8  Species delimitation

Author

Luís Valente

8.1 Species delimitation using the GMYC model

How many species of blue tits are there? We will use a model to delimit species based on the divergence between clades in the phylogeny. The GMYC model (Fujisawa & Barraclough 2013, Systematic Biology), which stands for “Generalized Mixed Yule Coalescent Approach”, is a likelihood method for delimiting species by fitting within- and between-species branching models to reconstructed gene trees.

Load the splits package (“SPecies’ LImits by Threshold Statistics”), which includes an R implementation of the GMYC model.

library(splits)

In case you haven’t done so above, remove the outgroup (delete all Parus individuals), by creating a new object without all the tips belonging to the outgroup.

cyanistes_ingroup<-drop.tip(cyanistes,c("Parus_major_major_KP759174.1",
                                         "Parus_major_DQ792786.1", 
                                         "Parus_major_DQ792787.1",
                                         "Parus_major_EU167009.1", 
                                         "Parus_major_KJ456375.1"))

Now we can fit the GMYC model to the data.

cyanistes_gmyc <- gmyc(cyanistes_ingroup)

Let’s look at the output from running the model. How many clusters are identified? What do these clusters mean?

summary(cyanistes_gmyc)

View which tips in the tree are assigned to each cluster

spec.list(cyanistes_gmyc)

Visualize the results of the GMYC model (Hit return to view the different plots). May require some adjusting on your screen.

plot(cyanistes_gmyc)

  • How many “species” does the model identify?

  • Do the clusters match species based on the tip names?

  • How many endemic species of Cyanistes are there in the Canary Islands?

  • How many endemic subspecies?

  • What other sources of evidence would be useful to define species of blue tits in the Canarian archipelago?

  • Would you recommend a taxonomic revision of this group?

  • What species would you give priority to conservation (if any)?