etc).

```{r, echo=F}
library(ape)
Insula_tree<-read.nexus("data/Insula.tre")
plot(Insula_tree)
```

-   [Insula_checklist.xlsx](data/Insula_checklist.xlsx): A species checklist including the distribution, endemicity status as well as the species that are missing from the phylogeny but which should be considered in the DAISIE analyses.

-   [Figure_Insula_Tip_states.pdf](data/Figure_Insula_Tip_states.pdf): A figure of the phylogeny with the tips coloured by the island where the species occurs.

![Phylogeny showing the geographical distribution of the extant species](images/Figure_Insula_tip_states.png)

-   [Figure_Insula_ancestral_state_reconstruction.pdf](data/Figure_Insula_ancestral_state_reconstruction.pdf): A figure of an ancestral range reconstruction for the genus.

![Ancestral area reconstruction](images/Figure_Insula_ancestral_state_reconstruction.png)

**Tips**:

For the DAISIE analyses use:

[Island age:]{.underline} 5 million years

[Mainland pool size]{.underline}: 1000 species

Don't forget to add the missing species.

**After the practical, a file with an example of how to run the *Insula* analyses will be provided, which can be used as a guideline in case you had difficulties completing the practical.**