Parameter Estimation under the MSci
We will use BPP to estimate the population size (theta), divergence times (tau), and introgression (phi) parameters for the following five species of budding yeast:
| Species name (acronym) |
|---|
| S. cerevisiae (Scer) |
| S. paradoxus (Spar) |
| S. mikatae (Smik) |
| S. kudriavzevii (Skud) |
| S. bayanus (Sbay) |
Phylogenetic studies on these taxa (Rokas et al., 2003, Edwards et al., 2007) have recovered conflicting topologies. In particular, regarding the relationships of the S. kudriavzevii and the S. bayanus to the rest of the species. Later on, it was shown that there is substantial introgression from S. kudriavzevii to S. bayanus (Wen and Nakhleh, 2018, Flouri et al,2020), which justifies the topological conflict when gene flow is ignored.
We assume the following MSC with introgression model:
Prepare for the exercise:
- Create a folder named
A00and navigate into it. - Download the corresponding Imap.txt and bpp_seqfile.txt and store them in you working directory
wget https://raw.githubusercontent.com/Pas-Kapli/bpp-tutorial/master/A00_Yeast/data/Imap.txt
wget https://raw.githubusercontent.com/Pas-Kapli/bpp-tutorial/master/A00_Yeast/data/bpp_seqfile.txt
The Imap and the sequence files are prepared in exactly the same way as we described before.