Evolutionary history of the Galápagos Rail revealed by ancient mitogenomes and modern samples

Beast v. 2.6.3 input (.xml) files and output (.log and .trees) files for phylogenetic analyses of rails, used to determined the evolutionary history of the Galápagos Rail Laterallus spilonota. There are two main datasets: coding sequences of the mitochondrial genome ('mtCDS'), partitioned per codon position, and a two mitochondrial/one nuclear marker dataset ('2mt1nc'). For each of the datasets, separate runs have been made in which the fossil calibration of Rallidae is applied to the stem of the present-day family ('calRallidaeStem') or the crown node ('calRallidaeCrown), and finally all runs have been replicated with three different starting seeds ('seed_NNNNNNNNN', with the different seeds 123456789, 456789123, and 789123456).

We provide raw output (.log and .raw.trees) as well as maximum clade credibility ('mcc') trees (.mcc.trees), calculated after discarding 10% of the trees as burn-in, using median ('heights_median') or mean ('heights_mean') node heights as estimated node age.

The runs used for Table 1 (and Figure 2) in the accompanying paper are:

Dataset mtCDS, Rallidae calibration of stem: seed 123456789

Dataset mtCDS, Rallidae calibration of crown: seed 456789123 

Dataset 2mt1nc, Rallidae calibration of stem: seed 789123456

Dataset 2mt1nc, Rallidae calibration of crown: seed 123456789

This version of the data includes Pellornis mikkelseni among the fossils making up the calibration distribution for crown Gruiformes. In a previous version of this data deposit, that data point was represented by Messelornis cristata (see accompanying paper).